From 84d0ca81ce0f49b36bcc28231a83d1561a73aea3 Mon Sep 17 00:00:00 2001 From: Sophie Yang <78716301+yangsophieee@users.noreply.github.com> Date: Wed, 18 Oct 2023 16:05:24 +1100 Subject: [PATCH 01/31] Check precedences of metadata (#99) Addresses #60, checking precedence of metadata fields across various sections of metadata are working correctly (e.g. location > trait metadata) - Added additional testing for checking precedence of metadata - Fixed an error with `dataset_test` where I didn't realise the data variable already uses `process_custom_code` so it was applying it twice - Removed old testing files - @ehwenk and I agree that trait metadata should probably take precedence over location metadata but we will leave this to a later date (trait metadata is read in via `process_parse_data` and location metadata replaces it afterwards in `dataset_process` around Line 141, so you'd have to move the location metadata part into `process_parse_data`, which will presumably require splitting location data into location properties vs the other variables and having them input at different times) --- R/process.R | 32 +- R/testdata.R | 1 - tests/testthat/examples/Test_2023_2/README.md | 9 +- tests/testthat/examples/Test_2023_2/data.csv | 94 ++-- .../examples/Test_2023_2/metadata.yml | 6 +- .../examples/Test_2023_2/output/traits.csv | 298 ++++++------ tests/testthat/examples/Test_2023_4/README.md | 7 +- tests/testthat/examples/Test_2023_4/data.csv | 458 +++++++++--------- .../examples/Test_2023_4/metadata.yml | 6 +- .../examples/Test_2023_4/output/traits.csv | 108 ++--- tests/testthat/examples/test1-data.csv | 46 -- tests/testthat/examples/test1-metadata.yml | 316 ------------ tests/testthat/examples/test2-data.csv | 46 -- tests/testthat/examples/test2-metadata.yml | 317 ------------ tests/testthat/examples/test2.1-metadata.yml | 317 ------------ tests/testthat/examples/test3-data.csv | 46 -- tests/testthat/examples/test3-metadata.yml | 318 ------------ tests/testthat/examples/test4-data.csv | 34 -- tests/testthat/examples/test4-metadata.yml | 195 -------- 19 files changed, 516 insertions(+), 2138 deletions(-) delete mode 100644 tests/testthat/examples/test1-data.csv delete mode 100644 tests/testthat/examples/test1-metadata.yml delete mode 100644 tests/testthat/examples/test2-data.csv delete mode 100644 tests/testthat/examples/test2-metadata.yml delete mode 100644 tests/testthat/examples/test2.1-metadata.yml delete mode 100644 tests/testthat/examples/test3-data.csv delete mode 100644 tests/testthat/examples/test3-metadata.yml delete mode 100644 tests/testthat/examples/test4-data.csv delete mode 100644 tests/testthat/examples/test4-metadata.yml diff --git a/R/process.R b/R/process.R index 915f318e..cc48594f 100644 --- a/R/process.R +++ b/R/process.R @@ -132,7 +132,9 @@ dataset_process <- function(filename_data_raw, } # Where missing, fill variables in traits table with values from locations - # Currently overwriting dataset-level column metadata -- NEED FIX + # Trait metadata should probably have precedence -- right now trait metadata + # is being read in during `process_parse_data` and getting overwritten here #TODO + if (nrow(locations) > 0) { vars <- c("basis_of_record", "life_stage", "collection_date", "measurement_remarks", "entity_type") @@ -149,8 +151,8 @@ dataset_process <- function(filename_data_raw, dplyr::select(dplyr::any_of(c("location_id", "col_tmp"))) %>% stats::na.omit() ) - # Use location level value if present - traits[[v]] <- ifelse(!is.na(traits_tmp[["col_tmp"]]), traits_tmp[["col_tmp"]], traits[[v]]) + # Use location level value if present + traits[[v]] <- ifelse(!is.na(traits_tmp[["col_tmp"]]), traits_tmp[["col_tmp"]], traits[[v]]) } } @@ -193,12 +195,14 @@ dataset_process <- function(filename_data_raw, taxonomic_updates <- traits %>% dplyr::select( - dplyr::all_of(c("dataset_id", "original_name", cleaned_name = "taxon_name", taxonomic_resolution = "taxonomic_resolution")) + dplyr::all_of( + c("dataset_id", "original_name", cleaned_name = "taxon_name", + taxonomic_resolution = "taxonomic_resolution")) ) %>% dplyr::distinct() %>% dplyr::arrange(.data$cleaned_name) - ## A temporary dataframe created to generate and bind method_id, + ## A temporary dataframe created to generate and bind `method_id`, ## for instances where the same trait is measured twice using different methods # Test ABRS_2023 @@ -314,7 +318,8 @@ dataset_build <- function( #' @return character text containing custom_R_code if custom_R_code is not empty, #' otherwise no changes are made process_custom_code <- function(txt) { - if (!is.null(txt) && !is.na(txt) && nchar(txt) > 0) { + + if (!is.null(txt) && !is.na(txt) && nchar(txt) > 0) { txt2 <- # Trim white space, quotes, new line from front and back @@ -324,17 +329,20 @@ process_custom_code <- function(txt) { # test: txt <-" '' \n Total of 23.5 bitcoins. " function(data) { - envir = new.env() - + envir <- new.env() # Read in extra functions used in custom R code - if(file.exists("R/custom_R_code.R")) { + if (file.exists("R/custom_R_code.R")) { source("R/custom_R_code.R", local = envir) } + eval(parse(text = txt2), envir = envir) + } - eval(parse(text = txt2), envir = envir)} } else { + identity + } + } #' Create entity id @@ -1921,13 +1929,13 @@ build_update_taxonomy <- function(austraits_raw, taxa) { taxon_rank = ifelse(!is.na(.data$taxon_rank), .data$taxonomic_resolution, .data$taxon_rank), # Field trinomial is only filled in if taxonomic resolution is an infraspecific name trinomial = ifelse(.data$taxon_rank %in% c("Subspecies", "Forma", "Varietas"), - stringr::str_split_fixed(.data$taxon_name, "\\[", 2)[,1] %>% stringr::str_trim(), NA), + stringr::str_split_fixed(.data$taxon_name, "\\[", 2)[, 1] %>% stringr::str_trim(), NA), # Field binomial is filled in if taxonomic resolution is an infraspecific name or a binomial # All taxon names that have "extra" information (beyond the actual name) have been formatted # to have that information in square brackets '[]', so these can be used as a delimitor to # extract the actual name binomial = ifelse(.data$taxon_rank %in% c("Species"), - stringr::str_split_fixed(.data$taxon_name, "\\[", 2)[,1] %>% stringr::str_trim(), NA), + stringr::str_split_fixed(.data$taxon_name, "\\[", 2)[, 1] %>% stringr::str_trim(), NA), binomial = ifelse(.data$taxon_rank %in% c("Subspecies", "Forma", "Varietas", "Series"), stringr::word(.data$taxon_name, start = 1, end = 2), .data$binomial), binomial = stringr::str_trim(.data$binomial), diff --git a/R/testdata.R b/R/testdata.R index 1009d625..d21d5539 100644 --- a/R/testdata.R +++ b/R/testdata.R @@ -756,7 +756,6 @@ dataset_test_worker <- # Check that special characters do not make it into the data expect_no_error( parsed_data <- data %>% - process_custom_code(metadata[["dataset"]][["custom_R_code"]])() %>% process_parse_data(dataset_id, metadata, contexts, schema), info = "`process_parse_data`") diff --git a/tests/testthat/examples/Test_2023_2/README.md b/tests/testthat/examples/Test_2023_2/README.md index 53a787c1..c3efb41c 100644 --- a/tests/testthat/examples/Test_2023_2/README.md +++ b/tests/testthat/examples/Test_2023_2/README.md @@ -11,11 +11,12 @@ This dataset is for testing the following, for wide datasets: - Check that `location_id` is NA for species `entity_type` measurements Test_2023_2 is a copy of Falster_2005_1 with the following modifications: -- Added `replicates` as a column, with also trait-level metadata (included some NAs) +- Added `replicates` as a column at the dataset level, with also trait-level metadata (included some NAs) - Added `basis_of_value` as a column at the trait level, with also some traits with fixed values (included some NAs) -- Added `value_type` as a column at the trait-level ("LASA1000"), not dataset-level (fixed value at dataset level) (included NAs in column) -- Added `basis_of_record`, `life_stage` as dataset-level, trait-level and location-level metadata -- Added `measurement_remarks` as location-level metadata +- Added `value_type` as a column at the trait level ("LASA1000"), not dataset-level (fixed value at dataset level) (included NAs in column) +- Added `basis_of_record` as dataset-level, trait-level and location-level metadata +- Added `measurement_remarks` as dataset-level column metadata, trait-level metadata and location-level metadata +- Added `life_stage` as dataset-level column metadata, location-level metadata and trait-level column metadata - Read in `entity_type` as a fixed value and renamed "Species" column to "species" - Added `source_id` column - Removed latitude and longitude fields for both locations diff --git a/tests/testthat/examples/Test_2023_2/data.csv b/tests/testthat/examples/Test_2023_2/data.csv index 3b3a76a3..62085e56 100644 --- a/tests/testthat/examples/Test_2023_2/data.csv +++ b/tests/testthat/examples/Test_2023_2/data.csv @@ -1,47 +1,47 @@ -species,species_abb,site,LMA (mg mm-2),Leaf nitrogen (mg mg-1),leaf size (mm2),wood density (mg mm-3),branch mass fraction,Seed mass (mg),LASA10,LASA250,LASA50,LASA1000,replicates,basis_of_value,value_type,life_stage,source_id,collection_date -Acacia celsa,acacel,Atherton,0.145,0.0214,2786,0.498,0.67,10.3,2977,7260,3722,6824,1,measurement,raw,adult,Test_2022,2004-02 -Acacia celsa,acacel,Atherton,0.145,0.0214,2786,0.498,0.67,10.3,2977,7260,3722,6824,1,measurement,raw,adult,Test_2022,2004-03 -Acronychia acidula,acraci,Atherton,0.085,0.0243,14302,0.525,0.48,,,7560,5541,9480,1,measurement,raw,adult,Test_2022, -Alphitonia petriei,alppet,Atherton,0.149,0.0163,6820,0.413,0.42,27.2,,4340,3313,4335,1,measurement,raw,adult,Test_2022, -Glochidion hylandii,glohyl,Atherton,0.106,0.0137,3209,0.566,0.41,10.41,1993,5075,5455,8664,3,measurement,mean,adult,Test_2002, -Homalanthus novoguineensis,omanov,Atherton,0.082,0.022,10682,0.319,0.47,7,,2136,2158,3307,3,model_derived,mean,seedling,Test_2002, -Melicope elleryana,melell,Atherton,0.075,0.0268,6955,0.346,0.58,1.61,,4201,2860,6119,3,unknown,mean,juvenile,Test_2002, -Neolitsea dealbata,neodea,Atherton,0.093,0.0164,5228,0.352,0.58,176.1,1686,2747,3049,7504,2,,mean,juvenile,Test_2002, -Polyscias australiana,polaus,Atherton,0.079,0.0154,6806,0.397,0.42,8.35,,6008,,6700,2,,mean,,Test_2002, -Psychotria sp Utchee Creek,psyspp,Atherton,0.108,0.0179,11157,0.582,0,23.09,,4977,2302,2037,,,mean,,Test_2002, -Rhodomyrtus trineura,rhotri,Atherton,0.129,0.0111,3401,0.763,0.34,,4321,3803,6088,6877,,,mean,,Test_2002, -Acmena graveolens,acmgra,Cape Tribulation,0.151,0.0155,5246,0.599,0.67,,,3057,2667,7156,,,,,Test_2002, -Aleurites rockinghamensis,aleroc,Cape Tribulation,0.113,0.0184,73984,0.28,0.02,7077,,4194,,6209,,,,,Test_2002, -Alstonia scholaris,alssch,Cape Tribulation,0.107,0.0223,6182,0.361,0.46,1.53,,1854,1682,3932,,,,,Test_2002, -Argyrodendron peralatum,argper,Cape Tribulation,0.244,0.0119,3201,0.726,0.71,433,,3832,1689,6718,,measurement,,,Test_2002, -Atractocarpus hirtus,atrhir,Cape Tribulation,0.072,0.0157,11374,0.804,0.28,,,7143,6727,6103,1,measurement,,,Test_2002, -Brombya platynema,bropla,Cape Tribulation,0.106,0.0188,8218,0.603,0.33,,,4261,3531,5377,1,measurement,,juvenile,Test_2002, -Cardwellia sublimis,carsub,Cape Tribulation,0.127,0.0128,4352,0.603,0.56,582.3,,6315,4880,8282,1,model_derived,,juvenile,Test_2022, -Castanospermum australe,casaus,Cape Tribulation,0.117,0.0237,2765,0.587,0.37,14851,,7329,,8869,3,model_derived,,juvenile,Test_2022, -Cleistanthus myrianthus,clemyr,Cape Tribulation,0.078,0.0228,4828,0.588,0.56,,3720,6084,5233,8559,3,measurement,raw,seedling,Test_2022, -Cryptocarya laevigata,crylae,Cape Tribulation,0.087,0.0156,2682,0.64,0.65,1281,1391,3297,4680,7588,3,measurement,maximum,seedling,Test_2022, -Cryptocarya mackinnoniana,crymac,Cape Tribulation,0.204,0.0152,10458,0.655,0.61,204,,3277,2325,8657,3,measurement,mean,seedling,Test_2022, -Cryptocarya murrayi,crymur,Cape Tribulation,0.155,0.0167,9960,0.674,0.39,,2693,5543,4298,5451,,measurement,mean,seedling,Test_2022, -Dendrocnide moroides,denmor,Cape Tribulation,0.052,0.0312,26454,0.23,0.46,0.71,,2372,,2090,,measurement,mean,seedling,Test_2022, -Elaeocarpus grandis,elaang,Cape Tribulation,0.122,0.0187,2762,0.499,0.47,3699,,2598,1748,4635,2,measurement,mean,seedling,Test_2022, -Endiandra leptodendron,endlep,Cape Tribulation,0.106,0.018,3987,0.611,0.68,,1492,2412,2783,7477,2,model_derived,mean,,Test_2022, -Endiandra microneura,endmic,Cape Tribulation,0.151,0.0177,3377,0.623,0.61,,3573,6344,3354,6235,2,unknown,mean,,Test_2022, -Gillbeea adenopetala,gilade,Cape Tribulation,0.126,0.0096,3678,0.43,0.46,15,,2863,3160,6549,2,unknown,mean,,Test_2022, -Haplostichanthus sp Coop. Ck,hapspp,Cape Tribulation,0.072,0.022,4685,0.668,0.36,,2430,12304,3282,2992,2,unknown,mean,,Test_2022, -Harpullia rhyticarpa,harrhy,Cape Tribulation,0.076,0.0174,40876,0.621,0.01,,,8971,5922,4669,2,unknown,mean,,Test_2022, -Hernandia albiflora,heralb,Cape Tribulation,0.069,0.0195,3806,0.447,0.33,,3123,4145,4643,6086,2,unknown,mean,,Test_2022, -Ixora biflora,ixobif,Cape Tribulation,0.081,0.01,2760,0.843,0.55,41.5,5244,3892,1969,8094,2,unknown,mean,adult,, -Lasianthus strigosus,lasstr,Cape Tribulation,0.055,0.0158,3313,0.684,0.15,7,1841,5100,2379,2731,2,unknown,mean,adult,, -Litsea leefeana,litlee,Cape Tribulation,0.13,0.0144,3917,0.549,0.68,263.4,3984,4141,3816,9645,2,unknown,mean,adult,, -Macaranga tanarius,mactan,Cape Tribulation,0.104,0.0205,46676,0.344,0,,,3377,,3901,2,unknown,mean,adult,, -Mallotus mollissimus,malmol,Cape Tribulation,0.063,0.0352,16716,0.373,0.32,31.25,1788,5580,5163,7944,2,unknown,mean,adult,Test_2022, -Medicosma sessiliflora,medses,Cape Tribulation,0.106,0.0153,8164,0.69,0.65,,2844,9332,6514,10298,2,unknown,mean,adult,Test_2022, -Melastoma cyanoides,melaff,Cape Tribulation,0.046,0.0208,4009,0.381,0.6,0.07,2960,4057,4661,6637,2,unknown,mean,adult,Test_2022, -Myristica insipida,myrins,Cape Tribulation,0.106,0.0185,8379,0.433,0.51,1612,,6929,4852,9273,2,unknown,mean,adult,Test_2022, -Pittosporum rubiginosum,pitrub,Cape Tribulation,0.065,0.0143,9931,0.728,0.28,27.94,7428,7459,5265,6548,2,unknown,mean,adult,Test_2022, -Psychotria dallachiana,psydal,Cape Tribulation,0.079,0.0177,2495,0.612,0.33,,4290,5666,4916,4761,2,unknown,mean,adult,Test_2022, -Quassia baileyana,quabai,Cape Tribulation,0.086,0.023,9624,0.501,0.42,,,5867,3216,5719,2,unknown,mean,adult,Test_2022, -Rockinghamia angustifolia,rocang,Cape Tribulation,0.108,0.0158,10636,0.455,0.39,19.38,,5862,4611,6098,2,unknown,mean,adult,Test_2022, -Syzygium gustavioides,syzgus,Cape Tribulation,0.167,0.0129,3590,0.521,0.59,48000,2833,3121,3047,6584,2,unknown,mean,adult,Test_2022, -Syzygium sayeri,syzsay,Cape Tribulation,0.131,0.0137,2645,0.485,0.65,841,3929,5767,4939,9836,2,unknown,mean,adult,Test_2022, -Trema aspera,treasp,Cape Tribulation,0.053,0.0299,2071,0.357,0.53,5.12,3578,5291,5440,6695,2,unknown,mean,adult,Test_2022, +species,species_abb,site,LMA (mg mm-2),Leaf nitrogen (mg mg-1),leaf size (mm2),wood density (mg mm-3),branch mass fraction,Seed mass (mg),LASA10,LASA250,LASA50,LASA1000,replicates,basis_of_value,value_type,life_stage,life_stage_seed_mass,source_id,measurement_remarks,collection_date +Acacia celsa,acacel,Atherton,0.145,0.0214,2786,0.498,0.67,10.3,2977,7260,3722,6824,1,measurement,raw,adult,juvenile,Test_2022,,2004-02 +Acacia celsa,acacel,Atherton,0.145,0.0214,2786,0.498,0.67,10.3,2977,7260,3722,6824,1,measurement,raw,adult,juvenile,Test_2022,,2004-03 +Acronychia acidula,acraci,Atherton,0.085,0.0243,14302,0.525,0.48,,,7560,5541,9480,1,measurement,raw,adult,juvenile,Test_2022,, +Alphitonia petriei,alppet,Atherton,0.149,0.0163,6820,0.413,0.42,27.2,,4340,3313,4335,1,measurement,raw,adult,juvenile,Test_2022,, +Glochidion hylandii,glohyl,Atherton,0.106,0.0137,3209,0.566,0.41,10.41,1993,5075,5455,8664,3,measurement,mean,adult,juvenile,Test_2002,, +Homalanthus novoguineensis,omanov,Atherton,0.082,0.022,10682,0.319,0.47,7,,2136,2158,3307,3,model_derived,mean,seedling,,Test_2002,, +Melicope elleryana,melell,Atherton,0.075,0.0268,6955,0.346,0.58,1.61,,4201,2860,6119,3,unknown,mean,juvenile,,Test_2002,, +Neolitsea dealbata,neodea,Atherton,0.093,0.0164,5228,0.352,0.58,176.1,1686,2747,3049,7504,2,,mean,juvenile,,Test_2002,, +Polyscias australiana,polaus,Atherton,0.079,0.0154,6806,0.397,0.42,8.35,,6008,,6700,2,,mean,,,Test_2002,Test dataset-level measurement_remarks, +Psychotria sp Utchee Creek,psyspp,Atherton,0.108,0.0179,11157,0.582,0,23.09,,4977,2302,2037,,,mean,,,Test_2002,Test dataset-level measurement_remarks, +Rhodomyrtus trineura,rhotri,Atherton,0.129,0.0111,3401,0.763,0.34,,4321,3803,6088,6877,,,mean,,,Test_2002,Test dataset-level measurement_remarks, +Acmena graveolens,acmgra,Cape Tribulation,0.151,0.0155,5246,0.599,0.67,,,3057,2667,7156,,,,,,Test_2002,Test dataset-level measurement_remarks, +Aleurites rockinghamensis,aleroc,Cape Tribulation,0.113,0.0184,73984,0.28,0.02,7077,,4194,,6209,,,,,,Test_2002,Test dataset-level measurement_remarks, +Alstonia scholaris,alssch,Cape Tribulation,0.107,0.0223,6182,0.361,0.46,1.53,,1854,1682,3932,,,,,,Test_2002,Test dataset-level measurement_remarks, +Argyrodendron peralatum,argper,Cape Tribulation,0.244,0.0119,3201,0.726,0.71,433,,3832,1689,6718,,measurement,,,,Test_2002,Test dataset-level measurement_remarks, +Atractocarpus hirtus,atrhir,Cape Tribulation,0.072,0.0157,11374,0.804,0.28,,,7143,6727,6103,1,measurement,,,,Test_2002,Test dataset-level measurement_remarks, +Brombya platynema,bropla,Cape Tribulation,0.106,0.0188,8218,0.603,0.33,,,4261,3531,5377,1,measurement,,juvenile,,Test_2002,, +Cardwellia sublimis,carsub,Cape Tribulation,0.127,0.0128,4352,0.603,0.56,582.3,,6315,4880,8282,1,model_derived,,juvenile,,Test_2022,, +Castanospermum australe,casaus,Cape Tribulation,0.117,0.0237,2765,0.587,0.37,14851,,7329,,8869,3,model_derived,,juvenile,,Test_2022,, +Cleistanthus myrianthus,clemyr,Cape Tribulation,0.078,0.0228,4828,0.588,0.56,,3720,6084,5233,8559,3,measurement,raw,seedling,,Test_2022,, +Cryptocarya laevigata,crylae,Cape Tribulation,0.087,0.0156,2682,0.64,0.65,1281,1391,3297,4680,7588,3,measurement,maximum,seedling,,Test_2022,, +Cryptocarya mackinnoniana,crymac,Cape Tribulation,0.204,0.0152,10458,0.655,0.61,204,,3277,2325,8657,3,measurement,mean,seedling,,Test_2022,, +Cryptocarya murrayi,crymur,Cape Tribulation,0.155,0.0167,9960,0.674,0.39,,2693,5543,4298,5451,,measurement,mean,seedling,,Test_2022,, +Dendrocnide moroides,denmor,Cape Tribulation,0.052,0.0312,26454,0.23,0.46,0.71,,2372,,2090,,measurement,mean,seedling,,Test_2022,, +Elaeocarpus grandis,elaang,Cape Tribulation,0.122,0.0187,2762,0.499,0.47,3699,,2598,1748,4635,2,measurement,mean,seedling,,Test_2022,, +Endiandra leptodendron,endlep,Cape Tribulation,0.106,0.018,3987,0.611,0.68,,1492,2412,2783,7477,2,model_derived,mean,,,Test_2022,, +Endiandra microneura,endmic,Cape Tribulation,0.151,0.0177,3377,0.623,0.61,,3573,6344,3354,6235,2,unknown,mean,,,Test_2022,, +Gillbeea adenopetala,gilade,Cape Tribulation,0.126,0.0096,3678,0.43,0.46,15,,2863,3160,6549,2,unknown,mean,,,Test_2022,, +Haplostichanthus sp Coop. Ck,hapspp,Cape Tribulation,0.072,0.022,4685,0.668,0.36,,2430,12304,3282,2992,2,unknown,mean,,,Test_2022,, +Harpullia rhyticarpa,harrhy,Cape Tribulation,0.076,0.0174,40876,0.621,0.01,,,8971,5922,4669,2,unknown,mean,,,Test_2022,, +Hernandia albiflora,heralb,Cape Tribulation,0.069,0.0195,3806,0.447,0.33,,3123,4145,4643,6086,2,unknown,mean,,,Test_2022,, +Ixora biflora,ixobif,Cape Tribulation,0.081,0.01,2760,0.843,0.55,41.5,5244,3892,1969,8094,2,unknown,mean,adult,seedling,,, +Lasianthus strigosus,lasstr,Cape Tribulation,0.055,0.0158,3313,0.684,0.15,7,1841,5100,2379,2731,2,unknown,mean,adult,seedling,,, +Litsea leefeana,litlee,Cape Tribulation,0.13,0.0144,3917,0.549,0.68,263.4,3984,4141,3816,9645,2,unknown,mean,adult,seedling,,, +Macaranga tanarius,mactan,Cape Tribulation,0.104,0.0205,46676,0.344,0,,,3377,,3901,2,unknown,mean,adult,seedling,,, +Mallotus mollissimus,malmol,Cape Tribulation,0.063,0.0352,16716,0.373,0.32,31.25,1788,5580,5163,7944,2,unknown,mean,adult,,Test_2022,, +Medicosma sessiliflora,medses,Cape Tribulation,0.106,0.0153,8164,0.69,0.65,,2844,9332,6514,10298,2,unknown,mean,adult,,Test_2022,, +Melastoma cyanoides,melaff,Cape Tribulation,0.046,0.0208,4009,0.381,0.6,0.07,2960,4057,4661,6637,2,unknown,mean,adult,,Test_2022,, +Myristica insipida,myrins,Cape Tribulation,0.106,0.0185,8379,0.433,0.51,1612,,6929,4852,9273,2,unknown,mean,adult,,Test_2022,, +Pittosporum rubiginosum,pitrub,Cape Tribulation,0.065,0.0143,9931,0.728,0.28,27.94,7428,7459,5265,6548,2,unknown,mean,adult,,Test_2022,, +Psychotria dallachiana,psydal,Cape Tribulation,0.079,0.0177,2495,0.612,0.33,,4290,5666,4916,4761,2,unknown,mean,adult,,Test_2022,, +Quassia baileyana,quabai,Cape Tribulation,0.086,0.023,9624,0.501,0.42,,,5867,3216,5719,2,unknown,mean,adult,,Test_2022,, +Rockinghamia angustifolia,rocang,Cape Tribulation,0.108,0.0158,10636,0.455,0.39,19.38,,5862,4611,6098,2,unknown,mean,adult,,Test_2022,, +Syzygium gustavioides,syzgus,Cape Tribulation,0.167,0.0129,3590,0.521,0.59,48000,2833,3121,3047,6584,2,unknown,mean,adult,,Test_2022,, +Syzygium sayeri,syzsay,Cape Tribulation,0.131,0.0137,2645,0.485,0.65,841,3929,5767,4939,9836,2,unknown,mean,adult,,Test_2022,, +Trema aspera,treasp,Cape Tribulation,0.053,0.0299,2071,0.357,0.53,5.12,3578,5291,5440,6695,2,unknown,mean,adult,,Test_2022,, diff --git a/tests/testthat/examples/Test_2023_2/metadata.yml b/tests/testthat/examples/Test_2023_2/metadata.yml index 8367c051..0fdccb92 100644 --- a/tests/testthat/examples/Test_2023_2/metadata.yml +++ b/tests/testthat/examples/Test_2023_2/metadata.yml @@ -36,7 +36,8 @@ dataset: description: Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species. basis_of_record: field - life_stage: adult + life_stage: life_stage + measurement_remarks: measurement_remarks sampling_strategy: Nineteen species, ranging from early to late successional status, were selected using published sources (Hopkins & Graham 1987; Osunkoya 1996; Hyland et al. 1999). Species selected to represent the light gradient establish and mature @@ -111,6 +112,7 @@ traits: methods: Branch mass fraction was calculated as the mass side branches/total mass, on a carbon dry mass basis. The zero values are correct - these are plants with no branches. + measurement_remarks: Made-up remarks for `branch_mass_fraction` - var_in: Seed mass (mg) unit_in: mg trait_name: seed_dry_mass @@ -119,7 +121,7 @@ traits: replicates: unknown basis_of_record: literature basis_of_value: basis_of_value - life_stage: seedling + life_stage: life_stage_seed_mass methods: Mean oven-dried seed mass (including seed coat but excluding seed accessories) was estimated for all species with available field material. In total, collections for 17 of 47 species were made. Data for an additional 12 species were drawn from diff --git a/tests/testthat/examples/Test_2023_2/output/traits.csv b/tests/testthat/examples/Test_2023_2/output/traits.csv index 74ab8aec..3b955ce4 100644 --- a/tests/testthat/examples/Test_2023_2/output/traits.csv +++ b/tests/testthat/examples/Test_2023_2/output/traits.csv @@ -1,18 +1,18 @@ dataset_id,taxon_name,observation_id,trait_name,value,unit,entity_type,value_type,basis_of_value,replicates,basis_of_record,life_stage,population_id,individual_id,repeat_measurements_id,temporal_context_id,source_id,location_id,entity_context_id,plot_context_id,treatment_context_id,collection_date,measurement_remarks,method_id,method_context_id,original_name -Test_2023_2,Acacia celsa,001,branch_mass_fraction,0.67,mg/mg,population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,2004-02,,01,,Acacia celsa +Test_2023_2,Acacia celsa,001,branch_mass_fraction,0.67,mg/mg,population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,2004-02,Made-up remarks for `branch_mass_fraction`,01,,Acacia celsa Test_2023_2,Acacia celsa,001,huber_value,0.000335908632851864,mm2{sapwood}/mm2{leaf},population,raw,measurement,7,field,adult,01,,,,Test_2022,01,,,,2004-02,,01,,Acacia celsa Test_2023_2,Acacia celsa,001,huber_value,0.000137741046831956,mm2{sapwood}/mm2{leaf},population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,2004-02,,02,,Acacia celsa Test_2023_2,Acacia celsa,001,huber_value,0.000268672756582483,mm2{sapwood}/mm2{leaf},population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,2004-02,,03,,Acacia celsa Test_2023_2,Acacia celsa,001,huber_value,0.000146541617819461,mm2{sapwood}/mm2{leaf},population,mean,measurement,1,field,adult,01,,,,Test_2022,01,,,,2004-02,,04,,Acacia celsa Test_2023_2,Acacia celsa,001,huber_value,0.000146541617819461,mm2{sapwood}/mm2{leaf},population,maximum,measurement,1,field,adult,01,,,,Test_2022,01,,,,2004-02,,04,,Acacia celsa -Test_2023_2,Acacia celsa,002,branch_mass_fraction,0.67,mg/mg,population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,2004-03,,01,,Acacia celsa +Test_2023_2,Acacia celsa,002,branch_mass_fraction,0.67,mg/mg,population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,2004-03,Made-up remarks for `branch_mass_fraction`,01,,Acacia celsa Test_2023_2,Acacia celsa,002,huber_value,0.000335908632851864,mm2{sapwood}/mm2{leaf},population,raw,measurement,7,field,adult,01,,,,Test_2022,01,,,,2004-03,,01,,Acacia celsa Test_2023_2,Acacia celsa,002,huber_value,0.000137741046831956,mm2{sapwood}/mm2{leaf},population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,2004-03,,02,,Acacia celsa Test_2023_2,Acacia celsa,002,huber_value,0.000268672756582483,mm2{sapwood}/mm2{leaf},population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,2004-03,,03,,Acacia celsa Test_2023_2,Acacia celsa,002,huber_value,0.000146541617819461,mm2{sapwood}/mm2{leaf},population,mean,measurement,1,field,adult,01,,,,Test_2022,01,,,,2004-03,,04,,Acacia celsa Test_2023_2,Acacia celsa,002,huber_value,0.000146541617819461,mm2{sapwood}/mm2{leaf},population,maximum,measurement,1,field,adult,01,,,,Test_2022,01,,,,2004-03,,04,,Acacia celsa -Test_2023_2,Acacia celsa,003,seed_dry_mass,10.3,mg,population,raw,measurement,unknown,literature,seedling,01,,,,Test_2022,01,,,,2004-02,,01,,Acacia celsa -Test_2023_2,Acacia celsa,004,seed_dry_mass,10.3,mg,population,raw,measurement,unknown,literature,seedling,01,,,,Test_2022,01,,,,2004-03,,01,,Acacia celsa +Test_2023_2,Acacia celsa,003,seed_dry_mass,10.3,mg,population,raw,measurement,unknown,literature,juvenile,01,,,,Test_2022,01,,,,2004-02,,01,,Acacia celsa +Test_2023_2,Acacia celsa,004,seed_dry_mass,10.3,mg,population,raw,measurement,unknown,literature,juvenile,01,,,,Test_2022,01,,,,2004-03,,01,,Acacia celsa Test_2023_2,Acacia celsa,005,leaf_N_per_dry_mass,21.4,mg/g,species,raw,measurement,1,field,adult,,,,,Test_2022,,,,,2004-02,,01,,Acacia celsa Test_2023_2,Acacia celsa,005,leaf_area,2786,mm2,species,raw,measurement,1,field,adult,,,,,Test_2022,,,,,2004-02,,01,,Acacia celsa Test_2023_2,Acacia celsa,005,leaf_mass_per_area,145,g/m2,species,raw,measurement,1,field,adult,,,,,Test_2022,,,,,2004-02,,01,,Acacia celsa @@ -26,11 +26,11 @@ Test_2023_2,Acmena graveolens,007,huber_value,0.000139742873113471,mm2{sapwood}/ Test_2023_2,Acmena graveolens,007,huber_value,0.000139742873113471,mm2{sapwood}/mm2{leaf},population,maximum,,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Acmena graveolens Test_2023_2,Acmena graveolens,007,huber_value,0.000327118089630357,mm2{sapwood}/mm2{leaf},population,,,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Acmena graveolens Test_2023_2,Acmena graveolens,007,huber_value,0.000374953130858643,mm2{sapwood}/mm2{leaf},population,,,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Acmena graveolens -Test_2023_2,Acmena graveolens,008,leaf_N_per_dry_mass,15.5,mg/g,species,,,,field,adult,,,,,Test_2002,,,,,,,01,,Acmena graveolens -Test_2023_2,Acmena graveolens,008,leaf_area,5246,mm2,species,,,,field,adult,,,,,Test_2002,,,,,,,01,,Acmena graveolens -Test_2023_2,Acmena graveolens,008,leaf_mass_per_area,151,g/m2,species,,measurement,,field,adult,,,,,Test_2002,,,,,,,01,,Acmena graveolens -Test_2023_2,Acmena graveolens,008,wood_density,0.599,mg/mm3,species,,,,field,adult,,,,,Test_2002,,,,,,,01,,Acmena graveolens -Test_2023_2,Acronychia acidula,009,branch_mass_fraction,0.48,mg/mg,population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,,,01,,Acronychia acidula +Test_2023_2,Acmena graveolens,008,leaf_N_per_dry_mass,15.5,mg/g,species,,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Acmena graveolens +Test_2023_2,Acmena graveolens,008,leaf_area,5246,mm2,species,,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Acmena graveolens +Test_2023_2,Acmena graveolens,008,leaf_mass_per_area,151,g/m2,species,,measurement,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Acmena graveolens +Test_2023_2,Acmena graveolens,008,wood_density,0.599,mg/mm3,species,,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Acmena graveolens +Test_2023_2,Acronychia acidula,009,branch_mass_fraction,0.48,mg/mg,population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,,Made-up remarks for `branch_mass_fraction`,01,,Acronychia acidula Test_2023_2,Acronychia acidula,009,huber_value,0.000132275132275132,mm2{sapwood}/mm2{leaf},population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,,,02,,Acronychia acidula Test_2023_2,Acronychia acidula,009,huber_value,0.000180472838837755,mm2{sapwood}/mm2{leaf},population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,,,03,,Acronychia acidula Test_2023_2,Acronychia acidula,009,huber_value,0.000105485232067511,mm2{sapwood}/mm2{leaf},population,mean,measurement,1,field,adult,01,,,,Test_2022,01,,,,,,04,,Acronychia acidula @@ -44,16 +44,16 @@ Test_2023_2,Aleurites rockinghamensis,011,huber_value,0.000161056530842326,mm2{s Test_2023_2,Aleurites rockinghamensis,011,huber_value,0.000161056530842326,mm2{sapwood}/mm2{leaf},population,maximum,,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Aleurites rockinghamensis Test_2023_2,Aleurites rockinghamensis,011,huber_value,0.000238435860753457,mm2{sapwood}/mm2{leaf},population,,,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Aleurites rockinghamensis Test_2023_2,Aleurites rockinghamensis,011,seed_dry_mass,7077,mg,population,,,unknown,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Aleurites rockinghamensis -Test_2023_2,Aleurites rockinghamensis,012,leaf_N_per_dry_mass,18.4,mg/g,species,,,,field,adult,,,,,Test_2002,,,,,,,01,,Aleurites rockinghamensis -Test_2023_2,Aleurites rockinghamensis,012,leaf_area,73984,mm2,species,,,,field,adult,,,,,Test_2002,,,,,,,01,,Aleurites rockinghamensis -Test_2023_2,Aleurites rockinghamensis,012,leaf_mass_per_area,113,g/m2,species,,measurement,,field,adult,,,,,Test_2002,,,,,,,01,,Aleurites rockinghamensis -Test_2023_2,Aleurites rockinghamensis,012,wood_density,0.28,mg/mm3,species,,,,field,adult,,,,,Test_2002,,,,,,,01,,Aleurites rockinghamensis -Test_2023_2,Alphitonia petriei,013,branch_mass_fraction,0.42,mg/mg,population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,,,01,,Alphitonia petriei +Test_2023_2,Aleurites rockinghamensis,012,leaf_N_per_dry_mass,18.4,mg/g,species,,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Aleurites rockinghamensis +Test_2023_2,Aleurites rockinghamensis,012,leaf_area,73984,mm2,species,,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Aleurites rockinghamensis +Test_2023_2,Aleurites rockinghamensis,012,leaf_mass_per_area,113,g/m2,species,,measurement,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Aleurites rockinghamensis +Test_2023_2,Aleurites rockinghamensis,012,wood_density,0.28,mg/mm3,species,,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Aleurites rockinghamensis +Test_2023_2,Alphitonia petriei,013,branch_mass_fraction,0.42,mg/mg,population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,,Made-up remarks for `branch_mass_fraction`,01,,Alphitonia petriei Test_2023_2,Alphitonia petriei,013,huber_value,0.000230414746543779,mm2{sapwood}/mm2{leaf},population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,,,02,,Alphitonia petriei Test_2023_2,Alphitonia petriei,013,huber_value,0.000301841231512225,mm2{sapwood}/mm2{leaf},population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,,,03,,Alphitonia petriei Test_2023_2,Alphitonia petriei,013,huber_value,0.000230680507497116,mm2{sapwood}/mm2{leaf},population,mean,measurement,1,field,adult,01,,,,Test_2022,01,,,,,,04,,Alphitonia petriei Test_2023_2,Alphitonia petriei,013,huber_value,0.000230680507497116,mm2{sapwood}/mm2{leaf},population,maximum,measurement,1,field,adult,01,,,,Test_2022,01,,,,,,04,,Alphitonia petriei -Test_2023_2,Alphitonia petriei,014,seed_dry_mass,27.2,mg,population,raw,measurement,unknown,literature,seedling,01,,,,Test_2022,01,,,,,,01,,Alphitonia petriei +Test_2023_2,Alphitonia petriei,014,seed_dry_mass,27.2,mg,population,raw,measurement,unknown,literature,juvenile,01,,,,Test_2022,01,,,,,,01,,Alphitonia petriei Test_2023_2,Alphitonia petriei,015,leaf_N_per_dry_mass,16.3,mg/g,species,raw,measurement,1,field,adult,,,,,Test_2022,,,,,,,01,,Alphitonia petriei Test_2023_2,Alphitonia petriei,015,leaf_area,6820,mm2,species,raw,measurement,1,field,adult,,,,,Test_2022,,,,,,,01,,Alphitonia petriei Test_2023_2,Alphitonia petriei,015,leaf_mass_per_area,149,g/m2,species,raw,measurement,1,field,adult,,,,,Test_2022,,,,,,,01,,Alphitonia petriei @@ -64,67 +64,67 @@ Test_2023_2,Alstonia scholaris,016,huber_value,0.000254323499491353,mm2{sapwood} Test_2023_2,Alstonia scholaris,016,huber_value,0.000539374325782093,mm2{sapwood}/mm2{leaf},population,,,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Alstonia scholaris Test_2023_2,Alstonia scholaris,016,huber_value,0.000594530321046373,mm2{sapwood}/mm2{leaf},population,,,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Alstonia scholaris Test_2023_2,Alstonia scholaris,016,seed_dry_mass,1.53,mg,population,,,unknown,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Alstonia scholaris -Test_2023_2,Alstonia scholaris,017,leaf_N_per_dry_mass,22.3,mg/g,species,,,,field,adult,,,,,Test_2002,,,,,,,01,,Alstonia scholaris -Test_2023_2,Alstonia scholaris,017,leaf_area,6182,mm2,species,,,,field,adult,,,,,Test_2002,,,,,,,01,,Alstonia scholaris -Test_2023_2,Alstonia scholaris,017,leaf_mass_per_area,107,g/m2,species,,measurement,,field,adult,,,,,Test_2002,,,,,,,01,,Alstonia scholaris -Test_2023_2,Alstonia scholaris,017,wood_density,0.361,mg/mm3,species,,,,field,adult,,,,,Test_2002,,,,,,,01,,Alstonia scholaris +Test_2023_2,Alstonia scholaris,017,leaf_N_per_dry_mass,22.3,mg/g,species,,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Alstonia scholaris +Test_2023_2,Alstonia scholaris,017,leaf_area,6182,mm2,species,,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Alstonia scholaris +Test_2023_2,Alstonia scholaris,017,leaf_mass_per_area,107,g/m2,species,,measurement,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Alstonia scholaris +Test_2023_2,Alstonia scholaris,017,wood_density,0.361,mg/mm3,species,,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Alstonia scholaris Test_2023_2,Argyrodendron peralatum,018,branch_mass_fraction,0.71,mg/mg,population,,measurement,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Argyrodendron peralatum Test_2023_2,Argyrodendron peralatum,018,huber_value,0.000148853825543316,mm2{sapwood}/mm2{leaf},population,mean,measurement,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Argyrodendron peralatum Test_2023_2,Argyrodendron peralatum,018,huber_value,0.000148853825543316,mm2{sapwood}/mm2{leaf},population,maximum,measurement,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Argyrodendron peralatum Test_2023_2,Argyrodendron peralatum,018,huber_value,0.000260960334029228,mm2{sapwood}/mm2{leaf},population,,measurement,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Argyrodendron peralatum Test_2023_2,Argyrodendron peralatum,018,huber_value,0.00059206631142688,mm2{sapwood}/mm2{leaf},population,,measurement,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Argyrodendron peralatum Test_2023_2,Argyrodendron peralatum,018,seed_dry_mass,433,mg,population,,measurement,unknown,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Argyrodendron peralatum -Test_2023_2,Argyrodendron peralatum,019,leaf_N_per_dry_mass,11.9,mg/g,species,,measurement,,field,adult,,,,,Test_2002,,,,,,,01,,Argyrodendron peralatum -Test_2023_2,Argyrodendron peralatum,019,leaf_area,3201,mm2,species,,measurement,,field,adult,,,,,Test_2002,,,,,,,01,,Argyrodendron peralatum -Test_2023_2,Argyrodendron peralatum,019,leaf_mass_per_area,244,g/m2,species,,measurement,,field,adult,,,,,Test_2002,,,,,,,01,,Argyrodendron peralatum -Test_2023_2,Argyrodendron peralatum,019,wood_density,0.726,mg/mm3,species,,measurement,,field,adult,,,,,Test_2002,,,,,,,01,,Argyrodendron peralatum +Test_2023_2,Argyrodendron peralatum,019,leaf_N_per_dry_mass,11.9,mg/g,species,,measurement,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Argyrodendron peralatum +Test_2023_2,Argyrodendron peralatum,019,leaf_area,3201,mm2,species,,measurement,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Argyrodendron peralatum +Test_2023_2,Argyrodendron peralatum,019,leaf_mass_per_area,244,g/m2,species,,measurement,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Argyrodendron peralatum +Test_2023_2,Argyrodendron peralatum,019,wood_density,0.726,mg/mm3,species,,measurement,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Argyrodendron peralatum Test_2023_2,Atractocarpus hirtus,020,branch_mass_fraction,0.28,mg/mg,population,,measurement,1,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Atractocarpus hirtus Test_2023_2,Atractocarpus hirtus,020,huber_value,0.000163853842372604,mm2{sapwood}/mm2{leaf},population,mean,measurement,1,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Atractocarpus hirtus Test_2023_2,Atractocarpus hirtus,020,huber_value,0.000163853842372604,mm2{sapwood}/mm2{leaf},population,maximum,measurement,1,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Atractocarpus hirtus Test_2023_2,Atractocarpus hirtus,020,huber_value,0.000139997200055999,mm2{sapwood}/mm2{leaf},population,,measurement,1,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Atractocarpus hirtus Test_2023_2,Atractocarpus hirtus,020,huber_value,0.000148654675189535,mm2{sapwood}/mm2{leaf},population,,measurement,1,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Atractocarpus hirtus -Test_2023_2,Atractocarpus hirtus,021,leaf_N_per_dry_mass,15.7,mg/g,species,,measurement,1,field,adult,,,,,Test_2002,,,,,,,01,,Atractocarpus hirtus -Test_2023_2,Atractocarpus hirtus,021,leaf_area,11374,mm2,species,,measurement,1,field,adult,,,,,Test_2002,,,,,,,01,,Atractocarpus hirtus -Test_2023_2,Atractocarpus hirtus,021,leaf_mass_per_area,72,g/m2,species,,measurement,1,field,adult,,,,,Test_2002,,,,,,,01,,Atractocarpus hirtus -Test_2023_2,Atractocarpus hirtus,021,wood_density,0.804,mg/mm3,species,,measurement,1,field,adult,,,,,Test_2002,,,,,,,01,,Atractocarpus hirtus +Test_2023_2,Atractocarpus hirtus,021,leaf_N_per_dry_mass,15.7,mg/g,species,,measurement,1,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Atractocarpus hirtus +Test_2023_2,Atractocarpus hirtus,021,leaf_area,11374,mm2,species,,measurement,1,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Atractocarpus hirtus +Test_2023_2,Atractocarpus hirtus,021,leaf_mass_per_area,72,g/m2,species,,measurement,1,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Atractocarpus hirtus +Test_2023_2,Atractocarpus hirtus,021,wood_density,0.804,mg/mm3,species,,measurement,1,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Atractocarpus hirtus Test_2023_2,Brombya platynema,022,branch_mass_fraction,0.33,mg/mg,population,,measurement,1,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Brombya platynema Test_2023_2,Brombya platynema,022,huber_value,0.000185977310768086,mm2{sapwood}/mm2{leaf},population,mean,measurement,1,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Brombya platynema Test_2023_2,Brombya platynema,022,huber_value,0.000185977310768086,mm2{sapwood}/mm2{leaf},population,maximum,measurement,1,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Brombya platynema Test_2023_2,Brombya platynema,022,huber_value,0.000234686693264492,mm2{sapwood}/mm2{leaf},population,,measurement,1,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Brombya platynema Test_2023_2,Brombya platynema,022,huber_value,0.000283205890682526,mm2{sapwood}/mm2{leaf},population,,measurement,1,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Brombya platynema -Test_2023_2,Brombya platynema,023,leaf_N_per_dry_mass,18.8,mg/g,species,,measurement,1,field,adult,,,,,Test_2002,,,,,,,01,,Brombya platynema -Test_2023_2,Brombya platynema,023,leaf_area,8218,mm2,species,,measurement,1,field,adult,,,,,Test_2002,,,,,,,01,,Brombya platynema -Test_2023_2,Brombya platynema,023,leaf_mass_per_area,106,g/m2,species,,measurement,1,field,adult,,,,,Test_2002,,,,,,,01,,Brombya platynema -Test_2023_2,Brombya platynema,023,wood_density,0.603,mg/mm3,species,,measurement,1,field,adult,,,,,Test_2002,,,,,,,01,,Brombya platynema +Test_2023_2,Brombya platynema,023,leaf_N_per_dry_mass,18.8,mg/g,species,,measurement,1,field,juvenile,,,,,Test_2002,,,,,,,01,,Brombya platynema +Test_2023_2,Brombya platynema,023,leaf_area,8218,mm2,species,,measurement,1,field,juvenile,,,,,Test_2002,,,,,,,01,,Brombya platynema +Test_2023_2,Brombya platynema,023,leaf_mass_per_area,106,g/m2,species,,measurement,1,field,juvenile,,,,,Test_2002,,,,,,,01,,Brombya platynema +Test_2023_2,Brombya platynema,023,wood_density,0.603,mg/mm3,species,,measurement,1,field,juvenile,,,,,Test_2002,,,,,,,01,,Brombya platynema Test_2023_2,Cardwellia sublimis,024,branch_mass_fraction,0.56,mg/mg,population,,model_derived,1,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Cardwellia sublimis Test_2023_2,Cardwellia sublimis,024,huber_value,0.000120743781695243,mm2{sapwood}/mm2{leaf},population,mean,model_derived,1,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Cardwellia sublimis Test_2023_2,Cardwellia sublimis,024,huber_value,0.000120743781695243,mm2{sapwood}/mm2{leaf},population,maximum,model_derived,1,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Cardwellia sublimis Test_2023_2,Cardwellia sublimis,024,huber_value,0.000158353127474268,mm2{sapwood}/mm2{leaf},population,,model_derived,1,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Cardwellia sublimis Test_2023_2,Cardwellia sublimis,024,huber_value,0.000204918032786885,mm2{sapwood}/mm2{leaf},population,,model_derived,1,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Cardwellia sublimis Test_2023_2,Cardwellia sublimis,024,seed_dry_mass,582.3,mg,population,,model_derived,unknown,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Cardwellia sublimis -Test_2023_2,Cardwellia sublimis,025,leaf_N_per_dry_mass,12.8,mg/g,species,,model_derived,1,field,adult,,,,,Test_2022,,,,,,,01,,Cardwellia sublimis -Test_2023_2,Cardwellia sublimis,025,leaf_area,4352,mm2,species,,model_derived,1,field,adult,,,,,Test_2022,,,,,,,01,,Cardwellia sublimis -Test_2023_2,Cardwellia sublimis,025,leaf_mass_per_area,127,g/m2,species,,measurement,1,field,adult,,,,,Test_2022,,,,,,,01,,Cardwellia sublimis -Test_2023_2,Cardwellia sublimis,025,wood_density,0.603,mg/mm3,species,,model_derived,1,field,adult,,,,,Test_2022,,,,,,,01,,Cardwellia sublimis +Test_2023_2,Cardwellia sublimis,025,leaf_N_per_dry_mass,12.8,mg/g,species,,model_derived,1,field,juvenile,,,,,Test_2022,,,,,,,01,,Cardwellia sublimis +Test_2023_2,Cardwellia sublimis,025,leaf_area,4352,mm2,species,,model_derived,1,field,juvenile,,,,,Test_2022,,,,,,,01,,Cardwellia sublimis +Test_2023_2,Cardwellia sublimis,025,leaf_mass_per_area,127,g/m2,species,,measurement,1,field,juvenile,,,,,Test_2022,,,,,,,01,,Cardwellia sublimis +Test_2023_2,Cardwellia sublimis,025,wood_density,0.603,mg/mm3,species,,model_derived,1,field,juvenile,,,,,Test_2022,,,,,,,01,,Cardwellia sublimis Test_2023_2,Castanospermum australe,026,branch_mass_fraction,0.37,mg/mg,population,,model_derived,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Castanospermum australe Test_2023_2,Castanospermum australe,026,huber_value,0.000112752283233735,mm2{sapwood}/mm2{leaf},population,mean,model_derived,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Castanospermum australe Test_2023_2,Castanospermum australe,026,huber_value,0.000112752283233735,mm2{sapwood}/mm2{leaf},population,maximum,model_derived,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Castanospermum australe Test_2023_2,Castanospermum australe,026,huber_value,0.000136444262518761,mm2{sapwood}/mm2{leaf},population,,model_derived,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Castanospermum australe Test_2023_2,Castanospermum australe,026,seed_dry_mass,14851,mg,population,,model_derived,unknown,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Castanospermum australe -Test_2023_2,Castanospermum australe,027,leaf_N_per_dry_mass,23.7,mg/g,species,,model_derived,3,field,adult,,,,,Test_2022,,,,,,,01,,Castanospermum australe -Test_2023_2,Castanospermum australe,027,leaf_area,2765,mm2,species,,model_derived,3,field,adult,,,,,Test_2022,,,,,,,01,,Castanospermum australe -Test_2023_2,Castanospermum australe,027,leaf_mass_per_area,117,g/m2,species,,measurement,3,field,adult,,,,,Test_2022,,,,,,,01,,Castanospermum australe -Test_2023_2,Castanospermum australe,027,wood_density,0.587,mg/mm3,species,,model_derived,3,field,adult,,,,,Test_2022,,,,,,,01,,Castanospermum australe +Test_2023_2,Castanospermum australe,027,leaf_N_per_dry_mass,23.7,mg/g,species,,model_derived,3,field,juvenile,,,,,Test_2022,,,,,,,01,,Castanospermum australe +Test_2023_2,Castanospermum australe,027,leaf_area,2765,mm2,species,,model_derived,3,field,juvenile,,,,,Test_2022,,,,,,,01,,Castanospermum australe +Test_2023_2,Castanospermum australe,027,leaf_mass_per_area,117,g/m2,species,,measurement,3,field,juvenile,,,,,Test_2022,,,,,,,01,,Castanospermum australe +Test_2023_2,Castanospermum australe,027,wood_density,0.587,mg/mm3,species,,model_derived,3,field,juvenile,,,,,Test_2022,,,,,,,01,,Castanospermum australe Test_2023_2,Cleistanthus myrianthus,028,branch_mass_fraction,0.56,mg/mg,population,raw,measurement,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Cleistanthus myrianthus Test_2023_2,Cleistanthus myrianthus,028,huber_value,0.000268817204301075,mm2{sapwood}/mm2{leaf},population,raw,measurement,7,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Cleistanthus myrianthus Test_2023_2,Cleistanthus myrianthus,028,huber_value,0.000164365548980934,mm2{sapwood}/mm2{leaf},population,raw,measurement,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Cleistanthus myrianthus Test_2023_2,Cleistanthus myrianthus,028,huber_value,0.000191094974202178,mm2{sapwood}/mm2{leaf},population,raw,measurement,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Cleistanthus myrianthus Test_2023_2,Cleistanthus myrianthus,028,huber_value,0.000116836078981189,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Cleistanthus myrianthus Test_2023_2,Cleistanthus myrianthus,028,huber_value,0.000116836078981189,mm2{sapwood}/mm2{leaf},population,maximum,measurement,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Cleistanthus myrianthus -Test_2023_2,Cleistanthus myrianthus,029,leaf_N_per_dry_mass,22.8,mg/g,species,raw,measurement,3,field,adult,,,,,Test_2022,,,,,,,01,,Cleistanthus myrianthus -Test_2023_2,Cleistanthus myrianthus,029,leaf_area,4828,mm2,species,raw,measurement,3,field,adult,,,,,Test_2022,,,,,,,01,,Cleistanthus myrianthus -Test_2023_2,Cleistanthus myrianthus,029,leaf_mass_per_area,78,g/m2,species,raw,measurement,3,field,adult,,,,,Test_2022,,,,,,,01,,Cleistanthus myrianthus -Test_2023_2,Cleistanthus myrianthus,029,wood_density,0.588,mg/mm3,species,raw,measurement,3,field,adult,,,,,Test_2022,,,,,,,01,,Cleistanthus myrianthus +Test_2023_2,Cleistanthus myrianthus,029,leaf_N_per_dry_mass,22.8,mg/g,species,raw,measurement,3,field,seedling,,,,,Test_2022,,,,,,,01,,Cleistanthus myrianthus +Test_2023_2,Cleistanthus myrianthus,029,leaf_area,4828,mm2,species,raw,measurement,3,field,seedling,,,,,Test_2022,,,,,,,01,,Cleistanthus myrianthus +Test_2023_2,Cleistanthus myrianthus,029,leaf_mass_per_area,78,g/m2,species,raw,measurement,3,field,seedling,,,,,Test_2022,,,,,,,01,,Cleistanthus myrianthus +Test_2023_2,Cleistanthus myrianthus,029,wood_density,0.588,mg/mm3,species,raw,measurement,3,field,seedling,,,,,Test_2022,,,,,,,01,,Cleistanthus myrianthus Test_2023_2,Cryptocarya laevigata,030,branch_mass_fraction,0.65,mg/mg,population,maximum,measurement,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Cryptocarya laevigata Test_2023_2,Cryptocarya laevigata,030,huber_value,0.000131787032156036,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Cryptocarya laevigata Test_2023_2,Cryptocarya laevigata,030,huber_value,0.000718907260963336,mm2{sapwood}/mm2{leaf},population,maximum,measurement,7,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Cryptocarya laevigata @@ -132,86 +132,86 @@ Test_2023_2,Cryptocarya laevigata,030,huber_value,0.000303306035790112,mm2{sapwo Test_2023_2,Cryptocarya laevigata,030,huber_value,0.000213675213675214,mm2{sapwood}/mm2{leaf},population,maximum,measurement,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Cryptocarya laevigata Test_2023_2,Cryptocarya laevigata,030,huber_value,0.000131787032156036,mm2{sapwood}/mm2{leaf},population,maximum,measurement,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Cryptocarya laevigata Test_2023_2,Cryptocarya laevigata,030,seed_dry_mass,1281,mg,population,maximum,measurement,unknown,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Cryptocarya laevigata -Test_2023_2,Cryptocarya laevigata,031,leaf_N_per_dry_mass,15.6,mg/g,species,maximum,measurement,3,field,adult,,,,,Test_2022,,,,,,,01,,Cryptocarya laevigata -Test_2023_2,Cryptocarya laevigata,031,leaf_area,2682,mm2,species,maximum,measurement,3,field,adult,,,,,Test_2022,,,,,,,01,,Cryptocarya laevigata -Test_2023_2,Cryptocarya laevigata,031,leaf_mass_per_area,87,g/m2,species,maximum,measurement,3,field,adult,,,,,Test_2022,,,,,,,01,,Cryptocarya laevigata -Test_2023_2,Cryptocarya laevigata,031,wood_density,0.64,mg/mm3,species,maximum,measurement,3,field,adult,,,,,Test_2022,,,,,,,01,,Cryptocarya laevigata +Test_2023_2,Cryptocarya laevigata,031,leaf_N_per_dry_mass,15.6,mg/g,species,maximum,measurement,3,field,seedling,,,,,Test_2022,,,,,,,01,,Cryptocarya laevigata +Test_2023_2,Cryptocarya laevigata,031,leaf_area,2682,mm2,species,maximum,measurement,3,field,seedling,,,,,Test_2022,,,,,,,01,,Cryptocarya laevigata +Test_2023_2,Cryptocarya laevigata,031,leaf_mass_per_area,87,g/m2,species,maximum,measurement,3,field,seedling,,,,,Test_2022,,,,,,,01,,Cryptocarya laevigata +Test_2023_2,Cryptocarya laevigata,031,wood_density,0.64,mg/mm3,species,maximum,measurement,3,field,seedling,,,,,Test_2022,,,,,,,01,,Cryptocarya laevigata Test_2023_2,Cryptocarya mackinnoniana,032,branch_mass_fraction,0.61,mg/mg,population,mean,measurement,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Cryptocarya mackinnoniana Test_2023_2,Cryptocarya mackinnoniana,032,huber_value,0.000305157155935307,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Cryptocarya mackinnoniana Test_2023_2,Cryptocarya mackinnoniana,032,huber_value,0.00043010752688172,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Cryptocarya mackinnoniana Test_2023_2,Cryptocarya mackinnoniana,032,huber_value,0.000115513457317778,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Cryptocarya mackinnoniana Test_2023_2,Cryptocarya mackinnoniana,032,huber_value,0.000115513457317778,mm2{sapwood}/mm2{leaf},population,maximum,measurement,3,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Cryptocarya mackinnoniana Test_2023_2,Cryptocarya mackinnoniana,032,seed_dry_mass,204,mg,population,mean,measurement,unknown,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Cryptocarya mackinnoniana -Test_2023_2,Cryptocarya mackinnoniana,033,leaf_N_per_dry_mass,15.2,mg/g,species,mean,measurement,3,field,adult,,,,,Test_2022,,,,,,,01,,Cryptocarya mackinnoniana -Test_2023_2,Cryptocarya mackinnoniana,033,leaf_area,10458,mm2,species,mean,measurement,3,field,adult,,,,,Test_2022,,,,,,,01,,Cryptocarya mackinnoniana -Test_2023_2,Cryptocarya mackinnoniana,033,leaf_mass_per_area,204,g/m2,species,mean,measurement,3,field,adult,,,,,Test_2022,,,,,,,01,,Cryptocarya mackinnoniana -Test_2023_2,Cryptocarya mackinnoniana,033,wood_density,0.655,mg/mm3,species,mean,measurement,3,field,adult,,,,,Test_2022,,,,,,,01,,Cryptocarya mackinnoniana +Test_2023_2,Cryptocarya mackinnoniana,033,leaf_N_per_dry_mass,15.2,mg/g,species,mean,measurement,3,field,seedling,,,,,Test_2022,,,,,,,01,,Cryptocarya mackinnoniana +Test_2023_2,Cryptocarya mackinnoniana,033,leaf_area,10458,mm2,species,mean,measurement,3,field,seedling,,,,,Test_2022,,,,,,,01,,Cryptocarya mackinnoniana +Test_2023_2,Cryptocarya mackinnoniana,033,leaf_mass_per_area,204,g/m2,species,mean,measurement,3,field,seedling,,,,,Test_2022,,,,,,,01,,Cryptocarya mackinnoniana +Test_2023_2,Cryptocarya mackinnoniana,033,wood_density,0.655,mg/mm3,species,mean,measurement,3,field,seedling,,,,,Test_2022,,,,,,,01,,Cryptocarya mackinnoniana Test_2023_2,Cryptocarya murrayi,034,branch_mass_fraction,0.39,mg/mg,population,mean,measurement,,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Cryptocarya murrayi Test_2023_2,Cryptocarya murrayi,034,huber_value,0.000371333085777943,mm2{sapwood}/mm2{leaf},population,mean,measurement,7,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Cryptocarya murrayi Test_2023_2,Cryptocarya murrayi,034,huber_value,0.000180407721450478,mm2{sapwood}/mm2{leaf},population,mean,measurement,,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Cryptocarya murrayi Test_2023_2,Cryptocarya murrayi,034,huber_value,0.000232666356444858,mm2{sapwood}/mm2{leaf},population,mean,measurement,,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Cryptocarya murrayi Test_2023_2,Cryptocarya murrayi,034,huber_value,0.000183452577508714,mm2{sapwood}/mm2{leaf},population,mean,measurement,,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Cryptocarya murrayi Test_2023_2,Cryptocarya murrayi,034,huber_value,0.000183452577508714,mm2{sapwood}/mm2{leaf},population,maximum,measurement,,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Cryptocarya murrayi -Test_2023_2,Cryptocarya murrayi,035,leaf_N_per_dry_mass,16.7,mg/g,species,mean,measurement,,field,adult,,,,,Test_2022,,,,,,,01,,Cryptocarya murrayi -Test_2023_2,Cryptocarya murrayi,035,leaf_area,9960,mm2,species,mean,measurement,,field,adult,,,,,Test_2022,,,,,,,01,,Cryptocarya murrayi -Test_2023_2,Cryptocarya murrayi,035,leaf_mass_per_area,155,g/m2,species,mean,measurement,,field,adult,,,,,Test_2022,,,,,,,01,,Cryptocarya murrayi -Test_2023_2,Cryptocarya murrayi,035,wood_density,0.674,mg/mm3,species,mean,measurement,,field,adult,,,,,Test_2022,,,,,,,01,,Cryptocarya murrayi +Test_2023_2,Cryptocarya murrayi,035,leaf_N_per_dry_mass,16.7,mg/g,species,mean,measurement,,field,seedling,,,,,Test_2022,,,,,,,01,,Cryptocarya murrayi +Test_2023_2,Cryptocarya murrayi,035,leaf_area,9960,mm2,species,mean,measurement,,field,seedling,,,,,Test_2022,,,,,,,01,,Cryptocarya murrayi +Test_2023_2,Cryptocarya murrayi,035,leaf_mass_per_area,155,g/m2,species,mean,measurement,,field,seedling,,,,,Test_2022,,,,,,,01,,Cryptocarya murrayi +Test_2023_2,Cryptocarya murrayi,035,wood_density,0.674,mg/mm3,species,mean,measurement,,field,seedling,,,,,Test_2022,,,,,,,01,,Cryptocarya murrayi Test_2023_2,Dendrocnide moroides,036,branch_mass_fraction,0.46,mg/mg,population,mean,measurement,,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Dendrocnide moroides Test_2023_2,Dendrocnide moroides,036,huber_value,0.000421585160202361,mm2{sapwood}/mm2{leaf},population,mean,measurement,,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Dendrocnide moroides Test_2023_2,Dendrocnide moroides,036,huber_value,0.000478468899521531,mm2{sapwood}/mm2{leaf},population,mean,measurement,,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Dendrocnide moroides Test_2023_2,Dendrocnide moroides,036,huber_value,0.000478468899521531,mm2{sapwood}/mm2{leaf},population,maximum,measurement,,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Dendrocnide moroides Test_2023_2,Dendrocnide moroides,036,seed_dry_mass,0.71,mg,population,mean,measurement,unknown,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Dendrocnide moroides -Test_2023_2,Dendrocnide moroides,037,leaf_N_per_dry_mass,31.2,mg/g,species,mean,measurement,,field,adult,,,,,Test_2022,,,,,,,01,,Dendrocnide moroides -Test_2023_2,Dendrocnide moroides,037,leaf_area,26454,mm2,species,mean,measurement,,field,adult,,,,,Test_2022,,,,,,,01,,Dendrocnide moroides -Test_2023_2,Dendrocnide moroides,037,leaf_mass_per_area,52,g/m2,species,mean,measurement,,field,adult,,,,,Test_2022,,,,,,,01,,Dendrocnide moroides -Test_2023_2,Dendrocnide moroides,037,wood_density,0.23,mg/mm3,species,mean,measurement,,field,adult,,,,,Test_2022,,,,,,,01,,Dendrocnide moroides +Test_2023_2,Dendrocnide moroides,037,leaf_N_per_dry_mass,31.2,mg/g,species,mean,measurement,,field,seedling,,,,,Test_2022,,,,,,,01,,Dendrocnide moroides +Test_2023_2,Dendrocnide moroides,037,leaf_area,26454,mm2,species,mean,measurement,,field,seedling,,,,,Test_2022,,,,,,,01,,Dendrocnide moroides +Test_2023_2,Dendrocnide moroides,037,leaf_mass_per_area,52,g/m2,species,mean,measurement,,field,seedling,,,,,Test_2022,,,,,,,01,,Dendrocnide moroides +Test_2023_2,Dendrocnide moroides,037,wood_density,0.23,mg/mm3,species,mean,measurement,,field,seedling,,,,,Test_2022,,,,,,,01,,Dendrocnide moroides Test_2023_2,Elaeocarpus grandis,038,branch_mass_fraction,0.47,mg/mg,population,mean,measurement,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Elaeocarpus grandis Test_2023_2,Elaeocarpus grandis,038,huber_value,0.000384911470361817,mm2{sapwood}/mm2{leaf},population,mean,measurement,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Elaeocarpus grandis Test_2023_2,Elaeocarpus grandis,038,huber_value,0.0005720823798627,mm2{sapwood}/mm2{leaf},population,mean,measurement,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Elaeocarpus grandis Test_2023_2,Elaeocarpus grandis,038,huber_value,0.000215749730312837,mm2{sapwood}/mm2{leaf},population,mean,measurement,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Elaeocarpus grandis Test_2023_2,Elaeocarpus grandis,038,huber_value,0.000215749730312837,mm2{sapwood}/mm2{leaf},population,maximum,measurement,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Elaeocarpus grandis Test_2023_2,Elaeocarpus grandis,038,seed_dry_mass,3699,mg,population,mean,measurement,unknown,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Elaeocarpus grandis -Test_2023_2,Elaeocarpus grandis,039,leaf_N_per_dry_mass,18.7,mg/g,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Elaeocarpus grandis -Test_2023_2,Elaeocarpus grandis,039,leaf_area,2762,mm2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Elaeocarpus grandis -Test_2023_2,Elaeocarpus grandis,039,leaf_mass_per_area,122,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Elaeocarpus grandis -Test_2023_2,Elaeocarpus grandis,039,wood_density,0.499,mg/mm3,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Elaeocarpus grandis +Test_2023_2,Elaeocarpus grandis,039,leaf_N_per_dry_mass,18.7,mg/g,species,mean,measurement,2,field,seedling,,,,,Test_2022,,,,,,,01,,Elaeocarpus grandis +Test_2023_2,Elaeocarpus grandis,039,leaf_area,2762,mm2,species,mean,measurement,2,field,seedling,,,,,Test_2022,,,,,,,01,,Elaeocarpus grandis +Test_2023_2,Elaeocarpus grandis,039,leaf_mass_per_area,122,g/m2,species,mean,measurement,2,field,seedling,,,,,Test_2022,,,,,,,01,,Elaeocarpus grandis +Test_2023_2,Elaeocarpus grandis,039,wood_density,0.499,mg/mm3,species,mean,measurement,2,field,seedling,,,,,Test_2022,,,,,,,01,,Elaeocarpus grandis Test_2023_2,Endiandra leptodendron,040,branch_mass_fraction,0.68,mg/mg,population,mean,model_derived,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Endiandra leptodendron Test_2023_2,Endiandra leptodendron,040,huber_value,0.000670241286863271,mm2{sapwood}/mm2{leaf},population,mean,model_derived,7,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Endiandra leptodendron Test_2023_2,Endiandra leptodendron,040,huber_value,0.000414593698175788,mm2{sapwood}/mm2{leaf},population,mean,model_derived,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Endiandra leptodendron Test_2023_2,Endiandra leptodendron,040,huber_value,0.000359324469996407,mm2{sapwood}/mm2{leaf},population,mean,model_derived,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Endiandra leptodendron Test_2023_2,Endiandra leptodendron,040,huber_value,0.00013374348000535,mm2{sapwood}/mm2{leaf},population,mean,model_derived,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Endiandra leptodendron Test_2023_2,Endiandra leptodendron,040,huber_value,0.00013374348000535,mm2{sapwood}/mm2{leaf},population,maximum,model_derived,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Endiandra leptodendron -Test_2023_2,Endiandra leptodendron,041,leaf_N_per_dry_mass,18,mg/g,species,mean,model_derived,2,field,adult,,,,,Test_2022,,,,,,,01,,Endiandra leptodendron -Test_2023_2,Endiandra leptodendron,041,leaf_area,3987,mm2,species,mean,model_derived,2,field,adult,,,,,Test_2022,,,,,,,01,,Endiandra leptodendron -Test_2023_2,Endiandra leptodendron,041,leaf_mass_per_area,106,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Endiandra leptodendron -Test_2023_2,Endiandra leptodendron,041,wood_density,0.611,mg/mm3,species,mean,model_derived,2,field,adult,,,,,Test_2022,,,,,,,01,,Endiandra leptodendron +Test_2023_2,Endiandra leptodendron,041,leaf_N_per_dry_mass,18,mg/g,species,mean,model_derived,2,field,,,,,,Test_2022,,,,,,,01,,Endiandra leptodendron +Test_2023_2,Endiandra leptodendron,041,leaf_area,3987,mm2,species,mean,model_derived,2,field,,,,,,Test_2022,,,,,,,01,,Endiandra leptodendron +Test_2023_2,Endiandra leptodendron,041,leaf_mass_per_area,106,g/m2,species,mean,measurement,2,field,,,,,,Test_2022,,,,,,,01,,Endiandra leptodendron +Test_2023_2,Endiandra leptodendron,041,wood_density,0.611,mg/mm3,species,mean,model_derived,2,field,,,,,,Test_2022,,,,,,,01,,Endiandra leptodendron Test_2023_2,Endiandra microneura,042,branch_mass_fraction,0.61,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Endiandra microneura Test_2023_2,Endiandra microneura,042,huber_value,0.000279876854184159,mm2{sapwood}/mm2{leaf},population,mean,unknown,7,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Endiandra microneura Test_2023_2,Endiandra microneura,042,huber_value,0.000157629255989912,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Endiandra microneura Test_2023_2,Endiandra microneura,042,huber_value,0.000298151460942159,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Endiandra microneura Test_2023_2,Endiandra microneura,042,huber_value,0.000160384923817161,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Endiandra microneura Test_2023_2,Endiandra microneura,042,huber_value,0.000160384923817161,mm2{sapwood}/mm2{leaf},population,maximum,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Endiandra microneura -Test_2023_2,Endiandra microneura,043,leaf_N_per_dry_mass,17.7,mg/g,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Endiandra microneura -Test_2023_2,Endiandra microneura,043,leaf_area,3377,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Endiandra microneura -Test_2023_2,Endiandra microneura,043,leaf_mass_per_area,151,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Endiandra microneura -Test_2023_2,Endiandra microneura,043,wood_density,0.623,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Endiandra microneura +Test_2023_2,Endiandra microneura,043,leaf_N_per_dry_mass,17.7,mg/g,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Endiandra microneura +Test_2023_2,Endiandra microneura,043,leaf_area,3377,mm2,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Endiandra microneura +Test_2023_2,Endiandra microneura,043,leaf_mass_per_area,151,g/m2,species,mean,measurement,2,field,,,,,,Test_2022,,,,,,,01,,Endiandra microneura +Test_2023_2,Endiandra microneura,043,wood_density,0.623,mg/mm3,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Endiandra microneura Test_2023_2,Gillbeea adenopetala,044,branch_mass_fraction,0.46,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Gillbeea adenopetala Test_2023_2,Gillbeea adenopetala,044,huber_value,0.000349283967865875,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Gillbeea adenopetala Test_2023_2,Gillbeea adenopetala,044,huber_value,0.000316455696202532,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Gillbeea adenopetala Test_2023_2,Gillbeea adenopetala,044,huber_value,0.000152695067949305,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Gillbeea adenopetala Test_2023_2,Gillbeea adenopetala,044,huber_value,0.000152695067949305,mm2{sapwood}/mm2{leaf},population,maximum,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Gillbeea adenopetala Test_2023_2,Gillbeea adenopetala,044,seed_dry_mass,15,mg,population,mean,unknown,unknown,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Gillbeea adenopetala -Test_2023_2,Gillbeea adenopetala,045,leaf_N_per_dry_mass,9.6,mg/g,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Gillbeea adenopetala -Test_2023_2,Gillbeea adenopetala,045,leaf_area,3678,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Gillbeea adenopetala -Test_2023_2,Gillbeea adenopetala,045,leaf_mass_per_area,126,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Gillbeea adenopetala -Test_2023_2,Gillbeea adenopetala,045,wood_density,0.43,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Gillbeea adenopetala -Test_2023_2,Glochidion hylandii,046,branch_mass_fraction,0.41,mg/mg,population,mean,measurement,3,field,adult,01,,,,Test_2002,01,,,,,,01,,Glochidion hylandii +Test_2023_2,Gillbeea adenopetala,045,leaf_N_per_dry_mass,9.6,mg/g,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Gillbeea adenopetala +Test_2023_2,Gillbeea adenopetala,045,leaf_area,3678,mm2,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Gillbeea adenopetala +Test_2023_2,Gillbeea adenopetala,045,leaf_mass_per_area,126,g/m2,species,mean,measurement,2,field,,,,,,Test_2022,,,,,,,01,,Gillbeea adenopetala +Test_2023_2,Gillbeea adenopetala,045,wood_density,0.43,mg/mm3,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Gillbeea adenopetala +Test_2023_2,Glochidion hylandii,046,branch_mass_fraction,0.41,mg/mg,population,mean,measurement,3,field,adult,01,,,,Test_2002,01,,,,,Made-up remarks for `branch_mass_fraction`,01,,Glochidion hylandii Test_2023_2,Glochidion hylandii,046,huber_value,0.000501756146512795,mm2{sapwood}/mm2{leaf},population,mean,measurement,7,field,adult,01,,,,Test_2002,01,,,,,,01,,Glochidion hylandii Test_2023_2,Glochidion hylandii,046,huber_value,0.000197044334975369,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,01,,,,Test_2002,01,,,,,,02,,Glochidion hylandii Test_2023_2,Glochidion hylandii,046,huber_value,0.000183318056828598,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,01,,,,Test_2002,01,,,,,,03,,Glochidion hylandii Test_2023_2,Glochidion hylandii,046,huber_value,0.000115420129270545,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,01,,,,Test_2002,01,,,,,,04,,Glochidion hylandii Test_2023_2,Glochidion hylandii,046,huber_value,0.000115420129270545,mm2{sapwood}/mm2{leaf},population,maximum,measurement,3,field,adult,01,,,,Test_2002,01,,,,,,04,,Glochidion hylandii -Test_2023_2,Glochidion hylandii,047,seed_dry_mass,10.41,mg,population,mean,measurement,unknown,literature,seedling,01,,,,Test_2002,01,,,,,,01,,Glochidion hylandii +Test_2023_2,Glochidion hylandii,047,seed_dry_mass,10.41,mg,population,mean,measurement,unknown,literature,juvenile,01,,,,Test_2002,01,,,,,,01,,Glochidion hylandii Test_2023_2,Glochidion hylandii,048,leaf_N_per_dry_mass,13.7,mg/g,species,mean,measurement,3,field,adult,,,,,Test_2002,,,,,,,01,,Glochidion hylandii Test_2023_2,Glochidion hylandii,048,leaf_area,3209,mm2,species,mean,measurement,3,field,adult,,,,,Test_2002,,,,,,,01,,Glochidion hylandii Test_2023_2,Glochidion hylandii,048,leaf_mass_per_area,106,g/m2,species,mean,measurement,3,field,adult,,,,,Test_2002,,,,,,,01,,Glochidion hylandii @@ -222,39 +222,39 @@ Test_2023_2,Haplostichanthus submontanus,049,huber_value,8.12743823146944e-05,mm Test_2023_2,Haplostichanthus submontanus,049,huber_value,0.000304692260816575,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Haplostichanthus sp Coop. Ck Test_2023_2,Haplostichanthus submontanus,049,huber_value,0.000334224598930481,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Haplostichanthus sp Coop. Ck Test_2023_2,Haplostichanthus submontanus,049,huber_value,0.000334224598930481,mm2{sapwood}/mm2{leaf},population,maximum,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Haplostichanthus sp Coop. Ck -Test_2023_2,Haplostichanthus submontanus,050,leaf_N_per_dry_mass,22,mg/g,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Haplostichanthus sp Coop. Ck -Test_2023_2,Haplostichanthus submontanus,050,leaf_area,4685,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Haplostichanthus sp Coop. Ck -Test_2023_2,Haplostichanthus submontanus,050,leaf_mass_per_area,72,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Haplostichanthus sp Coop. Ck -Test_2023_2,Haplostichanthus submontanus,050,wood_density,0.668,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Haplostichanthus sp Coop. Ck +Test_2023_2,Haplostichanthus submontanus,050,leaf_N_per_dry_mass,22,mg/g,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Haplostichanthus sp Coop. Ck +Test_2023_2,Haplostichanthus submontanus,050,leaf_area,4685,mm2,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Haplostichanthus sp Coop. Ck +Test_2023_2,Haplostichanthus submontanus,050,leaf_mass_per_area,72,g/m2,species,mean,measurement,2,field,,,,,,Test_2022,,,,,,,01,,Haplostichanthus sp Coop. Ck +Test_2023_2,Haplostichanthus submontanus,050,wood_density,0.668,mg/mm3,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Haplostichanthus sp Coop. Ck Test_2023_2,Harpullia rhyticarpa,051,branch_mass_fraction,0.01,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Harpullia rhyticarpa Test_2023_2,Harpullia rhyticarpa,051,huber_value,0.000111470293166871,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Harpullia rhyticarpa Test_2023_2,Harpullia rhyticarpa,051,huber_value,0.000168861870989531,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Harpullia rhyticarpa Test_2023_2,Harpullia rhyticarpa,051,huber_value,0.000214178624973228,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Harpullia rhyticarpa Test_2023_2,Harpullia rhyticarpa,051,huber_value,0.000214178624973228,mm2{sapwood}/mm2{leaf},population,maximum,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Harpullia rhyticarpa -Test_2023_2,Harpullia rhyticarpa,052,leaf_N_per_dry_mass,17.4,mg/g,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Harpullia rhyticarpa -Test_2023_2,Harpullia rhyticarpa,052,leaf_area,40876,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Harpullia rhyticarpa -Test_2023_2,Harpullia rhyticarpa,052,leaf_mass_per_area,76,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Harpullia rhyticarpa -Test_2023_2,Harpullia rhyticarpa,052,wood_density,0.621,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Harpullia rhyticarpa +Test_2023_2,Harpullia rhyticarpa,052,leaf_N_per_dry_mass,17.4,mg/g,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Harpullia rhyticarpa +Test_2023_2,Harpullia rhyticarpa,052,leaf_area,40876,mm2,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Harpullia rhyticarpa +Test_2023_2,Harpullia rhyticarpa,052,leaf_mass_per_area,76,g/m2,species,mean,measurement,2,field,,,,,,Test_2022,,,,,,,01,,Harpullia rhyticarpa +Test_2023_2,Harpullia rhyticarpa,052,wood_density,0.621,mg/mm3,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Harpullia rhyticarpa Test_2023_2,Hernandia albiflora,053,branch_mass_fraction,0.33,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Hernandia albiflora Test_2023_2,Hernandia albiflora,053,huber_value,0.00032020493115594,mm2{sapwood}/mm2{leaf},population,mean,unknown,7,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Hernandia albiflora Test_2023_2,Hernandia albiflora,053,huber_value,0.000241254523522316,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Hernandia albiflora Test_2023_2,Hernandia albiflora,053,huber_value,0.000215377988369589,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Hernandia albiflora Test_2023_2,Hernandia albiflora,053,huber_value,0.000164311534669734,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Hernandia albiflora Test_2023_2,Hernandia albiflora,053,huber_value,0.000164311534669734,mm2{sapwood}/mm2{leaf},population,maximum,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Hernandia albiflora -Test_2023_2,Hernandia albiflora,054,leaf_N_per_dry_mass,19.5,mg/g,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Hernandia albiflora -Test_2023_2,Hernandia albiflora,054,leaf_area,3806,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Hernandia albiflora -Test_2023_2,Hernandia albiflora,054,leaf_mass_per_area,69,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Hernandia albiflora -Test_2023_2,Hernandia albiflora,054,wood_density,0.447,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Hernandia albiflora -Test_2023_2,Homalanthus novo-guineensis,055,branch_mass_fraction,0.47,mg/mg,population,mean,model_derived,3,field,adult,01,,,,Test_2002,01,,,,,,01,,Homalanthus novoguineensis -Test_2023_2,Homalanthus novo-guineensis,055,huber_value,0.000468164794007491,mm2{sapwood}/mm2{leaf},population,mean,model_derived,3,field,adult,01,,,,Test_2002,01,,,,,,02,,Homalanthus novoguineensis -Test_2023_2,Homalanthus novo-guineensis,055,huber_value,0.00046339202965709,mm2{sapwood}/mm2{leaf},population,mean,model_derived,3,field,adult,01,,,,Test_2002,01,,,,,,03,,Homalanthus novoguineensis -Test_2023_2,Homalanthus novo-guineensis,055,huber_value,0.000302388872089507,mm2{sapwood}/mm2{leaf},population,mean,model_derived,3,field,adult,01,,,,Test_2002,01,,,,,,04,,Homalanthus novoguineensis -Test_2023_2,Homalanthus novo-guineensis,055,huber_value,0.000302388872089507,mm2{sapwood}/mm2{leaf},population,maximum,model_derived,3,field,adult,01,,,,Test_2002,01,,,,,,04,,Homalanthus novoguineensis -Test_2023_2,Homalanthus novo-guineensis,056,seed_dry_mass,7,mg,population,mean,model_derived,unknown,literature,seedling,01,,,,Test_2002,01,,,,,,01,,Homalanthus novoguineensis -Test_2023_2,Homalanthus novo-guineensis,057,leaf_N_per_dry_mass,22,mg/g,species,mean,model_derived,3,field,adult,,,,,Test_2002,,,,,,,01,,Homalanthus novoguineensis -Test_2023_2,Homalanthus novo-guineensis,057,leaf_area,10682,mm2,species,mean,model_derived,3,field,adult,,,,,Test_2002,,,,,,,01,,Homalanthus novoguineensis -Test_2023_2,Homalanthus novo-guineensis,057,leaf_mass_per_area,82,g/m2,species,mean,measurement,3,field,adult,,,,,Test_2002,,,,,,,01,,Homalanthus novoguineensis -Test_2023_2,Homalanthus novo-guineensis,057,wood_density,0.319,mg/mm3,species,mean,model_derived,3,field,adult,,,,,Test_2002,,,,,,,01,,Homalanthus novoguineensis +Test_2023_2,Hernandia albiflora,054,leaf_N_per_dry_mass,19.5,mg/g,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Hernandia albiflora +Test_2023_2,Hernandia albiflora,054,leaf_area,3806,mm2,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Hernandia albiflora +Test_2023_2,Hernandia albiflora,054,leaf_mass_per_area,69,g/m2,species,mean,measurement,2,field,,,,,,Test_2022,,,,,,,01,,Hernandia albiflora +Test_2023_2,Hernandia albiflora,054,wood_density,0.447,mg/mm3,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Hernandia albiflora +Test_2023_2,Homalanthus novo-guineensis,055,seed_dry_mass,7,mg,population,mean,model_derived,unknown,literature,,01,,,,Test_2002,01,,,,,,01,,Homalanthus novoguineensis +Test_2023_2,Homalanthus novo-guineensis,056,branch_mass_fraction,0.47,mg/mg,population,mean,model_derived,3,field,seedling,01,,,,Test_2002,01,,,,,Made-up remarks for `branch_mass_fraction`,01,,Homalanthus novoguineensis +Test_2023_2,Homalanthus novo-guineensis,056,huber_value,0.000468164794007491,mm2{sapwood}/mm2{leaf},population,mean,model_derived,3,field,seedling,01,,,,Test_2002,01,,,,,,02,,Homalanthus novoguineensis +Test_2023_2,Homalanthus novo-guineensis,056,huber_value,0.00046339202965709,mm2{sapwood}/mm2{leaf},population,mean,model_derived,3,field,seedling,01,,,,Test_2002,01,,,,,,03,,Homalanthus novoguineensis +Test_2023_2,Homalanthus novo-guineensis,056,huber_value,0.000302388872089507,mm2{sapwood}/mm2{leaf},population,mean,model_derived,3,field,seedling,01,,,,Test_2002,01,,,,,,04,,Homalanthus novoguineensis +Test_2023_2,Homalanthus novo-guineensis,056,huber_value,0.000302388872089507,mm2{sapwood}/mm2{leaf},population,maximum,model_derived,3,field,seedling,01,,,,Test_2002,01,,,,,,04,,Homalanthus novoguineensis +Test_2023_2,Homalanthus novo-guineensis,057,leaf_N_per_dry_mass,22,mg/g,species,mean,model_derived,3,field,seedling,,,,,Test_2002,,,,,,,01,,Homalanthus novoguineensis +Test_2023_2,Homalanthus novo-guineensis,057,leaf_area,10682,mm2,species,mean,model_derived,3,field,seedling,,,,,Test_2002,,,,,,,01,,Homalanthus novoguineensis +Test_2023_2,Homalanthus novo-guineensis,057,leaf_mass_per_area,82,g/m2,species,mean,measurement,3,field,seedling,,,,,Test_2002,,,,,,,01,,Homalanthus novoguineensis +Test_2023_2,Homalanthus novo-guineensis,057,wood_density,0.319,mg/mm3,species,mean,model_derived,3,field,seedling,,,,,Test_2002,,,,,,,01,,Homalanthus novoguineensis Test_2023_2,Ixora biflora,058,branch_mass_fraction,0.55,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Ixora biflora Test_2023_2,Ixora biflora,058,huber_value,0.0001906941266209,mm2{sapwood}/mm2{leaf},population,mean,unknown,7,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Ixora biflora Test_2023_2,Ixora biflora,058,huber_value,0.00025693730729702,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Ixora biflora @@ -328,16 +328,16 @@ Test_2023_2,Melastoma cyanoides,071,leaf_N_per_dry_mass,20.8,mg/g,species,mean,u Test_2023_2,Melastoma cyanoides,071,leaf_area,4009,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Melastoma cyanoides Test_2023_2,Melastoma cyanoides,071,leaf_mass_per_area,46,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Melastoma cyanoides Test_2023_2,Melastoma cyanoides,071,wood_density,0.381,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Melastoma cyanoides -Test_2023_2,Melicope elleryana,072,branch_mass_fraction,0.58,mg/mg,population,mean,unknown,3,field,adult,01,,,,Test_2002,01,,,,,,01,,Melicope elleryana -Test_2023_2,Melicope elleryana,072,huber_value,0.000238038562247084,mm2{sapwood}/mm2{leaf},population,mean,unknown,3,field,adult,01,,,,Test_2002,01,,,,,,02,,Melicope elleryana -Test_2023_2,Melicope elleryana,072,huber_value,0.00034965034965035,mm2{sapwood}/mm2{leaf},population,mean,unknown,3,field,adult,01,,,,Test_2002,01,,,,,,03,,Melicope elleryana -Test_2023_2,Melicope elleryana,072,huber_value,0.000163425396306586,mm2{sapwood}/mm2{leaf},population,mean,unknown,3,field,adult,01,,,,Test_2002,01,,,,,,04,,Melicope elleryana -Test_2023_2,Melicope elleryana,072,huber_value,0.000163425396306586,mm2{sapwood}/mm2{leaf},population,maximum,unknown,3,field,adult,01,,,,Test_2002,01,,,,,,04,,Melicope elleryana -Test_2023_2,Melicope elleryana,073,seed_dry_mass,1.61,mg,population,mean,unknown,unknown,literature,seedling,01,,,,Test_2002,01,,,,,,01,,Melicope elleryana -Test_2023_2,Melicope elleryana,074,leaf_N_per_dry_mass,26.8,mg/g,species,mean,unknown,3,field,adult,,,,,Test_2002,,,,,,,01,,Melicope elleryana -Test_2023_2,Melicope elleryana,074,leaf_area,6955,mm2,species,mean,unknown,3,field,adult,,,,,Test_2002,,,,,,,01,,Melicope elleryana -Test_2023_2,Melicope elleryana,074,leaf_mass_per_area,75,g/m2,species,mean,measurement,3,field,adult,,,,,Test_2002,,,,,,,01,,Melicope elleryana -Test_2023_2,Melicope elleryana,074,wood_density,0.346,mg/mm3,species,mean,unknown,3,field,adult,,,,,Test_2002,,,,,,,01,,Melicope elleryana +Test_2023_2,Melicope elleryana,072,seed_dry_mass,1.61,mg,population,mean,unknown,unknown,literature,,01,,,,Test_2002,01,,,,,,01,,Melicope elleryana +Test_2023_2,Melicope elleryana,073,branch_mass_fraction,0.58,mg/mg,population,mean,unknown,3,field,juvenile,01,,,,Test_2002,01,,,,,Made-up remarks for `branch_mass_fraction`,01,,Melicope elleryana +Test_2023_2,Melicope elleryana,073,huber_value,0.000238038562247084,mm2{sapwood}/mm2{leaf},population,mean,unknown,3,field,juvenile,01,,,,Test_2002,01,,,,,,02,,Melicope elleryana +Test_2023_2,Melicope elleryana,073,huber_value,0.00034965034965035,mm2{sapwood}/mm2{leaf},population,mean,unknown,3,field,juvenile,01,,,,Test_2002,01,,,,,,03,,Melicope elleryana +Test_2023_2,Melicope elleryana,073,huber_value,0.000163425396306586,mm2{sapwood}/mm2{leaf},population,mean,unknown,3,field,juvenile,01,,,,Test_2002,01,,,,,,04,,Melicope elleryana +Test_2023_2,Melicope elleryana,073,huber_value,0.000163425396306586,mm2{sapwood}/mm2{leaf},population,maximum,unknown,3,field,juvenile,01,,,,Test_2002,01,,,,,,04,,Melicope elleryana +Test_2023_2,Melicope elleryana,074,leaf_N_per_dry_mass,26.8,mg/g,species,mean,unknown,3,field,juvenile,,,,,Test_2002,,,,,,,01,,Melicope elleryana +Test_2023_2,Melicope elleryana,074,leaf_area,6955,mm2,species,mean,unknown,3,field,juvenile,,,,,Test_2002,,,,,,,01,,Melicope elleryana +Test_2023_2,Melicope elleryana,074,leaf_mass_per_area,75,g/m2,species,mean,measurement,3,field,juvenile,,,,,Test_2002,,,,,,,01,,Melicope elleryana +Test_2023_2,Melicope elleryana,074,wood_density,0.346,mg/mm3,species,mean,unknown,3,field,juvenile,,,,,Test_2002,,,,,,,01,,Melicope elleryana Test_2023_2,Myristica insipida,075,branch_mass_fraction,0.51,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Myristica insipida Test_2023_2,Myristica insipida,075,huber_value,0.000144320969836917,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Myristica insipida Test_2023_2,Myristica insipida,075,huber_value,0.000206100577081616,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Myristica insipida @@ -348,17 +348,17 @@ Test_2023_2,Myristica insipida,076,leaf_N_per_dry_mass,18.5,mg/g,species,mean,un Test_2023_2,Myristica insipida,076,leaf_area,8379,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Myristica insipida Test_2023_2,Myristica insipida,076,leaf_mass_per_area,106,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Myristica insipida Test_2023_2,Myristica insipida,076,wood_density,0.433,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Myristica insipida -Test_2023_2,Neolitsea dealbata,077,branch_mass_fraction,0.58,mg/mg,population,mean,,2,field,adult,01,,,,Test_2002,01,,,,,,01,,Neolitsea dealbata -Test_2023_2,Neolitsea dealbata,077,huber_value,0.000593119810201661,mm2{sapwood}/mm2{leaf},population,mean,,7,field,adult,01,,,,Test_2002,01,,,,,,01,,Neolitsea dealbata -Test_2023_2,Neolitsea dealbata,077,huber_value,0.000364033491081179,mm2{sapwood}/mm2{leaf},population,mean,,2,field,adult,01,,,,Test_2002,01,,,,,,02,,Neolitsea dealbata -Test_2023_2,Neolitsea dealbata,077,huber_value,0.00032797638570023,mm2{sapwood}/mm2{leaf},population,mean,,2,field,adult,01,,,,Test_2002,01,,,,,,03,,Neolitsea dealbata -Test_2023_2,Neolitsea dealbata,077,huber_value,0.000133262260127932,mm2{sapwood}/mm2{leaf},population,mean,,2,field,adult,01,,,,Test_2002,01,,,,,,04,,Neolitsea dealbata -Test_2023_2,Neolitsea dealbata,077,huber_value,0.000133262260127932,mm2{sapwood}/mm2{leaf},population,maximum,,2,field,adult,01,,,,Test_2002,01,,,,,,04,,Neolitsea dealbata -Test_2023_2,Neolitsea dealbata,078,seed_dry_mass,176.1,mg,population,mean,,unknown,literature,seedling,01,,,,Test_2002,01,,,,,,01,,Neolitsea dealbata -Test_2023_2,Neolitsea dealbata,079,leaf_N_per_dry_mass,16.4,mg/g,species,mean,,2,field,adult,,,,,Test_2002,,,,,,,01,,Neolitsea dealbata -Test_2023_2,Neolitsea dealbata,079,leaf_area,5228,mm2,species,mean,,2,field,adult,,,,,Test_2002,,,,,,,01,,Neolitsea dealbata -Test_2023_2,Neolitsea dealbata,079,leaf_mass_per_area,93,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2002,,,,,,,01,,Neolitsea dealbata -Test_2023_2,Neolitsea dealbata,079,wood_density,0.352,mg/mm3,species,mean,,2,field,adult,,,,,Test_2002,,,,,,,01,,Neolitsea dealbata +Test_2023_2,Neolitsea dealbata,077,seed_dry_mass,176.1,mg,population,mean,,unknown,literature,,01,,,,Test_2002,01,,,,,,01,,Neolitsea dealbata +Test_2023_2,Neolitsea dealbata,078,branch_mass_fraction,0.58,mg/mg,population,mean,,2,field,juvenile,01,,,,Test_2002,01,,,,,Made-up remarks for `branch_mass_fraction`,01,,Neolitsea dealbata +Test_2023_2,Neolitsea dealbata,078,huber_value,0.000593119810201661,mm2{sapwood}/mm2{leaf},population,mean,,7,field,juvenile,01,,,,Test_2002,01,,,,,,01,,Neolitsea dealbata +Test_2023_2,Neolitsea dealbata,078,huber_value,0.000364033491081179,mm2{sapwood}/mm2{leaf},population,mean,,2,field,juvenile,01,,,,Test_2002,01,,,,,,02,,Neolitsea dealbata +Test_2023_2,Neolitsea dealbata,078,huber_value,0.00032797638570023,mm2{sapwood}/mm2{leaf},population,mean,,2,field,juvenile,01,,,,Test_2002,01,,,,,,03,,Neolitsea dealbata +Test_2023_2,Neolitsea dealbata,078,huber_value,0.000133262260127932,mm2{sapwood}/mm2{leaf},population,mean,,2,field,juvenile,01,,,,Test_2002,01,,,,,,04,,Neolitsea dealbata +Test_2023_2,Neolitsea dealbata,078,huber_value,0.000133262260127932,mm2{sapwood}/mm2{leaf},population,maximum,,2,field,juvenile,01,,,,Test_2002,01,,,,,,04,,Neolitsea dealbata +Test_2023_2,Neolitsea dealbata,079,leaf_N_per_dry_mass,16.4,mg/g,species,mean,,2,field,juvenile,,,,,Test_2002,,,,,,,01,,Neolitsea dealbata +Test_2023_2,Neolitsea dealbata,079,leaf_area,5228,mm2,species,mean,,2,field,juvenile,,,,,Test_2002,,,,,,,01,,Neolitsea dealbata +Test_2023_2,Neolitsea dealbata,079,leaf_mass_per_area,93,g/m2,species,mean,measurement,2,field,juvenile,,,,,Test_2002,,,,,,,01,,Neolitsea dealbata +Test_2023_2,Neolitsea dealbata,079,wood_density,0.352,mg/mm3,species,mean,,2,field,juvenile,,,,,Test_2002,,,,,,,01,,Neolitsea dealbata Test_2023_2,Pittosporum rubiginosum,080,branch_mass_fraction,0.28,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Pittosporum rubiginosum Test_2023_2,Pittosporum rubiginosum,080,huber_value,0.000134625740441572,mm2{sapwood}/mm2{leaf},population,mean,unknown,7,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Pittosporum rubiginosum Test_2023_2,Pittosporum rubiginosum,080,huber_value,0.000134066228716986,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Pittosporum rubiginosum @@ -370,15 +370,15 @@ Test_2023_2,Pittosporum rubiginosum,081,leaf_N_per_dry_mass,14.3,mg/g,species,me Test_2023_2,Pittosporum rubiginosum,081,leaf_area,9931,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Pittosporum rubiginosum Test_2023_2,Pittosporum rubiginosum,081,leaf_mass_per_area,65,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Pittosporum rubiginosum Test_2023_2,Pittosporum rubiginosum,081,wood_density,0.728,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Pittosporum rubiginosum -Test_2023_2,Polyscias australiana,082,branch_mass_fraction,0.42,mg/mg,population,mean,,2,field,adult,01,,,,Test_2002,01,,,,,,01,,Polyscias australiana -Test_2023_2,Polyscias australiana,082,huber_value,0.000166444740346205,mm2{sapwood}/mm2{leaf},population,mean,,2,field,adult,01,,,,Test_2002,01,,,,,,02,,Polyscias australiana -Test_2023_2,Polyscias australiana,082,huber_value,0.000149253731343284,mm2{sapwood}/mm2{leaf},population,mean,,2,field,adult,01,,,,Test_2002,01,,,,,,04,,Polyscias australiana -Test_2023_2,Polyscias australiana,082,huber_value,0.000149253731343284,mm2{sapwood}/mm2{leaf},population,maximum,,2,field,adult,01,,,,Test_2002,01,,,,,,04,,Polyscias australiana -Test_2023_2,Polyscias australiana,083,seed_dry_mass,8.35,mg,population,mean,,unknown,literature,seedling,01,,,,Test_2002,01,,,,,,01,,Polyscias australiana -Test_2023_2,Polyscias australiana,084,leaf_N_per_dry_mass,15.4,mg/g,species,mean,,2,field,adult,,,,,Test_2002,,,,,,,01,,Polyscias australiana -Test_2023_2,Polyscias australiana,084,leaf_area,6806,mm2,species,mean,,2,field,adult,,,,,Test_2002,,,,,,,01,,Polyscias australiana -Test_2023_2,Polyscias australiana,084,leaf_mass_per_area,79,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2002,,,,,,,01,,Polyscias australiana -Test_2023_2,Polyscias australiana,084,wood_density,0.397,mg/mm3,species,mean,,2,field,adult,,,,,Test_2002,,,,,,,01,,Polyscias australiana +Test_2023_2,Polyscias australiana,082,branch_mass_fraction,0.42,mg/mg,population,mean,,2,field,,01,,,,Test_2002,01,,,,,Made-up remarks for `branch_mass_fraction`,01,,Polyscias australiana +Test_2023_2,Polyscias australiana,082,huber_value,0.000166444740346205,mm2{sapwood}/mm2{leaf},population,mean,,2,field,,01,,,,Test_2002,01,,,,,Test dataset-level measurement_remarks,02,,Polyscias australiana +Test_2023_2,Polyscias australiana,082,huber_value,0.000149253731343284,mm2{sapwood}/mm2{leaf},population,mean,,2,field,,01,,,,Test_2002,01,,,,,Test dataset-level measurement_remarks,04,,Polyscias australiana +Test_2023_2,Polyscias australiana,082,huber_value,0.000149253731343284,mm2{sapwood}/mm2{leaf},population,maximum,,2,field,,01,,,,Test_2002,01,,,,,Test dataset-level measurement_remarks,04,,Polyscias australiana +Test_2023_2,Polyscias australiana,083,seed_dry_mass,8.35,mg,population,mean,,unknown,literature,,01,,,,Test_2002,01,,,,,Test dataset-level measurement_remarks,01,,Polyscias australiana +Test_2023_2,Polyscias australiana,084,leaf_N_per_dry_mass,15.4,mg/g,species,mean,,2,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Polyscias australiana +Test_2023_2,Polyscias australiana,084,leaf_area,6806,mm2,species,mean,,2,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Polyscias australiana +Test_2023_2,Polyscias australiana,084,leaf_mass_per_area,79,g/m2,species,mean,measurement,2,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Polyscias australiana +Test_2023_2,Polyscias australiana,084,wood_density,0.397,mg/mm3,species,mean,,2,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Polyscias australiana Test_2023_2,Psychotria dallachiana,085,branch_mass_fraction,0.33,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Psychotria dallachiana Test_2023_2,Psychotria dallachiana,085,huber_value,0.000233100233100233,mm2{sapwood}/mm2{leaf},population,mean,unknown,7,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Psychotria dallachiana Test_2023_2,Psychotria dallachiana,085,huber_value,0.000176491351923756,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Psychotria dallachiana @@ -389,16 +389,16 @@ Test_2023_2,Psychotria dallachiana,086,leaf_N_per_dry_mass,17.7,mg/g,species,mea Test_2023_2,Psychotria dallachiana,086,leaf_area,2495,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Psychotria dallachiana Test_2023_2,Psychotria dallachiana,086,leaf_mass_per_area,79,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Psychotria dallachiana Test_2023_2,Psychotria dallachiana,086,wood_density,0.612,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Psychotria dallachiana -Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),087,branch_mass_fraction,0,mg/mg,population,mean,,,field,adult,01,,,,Test_2002,01,,,,,,01,,Psychotria sp Utchee Creek -Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),087,huber_value,0.000200924251557163,mm2{sapwood}/mm2{leaf},population,mean,,,field,adult,01,,,,Test_2002,01,,,,,,02,,Psychotria sp Utchee Creek -Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),087,huber_value,0.000434404865334492,mm2{sapwood}/mm2{leaf},population,mean,,,field,adult,01,,,,Test_2002,01,,,,,,03,,Psychotria sp Utchee Creek -Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),087,huber_value,0.000490918016691213,mm2{sapwood}/mm2{leaf},population,mean,,,field,adult,01,,,,Test_2002,01,,,,,,04,,Psychotria sp Utchee Creek -Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),087,huber_value,0.000490918016691213,mm2{sapwood}/mm2{leaf},population,maximum,,,field,adult,01,,,,Test_2002,01,,,,,,04,,Psychotria sp Utchee Creek -Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),088,seed_dry_mass,23.09,mg,population,mean,,unknown,literature,seedling,01,,,,Test_2002,01,,,,,,01,,Psychotria sp Utchee Creek -Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),089,leaf_N_per_dry_mass,17.9,mg/g,species,mean,,,field,adult,,,,,Test_2002,,,,,,,01,,Psychotria sp Utchee Creek -Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),089,leaf_area,11157,mm2,species,mean,,,field,adult,,,,,Test_2002,,,,,,,01,,Psychotria sp Utchee Creek -Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),089,leaf_mass_per_area,108,g/m2,species,mean,measurement,,field,adult,,,,,Test_2002,,,,,,,01,,Psychotria sp Utchee Creek -Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),089,wood_density,0.582,mg/mm3,species,mean,,,field,adult,,,,,Test_2002,,,,,,,01,,Psychotria sp Utchee Creek +Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),087,branch_mass_fraction,0,mg/mg,population,mean,,,field,,01,,,,Test_2002,01,,,,,Made-up remarks for `branch_mass_fraction`,01,,Psychotria sp Utchee Creek +Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),087,huber_value,0.000200924251557163,mm2{sapwood}/mm2{leaf},population,mean,,,field,,01,,,,Test_2002,01,,,,,Test dataset-level measurement_remarks,02,,Psychotria sp Utchee Creek +Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),087,huber_value,0.000434404865334492,mm2{sapwood}/mm2{leaf},population,mean,,,field,,01,,,,Test_2002,01,,,,,Test dataset-level measurement_remarks,03,,Psychotria sp Utchee Creek +Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),087,huber_value,0.000490918016691213,mm2{sapwood}/mm2{leaf},population,mean,,,field,,01,,,,Test_2002,01,,,,,Test dataset-level measurement_remarks,04,,Psychotria sp Utchee Creek +Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),087,huber_value,0.000490918016691213,mm2{sapwood}/mm2{leaf},population,maximum,,,field,,01,,,,Test_2002,01,,,,,Test dataset-level measurement_remarks,04,,Psychotria sp Utchee Creek +Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),088,seed_dry_mass,23.09,mg,population,mean,,unknown,literature,,01,,,,Test_2002,01,,,,,Test dataset-level measurement_remarks,01,,Psychotria sp Utchee Creek +Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),089,leaf_N_per_dry_mass,17.9,mg/g,species,mean,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Psychotria sp Utchee Creek +Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),089,leaf_area,11157,mm2,species,mean,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Psychotria sp Utchee Creek +Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),089,leaf_mass_per_area,108,g/m2,species,mean,measurement,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Psychotria sp Utchee Creek +Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),089,wood_density,0.582,mg/mm3,species,mean,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Psychotria sp Utchee Creek Test_2023_2,Quassia baileyana,090,branch_mass_fraction,0.42,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Quassia baileyana Test_2023_2,Quassia baileyana,090,huber_value,0.000170444861087438,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Quassia baileyana Test_2023_2,Quassia baileyana,090,huber_value,0.000310945273631841,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Quassia baileyana @@ -408,16 +408,16 @@ Test_2023_2,Quassia baileyana,091,leaf_N_per_dry_mass,23,mg/g,species,mean,unkno Test_2023_2,Quassia baileyana,091,leaf_area,9624,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Quassia baileyana Test_2023_2,Quassia baileyana,091,leaf_mass_per_area,86,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Quassia baileyana Test_2023_2,Quassia baileyana,091,wood_density,0.501,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Quassia baileyana -Test_2023_2,Rhodomyrtus trineura,092,branch_mass_fraction,0.34,mg/mg,population,mean,,,field,adult,01,,,,Test_2002,01,,,,,,01,,Rhodomyrtus trineura -Test_2023_2,Rhodomyrtus trineura,092,huber_value,0.000231427910205971,mm2{sapwood}/mm2{leaf},population,mean,,7,field,adult,01,,,,Test_2002,01,,,,,,01,,Rhodomyrtus trineura -Test_2023_2,Rhodomyrtus trineura,092,huber_value,0.000262950302392848,mm2{sapwood}/mm2{leaf},population,mean,,,field,adult,01,,,,Test_2002,01,,,,,,02,,Rhodomyrtus trineura -Test_2023_2,Rhodomyrtus trineura,092,huber_value,0.000164257555847569,mm2{sapwood}/mm2{leaf},population,mean,,,field,adult,01,,,,Test_2002,01,,,,,,03,,Rhodomyrtus trineura -Test_2023_2,Rhodomyrtus trineura,092,huber_value,0.00014541224371092,mm2{sapwood}/mm2{leaf},population,mean,,,field,adult,01,,,,Test_2002,01,,,,,,04,,Rhodomyrtus trineura -Test_2023_2,Rhodomyrtus trineura,092,huber_value,0.00014541224371092,mm2{sapwood}/mm2{leaf},population,maximum,,,field,adult,01,,,,Test_2002,01,,,,,,04,,Rhodomyrtus trineura -Test_2023_2,Rhodomyrtus trineura,093,leaf_N_per_dry_mass,11.1,mg/g,species,mean,,,field,adult,,,,,Test_2002,,,,,,,01,,Rhodomyrtus trineura -Test_2023_2,Rhodomyrtus trineura,093,leaf_area,3401,mm2,species,mean,,,field,adult,,,,,Test_2002,,,,,,,01,,Rhodomyrtus trineura -Test_2023_2,Rhodomyrtus trineura,093,leaf_mass_per_area,129,g/m2,species,mean,measurement,,field,adult,,,,,Test_2002,,,,,,,01,,Rhodomyrtus trineura -Test_2023_2,Rhodomyrtus trineura,093,wood_density,0.763,mg/mm3,species,mean,,,field,adult,,,,,Test_2002,,,,,,,01,,Rhodomyrtus trineura +Test_2023_2,Rhodomyrtus trineura,092,branch_mass_fraction,0.34,mg/mg,population,mean,,,field,,01,,,,Test_2002,01,,,,,Made-up remarks for `branch_mass_fraction`,01,,Rhodomyrtus trineura +Test_2023_2,Rhodomyrtus trineura,092,huber_value,0.000231427910205971,mm2{sapwood}/mm2{leaf},population,mean,,7,field,,01,,,,Test_2002,01,,,,,Test dataset-level measurement_remarks,01,,Rhodomyrtus trineura +Test_2023_2,Rhodomyrtus trineura,092,huber_value,0.000262950302392848,mm2{sapwood}/mm2{leaf},population,mean,,,field,,01,,,,Test_2002,01,,,,,Test dataset-level measurement_remarks,02,,Rhodomyrtus trineura +Test_2023_2,Rhodomyrtus trineura,092,huber_value,0.000164257555847569,mm2{sapwood}/mm2{leaf},population,mean,,,field,,01,,,,Test_2002,01,,,,,Test dataset-level measurement_remarks,03,,Rhodomyrtus trineura +Test_2023_2,Rhodomyrtus trineura,092,huber_value,0.00014541224371092,mm2{sapwood}/mm2{leaf},population,mean,,,field,,01,,,,Test_2002,01,,,,,Test dataset-level measurement_remarks,04,,Rhodomyrtus trineura +Test_2023_2,Rhodomyrtus trineura,092,huber_value,0.00014541224371092,mm2{sapwood}/mm2{leaf},population,maximum,,,field,,01,,,,Test_2002,01,,,,,Test dataset-level measurement_remarks,04,,Rhodomyrtus trineura +Test_2023_2,Rhodomyrtus trineura,093,leaf_N_per_dry_mass,11.1,mg/g,species,mean,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Rhodomyrtus trineura +Test_2023_2,Rhodomyrtus trineura,093,leaf_area,3401,mm2,species,mean,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Rhodomyrtus trineura +Test_2023_2,Rhodomyrtus trineura,093,leaf_mass_per_area,129,g/m2,species,mean,measurement,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Rhodomyrtus trineura +Test_2023_2,Rhodomyrtus trineura,093,wood_density,0.763,mg/mm3,species,mean,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Rhodomyrtus trineura Test_2023_2,Rockinghamia angustifolia,094,branch_mass_fraction,0.39,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Rockinghamia angustifolia Test_2023_2,Rockinghamia angustifolia,094,huber_value,0.000170590242238144,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Rockinghamia angustifolia Test_2023_2,Rockinghamia angustifolia,094,huber_value,0.000216872695727608,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Rockinghamia angustifolia diff --git a/tests/testthat/examples/Test_2023_4/README.md b/tests/testthat/examples/Test_2023_4/README.md index 873407ef..363d23c1 100644 --- a/tests/testthat/examples/Test_2023_4/README.md +++ b/tests/testthat/examples/Test_2023_4/README.md @@ -15,9 +15,10 @@ Test_2023_4 is a copy of NHNSW_2023 with the following modifications: - Added `entity_type` as a column, and read in as a dataset-level column with also trait-level and location-level metadata (included some NAs) - Read `value_type` as a column and as fixed values at the trait level - Added `basis_of_value` and `basis_of_record` as columns at the trait-level, with a fixed value at the dataset level for the latter (included NAs in column) (and missing `basis_of_record` for `fruit_width`) -- Added `life_stage` as dataset-level, trait-level and location-level metadata -- Added `replicates` as dataset-level and location-level metadata -- Added `measurement_remarks` as dataset-level and location-level metadata +- Added `replicates` as dataset-level and trait-level metadata +- Added `life_stage` as dataset-level column metadata, fixed trait-level and location-level metadata +- Added `measurement_remarks` as dataset-level column metadata, fixed location-level metadata and trait-level column metadata #TODO +- Added `collection_date` as location-level metadata (set as NA at dataset level because otherwise `custom_R_code` won't be detected correctly -- see `read_metadata` function) - Removed trait-level `unit_in` for `fruit_colour` and `fruit_length` and instead read their units in from a column at the dataset level - Converted some `fruit_length` units to cm (and changed the "units" column) - For `fruit_width`, put `units` column to NA using `custom_R_code` to test that units are read in at the trait level while they are NA in the column at the dataset level diff --git a/tests/testthat/examples/Test_2023_4/data.csv b/tests/testthat/examples/Test_2023_4/data.csv index b6280ea4..bf3ae68b 100644 --- a/tests/testthat/examples/Test_2023_4/data.csv +++ b/tests/testthat/examples/Test_2023_4/data.csv @@ -1,229 +1,229 @@ -source,test_location,taxon_name,trait_name,category,trait_value,flora_value,units,value_type,test_entity_type,test_basis_of_value,test_basis_of_record,source_id,individual_id,collection_date -PlantNET_flora,australia,Exocarpos homalocladus,fruit_width,drupe,8,,mm,maximum,species,measurement,,Test_2000,, -PlantNET_flora,australia,Lepidosperma gladiatum,fruit_length,nut,0.3,,cm,maximum,species,measurement,literature,Test_2000,, -PlantNET_flora,australia_2,Imperata cylindrica,fruit_length,caryopsis,0.1,,cm,minimum,individual,measurement,literature,Test_2000,,2006-03 -PlantNET_flora,australia_2,Imperata cylindrica,fruit_length,caryopsis,0.1,,cm,minimum,individual,measurement,literature,Test_2000,,2007-03 -PlantNET_flora,australia,Gentianella barringtonensis,fruit_colour,,brown,inferred_from_genus,,minimum,species,,literature,,, -PlantNET_flora,australia,Acacia bulgaensis,fruit_length,pods,95,,mm,minimum,metapopulation,measurement,literature,,, -PlantNET_flora,australia,Sparaxis bulbifera,fruit_colour,,green,green,,minimum,metapopulation,,field,,, -PlantNET_flora,australia,Psoralea pinnata,fruit_width,fruits,2.5,,mm,minimum,metapopulation,,field,Test_2003,, -PlantNET_flora,australia,Eucalyptus dorrigoensis,fruit_length,fruit,0.5,,cm,minimum,species,measurement,field_experiment,Test_2003,, -PlantNET_flora,australia,Alectryon subdentatus,fruit_length,capsule,0.8,,cm,minimum,species,measurement,,Test_2003,,2008-01 -PlantNET_flora,australia,Alectryon subdentatus,fruit_length,capsule,0.8,,cm,minimum,species,measurement,,Test_2003,,2009-01 -PlantNET_flora,,Acacia crassa,fruit_length,pods,40,,mm,minimum,species,expert_score,field,Test_2003,, -PlantNET_flora,,Commersonia amystia,fruit_width,capsule,13,,mm,maximum,species,unknown,field,Test_2003,, -PlantNET_flora,,Gompholobium grandiflorum,fruit_length,pod,15,,mm,maximum,species,,,Test_2003,, -PlantNET_flora,australia_2,Crassula decumbens,fruit_dehiscence,,dehiscent,dehiscing,,mode,species,,,Test_2003,, -PlantNET_flora,australia_2,Chthonocephalus pseudevax,fruit_length,achenes,0.5,,mm,mode,,,,Test_2003,, -PlantNET_flora,australia_2,Amyema preissii,fruit_colour,,pink white,pink white,,mode,,,,Test_2003,, -PlantNET_flora,australia_2,Dichromochlamys dentatifolia,fruit_length,achenes,1.8,,mm,mode,,,field_experiment,Test_2003,, -PlantNET_flora,australia_2,Adriana tomentosa,fruit_width,capsule,12,,mm,mode,,,literature,Test_2003,, -PlantNET_flora,australia_2,Isotoma fluviatilis subsp. fluviatilis,fruit_width,capsule,3,,mm,mode,,,literature,Test_2003,, -PlantNET_flora,australia_2,Cassinia compacta,fruit_length,achenes,0.5,,mm,mode,,,literature,Test_2003,, -PlantNET_flora,australia_2,Mischocarpus australis,fruit_width,capsule,8,,mm,mode,,,literature,Test_2003,, -PlantNET_flora,australia_2,Eleocharis pallens,fruit_length,nut,1.4,,mm,mode,population,,literature,Test_2003,, -PlantNET_flora,australia_2,Hypoxis glabella var. glabella,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,population,unknown,literature,Test_2003,, -PlantNET_flora,australia_2,Crassula peduncularis,fruit_dehiscence,,dehiscent,splitting,,mode,population,expert_score,literature,Test_2003,, -PlantNET_flora,australia_2,Derris involuta,fruit_dehiscence,,indehiscent,inferred_from_genus,,mode,population,measurement,literature,Test_2003,, -PlantNET_flora,australia_2,Diodia,fruit_dehiscence,,indehiscent,indehiscent,,mode,genus,measurement,literature,Test_2003,, -PlantNET_flora,australia_2,Stellaria angustifolia subsp. angustifolia,fruit_length,capsule,8.5,,mm,mode,,measurement,literature,Test_2003,, -PlantNET_flora,australia_2,Pittosporum erioloma,fruit_dehiscence,,dehiscent,valves,,mode,,measurement,literature,Test_2003,, -PlantNET_flora,australia_2,Corymbia citriodora,fruit_length,fruit,15,,mm,mode,,measurement,literature,Test_2003,, -PlantNET_flora,australia_2,Pimelea ligustrina subsp. ligustrina,fruit_colour,,green,inferred_from_species,,mode,metapopulation,measurement,literature,Test_2003,, -PlantNET_flora,australia_2,Trifolium dubium,fruit_length,pod,2,,mm,mode,metapopulation,measurement,literature,Test_2003,, -PlantNET_flora,australia_2,Myoporum boninense subsp. australe,fruit_length,fruit,10,,mm,mode,metapopulation,measurement,literature,Test_2003,, -PlantNET_flora,australia_2,Arbutus unedo,fruit_colour,,red,red,,mode,metapopulation,measurement,,,, -PlantNET_flora,australia_2,Schoenus vaginatus,fruit_colour,,red yellow brown,red yellow brown,,mode,metapopulation,,,,, -PlantNET_flora,australia_2,Dodonaea petiolaris,fruit_length,capsule,16,,mm,mode,metapopulation,,,,, -PlantNET_flora,australia_2,Leptospermum continentale,fruit_length,fruit,6,,mm,mode,metapopulation,,,,, -PlantNET_flora,australia_2,Freesia hybrid,fruit_colour,,green,green,,mode,metapopulation,,,,, -PlantNET_flora,australia_2,Epilobium gunnianum,fruit_length,fruit,75,,mm,mode,metapopulation,,,,, -PlantNET_flora,australia_2,Dodonaea truncatiales,fruit_width,capsule,17,,mm,mode,metapopulation,,,,, -PlantNET_flora,australia_2,Thlaspi,fruit_dehiscence,,dehiscent,dehiscent,,mode,metapopulation,,,,, -PlantNET_flora,australia_2,Eucalyptus recurva,fruit_length,fruit,4,,mm,mode,metapopulation,,,Test_2000,, -PlantNET_flora,australia_2,Lotononis bainesii,fruit_length,pod,8,,mm,mode,metapopulation,,,Test_2000,, -PlantNET_flora,australia_2,Correa alba,fruit_length,fruit,5,,mm,mode,species,,,Test_2000,, -PlantNET_flora,australia_2,Commersonia salviifolia,fruit_width,capsule,5,,mm,mode,species,,,Test_2000,, -PlantNET_flora,australia_2,Carex cephalotes,fruit_length,utricles,2.5,,mm,,species,,,,, -PlantNET_flora,australia_2,Juncus acutus subsp. acutus,fruit_dehiscence,,dehiscent,inferred_from_family,,,species,,,,, -PlantNET_flora,australia_2,Thelymitra kangaloonica,fruit_length,capsules,12,,mm,,species,,,,, -PlantNET_flora,australia_2,Eucalyptus viminalis,fruit_width,fruit,4,,mm,,species,,,,, -PlantNET_flora,australia_2,Acronychia littoralis,fruit_width,fruit,20,,mm,,species,,,,, -PlantNET_flora,australia_2,Eucalyptus leucoxylon subsp. pruinosa,fruit_dehiscence,,dehiscent,valves,,,species,,,,, -PlantNET_flora,australia_2,Hibbertia crinita,fruit_dehiscence,,dehiscent,inferred_from_genus,,,species,,,,, -PlantNET_flora,australia_2,Crotalaria brevis,fruit_length,pods,6,,mm,mean,species,,,,, -PlantNET_flora,australia_2,Spergularia diandra,fruit_dehiscence,,dehiscent,inferred_from_genus,,mean,species,,,,, -PlantNET_flora,australia_2,Hypericum elodes,fruit_length,capsule,4,,mm,mean,species,,,,, -PlantNET_flora,australia_2,Hakea macraeana,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,, -PlantNET_flora,australia_2,Dillwynia cinerascens,fruit_length,pod,5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Lupinus polyphyllus,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,, -PlantNET_flora,australia_2,Potamogeton australiensis,fruit_length,fruit,4,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Hypoxis,fruit_dehiscence,,dehiscent,dehiscing,,mode,species,,,,, -PlantNET_flora,australia_2,Carex raleighii,fruit_length,utricles,2.5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Veronica catenata,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,, -PlantNET_flora,australia_2,Phlegmatospermum cochlearinum,fruit_length,silicula,10,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Australina pusilla,fruit_length,achene,1,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Schoenus lepidosperma,fruit_width,nut,2.5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Calendula arvensis,fruit_length,achenes,15,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Veronica derwentiana,fruit_length,capsule,2.8,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Gossia bidwillii,fruit_colour,,black,black,,mode,species,,,,, -PlantNET_flora,australia_2,Cyperus bulbosus,fruit_colour,,grey,greyish,,mode,species,,,,, -PlantNET_flora,australia_2,Eucalyptus youmanii,fruit_width,fruit,9,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Lobelia pedunculata,fruit_length,fruit,4,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Goodenia varia,fruit_length,fruit,10,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Convolvulus farinosus,fruit_width,capsule,6,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Freesia laxa,fruit_length,capsule,12,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Rhodamnia argentea,fruit_colour,,black,black,,mode,species,,,,, -PlantNET_flora,australia_2,Eremophila deserti,fruit_colour,,yellow black,yellow black,,mode,species,,,,, -PlantNET_flora,australia_2,Geijera salicifolia,fruit_width,fruit,6,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Endiandra globosa,fruit_width,fruit,50,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Thesium australe,fruit_width,fruit,2.5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Teucrium puberulum,fruit_width,drupe,4,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Davidsonia johnsonii,fruit_length,fruit,30,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Claoxylon australe,fruit_width,capsule,5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Cyperus sculptus,fruit_length,nut,1,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Cyperus laevigatus,fruit_width,nut,1.2,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Eucalyptus muelleriana,fruit_dehiscence,,dehiscent,valves,,mode,species,,,,, -PlantNET_flora,australia_2,Centranthera,fruit_dehiscence,,dehiscent,loculicidal,,mode,species,,,,, -PlantNET_flora,australia_2,Eucalyptus badjensis,fruit_length,fruit,5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Leucopogon amplexicaulis,fruit_length,fruit,3.5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Eucalyptus oblonga,fruit_length,fruit,8,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Lobelia trigonocaulis,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,, -PlantNET_flora,australia_2,Senecio longipilus,fruit_length,achenes,2.5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Burmannia disticha,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,, -PlantNET_flora,australia_2,Schoenus apogon,fruit_colour,,white,whitish,,mode,species,,,,, -PlantNET_flora,australia_2,Bursaria spinosa subsp. spinosa,fruit_width,capsules,9,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Pisum sativum var. arvense,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,, -PlantNET_flora,australia_2,Abildgaardia ovata,fruit_width,nut,1.2,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Leptospermum obovatum,fruit_width,fruit,8,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Hibiscus brachysiphonius,fruit_length,capsule,15,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Muehlenbeckia adpressa,fruit_colour,,brown black,brown black,,mode,species,,,,, -PlantNET_flora,australia_2,Salix alba,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,, -PlantNET_flora,australia_2,Isolepis montivaga,fruit_length,nut,0.9,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Leptomeria drupacea,fruit_length,drupe,6,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Elaeocarpus grandis,fruit_width,fruit,20,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Eucalyptus youmanii,fruit_length,fruit,12,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Carex leporina,fruit_length,utricles,3.5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Juncus kraussii,fruit_colour,,red yellow brown black,red golden brown blackish,,mode,species,,,,, -PlantNET_flora,australia_2,Eucalyptus nandewarica,fruit_length,fruit,3,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Eucalyptus yangoura,fruit_width,fruit,6,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Eucalyptus olida,fruit_length,fruit,5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Sida goniocarpa,fruit_width,fruit,7,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Dampiera fusca,fruit_colour,,brown,brownish,,mode,species,,,,, -PlantNET_flora,australia_2,Lepidium foliosum,fruit_length,silicula,4,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Alectryon coriaceus,fruit_length,capsule,7,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Styphelia viridis,fruit_length,fruit,10,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Lepidium oxytrichum,fruit_length,silicula,5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Rhodamnia argentea,fruit_length,fruit,6,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Rubus parvifolius,fruit_colour,,red,red,,mode,species,,,,, -PlantNET_flora,australia_2,Artanema,fruit_dehiscence,,dehiscent,valve,,mode,species,,,,, -PlantNET_flora,australia_2,Lepidium africanum,fruit_width,silicula,2,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Acacia leiocalyx subsp. leiocalyx,fruit_width,pods,4,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Plantago turrifera,fruit_length,capsule,3,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Crotalaria brevis,fruit_colour,,brown,brown,,mode,species,,,,, -PlantNET_flora,australia_2,Apophyllum anomalum,fruit_colour,,purple,purple,,mode,species,,,,, -PlantNET_flora,australia_2,Isotoma axillaris,fruit_length,capsule,7,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Eucalyptus camphora,fruit_length,fruit,4,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Medicago orbicularis,fruit_length,pod,7,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Acacia havilandiorum,fruit_width,pods,2,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Coprosma nivalis,fruit_colour,,purple grey,violet grey,,mode,species,,,,, -PlantNET_flora,australia_2,Swainsona cadellii,fruit_length,pod,25,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Paraserianthes lophantha,fruit_width,pod,25,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Crotalaria lanceolata,fruit_length,pod,20,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Nicotiana goodspeedii,fruit_length,capsule,5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Eucalyptus rossii,fruit_width,fruit,6,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Gentiana wingecarribiensis,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,, -PlantNET_flora,australia_2,Oxalis corniculata,fruit_width,fruit,1.5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Acacia gladiiformis,fruit_length,pods,150,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Escallonia bifida,fruit_length,capsule,3,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Crotalaria grahamiana,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,, -PlantNET_flora,australia_2,Acacia alpina,fruit_width,pods,3,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Sphaeromorphaea littoralis,fruit_length,achenes,1.3,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Picris barbarorum,fruit_length,cypselas,7.5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Acacia ramulosa var. ramulosa,fruit_length,pods,20,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Stypandra,fruit_colour,,black,black,,mode,species,,,,, -PlantNET_flora,australia_2,Eremophila oppositifolia,fruit_length,fruit,4,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Parkinsonia,fruit_dehiscence,,indehiscent,indehiscent,,mode,species,,,,, -PlantNET_flora,australia_2,Geranium purpureum subsp. purpureum,fruit_length,fruit,12,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Callistemon purpurascens,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,, -PlantNET_flora,australia_2,Acacia beadleana,fruit_width,pods,10.5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Polycarpon tetraphyllum,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,, -PlantNET_flora,australia_2,Schenkia australis,fruit_length,capsule,10,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Pultenaea ferruginea,fruit_length,pod,6,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Angophora leiocarpa,fruit_width,fruit,11,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Sisymbrium irio,fruit_length,siliqua,25,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Corymbia eximia,fruit_length,fruit,13,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Cylindropuntia kleiniae,fruit_length,fruits,20,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Hibiscus sturtii,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,, -PlantNET_flora,australia_2,Carex cephalotes,fruit_width,utricles,1,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Cyperus albostriatus,fruit_colour,,brown black,brown blackish,,mode,species,,,,, -PlantNET_flora,australia_2,Pandorea pandorana subsp. austrocaledonica,fruit_dehiscence,,dehiscent,valves,,mode,species,,,,, -PlantNET_flora,australia_2,Coprosma niphophila,fruit_colour,,red orange,red orange,,mode,species,,,,, -PlantNET_flora,australia_2,Wahlenbergia luteola,fruit_length,capsule,5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Libertia,fruit_dehiscence,,dehiscent,inferred_from_family,,mode,species,,,,, -PlantNET_flora,australia_2,Ammannia,fruit_dehiscence,,dehiscent,splitting,,mode,species,,,,, -PlantNET_flora,australia_2,Acacia myrtifolia,fruit_width,pods,5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Erigeron conyzoides,fruit_length,achenes,2.5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Scleria rugosa,fruit_length,nut,3,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Hemisteptia lyrata,fruit_length,achenes,2,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Dovyalis caffra,fruit_colour,,orange yellow,apricot yellow,,mode,species,,,,, -PlantNET_flora,australia_2,Carmichaelia exsul,fruit_length,pods,10,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Centaurium tenuiflorum,fruit_length,capsule,6,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Acacia spectabilis,fruit_length,pods,170,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Castanospermum australe,fruit_length,pod,100,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Parentucellia latifolia,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,, -PlantNET_flora,australia_2,Alectryon oleifolius,fruit_width,capsule,10,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Cyperus betchei,fruit_width,nut,0.4,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Endiandra muelleri,fruit_colour,,black,black,,mode,species,,,,, -PlantNET_flora,australia_2,Lantana montevidensis,fruit_colour,,purple black,purplish black,,mode,species,,,,, -PlantNET_flora,australia_2,Exocarpos sparteus,fruit_length,drupe,5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Acacia flexifolia,fruit_width,pods,2,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Eucalyptus scias,fruit_dehiscence,,dehiscent,valves,,mode,species,,,,, -PlantNET_flora,australia_2,Melichrus procumbens,fruit_length,fruit,4,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Pinus pinea,fruit_colour,,brown,brown,,mode,species,,,,, -PlantNET_flora,australia_2,Erythroxylum australe,fruit_width,drupe,4,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Schoenus brevifolius,fruit_width,nut,0.7,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Cestrum nocturnum,fruit_width,berry,8,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Acacia terminalis subsp. Glabrous form (M.Hancock 94),fruit_width,pods,14,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Rorippa gigantea,fruit_length,siliqua,15,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Dinosperma erythrococcum,fruit_length,follicles,5,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Grevillea scortechinii,fruit_colour,,red brown,reddish brown,,mode,species,,,,, -PlantNET_flora,australia_2,Ficus henneana,fruit_length,figs,15,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Sigesbeckia orientalis,fruit_length,achenes,3,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Indigofera triflora,fruit_length,pods,30,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Dillwynia floribunda,fruit_length,pod,4,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Lotus corniculatus,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,, -PlantNET_flora,australia_2,Eucalyptus pulverulenta,fruit_width,fruit,6,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Acacia caroleae,fruit_width,pods,2,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Geranium obtusisepalum,fruit_length,fruit,17,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Phyla nodiflora,fruit_width,fruit,2,,mm,mode,species,,,,, -PlantNET_flora,australia_2,Nicotiana glauca,fruit_length,capsule,1.3,,cm,mode,species,,,,, -PlantNET_flora,australia_2,Ipomoea cairica,fruit_length,capsule,1.1,,cm,mode,species,,,,, -PlantNET_flora,australia_2,Euphorbia inappendiculata var. queenslandica,fruit_length,capsule,0.15,,cm,mode,species,,,,, -PlantNET_flora,australia_2,Daviesia arenaria,fruit_length,pod,0.7,,cm,mode,species,,,,, -PlantNET_flora,australia_2,Nicotiana glauca,leaf_photosynthesis,,6,,,,individual,,,,, -PlantNET_flora,australia_2,Nicotiana glauca,leaf_photosynthesis,,4,,,,individual,,,,, -PlantNET_flora,australia_2,Nicotiana glauca,leaf_photosynthesis,,3.7,,,,individual,,,,, -PlantNET_flora,australia_2,Lotus corniculatus,leaf_photosynthesis,,5,,,,individual,,,,1, -PlantNET_flora,australia_2,Lotus corniculatus,leaf_photosynthesis,,4.4,,,,individual,,,,1, -PlantNET_flora,australia_2,Lotus corniculatus,leaf_photosynthesis,,2,,,,individual,,,,1, -PlantNET_flora,australia_2,Lotus corniculatus,leaf_photosynthesis,,0.9,,,,individual,,,,2, -PlantNET_flora,australia,Lotus corniculatus,leaf_stomatal_conductance,,0.3,,,,population,,,,, -PlantNET_flora,australia,Lotus corniculatus,leaf_stomatal_conductance,,0.2,,,,population,,,,, -PlantNET_flora,australia_2,Lotus corniculatus,leaf_stomatal_conductance,,0.5,,,,population,,,,, -PlantNET_flora,australia_2,Lotus corniculatus,leaf_stomatal_conductance,,0.44,,,,population,,,,, -PlantNET_flora,australia_2,Lotus corniculatus,leaf_stomatal_conductance,,0.3,,,,population,,,,, -PlantNET_flora,australia,Phyla nodiflora,leaf_stomatal_conductance,,0.2,,,,species,,,,, -PlantNET_flora,australia_2,Phyla nodiflora,leaf_stomatal_conductance,,0.1,,,,species,,,,, -PlantNET_flora,australia_2,Eucalyptus pulverulenta,leaf_stomatal_conductance,,0.3,,,,species,,,,, -PlantNET_flora,australia_2,Eucalyptus pulverulenta,leaf_stomatal_conductance,,0.6,,,,species,,,,, -PlantNET_flora,australia_2,Eucalyptus pulverulenta,leaf_stomatal_conductance,,0.7,,,,species,,,,, -PlantNET_flora,australia_2,Eucalyptus pulverulenta,leaf_stomatal_conductance,,0.88,,,,species,,,,, -PlantNET_flora,australia,Ipomoea cairica,leaf_stomatal_conductance_2,,0.6,,,,,,,,, -PlantNET_flora,australia,Ipomoea cairica,leaf_stomatal_conductance_2,,0.5,,,,,,,,, -PlantNET_flora,australia_2,Ipomoea cairica,leaf_stomatal_conductance_2,,0.42,,,,,,,,, -PlantNET_flora,australia_2,Phyla nodiflora,leaf_stomatal_conductance_2,,0.37,,,,,,,,, -PlantNET_flora,australia_2,Phyla nodiflora,leaf_stomatal_conductance_2,,0.6,,,,,,,,, -PlantNET_flora,,Hemisteptia lyrata,fruit_width_2,,1000--3000,,um,bin,species,,,,, -PlantNET_flora,,Dovyalis caffra,fruit_width_2,,2000--4000,,um,bin,species,,,,, -PlantNET_flora,,Carmichaelia exsul,fruit_width_2,,1000--2000,,um,bin,species,,,,, +source,test_location,taxon_name,trait_name,category,trait_value,flora_value,units,value_type,test_entity_type,test_basis_of_value,test_basis_of_record,source_id,individual_id,life_stage,measurement_remarks,measurement_remarks_fruit_dehiscence,collection_date +PlantNET_flora,australia,Exocarpos homalocladus,fruit_width,drupe,8,,mm,maximum,species,measurement,,Test_2000,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia,Lepidosperma gladiatum,fruit_length,nut,0.3,,cm,maximum,species,measurement,literature,Test_2000,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia,Imperata cylindrica,fruit_length,caryopsis,0.1,,cm,minimum,species,measurement,literature,Test_2000,,seedling,Part of Test Dataset 4,,2006-03 +PlantNET_flora,australia,Imperata cylindrica,fruit_length,caryopsis,0.1,,cm,minimum,species,measurement,literature,Test_2000,,seedling,Part of Test Dataset 4,,2007-03 +PlantNET_flora,australia,Gentianella barringtonensis,fruit_colour,,brown,inferred_from_genus,,minimum,species,,literature,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia,Acacia bulgaensis,fruit_length,pods,95,,mm,minimum,metapopulation,measurement,literature,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia,Sparaxis bulbifera,fruit_colour,,green,green,,minimum,metapopulation,,field,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia,Psoralea pinnata,fruit_width,fruits,2.5,,mm,minimum,metapopulation,,field,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia,Eucalyptus dorrigoensis,fruit_length,fruit,0.5,,cm,minimum,species,measurement,field_experiment,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia,Alectryon subdentatus,fruit_length,capsule,0.8,,cm,minimum,species,measurement,,Test_2003,,seedling,Part of Test Dataset 4,,2008-01 +PlantNET_flora,australia,Alectryon subdentatus,fruit_length,capsule,0.8,,cm,minimum,species,measurement,,Test_2003,,seedling,Part of Test Dataset 4,,2009-01 +PlantNET_flora,,Acacia crassa,fruit_length,pods,40,,mm,minimum,species,expert_score,field,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,,Commersonia amystia,fruit_width,capsule,13,,mm,maximum,species,unknown,field,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,,Gompholobium grandiflorum,fruit_length,pod,15,,mm,maximum,species,,,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia,Crassula decumbens,fruit_dehiscence,,dehiscent,dehiscing,,mode,population,,,Test_2003,,seedling,Part of Test Dataset 4,Remarks for `fruit_dehiscence`, +PlantNET_flora,australia_2,Chthonocephalus pseudevax,fruit_length,achenes,0.5,,mm,mode,,,,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Amyema preissii,fruit_colour,,pink white,pink white,,mode,,,,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Dichromochlamys dentatifolia,fruit_length,achenes,1.8,,mm,mode,,,field_experiment,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Adriana tomentosa,fruit_width,capsule,12,,mm,mode,,,literature,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Isotoma fluviatilis subsp. fluviatilis,fruit_width,capsule,3,,mm,mode,,,literature,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Cassinia compacta,fruit_length,achenes,0.5,,mm,mode,,,literature,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Mischocarpus australis,fruit_width,capsule,8,,mm,mode,,,literature,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eleocharis pallens,fruit_length,nut,1.4,,mm,mode,population,,literature,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Hypoxis glabella var. glabella,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,population,unknown,literature,Test_2003,,seedling,Part of Test Dataset 4,Remarks for `fruit_dehiscence`, +PlantNET_flora,australia_2,Crassula peduncularis,fruit_dehiscence,,dehiscent,splitting,,mode,population,expert_score,literature,Test_2003,,seedling,Part of Test Dataset 4,Remarks for `fruit_dehiscence`, +PlantNET_flora,australia_2,Derris involuta,fruit_dehiscence,,indehiscent,inferred_from_genus,,mode,population,measurement,literature,Test_2003,,seedling,Part of Test Dataset 4,Remarks for `fruit_dehiscence`, +PlantNET_flora,australia_2,Diodia,fruit_dehiscence,,indehiscent,indehiscent,,mode,genus,measurement,literature,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Stellaria angustifolia subsp. angustifolia,fruit_length,capsule,8.5,,mm,mode,,measurement,literature,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Pittosporum erioloma,fruit_dehiscence,,dehiscent,valves,,mode,,measurement,literature,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Corymbia citriodora,fruit_length,fruit,15,,mm,mode,,measurement,literature,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Pimelea ligustrina subsp. ligustrina,fruit_colour,,green,inferred_from_species,,mode,metapopulation,measurement,literature,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Trifolium dubium,fruit_length,pod,2,,mm,mode,metapopulation,measurement,literature,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Myoporum boninense subsp. australe,fruit_length,fruit,10,,mm,mode,metapopulation,measurement,literature,Test_2003,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Arbutus unedo,fruit_colour,,red,red,,mode,metapopulation,measurement,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Schoenus vaginatus,fruit_colour,,red yellow brown,red yellow brown,,mode,metapopulation,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Dodonaea petiolaris,fruit_length,capsule,16,,mm,mode,metapopulation,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Leptospermum continentale,fruit_length,fruit,6,,mm,mode,metapopulation,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Freesia hybrid,fruit_colour,,green,green,,mode,metapopulation,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Epilobium gunnianum,fruit_length,fruit,75,,mm,mode,metapopulation,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Dodonaea truncatiales,fruit_width,capsule,17,,mm,mode,metapopulation,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Thlaspi,fruit_dehiscence,,dehiscent,dehiscent,,mode,metapopulation,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus recurva,fruit_length,fruit,4,,mm,mode,metapopulation,,,Test_2000,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Lotononis bainesii,fruit_length,pod,8,,mm,mode,metapopulation,,,Test_2000,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Correa alba,fruit_length,fruit,5,,mm,mode,species,,,Test_2000,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Commersonia salviifolia,fruit_width,capsule,5,,mm,mode,species,,,Test_2000,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Carex cephalotes,fruit_length,utricles,2.5,,mm,,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Juncus acutus subsp. acutus,fruit_dehiscence,,dehiscent,inferred_from_family,,,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Thelymitra kangaloonica,fruit_length,capsules,12,,mm,,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus viminalis,fruit_width,fruit,4,,mm,,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Acronychia littoralis,fruit_width,fruit,20,,mm,,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus leucoxylon subsp. pruinosa,fruit_dehiscence,,dehiscent,valves,,,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Hibbertia crinita,fruit_dehiscence,,dehiscent,inferred_from_genus,,,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Crotalaria brevis,fruit_length,pods,6,,mm,mean,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Spergularia diandra,fruit_dehiscence,,dehiscent,inferred_from_genus,,mean,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Hypericum elodes,fruit_length,capsule,4,,mm,mean,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Hakea macraeana,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Dillwynia cinerascens,fruit_length,pod,5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Lupinus polyphyllus,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Potamogeton australiensis,fruit_length,fruit,4,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Hypoxis,fruit_dehiscence,,dehiscent,dehiscing,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Carex raleighii,fruit_length,utricles,2.5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Veronica catenata,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Phlegmatospermum cochlearinum,fruit_length,silicula,10,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Australina pusilla,fruit_length,achene,1,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Schoenus lepidosperma,fruit_width,nut,2.5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Calendula arvensis,fruit_length,achenes,15,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Veronica derwentiana,fruit_length,capsule,2.8,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Gossia bidwillii,fruit_colour,,black,black,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Cyperus bulbosus,fruit_colour,,grey,greyish,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus youmanii,fruit_width,fruit,9,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Lobelia pedunculata,fruit_length,fruit,4,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Goodenia varia,fruit_length,fruit,10,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Convolvulus farinosus,fruit_width,capsule,6,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Freesia laxa,fruit_length,capsule,12,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Rhodamnia argentea,fruit_colour,,black,black,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eremophila deserti,fruit_colour,,yellow black,yellow black,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Geijera salicifolia,fruit_width,fruit,6,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Endiandra globosa,fruit_width,fruit,50,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Thesium australe,fruit_width,fruit,2.5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Teucrium puberulum,fruit_width,drupe,4,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Davidsonia johnsonii,fruit_length,fruit,30,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Claoxylon australe,fruit_width,capsule,5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Cyperus sculptus,fruit_length,nut,1,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Cyperus laevigatus,fruit_width,nut,1.2,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus muelleriana,fruit_dehiscence,,dehiscent,valves,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Centranthera,fruit_dehiscence,,dehiscent,loculicidal,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus badjensis,fruit_length,fruit,5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Leucopogon amplexicaulis,fruit_length,fruit,3.5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus oblonga,fruit_length,fruit,8,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Lobelia trigonocaulis,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Senecio longipilus,fruit_length,achenes,2.5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Burmannia disticha,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Schoenus apogon,fruit_colour,,white,whitish,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Bursaria spinosa subsp. spinosa,fruit_width,capsules,9,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Pisum sativum var. arvense,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Abildgaardia ovata,fruit_width,nut,1.2,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Leptospermum obovatum,fruit_width,fruit,8,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Hibiscus brachysiphonius,fruit_length,capsule,15,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Muehlenbeckia adpressa,fruit_colour,,brown black,brown black,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Salix alba,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Isolepis montivaga,fruit_length,nut,0.9,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Leptomeria drupacea,fruit_length,drupe,6,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Elaeocarpus grandis,fruit_width,fruit,20,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus youmanii,fruit_length,fruit,12,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Carex leporina,fruit_length,utricles,3.5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Juncus kraussii,fruit_colour,,red yellow brown black,red golden brown blackish,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus nandewarica,fruit_length,fruit,3,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus yangoura,fruit_width,fruit,6,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus olida,fruit_length,fruit,5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Sida goniocarpa,fruit_width,fruit,7,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Dampiera fusca,fruit_colour,,brown,brownish,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Lepidium foliosum,fruit_length,silicula,4,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Alectryon coriaceus,fruit_length,capsule,7,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Styphelia viridis,fruit_length,fruit,10,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Lepidium oxytrichum,fruit_length,silicula,5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Rhodamnia argentea,fruit_length,fruit,6,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Rubus parvifolius,fruit_colour,,red,red,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Artanema,fruit_dehiscence,,dehiscent,valve,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Lepidium africanum,fruit_width,silicula,2,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Acacia leiocalyx subsp. leiocalyx,fruit_width,pods,4,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Plantago turrifera,fruit_length,capsule,3,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Crotalaria brevis,fruit_colour,,brown,brown,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Apophyllum anomalum,fruit_colour,,purple,purple,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Isotoma axillaris,fruit_length,capsule,7,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus camphora,fruit_length,fruit,4,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Medicago orbicularis,fruit_length,pod,7,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Acacia havilandiorum,fruit_width,pods,2,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Coprosma nivalis,fruit_colour,,purple grey,violet grey,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Swainsona cadellii,fruit_length,pod,25,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Paraserianthes lophantha,fruit_width,pod,25,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Crotalaria lanceolata,fruit_length,pod,20,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Nicotiana goodspeedii,fruit_length,capsule,5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus rossii,fruit_width,fruit,6,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Gentiana wingecarribiensis,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Oxalis corniculata,fruit_width,fruit,1.5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Acacia gladiiformis,fruit_length,pods,150,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Escallonia bifida,fruit_length,capsule,3,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Crotalaria grahamiana,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Acacia alpina,fruit_width,pods,3,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Sphaeromorphaea littoralis,fruit_length,achenes,1.3,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Picris barbarorum,fruit_length,cypselas,7.5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Acacia ramulosa var. ramulosa,fruit_length,pods,20,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Stypandra,fruit_colour,,black,black,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eremophila oppositifolia,fruit_length,fruit,4,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Parkinsonia,fruit_dehiscence,,indehiscent,indehiscent,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Geranium purpureum subsp. purpureum,fruit_length,fruit,12,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Callistemon purpurascens,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Acacia beadleana,fruit_width,pods,10.5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Polycarpon tetraphyllum,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Schenkia australis,fruit_length,capsule,10,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Pultenaea ferruginea,fruit_length,pod,6,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Angophora leiocarpa,fruit_width,fruit,11,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Sisymbrium irio,fruit_length,siliqua,25,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Corymbia eximia,fruit_length,fruit,13,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Cylindropuntia kleiniae,fruit_length,fruits,20,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Hibiscus sturtii,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Carex cephalotes,fruit_width,utricles,1,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Cyperus albostriatus,fruit_colour,,brown black,brown blackish,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Pandorea pandorana subsp. austrocaledonica,fruit_dehiscence,,dehiscent,valves,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Coprosma niphophila,fruit_colour,,red orange,red orange,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Wahlenbergia luteola,fruit_length,capsule,5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Libertia,fruit_dehiscence,,dehiscent,inferred_from_family,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Ammannia,fruit_dehiscence,,dehiscent,splitting,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Acacia myrtifolia,fruit_width,pods,5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Erigeron conyzoides,fruit_length,achenes,2.5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Scleria rugosa,fruit_length,nut,3,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Hemisteptia lyrata,fruit_length,achenes,2,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Dovyalis caffra,fruit_colour,,orange yellow,apricot yellow,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Carmichaelia exsul,fruit_length,pods,10,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Centaurium tenuiflorum,fruit_length,capsule,6,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Acacia spectabilis,fruit_length,pods,170,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Castanospermum australe,fruit_length,pod,100,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Parentucellia latifolia,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Alectryon oleifolius,fruit_width,capsule,10,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Cyperus betchei,fruit_width,nut,0.4,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Endiandra muelleri,fruit_colour,,black,black,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Lantana montevidensis,fruit_colour,,purple black,purplish black,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Exocarpos sparteus,fruit_length,drupe,5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Acacia flexifolia,fruit_width,pods,2,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus scias,fruit_dehiscence,,dehiscent,valves,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Melichrus procumbens,fruit_length,fruit,4,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Pinus pinea,fruit_colour,,brown,brown,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Erythroxylum australe,fruit_width,drupe,4,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Schoenus brevifolius,fruit_width,nut,0.7,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Cestrum nocturnum,fruit_width,berry,8,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Acacia terminalis subsp. Glabrous form (M.Hancock 94),fruit_width,pods,14,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Rorippa gigantea,fruit_length,siliqua,15,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Dinosperma erythrococcum,fruit_length,follicles,5,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Grevillea scortechinii,fruit_colour,,red brown,reddish brown,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Ficus henneana,fruit_length,figs,15,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Sigesbeckia orientalis,fruit_length,achenes,3,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Indigofera triflora,fruit_length,pods,30,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Dillwynia floribunda,fruit_length,pod,4,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Lotus corniculatus,fruit_dehiscence,,dehiscent,inferred_from_genus,,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus pulverulenta,fruit_width,fruit,6,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Acacia caroleae,fruit_width,pods,2,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Geranium obtusisepalum,fruit_length,fruit,17,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Phyla nodiflora,fruit_width,fruit,2,,mm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Nicotiana glauca,fruit_length,capsule,1.3,,cm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Ipomoea cairica,fruit_length,capsule,1.1,,cm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Euphorbia inappendiculata var. queenslandica,fruit_length,capsule,0.15,,cm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Daviesia arenaria,fruit_length,pod,0.7,,cm,mode,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Nicotiana glauca,leaf_photosynthesis,,6,,,,individual,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Nicotiana glauca,leaf_photosynthesis,,4,,,,individual,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Nicotiana glauca,leaf_photosynthesis,,3.7,,,,individual,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Lotus corniculatus,leaf_photosynthesis,,5,,,,individual,,,,1,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Lotus corniculatus,leaf_photosynthesis,,4.4,,,,individual,,,,1,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Lotus corniculatus,leaf_photosynthesis,,2,,,,individual,,,,1,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Lotus corniculatus,leaf_photosynthesis,,0.9,,,,individual,,,,2,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia,Lotus corniculatus,leaf_stomatal_conductance,,0.3,,,,population,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia,Lotus corniculatus,leaf_stomatal_conductance,,0.2,,,,population,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Lotus corniculatus,leaf_stomatal_conductance,,0.5,,,,population,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Lotus corniculatus,leaf_stomatal_conductance,,0.44,,,,population,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Lotus corniculatus,leaf_stomatal_conductance,,0.3,,,,population,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia,Phyla nodiflora,leaf_stomatal_conductance,,0.2,,,,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Phyla nodiflora,leaf_stomatal_conductance,,0.1,,,,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus pulverulenta,leaf_stomatal_conductance,,0.3,,,,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus pulverulenta,leaf_stomatal_conductance,,0.6,,,,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus pulverulenta,leaf_stomatal_conductance,,0.7,,,,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Eucalyptus pulverulenta,leaf_stomatal_conductance,,0.88,,,,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia,Ipomoea cairica,leaf_stomatal_conductance_2,,0.6,,,,,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia,Ipomoea cairica,leaf_stomatal_conductance_2,,0.5,,,,,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Ipomoea cairica,leaf_stomatal_conductance_2,,0.42,,,,,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Phyla nodiflora,leaf_stomatal_conductance_2,,0.37,,,,,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,australia_2,Phyla nodiflora,leaf_stomatal_conductance_2,,0.6,,,,,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,,Hemisteptia lyrata,fruit_width_2,,1000--3000,,um,bin,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,,Dovyalis caffra,fruit_width_2,,2000--4000,,um,bin,species,,,,,seedling,Part of Test Dataset 4,, +PlantNET_flora,,Carmichaelia exsul,fruit_width_2,,1000--2000,,um,bin,species,,,,,seedling,Part of Test Dataset 4,, diff --git a/tests/testthat/examples/Test_2023_4/metadata.yml b/tests/testthat/examples/Test_2023_4/metadata.yml index f1bc47ef..0c7be3a3 100644 --- a/tests/testthat/examples/Test_2023_4/metadata.yml +++ b/tests/testthat/examples/Test_2023_4/metadata.yml @@ -97,9 +97,9 @@ dataset: basis_of_record: field_experiment source_id: source_id description: Plant growth form data extracted from the NT Flora Online - life_stage: seedling + life_stage: life_stage replicates: 1 - measurement_remarks: Part of Test Dataset 4 + measurement_remarks: measurement_remarks sampling_strategy: This dataset is sourced from the PlantNet online flora (version date 2022-05-06). Briefly, the textual descriptions of each taxon were downloaded and organised into a tabular format of individual taxon names and their corresponding @@ -125,6 +125,7 @@ locations: description: First made-up location for testing entity_type: population life_stage: juvenile + collection_date: '2020' australia_2: latitude (deg): -27.158 longitude (deg): 142.685 @@ -198,6 +199,7 @@ traits: the kind of dehiscence e.g. scepticidal, loculicidal or possessing valves. basis_of_record: test_basis_of_record life_stage: adult + measurement_remarks: measurement_remarks_fruit_dehiscence - var_in: fruit_length trait_name: fruit_length unit_in: units diff --git a/tests/testthat/examples/Test_2023_4/output/traits.csv b/tests/testthat/examples/Test_2023_4/output/traits.csv index ba4fa405..ac42b70c 100644 --- a/tests/testthat/examples/Test_2023_4/output/traits.csv +++ b/tests/testthat/examples/Test_2023_4/output/traits.csv @@ -2,7 +2,7 @@ dataset_id,taxon_name,observation_id,trait_name,value,unit,entity_type,value_typ Test_2023_4,Abildgaardia ovata,001,fruit_width,1.2,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Abildgaardia ovata Test_2023_4,Acacia alpina,002,fruit_width,3,mm,species,mode,,1,field_experiment,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Acacia alpina Test_2023_4,Acacia beadleana,003,fruit_width,10.5,mm,species,mode,,1,field_experiment,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Acacia beadleana -Test_2023_4,Acacia bulgaensis,004,fruit_length,95,mm,population,minimum,measurement,1,literature,juvenile,01,,,,,01,02,,,,Part of Test Dataset 4,01,04,Acacia bulgaensis +Test_2023_4,Acacia bulgaensis,004,fruit_length,95,mm,population,minimum,measurement,1,literature,juvenile,01,,,,,01,02,,,2020,Part of Test Dataset 4,01,04,Acacia bulgaensis Test_2023_4,Acacia caroleae,005,fruit_width,2,mm,species,mode,,1,field_experiment,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Acacia caroleae Test_2023_4,Acacia crassa,006,fruit_length,40,mm,species,minimum,expert_score,1,field,seedling,,,,,Test_2003,,02,,,,Part of Test Dataset 4,01,04,Acacia crassa Test_2023_4,Acacia flexifolia,007,fruit_width,2,mm,species,mode,,1,field_experiment,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Acacia flexifolia @@ -22,12 +22,12 @@ Test_2023_4,Alectryon subdentatus,020,fruit_length,8,mm,species,minimum,measurem Test_2023_4,Amyema preissii,021,fruit_colour,pink white,,,mode,,1,,seedling,,,,,Test_2003,,02,,,,Part of Test Dataset 4,01,04,Amyema preissii Test_2023_4,Angophora leiocarpa,022,fruit_width,11,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Angophora leiocarpa Test_2023_4,Apophyllum anomalum,023,fruit_colour,purple,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Apophyllum anomalum -Test_2023_4,Arbutus unedo,024,fruit_colour,red,,metapopulation,mode,,1,,seedling,02,,,,,02,02,,,,From `australia_2` site,01,04,Arbutus unedo +Test_2023_4,Arbutus unedo,024,fruit_colour,red,,metapopulation,mode,,1,,seedling,03,,,,,02,02,,,,From `australia_2` site,01,04,Arbutus unedo Test_2023_4,Australina pusilla,025,fruit_length,1,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Australina pusilla -Test_2023_4,Burmannia disticha,026,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,02,Burmannia disticha +Test_2023_4,Burmannia disticha,026,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Burmannia disticha Test_2023_4,Bursaria spinosa subsp. spinosa,027,fruit_width,9,mm,species,mode,,1,field_experiment,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Bursaria spinosa subsp. spinosa Test_2023_4,Calendula arvensis,028,fruit_length,15,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Calendula arvensis -Test_2023_4,Callistemon purpurascens,029,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,02,Callistemon purpurascens +Test_2023_4,Callistemon purpurascens,029,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Callistemon purpurascens Test_2023_4,Carex cephalotes,030,fruit_length,2.5,mm,species,,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Carex cephalotes Test_2023_4,Carex cephalotes,031,fruit_width,1,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Carex cephalotes Test_2023_4,Carex leporina,032,fruit_length,3.5,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Carex leporina @@ -48,11 +48,11 @@ Test_2023_4,Coprosma nivalis,046,fruit_colour,grey purple,,species,mode,,1,,seed Test_2023_4,Correa alba,047,fruit_length,5,mm,species,mode,,1,,seedling,,,,,Test_2000,,01,,,,Part of Test Dataset 4,01,04,Correa alba Test_2023_4,Corymbia citriodora,048,fruit_length,15,mm,,mode,measurement,1,literature,seedling,,,,,Test_2003,,01,,,,Part of Test Dataset 4,01,04,Corymbia citriodora Test_2023_4,Corymbia eximia,049,fruit_length,13,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Corymbia eximia -Test_2023_4,Crassula decumbens,050,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,Test_2003,,02,,,,Part of Test Dataset 4,01,04,Crassula decumbens -Test_2023_4,Crassula peduncularis,051,fruit_dehiscence,dehiscent,,population,mode,,1,literature,adult,02,,,,Test_2003,02,02,,,,From `australia_2` site,01,04,Crassula peduncularis +Test_2023_4,Crassula decumbens,050,fruit_dehiscence,dehiscent,,population,mode,,1,,juvenile,01,,,,Test_2003,01,02,,,2020,Remarks for `fruit_dehiscence`,01,04,Crassula decumbens +Test_2023_4,Crassula peduncularis,051,fruit_dehiscence,dehiscent,,population,mode,,1,literature,adult,03,,,,Test_2003,02,02,,,,From `australia_2` site,01,04,Crassula peduncularis Test_2023_4,Crotalaria brevis,052,fruit_colour,brown,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Crotalaria brevis Test_2023_4,Crotalaria brevis,052,fruit_length,6,mm,species,mean,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Crotalaria brevis -Test_2023_4,Crotalaria grahamiana,053,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,02,Crotalaria grahamiana +Test_2023_4,Crotalaria grahamiana,053,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Crotalaria grahamiana Test_2023_4,Crotalaria lanceolata,054,fruit_length,20,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Crotalaria lanceolata Test_2023_4,Cylindropuntia kleiniae,055,fruit_length,20,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Cylindropuntia kleiniae Test_2023_4,Cyperus albostriatus,056,fruit_colour,black brown,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Cyperus albostriatus @@ -63,20 +63,20 @@ Test_2023_4,Cyperus sculptus,060,fruit_length,1,mm,species,mode,,1,,seedling,,,, Test_2023_4,Dampiera fusca,061,fruit_colour,brown,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Dampiera fusca Test_2023_4,Davidsonia johnsonii,062,fruit_length,30,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Davidsonia johnsonii Test_2023_4,Daviesia arenaria,063,fruit_length,7,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Daviesia arenaria -Test_2023_4,Derris involuta,064,fruit_dehiscence,indehiscent,,population,mode,,1,literature,adult,02,,,,Test_2003,02,02,,,,From `australia_2` site,01,02,Derris involuta +Test_2023_4,Derris involuta,064,fruit_dehiscence,indehiscent,,population,mode,,1,literature,adult,03,,,,Test_2003,02,02,,,,From `australia_2` site,01,02,Derris involuta Test_2023_4,Dichromochlamys dentatifolia,065,fruit_length,1.8,mm,,mode,,1,field_experiment,seedling,,,,,Test_2003,,01,,,,Part of Test Dataset 4,01,04,Dichromochlamys dentatifolia Test_2023_4,Dillwynia cinerascens,066,fruit_length,5,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Dillwynia cinerascens Test_2023_4,Dillwynia floribunda,067,fruit_length,4,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Dillwynia floribunda Test_2023_4,Dinosperma erythrococcum,068,fruit_length,5,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Dinosperma erythrococcum -Test_2023_4,Dodonaea petiolaris,069,fruit_length,16,mm,metapopulation,mode,,1,,seedling,02,,,,,02,01,,,,From `australia_2` site,01,04,Dodonaea petiolaris +Test_2023_4,Dodonaea petiolaris,069,fruit_length,16,mm,metapopulation,mode,,1,,seedling,03,,,,,02,01,,,,From `australia_2` site,01,04,Dodonaea petiolaris Test_2023_4,Dodonaea truncatiales,070,fruit_width,17,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Dodonaea truncatiales Test_2023_4,Dovyalis caffra,071,fruit_colour,orange yellow,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Dovyalis caffra Test_2023_4,Dovyalis caffra,072,fruit_width,2--4,mm,species,bin,,1,field_experiment,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Dovyalis caffra Test_2023_4,Elaeocarpus grandis,073,fruit_width,20,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Elaeocarpus grandis -Test_2023_4,Eleocharis pallens,074,fruit_length,1.4,mm,population,mode,,1,literature,seedling,02,,,,Test_2003,02,01,,,,From `australia_2` site,01,04,Eleocharis pallens +Test_2023_4,Eleocharis pallens,074,fruit_length,1.4,mm,population,mode,,1,literature,seedling,03,,,,Test_2003,02,01,,,,From `australia_2` site,01,04,Eleocharis pallens Test_2023_4,Endiandra globosa,075,fruit_width,50,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Endiandra globosa Test_2023_4,Endiandra muelleri,076,fruit_colour,black,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Endiandra muelleri -Test_2023_4,Epilobium gunnianum,077,fruit_length,75,mm,metapopulation,mode,,1,,seedling,02,,,,,02,01,,,,From `australia_2` site,01,04,Epilobium gunnianum +Test_2023_4,Epilobium gunnianum,077,fruit_length,75,mm,metapopulation,mode,,1,,seedling,03,,,,,02,01,,,,From `australia_2` site,01,04,Epilobium gunnianum Test_2023_4,Eremophila deserti,078,fruit_colour,black yellow,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Eremophila deserti Test_2023_4,Eremophila oppositifolia,079,fruit_length,4,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eremophila oppositifolia Test_2023_4,Erigeron conyzoides,080,fruit_length,2.5,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Erigeron conyzoides @@ -85,8 +85,8 @@ Test_2023_4,Escallonia bifida,082,fruit_length,3,mm,species,mode,,1,,seedling,,, Test_2023_4,Eucalyptus badjensis,083,fruit_length,5,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus badjensis Test_2023_4,Eucalyptus camphora,084,fruit_length,4,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus camphora Test_2023_4,Eucalyptus dorrigoensis,085,fruit_length,5,mm,species,minimum,measurement,1,field_experiment,seedling,,,,,Test_2003,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus dorrigoensis -Test_2023_4,Eucalyptus leucoxylon subsp. pruinosa,086,fruit_dehiscence,dehiscent,,species,,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,04,Eucalyptus leucoxylon subsp. pruinosa -Test_2023_4,Eucalyptus muelleriana,087,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,04,Eucalyptus muelleriana +Test_2023_4,Eucalyptus leucoxylon subsp. pruinosa,086,fruit_dehiscence,dehiscent,,species,,,1,,adult,,,,,,,02,,,,,01,04,Eucalyptus leucoxylon subsp. pruinosa +Test_2023_4,Eucalyptus muelleriana,087,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,04,Eucalyptus muelleriana Test_2023_4,Eucalyptus nandewarica,088,fruit_length,3,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus nandewarica Test_2023_4,Eucalyptus oblonga,089,fruit_length,8,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus oblonga Test_2023_4,Eucalyptus olida,090,fruit_length,5,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus olida @@ -95,9 +95,9 @@ Test_2023_4,Eucalyptus pulverulenta,092,leaf_stomatal_conductance,0.3,mol{H2O}/m Test_2023_4,Eucalyptus pulverulenta,092,leaf_stomatal_conductance,0.6,mol{H2O}/m2/s,species,raw,measurement,5,field_experiment,seedling,,,02,,,,02,,,,Part of Test Dataset 4,01,04,Eucalyptus pulverulenta Test_2023_4,Eucalyptus pulverulenta,092,leaf_stomatal_conductance,0.7,mol{H2O}/m2/s,species,raw,measurement,5,field_experiment,seedling,,,03,,,,02,,,,Part of Test Dataset 4,01,04,Eucalyptus pulverulenta Test_2023_4,Eucalyptus pulverulenta,092,leaf_stomatal_conductance,0.88,mol{H2O}/m2/s,species,raw,measurement,5,field_experiment,seedling,,,04,,,,02,,,,Part of Test Dataset 4,01,04,Eucalyptus pulverulenta -Test_2023_4,Eucalyptus recurva,093,fruit_length,4,mm,metapopulation,mode,,1,,seedling,02,,,,Test_2000,02,01,,,,From `australia_2` site,01,04,Eucalyptus recurva +Test_2023_4,Eucalyptus recurva,093,fruit_length,4,mm,metapopulation,mode,,1,,seedling,03,,,,Test_2000,02,01,,,,From `australia_2` site,01,04,Eucalyptus recurva Test_2023_4,Eucalyptus rossii,094,fruit_width,6,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus rossii -Test_2023_4,Eucalyptus scias,095,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,04,Eucalyptus scias +Test_2023_4,Eucalyptus scias,095,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,04,Eucalyptus scias Test_2023_4,Eucalyptus viminalis,096,fruit_width,4,mm,species,,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus viminalis Test_2023_4,Eucalyptus yangoura,097,fruit_width,6,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus yangoura Test_2023_4,Eucalyptus youmanii,098,fruit_length,12,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus youmanii @@ -106,10 +106,10 @@ Test_2023_4,Euphorbia inappendiculata var. queenslandica,100,fruit_length,1.5,mm Test_2023_4,Exocarpos homalocladus,101,fruit_width,8,mm,species,maximum,,1,field_experiment,seedling,,,,,Test_2000,,02,,,,Part of Test Dataset 4,01,04,Exocarpos homalocladus Test_2023_4,Exocarpos sparteus,102,fruit_length,5,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Exocarpos sparteus Test_2023_4,Ficus henneana,103,fruit_length,15,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Ficus henneana -Test_2023_4,Freesia hybrid,104,fruit_colour,green,,metapopulation,mode,,1,,seedling,02,,,,,02,02,,,,From `australia_2` site,01,04,Freesia hybrid +Test_2023_4,Freesia hybrid,104,fruit_colour,green,,metapopulation,mode,,1,,seedling,03,,,,,02,02,,,,From `australia_2` site,01,04,Freesia hybrid Test_2023_4,Freesia laxa,105,fruit_length,12,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Freesia laxa Test_2023_4,Geijera salicifolia,106,fruit_width,6,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Geijera salicifolia -Test_2023_4,Gentiana wingecarribiensis,107,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,02,Gentiana wingecarribiensis +Test_2023_4,Gentiana wingecarribiensis,107,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Gentiana wingecarribiensis Test_2023_4,Gentianella barringtonensis,108,fruit_colour,brown,,species,minimum,,1,literature,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,02,Gentianella barringtonensis Test_2023_4,Geranium obtusisepalum,109,fruit_length,17,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Geranium obtusisepalum Test_2023_4,Geranium purpureum subsp. purpureum,110,fruit_length,12,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Geranium purpureum subsp. purpureum @@ -117,16 +117,16 @@ Test_2023_4,Gompholobium grandiflorum,111,fruit_length,15,mm,species,maximum,,1, Test_2023_4,Goodenia varia,112,fruit_length,10,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Goodenia varia Test_2023_4,Gossia bidwillii,113,fruit_colour,black,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Gossia bidwillii Test_2023_4,Grevillea scortechinii,114,fruit_colour,brown red,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Grevillea scortechinii -Test_2023_4,Hakea macraeana,115,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,02,Hakea macraeana +Test_2023_4,Hakea macraeana,115,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Hakea macraeana Test_2023_4,Hemisteptia lyrata,116,fruit_length,2,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Hemisteptia lyrata Test_2023_4,Hemisteptia lyrata,117,fruit_width,1--3,mm,species,bin,,1,field_experiment,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Hemisteptia lyrata -Test_2023_4,Hibbertia crinita,118,fruit_dehiscence,dehiscent,,species,,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,02,Hibbertia crinita +Test_2023_4,Hibbertia crinita,118,fruit_dehiscence,dehiscent,,species,,,1,,adult,,,,,,,02,,,,,01,02,Hibbertia crinita Test_2023_4,Hibiscus brachysiphonius,119,fruit_length,15,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Hibiscus brachysiphonius -Test_2023_4,Hibiscus sturtii,120,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,02,Hibiscus sturtii +Test_2023_4,Hibiscus sturtii,120,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Hibiscus sturtii Test_2023_4,Hypericum elodes,121,fruit_length,4,mm,species,mean,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Hypericum elodes -Test_2023_4,Hypoxis glabella var. glabella,122,fruit_dehiscence,dehiscent,,population,mode,,1,literature,adult,02,,,,Test_2003,02,02,,,,From `australia_2` site,01,02,Hypoxis glabella var. glabella -Test_2023_4,Imperata cylindrica,123,fruit_length,1,mm,individual,minimum,measurement,1,literature,seedling,02,01,,,Test_2000,02,02,,,2006-03,From `australia_2` site,01,04,Imperata cylindrica -Test_2023_4,Imperata cylindrica,124,fruit_length,1,mm,individual,minimum,measurement,1,literature,seedling,02,01,,,Test_2000,02,02,,,2007-03,From `australia_2` site,01,04,Imperata cylindrica +Test_2023_4,Hypoxis glabella var. glabella,122,fruit_dehiscence,dehiscent,,population,mode,,1,literature,adult,03,,,,Test_2003,02,02,,,,From `australia_2` site,01,02,Hypoxis glabella var. glabella +Test_2023_4,Imperata cylindrica,123,fruit_length,1,mm,species,minimum,measurement,1,literature,seedling,,,,,Test_2000,,02,,,2006-03,Part of Test Dataset 4,01,04,Imperata cylindrica +Test_2023_4,Imperata cylindrica,124,fruit_length,1,mm,species,minimum,measurement,1,literature,seedling,,,,,Test_2000,,02,,,2007-03,Part of Test Dataset 4,01,04,Imperata cylindrica Test_2023_4,Indigofera triflora,125,fruit_length,30,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Indigofera triflora Test_2023_4,Ipomoea cairica,126,fruit_length,11,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Ipomoea cairica Test_2023_4,Ipomoea cairica,127,leaf_stomatal_conductance,0.6,mol{H2O}/m2/s,species,raw,measurement,5,field_experiment,seedling,,,,,,,02,,,,Part of Test Dataset 4,02,04,Ipomoea cairica @@ -135,7 +135,7 @@ Test_2023_4,Ipomoea cairica,127,leaf_stomatal_conductance,0.42,mol{H2O}/m2/s,spe Test_2023_4,Isolepis montivaga,128,fruit_length,0.9,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Isolepis montivaga Test_2023_4,Isotoma axillaris,129,fruit_length,7,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Isotoma axillaris Test_2023_4,Isotoma fluviatilis subsp. fluviatilis,130,fruit_width,3,mm,species,mode,,1,field_experiment,seedling,,,,,Test_2003,,01,,,,Part of Test Dataset 4,01,04,Isotoma fluviatilis subsp. fluviatilis -Test_2023_4,Juncus acutus subsp. acutus,131,fruit_dehiscence,dehiscent,,species,,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,01,Juncus acutus subsp. acutus +Test_2023_4,Juncus acutus subsp. acutus,131,fruit_dehiscence,dehiscent,,species,,,1,,adult,,,,,,,02,,,,,01,01,Juncus acutus subsp. acutus Test_2023_4,Juncus kraussii,132,fruit_colour,black brown red yellow,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Juncus kraussii Test_2023_4,Lantana montevidensis,133,fruit_colour,black purple,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Lantana montevidensis Test_2023_4,Lepidium africanum,134,fruit_width,2,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Lepidium africanum @@ -143,37 +143,37 @@ Test_2023_4,Lepidium foliosum,135,fruit_length,4,mm,species,mode,,1,,seedling,,, Test_2023_4,Lepidium oxytrichum,136,fruit_length,5,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Lepidium oxytrichum Test_2023_4,Lepidosperma gladiatum,137,fruit_length,3,mm,species,maximum,measurement,1,literature,seedling,,,,,Test_2000,,01,,,,Part of Test Dataset 4,01,04,Lepidosperma gladiatum Test_2023_4,Leptomeria drupacea,138,fruit_length,6,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Leptomeria drupacea -Test_2023_4,Leptospermum continentale,139,fruit_length,6,mm,metapopulation,mode,,1,,seedling,02,,,,,02,01,,,,From `australia_2` site,01,04,Leptospermum continentale +Test_2023_4,Leptospermum continentale,139,fruit_length,6,mm,metapopulation,mode,,1,,seedling,03,,,,,02,01,,,,From `australia_2` site,01,04,Leptospermum continentale Test_2023_4,Leptospermum obovatum,140,fruit_width,8,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Leptospermum obovatum Test_2023_4,Leucopogon amplexicaulis,141,fruit_length,3.5,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Leucopogon amplexicaulis Test_2023_4,Lobelia pedunculata,142,fruit_length,4,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Lobelia pedunculata -Test_2023_4,Lobelia trigonocaulis,143,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,02,Lobelia trigonocaulis -Test_2023_4,Lotononis bainesii,144,fruit_length,8,mm,metapopulation,mode,,1,,seedling,02,,,,Test_2000,02,02,,,,From `australia_2` site,01,04,Lotononis bainesii -Test_2023_4,Lotus corniculatus,145,leaf_stomatal_conductance,0.3,mol{H2O}/m2/s,population,raw,measurement,5,field_experiment,juvenile,01,,01,,,01,02,,,,Part of Test Dataset 4,01,04,Lotus corniculatus -Test_2023_4,Lotus corniculatus,145,leaf_stomatal_conductance,0.2,mol{H2O}/m2/s,population,raw,measurement,5,field_experiment,juvenile,01,,02,,,01,02,,,,Part of Test Dataset 4,01,04,Lotus corniculatus -Test_2023_4,Lotus corniculatus,146,leaf_photosynthesis,5,umol/m2/s,individual,raw,measurement,5,field_experiment,seedling,02,01,01,,,02,02,,,,From `australia_2` site,01,04,Lotus corniculatus -Test_2023_4,Lotus corniculatus,146,leaf_photosynthesis,4.4,umol/m2/s,individual,raw,measurement,5,field_experiment,seedling,02,01,02,,,02,02,,,,From `australia_2` site,01,04,Lotus corniculatus -Test_2023_4,Lotus corniculatus,146,leaf_photosynthesis,2,umol/m2/s,individual,raw,measurement,5,field_experiment,seedling,02,01,03,,,02,02,,,,From `australia_2` site,01,04,Lotus corniculatus -Test_2023_4,Lotus corniculatus,147,leaf_photosynthesis,0.9,umol/m2/s,individual,raw,measurement,5,field_experiment,seedling,02,02,01,,,02,02,,,,From `australia_2` site,01,04,Lotus corniculatus -Test_2023_4,Lotus corniculatus,148,leaf_stomatal_conductance,0.5,mol{H2O}/m2/s,population,raw,measurement,5,field_experiment,seedling,02,,01,,,02,02,,,,From `australia_2` site,01,04,Lotus corniculatus -Test_2023_4,Lotus corniculatus,148,leaf_stomatal_conductance,0.44,mol{H2O}/m2/s,population,raw,measurement,5,field_experiment,seedling,02,,02,,,02,02,,,,From `australia_2` site,01,04,Lotus corniculatus -Test_2023_4,Lotus corniculatus,148,leaf_stomatal_conductance,0.3,mol{H2O}/m2/s,population,raw,measurement,5,field_experiment,seedling,02,,03,,,02,02,,,,From `australia_2` site,01,04,Lotus corniculatus -Test_2023_4,Lotus corniculatus,149,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,02,Lotus corniculatus -Test_2023_4,Lupinus polyphyllus,150,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,02,Lupinus polyphyllus +Test_2023_4,Lobelia trigonocaulis,143,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Lobelia trigonocaulis +Test_2023_4,Lotononis bainesii,144,fruit_length,8,mm,metapopulation,mode,,1,,seedling,03,,,,Test_2000,02,02,,,,From `australia_2` site,01,04,Lotononis bainesii +Test_2023_4,Lotus corniculatus,145,leaf_stomatal_conductance,0.3,mol{H2O}/m2/s,population,raw,measurement,5,field_experiment,juvenile,01,,01,,,01,02,,,2020,Part of Test Dataset 4,01,04,Lotus corniculatus +Test_2023_4,Lotus corniculatus,145,leaf_stomatal_conductance,0.2,mol{H2O}/m2/s,population,raw,measurement,5,field_experiment,juvenile,01,,02,,,01,02,,,2020,Part of Test Dataset 4,01,04,Lotus corniculatus +Test_2023_4,Lotus corniculatus,146,leaf_photosynthesis,5,umol/m2/s,individual,raw,measurement,5,field_experiment,seedling,03,01,01,,,02,02,,,,From `australia_2` site,01,04,Lotus corniculatus +Test_2023_4,Lotus corniculatus,146,leaf_photosynthesis,4.4,umol/m2/s,individual,raw,measurement,5,field_experiment,seedling,03,01,02,,,02,02,,,,From `australia_2` site,01,04,Lotus corniculatus +Test_2023_4,Lotus corniculatus,146,leaf_photosynthesis,2,umol/m2/s,individual,raw,measurement,5,field_experiment,seedling,03,01,03,,,02,02,,,,From `australia_2` site,01,04,Lotus corniculatus +Test_2023_4,Lotus corniculatus,147,leaf_photosynthesis,0.9,umol/m2/s,individual,raw,measurement,5,field_experiment,seedling,03,02,01,,,02,02,,,,From `australia_2` site,01,04,Lotus corniculatus +Test_2023_4,Lotus corniculatus,148,leaf_stomatal_conductance,0.5,mol{H2O}/m2/s,population,raw,measurement,5,field_experiment,seedling,03,,01,,,02,02,,,,From `australia_2` site,01,04,Lotus corniculatus +Test_2023_4,Lotus corniculatus,148,leaf_stomatal_conductance,0.44,mol{H2O}/m2/s,population,raw,measurement,5,field_experiment,seedling,03,,02,,,02,02,,,,From `australia_2` site,01,04,Lotus corniculatus +Test_2023_4,Lotus corniculatus,148,leaf_stomatal_conductance,0.3,mol{H2O}/m2/s,population,raw,measurement,5,field_experiment,seedling,03,,03,,,02,02,,,,From `australia_2` site,01,04,Lotus corniculatus +Test_2023_4,Lotus corniculatus,149,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Lotus corniculatus +Test_2023_4,Lupinus polyphyllus,150,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Lupinus polyphyllus Test_2023_4,Medicago orbicularis,151,fruit_length,7,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Medicago orbicularis Test_2023_4,Melichrus procumbens,152,fruit_length,4,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Melichrus procumbens Test_2023_4,Mischocarpus australis,153,fruit_width,8,mm,species,mode,,1,field_experiment,seedling,,,,,Test_2003,,01,,,,Part of Test Dataset 4,01,04,Mischocarpus australis Test_2023_4,Muehlenbeckia adpressa,154,fruit_colour,black brown,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Muehlenbeckia adpressa -Test_2023_4,Myoporum boninense subsp. australe,155,fruit_length,10,mm,metapopulation,mode,measurement,1,literature,seedling,02,,,,Test_2003,02,01,,,,From `australia_2` site,01,04,Myoporum boninense subsp. australe -Test_2023_4,Nicotiana glauca,156,leaf_photosynthesis,6,umol/m2/s,individual,raw,measurement,5,field_experiment,seedling,02,01,01,,,02,02,,,,From `australia_2` site,01,04,Nicotiana glauca -Test_2023_4,Nicotiana glauca,156,leaf_photosynthesis,4,umol/m2/s,individual,raw,measurement,5,field_experiment,seedling,02,01,02,,,02,02,,,,From `australia_2` site,01,04,Nicotiana glauca -Test_2023_4,Nicotiana glauca,156,leaf_photosynthesis,3.7,umol/m2/s,individual,raw,measurement,5,field_experiment,seedling,02,01,03,,,02,02,,,,From `australia_2` site,01,04,Nicotiana glauca +Test_2023_4,Myoporum boninense subsp. australe,155,fruit_length,10,mm,metapopulation,mode,measurement,1,literature,seedling,03,,,,Test_2003,02,01,,,,From `australia_2` site,01,04,Myoporum boninense subsp. australe +Test_2023_4,Nicotiana glauca,156,leaf_photosynthesis,6,umol/m2/s,individual,raw,measurement,5,field_experiment,seedling,03,01,01,,,02,02,,,,From `australia_2` site,01,04,Nicotiana glauca +Test_2023_4,Nicotiana glauca,156,leaf_photosynthesis,4,umol/m2/s,individual,raw,measurement,5,field_experiment,seedling,03,01,02,,,02,02,,,,From `australia_2` site,01,04,Nicotiana glauca +Test_2023_4,Nicotiana glauca,156,leaf_photosynthesis,3.7,umol/m2/s,individual,raw,measurement,5,field_experiment,seedling,03,01,03,,,02,02,,,,From `australia_2` site,01,04,Nicotiana glauca Test_2023_4,Nicotiana glauca,157,fruit_length,13,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Nicotiana glauca Test_2023_4,Nicotiana goodspeedii,158,fruit_length,5,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Nicotiana goodspeedii Test_2023_4,Oxalis corniculata,159,fruit_width,1.5,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Oxalis corniculata -Test_2023_4,Pandorea pandorana subsp. austrocaledonica,160,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,04,Pandorea pandorana subsp. austrocaledonica +Test_2023_4,Pandorea pandorana subsp. austrocaledonica,160,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,04,Pandorea pandorana subsp. austrocaledonica Test_2023_4,Paraserianthes lophantha,161,fruit_width,25,mm,species,mode,,1,field_experiment,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Paraserianthes lophantha -Test_2023_4,Parentucellia latifolia,162,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,02,Parentucellia latifolia +Test_2023_4,Parentucellia latifolia,162,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Parentucellia latifolia Test_2023_4,Phlegmatospermum cochlearinum,163,fruit_length,10,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Phlegmatospermum cochlearinum Test_2023_4,Phyla nodiflora,164,fruit_width,2,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Phyla nodiflora Test_2023_4,Phyla nodiflora,165,leaf_stomatal_conductance,0.2,mol{H2O}/m2/s,species,raw,measurement,5,field_experiment,seedling,,,01,,,,02,,,,Part of Test Dataset 4,01,04,Phyla nodiflora @@ -181,12 +181,12 @@ Test_2023_4,Phyla nodiflora,165,leaf_stomatal_conductance,0.1,mol{H2O}/m2/s,spec Test_2023_4,Phyla nodiflora,165,leaf_stomatal_conductance,0.37,mol{H2O}/m2/s,species,raw,measurement,5,field_experiment,seedling,,,,,,,02,,,,Part of Test Dataset 4,02,04,Phyla nodiflora Test_2023_4,Phyla nodiflora,165,leaf_stomatal_conductance,0.6,mol{H2O}/m2/s,species,raw,measurement,5,field_experiment,seedling,,,,,,,02,,,,Part of Test Dataset 4,02,04,Phyla nodiflora Test_2023_4,Picris barbarorum,166,fruit_length,7.5,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Picris barbarorum -Test_2023_4,Pimelea ligustrina subsp. ligustrina,167,fruit_colour,green,,metapopulation,mode,,1,literature,seedling,02,,,,Test_2003,02,02,,,,From `australia_2` site,01,03,Pimelea ligustrina subsp. ligustrina +Test_2023_4,Pimelea ligustrina subsp. ligustrina,167,fruit_colour,green,,metapopulation,mode,,1,literature,seedling,03,,,,Test_2003,02,02,,,,From `australia_2` site,01,03,Pimelea ligustrina subsp. ligustrina Test_2023_4,Pinus pinea,168,fruit_colour,brown,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Pinus pinea -Test_2023_4,Pisum sativum var. arvense,169,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,02,Pisum sativum var. arvense -Test_2023_4,Pittosporum erioloma,170,fruit_dehiscence,dehiscent,,,mode,,1,literature,adult,,,,,Test_2003,,02,,,,Part of Test Dataset 4,01,04,Pittosporum erioloma +Test_2023_4,Pisum sativum var. arvense,169,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Pisum sativum var. arvense +Test_2023_4,Pittosporum erioloma,170,fruit_dehiscence,dehiscent,,,mode,,1,literature,adult,,,,,Test_2003,,02,,,,,01,04,Pittosporum erioloma Test_2023_4,Plantago turrifera,171,fruit_length,3,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Plantago turrifera -Test_2023_4,Polycarpon tetraphyllum,172,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,02,Polycarpon tetraphyllum +Test_2023_4,Polycarpon tetraphyllum,172,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Polycarpon tetraphyllum Test_2023_4,Potamogeton australiensis,173,fruit_length,4,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Potamogeton australiensis Test_2023_4,Psoralea pinnata,174,fruit_width,2.5,mm,species,minimum,,1,field_experiment,seedling,,,,,Test_2003,,01,,,,Part of Test Dataset 4,01,04,Psoralea pinnata Test_2023_4,Pultenaea ferruginea,175,fruit_length,6,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Pultenaea ferruginea @@ -194,19 +194,19 @@ Test_2023_4,Rhodamnia argentea,176,fruit_length,6,mm,species,mode,,1,,seedling,, Test_2023_4,Rhodamnia argentea,177,fruit_colour,black,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Rhodamnia argentea Test_2023_4,Rorippa gigantea,178,fruit_length,15,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Rorippa gigantea Test_2023_4,Rubus parvifolius,179,fruit_colour,red,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Rubus parvifolius -Test_2023_4,Salix alba,180,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,02,Salix alba +Test_2023_4,Salix alba,180,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Salix alba Test_2023_4,Schenkia australis,181,fruit_length,10,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Schenkia australis Test_2023_4,Schoenus apogon,182,fruit_colour,white,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Schoenus apogon Test_2023_4,Schoenus brevifolius,183,fruit_width,0.7,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Schoenus brevifolius Test_2023_4,Schoenus lepidosperma,184,fruit_width,2.5,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Schoenus lepidosperma -Test_2023_4,Schoenus vaginatus,185,fruit_colour,brown red yellow,,metapopulation,mode,,1,,seedling,02,,,,,02,02,,,,From `australia_2` site,01,04,Schoenus vaginatus +Test_2023_4,Schoenus vaginatus,185,fruit_colour,brown red yellow,,metapopulation,mode,,1,,seedling,03,,,,,02,02,,,,From `australia_2` site,01,04,Schoenus vaginatus Test_2023_4,Scleria rugosa,186,fruit_length,3,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Scleria rugosa Test_2023_4,Senecio longipilus,187,fruit_length,2.5,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Senecio longipilus Test_2023_4,Sida goniocarpa,188,fruit_width,7,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Sida goniocarpa Test_2023_4,Sigesbeckia orientalis,189,fruit_length,3,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Sigesbeckia orientalis Test_2023_4,Sisymbrium irio,190,fruit_length,25,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Sisymbrium irio -Test_2023_4,Sparaxis bulbifera,191,fruit_colour,green,,population,minimum,,1,field,juvenile,01,,,,,01,02,,,,Part of Test Dataset 4,01,04,Sparaxis bulbifera -Test_2023_4,Spergularia diandra,192,fruit_dehiscence,dehiscent,,species,mean,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,02,Spergularia diandra +Test_2023_4,Sparaxis bulbifera,191,fruit_colour,green,,population,minimum,,1,field,juvenile,01,,,,,01,02,,,2020,Part of Test Dataset 4,01,04,Sparaxis bulbifera +Test_2023_4,Spergularia diandra,192,fruit_dehiscence,dehiscent,,species,mean,,1,,adult,,,,,,,02,,,,,01,02,Spergularia diandra Test_2023_4,Sphaeromorphaea littoralis,193,fruit_length,1.3,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Sphaeromorphaea littoralis Test_2023_4,Stellaria angustifolia subsp. angustifolia,194,fruit_length,8.5,mm,,mode,measurement,1,literature,seedling,,,,,Test_2003,,01,,,,Part of Test Dataset 4,01,04,Stellaria angustifolia subsp. angustifolia Test_2023_4,Styphelia viridis,195,fruit_length,10,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Styphelia viridis @@ -214,7 +214,7 @@ Test_2023_4,Swainsona cadellii,196,fruit_length,25,mm,species,mode,,1,,seedling, Test_2023_4,Teucrium puberulum,197,fruit_width,4,mm,species,mode,,1,field_experiment,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Teucrium puberulum Test_2023_4,Thelymitra kangaloonica,198,fruit_length,12,mm,species,,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Thelymitra kangaloonica Test_2023_4,Thesium australe,199,fruit_width,2.5,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Thesium australe -Test_2023_4,Trifolium dubium,200,fruit_length,2,mm,metapopulation,mode,measurement,1,literature,seedling,02,,,,Test_2003,02,02,,,,From `australia_2` site,01,04,Trifolium dubium -Test_2023_4,Veronica catenata,201,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,Part of Test Dataset 4,01,02,Veronica catenata +Test_2023_4,Trifolium dubium,200,fruit_length,2,mm,metapopulation,mode,measurement,1,literature,seedling,03,,,,Test_2003,02,02,,,,From `australia_2` site,01,04,Trifolium dubium +Test_2023_4,Veronica catenata,201,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Veronica catenata Test_2023_4,Veronica derwentiana,202,fruit_length,2.8,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Veronica derwentiana Test_2023_4,Wahlenbergia luteola,203,fruit_length,5,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Wahlenbergia luteola diff --git a/tests/testthat/examples/test1-data.csv b/tests/testthat/examples/test1-data.csv deleted file mode 100644 index 6cfcbcb7..00000000 --- a/tests/testthat/examples/test1-data.csv +++ /dev/null @@ -1,46 +0,0 @@ -Species,species_abb,site,LMA (mg mm-2),Leaf nitrogen (mg mg-1),leaf size (mm2),wood density (mg mm-3),branch mass fraction,Seed mass (mg),LASA10,LASA250,LASA50,LASA1000 -Acacia celsa,acacel,Atherton,0.145,0.0214,2786,0.498,0.67,10.3,2977,7260,3722,6824 -Acronychia acidula,acraci,Atherton,0.085,0.0243,14302,0.525,0.48,,,7560,5541,9480 -Alphitonia petriei,alppet,Atherton,0.149,0.0163,6820,0.413,0.42,27.2,,4340,3313,4335 -Glochidion hylandii,glohyl,Atherton,0.106,0.0137,3209,0.566,0.41,10.41,1993,5075,5455,8664 -Homalanthus novoguineensis,omanov,Atherton,0.082,0.022,10682,0.319,0.47,7,,2136,2158,3307 -Melicope elleryana,melell,Atherton,0.075,0.0268,6955,0.346,0.58,1.61,,4201,2860,6119 -Neolitsea dealbata,neodea,Atherton,0.093,0.0164,5228,0.352,0.58,176.1,1686,2747,3049,7504 -Polyscias australiana,polaus,Atherton,0.079,0.0154,6806,0.397,0.42,8.35,,6008,,6700 -Psychotria sp Utchee Creek,psyspp,Atherton,0.108,0.0179,11157,0.582,0,23.09,,4977,2302,2037 -Rhodomyrtus trineura,rhotri,Atherton,0.129,0.0111,3401,0.763,0.34,,4321,3803,6088,6877 -Acmena graveolens,acmgra,Cape Tribulation,0.151,0.0155,5246,0.599,0.67,,,3057,2667,7156 -Aleurites rockinghamensis,aleroc,Cape Tribulation,0.113,0.0184,73984,0.28,0.02,7077,,4194,,6209 -Alstonia scholaris,alssch,Cape Tribulation,0.107,0.0223,6182,0.361,0.46,1.53,,1854,1682,3932 -Argyrodendron peralatum,argper,Cape Tribulation,0.244,0.0119,3201,0.726,0.71,433,,3832,1689,6718 -Atractocarpus hirtus,atrhir,Cape Tribulation,0.072,0.0157,11374,0.804,0.28,,,7143,6727,6103 -Brombya platynema,bropla,Cape Tribulation,0.106,0.0188,8218,0.603,0.33,,,4261,3531,5377 -Cardwellia sublimis,carsub,Cape Tribulation,0.127,0.0128,4352,0.603,0.56,582.3,,6315,4880,8282 -Castanospermum australe,casaus,Cape Tribulation,0.117,0.0237,2765,0.587,0.37,14851,,7329,,8869 -Cleistanthus myrianthus,clemyr,Cape Tribulation,0.078,0.0228,4828,0.588,0.56,,3720,6084,5233,8559 -Cryptocarya laevigata,crylae,Cape Tribulation,0.087,0.0156,2682,0.64,0.65,1281,1391,3297,4680,7588 -Cryptocarya mackinnoniana,crymac,Cape Tribulation,0.204,0.0152,10458,0.655,0.61,204,,3277,2325,8657 -Cryptocarya murrayi,crymur,Cape Tribulation,0.155,0.0167,9960,0.674,0.39,,2693,5543,4298,5451 -Dendrocnide moroides,denmor,Cape Tribulation,0.052,0.0312,26454,0.23,0.46,0.71,,2372,,2090 -Elaeocarpus grandis,elaang,Cape Tribulation,0.122,0.0187,2762,0.499,0.47,3699,,2598,1748,4635 -Endiandra leptodendron,endlep,Cape Tribulation,0.106,0.018,3987,0.611,0.68,,1492,2412,2783,7477 -Endiandra microneura,endmic,Cape Tribulation,0.151,0.0177,3377,0.623,0.61,,3573,6344,3354,6235 -Gillbeea adenopetala,gilade,Cape Tribulation,0.126,0.0096,3678,0.43,0.46,15,,2863,3160,6549 -Haplostichanthus sp Coop. Ck,hapspp,Cape Tribulation,0.072,0.022,4685,0.668,0.36,,2430,12304,3282,2992 -Harpullia rhyticarpa,harrhy,Cape Tribulation,0.076,0.0174,40876,0.621,0.01,,,8971,5922,4669 -Hernandia albiflora,heralb,Cape Tribulation,0.069,0.0195,3806,0.447,0.33,,3123,4145,4643,6086 -Ixora biflora,ixobif,Cape Tribulation,0.081,0.01,2760,0.843,0.55,41.5,5244,3892,1969,8094 -Lasianthus strigosus,lasstr,Cape Tribulation,0.055,0.0158,3313,0.684,0.15,7,1841,5100,2379,2731 -Litsea leefeana,litlee,Cape Tribulation,0.13,0.0144,3917,0.549,0.68,263.4,3984,4141,3816,9645 -Macaranga tanarius,mactan,Cape Tribulation,0.104,0.0205,46676,0.344,0,,,3377,,3901 -Mallotus mollissimus,malmol,Cape Tribulation,0.063,0.0352,16716,0.373,0.32,31.25,1788,5580,5163,7944 -Medicosma sessiliflora,medses,Cape Tribulation,0.106,0.0153,8164,0.69,0.65,,2844,9332,6514,10298 -Melastoma cyanoides,melaff,Cape Tribulation,0.046,0.0208,4009,0.381,0.6,0.07,2960,4057,4661,6637 -Myristica insipida,myrins,Cape Tribulation,0.106,0.0185,8379,0.433,0.51,1612,,6929,4852,9273 -Pittosporum rubiginosum,pitrub,Cape Tribulation,0.065,0.0143,9931,0.728,0.28,27.94,7428,7459,5265,6548 -Psychotria dallachiana,psydal,Cape Tribulation,0.079,0.0177,2495,0.612,0.33,,4290,5666,4916,4761 -Quassia baileyana,quabai,Cape Tribulation,0.086,0.023,9624,0.501,0.42,,,5867,3216,5719 -Rockinghamia angustifolia,rocang,Cape Tribulation,0.108,0.0158,10636,0.455,0.39,19.38,,5862,4611,6098 -Syzygium gustavioides,syzgus,Cape Tribulation,0.167,0.0129,3590,0.521,0.59,48000,2833,3121,3047,6584 -Syzygium sayeri,syzsay,Cape Tribulation,0.131,0.0137,2645,0.485,0.65,841,3929,5767,4939,9836 -Trema aspera,treasp,Cape Tribulation,0.053,0.0299,2071,0.357,0.53,5.12,3578,5291,5440,6695 diff --git a/tests/testthat/examples/test1-metadata.yml b/tests/testthat/examples/test1-metadata.yml deleted file mode 100644 index dbce2dff..00000000 --- a/tests/testthat/examples/test1-metadata.yml +++ /dev/null @@ -1,316 +0,0 @@ -source: - primary: - key: Falster_2005_1 - bibtype: Article - author: Daniel S. Falster, Mark Westoby - year: 2005 - title: Alternative height strategies among 45 dicot rain forest species from tropical - Queensland, Australia - journal: Journal of Ecology - volume: 93 - pages: 521--535 - publisher: Wiley-Blackwell - doi: 10.1111/j.0022-0477.2005.00992.x -contributors: - data_collectors: - - last_name: Falster - given_name: Daniel - ORCID: 0000-0002-9814-092X - affiliation: Evolution & Ecology Research Centre, School of Biological, Earth, - and Environmental Sciences, UNSW Sydney, Australia - additional_role: contact - - last_name: Westoby - given_name: Mark - ORCID: 0000-0001-7690-4530 - affiliation: Department of Biological Sciences, Macquarie University, Australia - dataset_curators: Elizabeth Wenk -dataset: - data_is_long_format: no - custom_R_code: .na - collection_date: 2004/2004 - taxon_name: Species - location_name: site - description: Investigation into trait values correlated with plant height along - light availability and successional gradients for far north Queensland species. - basis_of_record: field - life_stage: adult - sampling_strategy: Nineteen species, ranging from early to late successional status, - were selected using published sources (Hopkins & Graham 1987; Osunkoya 1996; Hyland - et al. 1999). Species selected to represent the light gradient establish and mature - in closed forest, where successional species are assumed absent. For inclusion - in this set we required that a species was known to establish and persist at low - light levels, as indicated either by published sources (Hyland et al. 1999; Osunkoya - 1996) or by scientists familiar with the vegetation (A Graham, J Wells, CSIRO - Atherton; R Jensen). Twenty-six species, experiencing a range of light levels - at maturity, from high (canopy trees) to low light (understorey shrubs), were - included. - original_file: Falster & Westoby 2005 J Ecol appendix.doc - notes: none -locations: - Atherton: - description: Tropical rain forest vegetation. - elevation (m): 800 - latitude (deg): -17.1166667 - longitude (deg): 145.65 - rainfall (mm): 2000 - Cape Tribulation: - description: Complex mesophyll vine forest in tropical rain forest. - elevation (m): 25 - latitude (deg): -16.1 - longitude (deg): 145.45 - rainfall (mm): 3500 -contexts: .na -traits: -- var_in: LMA (mg mm-2) - unit_in: mg/mm2 - trait_name: leaf_mass_per_area - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: LMA was calculated as the leaf dry mass (oven-dried for 48 hours at 65 - deg C) divided by leaf size. It was measured on the first five fully expanded - leaves at the tip of each individual. -- var_in: Leaf nitrogen (mg mg-1) - unit_in: mg/mg - trait_name: leaf_N_per_dry_mass - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: Leaves from all individuals per species were pooled and finely ground for - nitrogen analysis. Total nitrogen concentration (%) was measured using complete - combustion gas chromatography by Waite Analytical Services, Adelaide. The first - five fully expanded leaves at the tip of each individual were used for the analysis. -- var_in: leaf size (mm2) - unit_in: mm2 - trait_name: leaf_area - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: Leaf size was calculated as the one-sided leaf area (flat bed scanner). - It was measured on the first five fully expanded leaves at the tip of each individual. -- var_in: wood density (mg mm-3) - unit_in: mg/mm3 - trait_name: wood_density - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: Wood density was calculated using 40-60 mm stem segments taken 250 mm and - 1000 mm back along a branch from the branch tip. Fresh samples were refrigerated - before processing. After removing bark material, the volume of each wood sample - was determined using Archimedes' principle (Hacke et al. 2000). Samples were submerged - in a water-filled container on a balance. The weight change (mg) recorded during - submersion corresponds to the mass of water displaced, which can be converted - to a volume using the formula, displacement weight (mg)/0.998 (mg/mm3), where - 0.998 mg/mm3 is the density of water at 20 deg C. Samples were then dried for - 4 days at 60 deg C before weighing. -- var_in: branch mass fraction - unit_in: mg/mg - trait_name: branch_mass_fraction - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: Branch mass fraction was calculated as the mass side branches/total mass, - on a carbon dry mass basis. The zero values are correct - these are plants with - no branches. -- var_in: Seed mass (mg) - unit_in: mg - trait_name: seed_dry_mass - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: unknown - methods: Mean oven-dried seed mass (including seed coat but excluding seed accessories) - was estimated for all species with available field material. In total, collections - for 17 of 47 species were made. Data for an additional 12 species were drawn from - published (Osunkoya et al. 1994; Grubb et al. 1998) and unpublished (P. Juniper, - CSIRO Atherton) sources. -- var_in: LASA10 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a shoot whose sapwood had a cross sectional - area of 10 mm2. In detail from Wright_2006, which used this data, No single best - point exists to compare traits such as LM/ SM, LA/SM and LA/SA when considering - a set of species that varies widely in canopy architecture and typical maximum - height (here, approximately 20 cm to 85 m). We have used several approaches (Table - 1). In one study, we made measurements on the terminal twigs of each species, - i.e. on a relatively standard developmental unit (Westoby and Wright 2003). For - species at Ash, GLP, Myall and TRF, traits were measured at each of several different - distances back down the stem from the branch tip (Falster and Westoby 2005a, 2005b - and unpublished, Pickup et al. 2005). At GHP, RHM and RHW, traits were measured - at a standard sapwood cross-sectional area (10 mm2; Pickup et al. 2005). For the - present re-analysis, we took the raw data from the previous studies and, for every - species possible, calculated patterns of leaf and stem deployment at two standard - points: at 250 mm distance from the branch tip (Ash, GLP, Myall and TRF) and at - 10 mm2 stem (Ash, Myall, TRF) or sapwood (GHP, GLP, RHM, RHW) crosssectional area - (250 mm or 10 mm2 formulation denoted as subscript in trait abbreviations). This - was done as follows. For each individual plant, total leaf and stem dry mass at - 250 mm distance was estimated by straightline interpolation from values measured - at the nearest sampling points on either side of this distance. As the dry mass - data tended to display non-linear (power) relationships with distance from the - branch tip, the interpolated values were calculated from log10-log10- transformed - data, then back-transformed to the original scale. The same approach was used - for interpolating data to the standard stem (or sapwood) cross-sectional area. - For individuals where measurements had not been made on either side of the desired - point but the nearest measurement had been made within 25 mm of 250 mm or 1 mm2 - of 10 mm2 cross-section (i.e. within 10% of the desired point), we extrapolated - (rather than interpolated) the measured data to the standard point. This allowed - us to include a number of individuals and species for which interpolation was - not possible. Still, several large-leaved, large-stemmed species from the TRF - site could not be included in the 10-mm2 crosssection dataset. No unusual tendencies - in analyses, including the extrapolated data, were seen in comparison to analyses - including interpolated data only (details not shown). To illustrate how species'' - morphology varied at the two standard sampling points, species-mean stem cross-sectional - area varied between 1.2 and 258 mm2 at 250 mm distance from the branch tip, while - the distance from the branch tip at which stem cross-sectional area reached 10 - mm2 varied from 64 to 995 mm.' -- var_in: LASA250 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a 250 mm branch segment and sapwood cross-sectional - area was determined where the branch was cut. In detail from Wright_2006, which - used this data, No single best point exists to compare traits such as LM/ SM, - LA/SM and LA/SA when considering a set of species that varies widely in canopy - architecture and typical maximum height (here, approximately 20 cm to 85 m). We - have used several approaches (Table 1). In one study, we made measurements on - the terminal twigs of each species, i.e. on a relatively standard developmental - unit (Westoby and Wright 2003). For species at Ash, GLP, Myall and TRF, traits - were measured at each of several different distances back down the stem from the - branch tip (Falster and Westoby 2005a, 2005b and unpublished, Pickup et al. 2005). - At GHP, RHM and RHW, traits were measured at a standard sapwood cross-sectional - area (10 mm2; Pickup et al. 2005). For the present re-analysis, we took the raw - data from the previous studies and, for every species possible, calculated patterns - of leaf and stem deployment at two standard points: at 250 mm distance from the - branch tip (Ash, GLP, Myall and TRF) and at 10 mm2 stem (Ash, Myall, TRF) or sapwood - (GHP, GLP, RHM, RHW) crosssectional area (250 mm or 10 mm2 formulation denoted - as subscript in trait abbreviations). This was done as follows. For each individual - plant, total leaf and stem dry mass at 250 mm distance was estimated by straightline - interpolation from values measured at the nearest sampling points on either side - of this distance. As the dry mass data tended to display non-linear (power) relationships - with distance from the branch tip, the interpolated values were calculated from - log10-log10- transformed data, then back-transformed to the original scale. The - same approach was used for interpolating data to the standard stem (or sapwood) - cross-sectional area. For individuals where measurements had not been made on - either side of the desired point but the nearest measurement had been made within - 25 mm of 250 mm or 1 mm2 of 10 mm2 cross-section (i.e. within 10% of the desired - point), we extrapolated (rather than interpolated) the measured data to the standard - point. This allowed us to include a number of individuals and species for which - interpolation was not possible. Still, several large-leaved, large-stemmed species - from the TRF site could not be included in the 10-mm2 crosssection dataset. No - unusual tendencies in analyses, including the extrapolated data, were seen in - comparison to analyses including interpolated data only (details not shown). To - illustrate how species'' morphology varied at the two standard sampling points, - species-mean stem cross-sectional area varied between 1.2 and 258 mm2 at 250 mm - distance from the branch tip, while the distance from the branch tip at which - stem cross-sectional area reached 10 mm2 varied from 64 to 995 mm.' -- var_in: LASA50 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a 50 mm branch segment and sapwood cross-sectional - area was determined where the branch was cut. In detail from Wright_2006, which - used this data, No single best point exists to compare traits such as LM/ SM, - LA/SM and LA/SA when considering a set of species that varies widely in canopy - architecture and typical maximum height (here, approximately 20 cm to 85 m). We - have used several approaches (Table 1). In one study, we made measurements on - the terminal twigs of each species, i.e. on a relatively standard developmental - unit (Westoby and Wright 2003). For species at Ash, GLP, Myall and TRF, traits - were measured at each of several different distances back down the stem from the - branch tip (Falster and Westoby 2005a, 2005b and unpublished, Pickup et al. 2005). - At GHP, RHM and RHW, traits were measured at a standard sapwood cross-sectional - area (10 mm2; Pickup et al. 2005). For the present re-analysis, we took the raw - data from the previous studies and, for every species possible, calculated patterns - of leaf and stem deployment at two standard points: at 250 mm distance from the - branch tip (Ash, GLP, Myall and TRF) and at 10 mm2 stem (Ash, Myall, TRF) or sapwood - (GHP, GLP, RHM, RHW) crosssectional area (250 mm or 10 mm2 formulation denoted - as subscript in trait abbreviations). This was done as follows. For each individual - plant, total leaf and stem dry mass at 250 mm distance was estimated by straightline - interpolation from values measured at the nearest sampling points on either side - of this distance. As the dry mass data tended to display non-linear (power) relationships - with distance from the branch tip, the interpolated values were calculated from - log10-log10- transformed data, then back-transformed to the original scale. The - same approach was used for interpolating data to the standard stem (or sapwood) - cross-sectional area. For individuals where measurements had not been made on - either side of the desired point but the nearest measurement had been made within - 25 mm of 250 mm or 1 mm2 of 10 mm2 cross-section (i.e. within 10% of the desired - point), we extrapolated (rather than interpolated) the measured data to the standard - point. This allowed us to include a number of individuals and species for which - interpolation was not possible. Still, several large-leaved, large-stemmed species - from the TRF site could not be included in the 10-mm2 crosssection dataset. No - unusual tendencies in analyses, including the extrapolated data, were seen in - comparison to analyses including interpolated data only (details not shown). To - illustrate how species'' morphology varied at the two standard sampling points, - species-mean stem cross-sectional area varied between 1.2 and 258 mm2 at 250 mm - distance from the branch tip, while the distance from the branch tip at which - stem cross-sectional area reached 10 mm2 varied from 64 to 995 mm.' -- var_in: LASA1000 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a 1000 mm branch segment and sapwood cross-sectional - area was determined where the branch was cut. In detail from Wright_2006, which - used this data, No single best point exists to compare traits such as LM/ SM, - LA/SM and LA/SA when considering a set of species that varies widely in canopy - architecture and typical maximum height (here, approximately 20 cm to 85 m). We - have used several approaches (Table 1). In one study, we made measurements on - the terminal twigs of each species, i.e. on a relatively standard developmental - unit (Westoby and Wright 2003). For species at Ash, GLP, Myall and TRF, traits - were measured at each of several different distances back down the stem from the - branch tip (Falster and Westoby 2005a, 2005b and unpublished, Pickup et al. 2005). - At GHP, RHM and RHW, traits were measured at a standard sapwood cross-sectional - area (10 mm2; Pickup et al. 2005). For the present re-analysis, we took the raw - data from the previous studies and, for every species possible, calculated patterns - of leaf and stem deployment at two standard points: at 250 mm distance from the - branch tip (Ash, GLP, Myall and TRF) and at 10 mm2 stem (Ash, Myall, TRF) or sapwood - (GHP, GLP, RHM, RHW) crosssectional area (250 mm or 10 mm2 formulation denoted - as subscript in trait abbreviations). This was done as follows. For each individual - plant, total leaf and stem dry mass at 250 mm distance was estimated by straightline - interpolation from values measured at the nearest sampling points on either side - of this distance. As the dry mass data tended to display non-linear (power) relationships - with distance from the branch tip, the interpolated values were calculated from - log10-log10- transformed data, then back-transformed to the original scale. The - same approach was used for interpolating data to the standard stem (or sapwood) - cross-sectional area. For individuals where measurements had not been made on - either side of the desired point but the nearest measurement had been made within - 25 mm of 250 mm or 1 mm2 of 10 mm2 cross-section (i.e. within 10% of the desired - point), we extrapolated (rather than interpolated) the measured data to the standard - point. This allowed us to include a number of individuals and species for which - interpolation was not possible. Still, several large-leaved, large-stemmed species - from the TRF site could not be included in the 10-mm2 crosssection dataset. No - unusual tendencies in analyses, including the extrapolated data, were seen in - comparison to analyses including interpolated data only (details not shown). To - illustrate how species'' morphology varied at the two standard sampling points, - species-mean stem cross-sectional area varied between 1.2 and 258 mm2 at 250 mm - distance from the branch tip, while the distance from the branch tip at which - stem cross-sectional area reached 10 mm2 varied from 64 to 995 mm.' -substitutions: .na -taxonomic_updates: -- find: Homalanthus novoguineensis - replace: Homalanthus novo-guineensis - reason: Change spelling to align with known name in APC (Daniel Falster, 2020.05.22) -- find: Haplostichanthus sp Coop. Ck - replace: Haplostichanthus submontanus - reason: Align previous phrase name with current APC name (E. Wenk, 2020-05-25) -- find: Psychotria sp Utchee Creek - replace: Psychotria sp. Utchee Creek (H.Flecker NQNC5313) - reason: Align to name in APC (D Falster, 2020.05.23) -exclude_observations: .na -questions: .na diff --git a/tests/testthat/examples/test2-data.csv b/tests/testthat/examples/test2-data.csv deleted file mode 100644 index d9e9f1a3..00000000 --- a/tests/testthat/examples/test2-data.csv +++ /dev/null @@ -1,46 +0,0 @@ -Species,species_abb,site,LMA (mg mm-2),Leaf nitrogen (mg mg-1),leaf size (mm2),wood density (mg mm-3),branch mass fraction,Seed mass (mg),LASA10,LASA250,LASA50,LASA1000,basis_of_record,life_stage -Acacia celsa,acacel,Atherton,0.145,0.0214,2786,0.498,0.67,10.3,2977,7260,3722,6824,wild,seedling -Acronychia acidula,acraci,Atherton,0.085,0.0243,14302,0.525,0.48,,,7560,5541,9480,wild,seedling -Alphitonia petriei,alppet,Atherton,0.149,0.0163,6820,0.413,0.42,27.2,,4340,3313,4335,wild,seedling -Glochidion hylandii,glohyl,Atherton,0.106,0.0137,3209,0.566,0.41,10.41,1993,5075,5455,8664,wild,seedling -Homalanthus novoguineensis,omanov,Atherton,0.082,0.022,10682,0.319,0.47,7,,2136,2158,3307,wild,seedling -Melicope elleryana,melell,Atherton,0.075,0.0268,6955,0.346,0.58,1.61,,4201,2860,6119,wild,seedling -Neolitsea dealbata,neodea,Atherton,0.093,0.0164,5228,0.352,0.58,176.1,1686,2747,3049,7504,wild,seedling -Polyscias australiana,polaus,Atherton,0.079,0.0154,6806,0.397,0.42,8.35,,6008,,6700,wild,seedling -Psychotria sp Utchee Creek,psyspp,Atherton,0.108,0.0179,11157,0.582,0,23.09,,4977,2302,2037,wild,seedling -Rhodomyrtus trineura,rhotri,Atherton,0.129,0.0111,3401,0.763,0.34,,4321,3803,6088,6877,wild,seedling -Acmena graveolens,acmgra,Cape Tribulation,0.151,0.0155,5246,0.599,0.67,,,3057,2667,7156,wild,seedling -Aleurites rockinghamensis,aleroc,Cape Tribulation,0.113,0.0184,73984,0.28,0.02,7077,,4194,,6209,wild,seedling -Alstonia scholaris,alssch,Cape Tribulation,0.107,0.0223,6182,0.361,0.46,1.53,,1854,1682,3932,wild,seedling -Argyrodendron peralatum,argper,Cape Tribulation,0.244,0.0119,3201,0.726,0.71,433,,3832,1689,6718,wild,seedling -Atractocarpus hirtus,atrhir,Cape Tribulation,0.072,0.0157,11374,0.804,0.28,,,7143,6727,6103,wild,seedling -Brombya platynema,bropla,Cape Tribulation,0.106,0.0188,8218,0.603,0.33,,,4261,3531,5377,wild,seedling -Cardwellia sublimis,carsub,Cape Tribulation,0.127,0.0128,4352,0.603,0.56,582.3,,6315,4880,8282,wild,seedling -Castanospermum australe,casaus,Cape Tribulation,0.117,0.0237,2765,0.587,0.37,14851,,7329,,8869,wild,seedling -Cleistanthus myrianthus,clemyr,Cape Tribulation,0.078,0.0228,4828,0.588,0.56,,3720,6084,5233,8559,wild,seedling -Cryptocarya laevigata,crylae,Cape Tribulation,0.087,0.0156,2682,0.64,0.65,1281,1391,3297,4680,7588,wild,seedling -Cryptocarya mackinnoniana,crymac,Cape Tribulation,0.204,0.0152,10458,0.655,0.61,204,,3277,2325,8657,wild,seedling -Cryptocarya murrayi,crymur,Cape Tribulation,0.155,0.0167,9960,0.674,0.39,,2693,5543,4298,5451,wild,seedling -Dendrocnide moroides,denmor,Cape Tribulation,0.052,0.0312,26454,0.23,0.46,0.71,,2372,,2090,wild,seedling -Elaeocarpus grandis,elaang,Cape Tribulation,0.122,0.0187,2762,0.499,0.47,3699,,2598,1748,4635,wild,seedling -Endiandra leptodendron,endlep,Cape Tribulation,0.106,0.018,3987,0.611,0.68,,1492,2412,2783,7477,wild,seedling -Endiandra microneura,endmic,Cape Tribulation,0.151,0.0177,3377,0.623,0.61,,3573,6344,3354,6235,wild,seedling -Gillbeea adenopetala,gilade,Cape Tribulation,0.126,0.0096,3678,0.43,0.46,15,,2863,3160,6549,wild,seedling -Haplostichanthus sp Coop. Ck,hapspp,Cape Tribulation,0.072,0.022,4685,0.668,0.36,,2430,12304,3282,2992,wild,seedling -Harpullia rhyticarpa,harrhy,Cape Tribulation,0.076,0.0174,40876,0.621,0.01,,,8971,5922,4669,wild,seedling -Hernandia albiflora,heralb,Cape Tribulation,0.069,0.0195,3806,0.447,0.33,,3123,4145,4643,6086,wild,seedling -Ixora biflora,ixobif,Cape Tribulation,0.081,0.01,2760,0.843,0.55,41.5,5244,3892,1969,8094,wild,seedling -Lasianthus strigosus,lasstr,Cape Tribulation,0.055,0.0158,3313,0.684,0.15,7,1841,5100,2379,2731,wild,seedling -Litsea leefeana,litlee,Cape Tribulation,0.13,0.0144,3917,0.549,0.68,263.4,3984,4141,3816,9645,wild,seedling -Macaranga tanarius,mactan,Cape Tribulation,0.104,0.0205,46676,0.344,0,,,3377,,3901,wild,seedling -Mallotus mollissimus,malmol,Cape Tribulation,0.063,0.0352,16716,0.373,0.32,31.25,1788,5580,5163,7944,wild,seedling -Medicosma sessiliflora,medses,Cape Tribulation,0.106,0.0153,8164,0.69,0.65,,2844,9332,6514,10298,wild,seedling -Melastoma cyanoides,melaff,Cape Tribulation,0.046,0.0208,4009,0.381,0.6,0.07,2960,4057,4661,6637,wild,seedling -Myristica insipida,myrins,Cape Tribulation,0.106,0.0185,8379,0.433,0.51,1612,,6929,4852,9273,wild,seedling -Pittosporum rubiginosum,pitrub,Cape Tribulation,0.065,0.0143,9931,0.728,0.28,27.94,7428,7459,5265,6548,wild,seedling -Psychotria dallachiana,psydal,Cape Tribulation,0.079,0.0177,2495,0.612,0.33,,4290,5666,4916,4761,wild,seedling -Quassia baileyana,quabai,Cape Tribulation,0.086,0.023,9624,0.501,0.42,,,5867,3216,5719,wild,seedling -Rockinghamia angustifolia,rocang,Cape Tribulation,0.108,0.0158,10636,0.455,0.39,19.38,,5862,4611,6098,wild,seedling -Syzygium gustavioides,syzgus,Cape Tribulation,0.167,0.0129,3590,0.521,0.59,48000,2833,3121,3047,6584,wild,seedling -Syzygium sayeri,syzsay,Cape Tribulation,0.131,0.0137,2645,0.485,0.65,841,3929,5767,4939,9836,wild,seedling -Trema aspera,treasp,Cape Tribulation,0.053,0.0299,2071,0.357,0.53,5.12,3578,5291,5440,6695,wild,seedling diff --git a/tests/testthat/examples/test2-metadata.yml b/tests/testthat/examples/test2-metadata.yml deleted file mode 100644 index c89a96d6..00000000 --- a/tests/testthat/examples/test2-metadata.yml +++ /dev/null @@ -1,317 +0,0 @@ -source: - primary: - key: Falster_2005_1 - bibtype: Article - author: Daniel S. Falster, Mark Westoby - year: 2005 - title: Alternative height strategies among 45 dicot rain forest species from tropical - Queensland, Australia - journal: Journal of Ecology - volume: 93 - pages: 521--535 - publisher: Wiley-Blackwell - doi: 10.1111/j.0022-0477.2005.00992.x -contributors: - data_collectors: - - last_name: Falster - given_name: Daniel - ORCID: 0000-0002-9814-092X - affiliation: Evolution & Ecology Research Centre, School of Biological, Earth, - and Environmental Sciences, UNSW Sydney, Australia - additional_role: contact - - last_name: Westoby - given_name: Mark - ORCID: 0000-0001-7690-4530 - affiliation: Department of Biological Sciences, Macquarie University, Australia - dataset_curators: Elizabeth Wenk -dataset: - data_is_long_format: no - custom_R_code: .na - collection_date: 2004/2004 - taxon_name: Species - location_name: site - description: Investigation into trait values correlated with plant height along - light availability and successional gradients for far north Queensland species. - basis_of_record: field - life_stage: adult - sampling_strategy: Nineteen species, ranging from early to late successional status, - were selected using published sources (Hopkins & Graham 1987; Osunkoya 1996; Hyland - et al. 1999). Species selected to represent the light gradient establish and mature - in closed forest, where successional species are assumed absent. For inclusion - in this set we required that a species was known to establish and persist at low - light levels, as indicated either by published sources (Hyland et al. 1999; Osunkoya - 1996) or by scientists familiar with the vegetation (A Graham, J Wells, CSIRO - Atherton; R Jensen). Twenty-six species, experiencing a range of light levels - at maturity, from high (canopy trees) to low light (understorey shrubs), were - included. - original_file: Falster & Westoby 2005 J Ecol appendix.doc - notes: none -locations: - Atherton: - description: Tropical rain forest vegetation. - elevation (m): 800 - latitude (deg): -17.1166667 - longitude (deg): 145.65 - rainfall (mm): 2000 - Cape Tribulation: - description: Complex mesophyll vine forest in tropical rain forest. - elevation (m): 25 - latitude (deg): -16.1 - longitude (deg): 145.45 - rainfall (mm): 3500 -contexts: .na -traits: -- var_in: LMA (mg mm-2) - unit_in: mg/mm2 - trait_name: leaf_mass_per_area - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: LMA was calculated as the leaf dry mass (oven-dried for 48 hours at 65 - deg C) divided by leaf size. It was measured on the first five fully expanded - leaves at the tip of each individual. -- var_in: Leaf nitrogen (mg mg-1) - unit_in: mg/mg - trait_name: leaf_N_per_dry_mass - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - basis_of_record: lab - methods: Leaves from all individuals per species were pooled and finely ground for - nitrogen analysis. Total nitrogen concentration (%) was measured using complete - combustion gas chromatography by Waite Analytical Services, Adelaide. The first - five fully expanded leaves at the tip of each individual were used for the analysis. -- var_in: leaf size (mm2) - unit_in: mm2 - trait_name: leaf_area - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: Leaf size was calculated as the one-sided leaf area (flat bed scanner). - It was measured on the first five fully expanded leaves at the tip of each individual. -- var_in: wood density (mg mm-3) - unit_in: mg/mm3 - trait_name: wood_density - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: Wood density was calculated using 40-60 mm stem segments taken 250 mm and - 1000 mm back along a branch from the branch tip. Fresh samples were refrigerated - before processing. After removing bark material, the volume of each wood sample - was determined using Archimedes' principle (Hacke et al. 2000). Samples were submerged - in a water-filled container on a balance. The weight change (mg) recorded during - submersion corresponds to the mass of water displaced, which can be converted - to a volume using the formula, displacement weight (mg)/0.998 (mg/mm3), where - 0.998 mg/mm3 is the density of water at 20 deg C. Samples were then dried for - 4 days at 60 deg C before weighing. -- var_in: branch mass fraction - unit_in: mg/mg - trait_name: branch_mass_fraction - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: Branch mass fraction was calculated as the mass side branches/total mass, - on a carbon dry mass basis. The zero values are correct - these are plants with - no branches. -- var_in: Seed mass (mg) - unit_in: mg - trait_name: seed_dry_mass - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: unknown - methods: Mean oven-dried seed mass (including seed coat but excluding seed accessories) - was estimated for all species with available field material. In total, collections - for 17 of 47 species were made. Data for an additional 12 species were drawn from - published (Osunkoya et al. 1994; Grubb et al. 1998) and unpublished (P. Juniper, - CSIRO Atherton) sources. -- var_in: LASA10 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a shoot whose sapwood had a cross sectional - area of 10 mm2. In detail from Wright_2006, which used this data, No single best - point exists to compare traits such as LM/ SM, LA/SM and LA/SA when considering - a set of species that varies widely in canopy architecture and typical maximum - height (here, approximately 20 cm to 85 m). We have used several approaches (Table - 1). In one study, we made measurements on the terminal twigs of each species, - i.e. on a relatively standard developmental unit (Westoby and Wright 2003). For - species at Ash, GLP, Myall and TRF, traits were measured at each of several different - distances back down the stem from the branch tip (Falster and Westoby 2005a, 2005b - and unpublished, Pickup et al. 2005). At GHP, RHM and RHW, traits were measured - at a standard sapwood cross-sectional area (10 mm2; Pickup et al. 2005). For the - present re-analysis, we took the raw data from the previous studies and, for every - species possible, calculated patterns of leaf and stem deployment at two standard - points: at 250 mm distance from the branch tip (Ash, GLP, Myall and TRF) and at - 10 mm2 stem (Ash, Myall, TRF) or sapwood (GHP, GLP, RHM, RHW) crosssectional area - (250 mm or 10 mm2 formulation denoted as subscript in trait abbreviations). This - was done as follows. For each individual plant, total leaf and stem dry mass at - 250 mm distance was estimated by straightline interpolation from values measured - at the nearest sampling points on either side of this distance. As the dry mass - data tended to display non-linear (power) relationships with distance from the - branch tip, the interpolated values were calculated from log10-log10- transformed - data, then back-transformed to the original scale. The same approach was used - for interpolating data to the standard stem (or sapwood) cross-sectional area. - For individuals where measurements had not been made on either side of the desired - point but the nearest measurement had been made within 25 mm of 250 mm or 1 mm2 - of 10 mm2 cross-section (i.e. within 10% of the desired point), we extrapolated - (rather than interpolated) the measured data to the standard point. This allowed - us to include a number of individuals and species for which interpolation was - not possible. Still, several large-leaved, large-stemmed species from the TRF - site could not be included in the 10-mm2 crosssection dataset. No unusual tendencies - in analyses, including the extrapolated data, were seen in comparison to analyses - including interpolated data only (details not shown). To illustrate how species'' - morphology varied at the two standard sampling points, species-mean stem cross-sectional - area varied between 1.2 and 258 mm2 at 250 mm distance from the branch tip, while - the distance from the branch tip at which stem cross-sectional area reached 10 - mm2 varied from 64 to 995 mm.' -- var_in: LASA250 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a 250 mm branch segment and sapwood cross-sectional - area was determined where the branch was cut. In detail from Wright_2006, which - used this data, No single best point exists to compare traits such as LM/ SM, - LA/SM and LA/SA when considering a set of species that varies widely in canopy - architecture and typical maximum height (here, approximately 20 cm to 85 m). We - have used several approaches (Table 1). In one study, we made measurements on - the terminal twigs of each species, i.e. on a relatively standard developmental - unit (Westoby and Wright 2003). For species at Ash, GLP, Myall and TRF, traits - were measured at each of several different distances back down the stem from the - branch tip (Falster and Westoby 2005a, 2005b and unpublished, Pickup et al. 2005). - At GHP, RHM and RHW, traits were measured at a standard sapwood cross-sectional - area (10 mm2; Pickup et al. 2005). For the present re-analysis, we took the raw - data from the previous studies and, for every species possible, calculated patterns - of leaf and stem deployment at two standard points: at 250 mm distance from the - branch tip (Ash, GLP, Myall and TRF) and at 10 mm2 stem (Ash, Myall, TRF) or sapwood - (GHP, GLP, RHM, RHW) crosssectional area (250 mm or 10 mm2 formulation denoted - as subscript in trait abbreviations). This was done as follows. For each individual - plant, total leaf and stem dry mass at 250 mm distance was estimated by straightline - interpolation from values measured at the nearest sampling points on either side - of this distance. As the dry mass data tended to display non-linear (power) relationships - with distance from the branch tip, the interpolated values were calculated from - log10-log10- transformed data, then back-transformed to the original scale. The - same approach was used for interpolating data to the standard stem (or sapwood) - cross-sectional area. For individuals where measurements had not been made on - either side of the desired point but the nearest measurement had been made within - 25 mm of 250 mm or 1 mm2 of 10 mm2 cross-section (i.e. within 10% of the desired - point), we extrapolated (rather than interpolated) the measured data to the standard - point. This allowed us to include a number of individuals and species for which - interpolation was not possible. Still, several large-leaved, large-stemmed species - from the TRF site could not be included in the 10-mm2 crosssection dataset. No - unusual tendencies in analyses, including the extrapolated data, were seen in - comparison to analyses including interpolated data only (details not shown). To - illustrate how species'' morphology varied at the two standard sampling points, - species-mean stem cross-sectional area varied between 1.2 and 258 mm2 at 250 mm - distance from the branch tip, while the distance from the branch tip at which - stem cross-sectional area reached 10 mm2 varied from 64 to 995 mm.' -- var_in: LASA50 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a 50 mm branch segment and sapwood cross-sectional - area was determined where the branch was cut. In detail from Wright_2006, which - used this data, No single best point exists to compare traits such as LM/ SM, - LA/SM and LA/SA when considering a set of species that varies widely in canopy - architecture and typical maximum height (here, approximately 20 cm to 85 m). We - have used several approaches (Table 1). In one study, we made measurements on - the terminal twigs of each species, i.e. on a relatively standard developmental - unit (Westoby and Wright 2003). For species at Ash, GLP, Myall and TRF, traits - were measured at each of several different distances back down the stem from the - branch tip (Falster and Westoby 2005a, 2005b and unpublished, Pickup et al. 2005). - At GHP, RHM and RHW, traits were measured at a standard sapwood cross-sectional - area (10 mm2; Pickup et al. 2005). For the present re-analysis, we took the raw - data from the previous studies and, for every species possible, calculated patterns - of leaf and stem deployment at two standard points: at 250 mm distance from the - branch tip (Ash, GLP, Myall and TRF) and at 10 mm2 stem (Ash, Myall, TRF) or sapwood - (GHP, GLP, RHM, RHW) crosssectional area (250 mm or 10 mm2 formulation denoted - as subscript in trait abbreviations). This was done as follows. For each individual - plant, total leaf and stem dry mass at 250 mm distance was estimated by straightline - interpolation from values measured at the nearest sampling points on either side - of this distance. As the dry mass data tended to display non-linear (power) relationships - with distance from the branch tip, the interpolated values were calculated from - log10-log10- transformed data, then back-transformed to the original scale. The - same approach was used for interpolating data to the standard stem (or sapwood) - cross-sectional area. For individuals where measurements had not been made on - either side of the desired point but the nearest measurement had been made within - 25 mm of 250 mm or 1 mm2 of 10 mm2 cross-section (i.e. within 10% of the desired - point), we extrapolated (rather than interpolated) the measured data to the standard - point. This allowed us to include a number of individuals and species for which - interpolation was not possible. Still, several large-leaved, large-stemmed species - from the TRF site could not be included in the 10-mm2 crosssection dataset. No - unusual tendencies in analyses, including the extrapolated data, were seen in - comparison to analyses including interpolated data only (details not shown). To - illustrate how species'' morphology varied at the two standard sampling points, - species-mean stem cross-sectional area varied between 1.2 and 258 mm2 at 250 mm - distance from the branch tip, while the distance from the branch tip at which - stem cross-sectional area reached 10 mm2 varied from 64 to 995 mm.' -- var_in: LASA1000 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a 1000 mm branch segment and sapwood cross-sectional - area was determined where the branch was cut. In detail from Wright_2006, which - used this data, No single best point exists to compare traits such as LM/ SM, - LA/SM and LA/SA when considering a set of species that varies widely in canopy - architecture and typical maximum height (here, approximately 20 cm to 85 m). We - have used several approaches (Table 1). In one study, we made measurements on - the terminal twigs of each species, i.e. on a relatively standard developmental - unit (Westoby and Wright 2003). For species at Ash, GLP, Myall and TRF, traits - were measured at each of several different distances back down the stem from the - branch tip (Falster and Westoby 2005a, 2005b and unpublished, Pickup et al. 2005). - At GHP, RHM and RHW, traits were measured at a standard sapwood cross-sectional - area (10 mm2; Pickup et al. 2005). For the present re-analysis, we took the raw - data from the previous studies and, for every species possible, calculated patterns - of leaf and stem deployment at two standard points: at 250 mm distance from the - branch tip (Ash, GLP, Myall and TRF) and at 10 mm2 stem (Ash, Myall, TRF) or sapwood - (GHP, GLP, RHM, RHW) crosssectional area (250 mm or 10 mm2 formulation denoted - as subscript in trait abbreviations). This was done as follows. For each individual - plant, total leaf and stem dry mass at 250 mm distance was estimated by straightline - interpolation from values measured at the nearest sampling points on either side - of this distance. As the dry mass data tended to display non-linear (power) relationships - with distance from the branch tip, the interpolated values were calculated from - log10-log10- transformed data, then back-transformed to the original scale. The - same approach was used for interpolating data to the standard stem (or sapwood) - cross-sectional area. For individuals where measurements had not been made on - either side of the desired point but the nearest measurement had been made within - 25 mm of 250 mm or 1 mm2 of 10 mm2 cross-section (i.e. within 10% of the desired - point), we extrapolated (rather than interpolated) the measured data to the standard - point. This allowed us to include a number of individuals and species for which - interpolation was not possible. Still, several large-leaved, large-stemmed species - from the TRF site could not be included in the 10-mm2 crosssection dataset. No - unusual tendencies in analyses, including the extrapolated data, were seen in - comparison to analyses including interpolated data only (details not shown). To - illustrate how species'' morphology varied at the two standard sampling points, - species-mean stem cross-sectional area varied between 1.2 and 258 mm2 at 250 mm - distance from the branch tip, while the distance from the branch tip at which - stem cross-sectional area reached 10 mm2 varied from 64 to 995 mm.' -substitutions: .na -taxonomic_updates: -- find: Homalanthus novoguineensis - replace: Homalanthus novo-guineensis - reason: Change spelling to align with known name in APC (Daniel Falster, 2020.05.22) -- find: Haplostichanthus sp Coop. Ck - replace: Haplostichanthus submontanus - reason: Align previous phrase name with current APC name (E. Wenk, 2020-05-25) -- find: Psychotria sp Utchee Creek - replace: Psychotria sp. Utchee Creek (H.Flecker NQNC5313) - reason: Align to name in APC (D Falster, 2020.05.23) -exclude_observations: .na -questions: .na diff --git a/tests/testthat/examples/test2.1-metadata.yml b/tests/testthat/examples/test2.1-metadata.yml deleted file mode 100644 index b8fdc9eb..00000000 --- a/tests/testthat/examples/test2.1-metadata.yml +++ /dev/null @@ -1,317 +0,0 @@ -source: - primary: - key: Falster_2005_1 - bibtype: Article - author: Daniel S. Falster, Mark Westoby - year: 2005 - title: Alternative height strategies among 45 dicot rain forest species from tropical - Queensland, Australia - journal: Journal of Ecology - volume: 93 - pages: 521--535 - publisher: Wiley-Blackwell - doi: 10.1111/j.0022-0477.2005.00992.x -contributors: - data_collectors: - - last_name: Falster - given_name: Daniel - ORCID: 0000-0002-9814-092X - affiliation: Evolution & Ecology Research Centre, School of Biological, Earth, - and Environmental Sciences, UNSW Sydney, Australia - additional_role: contact - - last_name: Westoby - given_name: Mark - ORCID: 0000-0001-7690-4530 - affiliation: Department of Biological Sciences, Macquarie University, Australia - dataset_curators: Elizabeth Wenk -dataset: - data_is_long_format: no - custom_R_code: .na - collection_date: 2004/2004 - taxon_name: Species - location_name: site - description: Investigation into trait values correlated with plant height along - light availability and successional gradients for far north Queensland species. - basis_of_record: basis_of_record - life_stage: life_stage - sampling_strategy: Nineteen species, ranging from early to late successional status, - were selected using published sources (Hopkins & Graham 1987; Osunkoya 1996; Hyland - et al. 1999). Species selected to represent the light gradient establish and mature - in closed forest, where successional species are assumed absent. For inclusion - in this set we required that a species was known to establish and persist at low - light levels, as indicated either by published sources (Hyland et al. 1999; Osunkoya - 1996) or by scientists familiar with the vegetation (A Graham, J Wells, CSIRO - Atherton; R Jensen). Twenty-six species, experiencing a range of light levels - at maturity, from high (canopy trees) to low light (understorey shrubs), were - included. - original_file: Falster & Westoby 2005 J Ecol appendix.doc - notes: none -locations: - Atherton: - description: Tropical rain forest vegetation. - elevation (m): 800 - latitude (deg): -17.1166667 - longitude (deg): 145.65 - rainfall (mm): 2000 - Cape Tribulation: - description: Complex mesophyll vine forest in tropical rain forest. - elevation (m): 25 - latitude (deg): -16.1 - longitude (deg): 145.45 - rainfall (mm): 3500 -contexts: .na -traits: -- var_in: LMA (mg mm-2) - unit_in: mg/mm2 - trait_name: leaf_mass_per_area - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: LMA was calculated as the leaf dry mass (oven-dried for 48 hours at 65 - deg C) divided by leaf size. It was measured on the first five fully expanded - leaves at the tip of each individual. -- var_in: Leaf nitrogen (mg mg-1) - unit_in: mg/mg - trait_name: leaf_N_per_dry_mass - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - basis_of_record: lab - methods: Leaves from all individuals per species were pooled and finely ground for - nitrogen analysis. Total nitrogen concentration (%) was measured using complete - combustion gas chromatography by Waite Analytical Services, Adelaide. The first - five fully expanded leaves at the tip of each individual were used for the analysis. -- var_in: leaf size (mm2) - unit_in: mm2 - trait_name: leaf_area - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: Leaf size was calculated as the one-sided leaf area (flat bed scanner). - It was measured on the first five fully expanded leaves at the tip of each individual. -- var_in: wood density (mg mm-3) - unit_in: mg/mm3 - trait_name: wood_density - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: Wood density was calculated using 40-60 mm stem segments taken 250 mm and - 1000 mm back along a branch from the branch tip. Fresh samples were refrigerated - before processing. After removing bark material, the volume of each wood sample - was determined using Archimedes' principle (Hacke et al. 2000). Samples were submerged - in a water-filled container on a balance. The weight change (mg) recorded during - submersion corresponds to the mass of water displaced, which can be converted - to a volume using the formula, displacement weight (mg)/0.998 (mg/mm3), where - 0.998 mg/mm3 is the density of water at 20 deg C. Samples were then dried for - 4 days at 60 deg C before weighing. -- var_in: branch mass fraction - unit_in: mg/mg - trait_name: branch_mass_fraction - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: Branch mass fraction was calculated as the mass side branches/total mass, - on a carbon dry mass basis. The zero values are correct - these are plants with - no branches. -- var_in: Seed mass (mg) - unit_in: mg - trait_name: seed_dry_mass - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: unknown - methods: Mean oven-dried seed mass (including seed coat but excluding seed accessories) - was estimated for all species with available field material. In total, collections - for 17 of 47 species were made. Data for an additional 12 species were drawn from - published (Osunkoya et al. 1994; Grubb et al. 1998) and unpublished (P. Juniper, - CSIRO Atherton) sources. -- var_in: LASA10 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a shoot whose sapwood had a cross sectional - area of 10 mm2. In detail from Wright_2006, which used this data, No single best - point exists to compare traits such as LM/ SM, LA/SM and LA/SA when considering - a set of species that varies widely in canopy architecture and typical maximum - height (here, approximately 20 cm to 85 m). We have used several approaches (Table - 1). In one study, we made measurements on the terminal twigs of each species, - i.e. on a relatively standard developmental unit (Westoby and Wright 2003). For - species at Ash, GLP, Myall and TRF, traits were measured at each of several different - distances back down the stem from the branch tip (Falster and Westoby 2005a, 2005b - and unpublished, Pickup et al. 2005). At GHP, RHM and RHW, traits were measured - at a standard sapwood cross-sectional area (10 mm2; Pickup et al. 2005). For the - present re-analysis, we took the raw data from the previous studies and, for every - species possible, calculated patterns of leaf and stem deployment at two standard - points: at 250 mm distance from the branch tip (Ash, GLP, Myall and TRF) and at - 10 mm2 stem (Ash, Myall, TRF) or sapwood (GHP, GLP, RHM, RHW) crosssectional area - (250 mm or 10 mm2 formulation denoted as subscript in trait abbreviations). This - was done as follows. For each individual plant, total leaf and stem dry mass at - 250 mm distance was estimated by straightline interpolation from values measured - at the nearest sampling points on either side of this distance. As the dry mass - data tended to display non-linear (power) relationships with distance from the - branch tip, the interpolated values were calculated from log10-log10- transformed - data, then back-transformed to the original scale. The same approach was used - for interpolating data to the standard stem (or sapwood) cross-sectional area. - For individuals where measurements had not been made on either side of the desired - point but the nearest measurement had been made within 25 mm of 250 mm or 1 mm2 - of 10 mm2 cross-section (i.e. within 10% of the desired point), we extrapolated - (rather than interpolated) the measured data to the standard point. This allowed - us to include a number of individuals and species for which interpolation was - not possible. Still, several large-leaved, large-stemmed species from the TRF - site could not be included in the 10-mm2 crosssection dataset. No unusual tendencies - in analyses, including the extrapolated data, were seen in comparison to analyses - including interpolated data only (details not shown). To illustrate how species'' - morphology varied at the two standard sampling points, species-mean stem cross-sectional - area varied between 1.2 and 258 mm2 at 250 mm distance from the branch tip, while - the distance from the branch tip at which stem cross-sectional area reached 10 - mm2 varied from 64 to 995 mm.' -- var_in: LASA250 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a 250 mm branch segment and sapwood cross-sectional - area was determined where the branch was cut. In detail from Wright_2006, which - used this data, No single best point exists to compare traits such as LM/ SM, - LA/SM and LA/SA when considering a set of species that varies widely in canopy - architecture and typical maximum height (here, approximately 20 cm to 85 m). We - have used several approaches (Table 1). In one study, we made measurements on - the terminal twigs of each species, i.e. on a relatively standard developmental - unit (Westoby and Wright 2003). For species at Ash, GLP, Myall and TRF, traits - were measured at each of several different distances back down the stem from the - branch tip (Falster and Westoby 2005a, 2005b and unpublished, Pickup et al. 2005). - At GHP, RHM and RHW, traits were measured at a standard sapwood cross-sectional - area (10 mm2; Pickup et al. 2005). For the present re-analysis, we took the raw - data from the previous studies and, for every species possible, calculated patterns - of leaf and stem deployment at two standard points: at 250 mm distance from the - branch tip (Ash, GLP, Myall and TRF) and at 10 mm2 stem (Ash, Myall, TRF) or sapwood - (GHP, GLP, RHM, RHW) crosssectional area (250 mm or 10 mm2 formulation denoted - as subscript in trait abbreviations). This was done as follows. For each individual - plant, total leaf and stem dry mass at 250 mm distance was estimated by straightline - interpolation from values measured at the nearest sampling points on either side - of this distance. As the dry mass data tended to display non-linear (power) relationships - with distance from the branch tip, the interpolated values were calculated from - log10-log10- transformed data, then back-transformed to the original scale. The - same approach was used for interpolating data to the standard stem (or sapwood) - cross-sectional area. For individuals where measurements had not been made on - either side of the desired point but the nearest measurement had been made within - 25 mm of 250 mm or 1 mm2 of 10 mm2 cross-section (i.e. within 10% of the desired - point), we extrapolated (rather than interpolated) the measured data to the standard - point. This allowed us to include a number of individuals and species for which - interpolation was not possible. Still, several large-leaved, large-stemmed species - from the TRF site could not be included in the 10-mm2 crosssection dataset. No - unusual tendencies in analyses, including the extrapolated data, were seen in - comparison to analyses including interpolated data only (details not shown). To - illustrate how species'' morphology varied at the two standard sampling points, - species-mean stem cross-sectional area varied between 1.2 and 258 mm2 at 250 mm - distance from the branch tip, while the distance from the branch tip at which - stem cross-sectional area reached 10 mm2 varied from 64 to 995 mm.' -- var_in: LASA50 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a 50 mm branch segment and sapwood cross-sectional - area was determined where the branch was cut. In detail from Wright_2006, which - used this data, No single best point exists to compare traits such as LM/ SM, - LA/SM and LA/SA when considering a set of species that varies widely in canopy - architecture and typical maximum height (here, approximately 20 cm to 85 m). We - have used several approaches (Table 1). In one study, we made measurements on - the terminal twigs of each species, i.e. on a relatively standard developmental - unit (Westoby and Wright 2003). For species at Ash, GLP, Myall and TRF, traits - were measured at each of several different distances back down the stem from the - branch tip (Falster and Westoby 2005a, 2005b and unpublished, Pickup et al. 2005). - At GHP, RHM and RHW, traits were measured at a standard sapwood cross-sectional - area (10 mm2; Pickup et al. 2005). For the present re-analysis, we took the raw - data from the previous studies and, for every species possible, calculated patterns - of leaf and stem deployment at two standard points: at 250 mm distance from the - branch tip (Ash, GLP, Myall and TRF) and at 10 mm2 stem (Ash, Myall, TRF) or sapwood - (GHP, GLP, RHM, RHW) crosssectional area (250 mm or 10 mm2 formulation denoted - as subscript in trait abbreviations). This was done as follows. For each individual - plant, total leaf and stem dry mass at 250 mm distance was estimated by straightline - interpolation from values measured at the nearest sampling points on either side - of this distance. As the dry mass data tended to display non-linear (power) relationships - with distance from the branch tip, the interpolated values were calculated from - log10-log10- transformed data, then back-transformed to the original scale. The - same approach was used for interpolating data to the standard stem (or sapwood) - cross-sectional area. For individuals where measurements had not been made on - either side of the desired point but the nearest measurement had been made within - 25 mm of 250 mm or 1 mm2 of 10 mm2 cross-section (i.e. within 10% of the desired - point), we extrapolated (rather than interpolated) the measured data to the standard - point. This allowed us to include a number of individuals and species for which - interpolation was not possible. Still, several large-leaved, large-stemmed species - from the TRF site could not be included in the 10-mm2 crosssection dataset. No - unusual tendencies in analyses, including the extrapolated data, were seen in - comparison to analyses including interpolated data only (details not shown). To - illustrate how species'' morphology varied at the two standard sampling points, - species-mean stem cross-sectional area varied between 1.2 and 258 mm2 at 250 mm - distance from the branch tip, while the distance from the branch tip at which - stem cross-sectional area reached 10 mm2 varied from 64 to 995 mm.' -- var_in: LASA1000 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a 1000 mm branch segment and sapwood cross-sectional - area was determined where the branch was cut. In detail from Wright_2006, which - used this data, No single best point exists to compare traits such as LM/ SM, - LA/SM and LA/SA when considering a set of species that varies widely in canopy - architecture and typical maximum height (here, approximately 20 cm to 85 m). We - have used several approaches (Table 1). In one study, we made measurements on - the terminal twigs of each species, i.e. on a relatively standard developmental - unit (Westoby and Wright 2003). For species at Ash, GLP, Myall and TRF, traits - were measured at each of several different distances back down the stem from the - branch tip (Falster and Westoby 2005a, 2005b and unpublished, Pickup et al. 2005). - At GHP, RHM and RHW, traits were measured at a standard sapwood cross-sectional - area (10 mm2; Pickup et al. 2005). For the present re-analysis, we took the raw - data from the previous studies and, for every species possible, calculated patterns - of leaf and stem deployment at two standard points: at 250 mm distance from the - branch tip (Ash, GLP, Myall and TRF) and at 10 mm2 stem (Ash, Myall, TRF) or sapwood - (GHP, GLP, RHM, RHW) crosssectional area (250 mm or 10 mm2 formulation denoted - as subscript in trait abbreviations). This was done as follows. For each individual - plant, total leaf and stem dry mass at 250 mm distance was estimated by straightline - interpolation from values measured at the nearest sampling points on either side - of this distance. As the dry mass data tended to display non-linear (power) relationships - with distance from the branch tip, the interpolated values were calculated from - log10-log10- transformed data, then back-transformed to the original scale. The - same approach was used for interpolating data to the standard stem (or sapwood) - cross-sectional area. For individuals where measurements had not been made on - either side of the desired point but the nearest measurement had been made within - 25 mm of 250 mm or 1 mm2 of 10 mm2 cross-section (i.e. within 10% of the desired - point), we extrapolated (rather than interpolated) the measured data to the standard - point. This allowed us to include a number of individuals and species for which - interpolation was not possible. Still, several large-leaved, large-stemmed species - from the TRF site could not be included in the 10-mm2 crosssection dataset. No - unusual tendencies in analyses, including the extrapolated data, were seen in - comparison to analyses including interpolated data only (details not shown). To - illustrate how species'' morphology varied at the two standard sampling points, - species-mean stem cross-sectional area varied between 1.2 and 258 mm2 at 250 mm - distance from the branch tip, while the distance from the branch tip at which - stem cross-sectional area reached 10 mm2 varied from 64 to 995 mm.' -substitutions: .na -taxonomic_updates: -- find: Homalanthus novoguineensis - replace: Homalanthus novo-guineensis - reason: Change spelling to align with known name in APC (Daniel Falster, 2020.05.22) -- find: Haplostichanthus sp Coop. Ck - replace: Haplostichanthus submontanus - reason: Align previous phrase name with current APC name (E. Wenk, 2020-05-25) -- find: Psychotria sp Utchee Creek - replace: Psychotria sp. Utchee Creek (H.Flecker NQNC5313) - reason: Align to name in APC (D Falster, 2020.05.23) -exclude_observations: .na -questions: .na diff --git a/tests/testthat/examples/test3-data.csv b/tests/testthat/examples/test3-data.csv deleted file mode 100644 index caa06bf4..00000000 --- a/tests/testthat/examples/test3-data.csv +++ /dev/null @@ -1,46 +0,0 @@ -Species,species_abb,site,LMA (mg mm-2),Leaf nitrogen (mg mg-1),leaf size (mm2),wood density (mg mm-3),branch mass fraction,Seed mass (mg),LASA10,LASA250,LASA50,LASA1000,basis_of_record -Acacia celsa,acacel,Atherton,0.145,0.0214,2786,0.498,0.67,10.3,2977,7260,3722,6824, -Acronychia acidula,acraci,Atherton,0.085,0.0243,14302,0.525,0.48,,,7560,5541,9480, -Alphitonia petriei,alppet,Atherton,0.149,0.0163,6820,0.413,0.42,27.2,,4340,3313,4335, -Glochidion hylandii,glohyl,Atherton,0.106,0.0137,3209,0.566,0.41,10.41,1993,5075,5455,8664, -Homalanthus novoguineensis,omanov,Atherton,0.082,0.022,10682,0.319,0.47,7,,2136,2158,3307, -Melicope elleryana,melell,Atherton,0.075,0.0268,6955,0.346,0.58,1.61,,4201,2860,6119, -Neolitsea dealbata,neodea,Atherton,0.093,0.0164,5228,0.352,0.58,176.1,1686,2747,3049,7504, -Polyscias australiana,polaus,Atherton,0.079,0.0154,6806,0.397,0.42,8.35,,6008,,6700, -Psychotria sp Utchee Creek,psyspp,Atherton,0.108,0.0179,11157,0.582,0,23.09,,4977,2302,2037, -Rhodomyrtus trineura,rhotri,Atherton,0.129,0.0111,3401,0.763,0.34,,4321,3803,6088,6877, -Acmena graveolens,acmgra,Cape Tribulation,0.151,0.0155,5246,0.599,0.67,,,3057,2667,7156, -Aleurites rockinghamensis,aleroc,Cape Tribulation,0.113,0.0184,73984,0.28,0.02,7077,,4194,,6209, -Alstonia scholaris,alssch,Cape Tribulation,0.107,0.0223,6182,0.361,0.46,1.53,,1854,1682,3932, -Argyrodendron peralatum,argper,Cape Tribulation,0.244,0.0119,3201,0.726,0.71,433,,3832,1689,6718, -Atractocarpus hirtus,atrhir,Cape Tribulation,0.072,0.0157,11374,0.804,0.28,,,7143,6727,6103, -Brombya platynema,bropla,Cape Tribulation,0.106,0.0188,8218,0.603,0.33,,,4261,3531,5377, -Cardwellia sublimis,carsub,Cape Tribulation,0.127,0.0128,4352,0.603,0.56,582.3,,6315,4880,8282, -Castanospermum australe,casaus,Cape Tribulation,0.117,0.0237,2765,0.587,0.37,14851,,7329,,8869, -Cleistanthus myrianthus,clemyr,Cape Tribulation,0.078,0.0228,4828,0.588,0.56,,3720,6084,5233,8559, -Cryptocarya laevigata,crylae,Cape Tribulation,0.087,0.0156,2682,0.64,0.65,1281,1391,3297,4680,7588, -Cryptocarya mackinnoniana,crymac,Cape Tribulation,0.204,0.0152,10458,0.655,0.61,204,,3277,2325,8657, -Cryptocarya murrayi,crymur,Cape Tribulation,0.155,0.0167,9960,0.674,0.39,,2693,5543,4298,5451, -Dendrocnide moroides,denmor,Cape Tribulation,0.052,0.0312,26454,0.23,0.46,0.71,,2372,,2090, -Elaeocarpus grandis,elaang,Cape Tribulation,0.122,0.0187,2762,0.499,0.47,3699,,2598,1748,4635, -Endiandra leptodendron,endlep,Cape Tribulation,0.106,0.018,3987,0.611,0.68,,1492,2412,2783,7477, -Endiandra microneura,endmic,Cape Tribulation,0.151,0.0177,3377,0.623,0.61,,3573,6344,3354,6235, -Gillbeea adenopetala,gilade,Cape Tribulation,0.126,0.0096,3678,0.43,0.46,15,,2863,3160,6549, -Haplostichanthus sp Coop. Ck,hapspp,Cape Tribulation,0.072,0.022,4685,0.668,0.36,,2430,12304,3282,2992, -Harpullia rhyticarpa,harrhy,Cape Tribulation,0.076,0.0174,40876,0.621,0.01,,,8971,5922,4669, -Hernandia albiflora,heralb,Cape Tribulation,0.069,0.0195,3806,0.447,0.33,,3123,4145,4643,6086, -Ixora biflora,ixobif,Cape Tribulation,0.081,0.01,2760,0.843,0.55,41.5,5244,3892,1969,8094, -Lasianthus strigosus,lasstr,Cape Tribulation,0.055,0.0158,3313,0.684,0.15,7,1841,5100,2379,2731, -Litsea leefeana,litlee,Cape Tribulation,0.13,0.0144,3917,0.549,0.68,263.4,3984,4141,3816,9645, -Macaranga tanarius,mactan,Cape Tribulation,0.104,0.0205,46676,0.344,0,,,3377,,3901, -Mallotus mollissimus,malmol,Cape Tribulation,0.063,0.0352,16716,0.373,0.32,31.25,1788,5580,5163,7944, -Medicosma sessiliflora,medses,Cape Tribulation,0.106,0.0153,8164,0.69,0.65,,2844,9332,6514,10298, -Melastoma cyanoides,melaff,Cape Tribulation,0.046,0.0208,4009,0.381,0.6,0.07,2960,4057,4661,6637, -Myristica insipida,myrins,Cape Tribulation,0.106,0.0185,8379,0.433,0.51,1612,,6929,4852,9273, -Pittosporum rubiginosum,pitrub,Cape Tribulation,0.065,0.0143,9931,0.728,0.28,27.94,7428,7459,5265,6548, -Psychotria dallachiana,psydal,Cape Tribulation,0.079,0.0177,2495,0.612,0.33,,4290,5666,4916,4761, -Quassia baileyana,quabai,Cape Tribulation,0.086,0.023,9624,0.501,0.42,,,5867,3216,5719, -Rockinghamia angustifolia,rocang,Cape Tribulation,0.108,0.0158,10636,0.455,0.39,19.38,,5862,4611,6098, -Syzygium gustavioides,syzgus,Cape Tribulation,0.167,0.0129,3590,0.521,0.59,48000,2833,3121,3047,6584, -Syzygium sayeri,syzsay,Cape Tribulation,0.131,0.0137,2645,0.485,0.65,841,3929,5767,4939,9836, -Trema aspera,treasp,Cape Tribulation,0.053,0.0299,2071,0.357,0.53,5.12,3578,5291,5440,6695,wild diff --git a/tests/testthat/examples/test3-metadata.yml b/tests/testthat/examples/test3-metadata.yml deleted file mode 100644 index d6f4dde8..00000000 --- a/tests/testthat/examples/test3-metadata.yml +++ /dev/null @@ -1,318 +0,0 @@ -source: - primary: - key: Falster_2005_1 - bibtype: Article - author: Daniel S. Falster, Mark Westoby - year: 2005 - title: Alternative height strategies among 45 dicot rain forest species from tropical - Queensland, Australia - journal: Journal of Ecology - volume: 93 - pages: 521--535 - publisher: Wiley-Blackwell - doi: 10.1111/j.0022-0477.2005.00992.x -contributors: - data_collectors: - - last_name: Falster - given_name: Daniel - ORCID: 0000-0002-9814-092X - affiliation: Evolution & Ecology Research Centre, School of Biological, Earth, - and Environmental Sciences, UNSW Sydney, Australia - additional_role: contact - - last_name: Westoby - given_name: Mark - ORCID: 0000-0001-7690-4530 - affiliation: Department of Biological Sciences, Macquarie University, Australia - dataset_curators: Elizabeth Wenk -dataset: - data_is_long_format: no - custom_R_code: .na - collection_date: 2004/2004 - taxon_name: Species - location_name: site - description: Investigation into trait values correlated with plant height along - light availability and successional gradients for far north Queensland species. - basis_of_record: basis_of_record - life_stage: life_stage - sampling_strategy: Nineteen species, ranging from early to late successional status, - were selected using published sources (Hopkins & Graham 1987; Osunkoya 1996; Hyland - et al. 1999). Species selected to represent the light gradient establish and mature - in closed forest, where successional species are assumed absent. For inclusion - in this set we required that a species was known to establish and persist at low - light levels, as indicated either by published sources (Hyland et al. 1999; Osunkoya - 1996) or by scientists familiar with the vegetation (A Graham, J Wells, CSIRO - Atherton; R Jensen). Twenty-six species, experiencing a range of light levels - at maturity, from high (canopy trees) to low light (understorey shrubs), were - included. - original_file: Falster & Westoby 2005 J Ecol appendix.doc - notes: none -locations: - Atherton: - description: Tropical rain forest vegetation. - elevation (m): 800 - latitude (deg): -17.1166667 - longitude (deg): 145.65 - rainfall (mm): 2000 - Cape Tribulation: - description: Complex mesophyll vine forest in tropical rain forest. - elevation (m): 25 - latitude (deg): -16.1 - longitude (deg): 145.45 - rainfall (mm): 3500 - basis_of_record: Cape_Tribulation -contexts: .na -traits: -- var_in: LMA (mg mm-2) - unit_in: mg/mm2 - trait_name: leaf_mass_per_area - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: LMA was calculated as the leaf dry mass (oven-dried for 48 hours at 65 - deg C) divided by leaf size. It was measured on the first five fully expanded - leaves at the tip of each individual. -- var_in: Leaf nitrogen (mg mg-1) - unit_in: mg/mg - trait_name: leaf_N_per_dry_mass - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - basis_of_record: lab - methods: Leaves from all individuals per species were pooled and finely ground for - nitrogen analysis. Total nitrogen concentration (%) was measured using complete - combustion gas chromatography by Waite Analytical Services, Adelaide. The first - five fully expanded leaves at the tip of each individual were used for the analysis. -- var_in: leaf size (mm2) - unit_in: mm2 - trait_name: leaf_area - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: Leaf size was calculated as the one-sided leaf area (flat bed scanner). - It was measured on the first five fully expanded leaves at the tip of each individual. -- var_in: wood density (mg mm-3) - unit_in: mg/mm3 - trait_name: wood_density - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: Wood density was calculated using 40-60 mm stem segments taken 250 mm and - 1000 mm back along a branch from the branch tip. Fresh samples were refrigerated - before processing. After removing bark material, the volume of each wood sample - was determined using Archimedes' principle (Hacke et al. 2000). Samples were submerged - in a water-filled container on a balance. The weight change (mg) recorded during - submersion corresponds to the mass of water displaced, which can be converted - to a volume using the formula, displacement weight (mg)/0.998 (mg/mm3), where - 0.998 mg/mm3 is the density of water at 20 deg C. Samples were then dried for - 4 days at 60 deg C before weighing. -- var_in: branch mass fraction - unit_in: mg/mg - trait_name: branch_mass_fraction - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: Branch mass fraction was calculated as the mass side branches/total mass, - on a carbon dry mass basis. The zero values are correct - these are plants with - no branches. -- var_in: Seed mass (mg) - unit_in: mg - trait_name: seed_dry_mass - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: unknown - methods: Mean oven-dried seed mass (including seed coat but excluding seed accessories) - was estimated for all species with available field material. In total, collections - for 17 of 47 species were made. Data for an additional 12 species were drawn from - published (Osunkoya et al. 1994; Grubb et al. 1998) and unpublished (P. Juniper, - CSIRO Atherton) sources. -- var_in: LASA10 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a shoot whose sapwood had a cross sectional - area of 10 mm2. In detail from Wright_2006, which used this data, No single best - point exists to compare traits such as LM/ SM, LA/SM and LA/SA when considering - a set of species that varies widely in canopy architecture and typical maximum - height (here, approximately 20 cm to 85 m). We have used several approaches (Table - 1). In one study, we made measurements on the terminal twigs of each species, - i.e. on a relatively standard developmental unit (Westoby and Wright 2003). For - species at Ash, GLP, Myall and TRF, traits were measured at each of several different - distances back down the stem from the branch tip (Falster and Westoby 2005a, 2005b - and unpublished, Pickup et al. 2005). At GHP, RHM and RHW, traits were measured - at a standard sapwood cross-sectional area (10 mm2; Pickup et al. 2005). For the - present re-analysis, we took the raw data from the previous studies and, for every - species possible, calculated patterns of leaf and stem deployment at two standard - points: at 250 mm distance from the branch tip (Ash, GLP, Myall and TRF) and at - 10 mm2 stem (Ash, Myall, TRF) or sapwood (GHP, GLP, RHM, RHW) crosssectional area - (250 mm or 10 mm2 formulation denoted as subscript in trait abbreviations). This - was done as follows. For each individual plant, total leaf and stem dry mass at - 250 mm distance was estimated by straightline interpolation from values measured - at the nearest sampling points on either side of this distance. As the dry mass - data tended to display non-linear (power) relationships with distance from the - branch tip, the interpolated values were calculated from log10-log10- transformed - data, then back-transformed to the original scale. The same approach was used - for interpolating data to the standard stem (or sapwood) cross-sectional area. - For individuals where measurements had not been made on either side of the desired - point but the nearest measurement had been made within 25 mm of 250 mm or 1 mm2 - of 10 mm2 cross-section (i.e. within 10% of the desired point), we extrapolated - (rather than interpolated) the measured data to the standard point. This allowed - us to include a number of individuals and species for which interpolation was - not possible. Still, several large-leaved, large-stemmed species from the TRF - site could not be included in the 10-mm2 crosssection dataset. No unusual tendencies - in analyses, including the extrapolated data, were seen in comparison to analyses - including interpolated data only (details not shown). To illustrate how species'' - morphology varied at the two standard sampling points, species-mean stem cross-sectional - area varied between 1.2 and 258 mm2 at 250 mm distance from the branch tip, while - the distance from the branch tip at which stem cross-sectional area reached 10 - mm2 varied from 64 to 995 mm.' -- var_in: LASA250 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a 250 mm branch segment and sapwood cross-sectional - area was determined where the branch was cut. In detail from Wright_2006, which - used this data, No single best point exists to compare traits such as LM/ SM, - LA/SM and LA/SA when considering a set of species that varies widely in canopy - architecture and typical maximum height (here, approximately 20 cm to 85 m). We - have used several approaches (Table 1). In one study, we made measurements on - the terminal twigs of each species, i.e. on a relatively standard developmental - unit (Westoby and Wright 2003). For species at Ash, GLP, Myall and TRF, traits - were measured at each of several different distances back down the stem from the - branch tip (Falster and Westoby 2005a, 2005b and unpublished, Pickup et al. 2005). - At GHP, RHM and RHW, traits were measured at a standard sapwood cross-sectional - area (10 mm2; Pickup et al. 2005). For the present re-analysis, we took the raw - data from the previous studies and, for every species possible, calculated patterns - of leaf and stem deployment at two standard points: at 250 mm distance from the - branch tip (Ash, GLP, Myall and TRF) and at 10 mm2 stem (Ash, Myall, TRF) or sapwood - (GHP, GLP, RHM, RHW) crosssectional area (250 mm or 10 mm2 formulation denoted - as subscript in trait abbreviations). This was done as follows. For each individual - plant, total leaf and stem dry mass at 250 mm distance was estimated by straightline - interpolation from values measured at the nearest sampling points on either side - of this distance. As the dry mass data tended to display non-linear (power) relationships - with distance from the branch tip, the interpolated values were calculated from - log10-log10- transformed data, then back-transformed to the original scale. The - same approach was used for interpolating data to the standard stem (or sapwood) - cross-sectional area. For individuals where measurements had not been made on - either side of the desired point but the nearest measurement had been made within - 25 mm of 250 mm or 1 mm2 of 10 mm2 cross-section (i.e. within 10% of the desired - point), we extrapolated (rather than interpolated) the measured data to the standard - point. This allowed us to include a number of individuals and species for which - interpolation was not possible. Still, several large-leaved, large-stemmed species - from the TRF site could not be included in the 10-mm2 crosssection dataset. No - unusual tendencies in analyses, including the extrapolated data, were seen in - comparison to analyses including interpolated data only (details not shown). To - illustrate how species'' morphology varied at the two standard sampling points, - species-mean stem cross-sectional area varied between 1.2 and 258 mm2 at 250 mm - distance from the branch tip, while the distance from the branch tip at which - stem cross-sectional area reached 10 mm2 varied from 64 to 995 mm.' -- var_in: LASA50 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a 50 mm branch segment and sapwood cross-sectional - area was determined where the branch was cut. In detail from Wright_2006, which - used this data, No single best point exists to compare traits such as LM/ SM, - LA/SM and LA/SA when considering a set of species that varies widely in canopy - architecture and typical maximum height (here, approximately 20 cm to 85 m). We - have used several approaches (Table 1). In one study, we made measurements on - the terminal twigs of each species, i.e. on a relatively standard developmental - unit (Westoby and Wright 2003). For species at Ash, GLP, Myall and TRF, traits - were measured at each of several different distances back down the stem from the - branch tip (Falster and Westoby 2005a, 2005b and unpublished, Pickup et al. 2005). - At GHP, RHM and RHW, traits were measured at a standard sapwood cross-sectional - area (10 mm2; Pickup et al. 2005). For the present re-analysis, we took the raw - data from the previous studies and, for every species possible, calculated patterns - of leaf and stem deployment at two standard points: at 250 mm distance from the - branch tip (Ash, GLP, Myall and TRF) and at 10 mm2 stem (Ash, Myall, TRF) or sapwood - (GHP, GLP, RHM, RHW) crosssectional area (250 mm or 10 mm2 formulation denoted - as subscript in trait abbreviations). This was done as follows. For each individual - plant, total leaf and stem dry mass at 250 mm distance was estimated by straightline - interpolation from values measured at the nearest sampling points on either side - of this distance. As the dry mass data tended to display non-linear (power) relationships - with distance from the branch tip, the interpolated values were calculated from - log10-log10- transformed data, then back-transformed to the original scale. The - same approach was used for interpolating data to the standard stem (or sapwood) - cross-sectional area. For individuals where measurements had not been made on - either side of the desired point but the nearest measurement had been made within - 25 mm of 250 mm or 1 mm2 of 10 mm2 cross-section (i.e. within 10% of the desired - point), we extrapolated (rather than interpolated) the measured data to the standard - point. This allowed us to include a number of individuals and species for which - interpolation was not possible. Still, several large-leaved, large-stemmed species - from the TRF site could not be included in the 10-mm2 crosssection dataset. No - unusual tendencies in analyses, including the extrapolated data, were seen in - comparison to analyses including interpolated data only (details not shown). To - illustrate how species'' morphology varied at the two standard sampling points, - species-mean stem cross-sectional area varied between 1.2 and 258 mm2 at 250 mm - distance from the branch tip, while the distance from the branch tip at which - stem cross-sectional area reached 10 mm2 varied from 64 to 995 mm.' -- var_in: LASA1000 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a 1000 mm branch segment and sapwood cross-sectional - area was determined where the branch was cut. In detail from Wright_2006, which - used this data, No single best point exists to compare traits such as LM/ SM, - LA/SM and LA/SA when considering a set of species that varies widely in canopy - architecture and typical maximum height (here, approximately 20 cm to 85 m). We - have used several approaches (Table 1). In one study, we made measurements on - the terminal twigs of each species, i.e. on a relatively standard developmental - unit (Westoby and Wright 2003). For species at Ash, GLP, Myall and TRF, traits - were measured at each of several different distances back down the stem from the - branch tip (Falster and Westoby 2005a, 2005b and unpublished, Pickup et al. 2005). - At GHP, RHM and RHW, traits were measured at a standard sapwood cross-sectional - area (10 mm2; Pickup et al. 2005). For the present re-analysis, we took the raw - data from the previous studies and, for every species possible, calculated patterns - of leaf and stem deployment at two standard points: at 250 mm distance from the - branch tip (Ash, GLP, Myall and TRF) and at 10 mm2 stem (Ash, Myall, TRF) or sapwood - (GHP, GLP, RHM, RHW) crosssectional area (250 mm or 10 mm2 formulation denoted - as subscript in trait abbreviations). This was done as follows. For each individual - plant, total leaf and stem dry mass at 250 mm distance was estimated by straightline - interpolation from values measured at the nearest sampling points on either side - of this distance. As the dry mass data tended to display non-linear (power) relationships - with distance from the branch tip, the interpolated values were calculated from - log10-log10- transformed data, then back-transformed to the original scale. The - same approach was used for interpolating data to the standard stem (or sapwood) - cross-sectional area. For individuals where measurements had not been made on - either side of the desired point but the nearest measurement had been made within - 25 mm of 250 mm or 1 mm2 of 10 mm2 cross-section (i.e. within 10% of the desired - point), we extrapolated (rather than interpolated) the measured data to the standard - point. This allowed us to include a number of individuals and species for which - interpolation was not possible. Still, several large-leaved, large-stemmed species - from the TRF site could not be included in the 10-mm2 crosssection dataset. No - unusual tendencies in analyses, including the extrapolated data, were seen in - comparison to analyses including interpolated data only (details not shown). To - illustrate how species'' morphology varied at the two standard sampling points, - species-mean stem cross-sectional area varied between 1.2 and 258 mm2 at 250 mm - distance from the branch tip, while the distance from the branch tip at which - stem cross-sectional area reached 10 mm2 varied from 64 to 995 mm.' -substitutions: .na -taxonomic_updates: -- find: Homalanthus novoguineensis - replace: Homalanthus novo-guineensis - reason: Change spelling to align with known name in APC (Daniel Falster, 2020.05.22) -- find: Haplostichanthus sp Coop. Ck - replace: Haplostichanthus submontanus - reason: Align previous phrase name with current APC name (E. Wenk, 2020-05-25) -- find: Psychotria sp Utchee Creek - replace: Psychotria sp. Utchee Creek (H.Flecker NQNC5313) - reason: Align to name in APC (D Falster, 2020.05.23) -exclude_observations: .na -questions: .na diff --git a/tests/testthat/examples/test4-data.csv b/tests/testthat/examples/test4-data.csv deleted file mode 100644 index 010dd375..00000000 --- a/tests/testthat/examples/test4-data.csv +++ /dev/null @@ -1,34 +0,0 @@ -PlotSite,Temp-trt,Chamber,Date,Curator,Species,treatment_context,month,Vcmax,Tleaf,Rd,lfN,N/area,A390,A630,LMA,Agrow,g_grow,Jmax,Jmax25,Vcmax25,Rd25,context,site_name,sex,fruit_colour -1,elevated,11,Dec 3 2010,K. Crous,Eucalyptus globulus,0C,DEC,112.03,27.46,-2.69,30.38999939,1.43,21.39999962,27.70000076,47.02,21.39999962,0.875999987,183.33,168.65,94.48,-2.27,elevated_temp_and_ambient_CO2_treatment_and_measured_in_DEC,Hawkesbury Forest Experiment site plot 1,male,red -6,ambient,7,Dec 3 2010,K. Crous,Eucalyptus globulus,0C,DEC,108.16,25.53,-1.74,33.5,1.71,19.20000076,29.70000076,50.94,19.20000076,0.31099999,169.43,162.8,104.21,-1.67,ambient_temp_and_ambient_CO2_treatment_and_measured_in_DEC,Hawkesbury Forest Experiment site plot 6,female,pink -12,ambient,5,Dec 10 2010,K. Crous,Eucalyptus globulus,0C,DEC,97.45,24.65,-1.01,34.81999969,1.84,22.89999962,29.39999962,52.86,22.89999962,0.49000001,168.79,170.02,99.89,-1.04,ambient_temp_and_ambient_CO2_treatment_and_measured_in_DEC,Hawkesbury Forest Experiment site plot 12,male,bl -16,elevated,1,Dec 9 2010,K. Crous,Eucalyptus globulus,0C,DEC,71.19,25.22,-1.06,31.86000061,1.17,16.5,21.89999962,36.83,16.5,0.370000005,114.32,115.16,70.12,-1.04,elevated_temp_and_ambient_CO2_treatment_and_measured_in_DEC,Hawkesbury Forest Experiment site plot 16,female,red -23,elevated,3,Dec 8 2010,K. Crous,Eucalyptus globulus,0C,DEC,70.67,24.95,-1.27,30.68000031,1.16,16.60000038,22.60000038,37.75,16.60000038,0.298000008,134.07,135.05,70.91,-1.28,elevated_temp_and_ambient_CO2_treatment_and_measured_in_DEC,Hawkesbury Forest Experiment site plot 23,male,pink -29,ambient,9,Dec 8 2010,K. Crous,Eucalyptus globulus,0C,DEC,97.19,25.15,-1.46,31.35000038,1.53,20.29999924,27.60000038,48.7,20.29999924,0.319000006,161.72,162.9,96.17,-1.44,ambient_temp_and_ambient_CO2_treatment_and_measured_in_DEC,Hawkesbury Forest Experiment site plot 29,female,bl -34,ambient,10,Dec 6 2010,K. Crous,Eucalyptus globulus,+C,DEC,81.19,25.12,-1.25,27.97999954,1.49,18.20000076,24.39999962,53.4,24.39999962,0.270000011,140.52,141.55,80.52,-1.24,ambient_temp_and_enriched_CO2_treatment_and_measured_in_DEC,Hawkesbury Forest Experiment site plot 34,male,red -38,ambient,2,Dec 2 2010,K. Crous,Eucalyptus globulus,+C,DEC,136.14,25.44,-3.67,28.54999924,1.8,26.5,35.20000076,63,35.20000076,0.970000029,226.35,228.01,131.98,-3.55,ambient_temp_and_enriched_CO2_treatment_and_measured_in_DEC,Hawkesbury Forest Experiment site plot 38,female,pink -42,ambient,12,Dec 7 2010,K. Crous,Eucalyptus globulus,+C,DEC,92.46,24.99,-1.55,28.88999939,1.61,21.5,27.60000038,55.6,27.60000038,0.298999995,162.83,164.03,92.54,-1.55,ambient_temp_and_enriched_CO2_treatment_and_measured_in_DEC,Hawkesbury Forest Experiment site plot 42,male,bl -47,elevated,4,Dec 6 2010,K. Crous,Eucalyptus globulus,+C,DEC,62.49,25.04,-1.09,23.37000084,0.97,16,22.29999924,41.54,22.29999924,0.527999997,120.24,121.12,62.3,-1.09,elevated_temp_and_enriched_CO2_treatment_and_measured_in_DEC,Hawkesbury Forest Experiment site plot 47,female,red -51,elevated,8,Dec 9 2010,K. Crous,Eucalyptus globulus,+C,DEC,97.59,24.97,-1.6,27.88999939,1.41,21.79999924,28.79999924,50.48,28.79999924,0.652999997,158.29,159.45,97.83,-1.61,elevated_temp_and_enriched_CO2_treatment_and_measured_in_DEC,Hawkesbury Forest Experiment site plot 51,male,pink -57,elevated,6,Dec 7 2010,K. Crous,Eucalyptus globulus,+C,DEC,58.53,25.14,-1.28,19.95000076,1.14,14.10000038,18.79999924,57.24,18.79999924,0.317999989,106.45,107.23,57.95,-1.27,elevated_temp_and_enriched_CO2_treatment_and_measured_in_DEC,Hawkesbury Forest Experiment site plot 57,female,bl -62,ambient,5,Feb 10 2011,K. Crous,Eucalyptus globulus,0C,FEB,84.42,25.11,-0.74,34.13999939,1.93,19.70000076,NA,56.67,19.70000076,0.500999987,116.47,117.32,83.79,-0.74,ambient_temp_and_ambient_CO2_treatment_and_measured_in_FEB,Hawkesbury Forest Experiment site plot 62,male,red -67,ambient,9,Feb 9 2011,K. Crous,Eucalyptus globulus,0C,FEB,88.13,25.14,-0.67,29.42000008,1.98,21.10000038,25.20000076,67.14,21.10000038,0.56400001,136.25,137.24,87.24,-0.67,ambient_temp_and_ambient_CO2_treatment_and_measured_in_FEB,Hawkesbury Forest Experiment site plot 67,female,pink -71,ambient,7,Feb 14 2011,K. Crous,Eucalyptus globulus,0C,FEB,70.34,25.03,-1.07,19.27000046,1.38,18,23.39999962,71.56,18,0.61500001,133.55,134.53,70.19,-1.07,ambient_temp_and_ambient_CO2_treatment_and_measured_in_FEB,Hawkesbury Forest Experiment site plot 71,male,bl -75,elevated,3,Feb 9 2011,K. Crous,Eucalyptus globulus,0C,FEB,64.55,25.15,-0.37,26.23999977,1.44,13.80000019,16.39999962,54.76,13.80000019,0.246999994,87.6,88.24,63.89,-0.36,elevated_temp_and_ambient_CO2_treatment_and_measured_in_FEB,Hawkesbury Forest Experiment site plot 75,female,red -80,elevated,1,Feb 12 2011,K. Crous,Eucalyptus globulus,0C,FEB,84.79,25.09,-1,27.14999962,1.47,19.89999962,24,54.08,19.89999962,0.469999999,129.42,130.37,84.26,-0.99,elevated_temp_and_ambient_CO2_treatment_and_measured_in_FEB,Hawkesbury Forest Experiment site plot 80,male,pink -87,ambient,2,Feb 15 2011,K. Crous,Eucalyptus globulus,+C,FEB,119.08,25.1,-1,33.99000168,2.38,30.00601959,39.74504089,70.15,39.74504089,1.057057858,235.65,237.38,118.26,-1,ambient_temp_and_enriched_CO2_treatment_and_measured_in_FEB,Hawkesbury Forest Experiment site plot 87,female,bl -91,ambient,10,Feb 11 2011,K. Crous,Eucalyptus globulus,+C,FEB,61.38,24.27,-1.5,19.46999931,2.06,11.79452896,18.0937233,105.77,18.0937233,0.135541379,125.19,132.61,64.59,-1.58,ambient_temp_and_enriched_CO2_treatment_and_measured_in_FEB,Hawkesbury Forest Experiment site plot 91,male,red -96,ambient,12,Feb 9 2011,K. Crous,Eucalyptus globulus,+C,FEB,93.17,24.87,-1.27,27.67000008,2.18,23,29.29999924,78.96,29.29999924,0.492000014,169.3,170.54,94.01,-1.28,ambient_temp_and_enriched_CO2_treatment_and_measured_in_FEB,Hawkesbury Forest Experiment site plot 96,female,pink -101,elevated,4,Feb 12 2011,K. Crous,Eucalyptus globulus,+C,FEB,74.68,25.02,-1.76,27.13999939,1.67,16.59725189,21.67111206,61.54,21.67111206,0.412641644,124.37,125.29,74.59,-1.76,elevated_temp_and_enriched_CO2_treatment_and_measured_in_FEB,Hawkesbury Forest Experiment site plot 101,male,bl -107,elevated,6,Feb 10 2011,K. Crous,Eucalyptus globulus,+C,FEB,94.92,24.96,-1.47,27.5,2.14,23.46526337,31.88568306,77.69,31.88568306,0.834146917,188.92,190.3,95.15,-1.47,elevated_temp_and_enriched_CO2_treatment_and_measured_in_FEB,Hawkesbury Forest Experiment site plot 107,female,red -115,elevated,11,Aug 26 2011,K. Crous,Eucalyptus globulus,0C,AUG,96.92,25.17,-1.86,24.19000053,2.08,20.20000076,29.10000038,86.08,20.20000076,0.300999999,202.48,203.97,95.8,-1.84,elevated_temp_and_ambient_CO2_treatment_and_measured_in_AUG,Hawkesbury Forest Experiment site plot 115,male,pink -120,elevated,3,Aug 29 2011,K. Crous,Eucalyptus globulus,0C,AUG,120.85,25,-2.4,33.52000046,3.42,21.89999962,30.29999924,101.91,21.89999962,0.270999998,212.14,213.7,120.82,-2.4,elevated_temp_and_ambient_CO2_treatment_and_measured_in_AUG,Hawkesbury Forest Experiment site plot 120,female,bl -125,ambient,7,Sep 2 2011,K. Crous,Eucalyptus globulus,0C,AUG,83.17,25.69,1.47,16.90999985,2.23,17.20000076,25.70000076,131.91,17.20000076,0.256999999,140.98,135.46,79.29,1.4,ambient_temp_and_ambient_CO2_treatment_and_measured_in_AUG,Hawkesbury Forest Experiment site plot 125,male,red -128,ambient,7,Sep 2 2011,K. Crous,Eucalyptus globulus,0C,AUG,78.21,24.93,-1.31,16.90999985,2.23,16.10000038,NA,131.91,16.10000038,0.672999978,141.86,142.9,78.62,-1.32,ambient_temp_and_ambient_CO2_treatment_and_measured_in_AUG,Hawkesbury Forest Experiment site plot 128,female,pink -130,ambient,5,Sep 5 2011,K. Crous,Eucalyptus globulus,0C,AUG,76.34,25.01,-1.3,21.13999939,2.6,17.79999924,21.5,123.21,17.79999924,0.38499999,144.64,145.7,76.29,-1.3,ambient_temp_and_ambient_CO2_treatment_and_measured_in_AUG,Hawkesbury Forest Experiment site plot 130,male,bl -134,ambient,9,Sep 5 2011,K. Crous,Eucalyptus globulus,0C,AUG,87.37,24.92,-2.34,14.38000011,1.82,14.39999962,21.20000076,126.51,14.39999962,0.123000003,143.32,144.37,87.86,-2.35,ambient_temp_and_ambient_CO2_treatment_and_measured_in_AUG,Hawkesbury Forest Experiment site plot 134,female,red -138,elevated,1,Sep 1 2011,K. Crous,Eucalyptus globulus,0C,AUG,104.74,24.97,-1.99,21.96999931,2.17,18.70000076,26,98.92,18.70000076,0.275999993,170.7,171.95,104.97,-2,elevated_temp_and_ambient_CO2_treatment_and_measured_in_AUG,Hawkesbury Forest Experiment site plot 138,male,pink -143,ambient,12,Sep 8 2011,K. Crous,Eucalyptus globulus,+C,AUG,66.33,25.01,-1.33,10.32999992,1.6,15.10000038,21.89999962,154.83,21.89999962,0.286000013,137.38,138.38,66.27,-1.33,ambient_temp_and_enriched_CO2_treatment_and_measured_in_AUG,Hawkesbury Forest Experiment site plot 143,female,bl -148,ambient,2,Sep 8 2011,K. Crous,Eucalyptus globulus,+C,AUG,88.76,24.99,-2.83,17.37000084,2.98,11.3,19.39999962,171.31,19.39999962,NA,169.71,170.95,88.84,-2.83,ambient_temp_and_enriched_CO2_treatment_and_measured_in_AUG,Hawkesbury Forest Experiment site plot 148,male,red -153,elevated,6,Sep 2 2011,K. Crous,Eucalyptus globulus,+C,AUG,98.92,25.61,-1.73,33.81000137,3.25,17.70000076,24.60000038,96.07,24.60000038,0.171000004,143.93,138.29,94.81,-1.66,elevated_temp_and_enriched_CO2_treatment_and_measured_in_AUG,Hawkesbury Forest Experiment site plot 153,female,pink -157,elevated,4,Sep 1 2011,K. Crous,Eucalyptus globulus,+C,AUG,31.44,25.18,-0.01,13.51000023,1.49,7.980000019,12,110.19,12,0.128000006,73.16,73.69,31.06,-0.01,elevated_temp_and_enriched_CO2_treatment_and_measured_in_AUG,Hawkesbury Forest Experiment site plot 157,male,bl diff --git a/tests/testthat/examples/test4-metadata.yml b/tests/testthat/examples/test4-metadata.yml deleted file mode 100644 index 146ae917..00000000 --- a/tests/testthat/examples/test4-metadata.yml +++ /dev/null @@ -1,195 +0,0 @@ -source: - primary: - key: Crous_2013 - bibtype: Article - year: '2013' - author: Kristine Y. Crous and Audrey G. Quentin and Yan-Shih Lin and Belinda E. - Medlyn and David G. Williams and Craig V. M. Barton and David S. Ellsworth - journal: Global Change Biology - title: Photosynthesis of temperate Eucalyptus globulus trees outside their native - range has limited adjustment to elevated CO2 and climate warming - volume: '19' - number: '12' - pages: 3790--3807 - doi: 10.1111/gcb.12314 -contributors: - data_collectors: - - last_name: Crous - given_name: Kristine - ORCID: 0000-0001-9478-7593 - affiliation: Hawkesbury Institute for the Environment, Western Sydney University, - Australia - additional_role: contact - dataset_curators: Elizabeth Wenk -dataset: - data_is_long_format: no - custom_R_code: ' - data %>% - mutate( - location_name = "Hawkesbury Forest Experiment site", - Date = Date %>% mdy(), - CO2_Treat = stringr::str_replace(treatment_context,"\\+C","added CO2"), - CO2_Treat = stringr::str_replace(CO2_Treat,"0C","ambient CO2") - ) - ' - collection_date: Date - taxon_name: Species - individual_id: Chamber - location_name: location_name - description: An experiment to investigate where Eucalyptus globulus, a widely planted - plantation species, would show high potential for acclimation of photosynthetic - traits across a wide range of growth conditions, including elevated [CO2] and - climate warming. - basis_of_record: lab - life_stage: sapling - sampling_strategy: Plant material Eucalyptus globulus ssp. globulus planting material - was obtained from a commercial tree nursery in Victoria as firstseason tube stock - seedlings. - original_file: Globulus_Austraits.xls - notes: A number of observations for 'leaf_light_respiration_per_area' are showing - up as duplicates, because the values adjusted to 25C and the raw values are sometimes - identical; both formulations are read into AusTraits, but the data are in separate - columns. -locations: - Hawkesbury Forest Experiment site: - latitude (deg): -33.6108111 - longitude (deg): 150.7410417 - description: tall closed tree chambers -contexts: -- context_property: sampling season - category: temporal_context - var_in: month - values: - - find: AUG - value: August - description: August (late winter) - - find: DEC - value: December - description: December (early summer) - - find: FEB - value: February - description: February (late summer) -- context_property: temperature treatment - category: treatment_context - var_in: Temp-trt - values: - - find: ambient - value: ambient - description: Plants grown at ambient temperatures; Jan average max = 29.4 dec - C / July average min = 3.2 dec C. - - find: elevated - value: elevated - description: Plants grown 3 deg C above ambient temperatures. -- context_property: CO2 treatment - category: treatment_context - var_in: CO2_Treat - values: - - find: ambient CO2 - value: 400 ppm - description: Plants grown at ambient CO2 (400 ppm). - - find: added CO2 - value: 640 ppm - description: Plants grown at elevated CO2 (640 ppm); 240 ppm above ambient. -- context_property: measurement temperature - category: method_context - var_in: method_context - values: - - find: Measurement made at 20°C - value: 20°C - description: Measurement made at 20°C - - find: Measurement made at 25°C - value: 25°C - description: Measurement made at 25°C -traits: -- var_in: fruit_colour - unit_in: .na - trait_name: fruit_colour - entity_type: species - value_type: mode - basis_of_value: expert_score - replicates: .na - methods: a dummy variable for tests -- var_in: Vcmax - unit_in: umol/m2/s - trait_name: leaf_photosynthesis_Vcmax_per_area - entity_type: individual - value_type: maximum - basis_of_value: measurement - replicates: 1 - method_context: Measurement made at 20°C - methods: &fluorescence Controlled photosynthetic CO2 response curve measurements were made using - Li-Cor 6400 portable infrared gas analysers (LiCor Inc., Lincoln, NE, USA). CO2 - response curves of net CO2 assimilation (Anet) were developed at a constant temperature - (termed 'Anet-Ci curves') for intact leaves within each tree chamber. These Anet-Ci - curve measurements progressed at four to five specified leaf temperatures for - the same leaf (i.e. one leaf per chamber) in each of three seasons (early summer, - December 2010; late summer, February 2011; and late winter, August 2011). Each - Anet-Ci response curve started with a steady-state measurement at the growth [CO2] - (henceforth called 'Anet at the growth [CO2]') and then consisted of 11 additional - steps all measured at a constant set leaf temperature while using light-saturating - photon flux density (PFD) of 1800 umol m-2 s-1. There were at least five [CO2] - levels used in the linear part of the curve, and at least three steps measured - in the saturating part of the curve. These Anet-Ci response curves were measured - on a leaf at the lowest set temperature (20 deg C) and then repeated fourmore - times on the same leaf, each time at an increased leaf temperature for each curve - following a progression of 25, 30, 35 and 41 deg C. From Anet-Ci response measurements - conducted at the set leaf temperatures, the photosynthetic parameters Jmax and - Vcmax from the biochemical model of Farquhar et al. (1980) can be extracted (e.g. - see (Bernacchi et al., 2002, 2001; Medlyn et al., 2002a). During the leaf-level - measurements, the entire tree was subjected to similar air temperatures in the - whole-tree chambers during the measurements. The entire tree was exposed to each - set temperature for at least 0.5 h before leaf gas exchange measurements started, - resulting in approximately 1.5 h duration set at each temperature level. At each - temperature, the curve was started with a measurement of Anet at the growth [CO2] - using the [CO2] appropriate for the long-term treatment for each chamber tree. - See manuscript for additional details on how humidity was controlled in the experimental - chambers to minimize stomatal closure. -- var_in: lfN - unit_in: mg/g - trait_name: leaf_N_per_dry_mass - entity_type: individual - value_type: raw - basis_of_value: measurement - replicates: 1 - methods: Leaves were collected after each Anet-Ci curve in December, February and - August, for determination of leaf area on a Li- Cor leaf area metre (Li-Cor model - 3100, Lincoln, NE, USA) and then oven-dried at 70 deg C. At final harvest in November, - a random sample of 100 leaves from each of three crown positions was also collected, - and area was measured on each of these leaves. For Anet-Ci leaves, leaf mass per - area ratio (LMA) was recorded before samples were ground to a homogenous powder - to analyse for total %N and %C on a microdigestion apparatus interfacing a CHN - elemental analyser (TruSpec; LECO Corp., St. Joseph, MI, USA).; Regarding the - high leaf N values, the author notes, given that E globulus was moved 700 km north - of its native distribution, it may have adapted via a change in Nmass as we have - seen in other studies (Sharwood et al. 2014, Crous et al. 2017 Tree Phys). -- var_in: LMA - unit_in: g/m2 - trait_name: leaf_mass_per_area - entity_type: individual - value_type: raw - basis_of_value: measurement - replicates: 1 - methods: Leaves were collected after each Anet-Ci curve in December, February and - August, for determination of leaf area on a Li- Cor leaf area metre (Li-Cor model - 3100, Lincoln, NE, USA) and then oven-dried at 70 deg C. At final harvest in November, - a random sample of 100 leaves from each of three crown positions was also collected, - and area was measured on each of these leaves. For Anet-Ci leaves, leaf mass per - area ratio (LMA) was recorded before samples were ground to a homogenous powder - to analyse for total %N and %C on a microdigestion apparatus interfacing a CHN - elemental analyser (TruSpec; LECO Corp., St. Joseph, MI, USA). -- var_in: Vcmax25 - unit_in: umol/m2/s - trait_name: leaf_photosynthesis_Vcmax_per_area - entity_type: individual - value_type: raw - basis_of_value: measurement - replicates: 1 - method_context: Measurement made at 25°C - methods: *fluorescence -substitutions: -- trait_name: fruit_colour - find: bl - replace: black -taxonomic_updates: .na -exclude_observations: .na -questions: .na From e3e2254727c335eb863fd6a6ea616fead4ee513e Mon Sep 17 00:00:00 2001 From: Sophie Yang <78716301+yangsophieee@users.noreply.github.com> Date: Fri, 20 Oct 2023 15:58:44 +1100 Subject: [PATCH 02/31] Fix unit conversions warning (#100) The unit conversions warning (#65) was showing up again for both @ehwenk and me. It seems to me that there is something going on with the `mutate` `ifelse` statement not being vectorised in the expected way. I don't fully understand why it isn't working as expected but @dfalster suggested a fix (add `value_type` to the `group_by` variables) which seems to produce the right output. (The problem dataset was vanderMoezel_1987.) --- R/process.R | 35 ++++++++++++++++++----------------- 1 file changed, 18 insertions(+), 17 deletions(-) diff --git a/R/process.R b/R/process.R index cc48594f..95e08e0e 100644 --- a/R/process.R +++ b/R/process.R @@ -1188,28 +1188,29 @@ process_convert_units <- function(data, definitions, unit_conversion_functions) } f_range_bin <- function(value, name) { - - stringr::str_split(value, "\\-\\-") %>% # split into parts - purrr::map(f_standard, name) %>% # apply unit conversions to each - purrr::map_chr(~paste(.x, collapse = "--")) # paste back together + stringr::str_split(value, "\\-\\-") %>% # Split into parts + purrr::map(f_standard, name) %>% # Apply unit conversions to each + purrr::map_chr(~paste(.x, collapse = "--")) # Paste back together } # Split by unique unit conversions, to allow for as few calls as possible data <- data %>% - dplyr::group_by(.data$ucn, .data$to_convert) %>% + dplyr::group_by(.data$ucn, .data$to_convert, .data$value_type) %>% dplyr::mutate( - # standard conversion - value = ifelse(.data$to_convert == TRUE & # value requires conversion - !.data$value_type %in% c("bin", "range") & # value_type not a bin or range; those are converted below - !is.na(.data$value), # value not NA - the full matrix from data.csv file is still in data table - f_standard(.data$value, .data$ucn[1]), # convert value to appropriate units - .data$value), # if conditions not met, keep original value - # value is a range of bin - value = ifelse(.data$to_convert == TRUE & # value requires conversion - .data$value_type %in% c("bin", "range") & # value_type is a bin or range - !is.na(.data$value), # value not NA - the full matrix from data.csv file is still in data table - f_range_bin(.data$value, .data$ucn[1]), # convert value to appropriate units - .data$value), # if conditions not met, keep original value + # Standard conversion + value = ifelse( + .data$to_convert == TRUE & # Value requires conversion + !.data$value_type %in% c("bin", "range") & # `value_type` not a bin or range; those are converted below + !is.na(.data$value), # Value not NA - the full matrix from data.csv file is still in data table + f_standard(.data$value, .data$ucn[1]), # Convert value to appropriate units + .data$value), # If conditions not met, keep original value + # Value is a range or bin + value = ifelse( + .data$to_convert == TRUE & # Value requires conversion + .data$value_type %in% c("bin", "range") & # `value_type` is a bin or range + !is.na(.data$value), # Value not NA - the full matrix from data.csv file is still in data table + f_range_bin(.data$value, .data$ucn[1]), # Convert value to appropriate units + .data$value), # If conditions not met, keep original value unit = ifelse(.data$to_convert, .data$to, .data$unit_in) ) %>% dplyr::ungroup() %>% From ad4f4075301c703cf96b532ea41f3193f1ffb0cc Mon Sep 17 00:00:00 2001 From: Sophie Yang <78716301+yangsophieee@users.noreply.github.com> Date: Fri, 20 Oct 2023 16:12:27 +1100 Subject: [PATCH 03/31] Add test to check context values in metadata contexts are in data file (#104) - Closes #63 --- R/testdata.R | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/R/testdata.R b/R/testdata.R index d21d5539..6ac8c7ae 100644 --- a/R/testdata.R +++ b/R/testdata.R @@ -602,10 +602,20 @@ dataset_test_worker <- all(i), info = ifelse( "hms" %in% class(v), - sprintf("%s - context names from data file not present in metadata contexts: %s\n\n'%s' has been detected as a time data type and reformatted\n\t-> Please make sure context metadata matches reformatting", f, v[!i], j), - sprintf("%s - context names from data file not present in metadata contexts: %s", f, v[!i]) + sprintf("%s - context values from data file not present in metadata contexts: %s\n\n'%s' has been detected as a time data type and reformatted\n\t-> Please make sure context metadata matches reformatting", f, v[!i], j), + sprintf("%s - context values from data file not present in metadata contexts: %s", f, v[!i]) ) ) + + i <- contextsub[["find"]] %in% v + + expect_true( + all(i), + info = sprintf( + "%s - context values in metadata contexts not detected in context values from data file: %s", + f, contextsub[["find"]][!i]) + ) + } } @@ -726,8 +736,7 @@ dataset_test_worker <- info = paste0(files[2], " - column ", metadata[["dataset"]][["location_name"]], "not found in data") ) - v <- - (data[[metadata[["dataset"]][["location_name"]]]] %>% unique %>% na.omit) + v <- data[[metadata[["dataset"]][["location_name"]]]] %>% unique %>% na.omit i <- v %in% names(metadata$locations) expect_true(all(i), info = paste0(f, " - site names from data file not present in metadata: ", v[!i])) From eb0f81883f73e946ce6f5a2e08d7ae8856770c89 Mon Sep 17 00:00:00 2001 From: Sophie Yang <78716301+yangsophieee@users.noreply.github.com> Date: Fri, 20 Oct 2023 16:26:24 +1100 Subject: [PATCH 04/31] Create test for blank datasets (#103) Closes #4 - These changes address three scenarios: 1) all traits in the metadata have `trait_name` mapped to `.na`, leading to an empty traits table, 2) all traits have 'wrong' `trait_name`'s or `trait_name`'s not in the traits dictionary, leading to an empty traits table, 3) the units are so far off that all data are excluded - Picks up these issues with `dataset_test` (@ehwenk has done testing) --- R/process.R | 2 +- R/testdata.R | 91 +++++++++++++++++++++++++++++++--------------------- 2 files changed, 56 insertions(+), 37 deletions(-) diff --git a/R/process.R b/R/process.R index 95e08e0e..80e46b6a 100644 --- a/R/process.R +++ b/R/process.R @@ -680,7 +680,7 @@ process_create_context_ids <- function(data, contexts) { # Extract context columns context_cols <- data %>% - dplyr::select(dplyr::all_of(tmp$var_in)) %>% + dplyr::select(dplyr::any_of(tmp$var_in)) %>% dplyr::mutate(dplyr::across(everything(), as.character)) names(context_cols) <- tmp$context_property diff --git a/R/testdata.R b/R/testdata.R index 6ac8c7ae..1949d431 100644 --- a/R/testdata.R +++ b/R/testdata.R @@ -555,12 +555,16 @@ dataset_test_worker <- } # Traits - expect_list_elements_contains_names(metadata[["traits"]], - schema$metadata$elements$traits$elements[1:3] %>% names(), - info = paste0(f, " - traits")) - expect_list_elements_allowed_names(metadata[["traits"]], - c(schema$metadata$elements$traits$elements %>% names(), unique(contexts$var_in)), - info = paste0(f, " - traits")) + expect_list_elements_contains_names( + metadata[["traits"]], + schema$metadata$elements$traits$elements[1:3] %>% names(), + info = paste0(f, " - traits") + ) + expect_list_elements_allowed_names( + metadata[["traits"]], + c(schema$metadata$elements$traits$elements %>% names(), unique(contexts$var_in)), + info = paste0(f, " - traits") + ) expect_silent( traits <- traits.build::util_list_to_df2(metadata[["traits"]]) ) @@ -750,46 +754,61 @@ dataset_test_worker <- )) } - ## Check that dataset can pivot wider - expect_no_error(dataset <- test_build_dataset( - file.path(path_data, dataset_id, "metadata.yml"), - file.path(path_data, dataset_id, "data.csv"), - dataset_id, - get_schema("config/traits.yml", "traits"), - get_unit_conversions("config/unit_conversions.csv"), - get_schema(), - get_schema("config/metadata.yml", "metadata"), - read_csv_char("config/taxon_list.csv") - ), info = sprintf(" - cannot build %s", dataset_id)) - # Check that special characters do not make it into the data expect_no_error( parsed_data <- data %>% process_parse_data(dataset_id, metadata, contexts, schema), - info = "`process_parse_data`") + info = sprintf("%s - `process_parse_data` has an error", dataset_id)) expect_allowed_text( parsed_data$traits$value, is_data = TRUE, info = sprintf("%s", files[1]) ) - testthat::expect_equal( - dataset$traits %>% - select( - dplyr::all_of(c("dataset_id", "trait_name", "value", "observation_id", "value_type", - "repeat_measurements_id", "method_id", "method_context_id")) - ) %>% - tidyr::pivot_wider(names_from = "trait_name", values_from = "value", values_fn = length) %>% - tidyr::pivot_longer(cols = 7:ncol(.)) %>% - dplyr::rename(dplyr::all_of(c("trait_name" = "name", "number_of_duplicates" = "value"))) %>% - select( - dplyr::all_of(c("dataset_id", "trait_name", "number_of_duplicates", "observation_id", "value_type")), everything() - ) %>% - filter(.data$number_of_duplicates > 1) %>% - nrow(), - 0, # Expect nrow() = 0 - info = sprintf("Duplicate rows in %s detected; `traits` table cannot pivot wider", dataset_id) - ) + expect_false( + nrow(metadata[["traits"]] %>% util_list_to_df2() %>% dplyr::filter(!is.na(.data$trait_name))) == 0, + info = paste0(f, " - `traits` metadata only contains NA `trait_name`'s")) + + if (nrow(metadata[["traits"]] %>% util_list_to_df2() %>% dplyr::filter(!is.na(.data$trait_name))) > 0) { + # Test build dataset + expect_no_error( + dataset <- test_build_dataset( + file.path(path_data, dataset_id, "metadata.yml"), + file.path(path_data, dataset_id, "data.csv"), + dataset_id, + get_schema("config/traits.yml", "traits"), + get_unit_conversions("config/unit_conversions.csv"), + get_schema(), + get_schema("config/metadata.yml", "metadata"), + read_csv_char("config/taxon_list.csv") + ), + info = sprintf("%s - cannot build dataset", dataset_id)) + + # Check that traits table is not empty + expect_false(nrow(dataset$traits) == 0, info = sprintf("%s - `traits` table is empty", dataset_id)) + + # Check that dataset can pivot wider + if (nrow(dataset$traits) > 0) { + testthat::expect_equal( + dataset$traits %>% + select( + dplyr::all_of(c("dataset_id", "trait_name", "value", "observation_id", "value_type", + "repeat_measurements_id", "method_id", "method_context_id")) + ) %>% + tidyr::pivot_wider(names_from = "trait_name", values_from = "value", values_fn = length) %>% + tidyr::pivot_longer(cols = 7:ncol(.)) %>% + dplyr::rename(dplyr::all_of(c("trait_name" = "name", "number_of_duplicates" = "value"))) %>% + select( + dplyr::all_of(c("dataset_id", "trait_name", "number_of_duplicates", "observation_id", + "value_type")), everything() + ) %>% + filter(.data$number_of_duplicates > 1) %>% + nrow(), + 0, # Expect nrow() = 0 + info = sprintf("Duplicate rows in %s detected; `traits` table cannot pivot wider", dataset_id) + ) + } + } }) } From 8989d8b465f70dd2efa06f4eafe31010698a9d19 Mon Sep 17 00:00:00 2001 From: Sophie Yang <78716301+yangsophieee@users.noreply.github.com> Date: Fri, 20 Oct 2023 22:56:31 +1100 Subject: [PATCH 05/31] Generalised database and target names (#102) Closes #6 - Allows different databases to rename the database, instead of before using "austraits" - Default is just set to "database", @ehwenk and I decided against "traits" because "traits$traits" is confusing --- R/setup.R | 3 +++ inst/support/build_base.whisker | 10 +++++----- inst/support/build_furrr.whisker | 6 +++--- inst/support/build_remake.whisker | 14 +++++++------- tests/testthat/test-setup.R | 32 +++++++++++++++++++++++-------- 5 files changed, 42 insertions(+), 23 deletions(-) diff --git a/R/setup.R b/R/setup.R index ff82cad4..31d47785 100644 --- a/R/setup.R +++ b/R/setup.R @@ -1147,6 +1147,7 @@ metadata_find_taxonomic_change <- function(find, replace = NULL, studies = NULL) #' #' @param dataset_ids `dataset_id`'s to include; by default includes all #' @param method Approach to use in build +#' @param database_name Name of database to be built #' @param template Template used to build #' @param workers Number of workers/parallel processes to use when using #' method = "furrr" @@ -1155,6 +1156,7 @@ metadata_find_taxonomic_change <- function(find, replace = NULL, studies = NULL) #' @export build_setup_pipeline <- function(dataset_ids = dir("data"), method = "base", + database_name = "database", template = select_pipeline_template(method), workers = 1 ) { @@ -1185,6 +1187,7 @@ build_setup_pipeline <- function(dataset_ids = dir("data"), dataset_ids_vector = sprintf("c(%s)", sprintf("'%s'", dataset_ids) %>% paste(collapse = ", ")), path = path, + database_name = database_name, workers = workers ) diff --git a/inst/support/build_base.whisker b/inst/support/build_base.whisker index 81bbc5dd..a3b882a4 100644 --- a/inst/support/build_base.whisker +++ b/inst/support/build_base.whisker @@ -20,19 +20,19 @@ taxon_list <- read_csv_char("config/taxon_list.csv") {{/dataset_ids}} -austraits_raw <- build_combine( +{{database_name}}_raw <- build_combine( {{#dataset_ids}} - {{dataset_id}}, + {{dataset_id}}, {{/dataset_ids}} - NULL) + NULL) # Version information version_number <- util_get_version("config/metadata.yml") git_SHA <- util_get_SHA() # Combine all the source into one resource -austraits <- build_add_version(austraits_raw, version_number, git_SHA) +{{database_name}} <- build_add_version({{database_name}}_raw, version_number, git_SHA) # Save to file dir.create("export/data/curr", FALSE, TRUE) -saveRDS(austraits, "export/data/curr/austraits.rds") +saveRDS({{database_name}}, "export/data/curr/{{database_name}}.rds") diff --git a/inst/support/build_furrr.whisker b/inst/support/build_furrr.whisker index 2d27e979..22639625 100644 --- a/inst/support/build_furrr.whisker +++ b/inst/support/build_furrr.whisker @@ -35,15 +35,15 @@ plan(multisession, workers = {{workers}}) sources <- future_map(dataset_ids, f, .progress = TRUE) -austraits_raw <- build_combine(d = sources) +{{database_name}}_raw <- build_combine(d = sources) # Version information version_number <- util_get_version("config/metadata.yml") git_SHA <- util_get_SHA() # Combine all the source into one resource -austraits <- build_add_version(austraits_raw, version_number, git_SHA) +{{database_name}} <- build_add_version({{database_name}}_raw, version_number, git_SHA) # Save to file dir.create("export/data/curr", FALSE, TRUE) -saveRDS(austraits, "export/data/curr/austraits.rds") +saveRDS({{database_name}}, "export/data/curr/{{database_name}}.rds") diff --git a/inst/support/build_remake.whisker b/inst/support/build_remake.whisker index 4181fa1a..9229023b 100644 --- a/inst/support/build_remake.whisker +++ b/inst/support/build_remake.whisker @@ -10,8 +10,8 @@ targets: # Define generic targets all: depends: - - austraits - - export/data/curr/austraits.rds + - {{database_name}} + - export/data/curr/{{database_name}}.rds # Load data resources schema: @@ -52,7 +52,7 @@ targets: {{/dataset_ids}} - austraits_raw: + {{database_name}}_raw: command: > build_combine( {{#dataset_ids}} @@ -70,9 +70,9 @@ targets: - .git/index # Combine all the source into one resource - austraits: - command: build_add_version(austraits_raw, version_number, git_SHA) + {{database_name}}: + command: build_add_version({{database_name}}_raw, version_number, git_SHA) # Save to file - export/data/curr/austraits.rds: - command: saveRDS(austraits, target_name) + export/data/curr/{{database_name}}.rds: + command: saveRDS({{database_name}}, target_name) diff --git a/tests/testthat/test-setup.R b/tests/testthat/test-setup.R index 5221ef2b..d13cdfea 100644 --- a/tests/testthat/test-setup.R +++ b/tests/testthat/test-setup.R @@ -628,7 +628,7 @@ test_that("`build_setup_pipeline` is working", { expect_silent(suppressMessages(source("build.R", local = base_tmp_env))) targets <- c( - "austraits", "austraits_raw", "definitions", "git_SHA", "resource_metadata", "schema", "taxon_list", + "database", "database_raw", "definitions", "git_SHA", "resource_metadata", "schema", "taxon_list", "Test_2022", "Test_2022_config", "Test_2022_raw", "unit_conversions", "version_number" ) expect_equal(sort(names(base_tmp_env)), sort(targets)) @@ -644,7 +644,7 @@ test_that("`build_setup_pipeline` is working", { expect_silent(suppressMessages(source("build.R", local = furrr_tmp_env))) targets <- c( - "austraits", "austraits_raw", "dataset_ids", "f", "definitions", "git_SHA", "resource_metadata", + "database", "database_raw", "dataset_ids", "f", "definitions", "git_SHA", "resource_metadata", "schema", "sources", "taxon_list", "unit_conversions", "version_number" ) expect_equal(sort(names(furrr_tmp_env)), sort(targets)) @@ -656,8 +656,8 @@ test_that("`build_setup_pipeline` is working", { expect_true(file.exists("config/taxon_list.csv")) unlink(".remake", recursive = TRUE) - expect_silent(suppressMessages(austraits_raw <- remake::make("austraits_raw"))) - expect_silent(suppressMessages(austraits <- remake::make("austraits"))) + expect_silent(suppressMessages(austraits_raw <- remake::make("database_raw"))) + expect_silent(suppressMessages(austraits <- remake::make("database"))) # Test that austraits_raw has no version number or git_SHA expect_null(austraits_raw$build_info$version) @@ -674,14 +674,30 @@ test_that("`build_setup_pipeline` is working", { # Compare products from three methods, except `build_info` v <- setdiff(names(austraits), "build_info") - expect_equal(base_tmp_env$austraits[v], austraits[v]) - expect_equal(furrr_tmp_env$austraits[v], austraits[v]) + expect_equal(base_tmp_env$database[v], austraits[v]) + expect_equal(furrr_tmp_env$database[v], austraits[v]) + # Try building database with a different name with base method + expect_silent(suppressMessages(build_setup_pipeline(method = "base", database_name = "test_name"))) + + base_tmp_env <- new.env() + expect_silent(suppressMessages(source("build.R", local = base_tmp_env))) + + targets <- c( + "test_name", "test_name_raw", "definitions", "git_SHA", "resource_metadata", "schema", "taxon_list", + "Test_2022", "Test_2022_config", "Test_2022_raw", "unit_conversions", "version_number" + ) + expect_equal(sort(names(base_tmp_env)), sort(targets)) + + # Try building database with a different name with `remake` method + expect_silent(suppressMessages(build_setup_pipeline(method = "remake", database_name = "test_name"))) + expect_silent(suppressMessages(test_name_raw <- remake::make("test_name_raw"))) + expect_silent(suppressMessages(test_name <- remake::make("test_name"))) }) testthat::test_that("`dataset_find_taxon` is working", { - expect_silent(suppressMessages(austraits <- remake::make("austraits"))) + expect_silent(suppressMessages(austraits <- remake::make("test_name"))) taxon <- c("Acacia celsa", "Acronychia acidula", "Aleurites rockinghamensis", "Syzygium sayeri") expect_no_error(x <- dataset_find_taxon(taxon, austraits), label = "`dataset_find_taxon`") expect_equal(unname(x[[4]]), "Test_2022") @@ -690,7 +706,7 @@ testthat::test_that("`dataset_find_taxon` is working", { test_that("reports and plots are produced", { - expect_silent(suppressMessages(austraits <- remake::make("austraits"))) + expect_silent(suppressMessages(austraits <- remake::make("test_name"))) # Not testing right now #expect_no_error( #p <- From 7475433676a5ab3ee7511c1cdd78aefc3584d6cd Mon Sep 17 00:00:00 2001 From: Sophie Yang <78716301+yangsophieee@users.noreply.github.com> Date: Wed, 25 Oct 2023 10:31:40 +1100 Subject: [PATCH 06/31] Add function for identifying duplicates preventing pivot wider (#106) Closes #83 - Includes function for checking duplicates that prevent pivoting wider (helps users identify which rows are the problem when the `dataset_test` `pivot_wider` test fails) --- NAMESPACE | 1 + R/process.R | 34 +++++++++++++++++++++++++++++++++- man/build_setup_pipeline.Rd | 3 +++ man/check_duplicates.Rd | 22 ++++++++++++++++++++++ man/process_generate_id.Rd | 8 ++++---- man/traits.build-package.Rd | 3 ++- 6 files changed, 65 insertions(+), 6 deletions(-) create mode 100644 man/check_duplicates.Rd diff --git a/NAMESPACE b/NAMESPACE index d086bdd1..c8a2c101 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -5,6 +5,7 @@ export(build_add_version) export(build_combine) export(build_setup_pipeline) export(build_update_taxonomy) +export(check_duplicates) export(dataset_build) export(dataset_configure) export(dataset_find_taxon) diff --git a/R/process.R b/R/process.R index 80e46b6a..686de42a 100644 --- a/R/process.R +++ b/R/process.R @@ -1170,7 +1170,7 @@ process_convert_units <- function(data, definitions, unit_conversion_functions) ucn = process_unit_conversion_name(.data$unit_in, .data$to), type = util_extract_list_element(.data$i, definitions, "type"), to_convert = ifelse(is.na(.data$error), (.data$type == "numeric" & .data$unit_in != .data$to), FALSE), - unit_in = ifelse(.data$type == "categorical", NA, unit_in) + unit_in = ifelse(.data$type == "categorical", NA, .data$unit_in) ) # Identify anything problematic in conversions and drop @@ -2059,3 +2059,35 @@ write_plaintext <- function(austraits, path) { readr::write_csv(austraits[[v]], sprintf("%s/%s.csv", path, v), na = "") } } + +#' Identify duplicates preventing pivoting wider +#' +#' @param database_object Database object +#' @param dataset_ids `dataset_id`'s to check for duplicates; default is all of them +#' +#' @return Tibble with duplicates and pivot columns +#' @export +check_duplicates <- function( + database_object, + dataset_ids = unique(database_object$traits$dataset_id) +) { + + # Check for duplicates + database_object$traits %>% + filter(.data$dataset_id %in% dataset_ids) %>% + select( + # `taxon_name` and `original_name` are not needed for pivoting but are included for informative purposes + dplyr::all_of( + c("dataset_id", "trait_name", "value", "taxon_name", "original_name", "observation_id", + "value_type", "repeat_measurements_id", "method_id", "method_context_id")) + ) %>% + tidyr::pivot_wider(names_from = "trait_name", values_from = "value", values_fn = length) %>% + tidyr::pivot_longer(cols = 9:ncol(.)) %>% + dplyr::rename(dplyr::all_of(c("trait_name" = "name", "number_of_duplicates" = "value"))) %>% + select( + dplyr::all_of(c("dataset_id", "trait_name", "number_of_duplicates", + "taxon_name", "original_name", "observation_id", "value_type")), everything() + ) %>% + filter(.data$number_of_duplicates > 1) + +} diff --git a/man/build_setup_pipeline.Rd b/man/build_setup_pipeline.Rd index 828382ec..cb06b874 100644 --- a/man/build_setup_pipeline.Rd +++ b/man/build_setup_pipeline.Rd @@ -7,6 +7,7 @@ build_setup_pipeline( dataset_ids = dir("data"), method = "base", + database_name = "database", template = select_pipeline_template(method), workers = 1 ) @@ -16,6 +17,8 @@ build_setup_pipeline( \item{method}{Approach to use in build} +\item{database_name}{Name of database to be built} + \item{template}{Template used to build} \item{workers}{Number of workers/parallel processes to use when using diff --git a/man/check_duplicates.Rd b/man/check_duplicates.Rd new file mode 100644 index 00000000..adbdc869 --- /dev/null +++ b/man/check_duplicates.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/process.R +\name{check_duplicates} +\alias{check_duplicates} +\title{Identify duplicates preventing pivoting wider} +\usage{ +check_duplicates( + database_object, + dataset_ids = unique(database_object$traits$dataset_id) +) +} +\arguments{ +\item{database_object}{Database object} + +\item{dataset_ids}{`dataset_id`'s to check for duplicates; default is all of them} +} +\value{ +Tibble with duplicates and pivot columns +} +\description{ +Identify duplicates preventing pivoting wider +} diff --git a/man/process_generate_id.Rd b/man/process_generate_id.Rd index 08c300e5..463c460b 100644 --- a/man/process_generate_id.Rd +++ b/man/process_generate_id.Rd @@ -8,14 +8,14 @@ Determines number of 00s needed based on number of records} process_generate_id(x, prefix, sort = FALSE) } \arguments{ -\item{x}{vector of text to convert} +\item{x}{Vector of text to convert} -\item{prefix}{text to put before id integer} +\item{prefix}{Text to put before id integer} -\item{sort}{logical to indicate whether x should be sorted before ids are generated} +\item{sort}{Logical to indicate whether x should be sorted before ids are generated} } \value{ -vector of ids +Vector of ids } \description{ Function to generate sequence of integer ids from vector of names diff --git a/man/traits.build-package.Rd b/man/traits.build-package.Rd index 649aa8cf..5913f88d 100644 --- a/man/traits.build-package.Rd +++ b/man/traits.build-package.Rd @@ -6,7 +6,7 @@ \alias{traits.build-package} \title{traits.build: Package used to build an AusTraits data resource} \description{ -This package enbales harmonising of data from diverse sources. The code was originally built to support AusTraits, an open-source compilation of data on the traits of Australian plant species. For more information on AusTraits go to https://austraits.org. +This package enables harmonising of data from diverse sources. The code was originally built to support AusTraits, an open-source compilation of data on the traits of Australian plant species. For more information on AusTraits go to https://austraits.org. } \seealso{ Useful links: @@ -22,6 +22,7 @@ Useful links: Authors: \itemize{ \item Elizabeth Wenk (\href{https://orcid.org/0000-0001-5640-5910}{ORCID}) [curator] + \item Sophie Yang (\href{https://orcid.org/0000-0001-7328-345X}{ORCID}) [curator] } Other contributors: From 4a1674d45dbd9f6d2b0eed1487c3367f7525f83e Mon Sep 17 00:00:00 2001 From: Elizabeth Wenk Date: Fri, 27 Oct 2023 08:23:26 +1100 Subject: [PATCH 07/31] Update report_dataset.Rmd (#108) Fix error in renaming syntax introduced to reports at some point since June. --- inst/support/report_dataset.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/support/report_dataset.Rmd b/inst/support/report_dataset.Rmd index 187ec94d..baccdc9f 100644 --- a/inst/support/report_dataset.Rmd +++ b/inst/support/report_dataset.Rmd @@ -667,7 +667,7 @@ for (trait in traits_categorical) { "No substitutions were required to align the data for this trait with AusTraits allowed trait values."), ifelse(nrow(substitutions_for_trait) > 0, substitutions_for_trait %>% - rename(all_of("value in contributed data table" = find, "AusTraits aligned value" = replace)) %>% + rename(all_of(c("value in contributed data table" = "find", "AusTraits aligned value" = "replace"))) %>% my_kable_styling(), "" ), From 33dd832b0862f5c646c10e73d006a3640731a0fe Mon Sep 17 00:00:00 2001 From: Sophie Yang <78716301+yangsophieee@users.noreply.github.com> Date: Tue, 31 Oct 2023 10:02:59 +1100 Subject: [PATCH 08/31] Improve `dataset_test` failure messages (#109) Closes #48 - Removed the duplicate set of failure messages by switching from `default_reporter()` (`ProgressReporter`) to `CompactProgressReporter` - Swapped out `testthat` `expect_` functions for manually written expectations in order to fully customise failure messages and make them more accessible - Tidied all failure messages --- NAMESPACE | 4 - R/process.R | 9 +- R/setup.R | 6 +- R/testdata.R | 580 ++++++++++++++++++++---------------- man/dataset_test.Rd | 2 +- tests/testthat/functions.R | 53 ++-- tests/testthat/test-setup.R | 2 +- 7 files changed, 364 insertions(+), 292 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index c8a2c101..73a301f3 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -73,11 +73,7 @@ importFrom(styler,style_text) importFrom(testthat,compare) importFrom(testthat,context) importFrom(testthat,expect) -importFrom(testthat,expect_false) -importFrom(testthat,expect_named) importFrom(testthat,expect_silent) -importFrom(testthat,expect_true) -importFrom(testthat,expect_type) importFrom(testthat,local_edition) importFrom(testthat,test_that) importFrom(tidyr,spread) diff --git a/R/process.R b/R/process.R index 686de42a..b8044b50 100644 --- a/R/process.R +++ b/R/process.R @@ -580,7 +580,7 @@ process_generate_method_ids <- function(metadata_traits) { dplyr::filter(!is.na(.data$trait_name)) %>% dplyr::select(dplyr::all_of(c("trait_name", "methods"))) %>% dplyr::distinct() %>% - # Group by traits to generate ids. + # Group by traits to generate ids # This handles instances where multiple methods used for a single trait within a dataset dplyr::group_by(.data$trait_name) %>% dplyr::mutate(method_id = process_generate_id(.data$methods, "")) %>% @@ -632,7 +632,7 @@ process_format_contexts <- function(my_list, dataset_id, traits) { ## They are both the unique set of values in the column in the data.csv file if (all(!c("find", "value") %in% names(out))) { out <- out %>% - # The following line shouldn't be neeeded, as we tested this was missing for the if statement above + # The following line shouldn't be needed, as we tested this was missing for the if statement above dplyr::select(-any_of(c("value"))) %>% dplyr::left_join( by = "var_in", @@ -2055,7 +2055,10 @@ write_plaintext <- function(austraits, path) { RefManageR::WriteBib(austraits$sources, sprintf("%s/sources", path)) # Save tables - for (v in c("traits", "locations", "contexts", "methods", "excluded_data", "taxonomic_updates", "taxa", "contributors")) { + for (v in c( + "traits", "locations", "contexts", "methods", "excluded_data", + "taxonomic_updates", "taxa", "contributors") + ) { readr::write_csv(austraits[[v]], sprintf("%s/%s.csv", path, v), na = "") } } diff --git a/R/setup.R b/R/setup.R index 31d47785..67def924 100644 --- a/R/setup.R +++ b/R/setup.R @@ -399,7 +399,7 @@ metadata_add_locations <- function(dataset_id, location_data, user_responses = N red("with variables ") %+% green("'%s'\n\t") %+% red("Please complete information in %s"), blue(dataset_id), paste(names(metadata$locations), collapse = "', '"), - ifelse(is.na(keep[1]),"latitude (deg)', 'longitude (deg)', 'description",paste(keep, collapse = "', '")), + ifelse(is.na(keep[1]), "latitude (deg)', 'longitude (deg)', 'description", paste(keep, collapse = "', '")), blue(dataset_id %>% metadata_path_dataset_id()) ) ) @@ -459,8 +459,8 @@ metadata_add_contexts <- function(dataset_id, overwrite = FALSE, user_responses message( sprintf( - red("Existing context information detected, from the following columns in the dataset: ") %+% green("'%s'\n\t") %+% - red("Metadata is being appended; please review duplicates manually"), + red("Existing context information detected, from the following columns in the dataset: ") %+% + green("'%s'\n\t") %+% red("Metadata is being appended; please review duplicates manually"), contexts %>% purrr::map_chr(~.x[["var_in"]]) %>% paste(collapse = "', '")) ) } diff --git a/R/testdata.R b/R/testdata.R index 1949d431..4a5863da 100644 --- a/R/testdata.R +++ b/R/testdata.R @@ -14,7 +14,7 @@ dataset_test <- function(dataset_ids, path_config = "config", path_data = "data", - reporter = testthat::default_reporter()) { + reporter = testthat::CompactProgressReporter) { requireNamespace("testthat", quietly = TRUE) @@ -41,7 +41,7 @@ dataset_test <- #' @inheritParams dataset_test #' @param schema Data schema #' @param definitions Trait defininitons -#' @importFrom testthat local_edition compare expect expect_true expect_false expect_named test_that context expect_silent expect_type +#' @importFrom testthat local_edition compare expect test_that context expect_silent #' @importFrom rlang .data #' @importFrom stats na.omit dataset_test_worker <- @@ -55,91 +55,123 @@ dataset_test_worker <- # We're using 2nd edition of test that, which has "context" field # https://cran.r-project.org/web/packages/testthat/vignettes/third-edition.html + # Is there a reason to be using the 2nd edition, while context has been superseded in later versions? local_edition(2) - ## New expect_that helper functions; test that a number is in a range, - ## or that a range contains a number. - - expect_isin <- - function(object, - expected, - ..., - info = NULL, - label = NULL, - expected.label = NULL, - na.rm = TRUE) { + expect_is_in <- function(object, expected, ..., info, label, na.rm = TRUE) { + if (na.rm) object <- object[!is.na(object)] i <- object %in% expected comp <- compare(all(i), TRUE, ...) - expect(comp$equal, - sprintf( - "%s - should not contain: %s", - info, - paste(object[!i], collapse = ", ") - )) + expect( + comp$equal, + sprintf( + "%s - %s should not contain: %s", + info, label, + paste(object[!i], collapse = ", ") + )) invisible(object) } - # Expectation: one set contains the other - expect_contains <- function(object, expected, ..., info = NULL) { + expect_contains <- function(object, expected, ..., info) { + i <- expected %in% object comp <- compare(all(i), TRUE, ...) - expect(comp$equal, - sprintf( - "%s - does not contain: %s", - info, - paste(expected[!i], collapse = ", ") - )) + expect( + comp$equal, + sprintf("%s - does not contain: %s", info, paste(expected[!i], collapse = ", ")) + ) invisible(object) } - # Expectation: one set contains the other - expect_allowed <- function(object, allowed, ..., info = NULL) { + expect_allowed <- function(object, allowed, ..., info, label) { + i <- object %in% allowed comp <- compare(all(i), TRUE, ...) - expect(comp$equal, - sprintf( - "%s - includes invalid terms: %s", - info, - paste(object[!i], collapse = ", ") - )) + expect( + comp$equal, + sprintf( + "%s - %s include(s) invalid terms: %s", + info, label, + paste(object[!i], collapse = ", ") + )) invisible(object) } - expect_not_NA <- function(object, info = NULL, label = NULL) { + expect_equal <- function(object, expected, info) { + i <- object == expected + comp <- compare(all(i), TRUE) + expect(comp$equal, info) + } + + expect_true <- function(object, info) { + i <- object == TRUE + comp <- compare(all(i), TRUE) + expect(comp$equal, info) + } + + expect_false <- function(object, info) { + i <- object == FALSE + comp <- compare(all(i), TRUE) + expect(comp$equal, info) + } + + expect_named <- function(object, expected_names, info, label) { + + if (missing(expected_names)) { + expect( + !identical(names(object), NULL), + sprintf("%s - %s do not exist", info, label)) + } else { + expect( + identical(names(object), expected_names), + sprintf( + "%s\tnames of %s (%s) don't match %s", + info, + label, paste0("'", names(object), "'", collapse = ", "), + paste0("'", expected_names, "'", collapse = ", ") + ) + ) + } + } + + expect_type <- function(object, type, info, label) { + stopifnot(is.character(type), length(type) == 1) + expect( + identical(typeof(object), type), + sprintf("%s - %s has type %s, not %s", info, label, typeof(object), type) + ) + } + + expect_not_NA <- function(object, info, label) { i <- !is.na(object) comp <- compare(all(i), TRUE) - expect(comp$equal, - sprintf("%s - contains NAs: %s", info, label)) + expect(comp$equal, sprintf("%s - %s contain(s) NAs", info, label)) invisible(object) } - expect_length_zero <- function(object, info = NULL, label = NULL) { + expect_length_zero <- function(object, info, label) { comp <- compare(length(object), 0) - expect(comp$equal, - sprintf("%s: %s", info, label)) + expect(comp$equal, sprintf("%s: %s", info, label)) invisible(object) } - expect_unique <- function(object, info = NULL, label = NULL) { + expect_unique <- function(object, info, label) { x <- table(unlist(object)) i <- x == 1 comp <- compare(all(i), TRUE) - expect(comp$equal, - sprintf("%s - not unique: %s", info, paste(names(x)[!i], collapse = ", "))) + expect(comp$equal, sprintf("%s - %s not unique: %s", info, label, paste(names(x)[!i], collapse = ", "))) invisible(object) } - expect_allowed_text <- function(object, is_data = FALSE, - info = NULL, - label = NULL) { + expect_allowed_text <- function(object, is_data = FALSE, info, label) { if (length(object) > 0) { @@ -155,24 +187,23 @@ dataset_test_worker <- txt <- "\n" for (i in which(check)) { - txt <- sprintf("%s\t- ln %s: %s\n", - txt, - i, - colour_characters(object[[i]], which(disallowed[[i]]))) + txt <- sprintf( + "%s\t- ln %s: %s\n", + txt, i, colour_characters(object[[i]], which(disallowed[[i]]))) } if (is_data) { expect( identical(as.vector(all(!check)), TRUE), sprintf( - "%s - disallowed characters in data detected: %s\n\tPlease replace using `custom_R_code`", + "%s\tdisallowed characters in data detected: %s\n\tPlease replace using `custom_R_code`", info, txt ) ) } else { expect( identical(as.vector(all(!check)), TRUE), - sprintf("%s - disallowed characters detected: %s", info, txt) + sprintf("%s - disallowed characters in %s detected: \n%s", info, label, txt) ) } @@ -183,6 +214,7 @@ dataset_test_worker <- } colour_characters <- function(x, i = NULL) { + chars <- x %>% charToRaw() %>% lapply(rawToChar) %>% unlist() # Wrapper around characters to print as colour @@ -208,87 +240,77 @@ dataset_test_worker <- is_allowed <- i %in% charToRaw(exceptions) !(is_ascii | is_allowed) - } # Better than expect_silent as contains `info` and allows for complete failures - expect_no_error <- - function(object, regexp = NULL, ..., info = NULL, label = NULL) { - error <- tryCatch({ - object - NULL - }, error = function(e) { - e - }) - expect(is.null(error), - sprintf( - "%s threw an error: %s", - label, - paste(error$message, collapse = ",") - ), - info = info) - invisible(NULL) - } + expect_no_error <- function(object, ..., info) { + error <- tryCatch({ + object + NULL + }, error = function(e) { + e + }) + expect( + is.null(error), + sprintf("%s threw an error:\n\n" %+% red("%s"), info, paste(error, collapse = ","))) + invisible(NULL) + } expect_list_elements_contains_names <- function(object, expected, info) { for (i in seq_along(object)) expect_contains(names(object[[i]]), expected, info = paste(info, i)) - invisible(NULL) } - expect_list_elements_allowed_names <- function(object, allowed, info) { + expect_list_elements_allowed_names <- function(object, allowed, info, label) { for (i in seq_along(object)) - expect_allowed(names(object[[i]]), allowed, info = paste(info, i)) - + expect_allowed(names(object[[i]]), allowed, info = paste(info, i), label = "field names") invisible(NULL) } - test_dataframe_valid <- function(data, info) { - expect_not_NA(colnames(data), info = info) - expect_allowed_text(colnames(data), info = info) - expect_unique(colnames(data), info = info) - expect_true(is.data.frame(data), info = info) + expect_dataframe_valid <- function(data, info, label) { + expect_not_NA(colnames(data), info, label) + expect_allowed_text(colnames(data), info = info, label = label) + expect_unique(colnames(data), info, label) + expect_true(is.data.frame(data), info = sprintf("%s - is not a dataframe", info)) } # Function is assigned but not used - test_dataframe_named <- function(data, expected_colnames, info) { - test_dataframe_valid(data, info) - expect_named(data, expected_colnames, info = info) + expect_dataframe_named <- function(data, expected_colnames, info, label) { + expect_dataframe_valid(data, info, label) + expect_named(data, expected_colnames, info = info, label = label) } - test_dataframe_names_contain <- - function(data, expected_colnames, info) { - test_dataframe_valid(data, info) - expect_contains(names(data), expected_colnames, info = info) - } + expect_dataframe_names_contain <- function(data, expected_colnames, info, label) { + expect_dataframe_valid(data, info, label) + expect_contains(names(data), expected_colnames, info = info) + } - test_list <- function(data, info) { - expect_true(class(data) == "list", info = info) + expect_list <- function(data, info) { + expect_true(class(data) == "list", info = sprintf("%s - is not a list", info)) } - test_list_names_valid <- function(data, info) { - test_list(data, info) - expect_not_NA(names(data), info = info) - expect_allowed_text(names(data), info = info) - expect_unique(names(data), info = info) + expect_list_names_valid <- function(data, info, label) { + expect_list(data, info) + expect_not_NA(names(data), info = info, label = label) + expect_unique(names(data), info = info, label = label) } - test_list_named_exact <- function(data, expected_names, info) { - test_list_names_valid(data, info) - expect_named(data, expected_names, info = info) + expect_list_names_exact <- function(data, expected_names, info, label) { + expect_list_names_valid(data, info, label = label) + expect_named(data, expected_names, info = info, label = label) } - test_list_named_allowed <- function(data, allowed_names, info) { - test_list_names_valid(data, info) - expect_named(data) - expect_allowed(names(data), allowed_names, info = info) + expect_list_names_allowed <- function(data, allowed_names, info, label) { + expect_list_names_valid(data, info, label = label) + expect_named(data, info = info, label = label) + expect_allowed(names(data), allowed_names, info = info, label = label) } # Function is assigned but not used - test_list_named_contains <- function(data, expected_names, info) { - test_list_names_valid(data, info) - expect_named(data) + expect_list_names_contain <- function(data, expected_names, info, label) { + expect_list_names_valid(data, info, label = label) + expect_named(data, info = info, label = label) expect_contains(names(data), expected_names, info = info) } @@ -298,15 +320,15 @@ dataset_test_worker <- # Test it builds with no errors expect_no_error({ build_config <- dataset_configure(path_metadata, definitions) - }, info = paste(info, "config")) + }, info = "`dataset_configure`") expect_no_error({ build_dataset_raw <- dataset_process(path_data, build_config, schema, resource_metadata, unit_conversions) - }, info = paste(info, "dataset_process")) + }, info = "`dataset_process`") expect_no_error({ build_dataset <- build_update_taxonomy(build_dataset_raw, taxon_list) - }, info = paste(info, "update taxonomy")) + }, info = "`build_update_taxonomy`") build_dataset } @@ -324,131 +346,152 @@ dataset_test_worker <- # Exists files <- file.path(s, c("data.csv", "metadata.yml")) for (f in files) { - expect_true(file.exists(f), info = f) + expect_true(file.exists(f), info = sprintf("%s" %+% "\tfile does not exist", red(f))) } # Check for other files vals <- c("data.csv", "metadata.yml", "raw") - expect_isin(dir(s), vals, info = paste(f, "- disallowed files")) + expect_is_in( + dir(s), vals, + info = paste0(red(file.path(path_data, dataset_id)), "\tdisallowed files"), + label = "folder" + ) # `data.csv` f <- files[1] - # Time columns get reformatted expect_silent( - data <- read_csv(f, col_types = cols(), guess_max = 1e5, progress = FALSE) + data <- read_csv(f, col_types = cols(), guess_max = 1e5, progress = FALSE) # Time columns get reformatted ) + # Check no issues flagged when parsing file expect_no_error( readr::stop_for_problems(data), - info = sprintf( - "Problems present when reading data, run `read_csv(%s)` to investigate", - f - ) + info = sprintf(red("`read_csv(%s)`"), f) ) - test_dataframe_valid(data, info = f) + expect_dataframe_valid(data, info = paste0(red(f), "\tdata"), label = "column names") # Metadata f <- files[2] - expect_allowed_text(readLines(f, encoding = "UTF-8"), info = f) + expect_allowed_text(readLines(f, encoding = "UTF-8"), info = paste0(red(f), "\tmetadata"), label = "metadata") expect_silent(metadata <- yaml::read_yaml(f)) - test_list_named_exact(metadata, schema$metadata$elements %>% names(), info = f) + expect_list_names_exact( + metadata, schema$metadata$elements %>% names(), + info = red(f), label = "metadata sections" + ) # Custom R code txt <- metadata[["dataset"]][["custom_R_code"]] # Check that `custom_R_code` is immediately followed by `collection_date` - testthat::expect_equal( + expect_equal( metadata[["dataset"]][which(names(metadata[["dataset"]]) == "custom_R_code") + 1] %>% names(), "collection_date", - info = sprintf("%s - dataset: the `custom_R_code` field must be followed by `collection_date`", f) + info = sprintf("%s\tdataset - the `custom_R_code` field must be followed by `collection_date`", red(f)) ) - #expect_false(grepl("#", txt), label=paste0(files[3], "-custom_R_code cannot contain comments, except on last line")) - expect_no_error(process_custom_code(txt)(data), label = paste0(files[3], " - custom_R_code")) - # Apply custom manipulations - data <- process_custom_code(txt)(data) + expect_no_error(data <- process_custom_code(txt)(data), info = paste0(red(f), "\t`custom_R_code`")) # Source - test_list(metadata[["source"]], info = f) - test_list_names_valid(metadata[["source"]], info = f) + expect_list_names_valid(metadata[["source"]], info = sprintf("%s\tsource", red(f)), label = "field names") v <- names(metadata[["source"]]) i <- grepl("primary", v) | grepl("secondary", v) | grepl("original", v) - expect_contains(v, "primary", info = f) + expect_contains(v, "primary", info = paste0(red(f), "\tsource")) expect_true( sum(grepl("primary", v)) <= 1, - info = paste( - f, - "sources can have max 1 type labelled 'primary': ", - paste(v, collapse = ", ") - ) + info = paste0(red(f), "\tsources can have max 1 type labelled 'primary': ", paste(v, collapse = ", ")) ) - expect_true(all(i), - info = paste( - f, - "sources must be either primary or secondary:", - paste(v[!i], collapse = ", ") - )) + expect_true( + all(i), + info = paste0(red(f), "\tsources must be primary, secondary or original: ", paste(v[!i], collapse = ", ")) + ) vals <- c("key", "bibtype", "author", "title", "year") for (bib in names(metadata[["source"]])) { - expect_contains(names(metadata[["source"]][[bib]]), vals, info = f) + expect_contains( + names(metadata[["source"]][[bib]]), vals, + info = sprintf("%s\tsource '%s'", red(f), bib) + ) } keys <- unlist(lapply(metadata[["source"]], "[[", "key")) - expect_unique(keys, info = paste( - f, - "sources must have unique keys:", - paste(keys, collapse = ", ") - )) + expect_unique( + keys, + info = paste0(red(f), "\tsources"), + label = "keys" + ) # People - test_list(metadata[["contributors"]], info = f) + expect_list(metadata[["contributors"]], info = paste0(red(f), "\tcontributors")) - test_list_named_allowed(metadata[["contributors"]], - schema$metadata$elements$contributors$elements %>% names(), - info = f + expect_list_names_allowed( + metadata[["contributors"]], + schema$metadata$elements$contributors$elements %>% names(), + info = paste0(red(f), "\tcontributors"), label = "contributor type fields" ) # Data collectors if (!is.na(metadata[["contributors"]][["data_collectors"]][1])) { - test_list(metadata[["contributors"]][["data_collectors"]], info = f) + expect_list(metadata[["contributors"]][["data_collectors"]], info = paste0(red(f), "\tdata_collectors")) vars <- schema$metadata$elements$contributors$elements$data_collectors$elements %>% names() + for (i in seq_along(metadata[["contributors"]][["data_collectors"]])) { - test_list_named_allowed( + expect_list_names_allowed( metadata[["contributors"]][["data_collectors"]][[i]], - vars, info = paste(f, "data_collector", i) + vars, + info = paste0(red(f), "\tdata_collector ", i), label = "`data_collector` field names" + ) + + expect_contains( + metadata[["contributors"]][["data_collectors"]][[i]] %>% names(), vars[1:4], + info = sprintf("%s\tdata_collector %s", red(f), i) ) - expect_contains(metadata[["contributors"]][["data_collectors"]][[i]] %>% names(), vars[1:4]) } } # Dataset curators - expect_true(!is.null(metadata[["contributors"]][["dataset_curators"]])) - expect_type(metadata[["contributors"]][["dataset_curators"]], "character") + expect_true( + !is.null(metadata[["contributors"]][["dataset_curators"]]), + info = sprintf("%s\tcontributors - `dataset_curators` is missing", red(f)) + ) + expect_type( + metadata[["contributors"]][["dataset_curators"]], "character", + info = paste0(red(f), "\tcontributors"), label = "`dataset_curators`" + ) # Assistants if (!is.null(metadata[["contributors"]][["assistants"]][1])) - expect_type(metadata[["contributors"]][["assistants"]], "character") + expect_type( + metadata[["contributors"]][["assistants"]], "character", + info = paste0(red(f), "\tcontributors"), label = "`assistants`" + ) # Dataset + expect_list_names_allowed( + metadata[["dataset"]], + schema$metadata$elements$dataset$values %>% names(), + info = paste0(red(f), "\tdataset"), label = "`dataset` field names" + ) - test_list_named_allowed(metadata[["dataset"]], - schema$metadata$elements$dataset$values %>% names(), - info = paste0(f, " - dataset")) + expect_type( + metadata[["dataset"]][["data_is_long_format"]], "logical", + info = paste0(red(f), "\tdataset"), label = "`data_is_long_format`" + ) - expect_type(metadata[["dataset"]][["data_is_long_format"]], "logical") - expect_type(metadata[["dataset"]], "list") + expect_type( + metadata[["dataset"]], "list", + info = paste0(red(f), "\tdataset"), label = "metadata" + ) # Locations if (length(unlist(metadata[["locations"]])) > 1) { - test_list(metadata[["locations"]], info = f) + expect_list(metadata[["locations"]], info = paste0(red(f), "\tlocations")) expect_silent( locations <- @@ -457,18 +500,18 @@ dataset_test_worker <- process_add_all_columns(names(schema[["austraits"]][["elements"]][["locations"]][["elements"]])) ) - test_dataframe_names_contain( + expect_dataframe_names_contain( locations, c("dataset_id", "location_name", "location_property", "value"), - info = paste0(f, " - locations") + info = paste0(red(f), "\tlocations"), label = "field names" ) for (v in names(metadata$locations)) { - test_list(metadata[["locations"]][[v]], info = f) + expect_list(metadata[["locations"]][[v]], info = paste0(red(f), "\tlocation ", v)) expect_contains( names(metadata[["locations"]][[v]]), c("latitude (deg)", "longitude (deg)"), - info = paste0(f, " - locations: ", v) + info = paste0(red(f), "\tlocation '", v, "'") ) } } @@ -489,10 +532,11 @@ dataset_test_worker <- ## Check context details load if (nrow(contexts) > 0) { - test_dataframe_names_contain( + + expect_dataframe_names_contain( contexts, c("context_property", "category", "var_in"), - info = paste0(f, " - contexts") + info = paste0(red(f), "\tcontexts"), label = "field names" ) for (i in seq_along(metadata$contexts)) { @@ -507,44 +551,39 @@ dataset_test_worker <- if (!is.null(vals[[s]][["find"]])) { expect_false( is.na(vals[[s]][["find"]]), - info = paste0( - f, - sprintf("\tcontexts: `find` value in the `context_property` '%s' should not be NA\n\tPlease replace NAs with desired value using `custom_R_code`", - metadata$contexts[[i]][["context_property"]])) + info = paste0(red(f), + sprintf( + "\tcontexts - `find` value in the `context_property` '%s' should not be NA\n\tPlease replace NAs with desired value using `custom_R_code`", + metadata$contexts[[i]][["context_property"]])) ) } # Check that there are no `find` fields without accompanying `value` fields expect_false( !is.null(vals[[s]][["find"]]) && is.null(vals[[s]][["value"]]), - info = paste0( - f, + info = paste0(red(f), sprintf( - "\tcontexts: `find: %s` in the `context_property` '%s' is not accompanied by a `value` field", - vals[[s]][["find"]], metadata$contexts[[i]][["context_property"]] - )) + "\tcontexts - `find: %s` in the `context_property` '%s' is not accompanied by a `value` field", + vals[[s]][["find"]], metadata$contexts[[i]][["context_property"]])) ) # Check that there are no `description` fields with NA `value` fields if (!is.null(vals[[s]][["value"]]) && !is.null(vals[[s]][["description"]])) { expect_false( !is.na(vals[[s]][["description"]]) && is.na(vals[[s]][["value"]]), - info = paste0( - f, + info = paste0(red(f), sprintf( - "\tcontexts: `description: %s` in the `context_property` '%s' should not be accompanied by an NA `value` field\n\tPlease use `custom_R_code` to assign a proper value to NA fields", - vals[[s]][["description"]], metadata$contexts[[i]][["context_property"]] - )) + "\tcontexts - `description: %s` in the `context_property` '%s' should not be accompanied by an NA `value` field\n\tPlease use `custom_R_code` to assign a proper value to NA fields", + vals[[s]][["description"]], metadata$contexts[[i]][["context_property"]])) ) } # Check that there are no `description` fields without accompanying `find` and `value` fields expect_false( !is.null(vals[[s]][["description"]]) && is.null(vals[[s]][["find"]]) && is.null(vals[[s]][["value"]]), - info = paste0( - f, + info = paste0(red(f), sprintf( - "\tcontexts: `description: %s` in the `context_property` '%s' is not accompanied by `find` and `value` fields", + "\tcontexts - `description: %s` in the `context_property` '%s' is not accompanied by `find` and `value` fields", vals[[s]][["description"]], metadata$contexts[[i]][["context_property"]] ) ) @@ -558,21 +597,27 @@ dataset_test_worker <- expect_list_elements_contains_names( metadata[["traits"]], schema$metadata$elements$traits$elements[1:3] %>% names(), - info = paste0(f, " - traits") + info = paste0(red(f), "\ttrait") ) + expect_list_elements_allowed_names( metadata[["traits"]], c(schema$metadata$elements$traits$elements %>% names(), unique(contexts$var_in)), - info = paste0(f, " - traits") + info = paste0(red(f), "\ttrait") ) - expect_silent( - traits <- traits.build::util_list_to_df2(metadata[["traits"]]) + + expect_silent(traits <- traits.build::util_list_to_df2(metadata[["traits"]])) + + expect_true( + is.data.frame(traits), + info = paste0(red(f), "\ttraits - metadata cannot be converted to a dataframe") ) - expect_true(is.data.frame(traits)) - expect_isin(traits$trait_name, - definitions$elements %>% names(), - info = paste0(f, " - traits")) + expect_is_in( + traits$trait_name, definitions$elements %>% names(), + info = paste0(red(f), "\ttraits"), + label = "`trait_name`'s" + ) # Now that traits loaded, check details of context match if (nrow(contexts > 0)) { @@ -581,16 +626,15 @@ dataset_test_worker <- expect_contains( c(names(data), names(traits)), unique(contexts$var_in), - info = files[2] + info = paste0(red(files[1]), red(", "), red(files[2]), "\tdata and/or traits metadata") ) for (j in unique(contexts[["var_in"]])) { - contextsub <- - contexts %>% filter(var_in == j) - unique2 <- function(x) {unique(x[!is.na(x)])} + contextsub <- contexts %>% filter(var_in == j) + + unique2 <- function(x) unique(x[!is.na(x)]) # Context values align either with a column of data or a column of traits table - # Sophie - Not sure how context values can align with the latter? if (is.null(data[[j]])) { v <- traits[[j]] %>% unique2() } else { @@ -606,75 +650,95 @@ dataset_test_worker <- all(i), info = ifelse( "hms" %in% class(v), - sprintf("%s - context values from data file not present in metadata contexts: %s\n\n'%s' has been detected as a time data type and reformatted\n\t-> Please make sure context metadata matches reformatting", f, v[!i], j), - sprintf("%s - context values from data file not present in metadata contexts: %s", f, v[!i]) - ) + sprintf( + "%s\tcontexts - context values of '%s' from data file not present in metadata contexts: %s\n\n'%s' has been detected as a time data type and reformatted\n\t-> Please make sure context metadata matches reformatting", + red(f), j, v[!i], j), + sprintf( + "%s\tcontexts - context values of '%s' from data file not present in metadata: %s", + red(f), j, v[!i])) ) i <- contextsub[["find"]] %in% v expect_true( all(i), - info = sprintf( - "%s - context values in metadata contexts not detected in context values from data file: %s", - f, contextsub[["find"]][!i]) + info = ifelse( + !is.null(data[[j]]), + sprintf( + "%s\tcontexts - values of '%s' in metadata not detected in context values from data file: %s", + red(f), j, contextsub[["find"]][!i]), + sprintf( + "%s\tcontexts - values of '%s' in metadata not detected in context values from traits metadata: %s", + red(f), j, contextsub[["find"]][!i]) + ) ) - } } # Check value types in metadata and any columns of data - # XXXX To do -- also check for entity type, basis of value and any other columns + # XXXX TODO -- also check for entity type, basis of value and any other columns + # Note this only checks for `value_type` at the trait metadata level, which is appropriate for `value_type` + # but may not be appropriate for other fields on the TODO list if ("value_type" %in% names(traits)) { - i <- (traits$value_type %in% names(data)) + + i <- traits$value_type %in% names(data) value_type_fixed <- traits$value_type[!i] %>% unique() value_type_cols <- traits$value_type[i] %>% unique() - - expect_isin( + expect_is_in( value_type_fixed, schema$value_type$values %>% names, - info = paste0(f, " - value types") + info = paste0(red(f), "\ttraits"), label = "value types" ) if (length(value_type_cols) > 0) { for (v in value_type_cols) - expect_isin( + expect_is_in( data[[v]] %>% unique(), schema$value_type$values %>% names, - info = paste(f, v, " - value types columns") + info = sprintf("%s\t%s", red(files[1]), v), label = "value type column" ) } } # Substitutions + ## TODO do the same for `taxonomic_updates` and `exclude_observations`? if (!is.na(metadata[["substitutions"]][1])) { + expect_list_elements_contains_names( metadata[["substitutions"]], schema$metadata$elements$substitutions$values %>% names(), - "metadata - substitution #" + info = paste0(red(f), "\tsubstitution") + ) + expect_list_elements_allowed_names( + metadata[["substitutions"]], + schema$metadata$elements$substitutions$values %>% names(), + info = paste0(red(f), "\tsubstitution") + ) + trait_names <- sapply(metadata[["substitutions"]], "[[", "trait_name") + expect_is_in( + unique(trait_names), definitions$elements %>% names(), + info = paste0(red(f), "\tsubstitutions"), label = "`trait_name`'s" ) - trait_names <- - sapply(metadata[["substitutions"]], "[[", "trait_name") - expect_isin(unique(trait_names), - definitions$elements %>% names(), - info = paste0(f, " - substitutions - trait_name")) - expect_isin( - unique(trait_names), - unique(traits$trait_name), - info = paste0(f, " - substitutions - trait_name") + expect_is_in( + unique(trait_names), unique(traits$trait_name), + info = paste0(red(f), "\tsubstitutions"), label = "`trait_name`'s" ) # Check for allowable values of categorical variables expect_no_error( - x <- metadata[["substitutions"]] %>% util_list_to_df2() %>% split(.$trait_name)) + x <- metadata[["substitutions"]] %>% util_list_to_df2() %>% split(.$trait_name), + info = paste0(red(f), "\tconverting substitutions to a dataframe and splitting by `trait_name`") # Check + ) for (trait in names(x)) { + if (!is.null(definitions$elements[[trait]]) && definitions$elements[[trait]]$type == "categorical") { + to_check <- x[[trait]]$replace %>% unique() to_check <- to_check[!(grepl("^[YyNn]+$", to_check) & stringr::str_length(to_check) == 12)] allowable <- c(definitions$elements[[trait]]$allowed_values_levels %>% names(), NA) @@ -686,10 +750,8 @@ dataset_test_worker <- expect_length_zero( failing, info = sprintf( - "%s - substitutions for `%s` have invalid replacement values", - f, - trait - ), + "%s\tsubstitutions - `%s` has invalid replacement values", + red(f), trait), label = failing %>% paste(collapse = ", ") ) } @@ -698,22 +760,26 @@ dataset_test_worker <- ## Check config files contain all relevant columns if (metadata[["dataset"]][["data_is_long_format"]]) { - # Variable match - #expect_isin(names(metadata[["dataset"]]), c("taxon_name", "trait_name", "value","location_name", "individual_id", "context_name", "collection_date"), info=paste0(f, " - variable_match")) # For vertical datasets, expect all values of "trait column" found in traits var_out <- names(metadata[["dataset"]]) var_in <- unlist(metadata[["dataset"]]) i <- match("trait_name", var_out) values <- unique(data[[var_in[i]]]) - expect_contains(traits[["var_in"]], values, info = files[2]) + expect_contains( + traits[["var_in"]], values, + info = paste0(red(files[2]), "\ttraits") + ) + } else { - # Variable match - #expect_isin(names(metadata[["dataset"]]), c("taxon_name", "location_name", "individual_id", "context_name", "collection_date"), info=paste0(f, " - variable_match")) - # For wide datasets, expect variables in traits are header in the data + # For wide datasets, expect variables in traits are headers in the data values <- names(data) - expect_isin(traits[["var_in"]], values, info = files[2]) + expect_is_in( + traits[["var_in"]], values, + info = paste0(red(files[2]), "\ttraits"), label = "`var_in`" + ) + } @@ -727,49 +793,59 @@ dataset_test_worker <- ## For numeric trait data, check it looks reasonable & converts properly ## Check `location_name`'s are in locations dataset - if (length(unlist(metadata[["locations"]])) > 1) { + expect_true( !is.null(metadata[["dataset"]][["location_name"]]), - info = paste0(files[2], " - variable_match -> location_name is missing") + info = paste0(red(files[2]), "\tdataset - `location_name` is missing") ) expect_contains( names(data), metadata[["dataset"]][["location_name"]], - info = paste0(files[2], " - column ", metadata[["dataset"]][["location_name"]], "not found in data") + info = paste0( + red(files[2]), + "\tdataset - `location_name` column not found in data") ) v <- data[[metadata[["dataset"]][["location_name"]]]] %>% unique %>% na.omit i <- v %in% names(metadata$locations) - expect_true(all(i), - info = paste0(f, " - site names from data file not present in metadata: ", v[!i])) + expect_true( + all(i), + info = paste0( + red(f), + "\tlocations - location names from data file not present in metadata: ", + v[!i]) + ) i <- names(metadata$locations) %in% v - expect_true(all(i), - info = paste0( - f, - " - site names from metadata not present in data file: ", - names(metadata$locations)[!i] - )) + expect_true( + all(i), + info = paste0( + red(f), + "\tlocations - location names from metadata not present in data file: ", + names(metadata$locations)[!i]) + ) + } # Check that special characters do not make it into the data expect_no_error( parsed_data <- data %>% process_parse_data(dataset_id, metadata, contexts, schema), - info = sprintf("%s - `process_parse_data` has an error", dataset_id)) + info = sprintf("%s\t`process_parse_data`", red(dataset_id))) expect_allowed_text( parsed_data$traits$value, is_data = TRUE, - info = sprintf("%s", files[1]) + info = sprintf("%s", red(files[1])) ) expect_false( nrow(metadata[["traits"]] %>% util_list_to_df2() %>% dplyr::filter(!is.na(.data$trait_name))) == 0, - info = paste0(f, " - `traits` metadata only contains NA `trait_name`'s")) + info = paste0(red(f), "\ttraits - only contain NA `trait_name`'s")) if (nrow(metadata[["traits"]] %>% util_list_to_df2() %>% dplyr::filter(!is.na(.data$trait_name))) > 0) { + # Test build dataset expect_no_error( dataset <- test_build_dataset( @@ -782,14 +858,14 @@ dataset_test_worker <- get_schema("config/metadata.yml", "metadata"), read_csv_char("config/taxon_list.csv") ), - info = sprintf("%s - cannot build dataset", dataset_id)) + info = sprintf("%s\tbuilding dataset", red(dataset_id))) # Check that traits table is not empty - expect_false(nrow(dataset$traits) == 0, info = sprintf("%s - `traits` table is empty", dataset_id)) + expect_false(nrow(dataset$traits) == 0, info = sprintf("%s\t`traits` table is empty", red(dataset_id))) # Check that dataset can pivot wider if (nrow(dataset$traits) > 0) { - testthat::expect_equal( + expect_equal( dataset$traits %>% select( dplyr::all_of(c("dataset_id", "trait_name", "value", "observation_id", "value_type", @@ -805,7 +881,7 @@ dataset_test_worker <- filter(.data$number_of_duplicates > 1) %>% nrow(), 0, # Expect nrow() = 0 - info = sprintf("Duplicate rows in %s detected; `traits` table cannot pivot wider", dataset_id) + info = sprintf("%s\tduplicate rows detected; `traits` table cannot pivot wider", red(dataset_id)) ) } } diff --git a/man/dataset_test.Rd b/man/dataset_test.Rd index f21c0293..6317a675 100644 --- a/man/dataset_test.Rd +++ b/man/dataset_test.Rd @@ -8,7 +8,7 @@ dataset_test( dataset_ids, path_config = "config", path_data = "data", - reporter = testthat::default_reporter() + reporter = testthat::CompactProgressReporter ) } \arguments{ diff --git a/tests/testthat/functions.R b/tests/testthat/functions.R index 007fb864..79a0c89c 100644 --- a/tests/testthat/functions.R +++ b/tests/testthat/functions.R @@ -1,10 +1,7 @@ # Are these functions supposed to be the same as those in testdata.R? -# I think this function already exists in the package -# Better than expect_silent as contains `info` and allows for complete failures expect_no_error <- function(object, regexp = NULL, ..., info = NULL, label = NULL) { - error <- tryCatch({ object NULL @@ -28,8 +25,8 @@ expect_unique <- function(object, info = NULL, label = NULL) { invisible(object) } -# I think this already exists, with `testthat::expect_in`, should I remove and replace the others with this? -expect_isin <- function(object, expected, ..., info = NULL, label = NULL, + +expect_is_in <- function(object, expected, ..., info = NULL, label = NULL, expected.label = NULL, na.rm = TRUE) { if (na.rm) @@ -55,33 +52,33 @@ expect_not_NA <- function(object, info = NULL, label = NULL) { invisible(object) } -# This is easily replaced with expect_type right? -test_list <- function(data, info) { + +expect_list <- function(data, info) { expect_true(class(data) == "list", info = info) } -# Should these function names follow the expect_ syntax? -test_list_names_valid <- function(data, info) { - test_list(data, info) + +expect_list_names_valid <- function(data, info) { + expect_list(data, info) expect_not_NA(names(data), info = info) # expect_allowed_text(names(data), info = info) expect_unique(names(data), info = info) } -test_list_named <- function(data, expected_names, info) { - test_list_names_valid(data, info) +expect_named_list <- function(data, expected_names, info) { + expect_list_names_valid(data, info) expect_named(data, expected_names, info = info) } -test_list_named_contains <- function(data, expected_names, info) { - test_list_names_valid(data, info) - expect_isin(names(data), expected_names) +expect_list_names_contain <- function(data, expected_names, info) { + expect_list_names_valid(data, info) + expect_is_in(names(data), expected_names, info = info) } -test_dataframe_valid <- function(data, info) { +expect_dataframe_valid <- function(data, info) { expect_not_NA(colnames(data), info = info) # expect_allowed_text(colnames(data), info = info) expect_unique(colnames(data), info = info) @@ -89,10 +86,10 @@ test_dataframe_valid <- function(data, info) { } -test_dataframe_named <- function(data, expected_colnames, info) { +expect_dataframe_named <- function(data, expected_colnames, info) { # I think the ordering of naming currently matters, maybe we don't want that? # Affected by what order fields are entered into the metadata - test_dataframe_valid(data, info) + expect_dataframe_valid(data, info) expect_named(data, expected_colnames, info = info) } @@ -103,21 +100,22 @@ test_build_dataset <- function( # Test it builds with no errors expect_no_error({ build_config <- dataset_configure(path_metadata, definitions) - }, info = paste(info, "config")) + }, info = paste(info, "`dataset_configure`")) expect_no_error({ build_dataset_raw <- dataset_process(path_data, build_config, schema, resource_metadata, unit_conversions) - }, info = paste(info, "dataset_process")) + }, info = paste(info, "`dataset_process`")) expect_no_error({ build_dataset <- build_update_taxonomy(build_dataset_raw, taxon_list) - }, info = paste(info, "update taxonomy")) + }, info = paste(info, "`build_update_taxonomy`")) test_structure(build_dataset, info, schema, definitions, single_dataset = TRUE) build_dataset } + test_structure <- function( data, info, schema, definitions, single_dataset = TRUE) { @@ -131,26 +129,25 @@ test_structure <- function( # Test lists have the right objects comparison <- vars_austraits - test_list_named(data, comparison, info = c(info, " - main elements")) + expect_named_list(data, comparison, info = c(info, " - main elements")) # Test structure of tables for (v in vars_tables) { - comparison <- schema$austraits$elements[[v]]$elements %>% names() - - test_dataframe_named(data[[v]], comparison, info = paste(info, "- structure of", v)) + expect_dataframe_named(data[[v]], comparison, info = paste(info, "- structure of", v)) } # Contains allowed traits - expect_isin(data$traits$trait_name %>% unique(), definitions$elements %>% names(), info = paste("traits ", v)) + expect_is_in(data$traits$trait_name %>% unique(), definitions$elements %>% names(), info = paste("traits ", v)) } -## a helper function to determine if this is being run as part of a test + +## A helper function to determine if this is being run as part of a test is_testing_env <- function() { # Calling scope tb <- .traceback(x = 0) - # Check if called in testthat or interactive + # Check if called in `testthat` or interactive if (any(unlist(lapply(tb, function(x) any(grepl("test_env", x)))))) { return(TRUE) } else { diff --git a/tests/testthat/test-setup.R b/tests/testthat/test-setup.R index d13cdfea..bb2e353d 100644 --- a/tests/testthat/test-setup.R +++ b/tests/testthat/test-setup.R @@ -722,7 +722,7 @@ test_that("reports and plots are produced", { testthat::test_that("`dataset_test` is working", { # Expect error if no `dataset_ids` argument is input - expect_output(expect_error(dataset_test())) + expect_error(dataset_test()) expect_silent( out <- dataset_test("Test_2022", reporter = testthat::SilentReporter)) expect_in( From c2c1b59da38734b392d7ec6221d730465951d32f Mon Sep 17 00:00:00 2001 From: Elizabeth Wenk Date: Wed, 1 Nov 2023 10:11:06 +1100 Subject: [PATCH 09/31] Taxonomy documention & edits (#111) * Update `build_update_taxonomy` A much more simplified version of `build_update_taxonomy` has now been implemented which only requires three columns of information from `taxon_list.csv` - `taxon_name` (accepted name or other "best practise" name), `cleaned_name` (name following taxonomic updates in the metadata file), and `taxon_rank` of the taxon name. Other columns, such as `genus`, `family`, `taxon_id`, `scientific_name`, etc. must be present in the `taxon_list.csv` file to later appear in the database$taxa table. That means, much of the code that used to be part of `build_update_taxonomy` will now reside in a function `build_taxon_list` that must be tailored to each database and stored within that databases' R/ folder. The version that will compile the austraits.build database will be available in the coming weeks. All taxon_ranks should now be lowercase and in English: phylum, class, order, family. genus, species, subspecies, variety, form * Rework tests to accommodate new `build_update_taxonomy` scheme --- R/process.R | 159 ++------ inst/support/report_dataset.Rmd | 21 +- tests/testthat/config/taxon_list-orig.csv | 16 +- .../examples/Test_2023_1/metadata.yml | 3 + .../examples/Test_2023_1/output/taxa.csv | 90 ++--- .../Test_2023_1/output/taxonomic_updates.csv | 92 ++--- .../examples/Test_2023_2/metadata.yml | 3 + .../examples/Test_2023_2/output/taxa.csv | 92 ++--- .../Test_2023_2/output/taxonomic_updates.csv | 92 ++--- .../examples/Test_2023_3/metadata.yml | 150 +++---- .../examples/Test_2023_3/output/taxa.csv | 372 ++++++++--------- .../Test_2023_3/output/taxonomic_updates.csv | 376 +++++++++--------- .../examples/Test_2023_4/metadata.yml | 150 +++---- .../examples/Test_2023_4/output/taxa.csv | 376 +++++++++--------- .../Test_2023_4/output/taxonomic_updates.csv | 376 +++++++++--------- .../examples/Test_2023_5/metadata.yml | 3 + .../examples/Test_2023_7/output/taxa.csv | 6 +- .../Test_2023_7/output/taxonomic_updates.csv | 6 +- .../examples/Test_2023_8/output/taxa.csv | 6 +- .../Test_2023_8/output/taxonomic_updates.csv | 6 +- tests/testthat/functions.R | 6 +- tests/testthat/test-setup.R | 19 +- tests/testthat/test-xamples.R | 4 +- 23 files changed, 1180 insertions(+), 1244 deletions(-) diff --git a/R/process.R b/R/process.R index b8044b50..d7f209c2 100644 --- a/R/process.R +++ b/R/process.R @@ -1723,7 +1723,7 @@ process_taxonomic_updates <- function(data, metadata) { # Copy original species name to a new column out[["original_name"]] <- out[["taxon_name"]] - # Create a column for `taxnomic_resolution` + # Create a column for `taxonomic_resolution` out[["taxonomic_resolution"]] <- NA_character_ # Now make any replacements specified in metadata yaml @@ -1845,164 +1845,77 @@ build_combine <- function(..., d = list(...)) { #' @export build_update_taxonomy <- function(austraits_raw, taxa) { + columns_in_taxon_list <- names(taxa) + + # incoming table from austraits_raw is a list of all taxa for the study + # `original_name` and `cleaned_name` will be different if + # there were taxonomic_updates specified in metadata file austraits_raw$taxonomic_updates <- austraits_raw$taxonomic_updates %>% dplyr::left_join( by = "cleaned_name", taxa %>% dplyr::select( - dplyr::all_of(c("cleaned_name", "cleaned_scientific_name_id", "cleaned_name_taxonomic_status", - "cleaned_name_alternative_taxonomic_status", "taxon_id", "taxon_name", "taxon_rank"))) - ) %>% - dplyr::mutate( - taxonomic_resolution = ifelse( - !is.na(.data$taxonomic_resolution) & .data$taxonomic_resolution != .data$taxon_rank, - .data$taxon_rank, .data$taxonomic_resolution - ), - taxonomic_resolution = ifelse( - is.na(.data$taxonomic_resolution), - .data$taxon_rank, .data$taxonomic_resolution - ) - ) %>% + dplyr::all_of(c("cleaned_name", "taxon_name")) + )) %>% dplyr::distinct() %>% - dplyr::select(-dplyr::all_of(c("taxon_rank"))) %>% dplyr::arrange(.data$cleaned_name) - austraits_raw$traits <- austraits_raw$traits %>% dplyr::rename(dplyr::all_of(c("cleaned_name" = "taxon_name"))) %>% dplyr::left_join(by = "cleaned_name", - taxa %>% dplyr::select(dplyr::all_of(c("cleaned_name", "taxon_name", "taxon_rank"))) + taxa %>% dplyr::select(dplyr::all_of(c("cleaned_name", "taxon_name"))) ) %>% dplyr::select(dplyr::all_of(c("dataset_id", "taxon_name")), dplyr::everything()) %>% + # for taxa where there is no taxon_name to matched to a "cleaned_name", maintain the "cleaned_name" as the "taxon_name" dplyr::mutate( - taxon_name = ifelse(is.na(.data$taxon_name), .data$cleaned_name, .data$taxon_name), - taxon_name = ifelse(stringr::str_detect(.data$cleaned_name, "\\["), .data$cleaned_name, .data$taxon_name) + taxon_name = ifelse(is.na(.data$taxon_name), .data$cleaned_name, .data$taxon_name)#, ) %>% dplyr::select(-dplyr::all_of(c("cleaned_name"))) -# Names, identifiers for all genera - genera_tmp <- taxa %>% - dplyr::filter(.data$taxon_rank %in% c("Genus", "genus")) %>% - dplyr::select(dplyr::all_of(c("taxon_name", "family", "taxonomic_reference", "taxon_id", - "scientific_name_id", "taxonomic_status"))) %>% - dplyr::rename(dplyr::all_of(c( - "name_to_match_to" = "taxon_name", "taxonomic_reference_genus" = "taxonomic_reference", - "taxon_id_genus" = "taxon_id", "scientific_name_id_genus" = "scientific_name_id", - "taxonomic_status_genus" = "taxonomic_status" - ))) %>% - dplyr::distinct() - -# Names, identifiers for all families in APC - families_tmp <- taxa %>% - dplyr::filter(.data$taxon_rank %in% c("Familia", "family")) %>% - dplyr::select( - dplyr::all_of( - c(name_to_match_to = "taxon_name", taxonomic_reference_family = "taxonomic_reference", - taxon_id_family = "taxon_id", scientific_name_id_family = "scientific_name_id", - taxonomic_status_family = "taxonomic_status") - )) %>% - dplyr::distinct() - -### Fill in columns for trinomial, binomial, genus, and family, as appropriate - # and match additional taxon information to the most specific name - species_tmp <- austraits_raw$traits %>% dplyr::select(dplyr::all_of(c("taxon_name", "taxonomic_resolution"))) %>% dplyr::distinct() %>% util_df_convert_character() %>% - dplyr::left_join( - by = "taxon_name", - taxa %>% dplyr::select(dplyr::all_of(c("taxon_name", "taxon_rank", "family"))) %>% - dplyr::distinct() %>% util_df_convert_character() - ) - - - species_tmp <- species_tmp %>% dplyr::mutate( - # If no taxonomic resolution is specified, then the name's taxonomic resolution - # is the taxon_rank for the taxon name + # If no taxonomic resolution is specified from taxonomic_updates, + # then the name's taxonomic resolution is the taxon_rank for the taxon name. taxonomic_resolution = ifelse( .data$taxon_name %in% taxa$cleaned_name, taxa$taxon_rank[match(.data$taxon_name, taxa$cleaned_name)], .data$taxonomic_resolution), - taxon_rank = ifelse(!is.na(.data$taxon_rank), .data$taxonomic_resolution, .data$taxon_rank), - # Field trinomial is only filled in if taxonomic resolution is an infraspecific name - trinomial = ifelse(.data$taxon_rank %in% c("Subspecies", "Forma", "Varietas"), - stringr::str_split_fixed(.data$taxon_name, "\\[", 2)[, 1] %>% stringr::str_trim(), NA), - # Field binomial is filled in if taxonomic resolution is an infraspecific name or a binomial - # All taxon names that have "extra" information (beyond the actual name) have been formatted - # to have that information in square brackets '[]', so these can be used as a delimitor to - # extract the actual name - binomial = ifelse(.data$taxon_rank %in% c("Species"), - stringr::str_split_fixed(.data$taxon_name, "\\[", 2)[, 1] %>% stringr::str_trim(), NA), - binomial = ifelse(.data$taxon_rank %in% c("Subspecies", "Forma", "Varietas", "Series"), - stringr::word(.data$taxon_name, start = 1, end = 2), .data$binomial), - binomial = stringr::str_trim(.data$binomial), - # Genus filled in for all names that have a taxonomic of genus or more detailed - genus = ifelse( - !.data$taxon_rank %in% c("Familia", "family"), - ifelse(stringr::word(.data$taxon_name, 1) == "x", - stringr::word(.data$taxon_name, start = 1, end = 2), - stringr::word(.data$taxon_name, 1)), - NA), - family = ifelse(.data$taxon_rank %in% c("Familia", "family"), stringr::word(.data$taxon_name, 1), .data$family), - # Identify which name is to be matched to the various identifiers, distribution information, etc. in the taxa file - name_to_match_to = ifelse(.data$taxon_rank %in% c("Subspecies", "Forma", "Varietas"), .data$trinomial, NA), - name_to_match_to = ifelse( - is.na(.data$name_to_match_to) & .data$taxon_rank %in% c("Species"), - .data$binomial, .data$name_to_match_to), - name_to_match_to = ifelse( - is.na(.data$name_to_match_to) & .data$taxon_rank %in% c("genus", "Genus"), - .data$genus, .data$name_to_match_to), - name_to_match_to = ifelse( - is.na(.data$name_to_match_to) & is.na(.data$taxon_rank), - .data$genus, .data$name_to_match_to), - name_to_match_to = ifelse( - is.na(.data$name_to_match_to) & .data$taxon_rank %in% c("family", "Familia"), - .data$family, .data$name_to_match_to) - ) %>% - # Remove family, taxon_rank; they are about to be merged back in, but matches will now be possible to more rows - select(-dplyr::all_of(c("taxon_rank", "taxonomic_resolution"))) %>% - dplyr::rename("family_tmp" = "family") %>% - util_df_convert_character() %>% - # Merge in all data from taxa - dplyr::left_join(by = c("name_to_match_to" = "taxon_name"), - taxa %>% dplyr::select(-dplyr::contains("clean")) %>% dplyr::distinct() %>% util_df_convert_character() - ) %>% - dplyr::arrange(.data$taxon_name) %>% - # Merge in identifiers for genera & families - dplyr::left_join(by = c("name_to_match_to", "family"), genera_tmp) %>% - dplyr::left_join(by = "name_to_match_to", families_tmp) %>% - dplyr::mutate( - taxonomic_status = ifelse(.data$taxon_rank %in% c("Genus", "genus"), .data$taxonomic_status_genus, .data$taxonomic_status), - taxonomic_status = ifelse(.data$taxon_rank %in% c("Familia", "family"), .data$taxonomic_status_family, .data$taxonomic_status), - taxonomic_reference = ifelse(.data$taxon_rank %in% c("Genus", "genus"), .data$taxonomic_reference_genus, .data$taxonomic_reference), - taxonomic_reference = ifelse(.data$taxon_rank %in% c("Familia", "family"), .data$taxonomic_reference_family, .data$taxonomic_reference), - taxon_id = ifelse(.data$taxon_rank %in% c("Genus", "genus"), .data$taxon_id_genus, .data$taxon_id), - taxon_id = ifelse(.data$taxon_rank %in% c("Familia", "family"), .data$taxon_id_family, .data$taxon_id), - scientific_name_id = ifelse(.data$taxon_rank %in% c("Genus", "genus"), .data$scientific_name_id_genus, .data$scientific_name_id), - scientific_name_id = ifelse(.data$taxon_rank %in% c("Familia", "family"), .data$scientific_name_id_family, .data$scientific_name_id), - taxon_distribution = ifelse(.data$taxon_rank %in% c("Familia", "family", "Genus", "genus"), NA, .data$taxon_distribution), - establishment_means = ifelse(.data$taxon_rank %in% c("Familia", "family", "Genus", "genus"), NA, .data$establishment_means) - ) %>% - dplyr::select(dplyr::all_of(c("taxon_name", "taxonomic_reference", "taxon_rank", "trinomial", "binomial", - "genus", "family", "taxon_distribution", "establishment_means", - "taxonomic_status", "scientific_name", "scientific_name_authorship", "taxon_id", - "scientific_name_id"))) + taxon_rank = .data$taxonomic_resolution, + name_to_match_to = taxon_name, + # Create variable `name_to_match_to` which specifies the part of the taxon name to which matches can be made. + # This step requires taxon_rank. + name_to_match_to = stringr::str_replace(taxon_name, " \\[.+",""), + name_to_match_to = ifelse(!taxon_rank %in% c("species", "subspecies", "series", "variety", "form"), + stringr::word(taxon_name,1), name_to_match_to) + ) %>% + # Remove taxon_rank, as it is about to be merged back in, but matches will now be possible to more rows. + select(-dplyr::any_of(c("taxon_rank", "taxonomic_resolution"))) %>% + util_df_convert_character() %>% + # Merge in all data from taxa. + dplyr::left_join(by = c("taxon_name"), + taxa %>% dplyr::select(-dplyr::any_of(dplyr::contains("clean"))) %>% + dplyr::distinct(taxon_name, .keep_all = TRUE) %>% + util_df_convert_character() + ) %>% + dplyr::arrange(.data$taxon_name) %>% + dplyr::select(-dplyr::any_of(c("name_to_match_to"))) austraits_raw$taxa <- species_tmp %>% dplyr::bind_rows() %>% dplyr::arrange(.data$taxon_name) %>% - dplyr::distinct(.data$taxon_name, .keep_all = TRUE) - - # Only now, at the very end, can `taxonomic_resolution` be removed from the traits table + dplyr::distinct(.data$taxon_name, .keep_all = TRUE) %>% + dplyr::select(dplyr::any_of(columns_in_taxon_list)) + # Now `taxonomic_resolution` be removed from the traits table. austraits_raw$traits <- austraits_raw$traits %>% - dplyr::select(-dplyr::all_of(c("taxonomic_resolution", "taxon_rank"))) + dplyr::select(-dplyr::all_of(c("taxonomic_resolution"))) austraits_raw$excluded_data <- austraits_raw$excluded_data %>% diff --git a/inst/support/report_dataset.Rmd b/inst/support/report_dataset.Rmd index baccdc9f..bbb286ff 100644 --- a/inst/support/report_dataset.Rmd +++ b/inst/support/report_dataset.Rmd @@ -735,13 +735,16 @@ schema$austraits$elements$taxa$elements %>% Clicking on the name will take you to the relevant taxonomic record in the APC or APNI, where known: ```{r taxon_list2, results='asis', echo=FALSE} +taxa_columns <- names(data_study$taxa) + tmp <- data_study$taxa %>% select(one_of(names(schema$austraits$elements$taxa$elements))) if (nrow(tmp) < 10000) { tmp %>% mutate( - taxon_name = as_link(taxon_id, taxon_name)) %>% + taxon_name = ifelse("taxon_id" %in% taxa_columns, as_link(taxon_id, taxon_name), taxon_name) + ) %>% mutate(across(everything(), ~replace_na(.x, replace = ""))) %>% my_kable_styling() } else { @@ -761,13 +764,18 @@ To create the list of aligned taxa, we needed to make some taxonomic changes. Th Links on `cleaned_name` and `taxon_name` take you to the APC or APNI record for that name. ```{r} +taxa_columns <- names(data_study$taxa) + data_study$taxonomic_updates %>% select(-dataset_id) %>% filter(original_name != taxon_name) %>% mutate( + taxon_id = ifelse("taxon_id" %in% taxa_columns, data_study$taxa$taxon_id[match(taxon_name, data_study$taxa$taxon_name)], NA), + cleaned_name_taxonomic_status = ifelse("cleaned_name_taxonomic_status" %in% taxa_columns, cleaned_name_taxonomic_status, NA), + cleaned_name_alternative_taxonomic_status = ifelse("cleaned_name_alternative_taxonomic_status" %in% taxa_columns, cleaned_name_alternative_taxonomic_status, ""), d1 = purrr::map2_dbl(original_name, cleaned_name, ~adist(.x, .y)) %>% as.character() %>% str_replace("0", ""), d2 = purrr::map2_dbl(taxon_name, cleaned_name, ~adist(.x, .y)) %>% as.character() %>% str_replace("0", ""), - cleaned_name = as_link(cleaned_scientific_name_id, cleaned_name), - taxon_name = as_link(taxon_id, taxon_name), + cleaned_name = ifelse("cleaned_scientific_name_id" %in% taxa_columns, as_link(cleaned_scientific_name_id, cleaned_name), cleaned_name), + taxon_name = ifelse("taxon_id" %in% taxa_columns, as_link(taxon_id, taxon_name), taxon_name), cleaned_name_alternative_taxonomic_status = replace_na(cleaned_name_alternative_taxonomic_status, ""), `status cleaned name` = sprintf( "%s %s", cleaned_name_taxonomic_status, @@ -787,8 +795,13 @@ We were unable to find taxonomic matches for the following taxa in the data. Whe ```{r taxa_list3, results='asis', echo=FALSE} data_study$taxa %>% filter(is.na(taxon_id)) %>% + mutate( + genus = ifelse("genus" %in% taxa_columns, genus, NA), + binomial = ifelse("binomial" %in% taxa_columns, binomial, NA), + trinomial = ifelse("trinomial" %in% taxa_columns, trinomial, NA), + ) %>% select(one_of(names(schema$austraits$elements$taxa$elements))) %>% - select(-taxon_id, -scientific_name_id, -taxon_distribution, -establishment_means) %>% + dplyr::select(-dplyr::any_of(c("taxon_id", "scientific_name_id", "taxon_distribution", "establishment_means"))) %>% mutate(across(everything(), ~replace_na(.x, replace = ""))) %>% my_kable_styling() ``` diff --git a/tests/testthat/config/taxon_list-orig.csv b/tests/testthat/config/taxon_list-orig.csv index cd2622d4..7c050c58 100644 --- a/tests/testthat/config/taxon_list-orig.csv +++ b/tests/testthat/config/taxon_list-orig.csv @@ -1,8 +1,8 @@ -cleaned_name,taxonomic_reference,cleaned_scientific_name_id,cleaned_name_taxonomic_status,cleaned_name_alternative_taxonomic_status,taxon_name,taxon_id,scientific_name_authorship,taxon_rank,taxonomic_status,family,taxon_distribution,establishment_means,scientific_name,scientific_name_id -Acacia celsa,APC,https://id.biodiversity.org.au/name/apni/154988,accepted,NA,Acacia celsa,https://id.biodiversity.org.au/taxon/apni/51436506,Tindale,Species,accepted,Fabaceae,Qld,native,Acacia celsa Tindale,https://id.biodiversity.org.au/name/apni/154988 -Acronychia acidula,APC,https://id.biodiversity.org.au/name/apni/73794,accepted,NA,Acronychia acidula,https://id.biodiversity.org.au/node/apni/2913200,F.Muell.,Species,accepted,Rutaceae,Qld,native,Acronychia acidula F.Muell.,https://id.biodiversity.org.au/name/apni/73794 -Alphitonia petriei,APC,https://id.biodiversity.org.au/name/apni/82935,accepted,NA,Alphitonia petriei,https://id.biodiversity.org.au/node/apni/2887911,Braid & C.T.White,Species,accepted,Rhamnaceae,"Qld, NSW",native,Alphitonia petriei Braid & C.T.White,https://id.biodiversity.org.au/name/apni/82935 -Euodia elleryana,APC,https://id.biodiversity.org.au/name/apni/68475,nomenclatural synonym,NA,Melicope elleryana,https://id.biodiversity.org.au/node/apni/2913641,(F.Muell.) T.G.Hartley,Species,accepted,Rutaceae,"WA, NT, Qld, NSW",native,Melicope elleryana (F.Muell.) T.G.Hartley,https://id.biodiversity.org.au/name/apni/118560 -Evodiella muelleri,APC,https://id.biodiversity.org.au/name/apni/87175,taxonomic synonym,NA,Melicope elleryana,https://id.biodiversity.org.au/node/apni/2913641,(F.Muell.) T.G.Hartley,Species,accepted,Rutaceae,"WA, NT, Qld, NSW",native,Melicope elleryana (F.Muell.) T.G.Hartley,https://id.biodiversity.org.au/name/apni/118560 -Glochidion hylandii,APC,https://id.biodiversity.org.au/name/apni/78303,accepted,NA,Glochidion hylandii,https://id.biodiversity.org.au/node/apni/2889113,Airy Shaw,Species,accepted,Phyllanthaceae,Qld,native,Glochidion hylandii Airy Shaw,https://id.biodiversity.org.au/name/apni/78303 -Melicope elleryana,APC,https://id.biodiversity.org.au/name/apni/118560,accepted,NA,Melicope elleryana,https://id.biodiversity.org.au/node/apni/2913641,(F.Muell.) T.G.Hartley,Species,accepted,Rutaceae,"WA, NT, Qld, NSW",native,Melicope elleryana (F.Muell.) T.G.Hartley,https://id.biodiversity.org.au/name/apni/118560 +cleaned_name,taxon_name,taxonomic_reference,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution +Acacia celsa,Acacia celsa,APC,species,accepted,Acacia,Acacia celsa,,Fabaceae,https://id.biodiversity.org.au/taxon/apni/51436506,Qld +Acronychia acidula,Acronychia acidula,APC,species,accepted,Acronychia,Acronychia acidula,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913200,Qld +Alphitonia petriei,Alphitonia petriei,APC,species,accepted,Alphitonia,Alphitonia petriei,,Rhamnaceae,https://id.biodiversity.org.au/node/apni/2887911,"Qld, NSW" +Euodia elleryana,Melicope elleryana,APC,species,accepted,Melicope,Melicope elleryana,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913641,"WA, NT, Qld, NSW" +Evodiella muelleri,Melicope elleryana,APC,species,accepted,Melicope,Melicope elleryana,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913641,"WA, NT, Qld, NSW" +Glochidion hylandii,Glochidion hylandii,APC,species,accepted,Glochidion,Glochidion hylandii,,Phyllanthaceae,https://id.biodiversity.org.au/node/apni/2889113,Qld +Melicope elleryana,Melicope elleryana,APC,species,accepted,Melicope,Melicope elleryana,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913641,"WA, NT, Qld, NSW" diff --git a/tests/testthat/examples/Test_2023_1/metadata.yml b/tests/testthat/examples/Test_2023_1/metadata.yml index b87e9b1d..2f564f99 100644 --- a/tests/testthat/examples/Test_2023_1/metadata.yml +++ b/tests/testthat/examples/Test_2023_1/metadata.yml @@ -539,12 +539,15 @@ taxonomic_updates: - find: Homalanthus novoguineensis replace: Homalanthus novo-guineensis reason: Change spelling to align with known name in APC (Daniel Falster, 2020.05.22) + taxonomic_resolution: species - find: Haplostichanthus sp Coop. Ck replace: Haplostichanthus submontanus reason: Align previous phrase name with current APC name (E. Wenk, 2020-05-25) + taxonomic_resolution: species - find: Psychotria sp Utchee Creek replace: Psychotria sp. Utchee Creek (H.Flecker NQNC5313) reason: Align to name in APC (D Falster, 2020.05.23) + taxonomic_resolution: species exclude_observations: - variable: taxon_name find: Syzygium gustavioides diff --git a/tests/testthat/examples/Test_2023_1/output/taxa.csv b/tests/testthat/examples/Test_2023_1/output/taxa.csv index 6e5a7c6b..4c45bc9b 100644 --- a/tests/testthat/examples/Test_2023_1/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_1/output/taxa.csv @@ -1,45 +1,45 @@ -taxon_name,taxonomic_reference,taxon_rank,trinomial,binomial,genus,family,taxon_distribution,establishment_means,taxonomic_status,scientific_name,scientific_name_authorship,taxon_id,scientific_name_id -Acacia celsa,APC,Species,,Acacia celsa,Acacia,Fabaceae,Qld,native,accepted,Acacia celsa Tindale,Tindale,https://id.biodiversity.org.au/taxon/apni/51436506,https://id.biodiversity.org.au/name/apni/154988 -Acmena graveolens,,,,,Acmena,,,,,,,, -Acronychia acidula,APC,Species,,Acronychia acidula,Acronychia,Rutaceae,Qld,native,accepted,Acronychia acidula F.Muell.,F.Muell.,https://id.biodiversity.org.au/node/apni/2913200,https://id.biodiversity.org.au/name/apni/73794 -Aleurites rockinghamensis,,,,,Aleurites,,,,,,,, -Alphitonia petriei,APC,Species,,Alphitonia petriei,Alphitonia,Rhamnaceae,"Qld, NSW",native,accepted,Alphitonia petriei Braid & C.T.White,Braid & C.T.White,https://id.biodiversity.org.au/node/apni/2887911,https://id.biodiversity.org.au/name/apni/82935 -Alstonia scholaris,,,,,Alstonia,,,,,,,, -Argyrodendron peralatum,,,,,Argyrodendron,,,,,,,, -Atractocarpus hirtus,,,,,Atractocarpus,,,,,,,, -Brombya platynema,,,,,Brombya,,,,,,,, -Cardwellia sublimis,,,,,Cardwellia,,,,,,,, -Castanospermum australe,,,,,Castanospermum,,,,,,,, -Cleistanthus myrianthus,,,,,Cleistanthus,,,,,,,, -Cryptocarya laevigata,,,,,Cryptocarya,,,,,,,, -Cryptocarya mackinnoniana,,,,,Cryptocarya,,,,,,,, -Cryptocarya murrayi,,,,,Cryptocarya,,,,,,,, -Dendrocnide moroides,,,,,Dendrocnide,,,,,,,, -Elaeocarpus grandis,,,,,Elaeocarpus,,,,,,,, -Endiandra leptodendron,,,,,Endiandra,,,,,,,, -Endiandra microneura,,,,,Endiandra,,,,,,,, -Gillbeea adenopetala,,,,,Gillbeea,,,,,,,, -Glochidion hylandii,APC,Species,,Glochidion hylandii,Glochidion,Phyllanthaceae,Qld,native,accepted,Glochidion hylandii Airy Shaw,Airy Shaw,https://id.biodiversity.org.au/node/apni/2889113,https://id.biodiversity.org.au/name/apni/78303 -Haplostichanthus submontanus,,,,,Haplostichanthus,,,,,,,, -Harpullia rhyticarpa,,,,,Harpullia,,,,,,,, -Hernandia albiflora,,,,,Hernandia,,,,,,,, -Homalanthus novo-guineensis,,,,,Homalanthus,,,,,,,, -Ixora biflora,,,,,Ixora,,,,,,,, -Lasianthus strigosus,,,,,Lasianthus,,,,,,,, -Litsea leefeana,,,,,Litsea,,,,,,,, -Macaranga tanarius,,,,,Macaranga,,,,,,,, -Mallotus mollissimus,,,,,Mallotus,,,,,,,, -Medicosma sessiliflora,,,,,Medicosma,,,,,,,, -Melastoma cyanoides,,,,,Melastoma,,,,,,,, -Melicope elleryana,APC,Species,,Melicope elleryana,Melicope,Rutaceae,"WA, NT, Qld, NSW",native,accepted,Melicope elleryana (F.Muell.) T.G.Hartley,(F.Muell.) T.G.Hartley,https://id.biodiversity.org.au/node/apni/2913641,https://id.biodiversity.org.au/name/apni/118560 -Myristica insipida,,,,,Myristica,,,,,,,, -Neolitsea dealbata,,,,,Neolitsea,,,,,,,, -Pittosporum rubiginosum,,,,,Pittosporum,,,,,,,, -Polyscias australiana,,,,,Polyscias,,,,,,,, -Psychotria dallachiana,,,,,Psychotria,,,,,,,, -Psychotria sp. Utchee Creek (H.Flecker NQNC5313),,,,,Psychotria,,,,,,,, -Quassia baileyana,,,,,Quassia,,,,,,,, -Rhodomyrtus trineura,,,,,Rhodomyrtus,,,,,,,, -Rockinghamia angustifolia,,,,,Rockinghamia,,,,,,,, -Syzygium sayeri,,,,,Syzygium,,,,,,,, -Trema aspera,,,,,Trema,,,,,,,, +taxon_name,taxonomic_reference,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution +Acacia celsa,APC,species,accepted,Acacia,Acacia celsa,,Fabaceae,https://id.biodiversity.org.au/taxon/apni/51436506,Qld +Acmena graveolens,,,,,,,,, +Acronychia acidula,APC,species,accepted,Acronychia,Acronychia acidula,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913200,Qld +Aleurites rockinghamensis,,,,,,,,, +Alphitonia petriei,APC,species,accepted,Alphitonia,Alphitonia petriei,,Rhamnaceae,https://id.biodiversity.org.au/node/apni/2887911,"Qld, NSW" +Alstonia scholaris,,,,,,,,, +Argyrodendron peralatum,,,,,,,,, +Atractocarpus hirtus,,,,,,,,, +Brombya platynema,,,,,,,,, +Cardwellia sublimis,,,,,,,,, +Castanospermum australe,,,,,,,,, +Cleistanthus myrianthus,,,,,,,,, +Cryptocarya laevigata,,,,,,,,, +Cryptocarya mackinnoniana,,,,,,,,, +Cryptocarya murrayi,,,,,,,,, +Dendrocnide moroides,,,,,,,,, +Elaeocarpus grandis,,,,,,,,, +Endiandra leptodendron,,,,,,,,, +Endiandra microneura,,,,,,,,, +Gillbeea adenopetala,,,,,,,,, +Glochidion hylandii,APC,species,accepted,Glochidion,Glochidion hylandii,,Phyllanthaceae,https://id.biodiversity.org.au/node/apni/2889113,Qld +Haplostichanthus submontanus,,,,,,,,, +Harpullia rhyticarpa,,,,,,,,, +Hernandia albiflora,,,,,,,,, +Homalanthus novo-guineensis,,,,,,,,, +Ixora biflora,,,,,,,,, +Lasianthus strigosus,,,,,,,,, +Litsea leefeana,,,,,,,,, +Macaranga tanarius,,,,,,,,, +Mallotus mollissimus,,,,,,,,, +Medicosma sessiliflora,,,,,,,,, +Melastoma cyanoides,,,,,,,,, +Melicope elleryana,APC,species,accepted,Melicope,Melicope elleryana,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913641,"WA, NT, Qld, NSW" +Myristica insipida,,,,,,,,, +Neolitsea dealbata,,,,,,,,, +Pittosporum rubiginosum,,,,,,,,, +Polyscias australiana,,,,,,,,, +Psychotria dallachiana,,,,,,,,, +Psychotria sp. Utchee Creek (H.Flecker NQNC5313),,,,,,,,, +Quassia baileyana,,,,,,,,, +Rhodomyrtus trineura,,,,,,,,, +Rockinghamia angustifolia,,,,,,,,, +Syzygium sayeri,,,,,,,,, +Trema aspera,,,,,,,,, diff --git a/tests/testthat/examples/Test_2023_1/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_1/output/taxonomic_updates.csv index c80d5126..16b9b357 100644 --- a/tests/testthat/examples/Test_2023_1/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_1/output/taxonomic_updates.csv @@ -1,46 +1,46 @@ -dataset_id,original_name,cleaned_name,taxonomic_resolution,cleaned_scientific_name_id,cleaned_name_taxonomic_status,cleaned_name_alternative_taxonomic_status,taxon_id,taxon_name -Test_2023_1,Acacia celsa,Acacia celsa,Species,https://id.biodiversity.org.au/name/apni/154988,accepted,,https://id.biodiversity.org.au/taxon/apni/51436506,Acacia celsa -Test_2023_1,Acmena graveolens,Acmena graveolens,,,,,, -Test_2023_1,Acronychia acidula,Acronychia acidula,Species,https://id.biodiversity.org.au/name/apni/73794,accepted,,https://id.biodiversity.org.au/node/apni/2913200,Acronychia acidula -Test_2023_1,Aleurites rockinghamensis,Aleurites rockinghamensis,,,,,, -Test_2023_1,Alphitonia petriei,Alphitonia petriei,Species,https://id.biodiversity.org.au/name/apni/82935,accepted,,https://id.biodiversity.org.au/node/apni/2887911,Alphitonia petriei -Test_2023_1,Alstonia scholaris,Alstonia scholaris,,,,,, -Test_2023_1,Argyrodendron peralatum,Argyrodendron peralatum,,,,,, -Test_2023_1,Atractocarpus hirtus,Atractocarpus hirtus,,,,,, -Test_2023_1,Brombya platynema,Brombya platynema,,,,,, -Test_2023_1,Cardwellia sublimis,Cardwellia sublimis,,,,,, -Test_2023_1,Castanospermum australe,Castanospermum australe,,,,,, -Test_2023_1,Cleistanthus myrianthus,Cleistanthus myrianthus,,,,,, -Test_2023_1,Cryptocarya laevigata,Cryptocarya laevigata,,,,,, -Test_2023_1,Cryptocarya mackinnoniana,Cryptocarya mackinnoniana,,,,,, -Test_2023_1,Cryptocarya murrayi,Cryptocarya murrayi,,,,,, -Test_2023_1,Dendrocnide moroides,Dendrocnide moroides,,,,,, -Test_2023_1,Elaeocarpus grandis,Elaeocarpus grandis,,,,,, -Test_2023_1,Endiandra leptodendron,Endiandra leptodendron,,,,,, -Test_2023_1,Endiandra microneura,Endiandra microneura,,,,,, -Test_2023_1,Gillbeea adenopetala,Gillbeea adenopetala,,,,,, -Test_2023_1,Glochidion hylandii,Glochidion hylandii,Species,https://id.biodiversity.org.au/name/apni/78303,accepted,,https://id.biodiversity.org.au/node/apni/2889113,Glochidion hylandii -Test_2023_1,Haplostichanthus sp Coop. Ck,Haplostichanthus submontanus,,,,,, -Test_2023_1,Harpullia rhyticarpa,Harpullia rhyticarpa,,,,,, -Test_2023_1,Hernandia albiflora,Hernandia albiflora,,,,,, -Test_2023_1,Homalanthus novoguineensis,Homalanthus novo-guineensis,,,,,, -Test_2023_1,Ixora biflora,Ixora biflora,,,,,, -Test_2023_1,Lasianthus strigosus,Lasianthus strigosus,,,,,, -Test_2023_1,Litsea leefeana,Litsea leefeana,,,,,, -Test_2023_1,Macaranga tanarius,Macaranga tanarius,,,,,, -Test_2023_1,Mallotus mollissimus,Mallotus mollissimus,,,,,, -Test_2023_1,Medicosma sessiliflora,Medicosma sessiliflora,,,,,, -Test_2023_1,Melastoma cyanoides,Melastoma cyanoides,,,,,, -Test_2023_1,Melicope elleryana,Melicope elleryana,Species,https://id.biodiversity.org.au/name/apni/118560,accepted,,https://id.biodiversity.org.au/node/apni/2913641,Melicope elleryana -Test_2023_1,Myristica insipida,Myristica insipida,,,,,, -Test_2023_1,Neolitsea dealbata,Neolitsea dealbata,,,,,, -Test_2023_1,Pittosporum rubiginosum,Pittosporum rubiginosum,,,,,, -Test_2023_1,Polyscias australiana,Polyscias australiana,,,,,, -Test_2023_1,Psychotria dallachiana,Psychotria dallachiana,,,,,, -Test_2023_1,Psychotria sp Utchee Creek,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),,,,,, -Test_2023_1,Quassia baileyana,Quassia baileyana,,,,,, -Test_2023_1,Rhodomyrtus trineura,Rhodomyrtus trineura,,,,,, -Test_2023_1,Rockinghamia angustifolia,Rockinghamia angustifolia,,,,,, -Test_2023_1,Syzygium gustavioides,Syzygium gustavioides,,,,,, -Test_2023_1,Syzygium sayeri,Syzygium sayeri,,,,,, -Test_2023_1,Trema aspera,Trema aspera,,,,,, +dataset_id,original_name,cleaned_name,taxonomic_resolution,taxon_name +Test_2023_1,Acacia celsa,Acacia celsa,,Acacia celsa +Test_2023_1,Acmena graveolens,Acmena graveolens,, +Test_2023_1,Acronychia acidula,Acronychia acidula,,Acronychia acidula +Test_2023_1,Aleurites rockinghamensis,Aleurites rockinghamensis,, +Test_2023_1,Alphitonia petriei,Alphitonia petriei,,Alphitonia petriei +Test_2023_1,Alstonia scholaris,Alstonia scholaris,, +Test_2023_1,Argyrodendron peralatum,Argyrodendron peralatum,, +Test_2023_1,Atractocarpus hirtus,Atractocarpus hirtus,, +Test_2023_1,Brombya platynema,Brombya platynema,, +Test_2023_1,Cardwellia sublimis,Cardwellia sublimis,, +Test_2023_1,Castanospermum australe,Castanospermum australe,, +Test_2023_1,Cleistanthus myrianthus,Cleistanthus myrianthus,, +Test_2023_1,Cryptocarya laevigata,Cryptocarya laevigata,, +Test_2023_1,Cryptocarya mackinnoniana,Cryptocarya mackinnoniana,, +Test_2023_1,Cryptocarya murrayi,Cryptocarya murrayi,, +Test_2023_1,Dendrocnide moroides,Dendrocnide moroides,, +Test_2023_1,Elaeocarpus grandis,Elaeocarpus grandis,, +Test_2023_1,Endiandra leptodendron,Endiandra leptodendron,, +Test_2023_1,Endiandra microneura,Endiandra microneura,, +Test_2023_1,Gillbeea adenopetala,Gillbeea adenopetala,, +Test_2023_1,Glochidion hylandii,Glochidion hylandii,,Glochidion hylandii +Test_2023_1,Haplostichanthus sp Coop. Ck,Haplostichanthus submontanus,species, +Test_2023_1,Harpullia rhyticarpa,Harpullia rhyticarpa,, +Test_2023_1,Hernandia albiflora,Hernandia albiflora,, +Test_2023_1,Homalanthus novoguineensis,Homalanthus novo-guineensis,species, +Test_2023_1,Ixora biflora,Ixora biflora,, +Test_2023_1,Lasianthus strigosus,Lasianthus strigosus,, +Test_2023_1,Litsea leefeana,Litsea leefeana,, +Test_2023_1,Macaranga tanarius,Macaranga tanarius,, +Test_2023_1,Mallotus mollissimus,Mallotus mollissimus,, +Test_2023_1,Medicosma sessiliflora,Medicosma sessiliflora,, +Test_2023_1,Melastoma cyanoides,Melastoma cyanoides,, +Test_2023_1,Melicope elleryana,Melicope elleryana,,Melicope elleryana +Test_2023_1,Myristica insipida,Myristica insipida,, +Test_2023_1,Neolitsea dealbata,Neolitsea dealbata,, +Test_2023_1,Pittosporum rubiginosum,Pittosporum rubiginosum,, +Test_2023_1,Polyscias australiana,Polyscias australiana,, +Test_2023_1,Psychotria dallachiana,Psychotria dallachiana,, +Test_2023_1,Psychotria sp Utchee Creek,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),species, +Test_2023_1,Quassia baileyana,Quassia baileyana,, +Test_2023_1,Rhodomyrtus trineura,Rhodomyrtus trineura,, +Test_2023_1,Rockinghamia angustifolia,Rockinghamia angustifolia,, +Test_2023_1,Syzygium gustavioides,Syzygium gustavioides,, +Test_2023_1,Syzygium sayeri,Syzygium sayeri,, +Test_2023_1,Trema aspera,Trema aspera,, diff --git a/tests/testthat/examples/Test_2023_2/metadata.yml b/tests/testthat/examples/Test_2023_2/metadata.yml index 0fdccb92..297767dd 100644 --- a/tests/testthat/examples/Test_2023_2/metadata.yml +++ b/tests/testthat/examples/Test_2023_2/metadata.yml @@ -343,11 +343,14 @@ taxonomic_updates: - find: Homalanthus novoguineensis replace: Homalanthus novo-guineensis reason: Change spelling to align with known name in APC (Daniel Falster, 2020.05.22) + taxonomic_resolution: species - find: Haplostichanthus sp Coop. Ck replace: Haplostichanthus submontanus reason: Align previous phrase name with current APC name (E. Wenk, 2020-05-25) + taxonomic_resolution: species - find: Psychotria sp Utchee Creek replace: Psychotria sp. Utchee Creek (H.Flecker NQNC5313) reason: Align to name in APC (D Falster, 2020.05.23) + taxonomic_resolution: species exclude_observations: .na questions: .na diff --git a/tests/testthat/examples/Test_2023_2/output/taxa.csv b/tests/testthat/examples/Test_2023_2/output/taxa.csv index f141e5cb..7bd9228b 100644 --- a/tests/testthat/examples/Test_2023_2/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_2/output/taxa.csv @@ -1,46 +1,46 @@ -taxon_name,taxonomic_reference,taxon_rank,trinomial,binomial,genus,family,taxon_distribution,establishment_means,taxonomic_status,scientific_name,scientific_name_authorship,taxon_id,scientific_name_id -Acacia celsa,APC,Species,,Acacia celsa,Acacia,Fabaceae,Qld,native,accepted,Acacia celsa Tindale,Tindale,https://id.biodiversity.org.au/taxon/apni/51436506,https://id.biodiversity.org.au/name/apni/154988 -Acmena graveolens,,,,,Acmena,,,,,,,, -Acronychia acidula,APC,Species,,Acronychia acidula,Acronychia,Rutaceae,Qld,native,accepted,Acronychia acidula F.Muell.,F.Muell.,https://id.biodiversity.org.au/node/apni/2913200,https://id.biodiversity.org.au/name/apni/73794 -Aleurites rockinghamensis,,,,,Aleurites,,,,,,,, -Alphitonia petriei,APC,Species,,Alphitonia petriei,Alphitonia,Rhamnaceae,"Qld, NSW",native,accepted,Alphitonia petriei Braid & C.T.White,Braid & C.T.White,https://id.biodiversity.org.au/node/apni/2887911,https://id.biodiversity.org.au/name/apni/82935 -Alstonia scholaris,,,,,Alstonia,,,,,,,, -Argyrodendron peralatum,,,,,Argyrodendron,,,,,,,, -Atractocarpus hirtus,,,,,Atractocarpus,,,,,,,, -Brombya platynema,,,,,Brombya,,,,,,,, -Cardwellia sublimis,,,,,Cardwellia,,,,,,,, -Castanospermum australe,,,,,Castanospermum,,,,,,,, -Cleistanthus myrianthus,,,,,Cleistanthus,,,,,,,, -Cryptocarya laevigata,,,,,Cryptocarya,,,,,,,, -Cryptocarya mackinnoniana,,,,,Cryptocarya,,,,,,,, -Cryptocarya murrayi,,,,,Cryptocarya,,,,,,,, -Dendrocnide moroides,,,,,Dendrocnide,,,,,,,, -Elaeocarpus grandis,,,,,Elaeocarpus,,,,,,,, -Endiandra leptodendron,,,,,Endiandra,,,,,,,, -Endiandra microneura,,,,,Endiandra,,,,,,,, -Gillbeea adenopetala,,,,,Gillbeea,,,,,,,, -Glochidion hylandii,APC,Species,,Glochidion hylandii,Glochidion,Phyllanthaceae,Qld,native,accepted,Glochidion hylandii Airy Shaw,Airy Shaw,https://id.biodiversity.org.au/node/apni/2889113,https://id.biodiversity.org.au/name/apni/78303 -Haplostichanthus submontanus,,,,,Haplostichanthus,,,,,,,, -Harpullia rhyticarpa,,,,,Harpullia,,,,,,,, -Hernandia albiflora,,,,,Hernandia,,,,,,,, -Homalanthus novo-guineensis,,,,,Homalanthus,,,,,,,, -Ixora biflora,,,,,Ixora,,,,,,,, -Lasianthus strigosus,,,,,Lasianthus,,,,,,,, -Litsea leefeana,,,,,Litsea,,,,,,,, -Macaranga tanarius,,,,,Macaranga,,,,,,,, -Mallotus mollissimus,,,,,Mallotus,,,,,,,, -Medicosma sessiliflora,,,,,Medicosma,,,,,,,, -Melastoma cyanoides,,,,,Melastoma,,,,,,,, -Melicope elleryana,APC,Species,,Melicope elleryana,Melicope,Rutaceae,"WA, NT, Qld, NSW",native,accepted,Melicope elleryana (F.Muell.) T.G.Hartley,(F.Muell.) T.G.Hartley,https://id.biodiversity.org.au/node/apni/2913641,https://id.biodiversity.org.au/name/apni/118560 -Myristica insipida,,,,,Myristica,,,,,,,, -Neolitsea dealbata,,,,,Neolitsea,,,,,,,, -Pittosporum rubiginosum,,,,,Pittosporum,,,,,,,, -Polyscias australiana,,,,,Polyscias,,,,,,,, -Psychotria dallachiana,,,,,Psychotria,,,,,,,, -Psychotria sp. Utchee Creek (H.Flecker NQNC5313),,,,,Psychotria,,,,,,,, -Quassia baileyana,,,,,Quassia,,,,,,,, -Rhodomyrtus trineura,,,,,Rhodomyrtus,,,,,,,, -Rockinghamia angustifolia,,,,,Rockinghamia,,,,,,,, -Syzygium gustavioides,,,,,Syzygium,,,,,,,, -Syzygium sayeri,,,,,Syzygium,,,,,,,, -Trema aspera,,,,,Trema,,,,,,,, +taxon_name,taxonomic_reference,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution +Acacia celsa,APC,species,accepted,Acacia,Acacia celsa,,Fabaceae,https://id.biodiversity.org.au/taxon/apni/51436506,Qld +Acmena graveolens,,,,,,,,, +Acronychia acidula,APC,species,accepted,Acronychia,Acronychia acidula,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913200,Qld +Aleurites rockinghamensis,,,,,,,,, +Alphitonia petriei,APC,species,accepted,Alphitonia,Alphitonia petriei,,Rhamnaceae,https://id.biodiversity.org.au/node/apni/2887911,"Qld, NSW" +Alstonia scholaris,,,,,,,,, +Argyrodendron peralatum,,,,,,,,, +Atractocarpus hirtus,,,,,,,,, +Brombya platynema,,,,,,,,, +Cardwellia sublimis,,,,,,,,, +Castanospermum australe,,,,,,,,, +Cleistanthus myrianthus,,,,,,,,, +Cryptocarya laevigata,,,,,,,,, +Cryptocarya mackinnoniana,,,,,,,,, +Cryptocarya murrayi,,,,,,,,, +Dendrocnide moroides,,,,,,,,, +Elaeocarpus grandis,,,,,,,,, +Endiandra leptodendron,,,,,,,,, +Endiandra microneura,,,,,,,,, +Gillbeea adenopetala,,,,,,,,, +Glochidion hylandii,APC,species,accepted,Glochidion,Glochidion hylandii,,Phyllanthaceae,https://id.biodiversity.org.au/node/apni/2889113,Qld +Haplostichanthus submontanus,,,,,,,,, +Harpullia rhyticarpa,,,,,,,,, +Hernandia albiflora,,,,,,,,, +Homalanthus novo-guineensis,,,,,,,,, +Ixora biflora,,,,,,,,, +Lasianthus strigosus,,,,,,,,, +Litsea leefeana,,,,,,,,, +Macaranga tanarius,,,,,,,,, +Mallotus mollissimus,,,,,,,,, +Medicosma sessiliflora,,,,,,,,, +Melastoma cyanoides,,,,,,,,, +Melicope elleryana,APC,species,accepted,Melicope,Melicope elleryana,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913641,"WA, NT, Qld, NSW" +Myristica insipida,,,,,,,,, +Neolitsea dealbata,,,,,,,,, +Pittosporum rubiginosum,,,,,,,,, +Polyscias australiana,,,,,,,,, +Psychotria dallachiana,,,,,,,,, +Psychotria sp. Utchee Creek (H.Flecker NQNC5313),,,,,,,,, +Quassia baileyana,,,,,,,,, +Rhodomyrtus trineura,,,,,,,,, +Rockinghamia angustifolia,,,,,,,,, +Syzygium gustavioides,,,,,,,,, +Syzygium sayeri,,,,,,,,, +Trema aspera,,,,,,,,, diff --git a/tests/testthat/examples/Test_2023_2/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_2/output/taxonomic_updates.csv index 6a717ef1..288fcdf1 100644 --- a/tests/testthat/examples/Test_2023_2/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_2/output/taxonomic_updates.csv @@ -1,46 +1,46 @@ -dataset_id,original_name,cleaned_name,taxonomic_resolution,cleaned_scientific_name_id,cleaned_name_taxonomic_status,cleaned_name_alternative_taxonomic_status,taxon_id,taxon_name -Test_2023_2,Acacia celsa,Acacia celsa,Species,https://id.biodiversity.org.au/name/apni/154988,accepted,,https://id.biodiversity.org.au/taxon/apni/51436506,Acacia celsa -Test_2023_2,Acmena graveolens,Acmena graveolens,,,,,, -Test_2023_2,Acronychia acidula,Acronychia acidula,Species,https://id.biodiversity.org.au/name/apni/73794,accepted,,https://id.biodiversity.org.au/node/apni/2913200,Acronychia acidula -Test_2023_2,Aleurites rockinghamensis,Aleurites rockinghamensis,,,,,, -Test_2023_2,Alphitonia petriei,Alphitonia petriei,Species,https://id.biodiversity.org.au/name/apni/82935,accepted,,https://id.biodiversity.org.au/node/apni/2887911,Alphitonia petriei -Test_2023_2,Alstonia scholaris,Alstonia scholaris,,,,,, -Test_2023_2,Argyrodendron peralatum,Argyrodendron peralatum,,,,,, -Test_2023_2,Atractocarpus hirtus,Atractocarpus hirtus,,,,,, -Test_2023_2,Brombya platynema,Brombya platynema,,,,,, -Test_2023_2,Cardwellia sublimis,Cardwellia sublimis,,,,,, -Test_2023_2,Castanospermum australe,Castanospermum australe,,,,,, -Test_2023_2,Cleistanthus myrianthus,Cleistanthus myrianthus,,,,,, -Test_2023_2,Cryptocarya laevigata,Cryptocarya laevigata,,,,,, -Test_2023_2,Cryptocarya mackinnoniana,Cryptocarya mackinnoniana,,,,,, -Test_2023_2,Cryptocarya murrayi,Cryptocarya murrayi,,,,,, -Test_2023_2,Dendrocnide moroides,Dendrocnide moroides,,,,,, -Test_2023_2,Elaeocarpus grandis,Elaeocarpus grandis,,,,,, -Test_2023_2,Endiandra leptodendron,Endiandra leptodendron,,,,,, -Test_2023_2,Endiandra microneura,Endiandra microneura,,,,,, -Test_2023_2,Gillbeea adenopetala,Gillbeea adenopetala,,,,,, -Test_2023_2,Glochidion hylandii,Glochidion hylandii,Species,https://id.biodiversity.org.au/name/apni/78303,accepted,,https://id.biodiversity.org.au/node/apni/2889113,Glochidion hylandii -Test_2023_2,Haplostichanthus sp Coop. Ck,Haplostichanthus submontanus,,,,,, -Test_2023_2,Harpullia rhyticarpa,Harpullia rhyticarpa,,,,,, -Test_2023_2,Hernandia albiflora,Hernandia albiflora,,,,,, -Test_2023_2,Homalanthus novoguineensis,Homalanthus novo-guineensis,,,,,, -Test_2023_2,Ixora biflora,Ixora biflora,,,,,, -Test_2023_2,Lasianthus strigosus,Lasianthus strigosus,,,,,, -Test_2023_2,Litsea leefeana,Litsea leefeana,,,,,, -Test_2023_2,Macaranga tanarius,Macaranga tanarius,,,,,, -Test_2023_2,Mallotus mollissimus,Mallotus mollissimus,,,,,, -Test_2023_2,Medicosma sessiliflora,Medicosma sessiliflora,,,,,, -Test_2023_2,Melastoma cyanoides,Melastoma cyanoides,,,,,, -Test_2023_2,Melicope elleryana,Melicope elleryana,Species,https://id.biodiversity.org.au/name/apni/118560,accepted,,https://id.biodiversity.org.au/node/apni/2913641,Melicope elleryana -Test_2023_2,Myristica insipida,Myristica insipida,,,,,, -Test_2023_2,Neolitsea dealbata,Neolitsea dealbata,,,,,, -Test_2023_2,Pittosporum rubiginosum,Pittosporum rubiginosum,,,,,, -Test_2023_2,Polyscias australiana,Polyscias australiana,,,,,, -Test_2023_2,Psychotria dallachiana,Psychotria dallachiana,,,,,, -Test_2023_2,Psychotria sp Utchee Creek,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),,,,,, -Test_2023_2,Quassia baileyana,Quassia baileyana,,,,,, -Test_2023_2,Rhodomyrtus trineura,Rhodomyrtus trineura,,,,,, -Test_2023_2,Rockinghamia angustifolia,Rockinghamia angustifolia,,,,,, -Test_2023_2,Syzygium gustavioides,Syzygium gustavioides,,,,,, -Test_2023_2,Syzygium sayeri,Syzygium sayeri,,,,,, -Test_2023_2,Trema aspera,Trema aspera,,,,,, +dataset_id,original_name,cleaned_name,taxonomic_resolution,taxon_name +Test_2023_2,Acacia celsa,Acacia celsa,,Acacia celsa +Test_2023_2,Acmena graveolens,Acmena graveolens,, +Test_2023_2,Acronychia acidula,Acronychia acidula,,Acronychia acidula +Test_2023_2,Aleurites rockinghamensis,Aleurites rockinghamensis,, +Test_2023_2,Alphitonia petriei,Alphitonia petriei,,Alphitonia petriei +Test_2023_2,Alstonia scholaris,Alstonia scholaris,, +Test_2023_2,Argyrodendron peralatum,Argyrodendron peralatum,, +Test_2023_2,Atractocarpus hirtus,Atractocarpus hirtus,, +Test_2023_2,Brombya platynema,Brombya platynema,, +Test_2023_2,Cardwellia sublimis,Cardwellia sublimis,, +Test_2023_2,Castanospermum australe,Castanospermum australe,, +Test_2023_2,Cleistanthus myrianthus,Cleistanthus myrianthus,, +Test_2023_2,Cryptocarya laevigata,Cryptocarya laevigata,, +Test_2023_2,Cryptocarya mackinnoniana,Cryptocarya mackinnoniana,, +Test_2023_2,Cryptocarya murrayi,Cryptocarya murrayi,, +Test_2023_2,Dendrocnide moroides,Dendrocnide moroides,, +Test_2023_2,Elaeocarpus grandis,Elaeocarpus grandis,, +Test_2023_2,Endiandra leptodendron,Endiandra leptodendron,, +Test_2023_2,Endiandra microneura,Endiandra microneura,, +Test_2023_2,Gillbeea adenopetala,Gillbeea adenopetala,, +Test_2023_2,Glochidion hylandii,Glochidion hylandii,,Glochidion hylandii +Test_2023_2,Haplostichanthus sp Coop. Ck,Haplostichanthus submontanus,species, +Test_2023_2,Harpullia rhyticarpa,Harpullia rhyticarpa,, +Test_2023_2,Hernandia albiflora,Hernandia albiflora,, +Test_2023_2,Homalanthus novoguineensis,Homalanthus novo-guineensis,species, +Test_2023_2,Ixora biflora,Ixora biflora,, +Test_2023_2,Lasianthus strigosus,Lasianthus strigosus,, +Test_2023_2,Litsea leefeana,Litsea leefeana,, +Test_2023_2,Macaranga tanarius,Macaranga tanarius,, +Test_2023_2,Mallotus mollissimus,Mallotus mollissimus,, +Test_2023_2,Medicosma sessiliflora,Medicosma sessiliflora,, +Test_2023_2,Melastoma cyanoides,Melastoma cyanoides,, +Test_2023_2,Melicope elleryana,Melicope elleryana,,Melicope elleryana +Test_2023_2,Myristica insipida,Myristica insipida,, +Test_2023_2,Neolitsea dealbata,Neolitsea dealbata,, +Test_2023_2,Pittosporum rubiginosum,Pittosporum rubiginosum,, +Test_2023_2,Polyscias australiana,Polyscias australiana,, +Test_2023_2,Psychotria dallachiana,Psychotria dallachiana,, +Test_2023_2,Psychotria sp Utchee Creek,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),species, +Test_2023_2,Quassia baileyana,Quassia baileyana,, +Test_2023_2,Rhodomyrtus trineura,Rhodomyrtus trineura,, +Test_2023_2,Rockinghamia angustifolia,Rockinghamia angustifolia,, +Test_2023_2,Syzygium gustavioides,Syzygium gustavioides,, +Test_2023_2,Syzygium sayeri,Syzygium sayeri,, +Test_2023_2,Trema aspera,Trema aspera,, diff --git a/tests/testthat/examples/Test_2023_3/metadata.yml b/tests/testthat/examples/Test_2023_3/metadata.yml index 52082a50..15313841 100644 --- a/tests/testthat/examples/Test_2023_3/metadata.yml +++ b/tests/testthat/examples/Test_2023_3/metadata.yml @@ -232,23 +232,23 @@ taxonomic_updates: replace: Acaena x anserovina reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Acaena ovina replace: Acaena x ovina reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Acaena sp. Thredbo River Gorge (L.A.S.Johnson ;amp; E.F.Constable s.n., 19 Jan 1951) replace: Acaena sp. Thredbo River Gorge (L.A.S.Johnson & E.F.Constable s.n., 19 Jan 1951) reason: match_10_fuzzy. Imprecise fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Alstonia constricta f. Pubescent form replace: Alstonia constricta Pubescent form reason: match_08. Automatic alignment with synonymous name in APNI (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Arthropteris beckleri x tenella replace: Arthropteris x [Arthropteris beckleri x tenella; NHNSW_2022] reason: match_11. Rewording hybrid species name not in APC or APNI to indicate a @@ -258,52 +258,52 @@ taxonomic_updates: replace: Atriplex sp. B reason: match_19. Automatic alignment with species-level canonical name in APNI when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Banksia spinulosa var. collina-spinulosa intergrade replace: Banksia spinulosa var. collina reason: match_12. Automatic alignment with infraspecific canonical name in APC accepted when notes are ignored (2022-11-22) - taxonomic_resolution: Varietas + taxonomic_resolution: variety - find: Bertya tasmanica variant ;qu;Glabrous ovary;qu; replace: Bertya tasmanica var. Glabrous ovary (T.A.James 527 & M.J.Taylor) reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: Varietas + taxonomic_resolution: variety - find: Blechnum fullagarii replace: Blechnum fullagari reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Caladenia sp. A sensu Harden (1993) replace: Caladenia sp. A reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Centaurea sp. A sensu Murray (1992) replace: Centaurea sp. A reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Cephalomanes atrovirens subsp. atrovirens replace: Cephalomanes atrovirens reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Choretrum sp. Coxs Gap (B.J.Lepschi 4218 ;amp; T.R.Lally) replace: Choretrum sp. Coxs Gap (B.J.Lepschi 4218 & T.R.Lally) reason: match_10_fuzzy. Imprecise fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Cipadessa baccifera replace: Cipadessa baccifera reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Crocosmia crocosmiiflora replace: Crocosmia x crocosmiiflora reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Cyperus bowmannii replace: Cyperus bowmanni reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Cyperus sp. Stockton (K.L.Wilson 10541) replace: Cyperus sp. [Cyperus sp. Stockton (K.L.Wilson 10541); NHNSW_2022] reason: match_20. Rewording name to be recognised as genus rank, with genus accepted @@ -312,75 +312,75 @@ taxonomic_updates: - find: Dillwynia sp. Ebor (P.C.Jobson 5318 ;amp; S.A.Mills) replace: Dillwynia sp. Ebor (P.C.Jobson 5318 & S.A.Mills) reason: match_17_fuzzy. Imprecise fuzzy alignment with canonical name in APNI (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Epidendrum radicans x secundum hybrid complex replace: Epidendrum radicans x Epidendrum secundum reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Eriochilus cucullatus complex replace: Eriochilus cucullatus reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Eucalyptus conjuncta replace: Eucalyptus x conjuncta reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Eucalyptus dealbata subsp. dealbata replace: Eucalyptus dealbata var. dealbata reason: match_06. Automatic alignment with synonymous term among known canonical names APC (2022-11-21) - taxonomic_resolution: Varietas + taxonomic_resolution: variety - find: Flacourtia sp. shiptons flat l w jessup gj.d3200 replace: Flacourtia sp. Shiptons Flat (L.W.Jessup+ GJD3200) reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Genoplesium cuspidatum replace: Genoplesium sp. Cuspidata (L.M.Copeland 3858) reason: match_15_fuzzy. Fuzzy match alignment with species-level canonical name in `APC known` when everything except first 2 words ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Genoplesium sp. Charmhaven (NSW896673) replace: Genoplesium sp. Charmhaven (NSW 896673) reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Glycine pacifica replace: Glycine pacifica (Grace 946) reason: match_19. Automatic alignment with species-level canonical name in APNI when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Hibbertia sp. B sensu Harden (1990) replace: Hibbertia sp. B reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Hibbertia stricta subsp. stricta replace: Hibbertia stricta var. stricta reason: match_06. Automatic alignment with synonymous term among known canonical names APC (2022-11-21) - taxonomic_resolution: Varietas + taxonomic_resolution: variety - find: Hoffmannseggia glauca replace: Hoffmannseggia glauca reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Houttuynia cordata replace: Houttuynia cordata reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Impatiens balfouri replace: Impatiens balfourii reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Kunzea capitata subsp. capitata replace: Kunzea capitata var. capitata reason: match_06. Automatic alignment with synonymous term among known canonical names APC (2022-11-21) - taxonomic_resolution: Varietas + taxonomic_resolution: variety - find: Lenwebbia sp. Main Range (P.R.Sharpe 4877) replace: Lenwebbia sp. Main Range (P.R.Sharpe+ 4877) reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Lepidium sp. Cooma (J.H.Maiden NSW642748) replace: Lepidium sp. [Lepidium sp. Cooma (J.H.Maiden NSW642748); NHNSW_2022] reason: match_20. Rewording name to be recognised as genus rank, with genus accepted @@ -390,34 +390,34 @@ taxonomic_updates: replace: Leucopogon lanceolatus reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Luzula densiflora subsp. densiflora replace: Luzula densiflora reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Luzula flaccida subsp. flaccida replace: Leucas flaccida var. flaccida reason: match_10_fuzzy. Imprecise fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: Varietas + taxonomic_resolution: variety - find: Margyricarpus pinnatus replace: Margyricarpus pinnatus reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Muehlenbeckia diclina subsp. Gippsland (R.O.Makinson 1007) Makinson replace: Muehlenbeckia diclina subsp. Gippsland (R.O.Makinson 1007) reason: match_05. Automatic alignment with scientific name in APC accepted list (2022-11-21) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Muehlenbeckia diclina subsp. Pooncarie (W.E. Mulham W811) replace: Muehlenbeckia diclina subsp. Pooncarie (W.E.Mulham W811) reason: match_08. Automatic alignment with synonymous name in APNI (2022-11-21) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Myosotis laxa subsp. caespitosa replace: Myosotis laxa subsp. cespitosa reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Netrostylis sp. East Coast (D.E. Albrecht 597) replace: Netrostylis sp. [Netrostylis sp. East Coast (D.E. Albrecht 597); NHNSW_2022] reason: match_20. Rewording name to be recognised as genus rank, with genus in APNI @@ -427,7 +427,7 @@ taxonomic_updates: replace: Notelaea sp. A reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Opuntia sp. sensu I.Telford (1984) replace: Opuntia sp. [Opuntia sp. sensu I.Telford (1984); NHNSW_2022] reason: match_20. Rewording name to be recognised as genus rank, with genus accepted @@ -437,165 +437,165 @@ taxonomic_updates: replace: Owenia x reliqua reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Pelargonium asperum replace: Pelargonium x asperum reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Pimelea neo-anglica replace: Pimelea neoanglica reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Polyscias sambucifolia subsp. Long leaflets (P.G.Neish 208) Vic. Herbarium replace: Polyscias sambucifolia subsp. Long leaflets (P.G.Neish 208) reason: match_05. Automatic alignment with scientific name in APC accepted list (2022-11-21) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Pomaderris andromedifolia f. ;qu;andromedifolia;qu; replace: Pomaderris andromedifolia subsp. andromedifolia reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Pomaderris andromedifolia f. ;qu;narrow-leaved;qu; replace: Pomaderris andromedifolia f. 'narrow-leaved' reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: Forma + taxonomic_resolution: form - find: Pomaderris andromedifolia f. ;qu;small-leaved;qu; replace: Pomaderris andromedifolia subsp. andromedifolia reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Potamogeton tricarinatus auct. non F.Muell. ;amp; A.Benn. ex A.Benn. replace: Potamogeton tricarinatus reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Prasophyllum sp. A sensu Harden (1993) replace: Prasophyllum sp. A reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Pultenaea sp. Dingo Creek (M.A.M.Renner 9176 ;amp; J.M.Cohen) replace: Pultenaea sp. Dingo Creek (M.A.M.Renner 9176 & J.M.Cohen) reason: match_17_fuzzy. Imprecise fuzzy alignment with canonical name in APNI (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Pultenaea sp. Narrabri (R.G.Coveny 8811 ;amp; S.K.Roy) replace: Pultenaea sp. (Narrabri R.G.Coveny+ 8811) reason: match_12. Automatic alignment with infraspecific canonical name in APC known names when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Pultenaea sp. Newnes (I.R.Telford 5072 ;amp; M.D.Crisp) replace: Pultenaea sp. Newnes (I.R.Telford 5072 & M.D.Crisp) reason: match_17_fuzzy. Imprecise fuzzy alignment with canonical name in APNI (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Pultenaea sp. Shadowgraph Bluff (T. ;amp; J.Whaite 3455) replace: Pultenaea sp. Shadowgraph Bluff (T. & J.Whaite 3455) reason: match_17_fuzzy. Imprecise fuzzy alignment with canonical name in APNI (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Quassia sp. Moonee Creek (King s.n., Nov 1949) replace: Quassia sp. 'Moonee Creek' (King s.n., Nov 1949) reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Radermachera sinica replace: Radermachera sinica reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Rotheca myricoides subsp. myricoides replace: Rotheca myricoides reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Rubus loganobaccus replace: Rubus loganubaccus reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Salix matsudana x alba replace: Salix matsudana x Salix alba reason: Manual alignment with canonical hybrid species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Salix x fragilis var. fragilis replace: Salix x fragilis reason: Manual alignment with canonical hybrid species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Salix x sepulcralis var. chrysocoma replace: Salix x sepulcralis reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Salix x sepulcralis var. sepulcralis replace: Salix x sepulcralis reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Varietas + taxonomic_resolution: variety - find: Salvinia molesta replace: Salvinia x molesta reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Sarcocornia quinqueflora subsp. quinqueflora replace: Salicornia quinqueflora subsp. quinqueflora reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Scleranthus sp. Fitz;qu;s Hill (J.G.West 5342) replace: Scleranthus sp. Fitz's Hill (J.G.West 5342) reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Sebaea zeyheri subsp. cleistantha replace: Sebaea zeyheri reason: match_19. Automatic alignment with species-level canonical name in APNI when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Sida sp. B sensu Harden (1990) replace: Sida sp. B reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Sida sp. C sensu Harden (1990) replace: Sida sp. C reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Sorghum almum replace: Sorghum x almum reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Sorghum bicolor subsp. almum replace: Sorghum bicolor subsp. x almum reason: match_08. Automatic alignment with synonymous name in APNI (2022-11-22) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Sorghum bicolor subsp. drummondii replace: Sorghum bicolor subsp. x drummondii reason: match_12. Automatic alignment with infraspecific canonical name in APC known names when notes are ignored (2022-11-22) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Spiraea x billiardii replace: Spiraea x billardii reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Suaeda sp. A sensu Harden (1990) replace: Suaeda sp. A reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Teucrium sp. D sensu Conn (1992) replace: Teucrium sp. D Flora of New South Wales (S.A.Horton 4114) reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Thelymitra irregularis replace: Thelymitra x irregularis reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Thelymitra merraniae replace: Thelymitra merranae reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Thelymitra truncata replace: Thelymitra x truncata reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: X Triticosecale replace: x Triticosecale reason: Manual matched to genus for taxon that can't be matched to species (Elizabeth diff --git a/tests/testthat/examples/Test_2023_3/output/taxa.csv b/tests/testthat/examples/Test_2023_3/output/taxa.csv index 5b99552e..aaf603ba 100644 --- a/tests/testthat/examples/Test_2023_3/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_3/output/taxa.csv @@ -1,186 +1,186 @@ -taxon_name,taxonomic_reference,taxon_rank,trinomial,binomial,genus,family,taxon_distribution,establishment_means,taxonomic_status,scientific_name,scientific_name_authorship,taxon_id,scientific_name_id -Abildgaardia ovata,,,,,Abildgaardia,,,,,,,, -Acacia alpina,,,,,Acacia,,,,,,,, -Acacia beadleana,,,,,Acacia,,,,,,,, -Acacia bulgaensis,,,,,Acacia,,,,,,,, -Acacia caroleae,,,,,Acacia,,,,,,,, -Acacia crassa,,,,,Acacia,,,,,,,, -Acacia flexifolia,,,,,Acacia,,,,,,,, -Acacia gladiiformis,,,,,Acacia,,,,,,,, -Acacia havilandiorum,,,,,Acacia,,,,,,,, -Acacia leiocalyx subsp. leiocalyx,,,,,Acacia,,,,,,,, -Acacia myrtifolia,,,,,Acacia,,,,,,,, -Acacia ramulosa var. ramulosa,,,,,Acacia,,,,,,,, -Acacia spectabilis,,,,,Acacia,,,,,,,, -Acacia terminalis subsp. Glabrous form (M.Hancock 94),,,,,Acacia,,,,,,,, -Acronychia littoralis,,,,,Acronychia,,,,,,,, -Adriana tomentosa,,,,,Adriana,,,,,,,, -Alectryon coriaceus,,,,,Alectryon,,,,,,,, -Alectryon oleifolius,,,,,Alectryon,,,,,,,, -Alectryon subdentatus,,,,,Alectryon,,,,,,,, -Amyema preissii,,,,,Amyema,,,,,,,, -Angophora leiocarpa,,,,,Angophora,,,,,,,, -Apophyllum anomalum,,,,,Apophyllum,,,,,,,, -Arbutus unedo,,,,,Arbutus,,,,,,,, -Australina pusilla,,,,,Australina,,,,,,,, -Burmannia disticha,,,,,Burmannia,,,,,,,, -Bursaria spinosa subsp. spinosa,,,,,Bursaria,,,,,,,, -Calendula arvensis,,,,,Calendula,,,,,,,, -Callistemon purpurascens,,,,,Callistemon,,,,,,,, -Carex cephalotes,,,,,Carex,,,,,,,, -Carex leporina,,,,,Carex,,,,,,,, -Carex raleighii,,,,,Carex,,,,,,,, -Carmichaelia exsul,,,,,Carmichaelia,,,,,,,, -Cassinia compacta,,,,,Cassinia,,,,,,,, -Castanospermum australe,,,,,Castanospermum,,,,,,,, -Centaurium tenuiflorum,,,,,Centaurium,,,,,,,, -Cestrum nocturnum,,,,,Cestrum,,,,,,,, -Chthonocephalus pseudevax,,,,,Chthonocephalus,,,,,,,, -Claoxylon australe,,,,,Claoxylon,,,,,,,, -Commersonia amystia,,,,,Commersonia,,,,,,,, -Commersonia salviifolia,,,,,Commersonia,,,,,,,, -Convolvulus farinosus,,,,,Convolvulus,,,,,,,, -Coprosma niphophila,,,,,Coprosma,,,,,,,, -Coprosma nivalis,,,,,Coprosma,,,,,,,, -Correa alba,,,,,Correa,,,,,,,, -Corymbia citriodora,,,,,Corymbia,,,,,,,, -Corymbia eximia,,,,,Corymbia,,,,,,,, -Crassula decumbens,,,,,Crassula,,,,,,,, -Crassula peduncularis,,,,,Crassula,,,,,,,, -Crotalaria brevis,,,,,Crotalaria,,,,,,,, -Crotalaria grahamiana,,,,,Crotalaria,,,,,,,, -Crotalaria lanceolata,,,,,Crotalaria,,,,,,,, -Cylindropuntia kleiniae,,,,,Cylindropuntia,,,,,,,, -Cyperus albostriatus,,,,,Cyperus,,,,,,,, -Cyperus betchei,,,,,Cyperus,,,,,,,, -Cyperus bulbosus,,,,,Cyperus,,,,,,,, -Cyperus laevigatus,,,,,Cyperus,,,,,,,, -Cyperus sculptus,,,,,Cyperus,,,,,,,, -Dampiera fusca,,,,,Dampiera,,,,,,,, -Davidsonia johnsonii,,,,,Davidsonia,,,,,,,, -Daviesia arenaria,,,,,Daviesia,,,,,,,, -Derris involuta,,,,,Derris,,,,,,,, -Dichromochlamys dentatifolia,,,,,Dichromochlamys,,,,,,,, -Dillwynia cinerascens,,,,,Dillwynia,,,,,,,, -Dillwynia floribunda,,,,,Dillwynia,,,,,,,, -Dinosperma erythrococcum,,,,,Dinosperma,,,,,,,, -Dodonaea petiolaris,,,,,Dodonaea,,,,,,,, -Dodonaea truncatiales,,,,,Dodonaea,,,,,,,, -Dovyalis caffra,,,,,Dovyalis,,,,,,,, -Elaeocarpus grandis,,,,,Elaeocarpus,,,,,,,, -Eleocharis pallens,,,,,Eleocharis,,,,,,,, -Endiandra globosa,,,,,Endiandra,,,,,,,, -Endiandra muelleri,,,,,Endiandra,,,,,,,, -Epilobium gunnianum,,,,,Epilobium,,,,,,,, -Eremophila deserti,,,,,Eremophila,,,,,,,, -Eremophila oppositifolia,,,,,Eremophila,,,,,,,, -Erigeron conyzoides,,,,,Erigeron,,,,,,,, -Erythroxylum australe,,,,,Erythroxylum,,,,,,,, -Escallonia bifida,,,,,Escallonia,,,,,,,, -Eucalyptus badjensis,,,,,Eucalyptus,,,,,,,, -Eucalyptus camphora,,,,,Eucalyptus,,,,,,,, -Eucalyptus dorrigoensis,,,,,Eucalyptus,,,,,,,, -Eucalyptus leucoxylon subsp. pruinosa,,,,,Eucalyptus,,,,,,,, -Eucalyptus muelleriana,,,,,Eucalyptus,,,,,,,, -Eucalyptus nandewarica,,,,,Eucalyptus,,,,,,,, -Eucalyptus oblonga,,,,,Eucalyptus,,,,,,,, -Eucalyptus olida,,,,,Eucalyptus,,,,,,,, -Eucalyptus pulverulenta,,,,,Eucalyptus,,,,,,,, -Eucalyptus recurva,,,,,Eucalyptus,,,,,,,, -Eucalyptus rossii,,,,,Eucalyptus,,,,,,,, -Eucalyptus scias,,,,,Eucalyptus,,,,,,,, -Eucalyptus viminalis,,,,,Eucalyptus,,,,,,,, -Eucalyptus yangoura,,,,,Eucalyptus,,,,,,,, -Eucalyptus youmanii,,,,,Eucalyptus,,,,,,,, -Euphorbia inappendiculata var. queenslandica,,,,,Euphorbia,,,,,,,, -Exocarpos homalocladus,,,,,Exocarpos,,,,,,,, -Exocarpos sparteus,,,,,Exocarpos,,,,,,,, -Ficus henneana,,,,,Ficus,,,,,,,, -Freesia hybrid,,,,,Freesia,,,,,,,, -Freesia laxa,,,,,Freesia,,,,,,,, -Geijera salicifolia,,,,,Geijera,,,,,,,, -Gentiana wingecarribiensis,,,,,Gentiana,,,,,,,, -Geranium obtusisepalum,,,,,Geranium,,,,,,,, -Geranium purpureum subsp. purpureum,,,,,Geranium,,,,,,,, -Gompholobium grandiflorum,,,,,Gompholobium,,,,,,,, -Goodenia varia,,,,,Goodenia,,,,,,,, -Gossia bidwillii,,,,,Gossia,,,,,,,, -Grevillea scortechinii,,,,,Grevillea,,,,,,,, -Hakea macraeana,,,,,Hakea,,,,,,,, -Hemisteptia lyrata,,,,,Hemisteptia,,,,,,,, -Hibbertia crinita,,,,,Hibbertia,,,,,,,, -Hibiscus brachysiphonius,,,,,Hibiscus,,,,,,,, -Hibiscus sturtii,,,,,Hibiscus,,,,,,,, -Hypericum elodes,,,,,Hypericum,,,,,,,, -Hypoxis glabella var. glabella,,,,,Hypoxis,,,,,,,, -Imperata cylindrica,,,,,Imperata,,,,,,,, -Indigofera triflora,,,,,Indigofera,,,,,,,, -Ipomoea cairica,,,,,Ipomoea,,,,,,,, -Isolepis montivaga,,,,,Isolepis,,,,,,,, -Isotoma axillaris,,,,,Isotoma,,,,,,,, -Isotoma fluviatilis subsp. fluviatilis,,,,,Isotoma,,,,,,,, -Juncus acutus subsp. acutus,,,,,Juncus,,,,,,,, -Juncus kraussii,,,,,Juncus,,,,,,,, -Lantana montevidensis,,,,,Lantana,,,,,,,, -Lepidium africanum,,,,,Lepidium,,,,,,,, -Lepidium foliosum,,,,,Lepidium,,,,,,,, -Lepidium oxytrichum,,,,,Lepidium,,,,,,,, -Leptomeria drupacea,,,,,Leptomeria,,,,,,,, -Leptospermum continentale,,,,,Leptospermum,,,,,,,, -Leptospermum obovatum,,,,,Leptospermum,,,,,,,, -Leucopogon amplexicaulis,,,,,Leucopogon,,,,,,,, -Lobelia pedunculata,,,,,Lobelia,,,,,,,, -Lobelia trigonocaulis,,,,,Lobelia,,,,,,,, -Lotononis bainesii,,,,,Lotononis,,,,,,,, -Lotus corniculatus,,,,,Lotus,,,,,,,, -Lupinus polyphyllus,,,,,Lupinus,,,,,,,, -Medicago orbicularis,,,,,Medicago,,,,,,,, -Melichrus procumbens,,,,,Melichrus,,,,,,,, -Mischocarpus australis,,,,,Mischocarpus,,,,,,,, -Muehlenbeckia adpressa,,,,,Muehlenbeckia,,,,,,,, -Myoporum boninense subsp. australe,,,,,Myoporum,,,,,,,, -Nicotiana glauca,,,,,Nicotiana,,,,,,,, -Nicotiana goodspeedii,,,,,Nicotiana,,,,,,,, -Oxalis corniculata,,,,,Oxalis,,,,,,,, -Pandorea pandorana subsp. austrocaledonica,,,,,Pandorea,,,,,,,, -Paraserianthes lophantha,,,,,Paraserianthes,,,,,,,, -Parentucellia latifolia,,,,,Parentucellia,,,,,,,, -Phlegmatospermum cochlearinum,,,,,Phlegmatospermum,,,,,,,, -Phyla nodiflora,,,,,Phyla,,,,,,,, -Picris barbarorum,,,,,Picris,,,,,,,, -Pimelea ligustrina subsp. ligustrina,,,,,Pimelea,,,,,,,, -Pinus pinea,,,,,Pinus,,,,,,,, -Pisum sativum var. arvense,,,,,Pisum,,,,,,,, -Pittosporum erioloma,,,,,Pittosporum,,,,,,,, -Plantago turrifera,,,,,Plantago,,,,,,,, -Polycarpon tetraphyllum,,,,,Polycarpon,,,,,,,, -Potamogeton australiensis,,,,,Potamogeton,,,,,,,, -Psoralea pinnata,,,,,Psoralea,,,,,,,, -Pultenaea ferruginea,,,,,Pultenaea,,,,,,,, -Rhodamnia argentea,,,,,Rhodamnia,,,,,,,, -Rorippa gigantea,,,,,Rorippa,,,,,,,, -Rubus parvifolius,,,,,Rubus,,,,,,,, -Salix alba,,,,,Salix,,,,,,,, -Schenkia australis,,,,,Schenkia,,,,,,,, -Schoenus apogon,,,,,Schoenus,,,,,,,, -Schoenus brevifolius,,,,,Schoenus,,,,,,,, -Schoenus lepidosperma,,,,,Schoenus,,,,,,,, -Schoenus vaginatus,,,,,Schoenus,,,,,,,, -Scleria rugosa,,,,,Scleria,,,,,,,, -Senecio longipilus,,,,,Senecio,,,,,,,, -Sida goniocarpa,,,,,Sida,,,,,,,, -Sigesbeckia orientalis,,,,,Sigesbeckia,,,,,,,, -Sisymbrium irio,,,,,Sisymbrium,,,,,,,, -Sparaxis bulbifera,,,,,Sparaxis,,,,,,,, -Spergularia diandra,,,,,Spergularia,,,,,,,, -Sphaeromorphaea littoralis,,,,,Sphaeromorphaea,,,,,,,, -Stellaria angustifolia subsp. angustifolia,,,,,Stellaria,,,,,,,, -Styphelia viridis,,,,,Styphelia,,,,,,,, -Swainsona cadellii,,,,,Swainsona,,,,,,,, -Teucrium puberulum,,,,,Teucrium,,,,,,,, -Thelymitra kangaloonica,,,,,Thelymitra,,,,,,,, -Thesium australe,,,,,Thesium,,,,,,,, -Trifolium dubium,,,,,Trifolium,,,,,,,, -Veronica catenata,,,,,Veronica,,,,,,,, -Veronica derwentiana,,,,,Veronica,,,,,,,, -Wahlenbergia luteola,,,,,Wahlenbergia,,,,,,,, +taxon_name,taxonomic_reference,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution +Abildgaardia ovata,,,,,,,,, +Acacia alpina,,,,,,,,, +Acacia beadleana,,,,,,,,, +Acacia bulgaensis,,,,,,,,, +Acacia caroleae,,,,,,,,, +Acacia crassa,,,,,,,,, +Acacia flexifolia,,,,,,,,, +Acacia gladiiformis,,,,,,,,, +Acacia havilandiorum,,,,,,,,, +Acacia leiocalyx subsp. leiocalyx,,,,,,,,, +Acacia myrtifolia,,,,,,,,, +Acacia ramulosa var. ramulosa,,,,,,,,, +Acacia spectabilis,,,,,,,,, +Acacia terminalis subsp. Glabrous form (M.Hancock 94),,,,,,,,, +Acronychia littoralis,,,,,,,,, +Adriana tomentosa,,,,,,,,, +Alectryon coriaceus,,,,,,,,, +Alectryon oleifolius,,,,,,,,, +Alectryon subdentatus,,,,,,,,, +Amyema preissii,,,,,,,,, +Angophora leiocarpa,,,,,,,,, +Apophyllum anomalum,,,,,,,,, +Arbutus unedo,,,,,,,,, +Australina pusilla,,,,,,,,, +Burmannia disticha,,,,,,,,, +Bursaria spinosa subsp. spinosa,,,,,,,,, +Calendula arvensis,,,,,,,,, +Callistemon purpurascens,,,,,,,,, +Carex cephalotes,,,,,,,,, +Carex leporina,,,,,,,,, +Carex raleighii,,,,,,,,, +Carmichaelia exsul,,,,,,,,, +Cassinia compacta,,,,,,,,, +Castanospermum australe,,,,,,,,, +Centaurium tenuiflorum,,,,,,,,, +Cestrum nocturnum,,,,,,,,, +Chthonocephalus pseudevax,,,,,,,,, +Claoxylon australe,,,,,,,,, +Commersonia amystia,,,,,,,,, +Commersonia salviifolia,,,,,,,,, +Convolvulus farinosus,,,,,,,,, +Coprosma niphophila,,,,,,,,, +Coprosma nivalis,,,,,,,,, +Correa alba,,,,,,,,, +Corymbia citriodora,,,,,,,,, +Corymbia eximia,,,,,,,,, +Crassula decumbens,,,,,,,,, +Crassula peduncularis,,,,,,,,, +Crotalaria brevis,,,,,,,,, +Crotalaria grahamiana,,,,,,,,, +Crotalaria lanceolata,,,,,,,,, +Cylindropuntia kleiniae,,,,,,,,, +Cyperus albostriatus,,,,,,,,, +Cyperus betchei,,,,,,,,, +Cyperus bulbosus,,,,,,,,, +Cyperus laevigatus,,,,,,,,, +Cyperus sculptus,,,,,,,,, +Dampiera fusca,,,,,,,,, +Davidsonia johnsonii,,,,,,,,, +Daviesia arenaria,,,,,,,,, +Derris involuta,,,,,,,,, +Dichromochlamys dentatifolia,,,,,,,,, +Dillwynia cinerascens,,,,,,,,, +Dillwynia floribunda,,,,,,,,, +Dinosperma erythrococcum,,,,,,,,, +Dodonaea petiolaris,,,,,,,,, +Dodonaea truncatiales,,,,,,,,, +Dovyalis caffra,,,,,,,,, +Elaeocarpus grandis,,,,,,,,, +Eleocharis pallens,,,,,,,,, +Endiandra globosa,,,,,,,,, +Endiandra muelleri,,,,,,,,, +Epilobium gunnianum,,,,,,,,, +Eremophila deserti,,,,,,,,, +Eremophila oppositifolia,,,,,,,,, +Erigeron conyzoides,,,,,,,,, +Erythroxylum australe,,,,,,,,, +Escallonia bifida,,,,,,,,, +Eucalyptus badjensis,,,,,,,,, +Eucalyptus camphora,,,,,,,,, +Eucalyptus dorrigoensis,,,,,,,,, +Eucalyptus leucoxylon subsp. pruinosa,,,,,,,,, +Eucalyptus muelleriana,,,,,,,,, +Eucalyptus nandewarica,,,,,,,,, +Eucalyptus oblonga,,,,,,,,, +Eucalyptus olida,,,,,,,,, +Eucalyptus pulverulenta,,,,,,,,, +Eucalyptus recurva,,,,,,,,, +Eucalyptus rossii,,,,,,,,, +Eucalyptus scias,,,,,,,,, +Eucalyptus viminalis,,,,,,,,, +Eucalyptus yangoura,,,,,,,,, +Eucalyptus youmanii,,,,,,,,, +Euphorbia inappendiculata var. queenslandica,,,,,,,,, +Exocarpos homalocladus,,,,,,,,, +Exocarpos sparteus,,,,,,,,, +Ficus henneana,,,,,,,,, +Freesia hybrid,,,,,,,,, +Freesia laxa,,,,,,,,, +Geijera salicifolia,,,,,,,,, +Gentiana wingecarribiensis,,,,,,,,, +Geranium obtusisepalum,,,,,,,,, +Geranium purpureum subsp. purpureum,,,,,,,,, +Gompholobium grandiflorum,,,,,,,,, +Goodenia varia,,,,,,,,, +Gossia bidwillii,,,,,,,,, +Grevillea scortechinii,,,,,,,,, +Hakea macraeana,,,,,,,,, +Hemisteptia lyrata,,,,,,,,, +Hibbertia crinita,,,,,,,,, +Hibiscus brachysiphonius,,,,,,,,, +Hibiscus sturtii,,,,,,,,, +Hypericum elodes,,,,,,,,, +Hypoxis glabella var. glabella,,,,,,,,, +Imperata cylindrica,,,,,,,,, +Indigofera triflora,,,,,,,,, +Ipomoea cairica,,,,,,,,, +Isolepis montivaga,,,,,,,,, +Isotoma axillaris,,,,,,,,, +Isotoma fluviatilis subsp. fluviatilis,,,,,,,,, +Juncus acutus subsp. acutus,,,,,,,,, +Juncus kraussii,,,,,,,,, +Lantana montevidensis,,,,,,,,, +Lepidium africanum,,,,,,,,, +Lepidium foliosum,,,,,,,,, +Lepidium oxytrichum,,,,,,,,, +Leptomeria drupacea,,,,,,,,, +Leptospermum continentale,,,,,,,,, +Leptospermum obovatum,,,,,,,,, +Leucopogon amplexicaulis,,,,,,,,, +Lobelia pedunculata,,,,,,,,, +Lobelia trigonocaulis,,,,,,,,, +Lotononis bainesii,,,,,,,,, +Lotus corniculatus,,,,,,,,, +Lupinus polyphyllus,,,,,,,,, +Medicago orbicularis,,,,,,,,, +Melichrus procumbens,,,,,,,,, +Mischocarpus australis,,,,,,,,, +Muehlenbeckia adpressa,,,,,,,,, +Myoporum boninense subsp. australe,,,,,,,,, +Nicotiana glauca,,,,,,,,, +Nicotiana goodspeedii,,,,,,,,, +Oxalis corniculata,,,,,,,,, +Pandorea pandorana subsp. austrocaledonica,,,,,,,,, +Paraserianthes lophantha,,,,,,,,, +Parentucellia latifolia,,,,,,,,, +Phlegmatospermum cochlearinum,,,,,,,,, +Phyla nodiflora,,,,,,,,, +Picris barbarorum,,,,,,,,, +Pimelea ligustrina subsp. ligustrina,,,,,,,,, +Pinus pinea,,,,,,,,, +Pisum sativum var. arvense,,,,,,,,, +Pittosporum erioloma,,,,,,,,, +Plantago turrifera,,,,,,,,, +Polycarpon tetraphyllum,,,,,,,,, +Potamogeton australiensis,,,,,,,,, +Psoralea pinnata,,,,,,,,, +Pultenaea ferruginea,,,,,,,,, +Rhodamnia argentea,,,,,,,,, +Rorippa gigantea,,,,,,,,, +Rubus parvifolius,,,,,,,,, +Salix alba,,,,,,,,, +Schenkia australis,,,,,,,,, +Schoenus apogon,,,,,,,,, +Schoenus brevifolius,,,,,,,,, +Schoenus lepidosperma,,,,,,,,, +Schoenus vaginatus,,,,,,,,, +Scleria rugosa,,,,,,,,, +Senecio longipilus,,,,,,,,, +Sida goniocarpa,,,,,,,,, +Sigesbeckia orientalis,,,,,,,,, +Sisymbrium irio,,,,,,,,, +Sparaxis bulbifera,,,,,,,,, +Spergularia diandra,,,,,,,,, +Sphaeromorphaea littoralis,,,,,,,,, +Stellaria angustifolia subsp. angustifolia,,,,,,,,, +Styphelia viridis,,,,,,,,, +Swainsona cadellii,,,,,,,,, +Teucrium puberulum,,,,,,,,, +Thelymitra kangaloonica,,,,,,,,, +Thesium australe,,,,,,,,, +Trifolium dubium,,,,,,,,, +Veronica catenata,,,,,,,,, +Veronica derwentiana,,,,,,,,, +Wahlenbergia luteola,,,,,,,,, diff --git a/tests/testthat/examples/Test_2023_3/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_3/output/taxonomic_updates.csv index c9fcc126..63f7f5cd 100644 --- a/tests/testthat/examples/Test_2023_3/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_3/output/taxonomic_updates.csv @@ -1,188 +1,188 @@ -dataset_id,original_name,cleaned_name,taxonomic_resolution,cleaned_scientific_name_id,cleaned_name_taxonomic_status,cleaned_name_alternative_taxonomic_status,taxon_id,taxon_name -Test_2023_3,Abildgaardia ovata,Abildgaardia ovata,,,,,, -Test_2023_3,Acacia alpina,Acacia alpina,,,,,, -Test_2023_3,Acacia beadleana,Acacia beadleana,,,,,, -Test_2023_3,Acacia bulgaensis,Acacia bulgaensis,,,,,, -Test_2023_3,Acacia caroleae,Acacia caroleae,,,,,, -Test_2023_3,Acacia crassa,Acacia crassa,,,,,, -Test_2023_3,Acacia flexifolia,Acacia flexifolia,,,,,, -Test_2023_3,Acacia gladiiformis,Acacia gladiiformis,,,,,, -Test_2023_3,Acacia havilandiorum,Acacia havilandiorum,,,,,, -Test_2023_3,Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx subsp. leiocalyx,,,,,, -Test_2023_3,Acacia myrtifolia,Acacia myrtifolia,,,,,, -Test_2023_3,Acacia ramulosa var. ramulosa,Acacia ramulosa var. ramulosa,,,,,, -Test_2023_3,Acacia spectabilis,Acacia spectabilis,,,,,, -Test_2023_3,Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis subsp. Glabrous form (M.Hancock 94),,,,,, -Test_2023_3,Acronychia littoralis,Acronychia littoralis,,,,,, -Test_2023_3,Adriana tomentosa,Adriana tomentosa,,,,,, -Test_2023_3,Alectryon coriaceus,Alectryon coriaceus,,,,,, -Test_2023_3,Alectryon oleifolius,Alectryon oleifolius,,,,,, -Test_2023_3,Alectryon subdentatus,Alectryon subdentatus,,,,,, -Test_2023_3,Amyema preissii,Amyema preissii,,,,,, -Test_2023_3,Angophora leiocarpa,Angophora leiocarpa,,,,,, -Test_2023_3,Apophyllum anomalum,Apophyllum anomalum,,,,,, -Test_2023_3,Arbutus unedo,Arbutus unedo,,,,,, -Test_2023_3,Australina pusilla,Australina pusilla,,,,,, -Test_2023_3,Burmannia disticha,Burmannia disticha,,,,,, -Test_2023_3,Bursaria spinosa subsp. spinosa,Bursaria spinosa subsp. spinosa,,,,,, -Test_2023_3,Calendula arvensis,Calendula arvensis,,,,,, -Test_2023_3,Callistemon purpurascens,Callistemon purpurascens,,,,,, -Test_2023_3,Carex cephalotes,Carex cephalotes,,,,,, -Test_2023_3,Carex leporina,Carex leporina,,,,,, -Test_2023_3,Carex raleighii,Carex raleighii,,,,,, -Test_2023_3,Carmichaelia exsul,Carmichaelia exsul,,,,,, -Test_2023_3,Cassinia compacta,Cassinia compacta,,,,,, -Test_2023_3,Castanospermum australe,Castanospermum australe,,,,,, -Test_2023_3,Centaurium tenuiflorum,Centaurium tenuiflorum,,,,,, -Test_2023_3,Cestrum nocturnum,Cestrum nocturnum,,,,,, -Test_2023_3,Chthonocephalus pseudevax,Chthonocephalus pseudevax,,,,,, -Test_2023_3,Claoxylon australe,Claoxylon australe,,,,,, -Test_2023_3,Commersonia amystia,Commersonia amystia,,,,,, -Test_2023_3,Commersonia salviifolia,Commersonia salviifolia,,,,,, -Test_2023_3,Convolvulus farinosus,Convolvulus farinosus,,,,,, -Test_2023_3,Coprosma niphophila,Coprosma niphophila,,,,,, -Test_2023_3,Coprosma nivalis,Coprosma nivalis,,,,,, -Test_2023_3,Correa alba,Correa alba,,,,,, -Test_2023_3,Corymbia citriodora,Corymbia citriodora,,,,,, -Test_2023_3,Corymbia eximia,Corymbia eximia,,,,,, -Test_2023_3,Crassula decumbens,Crassula decumbens,,,,,, -Test_2023_3,Crassula peduncularis,Crassula peduncularis,,,,,, -Test_2023_3,Crotalaria brevis,Crotalaria brevis,,,,,, -Test_2023_3,Crotalaria grahamiana,Crotalaria grahamiana,,,,,, -Test_2023_3,Crotalaria lanceolata,Crotalaria lanceolata,,,,,, -Test_2023_3,Cylindropuntia kleiniae,Cylindropuntia kleiniae,,,,,, -Test_2023_3,Cyperus albostriatus,Cyperus albostriatus,,,,,, -Test_2023_3,Cyperus betchei,Cyperus betchei,,,,,, -Test_2023_3,Cyperus bulbosus,Cyperus bulbosus,,,,,, -Test_2023_3,Cyperus laevigatus,Cyperus laevigatus,,,,,, -Test_2023_3,Cyperus sculptus,Cyperus sculptus,,,,,, -Test_2023_3,Dampiera fusca,Dampiera fusca,,,,,, -Test_2023_3,Davidsonia johnsonii,Davidsonia johnsonii,,,,,, -Test_2023_3,Daviesia arenaria,Daviesia arenaria,,,,,, -Test_2023_3,Derris involuta,Derris involuta,,,,,, -Test_2023_3,Dichromochlamys dentatifolia,Dichromochlamys dentatifolia,,,,,, -Test_2023_3,Dillwynia cinerascens,Dillwynia cinerascens,,,,,, -Test_2023_3,Dillwynia floribunda,Dillwynia floribunda,,,,,, -Test_2023_3,Dinosperma erythrococcum,Dinosperma erythrococcum,,,,,, -Test_2023_3,Dodonaea petiolaris,Dodonaea petiolaris,,,,,, -Test_2023_3,Dodonaea truncatiales,Dodonaea truncatiales,,,,,, -Test_2023_3,Dovyalis caffra,Dovyalis caffra,,,,,, -Test_2023_3,Elaeocarpus grandis,Elaeocarpus grandis,,,,,, -Test_2023_3,Eleocharis pallens,Eleocharis pallens,,,,,, -Test_2023_3,Endiandra globosa,Endiandra globosa,,,,,, -Test_2023_3,Endiandra muelleri,Endiandra muelleri,,,,,, -Test_2023_3,Epilobium gunnianum,Epilobium gunnianum,,,,,, -Test_2023_3,Eremophila deserti,Eremophila deserti,,,,,, -Test_2023_3,Eremophila oppositifolia,Eremophila oppositifolia,,,,,, -Test_2023_3,Erigeron conyzoides,Erigeron conyzoides,,,,,, -Test_2023_3,Erythroxylum australe,Erythroxylum australe,,,,,, -Test_2023_3,Escallonia bifida,Escallonia bifida,,,,,, -Test_2023_3,Eucalyptus badjensis,Eucalyptus badjensis,,,,,, -Test_2023_3,Eucalyptus camphora,Eucalyptus camphora,,,,,, -Test_2023_3,Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,,,,,, -Test_2023_3,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,,,,,, -Test_2023_3,Eucalyptus muelleriana,Eucalyptus muelleriana,,,,,, -Test_2023_3,Eucalyptus nandewarica,Eucalyptus nandewarica,,,,,, -Test_2023_3,Eucalyptus oblonga,Eucalyptus oblonga,,,,,, -Test_2023_3,Eucalyptus olida,Eucalyptus olida,,,,,, -Test_2023_3,Eucalyptus pulverulenta,Eucalyptus pulverulenta,,,,,, -Test_2023_3,Eucalyptus recurva,Eucalyptus recurva,,,,,, -Test_2023_3,Eucalyptus rossii,Eucalyptus rossii,,,,,, -Test_2023_3,Eucalyptus scias,Eucalyptus scias,,,,,, -Test_2023_3,Eucalyptus viminalis,Eucalyptus viminalis,,,,,, -Test_2023_3,Eucalyptus yangoura,Eucalyptus yangoura,,,,,, -Test_2023_3,Eucalyptus youmanii,Eucalyptus youmanii,,,,,, -Test_2023_3,Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata var. queenslandica,,,,,, -Test_2023_3,Exocarpos homalocladus,Exocarpos homalocladus,,,,,, -Test_2023_3,Exocarpos sparteus,Exocarpos sparteus,,,,,, -Test_2023_3,Ficus henneana,Ficus henneana,,,,,, -Test_2023_3,Freesia hybrid,Freesia hybrid,,,,,, -Test_2023_3,Freesia laxa,Freesia laxa,,,,,, -Test_2023_3,Geijera salicifolia,Geijera salicifolia,,,,,, -Test_2023_3,Gentiana wingecarribiensis,Gentiana wingecarribiensis,,,,,, -Test_2023_3,Gentianella barringtonensis,Gentianella barringtonensis,,,,,, -Test_2023_3,Geranium obtusisepalum,Geranium obtusisepalum,,,,,, -Test_2023_3,Geranium purpureum subsp. purpureum,Geranium purpureum subsp. purpureum,,,,,, -Test_2023_3,Gompholobium grandiflorum,Gompholobium grandiflorum,,,,,, -Test_2023_3,Goodenia varia,Goodenia varia,,,,,, -Test_2023_3,Gossia bidwillii,Gossia bidwillii,,,,,, -Test_2023_3,Grevillea scortechinii,Grevillea scortechinii,,,,,, -Test_2023_3,Hakea macraeana,Hakea macraeana,,,,,, -Test_2023_3,Hemisteptia lyrata,Hemisteptia lyrata,,,,,, -Test_2023_3,Hibbertia crinita,Hibbertia crinita,,,,,, -Test_2023_3,Hibiscus brachysiphonius,Hibiscus brachysiphonius,,,,,, -Test_2023_3,Hibiscus sturtii,Hibiscus sturtii,,,,,, -Test_2023_3,Hypericum elodes,Hypericum elodes,,,,,, -Test_2023_3,Hypoxis glabella var. glabella,Hypoxis glabella var. glabella,,,,,, -Test_2023_3,Imperata cylindrica,Imperata cylindrica,,,,,, -Test_2023_3,Indigofera triflora,Indigofera triflora,,,,,, -Test_2023_3,Ipomoea cairica,Ipomoea cairica,,,,,, -Test_2023_3,Isolepis montivaga,Isolepis montivaga,,,,,, -Test_2023_3,Isotoma axillaris,Isotoma axillaris,,,,,, -Test_2023_3,Isotoma fluviatilis subsp. fluviatilis,Isotoma fluviatilis subsp. fluviatilis,,,,,, -Test_2023_3,Juncus acutus subsp. acutus,Juncus acutus subsp. acutus,,,,,, -Test_2023_3,Juncus kraussii,Juncus kraussii,,,,,, -Test_2023_3,Lantana montevidensis,Lantana montevidensis,,,,,, -Test_2023_3,Lepidium africanum,Lepidium africanum,,,,,, -Test_2023_3,Lepidium foliosum,Lepidium foliosum,,,,,, -Test_2023_3,Lepidium oxytrichum,Lepidium oxytrichum,,,,,, -Test_2023_3,Lepidosperma gladiatum,Lepidosperma gladiatum,,,,,, -Test_2023_3,Leptomeria drupacea,Leptomeria drupacea,,,,,, -Test_2023_3,Leptospermum continentale,Leptospermum continentale,,,,,, -Test_2023_3,Leptospermum obovatum,Leptospermum obovatum,,,,,, -Test_2023_3,Leucopogon amplexicaulis,Leucopogon amplexicaulis,,,,,, -Test_2023_3,Lobelia pedunculata,Lobelia pedunculata,,,,,, -Test_2023_3,Lobelia trigonocaulis,Lobelia trigonocaulis,,,,,, -Test_2023_3,Lotononis bainesii,Lotononis bainesii,,,,,, -Test_2023_3,Lotus corniculatus,Lotus corniculatus,,,,,, -Test_2023_3,Lupinus polyphyllus,Lupinus polyphyllus,,,,,, -Test_2023_3,Medicago orbicularis,Medicago orbicularis,,,,,, -Test_2023_3,Melichrus procumbens,Melichrus procumbens,,,,,, -Test_2023_3,Mischocarpus australis,Mischocarpus australis,,,,,, -Test_2023_3,Muehlenbeckia adpressa,Muehlenbeckia adpressa,,,,,, -Test_2023_3,Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,,,,,, -Test_2023_3,Nicotiana glauca,Nicotiana glauca,,,,,, -Test_2023_3,Nicotiana goodspeedii,Nicotiana goodspeedii,,,,,, -Test_2023_3,Oxalis corniculata,Oxalis corniculata,,,,,, -Test_2023_3,Pandorea pandorana subsp. austrocaledonica,Pandorea pandorana subsp. austrocaledonica,,,,,, -Test_2023_3,Paraserianthes lophantha,Paraserianthes lophantha,,,,,, -Test_2023_3,Parentucellia latifolia,Parentucellia latifolia,,,,,, -Test_2023_3,Phlegmatospermum cochlearinum,Phlegmatospermum cochlearinum,,,,,, -Test_2023_3,Phyla nodiflora,Phyla nodiflora,,,,,, -Test_2023_3,Picris barbarorum,Picris barbarorum,,,,,, -Test_2023_3,Pimelea ligustrina subsp. ligustrina,Pimelea ligustrina subsp. ligustrina,,,,,, -Test_2023_3,Pinus pinea,Pinus pinea,,,,,, -Test_2023_3,Pisum sativum var. arvense,Pisum sativum var. arvense,,,,,, -Test_2023_3,Pittosporum erioloma,Pittosporum erioloma,,,,,, -Test_2023_3,Plantago turrifera,Plantago turrifera,,,,,, -Test_2023_3,Polycarpon tetraphyllum,Polycarpon tetraphyllum,,,,,, -Test_2023_3,Potamogeton australiensis,Potamogeton australiensis,,,,,, -Test_2023_3,Psoralea pinnata,Psoralea pinnata,,,,,, -Test_2023_3,Pultenaea ferruginea,Pultenaea ferruginea,,,,,, -Test_2023_3,Rhodamnia argentea,Rhodamnia argentea,,,,,, -Test_2023_3,Rorippa gigantea,Rorippa gigantea,,,,,, -Test_2023_3,Rubus parvifolius,Rubus parvifolius,,,,,, -Test_2023_3,Salix alba,Salix alba,,,,,, -Test_2023_3,Schenkia australis,Schenkia australis,,,,,, -Test_2023_3,Schoenus apogon,Schoenus apogon,,,,,, -Test_2023_3,Schoenus brevifolius,Schoenus brevifolius,,,,,, -Test_2023_3,Schoenus lepidosperma,Schoenus lepidosperma,,,,,, -Test_2023_3,Schoenus vaginatus,Schoenus vaginatus,,,,,, -Test_2023_3,Scleria rugosa,Scleria rugosa,,,,,, -Test_2023_3,Senecio longipilus,Senecio longipilus,,,,,, -Test_2023_3,Sida goniocarpa,Sida goniocarpa,,,,,, -Test_2023_3,Sigesbeckia orientalis,Sigesbeckia orientalis,,,,,, -Test_2023_3,Sisymbrium irio,Sisymbrium irio,,,,,, -Test_2023_3,Sparaxis bulbifera,Sparaxis bulbifera,,,,,, -Test_2023_3,Spergularia diandra,Spergularia diandra,,,,,, -Test_2023_3,Sphaeromorphaea littoralis,Sphaeromorphaea littoralis,,,,,, -Test_2023_3,Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia subsp. angustifolia,,,,,, -Test_2023_3,Styphelia viridis,Styphelia viridis,,,,,, -Test_2023_3,Swainsona cadellii,Swainsona cadellii,,,,,, -Test_2023_3,Teucrium puberulum,Teucrium puberulum,,,,,, -Test_2023_3,Thelymitra kangaloonica,Thelymitra kangaloonica,,,,,, -Test_2023_3,Thesium australe,Thesium australe,,,,,, -Test_2023_3,Trifolium dubium,Trifolium dubium,,,,,, -Test_2023_3,Veronica catenata,Veronica catenata,,,,,, -Test_2023_3,Veronica derwentiana,Veronica derwentiana,,,,,, -Test_2023_3,Wahlenbergia luteola,Wahlenbergia luteola,,,,,, +dataset_id,original_name,cleaned_name,taxonomic_resolution,taxon_name +Test_2023_3,Abildgaardia ovata,Abildgaardia ovata,, +Test_2023_3,Acacia alpina,Acacia alpina,, +Test_2023_3,Acacia beadleana,Acacia beadleana,, +Test_2023_3,Acacia bulgaensis,Acacia bulgaensis,, +Test_2023_3,Acacia caroleae,Acacia caroleae,, +Test_2023_3,Acacia crassa,Acacia crassa,, +Test_2023_3,Acacia flexifolia,Acacia flexifolia,, +Test_2023_3,Acacia gladiiformis,Acacia gladiiformis,, +Test_2023_3,Acacia havilandiorum,Acacia havilandiorum,, +Test_2023_3,Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx subsp. leiocalyx,, +Test_2023_3,Acacia myrtifolia,Acacia myrtifolia,, +Test_2023_3,Acacia ramulosa var. ramulosa,Acacia ramulosa var. ramulosa,, +Test_2023_3,Acacia spectabilis,Acacia spectabilis,, +Test_2023_3,Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis subsp. Glabrous form (M.Hancock 94),, +Test_2023_3,Acronychia littoralis,Acronychia littoralis,, +Test_2023_3,Adriana tomentosa,Adriana tomentosa,, +Test_2023_3,Alectryon coriaceus,Alectryon coriaceus,, +Test_2023_3,Alectryon oleifolius,Alectryon oleifolius,, +Test_2023_3,Alectryon subdentatus,Alectryon subdentatus,, +Test_2023_3,Amyema preissii,Amyema preissii,, +Test_2023_3,Angophora leiocarpa,Angophora leiocarpa,, +Test_2023_3,Apophyllum anomalum,Apophyllum anomalum,, +Test_2023_3,Arbutus unedo,Arbutus unedo,, +Test_2023_3,Australina pusilla,Australina pusilla,, +Test_2023_3,Burmannia disticha,Burmannia disticha,, +Test_2023_3,Bursaria spinosa subsp. spinosa,Bursaria spinosa subsp. spinosa,, +Test_2023_3,Calendula arvensis,Calendula arvensis,, +Test_2023_3,Callistemon purpurascens,Callistemon purpurascens,, +Test_2023_3,Carex cephalotes,Carex cephalotes,, +Test_2023_3,Carex leporina,Carex leporina,, +Test_2023_3,Carex raleighii,Carex raleighii,, +Test_2023_3,Carmichaelia exsul,Carmichaelia exsul,, +Test_2023_3,Cassinia compacta,Cassinia compacta,, +Test_2023_3,Castanospermum australe,Castanospermum australe,, +Test_2023_3,Centaurium tenuiflorum,Centaurium tenuiflorum,, +Test_2023_3,Cestrum nocturnum,Cestrum nocturnum,, +Test_2023_3,Chthonocephalus pseudevax,Chthonocephalus pseudevax,, +Test_2023_3,Claoxylon australe,Claoxylon australe,, +Test_2023_3,Commersonia amystia,Commersonia amystia,, +Test_2023_3,Commersonia salviifolia,Commersonia salviifolia,, +Test_2023_3,Convolvulus farinosus,Convolvulus farinosus,, +Test_2023_3,Coprosma niphophila,Coprosma niphophila,, +Test_2023_3,Coprosma nivalis,Coprosma nivalis,, +Test_2023_3,Correa alba,Correa alba,, +Test_2023_3,Corymbia citriodora,Corymbia citriodora,, +Test_2023_3,Corymbia eximia,Corymbia eximia,, +Test_2023_3,Crassula decumbens,Crassula decumbens,, +Test_2023_3,Crassula peduncularis,Crassula peduncularis,, +Test_2023_3,Crotalaria brevis,Crotalaria brevis,, +Test_2023_3,Crotalaria grahamiana,Crotalaria grahamiana,, +Test_2023_3,Crotalaria lanceolata,Crotalaria lanceolata,, +Test_2023_3,Cylindropuntia kleiniae,Cylindropuntia kleiniae,, +Test_2023_3,Cyperus albostriatus,Cyperus albostriatus,, +Test_2023_3,Cyperus betchei,Cyperus betchei,, +Test_2023_3,Cyperus bulbosus,Cyperus bulbosus,, +Test_2023_3,Cyperus laevigatus,Cyperus laevigatus,, +Test_2023_3,Cyperus sculptus,Cyperus sculptus,, +Test_2023_3,Dampiera fusca,Dampiera fusca,, +Test_2023_3,Davidsonia johnsonii,Davidsonia johnsonii,, +Test_2023_3,Daviesia arenaria,Daviesia arenaria,, +Test_2023_3,Derris involuta,Derris involuta,, +Test_2023_3,Dichromochlamys dentatifolia,Dichromochlamys dentatifolia,, +Test_2023_3,Dillwynia cinerascens,Dillwynia cinerascens,, +Test_2023_3,Dillwynia floribunda,Dillwynia floribunda,, +Test_2023_3,Dinosperma erythrococcum,Dinosperma erythrococcum,, +Test_2023_3,Dodonaea petiolaris,Dodonaea petiolaris,, +Test_2023_3,Dodonaea truncatiales,Dodonaea truncatiales,, +Test_2023_3,Dovyalis caffra,Dovyalis caffra,, +Test_2023_3,Elaeocarpus grandis,Elaeocarpus grandis,, +Test_2023_3,Eleocharis pallens,Eleocharis pallens,, +Test_2023_3,Endiandra globosa,Endiandra globosa,, +Test_2023_3,Endiandra muelleri,Endiandra muelleri,, +Test_2023_3,Epilobium gunnianum,Epilobium gunnianum,, +Test_2023_3,Eremophila deserti,Eremophila deserti,, +Test_2023_3,Eremophila oppositifolia,Eremophila oppositifolia,, +Test_2023_3,Erigeron conyzoides,Erigeron conyzoides,, +Test_2023_3,Erythroxylum australe,Erythroxylum australe,, +Test_2023_3,Escallonia bifida,Escallonia bifida,, +Test_2023_3,Eucalyptus badjensis,Eucalyptus badjensis,, +Test_2023_3,Eucalyptus camphora,Eucalyptus camphora,, +Test_2023_3,Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,, +Test_2023_3,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,, +Test_2023_3,Eucalyptus muelleriana,Eucalyptus muelleriana,, +Test_2023_3,Eucalyptus nandewarica,Eucalyptus nandewarica,, +Test_2023_3,Eucalyptus oblonga,Eucalyptus oblonga,, +Test_2023_3,Eucalyptus olida,Eucalyptus olida,, +Test_2023_3,Eucalyptus pulverulenta,Eucalyptus pulverulenta,, +Test_2023_3,Eucalyptus recurva,Eucalyptus recurva,, +Test_2023_3,Eucalyptus rossii,Eucalyptus rossii,, +Test_2023_3,Eucalyptus scias,Eucalyptus scias,, +Test_2023_3,Eucalyptus viminalis,Eucalyptus viminalis,, +Test_2023_3,Eucalyptus yangoura,Eucalyptus yangoura,, +Test_2023_3,Eucalyptus youmanii,Eucalyptus youmanii,, +Test_2023_3,Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata var. queenslandica,, +Test_2023_3,Exocarpos homalocladus,Exocarpos homalocladus,, +Test_2023_3,Exocarpos sparteus,Exocarpos sparteus,, +Test_2023_3,Ficus henneana,Ficus henneana,, +Test_2023_3,Freesia hybrid,Freesia hybrid,, +Test_2023_3,Freesia laxa,Freesia laxa,, +Test_2023_3,Geijera salicifolia,Geijera salicifolia,, +Test_2023_3,Gentiana wingecarribiensis,Gentiana wingecarribiensis,, +Test_2023_3,Gentianella barringtonensis,Gentianella barringtonensis,, +Test_2023_3,Geranium obtusisepalum,Geranium obtusisepalum,, +Test_2023_3,Geranium purpureum subsp. purpureum,Geranium purpureum subsp. purpureum,, +Test_2023_3,Gompholobium grandiflorum,Gompholobium grandiflorum,, +Test_2023_3,Goodenia varia,Goodenia varia,, +Test_2023_3,Gossia bidwillii,Gossia bidwillii,, +Test_2023_3,Grevillea scortechinii,Grevillea scortechinii,, +Test_2023_3,Hakea macraeana,Hakea macraeana,, +Test_2023_3,Hemisteptia lyrata,Hemisteptia lyrata,, +Test_2023_3,Hibbertia crinita,Hibbertia crinita,, +Test_2023_3,Hibiscus brachysiphonius,Hibiscus brachysiphonius,, +Test_2023_3,Hibiscus sturtii,Hibiscus sturtii,, +Test_2023_3,Hypericum elodes,Hypericum elodes,, +Test_2023_3,Hypoxis glabella var. glabella,Hypoxis glabella var. glabella,, +Test_2023_3,Imperata cylindrica,Imperata cylindrica,, +Test_2023_3,Indigofera triflora,Indigofera triflora,, +Test_2023_3,Ipomoea cairica,Ipomoea cairica,, +Test_2023_3,Isolepis montivaga,Isolepis montivaga,, +Test_2023_3,Isotoma axillaris,Isotoma axillaris,, +Test_2023_3,Isotoma fluviatilis subsp. fluviatilis,Isotoma fluviatilis subsp. fluviatilis,, +Test_2023_3,Juncus acutus subsp. acutus,Juncus acutus subsp. acutus,, +Test_2023_3,Juncus kraussii,Juncus kraussii,, +Test_2023_3,Lantana montevidensis,Lantana montevidensis,, +Test_2023_3,Lepidium africanum,Lepidium africanum,, +Test_2023_3,Lepidium foliosum,Lepidium foliosum,, +Test_2023_3,Lepidium oxytrichum,Lepidium oxytrichum,, +Test_2023_3,Lepidosperma gladiatum,Lepidosperma gladiatum,, +Test_2023_3,Leptomeria drupacea,Leptomeria drupacea,, +Test_2023_3,Leptospermum continentale,Leptospermum continentale,, +Test_2023_3,Leptospermum obovatum,Leptospermum obovatum,, +Test_2023_3,Leucopogon amplexicaulis,Leucopogon amplexicaulis,, +Test_2023_3,Lobelia pedunculata,Lobelia pedunculata,, +Test_2023_3,Lobelia trigonocaulis,Lobelia trigonocaulis,, +Test_2023_3,Lotononis bainesii,Lotononis bainesii,, +Test_2023_3,Lotus corniculatus,Lotus corniculatus,, +Test_2023_3,Lupinus polyphyllus,Lupinus polyphyllus,, +Test_2023_3,Medicago orbicularis,Medicago orbicularis,, +Test_2023_3,Melichrus procumbens,Melichrus procumbens,, +Test_2023_3,Mischocarpus australis,Mischocarpus australis,, +Test_2023_3,Muehlenbeckia adpressa,Muehlenbeckia adpressa,, +Test_2023_3,Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,, +Test_2023_3,Nicotiana glauca,Nicotiana glauca,, +Test_2023_3,Nicotiana goodspeedii,Nicotiana goodspeedii,, +Test_2023_3,Oxalis corniculata,Oxalis corniculata,, +Test_2023_3,Pandorea pandorana subsp. austrocaledonica,Pandorea pandorana subsp. austrocaledonica,, +Test_2023_3,Paraserianthes lophantha,Paraserianthes lophantha,, +Test_2023_3,Parentucellia latifolia,Parentucellia latifolia,, +Test_2023_3,Phlegmatospermum cochlearinum,Phlegmatospermum cochlearinum,, +Test_2023_3,Phyla nodiflora,Phyla nodiflora,, +Test_2023_3,Picris barbarorum,Picris barbarorum,, +Test_2023_3,Pimelea ligustrina subsp. ligustrina,Pimelea ligustrina subsp. ligustrina,, +Test_2023_3,Pinus pinea,Pinus pinea,, +Test_2023_3,Pisum sativum var. arvense,Pisum sativum var. arvense,, +Test_2023_3,Pittosporum erioloma,Pittosporum erioloma,, +Test_2023_3,Plantago turrifera,Plantago turrifera,, +Test_2023_3,Polycarpon tetraphyllum,Polycarpon tetraphyllum,, +Test_2023_3,Potamogeton australiensis,Potamogeton australiensis,, +Test_2023_3,Psoralea pinnata,Psoralea pinnata,, +Test_2023_3,Pultenaea ferruginea,Pultenaea ferruginea,, +Test_2023_3,Rhodamnia argentea,Rhodamnia argentea,, +Test_2023_3,Rorippa gigantea,Rorippa gigantea,, +Test_2023_3,Rubus parvifolius,Rubus parvifolius,, +Test_2023_3,Salix alba,Salix alba,, +Test_2023_3,Schenkia australis,Schenkia australis,, +Test_2023_3,Schoenus apogon,Schoenus apogon,, +Test_2023_3,Schoenus brevifolius,Schoenus brevifolius,, +Test_2023_3,Schoenus lepidosperma,Schoenus lepidosperma,, +Test_2023_3,Schoenus vaginatus,Schoenus vaginatus,, +Test_2023_3,Scleria rugosa,Scleria rugosa,, +Test_2023_3,Senecio longipilus,Senecio longipilus,, +Test_2023_3,Sida goniocarpa,Sida goniocarpa,, +Test_2023_3,Sigesbeckia orientalis,Sigesbeckia orientalis,, +Test_2023_3,Sisymbrium irio,Sisymbrium irio,, +Test_2023_3,Sparaxis bulbifera,Sparaxis bulbifera,, +Test_2023_3,Spergularia diandra,Spergularia diandra,, +Test_2023_3,Sphaeromorphaea littoralis,Sphaeromorphaea littoralis,, +Test_2023_3,Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia subsp. angustifolia,, +Test_2023_3,Styphelia viridis,Styphelia viridis,, +Test_2023_3,Swainsona cadellii,Swainsona cadellii,, +Test_2023_3,Teucrium puberulum,Teucrium puberulum,, +Test_2023_3,Thelymitra kangaloonica,Thelymitra kangaloonica,, +Test_2023_3,Thesium australe,Thesium australe,, +Test_2023_3,Trifolium dubium,Trifolium dubium,, +Test_2023_3,Veronica catenata,Veronica catenata,, +Test_2023_3,Veronica derwentiana,Veronica derwentiana,, +Test_2023_3,Wahlenbergia luteola,Wahlenbergia luteola,, diff --git a/tests/testthat/examples/Test_2023_4/metadata.yml b/tests/testthat/examples/Test_2023_4/metadata.yml index 0c7be3a3..a3d9f303 100644 --- a/tests/testthat/examples/Test_2023_4/metadata.yml +++ b/tests/testthat/examples/Test_2023_4/metadata.yml @@ -256,23 +256,23 @@ taxonomic_updates: replace: Acaena x anserovina reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Acaena ovina replace: Acaena x ovina reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Acaena sp. Thredbo River Gorge (L.A.S.Johnson ;amp; E.F.Constable s.n., 19 Jan 1951) replace: Acaena sp. Thredbo River Gorge (L.A.S.Johnson & E.F.Constable s.n., 19 Jan 1951) reason: match_10_fuzzy. Imprecise fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Alstonia constricta f. Pubescent form replace: Alstonia constricta Pubescent form reason: match_08. Automatic alignment with synonymous name in APNI (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Arthropteris beckleri x tenella replace: Arthropteris x [Arthropteris beckleri x tenella; NHNSW_2022] reason: match_11. Rewording hybrid species name not in APC or APNI to indicate a @@ -282,52 +282,52 @@ taxonomic_updates: replace: Atriplex sp. B reason: match_19. Automatic alignment with species-level canonical name in APNI when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Banksia spinulosa var. collina-spinulosa intergrade replace: Banksia spinulosa var. collina reason: match_12. Automatic alignment with infraspecific canonical name in APC accepted when notes are ignored (2022-11-22) - taxonomic_resolution: Varietas + taxonomic_resolution: variety - find: Bertya tasmanica variant ;qu;Glabrous ovary;qu; replace: Bertya tasmanica var. Glabrous ovary (T.A.James 527 & M.J.Taylor) reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: Varietas + taxonomic_resolution: variety - find: Blechnum fullagarii replace: Blechnum fullagari reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Caladenia sp. A sensu Harden (1993) replace: Caladenia sp. A reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Centaurea sp. A sensu Murray (1992) replace: Centaurea sp. A reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Cephalomanes atrovirens subsp. atrovirens replace: Cephalomanes atrovirens reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Choretrum sp. Coxs Gap (B.J.Lepschi 4218 ;amp; T.R.Lally) replace: Choretrum sp. Coxs Gap (B.J.Lepschi 4218 & T.R.Lally) reason: match_10_fuzzy. Imprecise fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Cipadessa baccifera replace: Cipadessa baccifera reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Crocosmia crocosmiiflora replace: Crocosmia x crocosmiiflora reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Cyperus bowmannii replace: Cyperus bowmanni reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Cyperus sp. Stockton (K.L.Wilson 10541) replace: Cyperus sp. [Cyperus sp. Stockton (K.L.Wilson 10541); NHNSW_2022] reason: match_20. Rewording name to be recognised as genus rank, with genus accepted @@ -336,75 +336,75 @@ taxonomic_updates: - find: Dillwynia sp. Ebor (P.C.Jobson 5318 ;amp; S.A.Mills) replace: Dillwynia sp. Ebor (P.C.Jobson 5318 & S.A.Mills) reason: match_17_fuzzy. Imprecise fuzzy alignment with canonical name in APNI (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Epidendrum radicans x secundum hybrid complex replace: Epidendrum radicans x Epidendrum secundum reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Eriochilus cucullatus complex replace: Eriochilus cucullatus reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Eucalyptus conjuncta replace: Eucalyptus x conjuncta reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Eucalyptus dealbata subsp. dealbata replace: Eucalyptus dealbata var. dealbata reason: match_06. Automatic alignment with synonymous term among known canonical names APC (2022-11-21) - taxonomic_resolution: Varietas + taxonomic_resolution: variety - find: Flacourtia sp. shiptons flat l w jessup gj.d3200 replace: Flacourtia sp. Shiptons Flat (L.W.Jessup+ GJD3200) reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Genoplesium cuspidatum replace: Genoplesium sp. Cuspidata (L.M.Copeland 3858) reason: match_15_fuzzy. Fuzzy match alignment with species-level canonical name in `APC known` when everything except first 2 words ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Genoplesium sp. Charmhaven (NSW896673) replace: Genoplesium sp. Charmhaven (NSW 896673) reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Glycine pacifica replace: Glycine pacifica (Grace 946) reason: match_19. Automatic alignment with species-level canonical name in APNI when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Hibbertia sp. B sensu Harden (1990) replace: Hibbertia sp. B reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Hibbertia stricta subsp. stricta replace: Hibbertia stricta var. stricta reason: match_06. Automatic alignment with synonymous term among known canonical names APC (2022-11-21) - taxonomic_resolution: Varietas + taxonomic_resolution: variety - find: Hoffmannseggia glauca replace: Hoffmannseggia glauca reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Houttuynia cordata replace: Houttuynia cordata reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Impatiens balfouri replace: Impatiens balfourii reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Kunzea capitata subsp. capitata replace: Kunzea capitata var. capitata reason: match_06. Automatic alignment with synonymous term among known canonical names APC (2022-11-21) - taxonomic_resolution: Varietas + taxonomic_resolution: variety - find: Lenwebbia sp. Main Range (P.R.Sharpe 4877) replace: Lenwebbia sp. Main Range (P.R.Sharpe+ 4877) reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Lepidium sp. Cooma (J.H.Maiden NSW642748) replace: Lepidium sp. [Lepidium sp. Cooma (J.H.Maiden NSW642748); NHNSW_2022] reason: match_20. Rewording name to be recognised as genus rank, with genus accepted @@ -414,34 +414,34 @@ taxonomic_updates: replace: Leucopogon lanceolatus reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Luzula densiflora subsp. densiflora replace: Luzula densiflora reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Luzula flaccida subsp. flaccida replace: Leucas flaccida var. flaccida reason: match_10_fuzzy. Imprecise fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: Varietas + taxonomic_resolution: variety - find: Margyricarpus pinnatus replace: Margyricarpus pinnatus reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Muehlenbeckia diclina subsp. Gippsland (R.O.Makinson 1007) Makinson replace: Muehlenbeckia diclina subsp. Gippsland (R.O.Makinson 1007) reason: match_05. Automatic alignment with scientific name in APC accepted list (2022-11-21) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Muehlenbeckia diclina subsp. Pooncarie (W.E. Mulham W811) replace: Muehlenbeckia diclina subsp. Pooncarie (W.E.Mulham W811) reason: match_08. Automatic alignment with synonymous name in APNI (2022-11-21) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Myosotis laxa subsp. caespitosa replace: Myosotis laxa subsp. cespitosa reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Netrostylis sp. East Coast (D.E. Albrecht 597) replace: Netrostylis sp. [Netrostylis sp. East Coast (D.E. Albrecht 597); NHNSW_2022] reason: match_20. Rewording name to be recognised as genus rank, with genus in APNI @@ -451,7 +451,7 @@ taxonomic_updates: replace: Notelaea sp. A reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Opuntia sp. sensu I.Telford (1984) replace: Opuntia sp. [Opuntia sp. sensu I.Telford (1984); NHNSW_2022] reason: match_20. Rewording name to be recognised as genus rank, with genus accepted @@ -461,165 +461,165 @@ taxonomic_updates: replace: Owenia x reliqua reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Pelargonium asperum replace: Pelargonium x asperum reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Pimelea neo-anglica replace: Pimelea neoanglica reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Polyscias sambucifolia subsp. Long leaflets (P.G.Neish 208) Vic. Herbarium replace: Polyscias sambucifolia subsp. Long leaflets (P.G.Neish 208) reason: match_05. Automatic alignment with scientific name in APC accepted list (2022-11-21) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Pomaderris andromedifolia f. ;qu;andromedifolia;qu; replace: Pomaderris andromedifolia subsp. andromedifolia reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Pomaderris andromedifolia f. ;qu;narrow-leaved;qu; replace: Pomaderris andromedifolia f. 'narrow-leaved' reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: Forma + taxonomic_resolution: form - find: Pomaderris andromedifolia f. ;qu;small-leaved;qu; replace: Pomaderris andromedifolia subsp. andromedifolia reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Potamogeton tricarinatus auct. non F.Muell. ;amp; A.Benn. ex A.Benn. replace: Potamogeton tricarinatus reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Prasophyllum sp. A sensu Harden (1993) replace: Prasophyllum sp. A reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Pultenaea sp. Dingo Creek (M.A.M.Renner 9176 ;amp; J.M.Cohen) replace: Pultenaea sp. Dingo Creek (M.A.M.Renner 9176 & J.M.Cohen) reason: match_17_fuzzy. Imprecise fuzzy alignment with canonical name in APNI (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Pultenaea sp. Narrabri (R.G.Coveny 8811 ;amp; S.K.Roy) replace: Pultenaea sp. (Narrabri R.G.Coveny+ 8811) reason: match_12. Automatic alignment with infraspecific canonical name in APC known names when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Pultenaea sp. Newnes (I.R.Telford 5072 ;amp; M.D.Crisp) replace: Pultenaea sp. Newnes (I.R.Telford 5072 & M.D.Crisp) reason: match_17_fuzzy. Imprecise fuzzy alignment with canonical name in APNI (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Pultenaea sp. Shadowgraph Bluff (T. ;amp; J.Whaite 3455) replace: Pultenaea sp. Shadowgraph Bluff (T. & J.Whaite 3455) reason: match_17_fuzzy. Imprecise fuzzy alignment with canonical name in APNI (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Quassia sp. Moonee Creek (King s.n., Nov 1949) replace: Quassia sp. 'Moonee Creek' (King s.n., Nov 1949) reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Radermachera sinica replace: Radermachera sinica reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Rotheca myricoides subsp. myricoides replace: Rotheca myricoides reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Rubus loganobaccus replace: Rubus loganubaccus reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Salix matsudana x alba replace: Salix matsudana x Salix alba reason: Manual alignment with canonical hybrid species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Salix x fragilis var. fragilis replace: Salix x fragilis reason: Manual alignment with canonical hybrid species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Salix x sepulcralis var. chrysocoma replace: Salix x sepulcralis reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Salix x sepulcralis var. sepulcralis replace: Salix x sepulcralis reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: Varietas + taxonomic_resolution: variety - find: Salvinia molesta replace: Salvinia x molesta reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Sarcocornia quinqueflora subsp. quinqueflora replace: Salicornia quinqueflora subsp. quinqueflora reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Scleranthus sp. Fitz;qu;s Hill (J.G.West 5342) replace: Scleranthus sp. Fitz's Hill (J.G.West 5342) reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Sebaea zeyheri subsp. cleistantha replace: Sebaea zeyheri reason: match_19. Automatic alignment with species-level canonical name in APNI when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Sida sp. B sensu Harden (1990) replace: Sida sp. B reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Sida sp. C sensu Harden (1990) replace: Sida sp. C reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Sorghum almum replace: Sorghum x almum reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Sorghum bicolor subsp. almum replace: Sorghum bicolor subsp. x almum reason: match_08. Automatic alignment with synonymous name in APNI (2022-11-22) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Sorghum bicolor subsp. drummondii replace: Sorghum bicolor subsp. x drummondii reason: match_12. Automatic alignment with infraspecific canonical name in APC known names when notes are ignored (2022-11-22) - taxonomic_resolution: Subspecies + taxonomic_resolution: subspecies - find: Spiraea x billiardii replace: Spiraea x billardii reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Suaeda sp. A sensu Harden (1990) replace: Suaeda sp. A reason: match_14. Automatic alignment with species-level name known by APC when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Teucrium sp. D sensu Conn (1992) replace: Teucrium sp. D Flora of New South Wales (S.A.Horton 4114) reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-22) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Thelymitra irregularis replace: Thelymitra x irregularis reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Thelymitra merraniae replace: Thelymitra merranae reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: Thelymitra truncata replace: Thelymitra x truncata reason: match_14. Automatic alignment with species-level canonical name in APC accepted when notes are ignored (2022-11-21) - taxonomic_resolution: Species + taxonomic_resolution: species - find: X Triticosecale replace: x Triticosecale reason: Manual matched to genus for taxon that can't be matched to species (Elizabeth diff --git a/tests/testthat/examples/Test_2023_4/output/taxa.csv b/tests/testthat/examples/Test_2023_4/output/taxa.csv index 5aae630e..d63b8d6d 100644 --- a/tests/testthat/examples/Test_2023_4/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_4/output/taxa.csv @@ -1,188 +1,188 @@ -taxon_name,taxonomic_reference,taxon_rank,trinomial,binomial,genus,family,taxon_distribution,establishment_means,taxonomic_status,scientific_name,scientific_name_authorship,taxon_id,scientific_name_id -Abildgaardia ovata,,,,,Abildgaardia,,,,,,,, -Acacia alpina,,,,,Acacia,,,,,,,, -Acacia beadleana,,,,,Acacia,,,,,,,, -Acacia bulgaensis,,,,,Acacia,,,,,,,, -Acacia caroleae,,,,,Acacia,,,,,,,, -Acacia crassa,,,,,Acacia,,,,,,,, -Acacia flexifolia,,,,,Acacia,,,,,,,, -Acacia gladiiformis,,,,,Acacia,,,,,,,, -Acacia havilandiorum,,,,,Acacia,,,,,,,, -Acacia leiocalyx subsp. leiocalyx,,,,,Acacia,,,,,,,, -Acacia myrtifolia,,,,,Acacia,,,,,,,, -Acacia ramulosa var. ramulosa,,,,,Acacia,,,,,,,, -Acacia spectabilis,,,,,Acacia,,,,,,,, -Acacia terminalis subsp. Glabrous form (M.Hancock 94),,,,,Acacia,,,,,,,, -Acronychia littoralis,,,,,Acronychia,,,,,,,, -Adriana tomentosa,,,,,Adriana,,,,,,,, -Alectryon coriaceus,,,,,Alectryon,,,,,,,, -Alectryon oleifolius,,,,,Alectryon,,,,,,,, -Alectryon subdentatus,,,,,Alectryon,,,,,,,, -Amyema preissii,,,,,Amyema,,,,,,,, -Angophora leiocarpa,,,,,Angophora,,,,,,,, -Apophyllum anomalum,,,,,Apophyllum,,,,,,,, -Arbutus unedo,,,,,Arbutus,,,,,,,, -Australina pusilla,,,,,Australina,,,,,,,, -Burmannia disticha,,,,,Burmannia,,,,,,,, -Bursaria spinosa subsp. spinosa,,,,,Bursaria,,,,,,,, -Calendula arvensis,,,,,Calendula,,,,,,,, -Callistemon purpurascens,,,,,Callistemon,,,,,,,, -Carex cephalotes,,,,,Carex,,,,,,,, -Carex leporina,,,,,Carex,,,,,,,, -Carex raleighii,,,,,Carex,,,,,,,, -Carmichaelia exsul,,,,,Carmichaelia,,,,,,,, -Cassinia compacta,,,,,Cassinia,,,,,,,, -Castanospermum australe,,,,,Castanospermum,,,,,,,, -Centaurium tenuiflorum,,,,,Centaurium,,,,,,,, -Cestrum nocturnum,,,,,Cestrum,,,,,,,, -Chthonocephalus pseudevax,,,,,Chthonocephalus,,,,,,,, -Claoxylon australe,,,,,Claoxylon,,,,,,,, -Commersonia amystia,,,,,Commersonia,,,,,,,, -Commersonia salviifolia,,,,,Commersonia,,,,,,,, -Convolvulus farinosus,,,,,Convolvulus,,,,,,,, -Coprosma niphophila,,,,,Coprosma,,,,,,,, -Coprosma nivalis,,,,,Coprosma,,,,,,,, -Correa alba,,,,,Correa,,,,,,,, -Corymbia citriodora,,,,,Corymbia,,,,,,,, -Corymbia eximia,,,,,Corymbia,,,,,,,, -Crassula decumbens,,,,,Crassula,,,,,,,, -Crassula peduncularis,,,,,Crassula,,,,,,,, -Crotalaria brevis,,,,,Crotalaria,,,,,,,, -Crotalaria grahamiana,,,,,Crotalaria,,,,,,,, -Crotalaria lanceolata,,,,,Crotalaria,,,,,,,, -Cylindropuntia kleiniae,,,,,Cylindropuntia,,,,,,,, -Cyperus albostriatus,,,,,Cyperus,,,,,,,, -Cyperus betchei,,,,,Cyperus,,,,,,,, -Cyperus bulbosus,,,,,Cyperus,,,,,,,, -Cyperus laevigatus,,,,,Cyperus,,,,,,,, -Cyperus sculptus,,,,,Cyperus,,,,,,,, -Dampiera fusca,,,,,Dampiera,,,,,,,, -Davidsonia johnsonii,,,,,Davidsonia,,,,,,,, -Daviesia arenaria,,,,,Daviesia,,,,,,,, -Derris involuta,,,,,Derris,,,,,,,, -Dichromochlamys dentatifolia,,,,,Dichromochlamys,,,,,,,, -Dillwynia cinerascens,,,,,Dillwynia,,,,,,,, -Dillwynia floribunda,,,,,Dillwynia,,,,,,,, -Dinosperma erythrococcum,,,,,Dinosperma,,,,,,,, -Dodonaea petiolaris,,,,,Dodonaea,,,,,,,, -Dodonaea truncatiales,,,,,Dodonaea,,,,,,,, -Dovyalis caffra,,,,,Dovyalis,,,,,,,, -Elaeocarpus grandis,,,,,Elaeocarpus,,,,,,,, -Eleocharis pallens,,,,,Eleocharis,,,,,,,, -Endiandra globosa,,,,,Endiandra,,,,,,,, -Endiandra muelleri,,,,,Endiandra,,,,,,,, -Epilobium gunnianum,,,,,Epilobium,,,,,,,, -Eremophila deserti,,,,,Eremophila,,,,,,,, -Eremophila oppositifolia,,,,,Eremophila,,,,,,,, -Erigeron conyzoides,,,,,Erigeron,,,,,,,, -Erythroxylum australe,,,,,Erythroxylum,,,,,,,, -Escallonia bifida,,,,,Escallonia,,,,,,,, -Eucalyptus badjensis,,,,,Eucalyptus,,,,,,,, -Eucalyptus camphora,,,,,Eucalyptus,,,,,,,, -Eucalyptus dorrigoensis,,,,,Eucalyptus,,,,,,,, -Eucalyptus leucoxylon subsp. pruinosa,,,,,Eucalyptus,,,,,,,, -Eucalyptus muelleriana,,,,,Eucalyptus,,,,,,,, -Eucalyptus nandewarica,,,,,Eucalyptus,,,,,,,, -Eucalyptus oblonga,,,,,Eucalyptus,,,,,,,, -Eucalyptus olida,,,,,Eucalyptus,,,,,,,, -Eucalyptus pulverulenta,,,,,Eucalyptus,,,,,,,, -Eucalyptus recurva,,,,,Eucalyptus,,,,,,,, -Eucalyptus rossii,,,,,Eucalyptus,,,,,,,, -Eucalyptus scias,,,,,Eucalyptus,,,,,,,, -Eucalyptus viminalis,,,,,Eucalyptus,,,,,,,, -Eucalyptus yangoura,,,,,Eucalyptus,,,,,,,, -Eucalyptus youmanii,,,,,Eucalyptus,,,,,,,, -Euphorbia inappendiculata var. queenslandica,,,,,Euphorbia,,,,,,,, -Exocarpos homalocladus,,,,,Exocarpos,,,,,,,, -Exocarpos sparteus,,,,,Exocarpos,,,,,,,, -Ficus henneana,,,,,Ficus,,,,,,,, -Freesia hybrid,,,,,Freesia,,,,,,,, -Freesia laxa,,,,,Freesia,,,,,,,, -Geijera salicifolia,,,,,Geijera,,,,,,,, -Gentiana wingecarribiensis,,,,,Gentiana,,,,,,,, -Gentianella barringtonensis,,,,,Gentianella,,,,,,,, -Geranium obtusisepalum,,,,,Geranium,,,,,,,, -Geranium purpureum subsp. purpureum,,,,,Geranium,,,,,,,, -Gompholobium grandiflorum,,,,,Gompholobium,,,,,,,, -Goodenia varia,,,,,Goodenia,,,,,,,, -Gossia bidwillii,,,,,Gossia,,,,,,,, -Grevillea scortechinii,,,,,Grevillea,,,,,,,, -Hakea macraeana,,,,,Hakea,,,,,,,, -Hemisteptia lyrata,,,,,Hemisteptia,,,,,,,, -Hibbertia crinita,,,,,Hibbertia,,,,,,,, -Hibiscus brachysiphonius,,,,,Hibiscus,,,,,,,, -Hibiscus sturtii,,,,,Hibiscus,,,,,,,, -Hypericum elodes,,,,,Hypericum,,,,,,,, -Hypoxis glabella var. glabella,,,,,Hypoxis,,,,,,,, -Imperata cylindrica,,,,,Imperata,,,,,,,, -Indigofera triflora,,,,,Indigofera,,,,,,,, -Ipomoea cairica,,,,,Ipomoea,,,,,,,, -Isolepis montivaga,,,,,Isolepis,,,,,,,, -Isotoma axillaris,,,,,Isotoma,,,,,,,, -Isotoma fluviatilis subsp. fluviatilis,,,,,Isotoma,,,,,,,, -Juncus acutus subsp. acutus,,,,,Juncus,,,,,,,, -Juncus kraussii,,,,,Juncus,,,,,,,, -Lantana montevidensis,,,,,Lantana,,,,,,,, -Lepidium africanum,,,,,Lepidium,,,,,,,, -Lepidium foliosum,,,,,Lepidium,,,,,,,, -Lepidium oxytrichum,,,,,Lepidium,,,,,,,, -Lepidosperma gladiatum,,,,,Lepidosperma,,,,,,,, -Leptomeria drupacea,,,,,Leptomeria,,,,,,,, -Leptospermum continentale,,,,,Leptospermum,,,,,,,, -Leptospermum obovatum,,,,,Leptospermum,,,,,,,, -Leucopogon amplexicaulis,,,,,Leucopogon,,,,,,,, -Lobelia pedunculata,,,,,Lobelia,,,,,,,, -Lobelia trigonocaulis,,,,,Lobelia,,,,,,,, -Lotononis bainesii,,,,,Lotononis,,,,,,,, -Lotus corniculatus,,,,,Lotus,,,,,,,, -Lupinus polyphyllus,,,,,Lupinus,,,,,,,, -Medicago orbicularis,,,,,Medicago,,,,,,,, -Melichrus procumbens,,,,,Melichrus,,,,,,,, -Mischocarpus australis,,,,,Mischocarpus,,,,,,,, -Muehlenbeckia adpressa,,,,,Muehlenbeckia,,,,,,,, -Myoporum boninense subsp. australe,,,,,Myoporum,,,,,,,, -Nicotiana glauca,,,,,Nicotiana,,,,,,,, -Nicotiana goodspeedii,,,,,Nicotiana,,,,,,,, -Oxalis corniculata,,,,,Oxalis,,,,,,,, -Pandorea pandorana subsp. austrocaledonica,,,,,Pandorea,,,,,,,, -Paraserianthes lophantha,,,,,Paraserianthes,,,,,,,, -Parentucellia latifolia,,,,,Parentucellia,,,,,,,, -Phlegmatospermum cochlearinum,,,,,Phlegmatospermum,,,,,,,, -Phyla nodiflora,,,,,Phyla,,,,,,,, -Picris barbarorum,,,,,Picris,,,,,,,, -Pimelea ligustrina subsp. ligustrina,,,,,Pimelea,,,,,,,, -Pinus pinea,,,,,Pinus,,,,,,,, -Pisum sativum var. arvense,,,,,Pisum,,,,,,,, -Pittosporum erioloma,,,,,Pittosporum,,,,,,,, -Plantago turrifera,,,,,Plantago,,,,,,,, -Polycarpon tetraphyllum,,,,,Polycarpon,,,,,,,, -Potamogeton australiensis,,,,,Potamogeton,,,,,,,, -Psoralea pinnata,,,,,Psoralea,,,,,,,, -Pultenaea ferruginea,,,,,Pultenaea,,,,,,,, -Rhodamnia argentea,,,,,Rhodamnia,,,,,,,, -Rorippa gigantea,,,,,Rorippa,,,,,,,, -Rubus parvifolius,,,,,Rubus,,,,,,,, -Salix alba,,,,,Salix,,,,,,,, -Schenkia australis,,,,,Schenkia,,,,,,,, -Schoenus apogon,,,,,Schoenus,,,,,,,, -Schoenus brevifolius,,,,,Schoenus,,,,,,,, -Schoenus lepidosperma,,,,,Schoenus,,,,,,,, -Schoenus vaginatus,,,,,Schoenus,,,,,,,, -Scleria rugosa,,,,,Scleria,,,,,,,, -Senecio longipilus,,,,,Senecio,,,,,,,, -Sida goniocarpa,,,,,Sida,,,,,,,, -Sigesbeckia orientalis,,,,,Sigesbeckia,,,,,,,, -Sisymbrium irio,,,,,Sisymbrium,,,,,,,, -Sparaxis bulbifera,,,,,Sparaxis,,,,,,,, -Spergularia diandra,,,,,Spergularia,,,,,,,, -Sphaeromorphaea littoralis,,,,,Sphaeromorphaea,,,,,,,, -Stellaria angustifolia subsp. angustifolia,,,,,Stellaria,,,,,,,, -Styphelia viridis,,,,,Styphelia,,,,,,,, -Swainsona cadellii,,,,,Swainsona,,,,,,,, -Teucrium puberulum,,,,,Teucrium,,,,,,,, -Thelymitra kangaloonica,,,,,Thelymitra,,,,,,,, -Thesium australe,,,,,Thesium,,,,,,,, -Trifolium dubium,,,,,Trifolium,,,,,,,, -Veronica catenata,,,,,Veronica,,,,,,,, -Veronica derwentiana,,,,,Veronica,,,,,,,, -Wahlenbergia luteola,,,,,Wahlenbergia,,,,,,,, +taxon_name,taxonomic_reference,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution +Abildgaardia ovata,,,,,,,,, +Acacia alpina,,,,,,,,, +Acacia beadleana,,,,,,,,, +Acacia bulgaensis,,,,,,,,, +Acacia caroleae,,,,,,,,, +Acacia crassa,,,,,,,,, +Acacia flexifolia,,,,,,,,, +Acacia gladiiformis,,,,,,,,, +Acacia havilandiorum,,,,,,,,, +Acacia leiocalyx subsp. leiocalyx,,,,,,,,, +Acacia myrtifolia,,,,,,,,, +Acacia ramulosa var. ramulosa,,,,,,,,, +Acacia spectabilis,,,,,,,,, +Acacia terminalis subsp. Glabrous form (M.Hancock 94),,,,,,,,, +Acronychia littoralis,,,,,,,,, +Adriana tomentosa,,,,,,,,, +Alectryon coriaceus,,,,,,,,, +Alectryon oleifolius,,,,,,,,, +Alectryon subdentatus,,,,,,,,, +Amyema preissii,,,,,,,,, +Angophora leiocarpa,,,,,,,,, +Apophyllum anomalum,,,,,,,,, +Arbutus unedo,,,,,,,,, +Australina pusilla,,,,,,,,, +Burmannia disticha,,,,,,,,, +Bursaria spinosa subsp. spinosa,,,,,,,,, +Calendula arvensis,,,,,,,,, +Callistemon purpurascens,,,,,,,,, +Carex cephalotes,,,,,,,,, +Carex leporina,,,,,,,,, +Carex raleighii,,,,,,,,, +Carmichaelia exsul,,,,,,,,, +Cassinia compacta,,,,,,,,, +Castanospermum australe,,,,,,,,, +Centaurium tenuiflorum,,,,,,,,, +Cestrum nocturnum,,,,,,,,, +Chthonocephalus pseudevax,,,,,,,,, +Claoxylon australe,,,,,,,,, +Commersonia amystia,,,,,,,,, +Commersonia salviifolia,,,,,,,,, +Convolvulus farinosus,,,,,,,,, +Coprosma niphophila,,,,,,,,, +Coprosma nivalis,,,,,,,,, +Correa alba,,,,,,,,, +Corymbia citriodora,,,,,,,,, +Corymbia eximia,,,,,,,,, +Crassula decumbens,,,,,,,,, +Crassula peduncularis,,,,,,,,, +Crotalaria brevis,,,,,,,,, +Crotalaria grahamiana,,,,,,,,, +Crotalaria lanceolata,,,,,,,,, +Cylindropuntia kleiniae,,,,,,,,, +Cyperus albostriatus,,,,,,,,, +Cyperus betchei,,,,,,,,, +Cyperus bulbosus,,,,,,,,, +Cyperus laevigatus,,,,,,,,, +Cyperus sculptus,,,,,,,,, +Dampiera fusca,,,,,,,,, +Davidsonia johnsonii,,,,,,,,, +Daviesia arenaria,,,,,,,,, +Derris involuta,,,,,,,,, +Dichromochlamys dentatifolia,,,,,,,,, +Dillwynia cinerascens,,,,,,,,, +Dillwynia floribunda,,,,,,,,, +Dinosperma erythrococcum,,,,,,,,, +Dodonaea petiolaris,,,,,,,,, +Dodonaea truncatiales,,,,,,,,, +Dovyalis caffra,,,,,,,,, +Elaeocarpus grandis,,,,,,,,, +Eleocharis pallens,,,,,,,,, +Endiandra globosa,,,,,,,,, +Endiandra muelleri,,,,,,,,, +Epilobium gunnianum,,,,,,,,, +Eremophila deserti,,,,,,,,, +Eremophila oppositifolia,,,,,,,,, +Erigeron conyzoides,,,,,,,,, +Erythroxylum australe,,,,,,,,, +Escallonia bifida,,,,,,,,, +Eucalyptus badjensis,,,,,,,,, +Eucalyptus camphora,,,,,,,,, +Eucalyptus dorrigoensis,,,,,,,,, +Eucalyptus leucoxylon subsp. pruinosa,,,,,,,,, +Eucalyptus muelleriana,,,,,,,,, +Eucalyptus nandewarica,,,,,,,,, +Eucalyptus oblonga,,,,,,,,, +Eucalyptus olida,,,,,,,,, +Eucalyptus pulverulenta,,,,,,,,, +Eucalyptus recurva,,,,,,,,, +Eucalyptus rossii,,,,,,,,, +Eucalyptus scias,,,,,,,,, +Eucalyptus viminalis,,,,,,,,, +Eucalyptus yangoura,,,,,,,,, +Eucalyptus youmanii,,,,,,,,, +Euphorbia inappendiculata var. queenslandica,,,,,,,,, +Exocarpos homalocladus,,,,,,,,, +Exocarpos sparteus,,,,,,,,, +Ficus henneana,,,,,,,,, +Freesia hybrid,,,,,,,,, +Freesia laxa,,,,,,,,, +Geijera salicifolia,,,,,,,,, +Gentiana wingecarribiensis,,,,,,,,, +Gentianella barringtonensis,,,,,,,,, +Geranium obtusisepalum,,,,,,,,, +Geranium purpureum subsp. purpureum,,,,,,,,, +Gompholobium grandiflorum,,,,,,,,, +Goodenia varia,,,,,,,,, +Gossia bidwillii,,,,,,,,, +Grevillea scortechinii,,,,,,,,, +Hakea macraeana,,,,,,,,, +Hemisteptia lyrata,,,,,,,,, +Hibbertia crinita,,,,,,,,, +Hibiscus brachysiphonius,,,,,,,,, +Hibiscus sturtii,,,,,,,,, +Hypericum elodes,,,,,,,,, +Hypoxis glabella var. glabella,,,,,,,,, +Imperata cylindrica,,,,,,,,, +Indigofera triflora,,,,,,,,, +Ipomoea cairica,,,,,,,,, +Isolepis montivaga,,,,,,,,, +Isotoma axillaris,,,,,,,,, +Isotoma fluviatilis subsp. fluviatilis,,,,,,,,, +Juncus acutus subsp. acutus,,,,,,,,, +Juncus kraussii,,,,,,,,, +Lantana montevidensis,,,,,,,,, +Lepidium africanum,,,,,,,,, +Lepidium foliosum,,,,,,,,, +Lepidium oxytrichum,,,,,,,,, +Lepidosperma gladiatum,,,,,,,,, +Leptomeria drupacea,,,,,,,,, +Leptospermum continentale,,,,,,,,, +Leptospermum obovatum,,,,,,,,, +Leucopogon amplexicaulis,,,,,,,,, +Lobelia pedunculata,,,,,,,,, +Lobelia trigonocaulis,,,,,,,,, +Lotononis bainesii,,,,,,,,, +Lotus corniculatus,,,,,,,,, +Lupinus polyphyllus,,,,,,,,, +Medicago orbicularis,,,,,,,,, +Melichrus procumbens,,,,,,,,, +Mischocarpus australis,,,,,,,,, +Muehlenbeckia adpressa,,,,,,,,, +Myoporum boninense subsp. australe,,,,,,,,, +Nicotiana glauca,,,,,,,,, +Nicotiana goodspeedii,,,,,,,,, +Oxalis corniculata,,,,,,,,, +Pandorea pandorana subsp. austrocaledonica,,,,,,,,, +Paraserianthes lophantha,,,,,,,,, +Parentucellia latifolia,,,,,,,,, +Phlegmatospermum cochlearinum,,,,,,,,, +Phyla nodiflora,,,,,,,,, +Picris barbarorum,,,,,,,,, +Pimelea ligustrina subsp. ligustrina,,,,,,,,, +Pinus pinea,,,,,,,,, +Pisum sativum var. arvense,,,,,,,,, +Pittosporum erioloma,,,,,,,,, +Plantago turrifera,,,,,,,,, +Polycarpon tetraphyllum,,,,,,,,, +Potamogeton australiensis,,,,,,,,, +Psoralea pinnata,,,,,,,,, +Pultenaea ferruginea,,,,,,,,, +Rhodamnia argentea,,,,,,,,, +Rorippa gigantea,,,,,,,,, +Rubus parvifolius,,,,,,,,, +Salix alba,,,,,,,,, +Schenkia australis,,,,,,,,, +Schoenus apogon,,,,,,,,, +Schoenus brevifolius,,,,,,,,, +Schoenus lepidosperma,,,,,,,,, +Schoenus vaginatus,,,,,,,,, +Scleria rugosa,,,,,,,,, +Senecio longipilus,,,,,,,,, +Sida goniocarpa,,,,,,,,, +Sigesbeckia orientalis,,,,,,,,, +Sisymbrium irio,,,,,,,,, +Sparaxis bulbifera,,,,,,,,, +Spergularia diandra,,,,,,,,, +Sphaeromorphaea littoralis,,,,,,,,, +Stellaria angustifolia subsp. angustifolia,,,,,,,,, +Styphelia viridis,,,,,,,,, +Swainsona cadellii,,,,,,,,, +Teucrium puberulum,,,,,,,,, +Thelymitra kangaloonica,,,,,,,,, +Thesium australe,,,,,,,,, +Trifolium dubium,,,,,,,,, +Veronica catenata,,,,,,,,, +Veronica derwentiana,,,,,,,,, +Wahlenbergia luteola,,,,,,,,, diff --git a/tests/testthat/examples/Test_2023_4/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_4/output/taxonomic_updates.csv index 66128283..84c0ae9c 100644 --- a/tests/testthat/examples/Test_2023_4/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_4/output/taxonomic_updates.csv @@ -1,188 +1,188 @@ -dataset_id,original_name,cleaned_name,taxonomic_resolution,cleaned_scientific_name_id,cleaned_name_taxonomic_status,cleaned_name_alternative_taxonomic_status,taxon_id,taxon_name -Test_2023_4,Abildgaardia ovata,Abildgaardia ovata,,,,,, -Test_2023_4,Acacia alpina,Acacia alpina,,,,,, -Test_2023_4,Acacia beadleana,Acacia beadleana,,,,,, -Test_2023_4,Acacia bulgaensis,Acacia bulgaensis,,,,,, -Test_2023_4,Acacia caroleae,Acacia caroleae,,,,,, -Test_2023_4,Acacia crassa,Acacia crassa,,,,,, -Test_2023_4,Acacia flexifolia,Acacia flexifolia,,,,,, -Test_2023_4,Acacia gladiiformis,Acacia gladiiformis,,,,,, -Test_2023_4,Acacia havilandiorum,Acacia havilandiorum,,,,,, -Test_2023_4,Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx subsp. leiocalyx,,,,,, -Test_2023_4,Acacia myrtifolia,Acacia myrtifolia,,,,,, -Test_2023_4,Acacia ramulosa var. ramulosa,Acacia ramulosa var. ramulosa,,,,,, -Test_2023_4,Acacia spectabilis,Acacia spectabilis,,,,,, -Test_2023_4,Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis subsp. Glabrous form (M.Hancock 94),,,,,, -Test_2023_4,Acronychia littoralis,Acronychia littoralis,,,,,, -Test_2023_4,Adriana tomentosa,Adriana tomentosa,,,,,, -Test_2023_4,Alectryon coriaceus,Alectryon coriaceus,,,,,, -Test_2023_4,Alectryon oleifolius,Alectryon oleifolius,,,,,, -Test_2023_4,Alectryon subdentatus,Alectryon subdentatus,,,,,, -Test_2023_4,Amyema preissii,Amyema preissii,,,,,, -Test_2023_4,Angophora leiocarpa,Angophora leiocarpa,,,,,, -Test_2023_4,Apophyllum anomalum,Apophyllum anomalum,,,,,, -Test_2023_4,Arbutus unedo,Arbutus unedo,,,,,, -Test_2023_4,Australina pusilla,Australina pusilla,,,,,, -Test_2023_4,Burmannia disticha,Burmannia disticha,,,,,, -Test_2023_4,Bursaria spinosa subsp. spinosa,Bursaria spinosa subsp. spinosa,,,,,, -Test_2023_4,Calendula arvensis,Calendula arvensis,,,,,, -Test_2023_4,Callistemon purpurascens,Callistemon purpurascens,,,,,, -Test_2023_4,Carex cephalotes,Carex cephalotes,,,,,, -Test_2023_4,Carex leporina,Carex leporina,,,,,, -Test_2023_4,Carex raleighii,Carex raleighii,,,,,, -Test_2023_4,Carmichaelia exsul,Carmichaelia exsul,,,,,, -Test_2023_4,Cassinia compacta,Cassinia compacta,,,,,, -Test_2023_4,Castanospermum australe,Castanospermum australe,,,,,, -Test_2023_4,Centaurium tenuiflorum,Centaurium tenuiflorum,,,,,, -Test_2023_4,Cestrum nocturnum,Cestrum nocturnum,,,,,, -Test_2023_4,Chthonocephalus pseudevax,Chthonocephalus pseudevax,,,,,, -Test_2023_4,Claoxylon australe,Claoxylon australe,,,,,, -Test_2023_4,Commersonia amystia,Commersonia amystia,,,,,, -Test_2023_4,Commersonia salviifolia,Commersonia salviifolia,,,,,, -Test_2023_4,Convolvulus farinosus,Convolvulus farinosus,,,,,, -Test_2023_4,Coprosma niphophila,Coprosma niphophila,,,,,, -Test_2023_4,Coprosma nivalis,Coprosma nivalis,,,,,, -Test_2023_4,Correa alba,Correa alba,,,,,, -Test_2023_4,Corymbia citriodora,Corymbia citriodora,,,,,, -Test_2023_4,Corymbia eximia,Corymbia eximia,,,,,, -Test_2023_4,Crassula decumbens,Crassula decumbens,,,,,, -Test_2023_4,Crassula peduncularis,Crassula peduncularis,,,,,, -Test_2023_4,Crotalaria brevis,Crotalaria brevis,,,,,, -Test_2023_4,Crotalaria grahamiana,Crotalaria grahamiana,,,,,, -Test_2023_4,Crotalaria lanceolata,Crotalaria lanceolata,,,,,, -Test_2023_4,Cylindropuntia kleiniae,Cylindropuntia kleiniae,,,,,, -Test_2023_4,Cyperus albostriatus,Cyperus albostriatus,,,,,, -Test_2023_4,Cyperus betchei,Cyperus betchei,,,,,, -Test_2023_4,Cyperus bulbosus,Cyperus bulbosus,,,,,, -Test_2023_4,Cyperus laevigatus,Cyperus laevigatus,,,,,, -Test_2023_4,Cyperus sculptus,Cyperus sculptus,,,,,, -Test_2023_4,Dampiera fusca,Dampiera fusca,,,,,, -Test_2023_4,Davidsonia johnsonii,Davidsonia johnsonii,,,,,, -Test_2023_4,Daviesia arenaria,Daviesia arenaria,,,,,, -Test_2023_4,Derris involuta,Derris involuta,,,,,, -Test_2023_4,Dichromochlamys dentatifolia,Dichromochlamys dentatifolia,,,,,, -Test_2023_4,Dillwynia cinerascens,Dillwynia cinerascens,,,,,, -Test_2023_4,Dillwynia floribunda,Dillwynia floribunda,,,,,, -Test_2023_4,Dinosperma erythrococcum,Dinosperma erythrococcum,,,,,, -Test_2023_4,Dodonaea petiolaris,Dodonaea petiolaris,,,,,, -Test_2023_4,Dodonaea truncatiales,Dodonaea truncatiales,,,,,, -Test_2023_4,Dovyalis caffra,Dovyalis caffra,,,,,, -Test_2023_4,Elaeocarpus grandis,Elaeocarpus grandis,,,,,, -Test_2023_4,Eleocharis pallens,Eleocharis pallens,,,,,, -Test_2023_4,Endiandra globosa,Endiandra globosa,,,,,, -Test_2023_4,Endiandra muelleri,Endiandra muelleri,,,,,, -Test_2023_4,Epilobium gunnianum,Epilobium gunnianum,,,,,, -Test_2023_4,Eremophila deserti,Eremophila deserti,,,,,, -Test_2023_4,Eremophila oppositifolia,Eremophila oppositifolia,,,,,, -Test_2023_4,Erigeron conyzoides,Erigeron conyzoides,,,,,, -Test_2023_4,Erythroxylum australe,Erythroxylum australe,,,,,, -Test_2023_4,Escallonia bifida,Escallonia bifida,,,,,, -Test_2023_4,Eucalyptus badjensis,Eucalyptus badjensis,,,,,, -Test_2023_4,Eucalyptus camphora,Eucalyptus camphora,,,,,, -Test_2023_4,Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,,,,,, -Test_2023_4,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,,,,,, -Test_2023_4,Eucalyptus muelleriana,Eucalyptus muelleriana,,,,,, -Test_2023_4,Eucalyptus nandewarica,Eucalyptus nandewarica,,,,,, -Test_2023_4,Eucalyptus oblonga,Eucalyptus oblonga,,,,,, -Test_2023_4,Eucalyptus olida,Eucalyptus olida,,,,,, -Test_2023_4,Eucalyptus pulverulenta,Eucalyptus pulverulenta,,,,,, -Test_2023_4,Eucalyptus recurva,Eucalyptus recurva,,,,,, -Test_2023_4,Eucalyptus rossii,Eucalyptus rossii,,,,,, -Test_2023_4,Eucalyptus scias,Eucalyptus scias,,,,,, -Test_2023_4,Eucalyptus viminalis,Eucalyptus viminalis,,,,,, -Test_2023_4,Eucalyptus yangoura,Eucalyptus yangoura,,,,,, -Test_2023_4,Eucalyptus youmanii,Eucalyptus youmanii,,,,,, -Test_2023_4,Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata var. queenslandica,,,,,, -Test_2023_4,Exocarpos homalocladus,Exocarpos homalocladus,,,,,, -Test_2023_4,Exocarpos sparteus,Exocarpos sparteus,,,,,, -Test_2023_4,Ficus henneana,Ficus henneana,,,,,, -Test_2023_4,Freesia hybrid,Freesia hybrid,,,,,, -Test_2023_4,Freesia laxa,Freesia laxa,,,,,, -Test_2023_4,Geijera salicifolia,Geijera salicifolia,,,,,, -Test_2023_4,Gentiana wingecarribiensis,Gentiana wingecarribiensis,,,,,, -Test_2023_4,Gentianella barringtonensis,Gentianella barringtonensis,,,,,, -Test_2023_4,Geranium obtusisepalum,Geranium obtusisepalum,,,,,, -Test_2023_4,Geranium purpureum subsp. purpureum,Geranium purpureum subsp. purpureum,,,,,, -Test_2023_4,Gompholobium grandiflorum,Gompholobium grandiflorum,,,,,, -Test_2023_4,Goodenia varia,Goodenia varia,,,,,, -Test_2023_4,Gossia bidwillii,Gossia bidwillii,,,,,, -Test_2023_4,Grevillea scortechinii,Grevillea scortechinii,,,,,, -Test_2023_4,Hakea macraeana,Hakea macraeana,,,,,, -Test_2023_4,Hemisteptia lyrata,Hemisteptia lyrata,,,,,, -Test_2023_4,Hibbertia crinita,Hibbertia crinita,,,,,, -Test_2023_4,Hibiscus brachysiphonius,Hibiscus brachysiphonius,,,,,, -Test_2023_4,Hibiscus sturtii,Hibiscus sturtii,,,,,, -Test_2023_4,Hypericum elodes,Hypericum elodes,,,,,, -Test_2023_4,Hypoxis glabella var. glabella,Hypoxis glabella var. glabella,,,,,, -Test_2023_4,Imperata cylindrica,Imperata cylindrica,,,,,, -Test_2023_4,Indigofera triflora,Indigofera triflora,,,,,, -Test_2023_4,Ipomoea cairica,Ipomoea cairica,,,,,, -Test_2023_4,Isolepis montivaga,Isolepis montivaga,,,,,, -Test_2023_4,Isotoma axillaris,Isotoma axillaris,,,,,, -Test_2023_4,Isotoma fluviatilis subsp. fluviatilis,Isotoma fluviatilis subsp. fluviatilis,,,,,, -Test_2023_4,Juncus acutus subsp. acutus,Juncus acutus subsp. acutus,,,,,, -Test_2023_4,Juncus kraussii,Juncus kraussii,,,,,, -Test_2023_4,Lantana montevidensis,Lantana montevidensis,,,,,, -Test_2023_4,Lepidium africanum,Lepidium africanum,,,,,, -Test_2023_4,Lepidium foliosum,Lepidium foliosum,,,,,, -Test_2023_4,Lepidium oxytrichum,Lepidium oxytrichum,,,,,, -Test_2023_4,Lepidosperma gladiatum,Lepidosperma gladiatum,,,,,, -Test_2023_4,Leptomeria drupacea,Leptomeria drupacea,,,,,, -Test_2023_4,Leptospermum continentale,Leptospermum continentale,,,,,, -Test_2023_4,Leptospermum obovatum,Leptospermum obovatum,,,,,, -Test_2023_4,Leucopogon amplexicaulis,Leucopogon amplexicaulis,,,,,, -Test_2023_4,Lobelia pedunculata,Lobelia pedunculata,,,,,, -Test_2023_4,Lobelia trigonocaulis,Lobelia trigonocaulis,,,,,, -Test_2023_4,Lotononis bainesii,Lotononis bainesii,,,,,, -Test_2023_4,Lotus corniculatus,Lotus corniculatus,,,,,, -Test_2023_4,Lupinus polyphyllus,Lupinus polyphyllus,,,,,, -Test_2023_4,Medicago orbicularis,Medicago orbicularis,,,,,, -Test_2023_4,Melichrus procumbens,Melichrus procumbens,,,,,, -Test_2023_4,Mischocarpus australis,Mischocarpus australis,,,,,, -Test_2023_4,Muehlenbeckia adpressa,Muehlenbeckia adpressa,,,,,, -Test_2023_4,Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,,,,,, -Test_2023_4,Nicotiana glauca,Nicotiana glauca,,,,,, -Test_2023_4,Nicotiana goodspeedii,Nicotiana goodspeedii,,,,,, -Test_2023_4,Oxalis corniculata,Oxalis corniculata,,,,,, -Test_2023_4,Pandorea pandorana subsp. austrocaledonica,Pandorea pandorana subsp. austrocaledonica,,,,,, -Test_2023_4,Paraserianthes lophantha,Paraserianthes lophantha,,,,,, -Test_2023_4,Parentucellia latifolia,Parentucellia latifolia,,,,,, -Test_2023_4,Phlegmatospermum cochlearinum,Phlegmatospermum cochlearinum,,,,,, -Test_2023_4,Phyla nodiflora,Phyla nodiflora,,,,,, -Test_2023_4,Picris barbarorum,Picris barbarorum,,,,,, -Test_2023_4,Pimelea ligustrina subsp. ligustrina,Pimelea ligustrina subsp. ligustrina,,,,,, -Test_2023_4,Pinus pinea,Pinus pinea,,,,,, -Test_2023_4,Pisum sativum var. arvense,Pisum sativum var. arvense,,,,,, -Test_2023_4,Pittosporum erioloma,Pittosporum erioloma,,,,,, -Test_2023_4,Plantago turrifera,Plantago turrifera,,,,,, -Test_2023_4,Polycarpon tetraphyllum,Polycarpon tetraphyllum,,,,,, -Test_2023_4,Potamogeton australiensis,Potamogeton australiensis,,,,,, -Test_2023_4,Psoralea pinnata,Psoralea pinnata,,,,,, -Test_2023_4,Pultenaea ferruginea,Pultenaea ferruginea,,,,,, -Test_2023_4,Rhodamnia argentea,Rhodamnia argentea,,,,,, -Test_2023_4,Rorippa gigantea,Rorippa gigantea,,,,,, -Test_2023_4,Rubus parvifolius,Rubus parvifolius,,,,,, -Test_2023_4,Salix alba,Salix alba,,,,,, -Test_2023_4,Schenkia australis,Schenkia australis,,,,,, -Test_2023_4,Schoenus apogon,Schoenus apogon,,,,,, -Test_2023_4,Schoenus brevifolius,Schoenus brevifolius,,,,,, -Test_2023_4,Schoenus lepidosperma,Schoenus lepidosperma,,,,,, -Test_2023_4,Schoenus vaginatus,Schoenus vaginatus,,,,,, -Test_2023_4,Scleria rugosa,Scleria rugosa,,,,,, -Test_2023_4,Senecio longipilus,Senecio longipilus,,,,,, -Test_2023_4,Sida goniocarpa,Sida goniocarpa,,,,,, -Test_2023_4,Sigesbeckia orientalis,Sigesbeckia orientalis,,,,,, -Test_2023_4,Sisymbrium irio,Sisymbrium irio,,,,,, -Test_2023_4,Sparaxis bulbifera,Sparaxis bulbifera,,,,,, -Test_2023_4,Spergularia diandra,Spergularia diandra,,,,,, -Test_2023_4,Sphaeromorphaea littoralis,Sphaeromorphaea littoralis,,,,,, -Test_2023_4,Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia subsp. angustifolia,,,,,, -Test_2023_4,Styphelia viridis,Styphelia viridis,,,,,, -Test_2023_4,Swainsona cadellii,Swainsona cadellii,,,,,, -Test_2023_4,Teucrium puberulum,Teucrium puberulum,,,,,, -Test_2023_4,Thelymitra kangaloonica,Thelymitra kangaloonica,,,,,, -Test_2023_4,Thesium australe,Thesium australe,,,,,, -Test_2023_4,Trifolium dubium,Trifolium dubium,,,,,, -Test_2023_4,Veronica catenata,Veronica catenata,,,,,, -Test_2023_4,Veronica derwentiana,Veronica derwentiana,,,,,, -Test_2023_4,Wahlenbergia luteola,Wahlenbergia luteola,,,,,, +dataset_id,original_name,cleaned_name,taxonomic_resolution,taxon_name +Test_2023_4,Abildgaardia ovata,Abildgaardia ovata,, +Test_2023_4,Acacia alpina,Acacia alpina,, +Test_2023_4,Acacia beadleana,Acacia beadleana,, +Test_2023_4,Acacia bulgaensis,Acacia bulgaensis,, +Test_2023_4,Acacia caroleae,Acacia caroleae,, +Test_2023_4,Acacia crassa,Acacia crassa,, +Test_2023_4,Acacia flexifolia,Acacia flexifolia,, +Test_2023_4,Acacia gladiiformis,Acacia gladiiformis,, +Test_2023_4,Acacia havilandiorum,Acacia havilandiorum,, +Test_2023_4,Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx subsp. leiocalyx,, +Test_2023_4,Acacia myrtifolia,Acacia myrtifolia,, +Test_2023_4,Acacia ramulosa var. ramulosa,Acacia ramulosa var. ramulosa,, +Test_2023_4,Acacia spectabilis,Acacia spectabilis,, +Test_2023_4,Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis subsp. Glabrous form (M.Hancock 94),, +Test_2023_4,Acronychia littoralis,Acronychia littoralis,, +Test_2023_4,Adriana tomentosa,Adriana tomentosa,, +Test_2023_4,Alectryon coriaceus,Alectryon coriaceus,, +Test_2023_4,Alectryon oleifolius,Alectryon oleifolius,, +Test_2023_4,Alectryon subdentatus,Alectryon subdentatus,, +Test_2023_4,Amyema preissii,Amyema preissii,, +Test_2023_4,Angophora leiocarpa,Angophora leiocarpa,, +Test_2023_4,Apophyllum anomalum,Apophyllum anomalum,, +Test_2023_4,Arbutus unedo,Arbutus unedo,, +Test_2023_4,Australina pusilla,Australina pusilla,, +Test_2023_4,Burmannia disticha,Burmannia disticha,, +Test_2023_4,Bursaria spinosa subsp. spinosa,Bursaria spinosa subsp. spinosa,, +Test_2023_4,Calendula arvensis,Calendula arvensis,, +Test_2023_4,Callistemon purpurascens,Callistemon purpurascens,, +Test_2023_4,Carex cephalotes,Carex cephalotes,, +Test_2023_4,Carex leporina,Carex leporina,, +Test_2023_4,Carex raleighii,Carex raleighii,, +Test_2023_4,Carmichaelia exsul,Carmichaelia exsul,, +Test_2023_4,Cassinia compacta,Cassinia compacta,, +Test_2023_4,Castanospermum australe,Castanospermum australe,, +Test_2023_4,Centaurium tenuiflorum,Centaurium tenuiflorum,, +Test_2023_4,Cestrum nocturnum,Cestrum nocturnum,, +Test_2023_4,Chthonocephalus pseudevax,Chthonocephalus pseudevax,, +Test_2023_4,Claoxylon australe,Claoxylon australe,, +Test_2023_4,Commersonia amystia,Commersonia amystia,, +Test_2023_4,Commersonia salviifolia,Commersonia salviifolia,, +Test_2023_4,Convolvulus farinosus,Convolvulus farinosus,, +Test_2023_4,Coprosma niphophila,Coprosma niphophila,, +Test_2023_4,Coprosma nivalis,Coprosma nivalis,, +Test_2023_4,Correa alba,Correa alba,, +Test_2023_4,Corymbia citriodora,Corymbia citriodora,, +Test_2023_4,Corymbia eximia,Corymbia eximia,, +Test_2023_4,Crassula decumbens,Crassula decumbens,, +Test_2023_4,Crassula peduncularis,Crassula peduncularis,, +Test_2023_4,Crotalaria brevis,Crotalaria brevis,, +Test_2023_4,Crotalaria grahamiana,Crotalaria grahamiana,, +Test_2023_4,Crotalaria lanceolata,Crotalaria lanceolata,, +Test_2023_4,Cylindropuntia kleiniae,Cylindropuntia kleiniae,, +Test_2023_4,Cyperus albostriatus,Cyperus albostriatus,, +Test_2023_4,Cyperus betchei,Cyperus betchei,, +Test_2023_4,Cyperus bulbosus,Cyperus bulbosus,, +Test_2023_4,Cyperus laevigatus,Cyperus laevigatus,, +Test_2023_4,Cyperus sculptus,Cyperus sculptus,, +Test_2023_4,Dampiera fusca,Dampiera fusca,, +Test_2023_4,Davidsonia johnsonii,Davidsonia johnsonii,, +Test_2023_4,Daviesia arenaria,Daviesia arenaria,, +Test_2023_4,Derris involuta,Derris involuta,, +Test_2023_4,Dichromochlamys dentatifolia,Dichromochlamys dentatifolia,, +Test_2023_4,Dillwynia cinerascens,Dillwynia cinerascens,, +Test_2023_4,Dillwynia floribunda,Dillwynia floribunda,, +Test_2023_4,Dinosperma erythrococcum,Dinosperma erythrococcum,, +Test_2023_4,Dodonaea petiolaris,Dodonaea petiolaris,, +Test_2023_4,Dodonaea truncatiales,Dodonaea truncatiales,, +Test_2023_4,Dovyalis caffra,Dovyalis caffra,, +Test_2023_4,Elaeocarpus grandis,Elaeocarpus grandis,, +Test_2023_4,Eleocharis pallens,Eleocharis pallens,, +Test_2023_4,Endiandra globosa,Endiandra globosa,, +Test_2023_4,Endiandra muelleri,Endiandra muelleri,, +Test_2023_4,Epilobium gunnianum,Epilobium gunnianum,, +Test_2023_4,Eremophila deserti,Eremophila deserti,, +Test_2023_4,Eremophila oppositifolia,Eremophila oppositifolia,, +Test_2023_4,Erigeron conyzoides,Erigeron conyzoides,, +Test_2023_4,Erythroxylum australe,Erythroxylum australe,, +Test_2023_4,Escallonia bifida,Escallonia bifida,, +Test_2023_4,Eucalyptus badjensis,Eucalyptus badjensis,, +Test_2023_4,Eucalyptus camphora,Eucalyptus camphora,, +Test_2023_4,Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,, +Test_2023_4,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,, +Test_2023_4,Eucalyptus muelleriana,Eucalyptus muelleriana,, +Test_2023_4,Eucalyptus nandewarica,Eucalyptus nandewarica,, +Test_2023_4,Eucalyptus oblonga,Eucalyptus oblonga,, +Test_2023_4,Eucalyptus olida,Eucalyptus olida,, +Test_2023_4,Eucalyptus pulverulenta,Eucalyptus pulverulenta,, +Test_2023_4,Eucalyptus recurva,Eucalyptus recurva,, +Test_2023_4,Eucalyptus rossii,Eucalyptus rossii,, +Test_2023_4,Eucalyptus scias,Eucalyptus scias,, +Test_2023_4,Eucalyptus viminalis,Eucalyptus viminalis,, +Test_2023_4,Eucalyptus yangoura,Eucalyptus yangoura,, +Test_2023_4,Eucalyptus youmanii,Eucalyptus youmanii,, +Test_2023_4,Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata var. queenslandica,, +Test_2023_4,Exocarpos homalocladus,Exocarpos homalocladus,, +Test_2023_4,Exocarpos sparteus,Exocarpos sparteus,, +Test_2023_4,Ficus henneana,Ficus henneana,, +Test_2023_4,Freesia hybrid,Freesia hybrid,, +Test_2023_4,Freesia laxa,Freesia laxa,, +Test_2023_4,Geijera salicifolia,Geijera salicifolia,, +Test_2023_4,Gentiana wingecarribiensis,Gentiana wingecarribiensis,, +Test_2023_4,Gentianella barringtonensis,Gentianella barringtonensis,, +Test_2023_4,Geranium obtusisepalum,Geranium obtusisepalum,, +Test_2023_4,Geranium purpureum subsp. purpureum,Geranium purpureum subsp. purpureum,, +Test_2023_4,Gompholobium grandiflorum,Gompholobium grandiflorum,, +Test_2023_4,Goodenia varia,Goodenia varia,, +Test_2023_4,Gossia bidwillii,Gossia bidwillii,, +Test_2023_4,Grevillea scortechinii,Grevillea scortechinii,, +Test_2023_4,Hakea macraeana,Hakea macraeana,, +Test_2023_4,Hemisteptia lyrata,Hemisteptia lyrata,, +Test_2023_4,Hibbertia crinita,Hibbertia crinita,, +Test_2023_4,Hibiscus brachysiphonius,Hibiscus brachysiphonius,, +Test_2023_4,Hibiscus sturtii,Hibiscus sturtii,, +Test_2023_4,Hypericum elodes,Hypericum elodes,, +Test_2023_4,Hypoxis glabella var. glabella,Hypoxis glabella var. glabella,, +Test_2023_4,Imperata cylindrica,Imperata cylindrica,, +Test_2023_4,Indigofera triflora,Indigofera triflora,, +Test_2023_4,Ipomoea cairica,Ipomoea cairica,, +Test_2023_4,Isolepis montivaga,Isolepis montivaga,, +Test_2023_4,Isotoma axillaris,Isotoma axillaris,, +Test_2023_4,Isotoma fluviatilis subsp. fluviatilis,Isotoma fluviatilis subsp. fluviatilis,, +Test_2023_4,Juncus acutus subsp. acutus,Juncus acutus subsp. acutus,, +Test_2023_4,Juncus kraussii,Juncus kraussii,, +Test_2023_4,Lantana montevidensis,Lantana montevidensis,, +Test_2023_4,Lepidium africanum,Lepidium africanum,, +Test_2023_4,Lepidium foliosum,Lepidium foliosum,, +Test_2023_4,Lepidium oxytrichum,Lepidium oxytrichum,, +Test_2023_4,Lepidosperma gladiatum,Lepidosperma gladiatum,, +Test_2023_4,Leptomeria drupacea,Leptomeria drupacea,, +Test_2023_4,Leptospermum continentale,Leptospermum continentale,, +Test_2023_4,Leptospermum obovatum,Leptospermum obovatum,, +Test_2023_4,Leucopogon amplexicaulis,Leucopogon amplexicaulis,, +Test_2023_4,Lobelia pedunculata,Lobelia pedunculata,, +Test_2023_4,Lobelia trigonocaulis,Lobelia trigonocaulis,, +Test_2023_4,Lotononis bainesii,Lotononis bainesii,, +Test_2023_4,Lotus corniculatus,Lotus corniculatus,, +Test_2023_4,Lupinus polyphyllus,Lupinus polyphyllus,, +Test_2023_4,Medicago orbicularis,Medicago orbicularis,, +Test_2023_4,Melichrus procumbens,Melichrus procumbens,, +Test_2023_4,Mischocarpus australis,Mischocarpus australis,, +Test_2023_4,Muehlenbeckia adpressa,Muehlenbeckia adpressa,, +Test_2023_4,Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,, +Test_2023_4,Nicotiana glauca,Nicotiana glauca,, +Test_2023_4,Nicotiana goodspeedii,Nicotiana goodspeedii,, +Test_2023_4,Oxalis corniculata,Oxalis corniculata,, +Test_2023_4,Pandorea pandorana subsp. austrocaledonica,Pandorea pandorana subsp. austrocaledonica,, +Test_2023_4,Paraserianthes lophantha,Paraserianthes lophantha,, +Test_2023_4,Parentucellia latifolia,Parentucellia latifolia,, +Test_2023_4,Phlegmatospermum cochlearinum,Phlegmatospermum cochlearinum,, +Test_2023_4,Phyla nodiflora,Phyla nodiflora,, +Test_2023_4,Picris barbarorum,Picris barbarorum,, +Test_2023_4,Pimelea ligustrina subsp. ligustrina,Pimelea ligustrina subsp. ligustrina,, +Test_2023_4,Pinus pinea,Pinus pinea,, +Test_2023_4,Pisum sativum var. arvense,Pisum sativum var. arvense,, +Test_2023_4,Pittosporum erioloma,Pittosporum erioloma,, +Test_2023_4,Plantago turrifera,Plantago turrifera,, +Test_2023_4,Polycarpon tetraphyllum,Polycarpon tetraphyllum,, +Test_2023_4,Potamogeton australiensis,Potamogeton australiensis,, +Test_2023_4,Psoralea pinnata,Psoralea pinnata,, +Test_2023_4,Pultenaea ferruginea,Pultenaea ferruginea,, +Test_2023_4,Rhodamnia argentea,Rhodamnia argentea,, +Test_2023_4,Rorippa gigantea,Rorippa gigantea,, +Test_2023_4,Rubus parvifolius,Rubus parvifolius,, +Test_2023_4,Salix alba,Salix alba,, +Test_2023_4,Schenkia australis,Schenkia australis,, +Test_2023_4,Schoenus apogon,Schoenus apogon,, +Test_2023_4,Schoenus brevifolius,Schoenus brevifolius,, +Test_2023_4,Schoenus lepidosperma,Schoenus lepidosperma,, +Test_2023_4,Schoenus vaginatus,Schoenus vaginatus,, +Test_2023_4,Scleria rugosa,Scleria rugosa,, +Test_2023_4,Senecio longipilus,Senecio longipilus,, +Test_2023_4,Sida goniocarpa,Sida goniocarpa,, +Test_2023_4,Sigesbeckia orientalis,Sigesbeckia orientalis,, +Test_2023_4,Sisymbrium irio,Sisymbrium irio,, +Test_2023_4,Sparaxis bulbifera,Sparaxis bulbifera,, +Test_2023_4,Spergularia diandra,Spergularia diandra,, +Test_2023_4,Sphaeromorphaea littoralis,Sphaeromorphaea littoralis,, +Test_2023_4,Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia subsp. angustifolia,, +Test_2023_4,Styphelia viridis,Styphelia viridis,, +Test_2023_4,Swainsona cadellii,Swainsona cadellii,, +Test_2023_4,Teucrium puberulum,Teucrium puberulum,, +Test_2023_4,Thelymitra kangaloonica,Thelymitra kangaloonica,, +Test_2023_4,Thesium australe,Thesium australe,, +Test_2023_4,Trifolium dubium,Trifolium dubium,, +Test_2023_4,Veronica catenata,Veronica catenata,, +Test_2023_4,Veronica derwentiana,Veronica derwentiana,, +Test_2023_4,Wahlenbergia luteola,Wahlenbergia luteola,, diff --git a/tests/testthat/examples/Test_2023_5/metadata.yml b/tests/testthat/examples/Test_2023_5/metadata.yml index a9796195..e3e536d9 100644 --- a/tests/testthat/examples/Test_2023_5/metadata.yml +++ b/tests/testthat/examples/Test_2023_5/metadata.yml @@ -306,11 +306,14 @@ taxonomic_updates: - find: Homalanthus novoguineensis replace: Homalanthus novo-guineensis reason: Change spelling to align with known name in APC (Daniel Falster, 2020.05.22) + taxonomic_resolution: species - find: Haplostichanthus sp Coop. Ck replace: Haplostichanthus submontanus reason: Align previous phrase name with current APC name (E. Wenk, 2020-05-25) + taxonomic_resolution: species - find: Psychotria sp Utchee Creek replace: Psychotria sp. Utchee Creek (H.Flecker NQNC5313) reason: Align to name in APC (D Falster, 2020.05.23) + taxonomic_resolution: species exclude_observations: .na questions: .na diff --git a/tests/testthat/examples/Test_2023_7/output/taxa.csv b/tests/testthat/examples/Test_2023_7/output/taxa.csv index 4e7f5169..a44dfc90 100644 --- a/tests/testthat/examples/Test_2023_7/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_7/output/taxa.csv @@ -1,3 +1,3 @@ -taxon_name,taxonomic_reference,taxon_rank,trinomial,binomial,genus,family,taxon_distribution,establishment_means,taxonomic_status,scientific_name,scientific_name_authorship,taxon_id,scientific_name_id -Eucalyptus miniata,,,,,Eucalyptus,,,,,,,, -Eucalyptus tetrodonta,,,,,Eucalyptus,,,,,,,, +taxon_name,taxonomic_reference,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution +Eucalyptus miniata,,,,,,,,, +Eucalyptus tetrodonta,,,,,,,,, diff --git a/tests/testthat/examples/Test_2023_7/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_7/output/taxonomic_updates.csv index c7d54a2d..23f82fa4 100644 --- a/tests/testthat/examples/Test_2023_7/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_7/output/taxonomic_updates.csv @@ -1,3 +1,3 @@ -dataset_id,original_name,cleaned_name,taxonomic_resolution,cleaned_scientific_name_id,cleaned_name_taxonomic_status,cleaned_name_alternative_taxonomic_status,taxon_id,taxon_name -Test_2023_7,Eucalyptus miniata,Eucalyptus miniata,,,,,, -Test_2023_7,Eucalyptus tetrodonta,Eucalyptus tetrodonta,,,,,, +dataset_id,original_name,cleaned_name,taxonomic_resolution,taxon_name +Test_2023_7,Eucalyptus miniata,Eucalyptus miniata,, +Test_2023_7,Eucalyptus tetrodonta,Eucalyptus tetrodonta,, diff --git a/tests/testthat/examples/Test_2023_8/output/taxa.csv b/tests/testthat/examples/Test_2023_8/output/taxa.csv index 4e7f5169..a44dfc90 100644 --- a/tests/testthat/examples/Test_2023_8/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_8/output/taxa.csv @@ -1,3 +1,3 @@ -taxon_name,taxonomic_reference,taxon_rank,trinomial,binomial,genus,family,taxon_distribution,establishment_means,taxonomic_status,scientific_name,scientific_name_authorship,taxon_id,scientific_name_id -Eucalyptus miniata,,,,,Eucalyptus,,,,,,,, -Eucalyptus tetrodonta,,,,,Eucalyptus,,,,,,,, +taxon_name,taxonomic_reference,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution +Eucalyptus miniata,,,,,,,,, +Eucalyptus tetrodonta,,,,,,,,, diff --git a/tests/testthat/examples/Test_2023_8/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_8/output/taxonomic_updates.csv index 12ad29b0..d1b3b79e 100644 --- a/tests/testthat/examples/Test_2023_8/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_8/output/taxonomic_updates.csv @@ -1,3 +1,3 @@ -dataset_id,original_name,cleaned_name,taxonomic_resolution,cleaned_scientific_name_id,cleaned_name_taxonomic_status,cleaned_name_alternative_taxonomic_status,taxon_id,taxon_name -Test_2023_8,Eucalyptus miniata,Eucalyptus miniata,,,,,, -Test_2023_8,Eucalyptus tetrodonta,Eucalyptus tetrodonta,,,,,, +dataset_id,original_name,cleaned_name,taxonomic_resolution,taxon_name +Test_2023_8,Eucalyptus miniata,Eucalyptus miniata,, +Test_2023_8,Eucalyptus tetrodonta,Eucalyptus tetrodonta,, diff --git a/tests/testthat/functions.R b/tests/testthat/functions.R index 79a0c89c..0e8a3dc5 100644 --- a/tests/testthat/functions.R +++ b/tests/testthat/functions.R @@ -124,7 +124,7 @@ test_structure <- function( vars_tables <- vars_austraits %>% - subset(., !(. %in% c("dataset_id", "definitions", "schema", "sources", "metadata", "build_info"))) + subset(., !(. %in% c("dataset_id", "definitions", "schema", "sources", "metadata", "build_info", "taxonomic_updates", "taxa"))) # Test lists have the right objects comparison <- vars_austraits @@ -137,6 +137,10 @@ test_structure <- function( expect_dataframe_named(data[[v]], comparison, info = paste(info, "- structure of", v)) } + # Test that minimum expected columns are in taxa, taxonomic_updates tables + expect_contains(names(data[["taxa"]]), c("taxon_name", "taxon_rank")) + expect_contains(names(data[["taxonomic_updates"]]), c("dataset_id", "original_name", "cleaned_name", "taxon_name", "taxonomic_resolution")) + # Contains allowed traits expect_is_in(data$traits$trait_name %>% unique(), definitions$elements %>% names(), info = paste("traits ", v)) } diff --git a/tests/testthat/test-setup.R b/tests/testthat/test-setup.R index bb2e353d..12d1ae13 100644 --- a/tests/testthat/test-setup.R +++ b/tests/testthat/test-setup.R @@ -608,19 +608,14 @@ test_that("`build_setup_pipeline` is working", { ## Check details on taxon list expect_silent(taxa1 <- read_csv_char("config/taxon_list.csv")) - vars <- - c("cleaned_name", "taxonomic_reference", "cleaned_scientific_name_id", - "cleaned_name_taxonomic_status", "cleaned_name_alternative_taxonomic_status", - "taxon_name", "taxon_id", "scientific_name_authorship", "taxon_rank", - "taxonomic_status", "family", "taxon_distribution", "establishment_means", - "scientific_name", "scientific_name_id") - expect_named(taxa1, vars) - expect_length(taxa1, 15) + vars <- c("taxon_name", "cleaned_name", "taxon_rank") + expect_contains(names(taxa1), vars) + expect_true(length(names(taxa1)) > 2) expect_true(nrow(taxa1) == 0) expect_true(file.copy("config/taxon_list-orig.csv", "config/taxon_list.csv", TRUE)) expect_silent(taxa2 <- read_csv_char("config/taxon_list.csv")) - expect_named(taxa2, vars) - expect_length(taxa2, 15) + expect_contains(names(taxa2), vars) + expect_true(length(names(taxa2)) > 2) expect_true(nrow(taxa2) == 7) ## Now try building in a controlled env, using base method @@ -668,8 +663,8 @@ test_that("`build_setup_pipeline` is working", { expect_equal(austraits$build_info$git_SHA, sha) expect_equal(austraits$build_info$git_SHA, "6c73238d8d048781d9a4f5239a03813be313f0dd") - expect_length(austraits_raw$taxa, 14) - expect_length(austraits$taxa, 14) + #expect_length(austraits_raw$taxa, 14) #not valid test with new `build_update_taxonomy setup` + #expect_length(austraits$taxa, 14) #not valid test with new `build_update_taxonomy setup` expect_equal(nrow(austraits$taxa), nrow(austraits_raw$taxa)) # Compare products from three methods, except `build_info` diff --git a/tests/testthat/test-xamples.R b/tests/testthat/test-xamples.R index ac1c0c74..5ea7332c 100644 --- a/tests/testthat/test-xamples.R +++ b/tests/testthat/test-xamples.R @@ -24,9 +24,11 @@ testthat::test_that("Test Dataset 1 builds correctly", { info = "Building Test Dataset 1") # Expected output + tables <- c("traits", "locations", "contexts", "methods", "excluded_data", "taxonomic_updates", "taxa", "contributors") - expect_no_error( + + expect_no_error( expected_output <- purrr::map( tables, ~read_csv(sprintf("examples/Test_2023_1/output/%s.csv", .x), col_types = cols(.default = "c"))), From d72638c068ee92b84be1ca0f273606de2ffe76c1 Mon Sep 17 00:00:00 2001 From: Elizabeth Wenk Date: Wed, 1 Nov 2023 11:39:27 +1100 Subject: [PATCH 10/31] Update taxonomic_updates functions (#113) edits to taxonomic_updates functions to:: - ensure updates are read into metadata in alphabetical order (to ensure additional updates are slotted into the correct location) - remove any updates where find = replace - offer functionality to overwrite vs not overwrite existing taxonomic updates - remove unnecessary `group_split` and `lapply` code --- R/setup.R | 35 +++++++++++++++++++++------- man/metadata_add_taxonomic_change.Rd | 5 +++- tests/testthat/test-setup.R | 2 +- 3 files changed, 31 insertions(+), 11 deletions(-) diff --git a/R/setup.R b/R/setup.R index 67def924..ebf6db20 100644 --- a/R/setup.R +++ b/R/setup.R @@ -869,10 +869,11 @@ metadata_add_substitutions_table <- function(dataframe_of_substitutions, dataset #' @param reason Reason for taxonomic change #' @param taxonomic_resolution The rank of the most specific taxon name (or scientific name) #' to which a submitted orignal name resolves +#' @param overwrite Parameter indicating whether preexisting find-replace entries should be overwritten. Defaults to `true` #' #' @return `metadata.yml` file with taxonomic change added #' @export -metadata_add_taxonomic_change <- function(dataset_id, find, replace, reason, taxonomic_resolution) { +metadata_add_taxonomic_change <- function(dataset_id, find, replace, reason, taxonomic_resolution, overwrite = TRUE) { if (length(replace) > 1) { stop(sprintf(red("Cannot replace with two names! (for ") %+% green("'%s' ") %+% red("-> ") %+% @@ -881,21 +882,36 @@ metadata_add_taxonomic_change <- function(dataset_id, find, replace, reason, tax set_name <- "taxonomic_updates" metadata <- read_metadata_dataset(dataset_id) - to_add <- list(find = find, replace = replace, reason = reason, taxonomic_resolution = taxonomic_resolution) + to_add <- dplyr::tibble(find = find, replace = replace, reason = reason, taxonomic_resolution = taxonomic_resolution) # Add `set_name` category if it doesn't yet exist if (all(is.na(metadata[[set_name]]))) { - metadata[[set_name]] <- list() + data <- to_add } else { + data <- util_list_to_df2(metadata[[set_name]]) # Check if find record already exists for that trait - data <- util_list_to_df2(metadata[[set_name]]) if (find %in% data$find) { - message(sprintf(red("Substitution already exists for ") %+% green("'%s'"), find)) - return(invisible()) + # If overwrite set to false, don't add a new substitution + if (overwrite == FALSE) { + message(sprintf(red("Substitution already exists for ") %+% green("'%s'"), find)) + return(invisible()) + # Default is to overwrite existing substitution + } else { + message(sprintf(red("Existing substitution will be overwritten for ") %+% green("'%s'"), find)) + data <- data %>% + filter(find != to_add$find) %>% + dplyr::bind_rows(to_add) %>% + filter(!find == replace) %>% + arrange(.data$find) + } + } else { + data <- dplyr::bind_rows(data, to_add) %>% + filter(!find == replace) %>% + arrange(.data$find) } } - metadata[[set_name]] <- util_append_to_list(metadata[[set_name]], to_add) + metadata[[set_name]] <- data message( sprintf(red("\tAdding taxonomic change in %s") %+% red(": ") %+% green("'%s'") %+% red(" -> ") %+% @@ -903,6 +919,7 @@ metadata_add_taxonomic_change <- function(dataset_id, find, replace, reason, tax blue(dataset_id), find, replace, reason) ) + # Write metadata write_metadata_dataset(metadata, dataset_id) } @@ -949,11 +966,11 @@ metadata_add_taxonomic_changes_list <- function(dataset_id, taxonomic_updates) { )) } # Write new taxonomic updates to metadata - metadata$taxonomic_updates <- existing_updates %>% dplyr::group_split(.data$find) %>% lapply(as.list) + metadata$taxonomic_updates <- existing_updates %>% arrange(.data$find) %>% filter(!find == replace) } else { # Read in dataframe of taxonomic changes, split into single-row lists, and add to metadata file - metadata$taxonomic_updates <- taxonomic_updates %>% dplyr::group_split(.data$find) %>% lapply(as.list) + metadata$taxonomic_updates <- taxonomic_updates %>% filter(!find == replace) } diff --git a/man/metadata_add_taxonomic_change.Rd b/man/metadata_add_taxonomic_change.Rd index f812d465..b7c0cc6c 100644 --- a/man/metadata_add_taxonomic_change.Rd +++ b/man/metadata_add_taxonomic_change.Rd @@ -9,7 +9,8 @@ metadata_add_taxonomic_change( find, replace, reason, - taxonomic_resolution + taxonomic_resolution, + overwrite = TRUE ) } \arguments{ @@ -23,6 +24,8 @@ metadata_add_taxonomic_change( \item{taxonomic_resolution}{The rank of the most specific taxon name (or scientific name) to which a submitted orignal name resolves} + +\item{overwrite}{Parameter indicating whether preexisting find-replace entries should be overwritten. Defaults to `true`} } \value{ `metadata.yml` file with taxonomic change added diff --git a/tests/testthat/test-setup.R b/tests/testthat/test-setup.R index 12d1ae13..35a209eb 100644 --- a/tests/testthat/test-setup.R +++ b/tests/testthat/test-setup.R @@ -461,7 +461,7 @@ test_that("`metadata_add_taxonomic_change` is working", { # Test if taxonomic substitution already exists expect_message( - metadata_add_taxonomic_change("Test_2022", "flower", "tree", "leaves", "test resolution"), + metadata_add_taxonomic_change("Test_2022", "flower", "tree", "leaves", "test resolution",overwrite=FALSE), ".*(?=Substitution already exists for )", perl = TRUE ) # Expect that second substitution should not exist From 31f2000048e981b4ac144110a66f78d28526c118 Mon Sep 17 00:00:00 2001 From: Elizabeth Wenk Date: Wed, 1 Nov 2023 19:14:54 +1100 Subject: [PATCH 11/31] rename fields (#114) * rename fields taxonomic_reference -> taxonomic_dataset cleaned_name -> aligned_name (and variants thereof) (Have reverted to a simpler commit - have not added `aligned_name` to columns in the taxa table.) --- R/process.R | 36 +++++++++---------- R/setup.R | 10 +++--- docs/reference/util_strip_taxon_names.html | 4 +-- inst/support/report_dataset.Rmd | 28 +++++++-------- inst/support/traits.build_schema.yml | 10 +++--- tests/testthat/config/taxon_list-orig.csv | 2 +- .../examples/Test_2023_1/output/taxa.csv | 2 +- .../Test_2023_1/output/taxonomic_updates.csv | 2 +- .../examples/Test_2023_2/output/taxa.csv | 2 +- .../Test_2023_2/output/taxonomic_updates.csv | 2 +- .../examples/Test_2023_3/output/taxa.csv | 2 +- .../Test_2023_3/output/taxonomic_updates.csv | 2 +- .../examples/Test_2023_4/output/taxa.csv | 2 +- .../Test_2023_4/output/taxonomic_updates.csv | 2 +- .../examples/Test_2023_7/output/taxa.csv | 2 +- .../Test_2023_7/output/taxonomic_updates.csv | 2 +- .../examples/Test_2023_8/output/taxa.csv | 2 +- .../Test_2023_8/output/taxonomic_updates.csv | 2 +- .../examples/Test_2023_9/output/taxa.csv | 2 +- .../Test_2023_9/output/taxonomic_updates.csv | 2 +- tests/testthat/functions.R | 2 +- tests/testthat/test-setup.R | 2 +- 22 files changed, 61 insertions(+), 61 deletions(-) diff --git a/R/process.R b/R/process.R index d7f209c2..6bf09984 100644 --- a/R/process.R +++ b/R/process.R @@ -190,17 +190,17 @@ dataset_process <- function(filename_data_raw, # Record methods methods <- process_format_methods(metadata, dataset_id, sources, contributors) - + # Retrieve taxonomic details for known species taxonomic_updates <- traits %>% dplyr::select( dplyr::all_of( - c("dataset_id", "original_name", cleaned_name = "taxon_name", + c("dataset_id", "original_name", aligned_name = "taxon_name", taxonomic_resolution = "taxonomic_resolution")) ) %>% dplyr::distinct() %>% - dplyr::arrange(.data$cleaned_name) + dplyr::arrange(.data$aligned_name) ## A temporary dataframe created to generate and bind `method_id`, ## for instances where the same trait is measured twice using different methods @@ -248,7 +248,7 @@ dataset_process <- function(filename_data_raw, dplyr::select(-dplyr::all_of(c("unit_in"))), taxonomic_updates = taxonomic_updates, taxa = taxonomic_updates %>% - dplyr::select(dplyr::all_of(c(taxon_name = "cleaned_name"))) %>% + dplyr::select(dplyr::all_of(c(taxon_name = "aligned_name"))) %>% dplyr::distinct(), contributors = contributors, sources = sources, @@ -1848,30 +1848,30 @@ build_update_taxonomy <- function(austraits_raw, taxa) { columns_in_taxon_list <- names(taxa) # incoming table from austraits_raw is a list of all taxa for the study - # `original_name` and `cleaned_name` will be different if + # `original_name` and `aligned_name` will be different if # there were taxonomic_updates specified in metadata file austraits_raw$taxonomic_updates <- austraits_raw$taxonomic_updates %>% dplyr::left_join( - by = "cleaned_name", + by = "aligned_name", taxa %>% dplyr::select( - dplyr::all_of(c("cleaned_name", "taxon_name")) + dplyr::all_of(c("aligned_name", "taxon_name")) )) %>% dplyr::distinct() %>% - dplyr::arrange(.data$cleaned_name) + dplyr::arrange(.data$aligned_name) austraits_raw$traits <- austraits_raw$traits %>% - dplyr::rename(dplyr::all_of(c("cleaned_name" = "taxon_name"))) %>% - dplyr::left_join(by = "cleaned_name", - taxa %>% dplyr::select(dplyr::all_of(c("cleaned_name", "taxon_name"))) + dplyr::rename(dplyr::all_of(c("aligned_name" = "taxon_name"))) %>% + dplyr::left_join(by = "aligned_name", + taxa %>% dplyr::select(dplyr::all_of(c("aligned_name", "taxon_name"))) ) %>% dplyr::select(dplyr::all_of(c("dataset_id", "taxon_name")), dplyr::everything()) %>% - # for taxa where there is no taxon_name to matched to a "cleaned_name", maintain the "cleaned_name" as the "taxon_name" + # for taxa where there is no taxon_name to matched to a "aligned_name", maintain the "aligned_name" as the "taxon_name" dplyr::mutate( - taxon_name = ifelse(is.na(.data$taxon_name), .data$cleaned_name, .data$taxon_name)#, + taxon_name = ifelse(is.na(.data$taxon_name), .data$aligned_name, .data$taxon_name)#, ) %>% - dplyr::select(-dplyr::all_of(c("cleaned_name"))) + dplyr::select(-dplyr::all_of(c("aligned_name"))) species_tmp <- austraits_raw$traits %>% @@ -1882,8 +1882,8 @@ build_update_taxonomy <- function(austraits_raw, taxa) { # If no taxonomic resolution is specified from taxonomic_updates, # then the name's taxonomic resolution is the taxon_rank for the taxon name. taxonomic_resolution = ifelse( - .data$taxon_name %in% taxa$cleaned_name, - taxa$taxon_rank[match(.data$taxon_name, taxa$cleaned_name)], + .data$taxon_name %in% taxa$aligned_name, + taxa$taxon_rank[match(.data$taxon_name, taxa$aligned_name)], .data$taxonomic_resolution), taxon_rank = .data$taxonomic_resolution, name_to_match_to = taxon_name, @@ -1898,12 +1898,12 @@ build_update_taxonomy <- function(austraits_raw, taxa) { util_df_convert_character() %>% # Merge in all data from taxa. dplyr::left_join(by = c("taxon_name"), - taxa %>% dplyr::select(-dplyr::any_of(dplyr::contains("clean"))) %>% + taxa %>% dplyr::select(-dplyr::any_of(dplyr::contains("align"))) %>% dplyr::distinct(taxon_name, .keep_all = TRUE) %>% util_df_convert_character() ) %>% dplyr::arrange(.data$taxon_name) %>% - dplyr::select(-dplyr::any_of(c("name_to_match_to"))) + dplyr::select(-dplyr::any_of(c("name_to_match_to", "aligned_name"))) austraits_raw$taxa <- species_tmp %>% diff --git a/R/setup.R b/R/setup.R index ebf6db20..b7a683a9 100644 --- a/R/setup.R +++ b/R/setup.R @@ -1243,11 +1243,11 @@ build_setup_pipeline <- function(dataset_ids = dir("data"), if (!file.exists(filename)) { dplyr::tibble( - cleaned_name = character(), - taxonomic_reference = character(), - cleaned_scientific_name_id = character(), - cleaned_name_taxonomic_status = character(), - cleaned_name_alternative_taxonomic_status = character(), + aligned_name = character(), + taxonomic_dataset = character(), + aligned_scientific_name_id = character(), + aligned_name_taxonomic_status = character(), + aligned_name_alternative_taxonomic_status = character(), taxon_name = character(), taxon_id = character(), scientific_name_authorship = character(), diff --git a/docs/reference/util_strip_taxon_names.html b/docs/reference/util_strip_taxon_names.html index a0fac253..a6bda87a 100644 --- a/docs/reference/util_strip_taxon_names.html +++ b/docs/reference/util_strip_taxon_names.html @@ -83,14 +83,14 @@

Strip scientific names of formatting and abbreviations

Arguments

x
-

Vector of names to clean

+

Vector of names to align

Value

-

Vector of cleaned names

+

Vector of aligned names

diff --git a/inst/support/report_dataset.Rmd b/inst/support/report_dataset.Rmd index bbb286ff..adb388ea 100644 --- a/inst/support/report_dataset.Rmd +++ b/inst/support/report_dataset.Rmd @@ -758,10 +758,10 @@ if (nrow(tmp) < 10000) { To create the list of aligned taxa, we needed to make some taxonomic changes. This involved two stages. -* **Stage 1**: Where possible (i.e. there was no or only a few characters difference), the name you supplied was matched automatically with a known name in APC or APNI. In other cases we may have aligned the taxa by searching for an appropriate match. Such changes are documented in the study metadata file. The variable `cleaned_name` shows the updated name. The variable `d1` shows the number of characters difference between the `original_name` and `cleaned_name`. -* **Stage 2**: Once aligned with a known name, we used the APC to update the `cleaned_name` to an accepted name. The taxonomic status of the cleaned name is indicated in column `status cleaned name`. If accepted, no change was made. If it is a synonym or otherwise, the name was changed according to the recommendation given in the APC. Where they existed, we preferred to take the accepted status of an `cleaned_name`, if it existed. Alternative status values are indicated in brackets. This indicate if alternative uses of the name were ever applied. +* **Stage 1**: Where possible (i.e. there was no or only a few characters difference), the name you supplied was matched automatically with a known name in APC or APNI. In other cases we may have aligned the taxa by searching for an appropriate match. Such changes are documented in the study metadata file. The variable `aligned_name` shows the updated name. The variable `d1` shows the number of characters difference between the `original_name` and `aligned_name`. +* **Stage 2**: Once aligned with a known name, we used the APC to update the `aligned_name` to an accepted name. The taxonomic status of the aligned name is indicated in column `status aligned name`. If accepted, no change was made. If it is a synonym or otherwise, the name was changed according to the recommendation given in the APC. Where they existed, we preferred to take the accepted status of an `aligned_name`, if it existed. Alternative status values are indicated in brackets. This indicate if alternative uses of the name were ever applied. -Links on `cleaned_name` and `taxon_name` take you to the APC or APNI record for that name. +Links on `aligned_name` and `taxon_name` take you to the APC or APNI record for that name. ```{r} taxa_columns <- names(data_study$taxa) @@ -770,20 +770,20 @@ data_study$taxonomic_updates %>% select(-dataset_id) %>% filter(original_name != taxon_name) %>% mutate( taxon_id = ifelse("taxon_id" %in% taxa_columns, data_study$taxa$taxon_id[match(taxon_name, data_study$taxa$taxon_name)], NA), - cleaned_name_taxonomic_status = ifelse("cleaned_name_taxonomic_status" %in% taxa_columns, cleaned_name_taxonomic_status, NA), - cleaned_name_alternative_taxonomic_status = ifelse("cleaned_name_alternative_taxonomic_status" %in% taxa_columns, cleaned_name_alternative_taxonomic_status, ""), - d1 = purrr::map2_dbl(original_name, cleaned_name, ~adist(.x, .y)) %>% as.character() %>% str_replace("0", ""), - d2 = purrr::map2_dbl(taxon_name, cleaned_name, ~adist(.x, .y)) %>% as.character() %>% str_replace("0", ""), - cleaned_name = ifelse("cleaned_scientific_name_id" %in% taxa_columns, as_link(cleaned_scientific_name_id, cleaned_name), cleaned_name), + aligned_name_taxonomic_status = ifelse("aligned_name_taxonomic_status" %in% taxa_columns, aligned_name_taxonomic_status, NA), + aligned_name_alternative_taxonomic_status = ifelse("aligned_name_alternative_taxonomic_status" %in% taxa_columns, aligned_name_alternative_taxonomic_status, ""), + d1 = purrr::map2_dbl(original_name, aligned_name, ~adist(.x, .y)) %>% as.character() %>% str_replace("0", ""), + d2 = purrr::map2_dbl(taxon_name, aligned_name, ~adist(.x, .y)) %>% as.character() %>% str_replace("0", ""), + aligned_name = ifelse("aligned_scientific_name_id" %in% taxa_columns, as_link(aligned_scientific_name_id, aligned_name), aligned_name), taxon_name = ifelse("taxon_id" %in% taxa_columns, as_link(taxon_id, taxon_name), taxon_name), - cleaned_name_alternative_taxonomic_status = replace_na(cleaned_name_alternative_taxonomic_status, ""), - `status cleaned name` = sprintf( - "%s %s", cleaned_name_taxonomic_status, - ifelse(cleaned_name_alternative_taxonomic_status == "", - "", paste("(", cleaned_name_alternative_taxonomic_status, ")")) + aligned_name_alternative_taxonomic_status = replace_na(aligned_name_alternative_taxonomic_status, ""), + `status aligned name` = sprintf( + "%s %s", aligned_name_taxonomic_status, + ifelse(aligned_name_alternative_taxonomic_status == "", + "", paste("(", aligned_name_alternative_taxonomic_status, ")")) ) ) %>% - select(original_name, d1, cleaned_name, d2, taxon_name, `status cleaned name`) %>% + select(original_name, d1, aligned_name, d2, taxon_name, `status aligned name`) %>% mutate(across(everything(), ~replace_na(.x, replace = ""))) %>% my_kable_styling() ``` diff --git a/inst/support/traits.build_schema.yml b/inst/support/traits.build_schema.yml index 59334c6f..573f6d8c 100644 --- a/inst/support/traits.build_schema.yml +++ b/inst/support/traits.build_schema.yml @@ -158,11 +158,11 @@ austraits: elements: dataset_id: *dataset_id original_name: *original_name - cleaned_name: The taxon name without authorship after implementing automated syntax standardisation and spelling changes as well as manually encoded syntax alignments for this taxon in the metadata file for the corresponding `dataset_id`. This name has not yet been matched to the currently accepted (botanical) or valid (zoological) taxon name in cases where there are taxonomic synonyms, isonyms, orthographic variants, etc. + aligned_name: The taxon name without authorship after implementing automated syntax standardisation and spelling changes as well as manually encoded syntax alignments for this taxon in the metadata file for the corresponding `dataset_id`. This name has not yet been matched to the currently accepted (botanical) or valid (zoological) taxon name in cases where there are taxonomic synonyms, isonyms, orthographic variants, etc. taxonomic_resolution: &taxonomic_resolution The rank of the most specific taxon name (or scientific name) to which a submitted orignal name resolves. - cleaned_scientific_name_id: An identifier for the cleaned name before it is updated to the currently accepted name usage. This may be a global unique identifier or an identifier specific to the data set. Must be resolvable within this dataset. - cleaned_name_taxonomic_status: The status of the use of the `cleaned_name` as a label for a taxon. Requires taxonomic opinion to define the scope of a taxon. Rules of priority then are used to define the taxonomic status of the nomenclature contained in that scope, combined with the experts opinion. It must be linked to a specific taxonomic reference that defines the concept. - cleaned_name_alternative_taxonomic_status: The taxonomic status of alternative taxonomic records with `cleaned_name` as the accepted (botanical) or valid (zoological) taxon name. + aligned_scientific_name_id: An identifier for the aligned name before it is updated to the currently accepted name usage. This may be a global unique identifier or an identifier specific to the data set. Must be resolvable within this dataset. + aligned_name_taxonomic_status: The status of the use of the `aligned_name` as a label for a taxon. Requires taxonomic opinion to define the scope of a taxon. Rules of priority then are used to define the taxonomic status of the nomenclature contained in that scope, combined with the experts opinion. It must be linked to a specific taxonomic reference that defines the concept. + aligned_name_alternative_taxonomic_status: The taxonomic status of alternative taxonomic records with `aligned_name` as the accepted (botanical) or valid (zoological) taxon name. taxon_id: &taxon_id An identifier for the set of taxon information (data associated with the taxon class). May be a global unique identifier or an identifier specific to the data set. Must be resolvable within this dataset. taxon_name: *taxon_name taxa: @@ -170,7 +170,7 @@ austraits: type: table elements: taxon_name: *taxon_name - taxonomic_reference: Name of the taxonomy (tree) that contains this concept. ie. APC, AusMoss etc. + taxonomic_dataset: Name of the taxonomy (tree) that contains this concept. ie. APC, AusMoss etc. taxon_rank: The taxonomic rank of the most specific name in the scientific name. trinomial: The infraspecific taxon name match for an original name. This column is assigned `na` for taxon name that are at a broader taxonomic_resolution. binomial: The species-level taxon name match for an original name. This column is assigned `na` for taxon name that are at a broader taxonomic_resolution. diff --git a/tests/testthat/config/taxon_list-orig.csv b/tests/testthat/config/taxon_list-orig.csv index 7c050c58..8bbfcfee 100644 --- a/tests/testthat/config/taxon_list-orig.csv +++ b/tests/testthat/config/taxon_list-orig.csv @@ -1,4 +1,4 @@ -cleaned_name,taxon_name,taxonomic_reference,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution +aligned_name,taxon_name,taxonomic_dataset,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution Acacia celsa,Acacia celsa,APC,species,accepted,Acacia,Acacia celsa,,Fabaceae,https://id.biodiversity.org.au/taxon/apni/51436506,Qld Acronychia acidula,Acronychia acidula,APC,species,accepted,Acronychia,Acronychia acidula,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913200,Qld Alphitonia petriei,Alphitonia petriei,APC,species,accepted,Alphitonia,Alphitonia petriei,,Rhamnaceae,https://id.biodiversity.org.au/node/apni/2887911,"Qld, NSW" diff --git a/tests/testthat/examples/Test_2023_1/output/taxa.csv b/tests/testthat/examples/Test_2023_1/output/taxa.csv index 4c45bc9b..74892a9c 100644 --- a/tests/testthat/examples/Test_2023_1/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_1/output/taxa.csv @@ -1,4 +1,4 @@ -taxon_name,taxonomic_reference,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution +taxon_name,taxonomic_dataset,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution Acacia celsa,APC,species,accepted,Acacia,Acacia celsa,,Fabaceae,https://id.biodiversity.org.au/taxon/apni/51436506,Qld Acmena graveolens,,,,,,,,, Acronychia acidula,APC,species,accepted,Acronychia,Acronychia acidula,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913200,Qld diff --git a/tests/testthat/examples/Test_2023_1/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_1/output/taxonomic_updates.csv index 16b9b357..e2355297 100644 --- a/tests/testthat/examples/Test_2023_1/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_1/output/taxonomic_updates.csv @@ -1,4 +1,4 @@ -dataset_id,original_name,cleaned_name,taxonomic_resolution,taxon_name +dataset_id,original_name,aligned_name,taxonomic_resolution,taxon_name Test_2023_1,Acacia celsa,Acacia celsa,,Acacia celsa Test_2023_1,Acmena graveolens,Acmena graveolens,, Test_2023_1,Acronychia acidula,Acronychia acidula,,Acronychia acidula diff --git a/tests/testthat/examples/Test_2023_2/output/taxa.csv b/tests/testthat/examples/Test_2023_2/output/taxa.csv index 7bd9228b..84196068 100644 --- a/tests/testthat/examples/Test_2023_2/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_2/output/taxa.csv @@ -1,4 +1,4 @@ -taxon_name,taxonomic_reference,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution +taxon_name,taxonomic_dataset,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution Acacia celsa,APC,species,accepted,Acacia,Acacia celsa,,Fabaceae,https://id.biodiversity.org.au/taxon/apni/51436506,Qld Acmena graveolens,,,,,,,,, Acronychia acidula,APC,species,accepted,Acronychia,Acronychia acidula,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913200,Qld diff --git a/tests/testthat/examples/Test_2023_2/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_2/output/taxonomic_updates.csv index 288fcdf1..35d71e1c 100644 --- a/tests/testthat/examples/Test_2023_2/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_2/output/taxonomic_updates.csv @@ -1,4 +1,4 @@ -dataset_id,original_name,cleaned_name,taxonomic_resolution,taxon_name +dataset_id,original_name,aligned_name,taxonomic_resolution,taxon_name Test_2023_2,Acacia celsa,Acacia celsa,,Acacia celsa Test_2023_2,Acmena graveolens,Acmena graveolens,, Test_2023_2,Acronychia acidula,Acronychia acidula,,Acronychia acidula diff --git a/tests/testthat/examples/Test_2023_3/output/taxa.csv b/tests/testthat/examples/Test_2023_3/output/taxa.csv index aaf603ba..29fddfe3 100644 --- a/tests/testthat/examples/Test_2023_3/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_3/output/taxa.csv @@ -1,4 +1,4 @@ -taxon_name,taxonomic_reference,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution +taxon_name,taxonomic_dataset,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution Abildgaardia ovata,,,,,,,,, Acacia alpina,,,,,,,,, Acacia beadleana,,,,,,,,, diff --git a/tests/testthat/examples/Test_2023_3/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_3/output/taxonomic_updates.csv index 63f7f5cd..c1f14ddf 100644 --- a/tests/testthat/examples/Test_2023_3/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_3/output/taxonomic_updates.csv @@ -1,4 +1,4 @@ -dataset_id,original_name,cleaned_name,taxonomic_resolution,taxon_name +dataset_id,original_name,aligned_name,taxonomic_resolution,taxon_name Test_2023_3,Abildgaardia ovata,Abildgaardia ovata,, Test_2023_3,Acacia alpina,Acacia alpina,, Test_2023_3,Acacia beadleana,Acacia beadleana,, diff --git a/tests/testthat/examples/Test_2023_4/output/taxa.csv b/tests/testthat/examples/Test_2023_4/output/taxa.csv index d63b8d6d..6f392a80 100644 --- a/tests/testthat/examples/Test_2023_4/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_4/output/taxa.csv @@ -1,4 +1,4 @@ -taxon_name,taxonomic_reference,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution +taxon_name,taxonomic_dataset,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution Abildgaardia ovata,,,,,,,,, Acacia alpina,,,,,,,,, Acacia beadleana,,,,,,,,, diff --git a/tests/testthat/examples/Test_2023_4/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_4/output/taxonomic_updates.csv index 84c0ae9c..a9c0b2f7 100644 --- a/tests/testthat/examples/Test_2023_4/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_4/output/taxonomic_updates.csv @@ -1,4 +1,4 @@ -dataset_id,original_name,cleaned_name,taxonomic_resolution,taxon_name +dataset_id,original_name,aligned_name,taxonomic_resolution,taxon_name Test_2023_4,Abildgaardia ovata,Abildgaardia ovata,, Test_2023_4,Acacia alpina,Acacia alpina,, Test_2023_4,Acacia beadleana,Acacia beadleana,, diff --git a/tests/testthat/examples/Test_2023_7/output/taxa.csv b/tests/testthat/examples/Test_2023_7/output/taxa.csv index a44dfc90..2af805f4 100644 --- a/tests/testthat/examples/Test_2023_7/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_7/output/taxa.csv @@ -1,3 +1,3 @@ -taxon_name,taxonomic_reference,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution +taxon_name,taxonomic_dataset,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution Eucalyptus miniata,,,,,,,,, Eucalyptus tetrodonta,,,,,,,,, diff --git a/tests/testthat/examples/Test_2023_7/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_7/output/taxonomic_updates.csv index 23f82fa4..90f4fda9 100644 --- a/tests/testthat/examples/Test_2023_7/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_7/output/taxonomic_updates.csv @@ -1,3 +1,3 @@ -dataset_id,original_name,cleaned_name,taxonomic_resolution,taxon_name +dataset_id,original_name,aligned_name,taxonomic_resolution,taxon_name Test_2023_7,Eucalyptus miniata,Eucalyptus miniata,, Test_2023_7,Eucalyptus tetrodonta,Eucalyptus tetrodonta,, diff --git a/tests/testthat/examples/Test_2023_8/output/taxa.csv b/tests/testthat/examples/Test_2023_8/output/taxa.csv index a44dfc90..2af805f4 100644 --- a/tests/testthat/examples/Test_2023_8/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_8/output/taxa.csv @@ -1,3 +1,3 @@ -taxon_name,taxonomic_reference,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution +taxon_name,taxonomic_dataset,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution Eucalyptus miniata,,,,,,,,, Eucalyptus tetrodonta,,,,,,,,, diff --git a/tests/testthat/examples/Test_2023_8/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_8/output/taxonomic_updates.csv index d1b3b79e..99b177ae 100644 --- a/tests/testthat/examples/Test_2023_8/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_8/output/taxonomic_updates.csv @@ -1,3 +1,3 @@ -dataset_id,original_name,cleaned_name,taxonomic_resolution,taxon_name +dataset_id,original_name,aligned_name,taxonomic_resolution,taxon_name Test_2023_8,Eucalyptus miniata,Eucalyptus miniata,, Test_2023_8,Eucalyptus tetrodonta,Eucalyptus tetrodonta,, diff --git a/tests/testthat/examples/Test_2023_9/output/taxa.csv b/tests/testthat/examples/Test_2023_9/output/taxa.csv index f141e5cb..fa1d9b6f 100644 --- a/tests/testthat/examples/Test_2023_9/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_9/output/taxa.csv @@ -1,4 +1,4 @@ -taxon_name,taxonomic_reference,taxon_rank,trinomial,binomial,genus,family,taxon_distribution,establishment_means,taxonomic_status,scientific_name,scientific_name_authorship,taxon_id,scientific_name_id +taxon_name,taxonomic_dataset,taxon_rank,trinomial,binomial,genus,family,taxon_distribution,establishment_means,taxonomic_status,scientific_name,scientific_name_authorship,taxon_id,scientific_name_id Acacia celsa,APC,Species,,Acacia celsa,Acacia,Fabaceae,Qld,native,accepted,Acacia celsa Tindale,Tindale,https://id.biodiversity.org.au/taxon/apni/51436506,https://id.biodiversity.org.au/name/apni/154988 Acmena graveolens,,,,,Acmena,,,,,,,, Acronychia acidula,APC,Species,,Acronychia acidula,Acronychia,Rutaceae,Qld,native,accepted,Acronychia acidula F.Muell.,F.Muell.,https://id.biodiversity.org.au/node/apni/2913200,https://id.biodiversity.org.au/name/apni/73794 diff --git a/tests/testthat/examples/Test_2023_9/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_9/output/taxonomic_updates.csv index c80d5126..de0f2e4c 100644 --- a/tests/testthat/examples/Test_2023_9/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_9/output/taxonomic_updates.csv @@ -1,4 +1,4 @@ -dataset_id,original_name,cleaned_name,taxonomic_resolution,cleaned_scientific_name_id,cleaned_name_taxonomic_status,cleaned_name_alternative_taxonomic_status,taxon_id,taxon_name +dataset_id,original_name,aligned_name,taxonomic_resolution,aligned_scientific_name_id,aligned_name_taxonomic_status,aligned_name_alternative_taxonomic_status,taxon_id,taxon_name Test_2023_1,Acacia celsa,Acacia celsa,Species,https://id.biodiversity.org.au/name/apni/154988,accepted,,https://id.biodiversity.org.au/taxon/apni/51436506,Acacia celsa Test_2023_1,Acmena graveolens,Acmena graveolens,,,,,, Test_2023_1,Acronychia acidula,Acronychia acidula,Species,https://id.biodiversity.org.au/name/apni/73794,accepted,,https://id.biodiversity.org.au/node/apni/2913200,Acronychia acidula diff --git a/tests/testthat/functions.R b/tests/testthat/functions.R index 0e8a3dc5..c4ae1d6b 100644 --- a/tests/testthat/functions.R +++ b/tests/testthat/functions.R @@ -139,7 +139,7 @@ test_structure <- function( # Test that minimum expected columns are in taxa, taxonomic_updates tables expect_contains(names(data[["taxa"]]), c("taxon_name", "taxon_rank")) - expect_contains(names(data[["taxonomic_updates"]]), c("dataset_id", "original_name", "cleaned_name", "taxon_name", "taxonomic_resolution")) + expect_contains(names(data[["taxonomic_updates"]]), c("dataset_id", "original_name", "aligned_name", "taxon_name", "taxonomic_resolution")) # Contains allowed traits expect_is_in(data$traits$trait_name %>% unique(), definitions$elements %>% names(), info = paste("traits ", v)) diff --git a/tests/testthat/test-setup.R b/tests/testthat/test-setup.R index 35a209eb..a13a70b4 100644 --- a/tests/testthat/test-setup.R +++ b/tests/testthat/test-setup.R @@ -608,7 +608,7 @@ test_that("`build_setup_pipeline` is working", { ## Check details on taxon list expect_silent(taxa1 <- read_csv_char("config/taxon_list.csv")) - vars <- c("taxon_name", "cleaned_name", "taxon_rank") + vars <- c("taxon_name", "aligned_name", "taxon_rank") expect_contains(names(taxa1), vars) expect_true(length(names(taxa1)) > 2) expect_true(nrow(taxa1) == 0) From d3e1416ed1b2574af9b8bc1c7344fedd89acb9d8 Mon Sep 17 00:00:00 2001 From: Elizabeth Wenk Date: Wed, 1 Nov 2023 21:21:08 +1100 Subject: [PATCH 12/31] Excluded observations fix (#116) Taxon names explicitly excluded under `exclude observations` are now also excluded from the taxonomic updates table Closes issue #115 --- R/process.R | 16 ++++++++++++++++ .../Test_2023_1/output/taxonomic_updates.csv | 1 - 2 files changed, 16 insertions(+), 1 deletion(-) diff --git a/R/process.R b/R/process.R index 6bf09984..1d037273 100644 --- a/R/process.R +++ b/R/process.R @@ -202,6 +202,22 @@ dataset_process <- function(filename_data_raw, dplyr::distinct() %>% dplyr::arrange(.data$aligned_name) + # Taxon names explicitly excluded in metadata also excluded from taxonomic updates table. + if (!is.na(metadata[["exclude_observations"]][1])) { + taxa_to_exclude <- + metadata[["exclude_observations"]] %>% + traits.build::util_list_to_df2() %>% + dplyr::mutate( + find = stringr::str_split(find, ", ") + ) %>% + tidyr::unnest_longer(find) %>% + dplyr::filter(variable == "taxon_name") + + taxonomic_updates <- + taxonomic_updates %>% + dplyr::filter(!aligned_name %in% taxa_to_exclude$find) + } + ## A temporary dataframe created to generate and bind `method_id`, ## for instances where the same trait is measured twice using different methods diff --git a/tests/testthat/examples/Test_2023_1/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_1/output/taxonomic_updates.csv index e2355297..8a92fb23 100644 --- a/tests/testthat/examples/Test_2023_1/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_1/output/taxonomic_updates.csv @@ -41,6 +41,5 @@ Test_2023_1,Psychotria sp Utchee Creek,Psychotria sp. Utchee Creek (H.Flecker NQ Test_2023_1,Quassia baileyana,Quassia baileyana,, Test_2023_1,Rhodomyrtus trineura,Rhodomyrtus trineura,, Test_2023_1,Rockinghamia angustifolia,Rockinghamia angustifolia,, -Test_2023_1,Syzygium gustavioides,Syzygium gustavioides,, Test_2023_1,Syzygium sayeri,Syzygium sayeri,, Test_2023_1,Trema aspera,Trema aspera,, From a7e4730a96269ace182465d42b4ee0eb1cb80fff Mon Sep 17 00:00:00 2001 From: Elizabeth Wenk Date: Fri, 3 Nov 2023 10:01:17 +1100 Subject: [PATCH 13/31] Taxonomic updates fixes (#119) Two fixes: Added align_name to group_by argument to ensure dataset_id correctly attributed to original_name by aligned_name combinations. (Closes issue #117) Filter taxonomic_updates to only include taxa for which trait data exists, NOTE: the taxa table still includes taxa in excluded data, but not taxon names that are in a data.csv file but for which no data (in traits table or excluded data table) exists --- R/process.R | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/R/process.R b/R/process.R index 1d037273..0aad981a 100644 --- a/R/process.R +++ b/R/process.R @@ -262,7 +262,8 @@ dataset_process <- function(filename_data_raw, dplyr::filter(!is.na(.data$error)) %>% dplyr::select(dplyr::all_of(c("error")), everything()) %>% dplyr::select(-dplyr::all_of(c("unit_in"))), - taxonomic_updates = taxonomic_updates, + taxonomic_updates = taxonomic_updates %>% + dplyr::filter(aligned_name %in% traits$taxon_name), taxa = taxonomic_updates %>% dplyr::select(dplyr::all_of(c(taxon_name = "aligned_name"))) %>% dplyr::distinct(), @@ -1811,11 +1812,11 @@ build_combine <- function(..., d = list(...)) { # Taxonomy taxonomic_updates <- combine("taxonomic_updates", d) %>% - dplyr::group_by(.data$original_name, .data$taxon_name, .data$taxonomic_resolution) %>% + dplyr::group_by(.data$original_name, .data$aligned_name, .data$taxon_name, .data$taxonomic_resolution) %>% dplyr::mutate(dataset_id = paste(.data$dataset_id, collapse = " ")) %>% dplyr::ungroup() %>% dplyr::distinct() %>% - dplyr::arrange(.data$original_name, .data$taxon_name, .data$taxonomic_resolution) + dplyr::arrange(.data$original_name, .data$aligned_name, .data$taxon_name, .data$taxonomic_resolution) # Metadata contributors <- combine("contributors", d) From 791c8a5fb7c88440cff5a493b8ac9cb099069a04 Mon Sep 17 00:00:00 2001 From: Daniel Falster Date: Fri, 10 Nov 2023 20:53:15 +1100 Subject: [PATCH 14/31] Remove dependency on {austraits} by importing plot (#121) * Import plot_trait_distribution_beeswarm and dependencies * Add test for function --------- Co-authored-by: yangsophieee --- DESCRIPTION | 8 +- NAMESPACE | 1 + R/plot_trait_beeswarm.R | 156 ++++++++++++++++++++++++ R/setup.R | 4 +- R/traits.build-package.R | 3 +- inst/support/report_dataset.Rmd | 2 +- man/plot_trait_distribution_beeswarm.Rd | 36 ++++++ man/traits.build-package.Rd | 1 + tests/testthat/test-setup.R | 5 +- tests/testthat/test-usage.R | 9 ++ 10 files changed, 218 insertions(+), 7 deletions(-) create mode 100644 R/plot_trait_beeswarm.R create mode 100644 man/plot_trait_distribution_beeswarm.Rd create mode 100644 tests/testthat/test-usage.R diff --git a/DESCRIPTION b/DESCRIPTION index 41181596..0f748602 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -7,6 +7,7 @@ Authors@R: c( person(given = "Daniel", family = "Falster", role = c("cre", "aut"), email = "daniel.falster@unsw.edu.au", comment = c(ORCID = "0000-0002-9814-092X")), person(given = "Elizabeth", family = "Wenk", role = c("cur", "aut"), comment = c(ORCID = "0000-0001-5640-5910")), person(given = "Sophie", family = "Yang", role = c("cur", "aut"), comment = c(ORCID = "0000-0001-7328-345X")), + person(given = "Fonti", family = "Kar", role = c("aut", "ctb"), comment = c(ORCID = "0000-0002-2760-3974")), person("ARDC", role = c("fnd")), person("ARC", role = c("fnd")) ) @@ -28,6 +29,7 @@ Imports: kableExtra, magrittr, purrr, + forcats, RefManageR, rlang, rmarkdown, @@ -40,7 +42,6 @@ Imports: Suggests: furrr, remake, - austraits, leaflet, bibtex, knitr, @@ -49,10 +50,13 @@ Suggests: markdown, pkgdown, rcrossref, + ggplot2, + ggbeeswarm, + gridExtra, + scales, zip, covr Remotes: - traitecoevo/austraits@develop, richfitz/remake Encoding: UTF-8 VignetteBuilder: knitr diff --git a/NAMESPACE b/NAMESPACE index 73a301f3..24b2e431 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -30,6 +30,7 @@ export(metadata_exclude_observations) export(metadata_find_taxonomic_change) export(metadata_remove_taxonomic_change) export(metadata_update_taxonomic_change) +export(plot_trait_distribution_beeswarm) export(read_csv_char) export(read_metadata) export(util_df_to_list) diff --git a/R/plot_trait_beeswarm.R b/R/plot_trait_beeswarm.R new file mode 100644 index 00000000..2153e8cd --- /dev/null +++ b/R/plot_trait_beeswarm.R @@ -0,0 +1,156 @@ +#' @title Beeswarm Trait distribution +#' @description Plots distribution of trait values by a grouping variable using ggbeeswarm package +#' +#' @param austraits austraits data object +#' @param trait_name Name of trait to plot +#' @param y_axis_category One of `dataset_id`, `family` +#' @param highlight specify a group to highlight +#' @param hide_ids add label on y_axis? +#' +#' @export +#' +#' @examples +#' \dontrun{ +#' austraits %>% plot_trait_distribution_beeswarm("wood_density", "dataset_id", "Westoby_2014") +#' } +#' @author Daniel Falster - daniel.falster@unsw.edu.au +#' @export + +# +plot_trait_distribution_beeswarm <- function(austraits, trait_name, y_axis_category, highlight=NA, hide_ids = FALSE) { + + # Subset data to this trait + austraits_trait <- + austraits$traits %>% filter(trait_name == trait_name) %>% + mutate(value = as.numeric(.data$value)) + + my_shapes = c("_min" = 60, "_mean" = 16, "_max" =62, "unknown" = 18) + + as_shape <- function(value_type) { + p <- rep("unknown", length(value_type)) + + p[grepl("mean", value_type)] <- "_mean" #16 + p[grepl("min", value_type)] <- "_min" #60 + p[grepl("max", value_type)] <- "_max" #62 + factor(p, levels=names(my_shapes)) + } + + tax_info <- austraits$taxa + + data <- + austraits_trait %>% + dplyr::mutate(shapes = as_shape(.data$value_type)) %>% + dplyr::left_join(by = "taxon_name", tax_info) + + # Define grouping variables and derivatives + if(!y_axis_category %in% names(data)){ + stop("Incorrect grouping variable! Currently implemented for `family` or `dataset_id`") + } + + # define grouping variable, ordered by group-level by mean values + # use log_value where possible + if(min(data$value, na.rm=TRUE) > 0 ) { + data$value2 <- log10(data$value) + } else { + data$value2 <- data$value + } + data$Group = forcats::fct_reorder(data[[y_axis_category]], data$value2, na.rm=TRUE) + + n_group <- levels(data$Group) %>% length() + + # set colour to be alternating + data$colour = ifelse(data$Group %in% levels(data$Group)[seq(1, n_group, by=2)], + "a", "b") + + # set colour of group to highlight + if(!is.na(highlight) & highlight %in% data$Group) { + data <- dplyr::mutate(data, colour = ifelse(.data$Group %in% highlight, "c", .data$colour)) + } + + vals <- list(minimum = purrr::pluck(austraits, "definitions", trait_name, "allowed_values_min"), + maximum = purrr::pluck(austraits, "definitions", trait_name, "allowed_values_max")) + + range <- (vals$maximum/vals$minimum) + + # Check range on y-axis + y.text <- ifelse(n_group > 20, 0.75, 1) + heights = c(1, max(1, n_group/7)) + + # Top plot - plain histogram of data + p1 <- + ggplot2::ggplot(data, ggplot2::aes(x=.data$value)) + + ggplot2::geom_histogram(ggplot2::aes(y = ..density..), color="darkgrey", fill="darkgrey", bins=50) + + ggplot2::geom_density(color="black") + + ggplot2::xlab("") + ggplot2::ylab("All data") + + ggplot2::theme_bw() + + ggplot2::theme(legend.position = "none", + panel.grid.minor = ggplot2::element_blank(), + panel.grid.major = ggplot2::element_blank(), + axis.ticks.y= ggplot2::element_blank(), + axis.text= ggplot2::element_blank(), + panel.background = ggplot2::element_blank() + ) + # Second plot -- dots by groups, using ggbeeswarm package + p2 <- + ggplot2::ggplot(data, ggplot2::aes(x = .data$value, y = .data$Group, colour = .data$colour, shape = .data$shapes)) + + ggbeeswarm::geom_quasirandom(groupOnX=FALSE) + + ggplot2::ylab(paste("By ", y_axis_category)) + + # inclusion of custom shapes: for min, mean, unknown + # NB: this single line of code makes function about 4-5 slower for some reason + ggplot2::scale_shape_manual(values = my_shapes) + + ggplot2::theme_bw() + + ggplot2::theme(legend.position = "none", + panel.grid.major.x = ggplot2::element_blank(), + panel.grid.minor.x = ggplot2::element_blank(), + axis.text.x = ggplot2::element_text(size=ggplot2::rel(1.25)), + axis.text.y = ggplot2::element_text(size=ggplot2::rel(y.text)) + ) #+ + # guides(colour=FALSE) + + + if(hide_ids) { + p2 <- p2 + ggplot2::theme(axis.text.y = ggplot2::element_blank()) + } + + #Sourced from https://gist.github.com/bbolker/5ba6a37d64b06a176e320b2b696b6733 + scientific_10 <- function(x,suppress_ones=TRUE) { + s <- scales::scientific_format()(x) + ## substitute for exact zeros + s[s=="0e+00"] <- "0" + ## regex: [+]? = "zero or one occurrences of '+'" + s2 <- gsub("e[+]?", " %*% 10^", s ) + ## suppress 1 x + if (suppress_ones) s2 <- gsub("1 %\\*% +","",s2) + parse(text=s2) + } + + # Define scale on x-axis and transform to log if required + if(vals$minimum !=0 & range > 20) { + #log transformation + p1 <- p1 + + ggplot2::scale_x_log10(name="", + breaks = scales::breaks_log(), + labels = scientific_10, + limits=c(vals$minimum, vals$maximum)) + p2 <- p2 + + ggplot2::scale_x_log10(name=paste(trait_name, ' (', data$unit[1], ')'), + breaks = scales::breaks_log(), + labels = scientific_10, + limits=c(vals$minimum, vals$maximum)) + } else { + p1 <- p1 + ggplot2::scale_x_continuous(limits=c(vals$minimum, vals$maximum)) + p2 <- p2 + ggplot2::scale_x_continuous(limits=c(vals$minimum, vals$maximum)) + + ggplot2::xlab(paste(trait_name, ' (', data$unit[1], ')')) + + } + + # combine plots + # Might be a better way to do this with other packages? + + f <- function(x) {suppressWarnings(ggplot2::ggplot_gtable(ggplot2::ggplot_build(x)))} + p1 <- f(p1) + p2 <- f(p2) + # Fix width of second plot to be same as bottom using ggplot_table + p1$widths[2:3] <- p2$widths[2:3] + gridExtra::grid.arrange(p1, p2, nrow=2, widths=c(1), heights=heights) +} diff --git a/R/setup.R b/R/setup.R index b7a683a9..f53d9bea 100644 --- a/R/setup.R +++ b/R/setup.R @@ -966,11 +966,11 @@ metadata_add_taxonomic_changes_list <- function(dataset_id, taxonomic_updates) { )) } # Write new taxonomic updates to metadata - metadata$taxonomic_updates <- existing_updates %>% arrange(.data$find) %>% filter(!find == replace) + metadata$taxonomic_updates <- existing_updates %>% dplyr::arrange(.data$find) %>% filter(!.data$find == .data$replace) } else { # Read in dataframe of taxonomic changes, split into single-row lists, and add to metadata file - metadata$taxonomic_updates <- taxonomic_updates %>% filter(!find == replace) + metadata$taxonomic_updates <- taxonomic_updates %>% dplyr::filter(!.data$find == .data$replace) } diff --git a/R/traits.build-package.R b/R/traits.build-package.R index bc459a29..05cb9975 100644 --- a/R/traits.build-package.R +++ b/R/traits.build-package.R @@ -11,6 +11,7 @@ NULL utils::globalVariables( c( ".", - ".data" + ".data", + "..density.." ) ) diff --git a/inst/support/report_dataset.Rmd b/inst/support/report_dataset.Rmd index adb388ea..e38efc2d 100644 --- a/inst/support/report_dataset.Rmd +++ b/inst/support/report_dataset.Rmd @@ -567,7 +567,7 @@ if (nrow(filter(data_study$excluded_data, error == "Value out of allowable range writeLines() } - austraits::plot_trait_distribution_beeswarm(austraits, trait, "dataset_id", highlight = dataset_id, hide_ids = TRUE) + plot_trait_distribution_beeswarm(austraits, trait, "dataset_id", highlight = dataset_id, hide_ids = TRUE) writeLines(c("")) diff --git a/man/plot_trait_distribution_beeswarm.Rd b/man/plot_trait_distribution_beeswarm.Rd new file mode 100644 index 00000000..fe8d83cb --- /dev/null +++ b/man/plot_trait_distribution_beeswarm.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/plot_trait_beeswarm.R +\name{plot_trait_distribution_beeswarm} +\alias{plot_trait_distribution_beeswarm} +\title{Beeswarm Trait distribution} +\usage{ +plot_trait_distribution_beeswarm( + austraits, + trait_name, + y_axis_category, + highlight = NA, + hide_ids = FALSE +) +} +\arguments{ +\item{austraits}{austraits data object} + +\item{trait_name}{Name of trait to plot} + +\item{y_axis_category}{One of `dataset_id`, `family`} + +\item{highlight}{specify a group to highlight} + +\item{hide_ids}{add label on y_axis?} +} +\description{ +Plots distribution of trait values by a grouping variable using ggbeeswarm package +} +\examples{ +\dontrun{ +austraits \%>\% plot_trait_distribution_beeswarm("wood_density", "dataset_id", "Westoby_2014") +} +} +\author{ +Daniel Falster - daniel.falster@unsw.edu.au +} diff --git a/man/traits.build-package.Rd b/man/traits.build-package.Rd index 5913f88d..15836a12 100644 --- a/man/traits.build-package.Rd +++ b/man/traits.build-package.Rd @@ -23,6 +23,7 @@ Authors: \itemize{ \item Elizabeth Wenk (\href{https://orcid.org/0000-0001-5640-5910}{ORCID}) [curator] \item Sophie Yang (\href{https://orcid.org/0000-0001-7328-345X}{ORCID}) [curator] + \item Fonti Kar (\href{https://orcid.org/0000-0002-2760-3974}{ORCID}) [contributor] } Other contributors: diff --git a/tests/testthat/test-setup.R b/tests/testthat/test-setup.R index a13a70b4..aabd3d76 100644 --- a/tests/testthat/test-setup.R +++ b/tests/testthat/test-setup.R @@ -654,6 +654,9 @@ test_that("`build_setup_pipeline` is working", { expect_silent(suppressMessages(austraits_raw <- remake::make("database_raw"))) expect_silent(suppressMessages(austraits <- remake::make("database"))) + # Save output for future tests on database + saveRDS(austraits, "test_austraits.rds") + # Test that austraits_raw has no version number or git_SHA expect_null(austraits_raw$build_info$version) expect_null(austraits_raw$build_info$git_SHA) @@ -705,7 +708,7 @@ test_that("reports and plots are produced", { # Not testing right now #expect_no_error( #p <- - #austraits::plot_trait_distribution_beeswarm( + #plot_trait_distribution_beeswarm( #austraits, "huber_value", "dataset_id", highlight = "Test_2022", hide_ids = TRUE) #) expect_silent( diff --git a/tests/testthat/test-usage.R b/tests/testthat/test-usage.R new file mode 100644 index 00000000..1b198830 --- /dev/null +++ b/tests/testthat/test-usage.R @@ -0,0 +1,9 @@ + + +austraits <- readRDS("test_austraits.rds") +# This file tests usage of the database +# Note, requires existnec of "test_austraits.rds", generated from `test-process.R` + +test_that("plots", { + expect_invisible(suppressMessages(austraits %>% plot_trait_distribution_beeswarm("wood_density", "dataset_id", "Test_2022"))) +}) From 906713c2292405af1b73f2a61eb0d2412140aa35 Mon Sep 17 00:00:00 2001 From: Daniel Falster Date: Fri, 10 Nov 2023 21:07:59 +1100 Subject: [PATCH 15/31] fix rcmdcheck issues (#122) --- R/process.R | 20 ++++++++++---------- R/setup.R | 7 +++---- 2 files changed, 13 insertions(+), 14 deletions(-) diff --git a/R/process.R b/R/process.R index 0aad981a..d485efc4 100644 --- a/R/process.R +++ b/R/process.R @@ -208,14 +208,14 @@ dataset_process <- function(filename_data_raw, metadata[["exclude_observations"]] %>% traits.build::util_list_to_df2() %>% dplyr::mutate( - find = stringr::str_split(find, ", ") + find = stringr::str_split(.data$find, ", ") ) %>% - tidyr::unnest_longer(find) %>% - dplyr::filter(variable == "taxon_name") + tidyr::unnest_longer(.data$find) %>% + dplyr::filter(.data$variable == "taxon_name") taxonomic_updates <- taxonomic_updates %>% - dplyr::filter(!aligned_name %in% taxa_to_exclude$find) + dplyr::filter(!.data$aligned_name %in% taxa_to_exclude$find) } ## A temporary dataframe created to generate and bind `method_id`, @@ -263,7 +263,7 @@ dataset_process <- function(filename_data_raw, dplyr::select(dplyr::all_of(c("error")), everything()) %>% dplyr::select(-dplyr::all_of(c("unit_in"))), taxonomic_updates = taxonomic_updates %>% - dplyr::filter(aligned_name %in% traits$taxon_name), + dplyr::filter(.data$aligned_name %in% traits$taxon_name), taxa = taxonomic_updates %>% dplyr::select(dplyr::all_of(c(taxon_name = "aligned_name"))) %>% dplyr::distinct(), @@ -1903,12 +1903,12 @@ build_update_taxonomy <- function(austraits_raw, taxa) { taxa$taxon_rank[match(.data$taxon_name, taxa$aligned_name)], .data$taxonomic_resolution), taxon_rank = .data$taxonomic_resolution, - name_to_match_to = taxon_name, + name_to_match_to = .data$taxon_name, # Create variable `name_to_match_to` which specifies the part of the taxon name to which matches can be made. # This step requires taxon_rank. - name_to_match_to = stringr::str_replace(taxon_name, " \\[.+",""), - name_to_match_to = ifelse(!taxon_rank %in% c("species", "subspecies", "series", "variety", "form"), - stringr::word(taxon_name,1), name_to_match_to) + name_to_match_to = stringr::str_replace(.data$taxon_name, " \\[.+",""), + name_to_match_to = ifelse(!.data$taxon_rank %in% c("species", "subspecies", "series", "variety", "form"), + stringr::word(.data$taxon_name,1), .data$name_to_match_to) ) %>% # Remove taxon_rank, as it is about to be merged back in, but matches will now be possible to more rows. select(-dplyr::any_of(c("taxon_rank", "taxonomic_resolution"))) %>% @@ -1916,7 +1916,7 @@ build_update_taxonomy <- function(austraits_raw, taxa) { # Merge in all data from taxa. dplyr::left_join(by = c("taxon_name"), taxa %>% dplyr::select(-dplyr::any_of(dplyr::contains("align"))) %>% - dplyr::distinct(taxon_name, .keep_all = TRUE) %>% + dplyr::distinct(.data$taxon_name, .keep_all = TRUE) %>% util_df_convert_character() ) %>% dplyr::arrange(.data$taxon_name) %>% diff --git a/R/setup.R b/R/setup.R index f53d9bea..a63b60dd 100644 --- a/R/setup.R +++ b/R/setup.R @@ -899,14 +899,14 @@ metadata_add_taxonomic_change <- function(dataset_id, find, replace, reason, tax } else { message(sprintf(red("Existing substitution will be overwritten for ") %+% green("'%s'"), find)) data <- data %>% - filter(find != to_add$find) %>% + filter(.data$find != to_add$find) %>% dplyr::bind_rows(to_add) %>% - filter(!find == replace) %>% + filter(!.data$find == replace) %>% arrange(.data$find) } } else { data <- dplyr::bind_rows(data, to_add) %>% - filter(!find == replace) %>% + filter(!.data$find == replace) %>% arrange(.data$find) } } @@ -971,7 +971,6 @@ metadata_add_taxonomic_changes_list <- function(dataset_id, taxonomic_updates) { # Read in dataframe of taxonomic changes, split into single-row lists, and add to metadata file metadata$taxonomic_updates <- taxonomic_updates %>% dplyr::filter(!.data$find == .data$replace) - } # Write metadata From d0b132e48355d5505e8217062080649ef8cc9a64 Mon Sep 17 00:00:00 2001 From: Sophie Yang <78716301+yangsophieee@users.noreply.github.com> Date: Wed, 15 Nov 2023 13:38:11 +1100 Subject: [PATCH 16/31] Collapse duplicate categorical values within a row (#125) - Closes #120 --- R/process.R | 16 ++++++++-------- R/utils.R | 3 ++- .../examples/Test_2023_1/output/traits.csv | 2 +- 3 files changed, 11 insertions(+), 10 deletions(-) diff --git a/R/process.R b/R/process.R index d485efc4..e7995e0d 100644 --- a/R/process.R +++ b/R/process.R @@ -190,7 +190,7 @@ dataset_process <- function(filename_data_raw, # Record methods methods <- process_format_methods(metadata, dataset_id, sources, contributors) - + # Retrieve taxonomic details for known species taxonomic_updates <- traits %>% @@ -204,7 +204,7 @@ dataset_process <- function(filename_data_raw, # Taxon names explicitly excluded in metadata also excluded from taxonomic updates table. if (!is.na(metadata[["exclude_observations"]][1])) { - taxa_to_exclude <- + taxa_to_exclude <- metadata[["exclude_observations"]] %>% traits.build::util_list_to_df2() %>% dplyr::mutate( @@ -213,7 +213,7 @@ dataset_process <- function(filename_data_raw, tidyr::unnest_longer(.data$find) %>% dplyr::filter(.data$variable == "taxon_name") - taxonomic_updates <- + taxonomic_updates <- taxonomic_updates %>% dplyr::filter(!.data$aligned_name %in% taxa_to_exclude$find) } @@ -1863,10 +1863,10 @@ build_combine <- function(..., d = list(...)) { build_update_taxonomy <- function(austraits_raw, taxa) { columns_in_taxon_list <- names(taxa) - + # incoming table from austraits_raw is a list of all taxa for the study - # `original_name` and `aligned_name` will be different if - # there were taxonomic_updates specified in metadata file + # `original_name` and `aligned_name` will be different if + # there were taxonomic_updates specified in metadata file austraits_raw$taxonomic_updates <- austraits_raw$taxonomic_updates %>% dplyr::left_join( @@ -1896,7 +1896,7 @@ build_update_taxonomy <- function(austraits_raw, taxa) { dplyr::distinct() %>% util_df_convert_character() %>% dplyr::mutate( - # If no taxonomic resolution is specified from taxonomic_updates, + # If no taxonomic resolution is specified from taxonomic_updates, # then the name's taxonomic resolution is the taxon_rank for the taxon name. taxonomic_resolution = ifelse( .data$taxon_name %in% taxa$aligned_name, @@ -1907,7 +1907,7 @@ build_update_taxonomy <- function(austraits_raw, taxa) { # Create variable `name_to_match_to` which specifies the part of the taxon name to which matches can be made. # This step requires taxon_rank. name_to_match_to = stringr::str_replace(.data$taxon_name, " \\[.+",""), - name_to_match_to = ifelse(!.data$taxon_rank %in% c("species", "subspecies", "series", "variety", "form"), + name_to_match_to = ifelse(!.data$taxon_rank %in% c("species", "subspecies", "series", "variety", "form"), stringr::word(.data$taxon_name,1), .data$name_to_match_to) ) %>% # Remove taxon_rank, as it is about to be merged back in, but matches will now be possible to more rows. diff --git a/R/utils.R b/R/utils.R index 825f056d..c953ae43 100644 --- a/R/utils.R +++ b/R/utils.R @@ -102,9 +102,10 @@ util_separate_and_sort <- function(x, sep = " ") { # For those cells, split, sort then combine x[i] <- x[i] %>% stringr::str_split(" ") %>% - lapply(function(xi) xi %>% sort() %>% paste(collapse = " ")) %>% + lapply(function(xi) xi %>% sort() %>% unique() %>% paste(collapse = " ")) %>% unlist() x + } #' Convert dataframe to list diff --git a/tests/testthat/examples/Test_2023_1/output/traits.csv b/tests/testthat/examples/Test_2023_1/output/traits.csv index c9e22157..3a32e6e7 100644 --- a/tests/testthat/examples/Test_2023_1/output/traits.csv +++ b/tests/testthat/examples/Test_2023_1/output/traits.csv @@ -80,7 +80,7 @@ Test_2023_1,Alphitonia petriei,034,leaf_mass_per_area,149,g/m2,population,mean,m Test_2023_1,Alphitonia petriei,034,seed_dry_mass,27.2,mg,population,mean,measurement,3,field,adult,05,,,02,,01,14,03,02,2004/2004,from Falster_2005_1,01,,Alphitonia petriei Test_2023_1,Alphitonia petriei,034,seed_dry_mass,3--4,mg,population,bin,measurement,10,field,adult,05,,,02,,01,14,03,02,2004/2004,from Falster_2005_1,02,,Alphitonia petriei Test_2023_1,Alphitonia petriei,034,wood_density,0.413,mg/mm3,population,mean,measurement,3,field,adult,05,,,02,,01,14,03,02,2004/2004,from Falster_2005_1,01,,Alphitonia petriei -Test_2023_1,Alphitonia petriei,035,plant_growth_form,mallee mallee shrub tree tree,,species,mode,expert_score,3,field,adult,,,,02,,,14,03,02,2004/2004,from Falster_2005_1,01,,Alphitonia petriei +Test_2023_1,Alphitonia petriei,035,plant_growth_form,mallee shrub tree,,species,mode,expert_score,3,field,adult,,,,02,,,14,03,02,2004/2004,from Falster_2005_1,01,,Alphitonia petriei Test_2023_1,Alstonia scholaris,037,huber_value,0.000254323499491353,mm2{sapwood}/mm2{leaf},individual,mean,model_derived,5,field,adult,04,02,,,,02,11,,,2002/2002,made-up measurement remarks,05,,Alstonia scholaris Test_2023_1,Alstonia scholaris,038,leaf_length,40,mm,individual,mean,measurement,3,field,adult,04,02,,,,02,11,,,2004/2004,from Falster_2005_1,01,,Alstonia scholaris Test_2023_1,Alstonia scholaris,039,huber_value,0.000254323499491353,mm2{sapwood}/mm2{leaf},individual,raw,model_derived,5,field,adult,04,02,,,,02,11,,,,made-up measurement remarks,04,01,Alstonia scholaris From 27ecb286d3132df6d3b353dbad3879702bbbdc7a Mon Sep 17 00:00:00 2001 From: Elizabeth Wenk Date: Wed, 15 Nov 2023 14:22:28 +1100 Subject: [PATCH 17/31] rename function `build_update_taxonomy` (#127) rename function `build_update_taxonomy` to `dataset_update_taxonomy` to align with naming conventions. This function updates taxonomy of 1 dataset at a time --- NAMESPACE | 2 +- R/process.R | 6 +++--- R/testdata.R | 4 ++-- _pkgdown.yml | 2 +- inst/support/build_base.whisker | 2 +- inst/support/build_remake.whisker | 2 +- man/dataset_build.Rd | 2 +- ...{build_update_taxonomy.Rd => dataset_update_taxonomy.Rd} | 6 +++--- tests/testthat/functions.R | 4 ++-- tests/testthat/test-setup.R | 4 ++-- 10 files changed, 17 insertions(+), 17 deletions(-) rename man/{build_update_taxonomy.Rd => dataset_update_taxonomy.Rd} (79%) diff --git a/NAMESPACE b/NAMESPACE index 24b2e431..32130b93 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -4,7 +4,6 @@ export("%>%") export(build_add_version) export(build_combine) export(build_setup_pipeline) -export(build_update_taxonomy) export(check_duplicates) export(dataset_build) export(dataset_configure) @@ -12,6 +11,7 @@ export(dataset_find_taxon) export(dataset_process) export(dataset_report) export(dataset_test) +export(dataset_update_taxonomy) export(get_schema) export(get_unit_conversions) export(metadata_add_contexts) diff --git a/R/process.R b/R/process.R index e7995e0d..d3a00900 100644 --- a/R/process.R +++ b/R/process.R @@ -279,7 +279,7 @@ dataset_process <- function(filename_data_raw, #' Build dataset #' #' Build specified dataset. This function completes three steps, which can be executed separately if desired: -#' `dataset_configure`, `dataset_process`, `build_update_taxonomy` +#' `dataset_configure`, `dataset_process`, `dataset_update_taxonomy` #' #' @param filename_metadata Metadata yaml file for a given study #' @param filename_data_raw Raw `data.csv` file for any given study @@ -319,7 +319,7 @@ dataset_build <- function( dataset_raw <- dataset_process( filename_data_raw, dataset_config, schema, resource_metadata, unit_conversion_functions, filter_missing_values = filter_missing_values) - dataset <- build_update_taxonomy(dataset_raw, taxon_list) + dataset <- dataset_update_taxonomy(dataset_raw, taxon_list) dataset } @@ -1860,7 +1860,7 @@ build_combine <- function(..., d = list(...)) { #' @importFrom rlang .data #' #' @export -build_update_taxonomy <- function(austraits_raw, taxa) { +dataset_update_taxonomy <- function(austraits_raw, taxa) { columns_in_taxon_list <- names(taxa) diff --git a/R/testdata.R b/R/testdata.R index 4a5863da..146f56b5 100644 --- a/R/testdata.R +++ b/R/testdata.R @@ -327,8 +327,8 @@ dataset_test_worker <- }, info = "`dataset_process`") expect_no_error({ - build_dataset <- build_update_taxonomy(build_dataset_raw, taxon_list) - }, info = "`build_update_taxonomy`") + build_dataset <- dataset_update_taxonomy(build_dataset_raw, taxon_list) + }, info = "`dataset_update_taxonomy`") build_dataset } diff --git a/_pkgdown.yml b/_pkgdown.yml index 086c68e3..d1c1f42b 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -34,7 +34,7 @@ reference: - '`build_setup_pipeline`' - '`build_combine`' - '`build_add_version`' - - '`build_update_taxonomy`' + - '`dataset_update_taxonomy`' - '`dataset_build`' - '`dataset_configure`' - '`dataset_process`' diff --git a/inst/support/build_base.whisker b/inst/support/build_base.whisker index a3b882a4..c3820d5e 100644 --- a/inst/support/build_base.whisker +++ b/inst/support/build_base.whisker @@ -16,7 +16,7 @@ taxon_list <- read_csv_char("config/taxon_list.csv") {{#dataset_ids}} {{dataset_id}}_config <- dataset_configure("{{path}}/{{dataset_id}}/metadata.yml", definitions) {{dataset_id}}_raw <- dataset_process("{{path}}/{{dataset_id}}/data.csv", {{dataset_id}}_config, schema, resource_metadata, unit_conversions) -{{dataset_id}} <- build_update_taxonomy({{dataset_id}}_raw, taxon_list) +{{dataset_id}} <- dataset_update_taxonomy({{dataset_id}}_raw, taxon_list) {{/dataset_ids}} diff --git a/inst/support/build_remake.whisker b/inst/support/build_remake.whisker index 9229023b..a9f51ad1 100644 --- a/inst/support/build_remake.whisker +++ b/inst/support/build_remake.whisker @@ -46,7 +46,7 @@ targets: ) {{dataset_id}}: command: > - build_update_taxonomy({{dataset_id}}_raw, + dataset_update_taxonomy({{dataset_id}}_raw, taxon_list ) diff --git a/man/dataset_build.Rd b/man/dataset_build.Rd index 57981f2c..bd169099 100644 --- a/man/dataset_build.Rd +++ b/man/dataset_build.Rd @@ -38,7 +38,7 @@ List, AusTraits database object } \description{ Build specified dataset. This function completes three steps, which can be executed separately if desired: -`dataset_configure`, `dataset_process`, `build_update_taxonomy` +`dataset_configure`, `dataset_process`, `dataset_update_taxonomy` } \examples{ \dontrun{ diff --git a/man/build_update_taxonomy.Rd b/man/dataset_update_taxonomy.Rd similarity index 79% rename from man/build_update_taxonomy.Rd rename to man/dataset_update_taxonomy.Rd index 1ee59197..34e6ce89 100644 --- a/man/build_update_taxonomy.Rd +++ b/man/dataset_update_taxonomy.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/process.R -\name{build_update_taxonomy} -\alias{build_update_taxonomy} +\name{dataset_update_taxonomy} +\alias{dataset_update_taxonomy} \title{Apply taxonomic updates to austraits_raw} \usage{ -build_update_taxonomy(austraits_raw, taxa) +dataset_update_taxonomy(austraits_raw, taxa) } \arguments{ \item{austraits_raw}{AusTraits compiled data as a large list without taxonomic updates applied} diff --git a/tests/testthat/functions.R b/tests/testthat/functions.R index c4ae1d6b..53dd8428 100644 --- a/tests/testthat/functions.R +++ b/tests/testthat/functions.R @@ -107,8 +107,8 @@ test_build_dataset <- function( }, info = paste(info, "`dataset_process`")) expect_no_error({ - build_dataset <- build_update_taxonomy(build_dataset_raw, taxon_list) - }, info = paste(info, "`build_update_taxonomy`")) + build_dataset <- dataset_update_taxonomy(build_dataset_raw, taxon_list) + }, info = paste(info, "`dataset_update_taxonomy`")) test_structure(build_dataset, info, schema, definitions, single_dataset = TRUE) diff --git a/tests/testthat/test-setup.R b/tests/testthat/test-setup.R index aabd3d76..d5550862 100644 --- a/tests/testthat/test-setup.R +++ b/tests/testthat/test-setup.R @@ -666,8 +666,8 @@ test_that("`build_setup_pipeline` is working", { expect_equal(austraits$build_info$git_SHA, sha) expect_equal(austraits$build_info$git_SHA, "6c73238d8d048781d9a4f5239a03813be313f0dd") - #expect_length(austraits_raw$taxa, 14) #not valid test with new `build_update_taxonomy setup` - #expect_length(austraits$taxa, 14) #not valid test with new `build_update_taxonomy setup` + #expect_length(austraits_raw$taxa, 14) #not valid test with new `dataset_update_taxonomy setup` + #expect_length(austraits$taxa, 14) #not valid test with new `dataset_update_taxonomy setup` expect_equal(nrow(austraits$taxa), nrow(austraits_raw$taxa)) # Compare products from three methods, except `build_info` From 9a9be4c4450406e6fb20966d6d5184bbf5a2f77d Mon Sep 17 00:00:00 2001 From: Sophie Yang <78716301+yangsophieee@users.noreply.github.com> Date: Thu, 16 Nov 2023 10:20:40 +1100 Subject: [PATCH 18/31] Add `austraits` functions to `dataset_test` and allow trait values to be excluded in `exclude_observations` (#123) - Moved austraits functions `trait_pivot_wider` and `trait_pivot_longer` to traits.build in `pivot.R` and added testing within `dataset_test` - Moved code for testing pivot wider into standalone function called `check_pivot_wider()` - Allowed trait values to be excluded in `exclude_observations`, where previously only metadata fields/locations, etc. could be excluded - Added extra tests in `dataset_test` for `exclude_observations` and `taxonomic_updates` sections - Replaced `testthat` functions with own functions to enable customisation of failure messages - Regenerated `taxon_list.csv` for test datasets and documented method --- NAMESPACE | 3 + R/pivot.R | 138 +++++++ R/process.R | 23 +- R/reports.R | 28 +- R/setup.R | 10 +- R/testdata.R | 197 +++++++-- inst/support/traits.build_schema.yml | 15 +- man/check_pivot_wider.Rd | 17 + man/dataset_report.Rd | 20 +- man/db_traits_pivot_longer.Rd | 42 ++ man/db_traits_pivot_wider.Rd | 38 ++ man/metadata_create_template.Rd | 2 +- man/util_kable_styling_html.Rd | 2 +- tests/testthat/config/metadata.yml | 10 +- tests/testthat/config/taxon_list-orig.R | 16 +- tests/testthat/config/taxon_list-orig.csv | 241 ++++++++++- tests/testthat/examples/Test_2023_1/data.csv | 6 +- .../examples/Test_2023_1/metadata.yml | 16 +- .../Test_2023_1/output/excluded_data.csv | 21 +- .../examples/Test_2023_1/output/locations.csv | 3 + .../examples/Test_2023_1/output/metadata.yml | 2 +- .../examples/Test_2023_1/output/taxa.csv | 89 ++--- .../Test_2023_1/output/taxonomic_updates.csv | 78 ++-- .../examples/Test_2023_1/output/traits.csv | 121 +++--- .../examples/Test_2023_2/output/metadata.yml | 2 +- .../examples/Test_2023_2/output/taxa.csv | 92 ++--- .../Test_2023_2/output/taxonomic_updates.csv | 80 ++-- .../examples/Test_2023_2/output/traits.csv | 100 ++--- .../examples/Test_2023_3/output/metadata.yml | 2 +- .../examples/Test_2023_3/output/taxa.csv | 371 +++++++++-------- .../Test_2023_3/output/taxonomic_updates.csv | 374 ++++++++--------- .../examples/Test_2023_3/output/traits.csv | 20 +- .../examples/Test_2023_4/output/metadata.yml | 2 +- .../examples/Test_2023_4/output/taxa.csv | 375 +++++++++--------- .../Test_2023_4/output/taxonomic_updates.csv | 374 ++++++++--------- .../examples/Test_2023_4/output/traits.csv | 20 +- .../examples/Test_2023_7/output/metadata.yml | 2 +- .../examples/Test_2023_7/output/taxa.csv | 6 +- .../Test_2023_7/output/taxonomic_updates.csv | 4 +- .../examples/Test_2023_8/output/metadata.yml | 2 +- .../examples/Test_2023_8/output/taxa.csv | 6 +- .../Test_2023_8/output/taxonomic_updates.csv | 4 +- tests/testthat/test-setup.R | 4 +- 43 files changed, 1797 insertions(+), 1181 deletions(-) create mode 100644 R/pivot.R create mode 100644 man/check_pivot_wider.Rd create mode 100644 man/db_traits_pivot_longer.Rd create mode 100644 man/db_traits_pivot_wider.Rd diff --git a/NAMESPACE b/NAMESPACE index 32130b93..e0602133 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -5,6 +5,7 @@ export(build_add_version) export(build_combine) export(build_setup_pipeline) export(check_duplicates) +export(check_pivot_wider) export(dataset_build) export(dataset_configure) export(dataset_find_taxon) @@ -12,6 +13,8 @@ export(dataset_process) export(dataset_report) export(dataset_test) export(dataset_update_taxonomy) +export(db_traits_pivot_longer) +export(db_traits_pivot_wider) export(get_schema) export(get_unit_conversions) export(metadata_add_contexts) diff --git a/R/pivot.R b/R/pivot.R new file mode 100644 index 00000000..7ebf0f18 --- /dev/null +++ b/R/pivot.R @@ -0,0 +1,138 @@ +#' @title Test whether a dataset can pivot wider +#' +#' @description Test whether the traits table of a dataset can pivot wider with the minimum required columns. +#' +#' @param dataset Built dataset with `test_build_dataset` +#' +#' @return Number of rows with duplicates preventing pivoting wider +#' @export + +check_pivot_wider <- function(dataset) { + + duplicates <- dataset$traits %>% + select( + dplyr::all_of(c("dataset_id", "trait_name", "value", "observation_id", "value_type", + "repeat_measurements_id", "method_id", "method_context_id")) + ) %>% + tidyr::pivot_wider(names_from = "trait_name", values_from = "value", values_fn = length) %>% + tidyr::pivot_longer(cols = 7:ncol(.)) %>% + dplyr::rename(dplyr::all_of(c("trait_name" = "name", "number_of_duplicates" = "value"))) %>% + select( + dplyr::all_of(c("dataset_id", "trait_name", "number_of_duplicates", "observation_id", + "value_type")), everything() + ) %>% + filter(.data$number_of_duplicates > 1) %>% + nrow() + + if (duplicates == 0) { + invisible(TRUE) + } else { + invisible(FALSE) + } + +} + + +#' @title Pivot long format data into a wide format +#' +#' @description `trait_pivot_wider` "widens" long format data ("tidy data"). +#' +#' Databases built with `traits.build` are organised in a long format where observations are on different rows and the +#' type of observation is denoted by various identifying columns (e.g `trait_name`, `dataset_id`, +#' `observation_id`, etc.). +#' This function converts the data into wide format so that each trait in its own column. +#' +#' @param traits The traits table from database (list object) +#' @return A tibble in wide format +#' @details `trait_pivot_wider` will return a single wide tibble; note that some meta-data columns +#' (unit, replicates, measurement_remarks, basis_of_record, basis_of_value) will be excluded to +#' produce a useful wide tibble. +#' @examples +#' \dontrun{ +#' data <- austraits$traits %>% filter(dataset_id == "Falster_2003") +#' data # Long format +#' traits_wide <- trait_pivot_wider(data) +#' traits_wide # Wide format +#' } +#' @author Daniel Falster - daniel.falster@unsw.edu.au +#' @export +db_traits_pivot_wider <- function(traits) { + + metadata_cols <- c("unit", "replicates", "measurement_remarks", "basis_of_value") + + # A check for if there are more than 1 value_type for a given taxon_name, observation_id and method + check_value_type <- traits %>% + select(dplyr::all_of(c( + "trait_name", "value", "dataset_id", "observation_id", "method_id", "method_context_id", + "repeat_measurements_id", "value_type"))) %>% + dplyr::group_by( + .data$dataset_id, .data$observation_id, .data$method_id, + .data$method_context_id, .data$repeat_measurements_id) %>% + dplyr::summarise(n_value_type = length(unique(.data$value_type))) %>% + arrange(.data$observation_id) %>% + dplyr::filter(.data$n_value_type > 1) + + if (nrow(check_value_type) > 1) { + + traits %>% + tidyr::pivot_wider( + names_from = "trait_name", + values_from = "value", + id_cols = -dplyr::all_of(metadata_cols) + ) + + } else { + + metadata_cols <- c(metadata_cols, "value_type") + + traits %>% + tidyr::pivot_wider( + names_from = "trait_name", + values_from = "value", + id_cols = -dplyr::all_of(metadata_cols) + ) + } + +} + + +#' @title Pivot wide format data into a long format +#' +#' @description `trait_pivot_longer` "gathers" wide format data into a "tidy" format. +#' +#' This function converts the data into long format where observations are on different rows and the type of +#' observation is denoted by the `trait_name` column. +#' In other words, `trait_pivot_longer` reverts the actions of `trait_pivot_wider`. +#' @param wide_data Output from `trait_pivot_wider` (a tibble of wide data) +#' @return A tibble in long format +#' @details +#' `trait_pivot_longer` will return a tibble with fewer columns than the original traits table +#' The excluded columns include: "unit", "replicates", "measurement_remarks", "basis_of_record", +#' "basis_of_value" # Double check #TODO +#' +#' @examples +#' \dontrun{ +#' data <- austraits$traits %>% +#' filter(dataset_id == "Falster_2003") +#' data # Long format +#' traits_wide <- trait_pivot_wider(data) +#' traits_wide # Wide format +#' +#' values_long <- trait_pivot_longer(traits_wide) +#' } +#' @author Daniel Falster - daniel.falster@unsw.edu.au +#' @author Fonti Kar - fonti.kar@unsw.edu.au +#' @export +db_traits_pivot_longer <- function(wide_data) { + + # The start of the trait columns is after `original_name` + start_of_trait_cols <- which(names(wide_data) == "original_name") + 1 + + wide_data %>% + tidyr::pivot_longer( + cols = start_of_trait_cols:ncol(.), + names_to = "trait_name", + values_drop_na = TRUE + ) + +} diff --git a/R/process.R b/R/process.R index d3a00900..40463096 100644 --- a/R/process.R +++ b/R/process.R @@ -115,7 +115,7 @@ dataset_process <- function(filename_data_raw, "parsing_id", "location_name", "taxonomic_resolution", "methods", "unit_in") ) - # Replace location_name with a location_id + # Replace old `location_id` with a new `location_id` if (nrow(locations) > 0) { traits <- traits %>% @@ -900,12 +900,25 @@ process_flag_excluded_observations <- function(data, metadata) { fix <- split(fix, fix$variable) + traits <- metadata$traits %>% util_list_to_df2 + for (v in names(fix)) - data <- data %>% - dplyr::mutate( - error = ifelse(.data[[v]] %in% fix[[v]]$find, - "Observation excluded in metadata", .data$error)) + if (v %in% traits$trait_name) { + data <- data %>% + dplyr::mutate( + error = ifelse( + .data$trait_name == v & .data$value %in% fix[[v]]$find, + "Observation excluded in metadata", + .data$error)) + } else { + data <- data %>% + dplyr::mutate( + error = ifelse( + .data[[v]] %in% fix[[v]]$find, + "Observation excluded in metadata", + .data$error)) + } data } diff --git a/R/reports.R b/R/reports.R index dae6f66d..69e356f1 100644 --- a/R/reports.R +++ b/R/reports.R @@ -1,19 +1,19 @@ #' Build reports for listed datasets #' -#' Builds a detailed report for every dataset with a unique `dataset_id`, based on the template Rmd file provided. The reports are -#' rendered as html files and saved in the specified output folder. +#' Builds a detailed report for every dataset with a unique `dataset_id`, based on the template Rmd file provided. +#' The reports are rendered as html files and saved in the specified output folder. #' -#' @param dataset_id name of specific study/dataset -#' @param austraits compiled austraits database -#' @param overwrite logical value to determine whether to overwrite existing report, -#' @param output_path location where rendered report will be saved -#' @param input_file report script (.Rmd) file to build study report -#' @param quiet An option to suppress printing during rendering from knitr, pandoc command line and others. -#' @param keep keep intermediate Rmd file used? +#' @param dataset_id Name of specific study/dataset +#' @param austraits Compiled austraits database +#' @param overwrite Logical value to determine whether to overwrite existing report +#' @param output_path Location where rendered report will be saved +#' @param input_file Report script (.Rmd) file to build study report +#' @param quiet An option to suppress printing during rendering from knitr, pandoc command line and others +#' @param keep Keep intermediate Rmd file used? #' #' @rdname dataset_report -#' @return html file of the rendered report located in the specified output folder. +#' @return Html file of the rendered report located in the specified output folder #' @export dataset_report <- function(dataset_id, austraits, overwrite = FALSE, output_path = "export/reports", @@ -41,7 +41,7 @@ dataset_report_worker <- function(dataset_id, austraits, overwrite = FALSE, dir.create(output_path, FALSE, TRUE) } - # filenames + # Filenames input_Rmd <- sprintf("tmp_%s_report.Rmd", dataset_id) output_html <- sprintf("%s/%s.html", output_path, dataset_id) @@ -54,7 +54,7 @@ dataset_report_worker <- function(dataset_id, austraits, overwrite = FALSE, x[2] <- sprintf("title: Report on study `%s` from", dataset_id) writeLines(x, input_Rmd) - # knit and render. Note, call render directly + # Knit and render. Note, call render directly # in preference to knit, then render, as leaflet widget # requires this to work # Warning: result assigned but may not be used @@ -82,7 +82,7 @@ dataset_report_worker <- function(dataset_id, austraits, overwrite = FALSE, #' Format table with kable and default styling for html #' -#' @param ... arguments passed to `kableExtra::kable()` +#' @param ... Arguments passed to `kableExtra::kable()` #' @importFrom rlang .data #' @export util_kable_styling_html <- function(...) { @@ -94,6 +94,6 @@ util_kable_styling_html <- function(...) { position = "left" ) - # hack to add margin to plot + # Hack to add margin to plot gsub('style="width: auto ', 'style="margin-left:30px; width: auto ', txt) } diff --git a/R/setup.R b/R/setup.R index a63b60dd..1d6accf8 100644 --- a/R/setup.R +++ b/R/setup.R @@ -9,7 +9,7 @@ metadata_path_dataset_id <- function(dataset_id) { #' Create a template of file `metadata.yml` for specified `dataset_id` #' -#' Includes place-holders for major sections of the metadata +#' Includes place-holders for major sections of the metadata. #' #' @inheritParams metadata_path_dataset_id #' @param path Location of file where output is saved @@ -869,7 +869,7 @@ metadata_add_substitutions_table <- function(dataframe_of_substitutions, dataset #' @param reason Reason for taxonomic change #' @param taxonomic_resolution The rank of the most specific taxon name (or scientific name) #' to which a submitted orignal name resolves -#' @param overwrite Parameter indicating whether preexisting find-replace entries should be overwritten. Defaults to `true` +#' @param overwrite Parameter indicating whether preexisting find-replace entries should be overwritten. Defaults to `true` #' #' @return `metadata.yml` file with taxonomic change added #' @export @@ -888,7 +888,7 @@ metadata_add_taxonomic_change <- function(dataset_id, find, replace, reason, tax if (all(is.na(metadata[[set_name]]))) { data <- to_add } else { - data <- util_list_to_df2(metadata[[set_name]]) + data <- util_list_to_df2(metadata[[set_name]]) # Check if find record already exists for that trait if (find %in% data$find) { # If overwrite set to false, don't add a new substitution @@ -897,8 +897,8 @@ metadata_add_taxonomic_change <- function(dataset_id, find, replace, reason, tax return(invisible()) # Default is to overwrite existing substitution } else { - message(sprintf(red("Existing substitution will be overwritten for ") %+% green("'%s'"), find)) - data <- data %>% + message(sprintf(red("Existing substitution will be overwritten for ") %+% green("'%s'"), find)) + data <- data %>% filter(.data$find != to_add$find) %>% dplyr::bind_rows(to_add) %>% filter(!.data$find == replace) %>% diff --git a/R/testdata.R b/R/testdata.R index 146f56b5..b378a467 100644 --- a/R/testdata.R +++ b/R/testdata.R @@ -253,19 +253,36 @@ dataset_test_worker <- expect( is.null(error), sprintf("%s threw an error:\n\n" %+% red("%s"), info, paste(error, collapse = ","))) - invisible(NULL) + invisible(object) + } + + expect_no_warning <- function(object, ..., info) { + warning <- tryCatch({ + object + NULL + }, warning = function(w) { + w + }) + expect(is.null(warning), info) } expect_list_elements_contains_names <- function(object, expected, info) { for (i in seq_along(object)) expect_contains(names(object[[i]]), expected, info = paste(info, i)) - invisible(NULL) + invisible(object) } expect_list_elements_allowed_names <- function(object, allowed, info, label) { for (i in seq_along(object)) expect_allowed(names(object[[i]]), allowed, info = paste(info, i), label = "field names") - invisible(NULL) + invisible(object) + } + + expect_list_elements_exact_names <- function(object, expected, info) { + for (i in seq_along(object)) + expect_contains(names(object[[i]]), expected, info = paste(info, i)) + expect_allowed(names(object[[i]]), expected, info = paste(info, i), label = "field names") + invisible(object) } expect_dataframe_valid <- function(data, info, label) { @@ -596,7 +613,7 @@ dataset_test_worker <- # Traits expect_list_elements_contains_names( metadata[["traits"]], - schema$metadata$elements$traits$elements[1:3] %>% names(), + schema$metadata$elements$traits$elements[1:3] %>% names(), # Add `value_type` and `basis_of_value` info = paste0(red(f), "\ttrait") ) @@ -705,19 +722,14 @@ dataset_test_worker <- } # Substitutions - ## TODO do the same for `taxonomic_updates` and `exclude_observations`? if (!is.na(metadata[["substitutions"]][1])) { - expect_list_elements_contains_names( - metadata[["substitutions"]], - schema$metadata$elements$substitutions$values %>% names(), - info = paste0(red(f), "\tsubstitution") - ) - expect_list_elements_allowed_names( + expect_list_elements_exact_names( metadata[["substitutions"]], schema$metadata$elements$substitutions$values %>% names(), info = paste0(red(f), "\tsubstitution") ) + trait_names <- sapply(metadata[["substitutions"]], "[[", "trait_name") expect_is_in( unique(trait_names), definitions$elements %>% names(), @@ -731,7 +743,7 @@ dataset_test_worker <- # Check for allowable values of categorical variables expect_no_error( x <- metadata[["substitutions"]] %>% util_list_to_df2() %>% split(.$trait_name), - info = paste0(red(f), "\tconverting substitutions to a dataframe and splitting by `trait_name`") # Check + info = paste0(red(f), "\tconverting substitutions to a dataframe and splitting by `trait_name`") ) for (trait in names(x)) { @@ -758,6 +770,120 @@ dataset_test_worker <- } } + # Taxonomic updates + if (!is.na(metadata[["taxonomic_updates"]][1])) { + + expect_list_elements_exact_names( + metadata[["taxonomic_updates"]], + schema$metadata$elements$taxonomic_updates$values %>% names(), + info = paste0(red(f), "\ttaxonomic_update") + ) + taxon_names <- sapply(metadata[["taxonomic_updates"]], "[[", "find") + expect_is_in( + unique(taxon_names), data[[metadata[["dataset"]][["taxon_name"]]]] %>% unique(), + info = paste0(red(f), "\ttaxonomic_updates"), label = "`taxon_name`'s" + ) + + } + + # Check that special characters do not make it into the data + expect_no_error( + parsed_data <- data %>% + process_parse_data(dataset_id, metadata, contexts, schema), + info = sprintf("%s\t`process_parse_data`", red(dataset_id))) + + expect_allowed_text( + parsed_data$traits$value, is_data = TRUE, + info = sprintf("%s", red(files[1])) + ) + + # Process data so that you can check excluded observations + parsed_data <- + parsed_data$traits %>% + process_add_all_columns( + c(names(schema[["austraits"]][["elements"]][["traits"]][["elements"]]), + "parsing_id", "location_name", "taxonomic_resolution", "methods", "unit_in") + ) + + # Replace original `location_id` with a new `location_id` + if (nrow(locations) > 0) { + parsed_data <- + parsed_data %>% + dplyr::select(-dplyr::all_of(c("location_id"))) %>% + dplyr::left_join( + by = c("location_name"), + locations %>% dplyr::select(dplyr::all_of(c("location_name", "location_id"))) %>% dplyr::distinct() + ) + parsed_data <- + parsed_data %>% + mutate( + location_id = ifelse(.data$entity_type == "species", NA_character_, .data$location_id) + ) + } + + # Where missing, fill variables in traits table with values from locations + # Trait metadata should probably have precedence -- right now trait metadata + # is being read in during `process_parse_data` and getting overwritten here #TODO + # If process.R changes, this needs to be updated + if (nrow(locations) > 0) { + vars <- c("basis_of_record", "life_stage", "collection_date", + "measurement_remarks", "entity_type") + + for (v in vars) { + # Merge into traits from location level + if (v %in% unique(locations$location_property)) { + traits_tmp <- parsed_data %>% + dplyr::left_join( + by = "location_id", + locations %>% + tidyr::pivot_wider(names_from = "location_property", values_from = "value") %>% + mutate(col_tmp = .data[[v]]) %>% + dplyr::select(dplyr::any_of(c("location_id", "col_tmp"))) %>% + stats::na.omit() + ) + # Use location level value if present + parsed_data[[v]] <- ifelse(!is.na(traits_tmp[["col_tmp"]]), traits_tmp[["col_tmp"]], parsed_data[[v]]) + } + } + } + + # Excluded observations + if (!is.na(metadata[["exclude_observations"]][1])) { + + expect_list_elements_exact_names( + metadata[["exclude_observations"]], + schema$metadata$elements$exclude_observations$values %>% names(), + info = paste0(red(f), "\texclude_observations") + ) + + # Check for allowable values of categorical variables + expect_no_error( + x <- metadata[["exclude_observations"]] %>% util_list_to_df2() %>% split(.$variable), + info = paste0(red(f), "\tconverting `exclude_observations` to a dataframe and splitting by `variable`") + ) + + for (variable in names(x)) { + + find_values <- x[[variable]][["find"]] %>% unique() + + # If the variable to be excluded is a trait: + if (variable %in% traits$trait_name) { + expect_is_in( + find_values, + # Extract values from the data for that variable + parsed_data %>% filter(.data$trait_name == variable) %>% dplyr::pull(.data$value) %>% unique(), + info = paste0(red(f), "\texclude_observations"), label = sprintf("variable '%s'", variable) + ) + # If the variable to be excluded is `taxon_name`, `location_name` or other metadata fields + } else { + expect_is_in( + find_values, parsed_data %>% dplyr::pull(variable) %>% unique(), + info = paste0(red(f), "\texclude_observations"), label = sprintf("variable '%s'", variable) + ) + } + } + } + ## Check config files contain all relevant columns if (metadata[["dataset"]][["data_is_long_format"]]) { @@ -829,17 +955,6 @@ dataset_test_worker <- } - # Check that special characters do not make it into the data - expect_no_error( - parsed_data <- data %>% - process_parse_data(dataset_id, metadata, contexts, schema), - info = sprintf("%s\t`process_parse_data`", red(dataset_id))) - - expect_allowed_text( - parsed_data$traits$value, is_data = TRUE, - info = sprintf("%s", red(files[1])) - ) - expect_false( nrow(metadata[["traits"]] %>% util_list_to_df2() %>% dplyr::filter(!is.na(.data$trait_name))) == 0, info = paste0(red(f), "\ttraits - only contain NA `trait_name`'s")) @@ -865,25 +980,29 @@ dataset_test_worker <- # Check that dataset can pivot wider if (nrow(dataset$traits) > 0) { - expect_equal( - dataset$traits %>% - select( - dplyr::all_of(c("dataset_id", "trait_name", "value", "observation_id", "value_type", - "repeat_measurements_id", "method_id", "method_context_id")) - ) %>% - tidyr::pivot_wider(names_from = "trait_name", values_from = "value", values_fn = length) %>% - tidyr::pivot_longer(cols = 7:ncol(.)) %>% - dplyr::rename(dplyr::all_of(c("trait_name" = "name", "number_of_duplicates" = "value"))) %>% - select( - dplyr::all_of(c("dataset_id", "trait_name", "number_of_duplicates", "observation_id", - "value_type")), everything() - ) %>% - filter(.data$number_of_duplicates > 1) %>% - nrow(), - 0, # Expect nrow() = 0 + expect_true( + dataset %>% check_pivot_wider(), info = sprintf("%s\tduplicate rows detected; `traits` table cannot pivot wider", red(dataset_id)) ) } + + # Test `austraits` functions + # Testing per study, not on all studies combined (is this ideal?) + # I'm not testing whether the functions work as intended, just that they throw no error + + expect_no_warning( + dataset_wider <- db_traits_pivot_wider(dataset$traits), + info = paste0(red(dataset_id), "\t`db_traits_pivot_wider` threw a warning; duplicate rows detected") + ) + + if (exists("dataset_wider")) { + expect_no_warning( + expect_no_error( + dataset_longer <- db_traits_pivot_longer(dataset_wider), + info = paste0(red(dataset_id), "\t`db_traits_pivot_longer`")), + info = paste0(red(dataset_id), "\t`db_traits_pivot_longer` threw a warning") + ) + } } }) } diff --git a/inst/support/traits.build_schema.yml b/inst/support/traits.build_schema.yml index 573f6d8c..70f70809 100644 --- a/inst/support/traits.build_schema.yml +++ b/inst/support/traits.build_schema.yml @@ -42,7 +42,7 @@ basis_of_record: field_experiment: Traits were recorded on entities living under experimentally manipulated conditions in the field. captive_cultivated: Traits were recorded on entities living in a common garden, arboretum, or botanical or zoological garden. lab: Traits were recorded on entities growing in a lab, glasshouse or growth chamber. - preserved_specimen: Traits were recorded from specimens preserved in a collection, eg. herbarium or museum + preserved_specimen: Traits were recorded from specimens preserved in a collection, eg. herbarium or museum. literature: Traits were sourced from values reported in the literature, and where the basis of record is not otherwise known. #------------------------------------------------------------- @@ -77,7 +77,7 @@ austraits: entity_context_id: &entity_context_id A unique integer identifier indicating specific contextual properties of an individual, possibly including the individual's sex or caste (for social insects). plot_context_id: &plot_context_id A unique integer identifier for a plot, where a plot is a distinct collection of organisms within a single geographic location, such as plants growing on different aspects or blocks in an experiment. The identifier links to specific information in the context table. treatment_context_id: &treatment_context_id A unique integer identifier for a treatment, where a treatment is any experimental manipulation to an organism's growing/living conditions. The identifier links to specific information in the context table. - collection_date: &collection_date Date sample was taken, in the format `yyyy-mm-dd`, `yyyy-mm` or `yyyy`, depending on the resoluton specified. Alternatively an overall range for the study can be indicating, with the starting and ending sample date sepatated by a `/`, as in 2010-10/2011-03 + collection_date: &collection_date Date sample was taken, in the format `yyyy-mm-dd`, `yyyy-mm` or `yyyy`, depending on the resoluton specified. Alternatively an overall range for the study can be indicating, with the starting and ending sample date sepatated by a `/`, as in 2010-10/2011-03. measurement_remarks: &measurement_remarks Brief comments or notes accompanying the trait measurement. method_id: &method_id A unique integer identifier to distinguish between multiple sets of methods used to measure a single trait within the same dataset. The identifier links to specific information in the methods table. method_context_id: &method_context_id A unique integer identifier indicating a trait is measured multiple times on the same entity, with different methods used for each entry. This field is only used if a single trait is measured using multiple methods within the same dataset. The identifier links to specific information in the context table. @@ -88,7 +88,7 @@ austraits: elements: dataset_id: *dataset_id location_id: *location_id - location_name: &location_name location name + location_name: &location_name The location name. location_property: The location characteristic being recorded. The name should include units of measurement, e.g. `MAT (C)`. Ideally we have at least the following variables for each location, `longitude (deg)`, `latitude (deg)`, `description`. value: The measured value of a location property. contexts: @@ -383,7 +383,7 @@ metadata: context_property: The context property represented by the data in the column specified by `var_in`. category: The category of contextual data. Options are `plot` (a distinct collection of organisms within a single geographic location, such as plants growing on different aspects or blocks in an experiment), `treatment` (an experimental treatment), `entity_context` (contextual information to record about the entity the isn't documented elsewhere, including the entity's sex, caste), `temporal` (indicating when repeat observations are made on the same individual (or population, or taxon) across time) and `method` (indicating the same trait was measured on the same individual (or population, or taxon) using multiple methods). var_in: Name of column with contextual data in the original data submitted. - find: The contextual values in the original data submitted (optional) + find: The contextual values in the original data submitted (optional). value: The standardised contextual values, aligning syntax and wording with other studies. description: A description of the contextual values. traits: @@ -417,12 +417,13 @@ metadata: values: find: *original_name replace: *taxon_name - reason: Records why the change was implemented, e.g. `typos`, `taxonomic synonyms`, and `standardising spellings` + reason: Records why the change was implemented, e.g. `typos`, `taxonomic synonyms`, and `standardising spellings`. + taxonomic_resolution: The taxonomic rank of the most specific name that can be aligned. exclude_observations: description: A table of observations to remove from the compilation. type: array values: - variable: A variable from the traits table, typically `taxon_name` or `location_name` + variable: A variable from the traits table, typically `taxon_name` or `location_name`. find: Value of variable to remove. - reason: Records why the data was removed, e.g. `exotic` + reason: Records why the data was removed, e.g. `exotic`. questions: A place to record any queries we have about the dataset (recorded as a named array), including notes on any additional traits that may have been collected in the study but have not been incorporated into AusTraits. diff --git a/man/check_pivot_wider.Rd b/man/check_pivot_wider.Rd new file mode 100644 index 00000000..e8746b0f --- /dev/null +++ b/man/check_pivot_wider.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pivot.R +\name{check_pivot_wider} +\alias{check_pivot_wider} +\title{Test whether a dataset can pivot wider} +\usage{ +check_pivot_wider(dataset) +} +\arguments{ +\item{dataset}{Built dataset with `test_build_dataset`} +} +\value{ +Number of rows with duplicates preventing pivoting wider +} +\description{ +Test whether the traits table of a dataset can pivot wider with the minimum required columns. +} diff --git a/man/dataset_report.Rd b/man/dataset_report.Rd index 12de2543..93782e41 100644 --- a/man/dataset_report.Rd +++ b/man/dataset_report.Rd @@ -15,24 +15,24 @@ dataset_report( ) } \arguments{ -\item{dataset_id}{name of specific study/dataset} +\item{dataset_id}{Name of specific study/dataset} -\item{austraits}{compiled austraits database} +\item{austraits}{Compiled austraits database} -\item{overwrite}{logical value to determine whether to overwrite existing report,} +\item{overwrite}{Logical value to determine whether to overwrite existing report} -\item{output_path}{location where rendered report will be saved} +\item{output_path}{Location where rendered report will be saved} -\item{input_file}{report script (.Rmd) file to build study report} +\item{input_file}{Report script (.Rmd) file to build study report} -\item{quiet}{An option to suppress printing during rendering from knitr, pandoc command line and others.} +\item{quiet}{An option to suppress printing during rendering from knitr, pandoc command line and others} -\item{keep}{keep intermediate Rmd file used?} +\item{keep}{Keep intermediate Rmd file used?} } \value{ -html file of the rendered report located in the specified output folder. +Html file of the rendered report located in the specified output folder } \description{ -Builds a detailed report for every dataset with a unique `dataset_id`, based on the template Rmd file provided. The reports are -rendered as html files and saved in the specified output folder. +Builds a detailed report for every dataset with a unique `dataset_id`, based on the template Rmd file provided. +The reports are rendered as html files and saved in the specified output folder. } diff --git a/man/db_traits_pivot_longer.Rd b/man/db_traits_pivot_longer.Rd new file mode 100644 index 00000000..fd5f4932 --- /dev/null +++ b/man/db_traits_pivot_longer.Rd @@ -0,0 +1,42 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pivot.R +\name{db_traits_pivot_longer} +\alias{db_traits_pivot_longer} +\title{Pivot wide format data into a long format} +\usage{ +db_traits_pivot_longer(wide_data) +} +\arguments{ +\item{wide_data}{Output from `trait_pivot_wider` (a tibble of wide data)} +} +\value{ +A tibble in long format +} +\description{ +`trait_pivot_longer` "gathers" wide format data into a "tidy" format. + +This function converts the data into long format where observations are on different rows and the type of +observation is denoted by the `trait_name` column. +In other words, `trait_pivot_longer` reverts the actions of `trait_pivot_wider`. +} +\details{ +`trait_pivot_longer` will return a tibble with fewer columns than the original traits table +The excluded columns include: "unit", "replicates", "measurement_remarks", "basis_of_record", +"basis_of_value" # Double check #TODO +} +\examples{ +\dontrun{ +data <- austraits$traits \%>\% +filter(dataset_id == "Falster_2003") +data # Long format +traits_wide <- trait_pivot_wider(data) +traits_wide # Wide format + +values_long <- trait_pivot_longer(traits_wide) +} +} +\author{ +Daniel Falster - daniel.falster@unsw.edu.au + +Fonti Kar - fonti.kar@unsw.edu.au +} diff --git a/man/db_traits_pivot_wider.Rd b/man/db_traits_pivot_wider.Rd new file mode 100644 index 00000000..4756b738 --- /dev/null +++ b/man/db_traits_pivot_wider.Rd @@ -0,0 +1,38 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pivot.R +\name{db_traits_pivot_wider} +\alias{db_traits_pivot_wider} +\title{Pivot long format data into a wide format} +\usage{ +db_traits_pivot_wider(traits) +} +\arguments{ +\item{traits}{The traits table from database (list object)} +} +\value{ +A tibble in wide format +} +\description{ +`trait_pivot_wider` "widens" long format data ("tidy data"). + +Databases built with `traits.build` are organised in a long format where observations are on different rows and the +type of observation is denoted by various identifying columns (e.g `trait_name`, `dataset_id`, +`observation_id`, etc.). +This function converts the data into wide format so that each trait in its own column. +} +\details{ +`trait_pivot_wider` will return a single wide tibble; note that some meta-data columns +(unit, replicates, measurement_remarks, basis_of_record, basis_of_value) will be excluded to +produce a useful wide tibble. +} +\examples{ +\dontrun{ +data <- austraits$traits \%>\% filter(dataset_id == "Falster_2003") +data # Long format +traits_wide <- trait_pivot_wider(data) +traits_wide # Wide format +} +} +\author{ +Daniel Falster - daniel.falster@unsw.edu.au +} diff --git a/man/metadata_create_template.Rd b/man/metadata_create_template.Rd index deeeb771..6672dbb5 100644 --- a/man/metadata_create_template.Rd +++ b/man/metadata_create_template.Rd @@ -25,5 +25,5 @@ of variables, mainly for testing purposes} A yaml file template for metadata } \description{ -Includes place-holders for major sections of the metadata +Includes place-holders for major sections of the metadata. } diff --git a/man/util_kable_styling_html.Rd b/man/util_kable_styling_html.Rd index 048a4c8a..2db1548e 100644 --- a/man/util_kable_styling_html.Rd +++ b/man/util_kable_styling_html.Rd @@ -7,7 +7,7 @@ util_kable_styling_html(...) } \arguments{ -\item{...}{arguments passed to `kableExtra::kable()`} +\item{...}{Arguments passed to `kableExtra::kable()`} } \description{ Format table with kable and default styling for html diff --git a/tests/testthat/config/metadata.yml b/tests/testthat/config/metadata.yml index 53d2e49f..7b2ba21c 100644 --- a/tests/testthat/config/metadata.yml +++ b/tests/testthat/config/metadata.yml @@ -1,7 +1,7 @@ metadata: title: 'AusTraits: a curated plant trait database for the Australian flora' description: "AusTraits is a transformative database, containing measurements on the traits of Australia's plant taxa, standardised from hundreds of disconnected primary sources. While this repository contains the harmonised data, the raw data and code used to build the resource are also available on the project's GitHub repository,http://traitecoevo.github.io/traits.build. Further information on the project is available in the associated publication and at the project website https://austraits.org." - version: "4.0.0" + version: "5.0.0" doi: 10.5281/zenodo.5112001 structure_URI: https://github.com/traitecoevo/traits.build geo_location: @@ -9,7 +9,7 @@ metadata: geodetic_datum: EPSG:4326 language: en related_identifiers: - - related_identifier_type: url + - related_identifier_type: url identifier: https://github.com/traitecoevo/traits.build/tree/v3.0.2 relation_type: isCompiledBy resource_type: dataset @@ -21,7 +21,7 @@ metadata: publisher: Zenodo publication_date: 27 Nov 2022 license: - rights: CC-BY-4.0 + rights: CC-BY-4.0 rights_holder: Falster, Daniel rights_URI: https://creativecommons.org/licenses/by/4.0/ description: Under this license, the material can be copied and redistributed in any medium or format. It can be remixed, transformed, and built upon for any purpose, even commercially. Re-users must give appropriate credit, provide a link to the license, and indicate if changes were made. Re-users may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. @@ -50,7 +50,7 @@ metadata: award_IRI: purl.org/au-research/grants/arc/DE170100208 award_number: DE170100208 award_title: Discovery Early Career Researcher Award - - funder_name: Australian Research Council + - funder_name: Australian Research Council award_IRI: purl.org/au-research/grants/arc/FT160100113 award_number: FT160100113 award_title: Future Fellowship @@ -58,7 +58,7 @@ metadata: award_IRI: purl.org/au-research/grants/arc/FT100100910 award_number: FT100100910 award_title: Future Fellowship - creators: + creators: - last_name: Falster given_name: Daniel ORCID: 0000-0002-9814-092X diff --git a/tests/testthat/config/taxon_list-orig.R b/tests/testthat/config/taxon_list-orig.R index d674d0ce..29876ad3 100644 --- a/tests/testthat/config/taxon_list-orig.R +++ b/tests/testthat/config/taxon_list-orig.R @@ -1,7 +1,11 @@ -# to generate taxon_list-orig.csv -v1 <- read_csv("config/taxon_list.csv") -v2 <- read_csv("tests//testthat/config/taxon_list-orig.csv") -v1 %>% - filter(taxon_id %in% v2$taxon_id, taxonomic_status == "accepted") %>% - write_csv("tests/testthat/config/taxon_list-orig.csv") +# To generate taxon_list-orig.csv + +# Use Lizzy's `R/build_update_taxon_list.R` function + +# First move the test datasets to the tests/testthat/data folder +# Then source "build.R" and "R/build_update_taxon_list.R" in "tests/testthat" +# Run the function on the built test database with `replace = TRUE` +# (Remove the tests from the data folder afterwards) + +build_update_taxon_list(database, read_csv("config/taxon_list.csv"), replace = TRUE) diff --git a/tests/testthat/config/taxon_list-orig.csv b/tests/testthat/config/taxon_list-orig.csv index 8bbfcfee..764bc6b7 100644 --- a/tests/testthat/config/taxon_list-orig.csv +++ b/tests/testthat/config/taxon_list-orig.csv @@ -1,8 +1,233 @@ -aligned_name,taxon_name,taxonomic_dataset,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution -Acacia celsa,Acacia celsa,APC,species,accepted,Acacia,Acacia celsa,,Fabaceae,https://id.biodiversity.org.au/taxon/apni/51436506,Qld -Acronychia acidula,Acronychia acidula,APC,species,accepted,Acronychia,Acronychia acidula,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913200,Qld -Alphitonia petriei,Alphitonia petriei,APC,species,accepted,Alphitonia,Alphitonia petriei,,Rhamnaceae,https://id.biodiversity.org.au/node/apni/2887911,"Qld, NSW" -Euodia elleryana,Melicope elleryana,APC,species,accepted,Melicope,Melicope elleryana,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913641,"WA, NT, Qld, NSW" -Evodiella muelleri,Melicope elleryana,APC,species,accepted,Melicope,Melicope elleryana,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913641,"WA, NT, Qld, NSW" -Glochidion hylandii,Glochidion hylandii,APC,species,accepted,Glochidion,Glochidion hylandii,,Phyllanthaceae,https://id.biodiversity.org.au/node/apni/2889113,Qld -Melicope elleryana,Melicope elleryana,APC,species,accepted,Melicope,Melicope elleryana,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913641,"WA, NT, Qld, NSW" +original_name,aligned_name,taxon_name,taxon_name_alternatives,genus,family,taxon_rank,taxonomic_dataset,taxonomic_status,subclass,taxon_distribution,scientific_name,taxon_id,taxon_ID_genus,scientific_name_id,canonical_name,cleaned_scientific_name_id,aligned_name_taxonomic_status,aligned_name_taxon_id,taxon_id_family,trinomial,binomial,establishment_means +Abildgaardia ovata,Abildgaardia ovata,Abildgaardia ovata,NA,Abildgaardia,Cyperaceae,species,APC,accepted,Magnoliidae,"NT, Qld, NSW",Abildgaardia ovata (Burm.f.) Kral,https://id.biodiversity.org.au/node/apni/2919627,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/150737,Abildgaardia ovata,https://id.biodiversity.org.au/name/apni/150737,accepted,https://id.biodiversity.org.au/node/apni/2919627,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Abildgaardia ovata,native +Acacia alpina,Acacia alpina,Acacia alpina,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Acacia alpina F.Muell.,https://id.biodiversity.org.au/node/apni/2907301,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/58263,Acacia alpina,https://id.biodiversity.org.au/name/apni/58263,accepted,https://id.biodiversity.org.au/node/apni/2907301,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia alpina,native +Acacia beadleana,Acacia beadleana,Acacia beadleana,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Acacia beadleana R.H.Jones & J.J.Bruhl,https://id.biodiversity.org.au/node/apni/2902581,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/198624,Acacia beadleana,https://id.biodiversity.org.au/name/apni/165277,taxonomic synonym,https://id.biodiversity.org.au/instance/apni/949589,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia beadleana,native +Acacia bulgaensis,Acacia bulgaensis,Acacia bulgaensis,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Acacia bulgaensis Tindale & S.J.Davies,https://id.biodiversity.org.au/node/apni/2889179,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/117995,Acacia bulgaensis,https://id.biodiversity.org.au/name/apni/117995,accepted,https://id.biodiversity.org.au/node/apni/2889179,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia bulgaensis,native +Acacia caroleae,Acacia caroleae,Acacia caroleae,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acacia caroleae Pedley,https://id.biodiversity.org.au/node/apni/2894332,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/60225,Acacia caroleae,https://id.biodiversity.org.au/name/apni/60225,accepted,https://id.biodiversity.org.au/node/apni/2894332,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia caroleae,native +Acacia celsa,Acacia celsa,Acacia celsa,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,Qld,Acacia celsa Tindale,https://id.biodiversity.org.au/taxon/apni/51436506,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/154988,Acacia celsa,https://id.biodiversity.org.au/name/apni/154988,accepted,https://id.biodiversity.org.au/taxon/apni/51436506,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia celsa,native +Acacia crassa,Acacia crassa,Acacia crassa,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acacia crassa Pedley,https://id.biodiversity.org.au/node/apni/2919707,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/60887,Acacia crassa,https://id.biodiversity.org.au/name/apni/60887,accepted,https://id.biodiversity.org.au/node/apni/2919707,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia crassa,native +Acacia flexifolia,Acacia flexifolia,Acacia flexifolia,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic",Acacia flexifolia A.Cunn. ex Benth.,https://id.biodiversity.org.au/node/apni/2914740,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/63146,Acacia flexifolia,https://id.biodiversity.org.au/name/apni/63146,accepted,https://id.biodiversity.org.au/node/apni/2914740,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia flexifolia,native +Acacia gladiiformis,Acacia gladiiformis,Acacia gladiiformis,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acacia gladiiformis A.Cunn. ex Benth.,https://id.biodiversity.org.au/node/apni/2887779,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/63580,Acacia gladiiformis,https://id.biodiversity.org.au/name/apni/63580,accepted,https://id.biodiversity.org.au/node/apni/2887779,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia gladiiformis,native +Acacia havilandiorum,Acacia havilandiorum,Acacia havilandiorum,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic",Acacia havilandiorum Maiden,https://id.biodiversity.org.au/node/apni/2897713,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/135274,Acacia havilandiorum,https://id.biodiversity.org.au/name/apni/135274,accepted,https://id.biodiversity.org.au/node/apni/2897713,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia havilandiorum,native +Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx subsp. leiocalyx,NA,Acacia,Fabaceae,subspecies,APC,accepted,Magnoliidae,"Qld, NSW",Acacia leiocalyx (Domin) Pedley subsp. leiocalyx,https://id.biodiversity.org.au/node/apni/2894438,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/65375,Acacia leiocalyx subsp. leiocalyx,https://id.biodiversity.org.au/name/apni/65375,accepted,https://id.biodiversity.org.au/node/apni/2894438,https://id.biodiversity.org.au/taxon/apni/51702961,Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx,native +Acacia myrtifolia,Acacia myrtifolia,Acacia myrtifolia,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic, Tas",Acacia myrtifolia (Sm.) Willd.,https://id.biodiversity.org.au/node/apni/2901160,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/162110,Acacia myrtifolia,https://id.biodiversity.org.au/name/apni/162110,accepted,https://id.biodiversity.org.au/node/apni/2901160,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia myrtifolia,native +Acacia ramulosa var. ramulosa,Acacia ramulosa var. ramulosa,Acacia ramulosa var. ramulosa,NA,Acacia,Fabaceae,variety,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Acacia ramulosa W.Fitzg. var. ramulosa,https://id.biodiversity.org.au/node/apni/2915768,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/168882,Acacia ramulosa var. ramulosa,https://id.biodiversity.org.au/name/apni/168882,accepted,https://id.biodiversity.org.au/node/apni/2915768,https://id.biodiversity.org.au/taxon/apni/51702961,Acacia ramulosa var. ramulosa,Acacia ramulosa,native +Acacia spectabilis,Acacia spectabilis,Acacia spectabilis,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW (native and naturalised)",Acacia spectabilis A.Cunn. ex Benth.,https://id.biodiversity.org.au/node/apni/2918795,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/70543,Acacia spectabilis,https://id.biodiversity.org.au/name/apni/70543,accepted,https://id.biodiversity.org.au/node/apni/2918795,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia spectabilis,native and naturalised +Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis subsp. Glabrous form (M.Hancock 94),NA,Acacia,Fabaceae,subspecies,APC,accepted,Magnoliidae,"NSW, Vic, Tas",Acacia terminalis subsp. Glabrous form (M.Hancock 94) NSW Herbarium,https://id.biodiversity.org.au/node/apni/2886403,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/199841,Acacia terminalis subsp. Glabrous form (M.Hancock 94),https://id.biodiversity.org.au/name/apni/199841,accepted,https://id.biodiversity.org.au/node/apni/2886403,https://id.biodiversity.org.au/taxon/apni/51702961,Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis,native +Acronychia acidula,Acronychia acidula,Acronychia acidula,NA,Acronychia,Rutaceae,species,APC,accepted,Magnoliidae,Qld,Acronychia acidula F.Muell.,https://id.biodiversity.org.au/node/apni/2913200,https://id.biodiversity.org.au/taxon/apni/51446847,https://id.biodiversity.org.au/name/apni/73794,Acronychia acidula,https://id.biodiversity.org.au/name/apni/73794,accepted,https://id.biodiversity.org.au/node/apni/2913200,https://id.biodiversity.org.au/taxon/apni/51461748,NA,Acronychia acidula,native +Acronychia littoralis,Acronychia littoralis,Acronychia littoralis,NA,Acronychia,Rutaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acronychia littoralis T.G.Hartley & J.B.Williams,https://id.biodiversity.org.au/node/apni/2907701,https://id.biodiversity.org.au/taxon/apni/51446847,https://id.biodiversity.org.au/name/apni/73953,Acronychia littoralis,https://id.biodiversity.org.au/name/apni/73953,accepted,https://id.biodiversity.org.au/node/apni/2907701,https://id.biodiversity.org.au/taxon/apni/51461748,NA,Acronychia littoralis,native +Adriana tomentosa,Adriana tomentosa,Adriana tomentosa,NA,Adriana,Euphorbiaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, ACT, Vic",Adriana tomentosa Gaudich.,https://id.biodiversity.org.au/node/apni/2898187,https://id.biodiversity.org.au/node/apni/8408111,https://id.biodiversity.org.au/name/apni/77104,Adriana tomentosa,https://id.biodiversity.org.au/name/apni/77104,accepted,https://id.biodiversity.org.au/node/apni/2898187,https://id.biodiversity.org.au/taxon/apni/51442249,NA,Adriana tomentosa,native +Alectryon coriaceus,Alectryon coriaceus,Alectryon coriaceus,NA,Alectryon,Sapindaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Alectryon coriaceus (Benth.) Radlk.,https://id.biodiversity.org.au/node/apni/2891604,https://id.biodiversity.org.au/taxon/apni/51299789,https://id.biodiversity.org.au/name/apni/81043,Alectryon coriaceus,https://id.biodiversity.org.au/name/apni/81043,accepted,https://id.biodiversity.org.au/node/apni/2891604,https://id.biodiversity.org.au/taxon/apni/51447212,NA,Alectryon coriaceus,native +Alectryon oleifolius,Alectryon oleifolius,Alectryon oleifolius,NA,Alectryon,Sapindaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Alectryon oleifolius (Desf.) S.T.Reynolds,https://id.biodiversity.org.au/node/apni/2900874,https://id.biodiversity.org.au/taxon/apni/51299789,https://id.biodiversity.org.au/name/apni/81066,Alectryon oleifolius,https://id.biodiversity.org.au/name/apni/81066,accepted,https://id.biodiversity.org.au/node/apni/2900874,https://id.biodiversity.org.au/taxon/apni/51447212,NA,Alectryon oleifolius,native +Alectryon subdentatus,Alectryon subdentatus,Alectryon subdentatus,NA,Alectryon,Sapindaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Alectryon subdentatus (F.Muell. ex Benth.) Radlk.,https://id.biodiversity.org.au/node/apni/2890534,https://id.biodiversity.org.au/taxon/apni/51299789,https://id.biodiversity.org.au/name/apni/81114,Alectryon subdentatus,https://id.biodiversity.org.au/name/apni/81114,accepted,https://id.biodiversity.org.au/node/apni/2890534,https://id.biodiversity.org.au/taxon/apni/51447212,NA,Alectryon subdentatus,native +Aleurites rockinghamensis,Aleurites rockinghamensis,Aleurites rockinghamensis,NA,Aleurites,Euphorbiaceae,species,APC,accepted,Magnoliidae,Qld,Aleurites rockinghamensis (Baill.) P.I.Forst.,https://id.biodiversity.org.au/node/apni/2916622,https://id.biodiversity.org.au/node/apni/2900410,https://id.biodiversity.org.au/name/apni/171057,Aleurites rockinghamensis,https://id.biodiversity.org.au/name/apni/171057,accepted,https://id.biodiversity.org.au/node/apni/2916622,https://id.biodiversity.org.au/taxon/apni/51442249,NA,Aleurites rockinghamensis,native +Alphitonia petriei,Alphitonia petriei,Alphitonia petriei,NA,Alphitonia,Rhamnaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Alphitonia petriei Braid & C.T.White,https://id.biodiversity.org.au/node/apni/2887911,https://id.biodiversity.org.au/taxon/apni/51446205,https://id.biodiversity.org.au/name/apni/82935,Alphitonia petriei,https://id.biodiversity.org.au/name/apni/82935,accepted,https://id.biodiversity.org.au/node/apni/2887911,https://id.biodiversity.org.au/taxon/apni/51446206,NA,Alphitonia petriei,native +Alstonia scholaris,Alstonia scholaris,Alstonia scholaris,NA,Alstonia,Apocynaceae,species,APC,accepted,Magnoliidae,Qld,Alstonia scholaris (L.) R.Br.,https://id.biodiversity.org.au/node/apni/2916809,https://id.biodiversity.org.au/node/apni/6684160,https://id.biodiversity.org.au/name/apni/83915,Alstonia scholaris,https://id.biodiversity.org.au/name/apni/83915,accepted,https://id.biodiversity.org.au/node/apni/2916809,https://id.biodiversity.org.au/taxon/apni/51700686,NA,Alstonia scholaris,native +Amyema preissii,Amyema preissii,Amyema preissii,NA,Amyema,Loranthaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Amyema preissii (Miq.) Tiegh.,https://id.biodiversity.org.au/node/apni/2888430,https://id.biodiversity.org.au/taxon/apni/51438795,https://id.biodiversity.org.au/name/apni/87461,Amyema preissii,https://id.biodiversity.org.au/name/apni/87461,accepted,https://id.biodiversity.org.au/node/apni/2888430,https://id.biodiversity.org.au/taxon/apni/51438796,NA,Amyema preissii,native +Angophora leiocarpa,Angophora leiocarpa,Angophora leiocarpa,NA,Angophora,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Angophora leiocarpa (L.A.S.Johnson ex G.J.Leach) K.R.Thiele & Ladiges,https://id.biodiversity.org.au/node/apni/2894339,https://id.biodiversity.org.au/taxon/apni/51439560,https://id.biodiversity.org.au/name/apni/123435,Angophora leiocarpa,https://id.biodiversity.org.au/name/apni/123435,accepted,https://id.biodiversity.org.au/node/apni/2894339,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Angophora leiocarpa,native +Arbutus unedo,Arbutus unedo,Arbutus unedo,NA,Arbutus,Ericaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (doubtfully naturalised), NSW (doubtfully naturalised), ACT (doubtfully naturalised), Vic (naturalised), Tas (doubtfully naturalised)",Arbutus unedo L.,https://id.biodiversity.org.au/node/apni/2904939,https://id.biodiversity.org.au/node/apni/2892910,https://id.biodiversity.org.au/name/apni/98540,Arbutus unedo,https://id.biodiversity.org.au/name/apni/98540,accepted,https://id.biodiversity.org.au/node/apni/2904939,https://id.biodiversity.org.au/taxon/apni/51436079,NA,Arbutus unedo,naturalised +Argyrodendron peralatum,Argyrodendron peralatum,Argyrodendron peralatum,NA,Argyrodendron,Malvaceae,species,APC,accepted,Magnoliidae,Qld,Argyrodendron peralatum (F.M.Bailey) Edlin ex I.H.Boas,https://id.biodiversity.org.au/node/apni/2915243,https://id.biodiversity.org.au/taxon/apni/51288410,https://id.biodiversity.org.au/name/apni/100216,Argyrodendron peralatum,https://id.biodiversity.org.au/name/apni/100216,accepted,https://id.biodiversity.org.au/node/apni/2915243,https://id.biodiversity.org.au/taxon/apni/51439248,NA,Argyrodendron peralatum,native +Atractocarpus hirtus,Atractocarpus hirtus,Atractocarpus hirtus,NA,Atractocarpus,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Atractocarpus hirtus (F.Muell.) Puttock,https://id.biodiversity.org.au/node/apni/2910460,https://id.biodiversity.org.au/taxon/apni/51446611,https://id.biodiversity.org.au/name/apni/146883,Atractocarpus hirtus,https://id.biodiversity.org.au/name/apni/146883,accepted,https://id.biodiversity.org.au/node/apni/2910460,https://id.biodiversity.org.au/taxon/apni/51446612,NA,Atractocarpus hirtus,native +Australina pusilla,Australina pusilla,Australina pusilla,NA,Australina,Urticaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic, Tas",Australina pusilla (Poir.) Gaudich.,https://id.biodiversity.org.au/node/apni/2913845,https://id.biodiversity.org.au/node/apni/2907879,https://id.biodiversity.org.au/name/apni/113875,Australina pusilla,https://id.biodiversity.org.au/name/apni/113875,accepted,https://id.biodiversity.org.au/node/apni/2913845,https://id.biodiversity.org.au/taxon/apni/51662052,NA,Australina pusilla,native +Brombya platynema,Brombya platynema,Brombya platynema,NA,Brombya,Rutaceae,species,APC,accepted,Magnoliidae,Qld,Brombya platynema F.Muell.,https://id.biodiversity.org.au/node/apni/2890280,https://id.biodiversity.org.au/node/apni/7937668,https://id.biodiversity.org.au/name/apni/67607,Brombya platynema,https://id.biodiversity.org.au/name/apni/67607,accepted,https://id.biodiversity.org.au/node/apni/2890280,https://id.biodiversity.org.au/taxon/apni/51461748,NA,Brombya platynema,native +Burmannia disticha,Burmannia disticha,Burmannia disticha,NA,Burmannia,Burmanniaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Burmannia disticha L.,https://id.biodiversity.org.au/node/apni/2900088,https://id.biodiversity.org.au/node/apni/2915743,https://id.biodiversity.org.au/name/apni/70173,Burmannia disticha,https://id.biodiversity.org.au/name/apni/70173,accepted,https://id.biodiversity.org.au/node/apni/2900088,https://id.biodiversity.org.au/node/apni/2887196,NA,Burmannia disticha,native +Bursaria spinosa subsp. spinosa,Bursaria spinosa subsp. spinosa,Bursaria spinosa subsp. spinosa,NA,Bursaria,Pittosporaceae,subspecies,APC,accepted,Magnoliidae,"SA, Qld, NSW, Vic, Tas",Bursaria spinosa Cav. subsp. spinosa,https://id.biodiversity.org.au/taxon/apni/51442337,https://id.biodiversity.org.au/taxon/apni/51442339,https://id.biodiversity.org.au/name/apni/142036,Bursaria spinosa subsp. spinosa,https://id.biodiversity.org.au/name/apni/142036,accepted,https://id.biodiversity.org.au/taxon/apni/51442337,https://id.biodiversity.org.au/taxon/apni/51442315,Bursaria spinosa subsp. spinosa,Bursaria spinosa,native +Calendula arvensis,Calendula arvensis,Calendula arvensis,NA,Calendula,Asteraceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (naturalised), Tas (naturalised)",Calendula arvensis L.,https://id.biodiversity.org.au/node/apni/2891878,https://id.biodiversity.org.au/node/apni/2893748,https://id.biodiversity.org.au/name/apni/95042,Calendula arvensis,https://id.biodiversity.org.au/name/apni/95042,accepted,https://id.biodiversity.org.au/node/apni/2891878,https://id.biodiversity.org.au/taxon/apni/51695393,NA,Calendula arvensis,naturalised +Callistemon purpurascens,Callistemon purpurascens,Callistemon purpurascens,NA,Callistemon,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Callistemon purpurascens S.M.Douglas & S.David,https://id.biodiversity.org.au/taxon/apni/51288952,https://id.biodiversity.org.au/taxon/apni/51439657,https://id.biodiversity.org.au/name/apni/4630985,Callistemon purpurascens,https://id.biodiversity.org.au/name/apni/4630985,accepted,https://id.biodiversity.org.au/taxon/apni/51288952,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Callistemon purpurascens,native +Apophyllum anomalum,Apophyllum anomalum,Capparis anomala,NA,Capparis,Capparaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Capparis anomala (F.Muell.) Byng & Christenh.,https://id.biodiversity.org.au/taxon/apni/51432888,https://id.biodiversity.org.au/taxon/apni/51432886,https://id.biodiversity.org.au/name/apni/50561973,Capparis anomala,https://id.biodiversity.org.au/name/apni/97697,basionym,https://id.biodiversity.org.au/instance/apni/50562214,https://id.biodiversity.org.au/taxon/apni/51433682,NA,Capparis anomala,native +Cardwellia sublimis,Cardwellia sublimis,Cardwellia sublimis,NA,Cardwellia,Proteaceae,species,APC,accepted,Magnoliidae,Qld,Cardwellia sublimis F.Muell.,https://id.biodiversity.org.au/node/apni/2899253,https://id.biodiversity.org.au/node/apni/2908094,https://id.biodiversity.org.au/name/apni/109268,Cardwellia sublimis,https://id.biodiversity.org.au/name/apni/109268,accepted,https://id.biodiversity.org.au/node/apni/2899253,https://id.biodiversity.org.au/taxon/apni/51614274,NA,Cardwellia sublimis,native +Carex leporina,Carex leporina,Carex leporina,NA,Carex,Cyperaceae,species,APC,accepted,Magnoliidae,"NSW (naturalised), NI (naturalised), Vic (naturalised), Tas (naturalised)",Carex leporina L.,https://id.biodiversity.org.au/node/apni/2902492,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/135236,Carex leporina,https://id.biodiversity.org.au/name/apni/135236,accepted,https://id.biodiversity.org.au/node/apni/2902492,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Carex leporina,naturalised +Carex cephalotes,Carex cephalotes,Carex pyrenaica var. cephalotes,NA,Carex,Cyperaceae,variety,APC,accepted,Magnoliidae,"NSW, Vic, Tas",Carex pyrenaica var. cephalotes (F.Muell.) Kük.,https://id.biodiversity.org.au/node/apni/2892693,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/111655,Carex pyrenaica var. cephalotes,https://id.biodiversity.org.au/name/apni/110600,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/946222,https://id.biodiversity.org.au/taxon/apni/51460154,Carex pyrenaica var. cephalotes,Carex pyrenaica,native +Carex raleighii,Carex raleighii,Carex raleighii,NA,Carex,Cyperaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic, Tas",Carex raleighii Nelmes,https://id.biodiversity.org.au/node/apni/2910405,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/111690,Carex raleighii,https://id.biodiversity.org.au/name/apni/111690,accepted,https://id.biodiversity.org.au/node/apni/2910405,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Carex raleighii,native +Carmichaelia exsul,Carmichaelia exsul,Carmichaelia exsul,NA,Carmichaelia,Fabaceae,species,APC,accepted,Magnoliidae,LHI,Carmichaelia exsul F.Muell.,https://id.biodiversity.org.au/node/apni/2915240,https://id.biodiversity.org.au/node/apni/8138105,https://id.biodiversity.org.au/name/apni/112335,Carmichaelia exsul,https://id.biodiversity.org.au/name/apni/112335,accepted,https://id.biodiversity.org.au/node/apni/2915240,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Carmichaelia exsul,native +Cassinia compacta,Cassinia compacta,Cassinia compacta , Cassinia accipitrum (pro parte misapplied) | Cassinia straminea (pro parte misapplied) | Cassinia telfordii (pro parte misapplied) | Cassinia accipitrum (misapplied),Cassinia,Asteraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Cassinia compacta F.Muell.,https://id.biodiversity.org.au/node/apni/2909860,https://id.biodiversity.org.au/taxon/apni/51431788,https://id.biodiversity.org.au/name/apni/54723,Cassinia compacta [alternative possible names: Cassinia accipitrum (pro parte misapplied) | Cassinia straminea (pro parte misapplied) | Cassinia telfordii (pro parte misapplied) | Cassinia accipitrum (misapplied)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51695393,NA,Cassinia compacta,native +Castanospermum australe,Castanospermum australe,Castanospermum australe,NA,Castanospermum,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, NI (doubtfully naturalised)",Castanospermum australe A.Cunn. ex Mudie,https://id.biodiversity.org.au/node/apni/2894943,https://id.biodiversity.org.au/node/apni/7226268,https://id.biodiversity.org.au/name/apni/196675,Castanospermum australe,https://id.biodiversity.org.au/name/apni/196675,accepted,https://id.biodiversity.org.au/node/apni/2894943,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Castanospermum australe,native and naturalised +Centaurium tenuiflorum,Centaurium tenuiflorum,Centaurium tenuiflorum,NA,Centaurium,Gentianaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Centaurium tenuiflorum (Hoffmanns. & Link) Fritsch,https://id.biodiversity.org.au/node/apni/7385749,https://id.biodiversity.org.au/node/apni/7385753,https://id.biodiversity.org.au/name/apni/58491,Centaurium tenuiflorum,https://id.biodiversity.org.au/name/apni/58491,accepted,https://id.biodiversity.org.au/node/apni/7385749,https://id.biodiversity.org.au/taxon/apni/51436871,NA,Centaurium tenuiflorum,naturalised +Cestrum nocturnum,Cestrum nocturnum,Cestrum nocturnum,NA,Cestrum,Solanaceae,species,APC,accepted,Magnoliidae,"Qld (doubtfully naturalised), NSW (naturalised), NI (naturalised)",Cestrum nocturnum L.,https://id.biodiversity.org.au/node/apni/2911237,https://id.biodiversity.org.au/node/apni/2889884,https://id.biodiversity.org.au/name/apni/60565,Cestrum nocturnum,https://id.biodiversity.org.au/name/apni/60565,accepted,https://id.biodiversity.org.au/node/apni/2911237,https://id.biodiversity.org.au/taxon/apni/51447684,NA,Cestrum nocturnum,naturalised +Chthonocephalus pseudevax,Chthonocephalus pseudevax,Chthonocephalus pseudevax,NA,Chthonocephalus,Asteraceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Chthonocephalus pseudevax Steetz,https://id.biodiversity.org.au/node/apni/2917443,https://id.biodiversity.org.au/node/apni/2892496,https://id.biodiversity.org.au/name/apni/68863,Chthonocephalus pseudevax,https://id.biodiversity.org.au/name/apni/68863,accepted,https://id.biodiversity.org.au/node/apni/2917443,https://id.biodiversity.org.au/taxon/apni/51695393,NA,Chthonocephalus pseudevax,native +Claoxylon australe,Claoxylon australe,Claoxylon australe,NA,Claoxylon,Euphorbiaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Claoxylon australe Baill.,https://id.biodiversity.org.au/node/apni/2887203,https://id.biodiversity.org.au/node/apni/2920593,https://id.biodiversity.org.au/name/apni/70907,Claoxylon australe,https://id.biodiversity.org.au/name/apni/70907,accepted,https://id.biodiversity.org.au/node/apni/2887203,https://id.biodiversity.org.au/taxon/apni/51442249,NA,Claoxylon australe,native +Cleistanthus myrianthus,Cleistanthus myrianthus,Cleistanthus myrianthus,NA,Cleistanthus,Phyllanthaceae,species,APC,accepted,Magnoliidae,Qld,Cleistanthus myrianthus (Hassk.) Kurz,https://id.biodiversity.org.au/node/apni/2897700,https://id.biodiversity.org.au/node/apni/2914326,https://id.biodiversity.org.au/name/apni/71354,Cleistanthus myrianthus,https://id.biodiversity.org.au/name/apni/71354,accepted,https://id.biodiversity.org.au/node/apni/2897700,https://id.biodiversity.org.au/taxon/apni/51442162,NA,Cleistanthus myrianthus,native +Commersonia amystia,Commersonia amystia,Commersonia amystia,NA,Commersonia,Malvaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Commersonia amystia C.F.Wilkins & L.M.Copel.,https://id.biodiversity.org.au/node/apni/2904387,https://id.biodiversity.org.au/taxon/apni/51438976,https://id.biodiversity.org.au/name/apni/214136,Commersonia amystia,https://id.biodiversity.org.au/name/apni/214136,accepted,https://id.biodiversity.org.au/node/apni/2904387,https://id.biodiversity.org.au/taxon/apni/51439248,NA,Commersonia amystia,native +Commersonia salviifolia,Commersonia salviifolia,Commersonia salviifolia,NA,Commersonia,Malvaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Commersonia salviifolia (Hook. ex Steetz) F.Muell.,https://id.biodiversity.org.au/node/apni/2901795,https://id.biodiversity.org.au/taxon/apni/51438976,https://id.biodiversity.org.au/name/apni/75211,Commersonia salviifolia,https://id.biodiversity.org.au/name/apni/75211,accepted,https://id.biodiversity.org.au/node/apni/2901795,https://id.biodiversity.org.au/taxon/apni/51439248,NA,Commersonia salviifolia,native +Convolvulus farinosus,Convolvulus farinosus,Convolvulus farinosus,NA,Convolvulus,Convolvulaceae,species,APC,accepted,Magnoliidae,NSW (naturalised),Convolvulus farinosus L.,https://id.biodiversity.org.au/node/apni/2895672,https://id.biodiversity.org.au/taxon/apni/51298269,https://id.biodiversity.org.au/name/apni/206071,Convolvulus farinosus,https://id.biodiversity.org.au/name/apni/206071,accepted,https://id.biodiversity.org.au/node/apni/2895672,https://id.biodiversity.org.au/taxon/apni/51695210,NA,Convolvulus farinosus,naturalised +Coprosma niphophila,Coprosma niphophila,Coprosma niphophila,NA,Coprosma,Rubiaceae,species,APC,accepted,Magnoliidae,NSW,Coprosma niphophila Orchard,https://id.biodiversity.org.au/node/apni/2910618,https://id.biodiversity.org.au/node/apni/8135850,https://id.biodiversity.org.au/name/apni/78856,Coprosma niphophila,https://id.biodiversity.org.au/name/apni/78856,accepted,https://id.biodiversity.org.au/node/apni/2910618,https://id.biodiversity.org.au/taxon/apni/51446612,NA,Coprosma niphophila,native +Coprosma nivalis,Coprosma nivalis,Coprosma nivalis,NA,Coprosma,Rubiaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Coprosma nivalis W.R.B.Oliv.,https://id.biodiversity.org.au/node/apni/2915002,https://id.biodiversity.org.au/node/apni/8135850,https://id.biodiversity.org.au/name/apni/78866,Coprosma nivalis,https://id.biodiversity.org.au/name/apni/78866,accepted,https://id.biodiversity.org.au/node/apni/2915002,https://id.biodiversity.org.au/taxon/apni/51446612,NA,Coprosma nivalis,native +Correa alba,Correa alba,Correa alba,NA,Correa,Rutaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Correa alba Andrews,https://id.biodiversity.org.au/node/apni/2906721,https://id.biodiversity.org.au/taxon/apni/51447015,https://id.biodiversity.org.au/name/apni/80283,Correa alba,https://id.biodiversity.org.au/name/apni/80283,accepted,https://id.biodiversity.org.au/node/apni/2906721,https://id.biodiversity.org.au/taxon/apni/51461748,NA,Correa alba,native +Corymbia citriodora,Corymbia citriodora,Corymbia citriodora,NA,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (doubtfully naturalised), Qld, NSW (native and naturalised), Vic (naturalised)",Corymbia citriodora (Hook.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2912509,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119387,Corymbia citriodora,https://id.biodiversity.org.au/name/apni/119387,accepted,https://id.biodiversity.org.au/node/apni/2912509,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Corymbia citriodora,native and naturalised +Corymbia eximia,Corymbia eximia,Corymbia eximia,NA,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Corymbia eximia (Schauer) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2909833,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119402,Corymbia eximia,https://id.biodiversity.org.au/name/apni/119402,accepted,https://id.biodiversity.org.au/node/apni/2909833,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Corymbia eximia,native +Crassula decumbens,Crassula decumbens,Crassula decumbens,NA,Crassula,Crassulaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, ACT, Vic, Tas",Crassula decumbens Thunb.,https://id.biodiversity.org.au/node/apni/2889646,https://id.biodiversity.org.au/node/apni/2903354,https://id.biodiversity.org.au/name/apni/83855,Crassula decumbens,https://id.biodiversity.org.au/name/apni/83855,accepted,https://id.biodiversity.org.au/node/apni/2889646,https://id.biodiversity.org.au/taxon/apni/51270792,NA,Crassula decumbens,native +Crassula peduncularis,Crassula peduncularis,Crassula peduncularis,NA,Crassula,Crassulaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, ACT, Vic, Tas",Crassula peduncularis (Sm.) F.Meigen,https://id.biodiversity.org.au/node/apni/2895654,https://id.biodiversity.org.au/node/apni/2903354,https://id.biodiversity.org.au/name/apni/84005,Crassula peduncularis,https://id.biodiversity.org.au/name/apni/84005,accepted,https://id.biodiversity.org.au/node/apni/2895654,https://id.biodiversity.org.au/taxon/apni/51270792,NA,Crassula peduncularis,native +Crotalaria brevis,Crotalaria brevis,Crotalaria brevis,NA,Crotalaria,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Crotalaria brevis Domin,https://id.biodiversity.org.au/node/apni/2906180,https://id.biodiversity.org.au/taxon/apni/51300011,https://id.biodiversity.org.au/name/apni/85578,Crotalaria brevis,https://id.biodiversity.org.au/name/apni/85578,accepted,https://id.biodiversity.org.au/node/apni/2906180,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Crotalaria brevis,native +Crotalaria grahamiana,Crotalaria grahamiana,Crotalaria grahamiana,NA,Crotalaria,Fabaceae,species,APC,accepted,Magnoliidae,"Qld (naturalised), NSW (naturalised)",Crotalaria grahamiana Wight & Arn.,https://id.biodiversity.org.au/node/apni/2917131,https://id.biodiversity.org.au/taxon/apni/51300011,https://id.biodiversity.org.au/name/apni/85770,Crotalaria grahamiana,https://id.biodiversity.org.au/name/apni/85770,accepted,https://id.biodiversity.org.au/node/apni/2917131,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Crotalaria grahamiana,naturalised +Crotalaria lanceolata,Crotalaria lanceolata,Crotalaria lanceolata,NA,Crotalaria,Fabaceae,species,APC,accepted,Magnoliidae,"NT (naturalised), Qld (naturalised), NSW (naturalised), NI (naturalised)",Crotalaria lanceolata E.Mey.,https://id.biodiversity.org.au/node/apni/2887683,https://id.biodiversity.org.au/taxon/apni/51300011,https://id.biodiversity.org.au/name/apni/85830,Crotalaria lanceolata,https://id.biodiversity.org.au/name/apni/85830,accepted,https://id.biodiversity.org.au/node/apni/2887683,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Crotalaria lanceolata,naturalised +Cryptocarya laevigata,Cryptocarya laevigata,Cryptocarya laevigata,NA,Cryptocarya,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Cryptocarya laevigata Blume,https://id.biodiversity.org.au/node/apni/2903400,https://id.biodiversity.org.au/taxon/apni/51438401,https://id.biodiversity.org.au/name/apni/88410,Cryptocarya laevigata,https://id.biodiversity.org.au/name/apni/88410,accepted,https://id.biodiversity.org.au/node/apni/2903400,https://id.biodiversity.org.au/taxon/apni/51438397,NA,Cryptocarya laevigata,native +Cryptocarya mackinnoniana,Cryptocarya mackinnoniana,Cryptocarya mackinnoniana,NA,Cryptocarya,Lauraceae,species,APC,accepted,Magnoliidae,Qld,Cryptocarya mackinnoniana F.Muell.,https://id.biodiversity.org.au/node/apni/2914946,https://id.biodiversity.org.au/taxon/apni/51438401,https://id.biodiversity.org.au/name/apni/88421,Cryptocarya mackinnoniana,https://id.biodiversity.org.au/name/apni/88421,accepted,https://id.biodiversity.org.au/node/apni/2914946,https://id.biodiversity.org.au/taxon/apni/51438397,NA,Cryptocarya mackinnoniana,native +Cryptocarya murrayi,Cryptocarya murrayi,Cryptocarya murrayi,NA,Cryptocarya,Lauraceae,species,APC,accepted,Magnoliidae,Qld,Cryptocarya murrayi F.Muell.,https://id.biodiversity.org.au/node/apni/2910393,https://id.biodiversity.org.au/taxon/apni/51438401,https://id.biodiversity.org.au/name/apni/88472,Cryptocarya murrayi,https://id.biodiversity.org.au/name/apni/88472,accepted,https://id.biodiversity.org.au/node/apni/2910393,https://id.biodiversity.org.au/taxon/apni/51438397,NA,Cryptocarya murrayi,native +Cylindropuntia kleiniae,Cylindropuntia kleiniae,Cylindropuntia kleiniae,NA,Cylindropuntia,Cactaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised)",Cylindropuntia kleiniae (DC.) F.M.Knuth,https://id.biodiversity.org.au/taxon/apni/51432847,https://id.biodiversity.org.au/taxon/apni/51432841,https://id.biodiversity.org.au/name/apni/191050,Cylindropuntia kleiniae,https://id.biodiversity.org.au/name/apni/191050,accepted,https://id.biodiversity.org.au/taxon/apni/51432847,https://id.biodiversity.org.au/taxon/apni/51432828,NA,Cylindropuntia kleiniae,naturalised +Cyperus albostriatus,Cyperus albostriatus,Cyperus albostriatus,NA,Cyperus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised), NI (naturalised)",Cyperus albostriatus Schrad.,https://id.biodiversity.org.au/node/apni/2893623,https://id.biodiversity.org.au/taxon/apni/51434383,https://id.biodiversity.org.au/name/apni/96258,Cyperus albostriatus,https://id.biodiversity.org.au/name/apni/96258,accepted,https://id.biodiversity.org.au/node/apni/2893623,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Cyperus albostriatus,naturalised +Cyperus betchei,Cyperus betchei,Cyperus betchei,NA,Cyperus,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Cyperus betchei (Kük.) S.T.Blake,https://id.biodiversity.org.au/node/apni/2888104,https://id.biodiversity.org.au/taxon/apni/51434383,https://id.biodiversity.org.au/name/apni/96480,Cyperus betchei,https://id.biodiversity.org.au/name/apni/96480,accepted,https://id.biodiversity.org.au/node/apni/2888104,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Cyperus betchei,native +Cyperus bulbosus,Cyperus bulbosus,Cyperus bulbosus,NA,Cyperus,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Cyperus bulbosus Vahl,https://id.biodiversity.org.au/node/apni/2902422,https://id.biodiversity.org.au/taxon/apni/51434383,https://id.biodiversity.org.au/name/apni/96591,Cyperus bulbosus,https://id.biodiversity.org.au/name/apni/96591,accepted,https://id.biodiversity.org.au/node/apni/2902422,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Cyperus bulbosus,native +Cyperus laevigatus,Cyperus laevigatus,Cyperus laevigatus,NA,Cyperus,Cyperaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT, SA, Qld, NSW",Cyperus laevigatus L.,https://id.biodiversity.org.au/node/apni/2916573,https://id.biodiversity.org.au/taxon/apni/51434383,https://id.biodiversity.org.au/name/apni/97862,Cyperus laevigatus,https://id.biodiversity.org.au/name/apni/97862,accepted,https://id.biodiversity.org.au/node/apni/2916573,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Cyperus laevigatus,native and naturalised +Cyperus sculptus,Cyperus sculptus,Cyperus sculptus,NA,Cyperus,Cyperaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Cyperus sculptus S.T.Blake,https://id.biodiversity.org.au/node/apni/2902340,https://id.biodiversity.org.au/taxon/apni/51434383,https://id.biodiversity.org.au/name/apni/98972,Cyperus sculptus,https://id.biodiversity.org.au/name/apni/98972,accepted,https://id.biodiversity.org.au/node/apni/2902340,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Cyperus sculptus,native +Dampiera fusca,Dampiera fusca,Dampiera fusca,NA,Dampiera,Goodeniaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Dampiera fusca Rajput & Carolin,https://id.biodiversity.org.au/node/apni/2908327,https://id.biodiversity.org.au/taxon/apni/51437007,https://id.biodiversity.org.au/name/apni/78388,Dampiera fusca,https://id.biodiversity.org.au/name/apni/78388,accepted,https://id.biodiversity.org.au/node/apni/2908327,https://id.biodiversity.org.au/taxon/apni/51462931,NA,Dampiera fusca,native +Davidsonia johnsonii,Davidsonia johnsonii,Davidsonia johnsonii,NA,Davidsonia,Cunoniaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Davidsonia johnsonii J.B.Williams & G.Harden,https://id.biodiversity.org.au/taxon/apni/51434155,https://id.biodiversity.org.au/taxon/apni/51434156,https://id.biodiversity.org.au/name/apni/166907,Davidsonia johnsonii,https://id.biodiversity.org.au/name/apni/166907,accepted,https://id.biodiversity.org.au/taxon/apni/51434155,https://id.biodiversity.org.au/taxon/apni/51434138,NA,Davidsonia johnsonii,native +Daviesia arenaria,Daviesia arenaria,Daviesia arenaria,NA,Daviesia,Fabaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic",Daviesia arenaria Crisp,https://id.biodiversity.org.au/taxon/apni/51435880,https://id.biodiversity.org.au/taxon/apni/51461520,https://id.biodiversity.org.au/name/apni/82236,Daviesia arenaria,https://id.biodiversity.org.au/name/apni/82236,accepted,https://id.biodiversity.org.au/taxon/apni/51435880,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Daviesia arenaria,native +Dendrocnide moroides,Dendrocnide moroides,Dendrocnide moroides,NA,Dendrocnide,Urticaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Dendrocnide moroides (Wedd.) Chew,https://id.biodiversity.org.au/node/apni/2904177,https://id.biodiversity.org.au/taxon/apni/51448284,https://id.biodiversity.org.au/name/apni/86919,Dendrocnide moroides,https://id.biodiversity.org.au/name/apni/86919,accepted,https://id.biodiversity.org.au/node/apni/2904177,https://id.biodiversity.org.au/taxon/apni/51662052,NA,Dendrocnide moroides,native +Dichromochlamys dentatifolia,Dichromochlamys dentatifolia,Dichromochlamys dentatifolia,NA,Dichromochlamys,Asteraceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Dichromochlamys dentatifolia (F.Muell.) Dunlop,https://id.biodiversity.org.au/node/apni/2888915,https://id.biodiversity.org.au/node/apni/2894601,https://id.biodiversity.org.au/name/apni/102074,Dichromochlamys dentatifolia,https://id.biodiversity.org.au/name/apni/102074,accepted,https://id.biodiversity.org.au/node/apni/2888915,https://id.biodiversity.org.au/taxon/apni/51695393,NA,Dichromochlamys dentatifolia,native +Dillwynia cinerascens,Dillwynia cinerascens,Dillwynia cinerascens,NA,Dillwynia,Fabaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Dillwynia cinerascens R.Br.,https://id.biodiversity.org.au/node/apni/2920072,https://id.biodiversity.org.au/taxon/apni/51285570,https://id.biodiversity.org.au/name/apni/105476,Dillwynia cinerascens,https://id.biodiversity.org.au/name/apni/105476,accepted,https://id.biodiversity.org.au/node/apni/2920072,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Dillwynia cinerascens,native +Dillwynia floribunda,Dillwynia floribunda,Dillwynia floribunda,NA,Dillwynia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Dillwynia floribunda Sm.,https://id.biodiversity.org.au/node/apni/2892820,https://id.biodiversity.org.au/taxon/apni/51285570,https://id.biodiversity.org.au/name/apni/105728,Dillwynia floribunda,https://id.biodiversity.org.au/name/apni/105728,accepted,https://id.biodiversity.org.au/node/apni/2892820,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Dillwynia floribunda,native +Dinosperma erythrococcum,Dinosperma erythrococcum,Dinosperma erythrococcum,NA,Dinosperma,Rutaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Dinosperma erythrococcum (F.Muell.) T.G.Hartley,https://id.biodiversity.org.au/node/apni/2897246,https://id.biodiversity.org.au/node/apni/2900591,https://id.biodiversity.org.au/name/apni/157718,Dinosperma erythrococcum,https://id.biodiversity.org.au/name/apni/157718,accepted,https://id.biodiversity.org.au/node/apni/2897246,https://id.biodiversity.org.au/taxon/apni/51461748,NA,Dinosperma erythrococcum,native +Dodonaea petiolaris,Dodonaea petiolaris,Dodonaea petiolaris , Dodonaea viscosa subsp. mucronata (pro parte misapplied),Dodonaea,Sapindaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Dodonaea petiolaris F.Muell.,https://id.biodiversity.org.au/node/apni/2921131,https://id.biodiversity.org.au/taxon/apni/51447268,https://id.biodiversity.org.au/name/apni/72184,Dodonaea petiolaris [alternative possible names: Dodonaea viscosa subsp. mucronata (pro parte misapplied)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51447212,NA,Dodonaea petiolaris,native +Dodonaea truncatiales,Dodonaea truncatiales,Dodonaea truncatiales , Dodonaea heteromorpha (pro parte misapplied) | Dodonaea heteromorpha (misapplied),Dodonaea,Sapindaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Dodonaea truncatiales F.Muell.,https://id.biodiversity.org.au/node/apni/7870563,https://id.biodiversity.org.au/taxon/apni/51447268,https://id.biodiversity.org.au/name/apni/72648,Dodonaea truncatiales [alternative possible names: Dodonaea heteromorpha (pro parte misapplied) | Dodonaea heteromorpha (misapplied)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51447212,NA,Dodonaea truncatiales,native +Dovyalis caffra,Dovyalis caffra,Dovyalis caffra,NA,Dovyalis,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised)",Dovyalis caffra (Hook.f. & Harv.) Hook.f.,https://id.biodiversity.org.au/node/apni/2888866,https://id.biodiversity.org.au/node/apni/2897632,https://id.biodiversity.org.au/name/apni/199157,Dovyalis caffra,https://id.biodiversity.org.au/name/apni/86110,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/841664,https://id.biodiversity.org.au/taxon/apni/51436847,NA,Dovyalis caffra,naturalised +Elaeocarpus grandis,Elaeocarpus grandis,Elaeocarpus grandis,NA,Elaeocarpus,Elaeocarpaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Elaeocarpus grandis F.Muell.,https://id.biodiversity.org.au/node/apni/2895259,https://id.biodiversity.org.au/taxon/apni/51435153,https://id.biodiversity.org.au/name/apni/115772,Elaeocarpus grandis,https://id.biodiversity.org.au/name/apni/115772,accepted,https://id.biodiversity.org.au/node/apni/2895259,https://id.biodiversity.org.au/taxon/apni/51632282,NA,Elaeocarpus grandis,native +Eleocharis pallens,Eleocharis pallens,Eleocharis pallens,NA,Eleocharis,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Eleocharis pallens S.T.Blake,https://id.biodiversity.org.au/node/apni/2899827,https://id.biodiversity.org.au/taxon/apni/51434435,https://id.biodiversity.org.au/name/apni/67140,Eleocharis pallens,https://id.biodiversity.org.au/name/apni/67140,accepted,https://id.biodiversity.org.au/node/apni/2899827,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Eleocharis pallens,native +Endiandra globosa,Endiandra globosa,Endiandra globosa,NA,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Endiandra globosa Maiden & Betche,https://id.biodiversity.org.au/node/apni/2901094,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111780,Endiandra globosa,https://id.biodiversity.org.au/name/apni/111780,accepted,https://id.biodiversity.org.au/node/apni/2901094,https://id.biodiversity.org.au/taxon/apni/51438397,NA,Endiandra globosa,native +Endiandra leptodendron,Endiandra leptodendron,Endiandra leptodendron,NA,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,Qld,Endiandra leptodendron B.Hyland,https://id.biodiversity.org.au/node/apni/2910725,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111888,Endiandra leptodendron,https://id.biodiversity.org.au/name/apni/111888,accepted,https://id.biodiversity.org.au/node/apni/2910725,https://id.biodiversity.org.au/taxon/apni/51438397,NA,Endiandra leptodendron,native +Endiandra microneura,Endiandra microneura,Endiandra microneura,NA,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,Qld,Endiandra microneura C.T.White,https://id.biodiversity.org.au/node/apni/2899314,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111949,Endiandra microneura,https://id.biodiversity.org.au/name/apni/111949,accepted,https://id.biodiversity.org.au/node/apni/2899314,https://id.biodiversity.org.au/taxon/apni/51438397,NA,Endiandra microneura,native +Endiandra muelleri,Endiandra muelleri,Endiandra muelleri,NA,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Endiandra muelleri Meisn.,https://id.biodiversity.org.au/node/apni/2903619,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111996,Endiandra muelleri,https://id.biodiversity.org.au/name/apni/111996,accepted,https://id.biodiversity.org.au/node/apni/2903619,https://id.biodiversity.org.au/taxon/apni/51438397,NA,Endiandra muelleri,native +Epilobium gunnianum,Epilobium gunnianum,Epilobium gunnianum,NA,Epilobium,Onagraceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic, Tas",Epilobium gunnianum Hausskn.,https://id.biodiversity.org.au/node/apni/2903068,https://id.biodiversity.org.au/taxon/apni/51440863,https://id.biodiversity.org.au/name/apni/105579,Epilobium gunnianum,https://id.biodiversity.org.au/name/apni/105579,accepted,https://id.biodiversity.org.au/node/apni/2903068,https://id.biodiversity.org.au/taxon/apni/51440864,NA,Epilobium gunnianum,native +Eremophila deserti,Eremophila deserti,Eremophila deserti,NA,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila deserti (A.Cunn. ex Benth.) Chinnock,https://id.biodiversity.org.au/node/apni/2897363,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/123426,Eremophila deserti,https://id.biodiversity.org.au/name/apni/123426,accepted,https://id.biodiversity.org.au/node/apni/2897363,https://id.biodiversity.org.au/taxon/apni/51461527,NA,Eremophila deserti,native +Eremophila oppositifolia,Eremophila oppositifolia,Eremophila oppositifolia,NA,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila oppositifolia R.Br.,https://id.biodiversity.org.au/node/apni/7951462,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/114575,Eremophila oppositifolia,https://id.biodiversity.org.au/name/apni/114575,accepted,https://id.biodiversity.org.au/node/apni/7951462,https://id.biodiversity.org.au/taxon/apni/51461527,NA,Eremophila oppositifolia,native +Erigeron conyzoides,Erigeron conyzoides,Erigeron conyzoides,NA,Erigeron,Asteraceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Erigeron conyzoides F.Muell.,https://id.biodiversity.org.au/node/apni/2913579,https://id.biodiversity.org.au/taxon/apni/51432118,https://id.biodiversity.org.au/name/apni/73195,Erigeron conyzoides,https://id.biodiversity.org.au/name/apni/239637,taxonomic synonym,https://id.biodiversity.org.au/instance/apni/6407754,https://id.biodiversity.org.au/taxon/apni/51695393,NA,Erigeron conyzoides,native +Erythroxylum australe,Erythroxylum australe,Erythroxylum australe , Erythroxylum sp. Splityard Creek (L.Pedley 5360) (pro parte misapplied),Erythroxylum,Erythroxylaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Erythroxylum australe F.Muell.,https://id.biodiversity.org.au/node/apni/2912212,https://id.biodiversity.org.au/node/apni/2919669,https://id.biodiversity.org.au/name/apni/75959,Erythroxylum australe [alternative possible names: Erythroxylum sp. Splityard Creek (L.Pedley 5360) (pro parte misapplied)],NA,NA,NA,https://id.biodiversity.org.au/node/apni/2893375,NA,Erythroxylum australe,native +Escallonia bifida,Escallonia bifida,Escallonia bifida,NA,Escallonia,Escalloniaceae,species,APC,accepted,Magnoliidae,NSW (naturalised),Escallonia bifida Link & Otto,https://id.biodiversity.org.au/taxon/apni/51435441,https://id.biodiversity.org.au/taxon/apni/51435442,https://id.biodiversity.org.au/name/apni/116602,Escallonia bifida,https://id.biodiversity.org.au/name/apni/116602,accepted,https://id.biodiversity.org.au/taxon/apni/51435441,https://id.biodiversity.org.au/taxon/apni/51435443,NA,Escallonia bifida,naturalised +Eucalyptus badjensis,Eucalyptus badjensis,Eucalyptus badjensis,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus badjensis Beuzev. & M.B.Welch,https://id.biodiversity.org.au/node/apni/2912724,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/57323,Eucalyptus badjensis,https://id.biodiversity.org.au/name/apni/57323,accepted,https://id.biodiversity.org.au/node/apni/2912724,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus badjensis,native +Eucalyptus camphora,Eucalyptus camphora,Eucalyptus camphora,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic",Eucalyptus camphora R.T.Baker,https://id.biodiversity.org.au/node/apni/2891665,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/94439,Eucalyptus camphora,https://id.biodiversity.org.au/name/apni/94439,accepted,https://id.biodiversity.org.au/node/apni/2891665,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus camphora,native +Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus dorrigoensis (Blakely) L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2903351,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118668,Eucalyptus dorrigoensis,https://id.biodiversity.org.au/name/apni/118668,accepted,https://id.biodiversity.org.au/node/apni/2903351,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus dorrigoensis,native +Eucalyptus yangoura,Eucalyptus yangoura,Eucalyptus globoidea,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus globoidea Blakely,https://id.biodiversity.org.au/node/apni/5270850,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/61141,Eucalyptus globoidea,https://id.biodiversity.org.au/name/apni/92470,taxonomic synonym,https://id.biodiversity.org.au/instance/apni/853397,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus globoidea,native +Eucalyptus oblonga,Eucalyptus oblonga,Eucalyptus globoidea , Eucalyptus sparsifolia (pro parte taxonomic synonym),Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus globoidea Blakely,https://id.biodiversity.org.au/node/apni/5270850,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/61141,Eucalyptus globoidea [alternative possible names: Eucalyptus sparsifolia (pro parte taxonomic synonym)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus globoidea,native +Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,NA,Eucalyptus,Myrtaceae,subspecies,APC,accepted,Magnoliidae,"SA, NSW, Vic",Eucalyptus leucoxylon subsp. pruinosa (F.Muell. ex Miq.) Boland,https://id.biodiversity.org.au/node/apni/2908258,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/77407,Eucalyptus leucoxylon subsp. pruinosa,https://id.biodiversity.org.au/name/apni/77407,accepted,https://id.biodiversity.org.au/node/apni/2908258,https://id.biodiversity.org.au/taxon/apni/51702983,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon,native +Eucalyptus miniata,Eucalyptus miniata,Eucalyptus miniata,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus miniata A.Cunn. ex Schauer,https://id.biodiversity.org.au/node/apni/2889426,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/56460,Eucalyptus miniata,https://id.biodiversity.org.au/name/apni/56460,accepted,https://id.biodiversity.org.au/node/apni/2889426,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus miniata,native +Eucalyptus muelleriana,Eucalyptus muelleriana,Eucalyptus muelleriana,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus muelleriana A.W.Howitt,https://id.biodiversity.org.au/node/apni/2888508,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/56840,Eucalyptus muelleriana,https://id.biodiversity.org.au/name/apni/56840,accepted,https://id.biodiversity.org.au/node/apni/2888508,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus muelleriana,native +Eucalyptus nandewarica,Eucalyptus nandewarica,Eucalyptus nandewarica,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus nandewarica L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2897688,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118852,Eucalyptus nandewarica,https://id.biodiversity.org.au/name/apni/118852,accepted,https://id.biodiversity.org.au/node/apni/2897688,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus nandewarica,native +Eucalyptus olida,Eucalyptus olida,Eucalyptus olida,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus olida L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2914019,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118797,Eucalyptus olida,https://id.biodiversity.org.au/name/apni/118797,accepted,https://id.biodiversity.org.au/node/apni/2914019,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus olida,native +Eucalyptus pulverulenta,Eucalyptus pulverulenta,Eucalyptus pulverulenta,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus pulverulenta Sims,https://id.biodiversity.org.au/taxon/apni/51440675,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/106609,Eucalyptus pulverulenta,https://id.biodiversity.org.au/name/apni/106609,accepted,https://id.biodiversity.org.au/taxon/apni/51440675,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus pulverulenta,native +Eucalyptus recurva,Eucalyptus recurva,Eucalyptus recurva,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus recurva Crisp,https://id.biodiversity.org.au/node/apni/2892273,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/101532,Eucalyptus recurva,https://id.biodiversity.org.au/name/apni/101532,accepted,https://id.biodiversity.org.au/node/apni/2892273,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus recurva,native +Eucalyptus rossii,Eucalyptus rossii,Eucalyptus rossii,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus rossii R.T.Baker & H.G.Sm.,https://id.biodiversity.org.au/node/apni/2900822,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/58182,Eucalyptus rossii,https://id.biodiversity.org.au/name/apni/58182,accepted,https://id.biodiversity.org.au/node/apni/2900822,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus rossii,native +Eucalyptus scias,Eucalyptus scias,Eucalyptus scias,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus scias L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2893839,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118833,Eucalyptus scias,https://id.biodiversity.org.au/name/apni/118833,accepted,https://id.biodiversity.org.au/node/apni/2893839,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus scias,native +Eucalyptus tetrodonta,Eucalyptus tetrodonta,Eucalyptus tetrodonta,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus tetrodonta F.Muell.,https://id.biodiversity.org.au/node/apni/2905964,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/55572,Eucalyptus tetrodonta,https://id.biodiversity.org.au/name/apni/55572,accepted,https://id.biodiversity.org.au/node/apni/2905964,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus tetrodonta,native +Eucalyptus viminalis,Eucalyptus viminalis,Eucalyptus viminalis , Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied),Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic, Tas",Eucalyptus viminalis Labill.,https://id.biodiversity.org.au/taxon/apni/51290421,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/65838,Eucalyptus viminalis [alternative possible names: Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus viminalis,native +Eucalyptus youmanii,Eucalyptus youmanii,Eucalyptus youmanii,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Eucalyptus youmanii Blakely & McKie,https://id.biodiversity.org.au/node/apni/2916227,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/92496,Eucalyptus youmanii,https://id.biodiversity.org.au/name/apni/92496,accepted,https://id.biodiversity.org.au/node/apni/2916227,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus youmanii,native +Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata var. queenslandica,NA,Euphorbia,Euphorbiaceae,variety,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Euphorbia inappendiculata var. queenslandica Domin,https://id.biodiversity.org.au/node/apni/7200245,https://id.biodiversity.org.au/taxon/apni/51435529,https://id.biodiversity.org.au/name/apni/92612,Euphorbia inappendiculata var. queenslandica,https://id.biodiversity.org.au/name/apni/92612,accepted,https://id.biodiversity.org.au/node/apni/7200245,https://id.biodiversity.org.au/taxon/apni/51442249,Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata,native +Exocarpos homalocladus,Exocarpos homalocladus,Exocarpos homalocladus,NA,Exocarpos,Santalaceae,species,APC,accepted,Magnoliidae,LHI,Exocarpos homalocladus C.Moore & F.Muell.,https://id.biodiversity.org.au/node/apni/2898548,https://id.biodiversity.org.au/taxon/apni/51447153,https://id.biodiversity.org.au/name/apni/58158,Exocarpos homalocladus,https://id.biodiversity.org.au/name/apni/58158,accepted,https://id.biodiversity.org.au/node/apni/2898548,https://id.biodiversity.org.au/taxon/apni/51447154,NA,Exocarpos homalocladus,native +Exocarpos sparteus,Exocarpos sparteus,Exocarpos sparteus,NA,Exocarpos,Santalaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Exocarpos sparteus R.Br.,https://id.biodiversity.org.au/node/apni/2898676,https://id.biodiversity.org.au/taxon/apni/51447153,https://id.biodiversity.org.au/name/apni/58330,Exocarpos sparteus,https://id.biodiversity.org.au/name/apni/58330,accepted,https://id.biodiversity.org.au/node/apni/2898676,https://id.biodiversity.org.au/taxon/apni/51447154,NA,Exocarpos sparteus,native +Ficus henneana,Ficus henneana,Ficus henneana,NA,Ficus,Moraceae,species,APC,accepted,Magnoliidae,"NT, Qld, NSW",Ficus henneana Miq.,https://id.biodiversity.org.au/node/apni/2903067,https://id.biodiversity.org.au/taxon/apni/51439476,https://id.biodiversity.org.au/name/apni/91212,Ficus henneana,https://id.biodiversity.org.au/name/apni/91212,accepted,https://id.biodiversity.org.au/node/apni/2903067,https://id.biodiversity.org.au/taxon/apni/51439463,NA,Ficus henneana,native +Freesia laxa,Freesia laxa,Freesia laxa,NA,Freesia,Iridaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), Qld (naturalised), NSW (naturalised), NI (naturalised), Vic (naturalised)",Freesia laxa (Thunb.) Goldblatt & J.C.Manning,https://id.biodiversity.org.au/node/apni/2886987,https://id.biodiversity.org.au/node/apni/2913899,https://id.biodiversity.org.au/name/apni/200132,Freesia laxa,https://id.biodiversity.org.au/name/apni/200132,accepted,https://id.biodiversity.org.au/node/apni/2886987,https://id.biodiversity.org.au/taxon/apni/51438006,NA,Freesia laxa,naturalised +Freesia hybrid,Freesia hybrid,Freesia leichtlinii subsp. leichtlinii x Freesia leichtlinii subsp. alba,NA,Freesia,Iridaceae,subspecies,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised)",Freesia leichtlinii Klatt subsp. leichtlinii x Freesia leichtlinii subsp. alba (G.L.Mey.) J.C.Manning & Goldblatt,https://id.biodiversity.org.au/node/apni/2908401,https://id.biodiversity.org.au/node/apni/2913899,https://id.biodiversity.org.au/name/apni/241787,Freesia leichtlinii subsp. leichtlinii x Freesia leichtlinii subsp. alba,https://id.biodiversity.org.au/name/apni/171901,taxonomic synonym,https://id.biodiversity.org.au/instance/apni/953836,https://id.biodiversity.org.au/taxon/apni/51438006,Freesia leichtlinii subsp. leichtlinii x Freesia leichtlinii subsp. alba,Freesia leichtlinii,naturalised +Geijera salicifolia,Geijera salicifolia,Geijera salicifolia,NA,Geijera,Rutaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Geijera salicifolia Schott,https://id.biodiversity.org.au/node/apni/2901807,https://id.biodiversity.org.au/node/apni/2905474,https://id.biodiversity.org.au/name/apni/101381,Geijera salicifolia,https://id.biodiversity.org.au/name/apni/101381,accepted,https://id.biodiversity.org.au/node/apni/2901807,https://id.biodiversity.org.au/taxon/apni/51461748,NA,Geijera salicifolia,native +Gentiana wingecarribiensis,Gentiana wingecarribiensis,Gentiana wingecarribiensis,NA,Gentiana,Gentianaceae,species,APC,accepted,Magnoliidae,NSW,Gentiana wingecarribiensis L.G.Adams,https://id.biodiversity.org.au/node/apni/2915610,https://id.biodiversity.org.au/taxon/apni/51436928,https://id.biodiversity.org.au/name/apni/80378,Gentiana wingecarribiensis,https://id.biodiversity.org.au/name/apni/80378,accepted,https://id.biodiversity.org.au/node/apni/2915610,https://id.biodiversity.org.au/taxon/apni/51436871,NA,Gentiana wingecarribiensis,native +Gentianella barringtonensis,Gentianella barringtonensis,Gentianella barringtonensis,NA,Gentianella,Gentianaceae,species,APC,accepted,Magnoliidae,NSW,Gentianella barringtonensis (L.G.Adams) Glenny,https://id.biodiversity.org.au/taxon/apni/51301045,https://id.biodiversity.org.au/taxon/apni/51301038,https://id.biodiversity.org.au/name/apni/192277,Gentianella barringtonensis,https://id.biodiversity.org.au/name/apni/192277,accepted,https://id.biodiversity.org.au/taxon/apni/51301045,https://id.biodiversity.org.au/taxon/apni/51436871,NA,Gentianella barringtonensis,native +Geranium obtusisepalum,Geranium obtusisepalum,Geranium obtusisepalum,NA,Geranium,Geraniaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Geranium obtusisepalum Carolin,https://id.biodiversity.org.au/node/apni/2910251,https://id.biodiversity.org.au/taxon/apni/51436946,https://id.biodiversity.org.au/name/apni/82004,Geranium obtusisepalum,https://id.biodiversity.org.au/name/apni/82004,accepted,https://id.biodiversity.org.au/node/apni/2910251,https://id.biodiversity.org.au/taxon/apni/51436947,NA,Geranium obtusisepalum,native +Geranium purpureum subsp. purpureum,Geranium purpureum subsp. purpureum,Geranium purpureum,NA,Geranium,Geraniaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised)",Geranium purpureum Vill.,https://id.biodiversity.org.au/node/apni/2919721,https://id.biodiversity.org.au/taxon/apni/51436946,https://id.biodiversity.org.au/name/apni/82353,Geranium purpureum,https://id.biodiversity.org.au/name/apni/82382,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/895632,https://id.biodiversity.org.au/taxon/apni/51436947,NA,Geranium purpureum,naturalised +Gillbeea adenopetala,Gillbeea adenopetala,Gillbeea adenopetala,NA,Gillbeea,Cunoniaceae,species,APC,accepted,Magnoliidae,Qld,Gillbeea adenopetala F.Muell.,https://id.biodiversity.org.au/node/apni/2913815,https://id.biodiversity.org.au/node/apni/2918249,https://id.biodiversity.org.au/name/apni/98098,Gillbeea adenopetala,https://id.biodiversity.org.au/name/apni/98098,accepted,https://id.biodiversity.org.au/node/apni/2913815,https://id.biodiversity.org.au/taxon/apni/51434138,NA,Gillbeea adenopetala,native +Glochidion hylandii,Glochidion hylandii,Glochidion hylandii,NA,Glochidion,Phyllanthaceae,species,APC,accepted,Magnoliidae,Qld,Glochidion hylandii Airy Shaw,https://id.biodiversity.org.au/node/apni/2889113,https://id.biodiversity.org.au/node/apni/8387508,https://id.biodiversity.org.au/name/apni/78303,Glochidion hylandii,https://id.biodiversity.org.au/name/apni/78303,accepted,https://id.biodiversity.org.au/node/apni/2889113,https://id.biodiversity.org.au/taxon/apni/51442162,NA,Glochidion hylandii,native +Gompholobium grandiflorum,Gompholobium grandiflorum,Gompholobium grandiflorum,NA,Gompholobium,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Gompholobium grandiflorum Sm.,https://id.biodiversity.org.au/node/apni/2909013,https://id.biodiversity.org.au/taxon/apni/51436123,https://id.biodiversity.org.au/name/apni/65291,Gompholobium grandiflorum,https://id.biodiversity.org.au/name/apni/65291,accepted,https://id.biodiversity.org.au/node/apni/2909013,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Gompholobium grandiflorum,native +Goodenia varia,Goodenia varia,Goodenia varia,NA,Goodenia,Goodeniaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic",Goodenia varia R.Br.,https://id.biodiversity.org.au/node/apni/2910439,https://id.biodiversity.org.au/taxon/apni/51437012,https://id.biodiversity.org.au/name/apni/92079,Goodenia varia,https://id.biodiversity.org.au/name/apni/92079,accepted,https://id.biodiversity.org.au/node/apni/2910439,https://id.biodiversity.org.au/taxon/apni/51462931,NA,Goodenia varia,native +Gossia bidwillii,Gossia bidwillii,Gossia bidwillii,NA,Gossia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Gossia bidwillii (Benth.) N.Snow & Guymer,https://id.biodiversity.org.au/taxon/apni/51439972,https://id.biodiversity.org.au/taxon/apni/51439958,https://id.biodiversity.org.au/name/apni/180918,Gossia bidwillii,https://id.biodiversity.org.au/name/apni/180918,accepted,https://id.biodiversity.org.au/taxon/apni/51439972,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Gossia bidwillii,native +Grevillea scortechinii,Grevillea scortechinii,Grevillea scortechinii,NA,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Grevillea scortechinii (F.Muell. ex Scort.) F.Muell.,https://id.biodiversity.org.au/node/apni/2918803,https://id.biodiversity.org.au/taxon/apni/51445337,https://id.biodiversity.org.au/name/apni/63322,Grevillea scortechinii,https://id.biodiversity.org.au/name/apni/63322,accepted,https://id.biodiversity.org.au/node/apni/2918803,https://id.biodiversity.org.au/taxon/apni/51614274,NA,Grevillea scortechinii,native +Hakea macraeana,Hakea macraeana,Hakea macraeana , Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied),Hakea,Proteaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Hakea macraeana F.Muell.,https://id.biodiversity.org.au/node/apni/2895080,https://id.biodiversity.org.au/taxon/apni/51445456,https://id.biodiversity.org.au/name/apni/94862,Hakea macraeana [alternative possible names: Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51614274,NA,Hakea macraeana,native +Harpullia rhyticarpa,Harpullia rhyticarpa,Harpullia rhyticarpa,NA,Harpullia,Sapindaceae,species,APC,accepted,Magnoliidae,Qld,Harpullia rhyticarpa C.T.White & W.D.Francis,https://id.biodiversity.org.au/node/apni/2910766,https://id.biodiversity.org.au/taxon/apni/51447330,https://id.biodiversity.org.au/name/apni/108928,Harpullia rhyticarpa,https://id.biodiversity.org.au/name/apni/108928,accepted,https://id.biodiversity.org.au/node/apni/2910766,https://id.biodiversity.org.au/taxon/apni/51447212,NA,Harpullia rhyticarpa,native +Hemisteptia lyrata,Hemisteptia lyrata,Hemisteptia lyrata,NA,Hemisteptia,Asteraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Hemisteptia lyrata (Bunge) Fisch. & C.A.Mey.,https://id.biodiversity.org.au/taxon/apni/51268530,https://id.biodiversity.org.au/taxon/apni/51268531,https://id.biodiversity.org.au/name/apni/230066,Hemisteptia lyrata,https://id.biodiversity.org.au/name/apni/230066,accepted,https://id.biodiversity.org.au/taxon/apni/51268530,https://id.biodiversity.org.au/taxon/apni/51695393,NA,Hemisteptia lyrata,native +Hernandia albiflora,Hernandia albiflora,Hernandia albiflora,NA,Hernandia,Hernandiaceae,species,APC,accepted,Magnoliidae,Qld,Hernandia albiflora (C.T.White) Kubitzki,https://id.biodiversity.org.au/node/apni/2911354,https://id.biodiversity.org.au/taxon/apni/51437691,https://id.biodiversity.org.au/name/apni/92773,Hernandia albiflora,https://id.biodiversity.org.au/name/apni/92773,accepted,https://id.biodiversity.org.au/node/apni/2911354,https://id.biodiversity.org.au/taxon/apni/51437692,NA,Hernandia albiflora,native +Hibbertia crinita,Hibbertia crinita,Hibbertia crinita,NA,Hibbertia,Dilleniaceae,species,APC,accepted,Magnoliidae,"SA, Vic",Hibbertia crinita Toelken,https://id.biodiversity.org.au/node/apni/2899370,https://id.biodiversity.org.au/taxon/apni/51434912,https://id.biodiversity.org.au/name/apni/170069,Hibbertia crinita,https://id.biodiversity.org.au/name/apni/170069,accepted,https://id.biodiversity.org.au/node/apni/2899370,https://id.biodiversity.org.au/taxon/apni/51434913,NA,Hibbertia crinita,native +Hibiscus brachysiphonius,Hibiscus brachysiphonius,Hibiscus brachysiphonius,NA,Hibiscus,Malvaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Hibiscus brachysiphonius F.Muell.,https://id.biodiversity.org.au/node/apni/2891329,https://id.biodiversity.org.au/taxon/apni/51439316,https://id.biodiversity.org.au/name/apni/91736,Hibiscus brachysiphonius,https://id.biodiversity.org.au/name/apni/91736,accepted,https://id.biodiversity.org.au/node/apni/2891329,https://id.biodiversity.org.au/taxon/apni/51439248,NA,Hibiscus brachysiphonius,native +Hibiscus sturtii,Hibiscus sturtii,Hibiscus sturtii,NA,Hibiscus,Malvaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Hibiscus sturtii Hook.,https://id.biodiversity.org.au/taxon/apni/51439064,https://id.biodiversity.org.au/taxon/apni/51439316,https://id.biodiversity.org.au/name/apni/63902,Hibiscus sturtii,https://id.biodiversity.org.au/name/apni/63902,accepted,https://id.biodiversity.org.au/taxon/apni/51439064,https://id.biodiversity.org.au/taxon/apni/51439248,NA,Hibiscus sturtii,native +Homalanthus novoguineensis,Homalanthus novo-guineensis,Homalanthus novo-guineensis,NA,Homalanthus,Euphorbiaceae,species,APC,accepted,Magnoliidae,"WA (native and naturalised), NT, Qld",Homalanthus novo-guineensis (Warb.) Lauterb. & K.Schum.,https://id.biodiversity.org.au/node/apni/2888327,https://id.biodiversity.org.au/node/apni/4932846,https://id.biodiversity.org.au/name/apni/130383,Homalanthus novo-guineensis,https://id.biodiversity.org.au/name/apni/130383,accepted,https://id.biodiversity.org.au/node/apni/2888327,https://id.biodiversity.org.au/taxon/apni/51442249,NA,Homalanthus novo-guineensis,native and naturalised +Hypericum elodes,Hypericum elodes,Hypericum elodes,NA,Hypericum,Hypericaceae,species,APC,accepted,Magnoliidae,NSW (naturalised),Hypericum elodes L.,https://id.biodiversity.org.au/node/apni/2909044,https://id.biodiversity.org.au/taxon/apni/51433733,https://id.biodiversity.org.au/name/apni/136721,Hypericum elodes,https://id.biodiversity.org.au/name/apni/136721,accepted,https://id.biodiversity.org.au/node/apni/2909044,https://id.biodiversity.org.au/taxon/apni/51433734,NA,Hypericum elodes,naturalised +Imperata cylindrica,Imperata cylindrica,Imperata cylindrica,NA,Imperata,Poaceae,species,APC,accepted,Magnoliidae,"WA, CoI (naturalised), ChI (naturalised), NT, SA, Qld, NSW, LHI (naturalised), ACT, Vic, Tas",Imperata cylindrica (L.) P.Beauv.,https://id.biodiversity.org.au/node/apni/2920993,https://id.biodiversity.org.au/node/apni/2905343,https://id.biodiversity.org.au/name/apni/71806,Imperata cylindrica,https://id.biodiversity.org.au/name/apni/179218,taxonomic synonym,https://id.biodiversity.org.au/instance/apni/888976,https://id.biodiversity.org.au/taxon/apni/51644646,NA,Imperata cylindrica,native and naturalised +Indigofera triflora,Indigofera triflora,Indigofera triflora,NA,Indigofera,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Indigofera triflora Peter G.Wilson & Rowe,https://id.biodiversity.org.au/node/apni/2905193,https://id.biodiversity.org.au/taxon/apni/51436152,https://id.biodiversity.org.au/name/apni/189510,Indigofera triflora,https://id.biodiversity.org.au/name/apni/189510,accepted,https://id.biodiversity.org.au/node/apni/2905193,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Indigofera triflora,native +Ipomoea cairica,Ipomoea cairica,Ipomoea cairica,NA,Ipomoea,Convolvulaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), ChI (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), NI (naturalised)",Ipomoea cairica (L.) Sweet,https://id.biodiversity.org.au/node/apni/2897935,https://id.biodiversity.org.au/taxon/apni/51433921,https://id.biodiversity.org.au/name/apni/93713,Ipomoea cairica,https://id.biodiversity.org.au/name/apni/93713,accepted,https://id.biodiversity.org.au/node/apni/2897935,https://id.biodiversity.org.au/taxon/apni/51695210,NA,Ipomoea cairica,naturalised +Isolepis montivaga,Isolepis montivaga,Isolepis montivaga,NA,Isolepis,Cyperaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic, Tas",Isolepis montivaga (S.T.Blake) K.L.Wilson,https://id.biodiversity.org.au/node/apni/2921053,https://id.biodiversity.org.au/taxon/apni/51336324,https://id.biodiversity.org.au/name/apni/74456,Isolepis montivaga,https://id.biodiversity.org.au/name/apni/74456,accepted,https://id.biodiversity.org.au/node/apni/2921053,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Isolepis montivaga,native +Isotoma axillaris,Isotoma axillaris,Isotoma axillaris,NA,Isotoma,Campanulaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic",Isotoma axillaris Lindl.,https://id.biodiversity.org.au/node/apni/2902056,https://id.biodiversity.org.au/node/apni/2892848,https://id.biodiversity.org.au/name/apni/102004,Isotoma axillaris,https://id.biodiversity.org.au/name/apni/102004,accepted,https://id.biodiversity.org.au/node/apni/2902056,https://id.biodiversity.org.au/taxon/apni/51432853,NA,Isotoma axillaris,native +Isotoma fluviatilis subsp. fluviatilis,Isotoma fluviatilis subsp. fluviatilis,Isotoma fluviatilis subsp. fluviatilis,NA,Isotoma,Campanulaceae,subspecies,APC,accepted,Magnoliidae,NSW,Isotoma fluviatilis (R.Br.) F.Muell. ex Benth. subsp. fluviatilis,https://id.biodiversity.org.au/node/apni/2897543,https://id.biodiversity.org.au/node/apni/2892848,https://id.biodiversity.org.au/name/apni/102114,Isotoma fluviatilis subsp. fluviatilis,https://id.biodiversity.org.au/name/apni/102114,accepted,https://id.biodiversity.org.au/node/apni/2897543,https://id.biodiversity.org.au/taxon/apni/51432853,Isotoma fluviatilis subsp. fluviatilis,Isotoma fluviatilis,native +Ixora biflora,Ixora biflora,Ixora biflora,NA,Ixora,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Ixora biflora Fosberg,https://id.biodiversity.org.au/node/apni/2915627,https://id.biodiversity.org.au/taxon/apni/51446659,https://id.biodiversity.org.au/name/apni/90479,Ixora biflora,https://id.biodiversity.org.au/name/apni/90479,accepted,https://id.biodiversity.org.au/node/apni/2915627,https://id.biodiversity.org.au/taxon/apni/51446612,NA,Ixora biflora,native +Juncus acutus subsp. acutus,Juncus acutus subsp. acutus,Juncus acutus subsp. acutus,NA,Juncus,Juncaceae,subspecies,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), Qld (naturalised), NSW (naturalised), Vic (naturalised)",Juncus acutus L. subsp. acutus,https://id.biodiversity.org.au/node/apni/2887983,https://id.biodiversity.org.au/taxon/apni/51438170,https://id.biodiversity.org.au/name/apni/182490,Juncus acutus subsp. acutus,https://id.biodiversity.org.au/name/apni/182490,accepted,https://id.biodiversity.org.au/node/apni/2887983,https://id.biodiversity.org.au/taxon/apni/51438171,Juncus acutus subsp. acutus,Juncus acutus,naturalised +Juncus kraussii,Juncus kraussii,Juncus kraussii,NA,Juncus,Juncaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic, Tas",Juncus kraussii Hochst.,https://id.biodiversity.org.au/node/apni/2900900,https://id.biodiversity.org.au/taxon/apni/51438170,https://id.biodiversity.org.au/name/apni/55859,Juncus kraussii,https://id.biodiversity.org.au/name/apni/55859,accepted,https://id.biodiversity.org.au/node/apni/2900900,https://id.biodiversity.org.au/taxon/apni/51438171,NA,Juncus kraussii,native +Lantana montevidensis,Lantana montevidensis,Lantana montevidensis,NA,Lantana,Verbenaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), Qld (naturalised), NSW (naturalised), NI (doubtfully naturalised)",Lantana montevidensis (Spreng.) Briq.,https://id.biodiversity.org.au/node/apni/2894994,https://id.biodiversity.org.au/taxon/apni/51448661,https://id.biodiversity.org.au/name/apni/70044,Lantana montevidensis,https://id.biodiversity.org.au/name/apni/70044,accepted,https://id.biodiversity.org.au/node/apni/2894994,https://id.biodiversity.org.au/taxon/apni/51448662,NA,Lantana montevidensis,naturalised +Lasianthus strigosus,Lasianthus strigosus,Lasianthus chlorocarpus,NA,Lasianthus,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Lasianthus chlorocarpus K.Schum.,https://id.biodiversity.org.au/node/apni/7839740,https://id.biodiversity.org.au/node/apni/8136656,https://id.biodiversity.org.au/name/apni/219373,Lasianthus chlorocarpus,https://id.biodiversity.org.au/name/apni/71294,misapplied,https://id.biodiversity.org.au/instance/apni/7839725,https://id.biodiversity.org.au/taxon/apni/51446612,NA,Lasianthus chlorocarpus,native +Lepidium africanum,Lepidium africanum,Lepidium africanum,NA,Lepidium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Lepidium africanum (Burm.f.) DC.,https://id.biodiversity.org.au/node/apni/2887818,https://id.biodiversity.org.au/taxon/apni/51612686,https://id.biodiversity.org.au/name/apni/68961,Lepidium africanum,https://id.biodiversity.org.au/name/apni/68961,accepted,https://id.biodiversity.org.au/node/apni/2887818,https://id.biodiversity.org.au/taxon/apni/51612687,NA,Lepidium africanum,naturalised +Lepidium foliosum,Lepidium foliosum,Lepidium foliosum,NA,Lepidium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Lepidium foliosum Desv.,https://id.biodiversity.org.au/node/apni/2908453,https://id.biodiversity.org.au/taxon/apni/51612686,https://id.biodiversity.org.au/name/apni/69389,Lepidium foliosum,https://id.biodiversity.org.au/name/apni/69389,accepted,https://id.biodiversity.org.au/node/apni/2908453,https://id.biodiversity.org.au/taxon/apni/51612687,NA,Lepidium foliosum,native +Lepidium oxytrichum,Lepidium oxytrichum,Lepidium oxytrichum,NA,Lepidium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Lepidium oxytrichum Sprague,https://id.biodiversity.org.au/node/apni/2915883,https://id.biodiversity.org.au/taxon/apni/51612686,https://id.biodiversity.org.au/name/apni/84027,Lepidium oxytrichum,https://id.biodiversity.org.au/name/apni/84027,accepted,https://id.biodiversity.org.au/node/apni/2915883,https://id.biodiversity.org.au/taxon/apni/51612687,NA,Lepidium oxytrichum,native +Lepidosperma gladiatum,Lepidosperma gladiatum,Lepidosperma gladiatum,NA,Lepidosperma,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Lepidosperma gladiatum Labill.,https://id.biodiversity.org.au/node/apni/2896726,https://id.biodiversity.org.au/taxon/apni/51434499,https://id.biodiversity.org.au/name/apni/85937,Lepidosperma gladiatum,https://id.biodiversity.org.au/name/apni/85937,accepted,https://id.biodiversity.org.au/node/apni/2896726,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Lepidosperma gladiatum,native +Leptomeria drupacea,Leptomeria drupacea,Leptomeria drupacea,NA,Leptomeria,Santalaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic, Tas",Leptomeria drupacea (Labill.) Druce,https://id.biodiversity.org.au/node/apni/2892780,https://id.biodiversity.org.au/node/apni/2897704,https://id.biodiversity.org.au/name/apni/61625,Leptomeria drupacea,https://id.biodiversity.org.au/name/apni/61625,accepted,https://id.biodiversity.org.au/node/apni/2892780,https://id.biodiversity.org.au/taxon/apni/51447154,NA,Leptomeria drupacea,native +Leptospermum continentale,Leptospermum continentale,Leptospermum continentale,NA,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic",Leptospermum continentale Joy Thomps.,https://id.biodiversity.org.au/node/apni/2917147,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/81291,Leptospermum continentale,https://id.biodiversity.org.au/name/apni/81291,accepted,https://id.biodiversity.org.au/node/apni/2917147,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Leptospermum continentale,native +Leptospermum obovatum,Leptospermum obovatum,Leptospermum obovatum,NA,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Leptospermum obovatum Sweet,https://id.biodiversity.org.au/node/apni/2891711,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/99608,Leptospermum obovatum,https://id.biodiversity.org.au/name/apni/99608,accepted,https://id.biodiversity.org.au/node/apni/2891711,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Leptospermum obovatum,native +Leucopogon amplexicaulis,Leucopogon amplexicaulis,Leucopogon amplexicaulis,NA,Leucopogon,Ericaceae,species,APC,accepted,Magnoliidae,NSW,Leucopogon amplexicaulis (Rudge) R.Br.,https://id.biodiversity.org.au/node/apni/2896081,https://id.biodiversity.org.au/taxon/apni/51435325,https://id.biodiversity.org.au/name/apni/106715,Leucopogon amplexicaulis,https://id.biodiversity.org.au/name/apni/106715,accepted,https://id.biodiversity.org.au/node/apni/2896081,https://id.biodiversity.org.au/taxon/apni/51436079,NA,Leucopogon amplexicaulis,native +Litsea leefeana,Litsea leefeana,Litsea leefeana,NA,Litsea,Lauraceae,species,APC,accepted,Magnoliidae,Qld,Litsea leefeana (F.Muell.) Merr.,https://id.biodiversity.org.au/node/apni/2921063,https://id.biodiversity.org.au/taxon/apni/51438430,https://id.biodiversity.org.au/name/apni/81094,Litsea leefeana,https://id.biodiversity.org.au/name/apni/81094,accepted,https://id.biodiversity.org.au/node/apni/2921063,https://id.biodiversity.org.au/taxon/apni/51438397,NA,Litsea leefeana,native +Lobelia pedunculata,Lobelia pedunculata,Lobelia pedunculata,NA,Lobelia,Campanulaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic, Tas",Lobelia pedunculata R.Br.,https://id.biodiversity.org.au/node/apni/2901444,https://id.biodiversity.org.au/taxon/apni/51432852,https://id.biodiversity.org.au/name/apni/106999,Lobelia pedunculata,https://id.biodiversity.org.au/name/apni/106999,accepted,https://id.biodiversity.org.au/node/apni/2901444,https://id.biodiversity.org.au/taxon/apni/51432853,NA,Lobelia pedunculata,native +Lobelia trigonocaulis,Lobelia trigonocaulis,Lobelia trigonocaulis,NA,Lobelia,Campanulaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Lobelia trigonocaulis F.Muell.,https://id.biodiversity.org.au/node/apni/2901863,https://id.biodiversity.org.au/taxon/apni/51432852,https://id.biodiversity.org.au/name/apni/107808,Lobelia trigonocaulis,https://id.biodiversity.org.au/name/apni/107808,accepted,https://id.biodiversity.org.au/node/apni/2901863,https://id.biodiversity.org.au/taxon/apni/51432853,NA,Lobelia trigonocaulis,native +Lotononis bainesii,Lotononis bainesii,Lotononis bainesii,NA,Lotononis,Fabaceae,species,APC,accepted,Magnoliidae,"Qld (naturalised), NSW (naturalised)",Lotononis bainesii Baker,https://id.biodiversity.org.au/node/apni/2904277,https://id.biodiversity.org.au/node/apni/2898035,https://id.biodiversity.org.au/name/apni/109834,Lotononis bainesii,https://id.biodiversity.org.au/name/apni/109834,accepted,https://id.biodiversity.org.au/node/apni/2904277,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Lotononis bainesii,naturalised +Lotus corniculatus,Lotus corniculatus,Lotus corniculatus , Lotus preslii (pro parte misapplied) | Lotus uliginosus (pro parte misapplied),Lotus,Fabaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (formerly naturalised), NSW (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Lotus corniculatus L.,https://id.biodiversity.org.au/node/apni/2921302,https://id.biodiversity.org.au/taxon/apni/51436215,https://id.biodiversity.org.au/name/apni/110319,Lotus corniculatus [alternative possible names: Lotus preslii (pro parte misapplied) | Lotus uliginosus (pro parte misapplied)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Lotus corniculatus,naturalised +Lupinus polyphyllus,Lupinus polyphyllus,Lupinus polyphyllus,NA,Lupinus,Fabaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), Vic (naturalised)",Lupinus polyphyllus Lindl.,https://id.biodiversity.org.au/node/apni/2917429,https://id.biodiversity.org.au/node/apni/2918316,https://id.biodiversity.org.au/name/apni/100609,Lupinus polyphyllus,https://id.biodiversity.org.au/name/apni/100609,accepted,https://id.biodiversity.org.au/node/apni/2917429,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Lupinus polyphyllus,naturalised +Macaranga tanarius,Macaranga tanarius,Macaranga tanarius,NA,Macaranga,Euphorbiaceae,species,APC,accepted,Magnoliidae,"ChI, NT, Qld, NSW",Macaranga tanarius (L.) Müll.Arg.,https://id.biodiversity.org.au/node/apni/2902044,https://id.biodiversity.org.au/node/apni/2900788,https://id.biodiversity.org.au/name/apni/57015,Macaranga tanarius,https://id.biodiversity.org.au/name/apni/57015,accepted,https://id.biodiversity.org.au/node/apni/2902044,https://id.biodiversity.org.au/taxon/apni/51442249,NA,Macaranga tanarius,native +Mallotus mollissimus,Mallotus mollissimus,Mallotus mollissimus,NA,Mallotus,Euphorbiaceae,species,APC,accepted,Magnoliidae,Qld,Mallotus mollissimus (Geiseler) Airy Shaw,https://id.biodiversity.org.au/node/apni/2904445,https://id.biodiversity.org.au/taxon/apni/51284195,https://id.biodiversity.org.au/name/apni/59376,Mallotus mollissimus,https://id.biodiversity.org.au/name/apni/59376,accepted,https://id.biodiversity.org.au/node/apni/2904445,https://id.biodiversity.org.au/taxon/apni/51442249,NA,Mallotus mollissimus,native +Medicago orbicularis,Medicago orbicularis,Medicago orbicularis,NA,Medicago,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (formerly naturalised)",Medicago orbicularis (L.) Bartal.,https://id.biodiversity.org.au/node/apni/2901771,https://id.biodiversity.org.au/taxon/apni/51285690,https://id.biodiversity.org.au/name/apni/59568,Medicago orbicularis,https://id.biodiversity.org.au/name/apni/59568,accepted,https://id.biodiversity.org.au/node/apni/2901771,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Medicago orbicularis,naturalised +Medicosma sessiliflora,Medicosma sessiliflora,Medicosma sessiliflora,NA,Medicosma,Rutaceae,species,APC,accepted,Magnoliidae,Qld,Medicosma sessiliflora (C.T.White) T.G.Hartley,https://id.biodiversity.org.au/node/apni/2914896,https://id.biodiversity.org.au/taxon/apni/51446918,https://id.biodiversity.org.au/name/apni/73658,Medicosma sessiliflora,https://id.biodiversity.org.au/name/apni/73658,accepted,https://id.biodiversity.org.au/node/apni/2914896,https://id.biodiversity.org.au/taxon/apni/51461748,NA,Medicosma sessiliflora,native +Melastoma cyanoides,Melastoma cyanoides,Melastoma cyanoides,NA,Melastoma,Melastomataceae,species,APC,accepted,Magnoliidae,Qld,Melastoma cyanoides Sm.,https://id.biodiversity.org.au/node/apni/2895184,https://id.biodiversity.org.au/taxon/apni/51439399,https://id.biodiversity.org.au/name/apni/172752,Melastoma cyanoides,https://id.biodiversity.org.au/name/apni/172752,accepted,https://id.biodiversity.org.au/node/apni/2895184,https://id.biodiversity.org.au/taxon/apni/51439392,NA,Melastoma cyanoides,native +Melichrus procumbens,Melichrus procumbens,Melichrus procumbens,NA,Melichrus,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Melichrus procumbens (Cav.) Druce,https://id.biodiversity.org.au/node/apni/2905836,https://id.biodiversity.org.au/node/apni/2914566,https://id.biodiversity.org.au/name/apni/114051,Melichrus procumbens,https://id.biodiversity.org.au/name/apni/114051,accepted,https://id.biodiversity.org.au/node/apni/2905836,https://id.biodiversity.org.au/taxon/apni/51436079,NA,Melichrus procumbens,native +Melicope elleryana,Melicope elleryana,Melicope elleryana,NA,Melicope,Rutaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Melicope elleryana (F.Muell.) T.G.Hartley,https://id.biodiversity.org.au/node/apni/2913641,https://id.biodiversity.org.au/node/apni/2918609,https://id.biodiversity.org.au/name/apni/118560,Melicope elleryana,https://id.biodiversity.org.au/name/apni/118560,accepted,https://id.biodiversity.org.au/node/apni/2913641,https://id.biodiversity.org.au/taxon/apni/51461748,NA,Melicope elleryana,native +Mischocarpus australis,Mischocarpus australis,Mischocarpus australis,NA,Mischocarpus,Sapindaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Mischocarpus australis S.T.Reynolds,https://id.biodiversity.org.au/node/apni/2893744,https://id.biodiversity.org.au/taxon/apni/51389373,https://id.biodiversity.org.au/name/apni/115917,Mischocarpus australis,https://id.biodiversity.org.au/name/apni/115917,accepted,https://id.biodiversity.org.au/node/apni/2893744,https://id.biodiversity.org.au/taxon/apni/51447212,NA,Mischocarpus australis,native +Muehlenbeckia adpressa,Muehlenbeckia adpressa,Muehlenbeckia adpressa,NA,Muehlenbeckia,Polygonaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Muehlenbeckia adpressa (Labill.) Meisn.,https://id.biodiversity.org.au/node/apni/4750977,https://id.biodiversity.org.au/taxon/apni/51291654,https://id.biodiversity.org.au/name/apni/107852,Muehlenbeckia adpressa,https://id.biodiversity.org.au/name/apni/107852,accepted,https://id.biodiversity.org.au/node/apni/4750977,https://id.biodiversity.org.au/taxon/apni/51444856,NA,Muehlenbeckia adpressa,native +Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,NA,Myoporum,Scrophulariaceae,subspecies,APC,accepted,Magnoliidae,"Qld, NSW",Myoporum boninense subsp. australe Chinnock,https://id.biodiversity.org.au/node/apni/7957248,https://id.biodiversity.org.au/taxon/apni/51447443,https://id.biodiversity.org.au/name/apni/117892,Myoporum boninense subsp. australe,https://id.biodiversity.org.au/name/apni/117892,accepted,https://id.biodiversity.org.au/node/apni/7957248,https://id.biodiversity.org.au/taxon/apni/51461527,Myoporum boninense subsp. australe,Myoporum boninense,native +Myristica insipida,Myristica insipida,Myristica insipida,NA,Myristica,Myristicaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Myristica insipida R.Br.,https://id.biodiversity.org.au/node/apni/2902429,https://id.biodiversity.org.au/node/apni/2895962,https://id.biodiversity.org.au/name/apni/86064,Myristica insipida,https://id.biodiversity.org.au/name/apni/86064,accepted,https://id.biodiversity.org.au/node/apni/2902429,https://id.biodiversity.org.au/node/apni/2903136,NA,Myristica insipida,native +Neolitsea dealbata,Neolitsea dealbata,Neolitsea dealbata,NA,Neolitsea,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Neolitsea dealbata (R.Br.) Merr.,https://id.biodiversity.org.au/node/apni/2910025,https://id.biodiversity.org.au/node/apni/2914447,https://id.biodiversity.org.au/name/apni/79589,Neolitsea dealbata,https://id.biodiversity.org.au/name/apni/79589,accepted,https://id.biodiversity.org.au/node/apni/2910025,https://id.biodiversity.org.au/taxon/apni/51438397,NA,Neolitsea dealbata,native +Nicotiana glauca,Nicotiana glauca,Nicotiana glauca,NA,Nicotiana,Solanaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (naturalised)",Nicotiana glauca Graham,https://id.biodiversity.org.au/node/apni/2887606,https://id.biodiversity.org.au/taxon/apni/51447689,https://id.biodiversity.org.au/name/apni/77368,Nicotiana glauca,https://id.biodiversity.org.au/name/apni/77368,accepted,https://id.biodiversity.org.au/node/apni/2887606,https://id.biodiversity.org.au/taxon/apni/51447684,NA,Nicotiana glauca,naturalised +Nicotiana goodspeedii,Nicotiana goodspeedii,Nicotiana goodspeedii,NA,Nicotiana,Solanaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic",Nicotiana goodspeedii H.-M.Wheeler,https://id.biodiversity.org.au/node/apni/2908652,https://id.biodiversity.org.au/taxon/apni/51447689,https://id.biodiversity.org.au/name/apni/77381,Nicotiana goodspeedii,https://id.biodiversity.org.au/name/apni/77381,accepted,https://id.biodiversity.org.au/node/apni/2908652,https://id.biodiversity.org.au/taxon/apni/51447684,NA,Nicotiana goodspeedii,native +Oxalis corniculata,Oxalis corniculata,Oxalis corniculata,NA,Oxalis,Oxalidaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), ChI (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Oxalis corniculata L.,https://id.biodiversity.org.au/node/apni/2909588,https://id.biodiversity.org.au/taxon/apni/51442068,https://id.biodiversity.org.au/name/apni/89460,Oxalis corniculata,https://id.biodiversity.org.au/name/apni/89460,accepted,https://id.biodiversity.org.au/node/apni/2909588,https://id.biodiversity.org.au/taxon/apni/51442069,NA,Oxalis corniculata,naturalised +Pandorea pandorana subsp. austrocaledonica,Pandorea pandorana subsp. austrocaledonica,Pandorea pandorana,NA,Pandorea,Bignoniaceae,species,APC,accepted,Magnoliidae,"WA, SA (native and naturalised), Qld, NSW, LHI, NI (presumed extinct), Vic (native and naturalised), Tas",Pandorea pandorana (Andrews) Steenis,https://id.biodiversity.org.au/taxon/apni/51269199,https://id.biodiversity.org.au/taxon/apni/51269200,https://id.biodiversity.org.au/name/apni/91117,Pandorea pandorana,https://id.biodiversity.org.au/name/apni/141640,misapplied,https://id.biodiversity.org.au/instance/apni/51269194,https://id.biodiversity.org.au/taxon/apni/51439229,NA,Pandorea pandorana,native and naturalised +Paraserianthes lophantha,Paraserianthes lophantha,Paraserianthes lophantha,NA,Paraserianthes,Fabaceae,species,APC,accepted,Magnoliidae,"WA (native and naturalised), SA (naturalised), NSW (naturalised), NI (naturalised), Vic (naturalised), Tas (naturalised)",Paraserianthes lophantha (Willd.) I.C.Nielsen,https://id.biodiversity.org.au/taxon/apni/51286820,https://id.biodiversity.org.au/taxon/apni/51286819,https://id.biodiversity.org.au/name/apni/116755,Paraserianthes lophantha,https://id.biodiversity.org.au/name/apni/116755,accepted,https://id.biodiversity.org.au/taxon/apni/51286820,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Paraserianthes lophantha,native and naturalised +Parentucellia latifolia,Parentucellia latifolia,Parentucellia latifolia,NA,Parentucellia,Orobanchaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Parentucellia latifolia (L.) Caruel,https://id.biodiversity.org.au/taxon/apni/51291069,https://id.biodiversity.org.au/taxon/apni/51291062,https://id.biodiversity.org.au/name/apni/96753,Parentucellia latifolia,https://id.biodiversity.org.au/name/apni/96753,accepted,https://id.biodiversity.org.au/taxon/apni/51291069,https://id.biodiversity.org.au/taxon/apni/51291037,NA,Parentucellia latifolia,naturalised +Hypoxis glabella var. glabella,Hypoxis glabella var. glabella,Pauridia glabella var. glabella,NA,Pauridia,Hypoxidaceae,variety,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Pauridia glabella (R.Br.) Snijman & Kocyan var. glabella,https://id.biodiversity.org.au/node/apni/7455351,https://id.biodiversity.org.au/taxon/apni/51437983,https://id.biodiversity.org.au/name/apni/244102,Pauridia glabella var. glabella,https://id.biodiversity.org.au/name/apni/81442,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/7455341,https://id.biodiversity.org.au/taxon/apni/51437984,Pauridia glabella var. glabella,Pauridia glabella,native +Phlegmatospermum cochlearinum,Phlegmatospermum cochlearinum,Phlegmatospermum cochlearinum,NA,Phlegmatospermum,Brassicaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic",Phlegmatospermum cochlearinum (F.Muell.) O.E.Schulz,https://id.biodiversity.org.au/node/apni/2915554,https://id.biodiversity.org.au/node/apni/2897988,https://id.biodiversity.org.au/name/apni/81861,Phlegmatospermum cochlearinum,https://id.biodiversity.org.au/name/apni/81861,accepted,https://id.biodiversity.org.au/node/apni/2915554,https://id.biodiversity.org.au/taxon/apni/51612687,NA,Phlegmatospermum cochlearinum,native +Phyla nodiflora,Phyla nodiflora,Phyla nodiflora,NA,Phyla,Verbenaceae,species,APC,accepted,Magnoliidae,"WA (native and naturalised), CoI (naturalised), NT, Qld, NSW (naturalised)",Phyla nodiflora (L.) Greene,https://id.biodiversity.org.au/node/apni/2907374,https://id.biodiversity.org.au/node/apni/2892182,https://id.biodiversity.org.au/name/apni/74617,Phyla nodiflora,https://id.biodiversity.org.au/name/apni/74617,accepted,https://id.biodiversity.org.au/node/apni/2907374,https://id.biodiversity.org.au/taxon/apni/51448662,NA,Phyla nodiflora,native and naturalised +Picris barbarorum,Picris barbarorum,Picris barbarorum,NA,Picris,Asteraceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic (presumed extinct)",Picris barbarorum Lindl.,https://id.biodiversity.org.au/node/apni/2916052,https://id.biodiversity.org.au/node/apni/7890078,https://id.biodiversity.org.au/name/apni/110349,Picris barbarorum,https://id.biodiversity.org.au/name/apni/110349,accepted,https://id.biodiversity.org.au/node/apni/2916052,https://id.biodiversity.org.au/taxon/apni/51695393,NA,Picris barbarorum,native +Pimelea ligustrina subsp. ligustrina,Pimelea ligustrina subsp. ligustrina,Pimelea ligustrina subsp. ligustrina,NA,Pimelea,Thymelaeaceae,subspecies,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Pimelea ligustrina Labill. subsp. ligustrina,https://id.biodiversity.org.au/node/apni/2889686,https://id.biodiversity.org.au/taxon/apni/51449000,https://id.biodiversity.org.au/name/apni/69062,Pimelea ligustrina subsp. ligustrina,https://id.biodiversity.org.au/name/apni/69062,accepted,https://id.biodiversity.org.au/node/apni/2889686,https://id.biodiversity.org.au/taxon/apni/51449001,Pimelea ligustrina subsp. ligustrina,Pimelea ligustrina,native +Pinus pinea,Pinus pinea,Pinus pinea,NA,Pinus,Pinaceae,species,APC,accepted,Pinidae,"WA (naturalised), NSW (naturalised), Vic (naturalised)",Pinus pinea L.,https://id.biodiversity.org.au/node/apni/2904478,https://id.biodiversity.org.au/node/apni/2902806,https://id.biodiversity.org.au/name/apni/171468,Pinus pinea,https://id.biodiversity.org.au/name/apni/171468,accepted,https://id.biodiversity.org.au/node/apni/2904478,https://id.biodiversity.org.au/node/apni/7742574,NA,Pinus pinea,naturalised +Pisum sativum var. arvense,Pisum sativum var. arvense,Pisum sativum var. arvense,NA,Pisum,Fabaceae,variety,APC,accepted,Magnoliidae,NSW (naturalised),Pisum sativum var. arvense (L.) Poir.,https://id.biodiversity.org.au/node/apni/2920606,https://id.biodiversity.org.au/node/apni/2898529,https://id.biodiversity.org.au/name/apni/153418,Pisum sativum var. arvense,https://id.biodiversity.org.au/name/apni/153418,accepted,https://id.biodiversity.org.au/node/apni/2920606,https://id.biodiversity.org.au/taxon/apni/51702961,Pisum sativum var. arvense,Pisum sativum,naturalised +Pittosporum erioloma,Pittosporum erioloma,Pittosporum erioloma,NA,Pittosporum,Pittosporaceae,species,APC,accepted,Magnoliidae,LHI,Pittosporum erioloma C.Moore & F.Muell.,https://id.biodiversity.org.au/node/apni/2891204,https://id.biodiversity.org.au/taxon/apni/51442349,https://id.biodiversity.org.au/name/apni/99523,Pittosporum erioloma,https://id.biodiversity.org.au/name/apni/99523,accepted,https://id.biodiversity.org.au/node/apni/2891204,https://id.biodiversity.org.au/taxon/apni/51442315,NA,Pittosporum erioloma,native +Pittosporum rubiginosum,Pittosporum rubiginosum,Pittosporum rubiginosum,NA,Pittosporum,Pittosporaceae,species,APC,accepted,Magnoliidae,Qld,Pittosporum rubiginosum A.Cunn.,https://id.biodiversity.org.au/node/apni/2887772,https://id.biodiversity.org.au/taxon/apni/51442349,https://id.biodiversity.org.au/name/apni/100119,Pittosporum rubiginosum,https://id.biodiversity.org.au/name/apni/100119,accepted,https://id.biodiversity.org.au/node/apni/2887772,https://id.biodiversity.org.au/taxon/apni/51442315,NA,Pittosporum rubiginosum,native +Plantago turrifera,Plantago turrifera,Plantago turrifera,NA,Plantago,Plantaginaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW (native and naturalised), Vic","Plantago turrifera B.G.Briggs, Carolin & Pulley",https://id.biodiversity.org.au/node/apni/2895983,https://id.biodiversity.org.au/node/apni/7745425,https://id.biodiversity.org.au/name/apni/79077,Plantago turrifera,https://id.biodiversity.org.au/name/apni/79077,accepted,https://id.biodiversity.org.au/node/apni/2895983,https://id.biodiversity.org.au/taxon/apni/51699383,NA,Plantago turrifera,native and naturalised +Haplostichanthus sp Coop. Ck,Haplostichanthus submontanus,Polyalthia submontana,NA,Polyalthia,Annonaceae,species,APC,accepted,Magnoliidae,Qld,Polyalthia submontana (Jessup) B.Xue & R.M.K.Saunders,https://id.biodiversity.org.au/taxon/apni/51613975,https://id.biodiversity.org.au/taxon/apni/51613976,https://id.biodiversity.org.au/name/apni/246294,Polyalthia submontana,https://id.biodiversity.org.au/name/apni/191525,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/51430810,https://id.biodiversity.org.au/taxon/apni/51613977,NA,Polyalthia submontana,native +Polycarpon tetraphyllum,Polycarpon tetraphyllum,Polycarpon tetraphyllum,NA,Polycarpon,Caryophyllaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Polycarpon tetraphyllum (L.) L.,https://id.biodiversity.org.au/taxon/apni/51270276,https://id.biodiversity.org.au/taxon/apni/51270277,https://id.biodiversity.org.au/name/apni/107982,Polycarpon tetraphyllum,https://id.biodiversity.org.au/name/apni/107982,accepted,https://id.biodiversity.org.au/taxon/apni/51270276,https://id.biodiversity.org.au/taxon/apni/51432987,NA,Polycarpon tetraphyllum,naturalised +Polyscias australiana,Polyscias australiana,Polyscias australiana,NA,Polyscias,Araliaceae,species,APC,accepted,Magnoliidae,"NT, Qld",Polyscias australiana (F.Muell.) Philipson,https://id.biodiversity.org.au/node/apni/7223338,https://id.biodiversity.org.au/taxon/apni/51292784,https://id.biodiversity.org.au/name/apni/84802,Polyscias australiana,https://id.biodiversity.org.au/name/apni/84787,taxonomic synonym,https://id.biodiversity.org.au/instance/apni/941828,https://id.biodiversity.org.au/taxon/apni/51632289,NA,Polyscias australiana,native +Potamogeton australiensis,Potamogeton australiensis,Potamogeton australiensis,NA,Potamogeton,Potamogetonaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Potamogeton australiensis A.Benn.,https://id.biodiversity.org.au/node/apni/7808489,https://id.biodiversity.org.au/node/apni/8770682,https://id.biodiversity.org.au/name/apni/65827,Potamogeton australiensis,https://id.biodiversity.org.au/name/apni/65827,accepted,https://id.biodiversity.org.au/node/apni/7808489,https://id.biodiversity.org.au/taxon/apni/51353530,NA,Potamogeton australiensis,native +Psoralea pinnata,Psoralea pinnata,Psoralea pinnata,NA,Psoralea,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised), Tas (naturalised)",Psoralea pinnata L.,https://id.biodiversity.org.au/node/apni/2887023,https://id.biodiversity.org.au/node/apni/8771698,https://id.biodiversity.org.au/name/apni/88820,Psoralea pinnata,https://id.biodiversity.org.au/name/apni/88820,accepted,https://id.biodiversity.org.au/node/apni/2887023,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Psoralea pinnata,naturalised +Psychotria dallachiana,Psychotria dallachiana,Psychotria dallachiana,NA,Psychotria,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Psychotria dallachiana Benth.,https://id.biodiversity.org.au/node/apni/2890013,https://id.biodiversity.org.au/taxon/apni/51446698,https://id.biodiversity.org.au/name/apni/89074,Psychotria dallachiana,https://id.biodiversity.org.au/name/apni/89074,accepted,https://id.biodiversity.org.au/node/apni/2890013,https://id.biodiversity.org.au/taxon/apni/51446612,NA,Psychotria dallachiana,native +Psychotria sp Utchee Creek,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),Psychotria sp. Utchee Creek (H.Flecker NQNC5313),NA,Psychotria,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Psychotria sp. Utchee Creek (H.Flecker NQNC5313) Qld Herbarium,https://id.biodiversity.org.au/taxon/apni/51446727,https://id.biodiversity.org.au/taxon/apni/51446698,https://id.biodiversity.org.au/name/apni/218829,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),https://id.biodiversity.org.au/name/apni/218829,accepted,https://id.biodiversity.org.au/taxon/apni/51446727,https://id.biodiversity.org.au/taxon/apni/51446612,NA,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),native +Pultenaea ferruginea,Pultenaea ferruginea,Pultenaea ferruginea,NA,Pultenaea,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Pultenaea ferruginea Rudge,https://id.biodiversity.org.au/node/apni/2906803,https://id.biodiversity.org.au/taxon/apni/51436286,https://id.biodiversity.org.au/name/apni/59158,Pultenaea ferruginea,https://id.biodiversity.org.au/name/apni/59158,accepted,https://id.biodiversity.org.au/node/apni/2906803,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Pultenaea ferruginea,native +Rhodamnia argentea,Rhodamnia argentea,Rhodamnia argentea,NA,Rhodamnia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Rhodamnia argentea Benth.,https://id.biodiversity.org.au/node/apni/2919069,https://id.biodiversity.org.au/taxon/apni/51440311,https://id.biodiversity.org.au/name/apni/68532,Rhodamnia argentea,https://id.biodiversity.org.au/name/apni/68532,accepted,https://id.biodiversity.org.au/node/apni/2919069,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Rhodamnia argentea,native +Rhodomyrtus trineura,Rhodomyrtus trineura,Rhodomyrtus trineura,NA,Rhodomyrtus,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Rhodomyrtus trineura (F.Muell.) Benth.,https://id.biodiversity.org.au/taxon/apni/51441176,https://id.biodiversity.org.au/taxon/apni/51441177,https://id.biodiversity.org.au/name/apni/69289,Rhodomyrtus trineura,https://id.biodiversity.org.au/name/apni/69289,accepted,https://id.biodiversity.org.au/taxon/apni/51441176,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Rhodomyrtus trineura,native +Rockinghamia angustifolia,Rockinghamia angustifolia,Rockinghamia angustifolia,NA,Rockinghamia,Euphorbiaceae,species,APC,accepted,Magnoliidae,Qld,Rockinghamia angustifolia (Benth.) Airy Shaw,https://id.biodiversity.org.au/node/apni/2921179,https://id.biodiversity.org.au/node/apni/2892697,https://id.biodiversity.org.au/name/apni/61487,Rockinghamia angustifolia,https://id.biodiversity.org.au/name/apni/61487,accepted,https://id.biodiversity.org.au/node/apni/2921179,https://id.biodiversity.org.au/taxon/apni/51442249,NA,Rockinghamia angustifolia,native +Rorippa gigantea,Rorippa gigantea,Rorippa gigantea,NA,Rorippa,Brassicaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Rorippa gigantea (Hook.) Garn.-Jones,https://id.biodiversity.org.au/node/apni/2920330,https://id.biodiversity.org.au/node/apni/8442201,https://id.biodiversity.org.au/name/apni/75950,Rorippa gigantea,https://id.biodiversity.org.au/name/apni/75950,accepted,https://id.biodiversity.org.au/node/apni/2920330,https://id.biodiversity.org.au/taxon/apni/51612687,NA,Rorippa gigantea,native +Rubus parvifolius,Rubus parvifolius,Rubus parvifolius,NA,Rubus,Rosaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Rubus parvifolius L.,https://id.biodiversity.org.au/node/apni/2901867,https://id.biodiversity.org.au/taxon/apni/51446575,https://id.biodiversity.org.au/name/apni/85986,Rubus parvifolius,https://id.biodiversity.org.au/name/apni/85986,accepted,https://id.biodiversity.org.au/node/apni/2901867,https://id.biodiversity.org.au/taxon/apni/51446278,NA,Rubus parvifolius,native +Salix alba,Salix alba,Salix alba , NA,Salix,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised)",Salix alba L.,https://id.biodiversity.org.au/node/apni/2896377,https://id.biodiversity.org.au/node/apni/8905801,https://id.biodiversity.org.au/name/apni/59687,Salix alba [alternative possible names: NA],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51436847,NA,Salix alba,naturalised +Quassia baileyana,Quassia baileyana,Samadera baileyana,NA,Samadera,Simaroubaceae,species,APC,accepted,Magnoliidae,Qld,Samadera baileyana Oliv.,https://id.biodiversity.org.au/node/apni/2891526,https://id.biodiversity.org.au/node/apni/2900441,https://id.biodiversity.org.au/name/apni/60763,Samadera baileyana,https://id.biodiversity.org.au/name/apni/70084,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/897542,https://id.biodiversity.org.au/taxon/apni/51316490,NA,Samadera baileyana,native +Schenkia australis,Schenkia australis,Schenkia australis,NA,Schenkia,Gentianaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic, Tas",Schenkia australis (R.Br.) G.Mans.,https://id.biodiversity.org.au/taxon/apni/51436897,https://id.biodiversity.org.au/taxon/apni/51436898,https://id.biodiversity.org.au/name/apni/200895,Schenkia australis,https://id.biodiversity.org.au/name/apni/200895,accepted,https://id.biodiversity.org.au/taxon/apni/51436897,https://id.biodiversity.org.au/taxon/apni/51436871,NA,Schenkia australis,native +Schoenus apogon,Schoenus apogon,Schoenus apogon,NA,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Schoenus apogon Roem. & Schult.,https://id.biodiversity.org.au/node/apni/2908439,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/109452,Schoenus apogon,https://id.biodiversity.org.au/name/apni/109452,accepted,https://id.biodiversity.org.au/node/apni/2908439,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Schoenus apogon,native +Schoenus brevifolius,Schoenus brevifolius,Schoenus brevifolius,NA,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic, Tas",Schoenus brevifolius R.Br.,https://id.biodiversity.org.au/node/apni/2904000,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/109778,Schoenus brevifolius,https://id.biodiversity.org.au/name/apni/109778,accepted,https://id.biodiversity.org.au/node/apni/2904000,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Schoenus brevifolius,native +Schoenus lepidosperma,Schoenus lepidosperma,Schoenus lepidosperma,NA,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Schoenus lepidosperma (F.Muell.) K.L.Wilson,https://id.biodiversity.org.au/node/apni/2893030,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/141376,Schoenus lepidosperma,https://id.biodiversity.org.au/name/apni/243667,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/947513,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Schoenus lepidosperma,native +Schoenus vaginatus,Schoenus vaginatus,Schoenus vaginatus,NA,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Schoenus vaginatus F.Muell. ex Benth.,https://id.biodiversity.org.au/node/apni/2896591,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/113246,Schoenus vaginatus,https://id.biodiversity.org.au/name/apni/113246,accepted,https://id.biodiversity.org.au/node/apni/2896591,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Schoenus vaginatus,native +Scleria rugosa,Scleria rugosa,Scleria rugosa,NA,Scleria,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Scleria rugosa R.Br.,https://id.biodiversity.org.au/node/apni/2892143,https://id.biodiversity.org.au/taxon/apni/51434752,https://id.biodiversity.org.au/name/apni/64346,Scleria rugosa,https://id.biodiversity.org.au/name/apni/64346,accepted,https://id.biodiversity.org.au/node/apni/2892143,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Scleria rugosa,native +Senecio longipilus,Senecio longipilus,Senecio longipilus,NA,Senecio,Asteraceae,species,APC,accepted,Magnoliidae,"NSW, Tas",Senecio longipilus I.Thomps.,https://id.biodiversity.org.au/node/apni/2907653,https://id.biodiversity.org.au/taxon/apni/51614245,https://id.biodiversity.org.au/name/apni/189666,Senecio longipilus,https://id.biodiversity.org.au/name/apni/189666,accepted,https://id.biodiversity.org.au/node/apni/2907653,https://id.biodiversity.org.au/taxon/apni/51695393,NA,Senecio longipilus,native +Sida goniocarpa,Sida goniocarpa,Sida goniocarpa,NA,Sida,Malvaceae,species,APC,accepted,Magnoliidae,"NT, SA, Qld, NSW",Sida goniocarpa (Benth.) Domin,https://id.biodiversity.org.au/node/apni/2893354,https://id.biodiversity.org.au/taxon/apni/51439283,https://id.biodiversity.org.au/name/apni/73352,Sida goniocarpa,https://id.biodiversity.org.au/name/apni/73352,accepted,https://id.biodiversity.org.au/node/apni/2893354,https://id.biodiversity.org.au/taxon/apni/51439248,NA,Sida goniocarpa,native +Sigesbeckia orientalis,Sigesbeckia orientalis,Sigesbeckia orientalis,NA,Sigesbeckia,Asteraceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT, SA, Qld, NSW, NI (naturalised), ACT, Vic, Tas (doubtfully naturalised)",Sigesbeckia orientalis L.,https://id.biodiversity.org.au/node/apni/2920819,https://id.biodiversity.org.au/taxon/apni/51432306,https://id.biodiversity.org.au/name/apni/75539,Sigesbeckia orientalis,https://id.biodiversity.org.au/name/apni/75539,accepted,https://id.biodiversity.org.au/node/apni/2920819,https://id.biodiversity.org.au/taxon/apni/51695393,NA,Sigesbeckia orientalis,native and naturalised +Sisymbrium irio,Sisymbrium irio,Sisymbrium irio,NA,Sisymbrium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Sisymbrium irio L.,https://id.biodiversity.org.au/node/apni/2887936,https://id.biodiversity.org.au/node/apni/2921080,https://id.biodiversity.org.au/name/apni/78148,Sisymbrium irio,https://id.biodiversity.org.au/name/apni/78148,accepted,https://id.biodiversity.org.au/node/apni/2887936,https://id.biodiversity.org.au/taxon/apni/51612687,NA,Sisymbrium irio,naturalised +Derris involuta,Derris involuta,Solori involuta,NA,Solori,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Solori involuta (Sprague) Sirich. & Adema,https://id.biodiversity.org.au/taxon/apni/51311103,https://id.biodiversity.org.au/taxon/apni/51311094,https://id.biodiversity.org.au/name/apni/4447863,Solori involuta,https://id.biodiversity.org.au/name/apni/87525,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/51311098,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Solori involuta,native +Sparaxis bulbifera,Sparaxis bulbifera,Sparaxis bulbifera,NA,Sparaxis,Iridaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised), Tas (naturalised)",Sparaxis bulbifera (L.) Ker Gawl.,https://id.biodiversity.org.au/node/apni/2894715,https://id.biodiversity.org.au/taxon/apni/51438097,https://id.biodiversity.org.au/name/apni/68699,Sparaxis bulbifera,https://id.biodiversity.org.au/name/apni/68699,accepted,https://id.biodiversity.org.au/node/apni/2894715,https://id.biodiversity.org.au/taxon/apni/51438006,NA,Sparaxis bulbifera,naturalised +Spergularia diandra,Spergularia diandra,Spergularia diandra,NA,Spergularia,Caryophyllaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised)",Spergularia diandra (Guss.) Heldr.,https://id.biodiversity.org.au/node/apni/2886696,https://id.biodiversity.org.au/taxon/apni/51295406,https://id.biodiversity.org.au/name/apni/83464,Spergularia diandra,https://id.biodiversity.org.au/name/apni/83464,accepted,https://id.biodiversity.org.au/node/apni/2886696,https://id.biodiversity.org.au/taxon/apni/51432987,NA,Spergularia diandra,naturalised +Sphaeromorphaea littoralis,Sphaeromorphaea littoralis,Sphaeromorphaea littoralis,NA,Sphaeromorphaea,Asteraceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Sphaeromorphaea littoralis (Retz.) A.R.Bean,https://id.biodiversity.org.au/node/apni/7069871,https://id.biodiversity.org.au/node/apni/7071683,https://id.biodiversity.org.au/name/apni/246779,Sphaeromorphaea littoralis,https://id.biodiversity.org.au/name/apni/246779,accepted,https://id.biodiversity.org.au/node/apni/7069871,https://id.biodiversity.org.au/taxon/apni/51695393,NA,Sphaeromorphaea littoralis,native +Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia subsp. angustifolia,NA,Stellaria,Caryophyllaceae,subspecies,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Stellaria angustifolia Hook. subsp. angustifolia,https://id.biodiversity.org.au/node/apni/2890520,https://id.biodiversity.org.au/taxon/apni/51433015,https://id.biodiversity.org.au/name/apni/240421,Stellaria angustifolia subsp. angustifolia,https://id.biodiversity.org.au/name/apni/240421,accepted,https://id.biodiversity.org.au/node/apni/2890520,https://id.biodiversity.org.au/taxon/apni/51432987,Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia,native +Styphelia viridis,Styphelia viridis,Styphelia viridis,NA,Styphelia,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Styphelia viridis Andrews,https://id.biodiversity.org.au/node/apni/2912747,https://id.biodiversity.org.au/taxon/apni/51435346,https://id.biodiversity.org.au/name/apni/109318,Styphelia viridis,https://id.biodiversity.org.au/name/apni/109318,accepted,https://id.biodiversity.org.au/node/apni/2912747,https://id.biodiversity.org.au/taxon/apni/51436079,NA,Styphelia viridis,native +Swainsona cadellii,Swainsona cadellii,Swainsona cadellii,NA,Swainsona,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Swainsona cadellii F.Muell. ex C.Moore,https://id.biodiversity.org.au/node/apni/2904099,https://id.biodiversity.org.au/taxon/apni/51436313,https://id.biodiversity.org.au/name/apni/76870,Swainsona cadellii,https://id.biodiversity.org.au/name/apni/76870,accepted,https://id.biodiversity.org.au/node/apni/2904099,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Swainsona cadellii,native +Acmena graveolens,Acmena graveolens,Syzygium graveolens,NA,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium graveolens (F.M.Bailey) Craven & Biffin,https://id.biodiversity.org.au/node/apni/2920364,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/202985,Syzygium graveolens,https://id.biodiversity.org.au/name/apni/73535,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/891710,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Syzygium graveolens,native +Syzygium gustavioides,Syzygium gustavioides,Syzygium gustavioides,NA,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium gustavioides (F.M.Bailey) B.Hyland,https://id.biodiversity.org.au/taxon/apni/51429676,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/64722,Syzygium gustavioides,https://id.biodiversity.org.au/name/apni/64722,accepted,https://id.biodiversity.org.au/taxon/apni/51429676,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Syzygium gustavioides,native +Syzygium sayeri,Syzygium sayeri,Syzygium sayeri,NA,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium sayeri (F.Muell.) B.Hyland,https://id.biodiversity.org.au/node/apni/2888968,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/64837,Syzygium sayeri,https://id.biodiversity.org.au/name/apni/64837,accepted,https://id.biodiversity.org.au/node/apni/2888968,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Syzygium sayeri,native +Teucrium puberulum,Teucrium puberulum,Teucrium puberulum,NA,Teucrium,Lamiaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Teucrium puberulum (F.Muell.) Kattari & Bräuchler,https://id.biodiversity.org.au/taxon/apni/51288087,https://id.biodiversity.org.au/taxon/apni/51438311,https://id.biodiversity.org.au/name/apni/7660439,Teucrium puberulum,https://id.biodiversity.org.au/name/apni/7660439,accepted,https://id.biodiversity.org.au/taxon/apni/51288087,https://id.biodiversity.org.au/taxon/apni/51696573,NA,Teucrium puberulum,native +Thelymitra kangaloonica,Thelymitra kangaloonica,Thelymitra kangaloonica,NA,Thelymitra,Orchidaceae,species,APC,accepted,Magnoliidae,NSW,Thelymitra kangaloonica Jeanes,https://id.biodiversity.org.au/taxon/apni/51414328,https://id.biodiversity.org.au/taxon/apni/51631246,https://id.biodiversity.org.au/name/apni/233692,Thelymitra kangaloonica,https://id.biodiversity.org.au/name/apni/233692,accepted,https://id.biodiversity.org.au/taxon/apni/51414328,https://id.biodiversity.org.au/taxon/apni/51697009,NA,Thelymitra kangaloonica,native +Thesium australe,Thesium australe,Thesium australe,NA,Thesium,Santalaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic, Tas (presumed extinct)",Thesium australe R.Br.,https://id.biodiversity.org.au/node/apni/2891975,https://id.biodiversity.org.au/node/apni/2913858,https://id.biodiversity.org.au/name/apni/56224,Thesium australe,https://id.biodiversity.org.au/name/apni/56224,accepted,https://id.biodiversity.org.au/node/apni/2891975,https://id.biodiversity.org.au/taxon/apni/51447154,NA,Thesium australe,native +Trema aspera,Trema aspera,Trema tomentosa var. aspera,NA,Trema,Cannabaceae,variety,APC,accepted,Magnoliidae,"WA, Qld, NSW, Vic (presumed extinct)",Trema tomentosa var. aspera (Brongn.) Hewson,https://id.biodiversity.org.au/node/apni/2917190,https://id.biodiversity.org.au/node/apni/2913617,https://id.biodiversity.org.au/name/apni/206199,Trema tomentosa var. aspera,https://id.biodiversity.org.au/name/apni/101838,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/856997,https://id.biodiversity.org.au/taxon/apni/51269919,Trema tomentosa var. aspera,Trema tomentosa,native +Trifolium dubium,Trifolium dubium,Trifolium dubium,NA,Trifolium,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Trifolium dubium Sibth.,https://id.biodiversity.org.au/taxon/apni/51436351,https://id.biodiversity.org.au/taxon/apni/51436341,https://id.biodiversity.org.au/name/apni/115704,Trifolium dubium,https://id.biodiversity.org.au/name/apni/115704,accepted,https://id.biodiversity.org.au/taxon/apni/51436351,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Trifolium dubium,naturalised +Veronica catenata,Veronica catenata,Veronica catenata,NA,Veronica,Plantaginaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), Vic (naturalised)",Veronica catenata Pennell,https://id.biodiversity.org.au/node/apni/2897164,https://id.biodiversity.org.au/taxon/apni/51632390,https://id.biodiversity.org.au/name/apni/67965,Veronica catenata,https://id.biodiversity.org.au/name/apni/67965,accepted,https://id.biodiversity.org.au/node/apni/2897164,https://id.biodiversity.org.au/taxon/apni/51699383,NA,Veronica catenata,naturalised +Veronica derwentiana,Veronica derwentiana,Veronica derwentiana,NA,Veronica,Plantaginaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Veronica derwentiana Andrews,https://id.biodiversity.org.au/node/apni/2917078,https://id.biodiversity.org.au/taxon/apni/51632390,https://id.biodiversity.org.au/name/apni/68107,Veronica derwentiana,https://id.biodiversity.org.au/name/apni/68107,accepted,https://id.biodiversity.org.au/node/apni/2917078,https://id.biodiversity.org.au/taxon/apni/51699383,NA,Veronica derwentiana,native +Wahlenbergia luteola,Wahlenbergia luteola,Wahlenbergia luteola,NA,Wahlenbergia,Campanulaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic",Wahlenbergia luteola P.J.Sm.,https://id.biodiversity.org.au/node/apni/2916523,https://id.biodiversity.org.au/taxon/apni/51432869,https://id.biodiversity.org.au/name/apni/73194,Wahlenbergia luteola,https://id.biodiversity.org.au/name/apni/73194,accepted,https://id.biodiversity.org.au/node/apni/2916523,https://id.biodiversity.org.au/taxon/apni/51432853,NA,Wahlenbergia luteola,native diff --git a/tests/testthat/examples/Test_2023_1/data.csv b/tests/testthat/examples/Test_2023_1/data.csv index cb3913b8..bd88c4f6 100644 --- a/tests/testthat/examples/Test_2023_1/data.csv +++ b/tests/testthat/examples/Test_2023_1/data.csv @@ -35,8 +35,8 @@ Rhodomyrtus trineura,rhotri,Atherton,0.129,0.0111,3401,0.763,0.34,,4321,3803,608 Acmena graveolens,acmgra,Cape Tribulation,0.151,0.0155,5246,0.599,0.67,,,3057,2667,7156,,,,,male,,,,,1,10,4,cm,,,,,,,, Aleurites rockinghamensis,aleroc,Cape Tribulation,0.113,0.0184,73984,0.28,0.02,7077,,4194,,6209,,,summer,,male,,,,,1,2,4,cm,,,,,,,, Alstonia scholaris,alssch,Cape Tribulation,0.107,0.0223,6182,0.361,0.46,1.53,,1854,1682,3932,,,not observed,herbs,male,,,,,1,2,4,cm,,,,,,,, -Argyrodendron peralatum,argper,Cape Tribulation,0.244,0.0119,3201,0.726,0.71,433,,3832,1689,6718,,,,,male,,control,,,1,,4,cm,,,,,,,, -Atractocarpus hirtus,atrhir,Cape Tribulation,0.072,0.0157,11374,0.804,0.28,,,7143,6727,6103,,,,tree,male,,control,,,2,,4,cm,,,,,,,, +Argyrodendron peralatum,argper,Cape Tribulation,0.244,0.0119,3201,0.726,0.71,433,,3832,1689,6718,,,test excluded observation,,male,,control,,,1,,4,cm,,,,,,,, +Atractocarpus hirtus,atrhir,Cape Tribulation,0.072,0.0157,11374,0.804,0.28,,,7143,6727,6103,,,test excluded observation 2,tree,male,,control,,,2,,4,cm,,,,,,,, Brombya platynema,bropla,Cape Tribulation,0.106,0.0188,8218,0.603,0.33,,,4261,3531,5377,,,,tree,male,,high nutrient,,,,,4,cm,,,,,,,, Cardwellia sublimis,carsub,Cape Tribulation,0.127,0.0128,4352,0.603,0.56,582.3,,6315,4880,8282,,,,tree,male,,high nutrient,,,,,4,cm,,,,,,,, Castanospermum australe,casaus,Cape Tribulation,0.117,0.0237,2765,0.587,0.37,14851,,7329,,8869,,,,unknown,female,,low nutrient,,,2,5,4,cm,,,,,,,, @@ -45,7 +45,7 @@ Cryptocarya laevigata,crylae,Cape Tribulation,0.087,0.0156,2682,0.64,0.65,1281,1 Cryptocarya mackinnoniana,crymac,Cape Tribulation,0.204,0.0152,10458,0.655,0.61,204,,3277,2325,8657,,,,,,,,,,,5,40,mm,,,,,,,, Cryptocarya murrayi,crymur,Cape Tribulation,0.155,0.0167,9960,0.674,0.39,,2693,5543,4298,5451,,,,,,,,,,,,40,mm,,,,,,,, Dendrocnide moroides,denmor,Cape Tribulation,0.052,0.0312,26454,0.23,0.46,0.71,,2372,,2090,,,,,,,,,,,,40,mm,,,,,,,, -Elaeocarpus grandis,elaang,Cape Tribulation,0.122,0.0187,2762,0.499,0.47,3699,,2598,1748,4635,,,,,,,,,,,,40,mm,,,,,,,, +Elaeocarpus grandis,elaang,test_excluded_site,0.122,0.0187,2762,0.499,0.47,3699,,2598,1748,4635,,,,,,,,,,,,40,mm,,,,,,,, Endiandra leptodendron,endlep,Cape Tribulation,0.106,0.018,3987,0.611,0.68,,1492,2412,2783,7477,,,,,,,,,,,,40,mm,,,,,,,, Endiandra microneura,endmic,Cape Tribulation,0.151,0.0177,3377,0.623,0.61,,3573,6344,3354,6235,,,,,,,,,,,,40,mm,,,,,,,, Gillbeea adenopetala,gilade,Cape Tribulation,0.126,0.0096,3678,0.43,0.46,15,,2863,3160,6549,,,,,,,,,,,,40,mm,,,,,,,, diff --git a/tests/testthat/examples/Test_2023_1/metadata.yml b/tests/testthat/examples/Test_2023_1/metadata.yml index 2f564f99..688c31a1 100644 --- a/tests/testthat/examples/Test_2023_1/metadata.yml +++ b/tests/testthat/examples/Test_2023_1/metadata.yml @@ -31,6 +31,7 @@ dataset: mutate(across(`wood density (mg mm-3)`, as.character)) %>% mutate( wrong_trait_name = "test", + wrong_trait_name = ifelse(Species == "Trema aspera", "test excluded observation", wrong_trait_name), wood_density_dupe = `wood density (mg mm-3)`, no_unit_conversion = 2, LASA50_dupe = LASA50, @@ -71,6 +72,10 @@ locations: latitude (deg): .na longitude (deg): .na rainfall (mm): 3500 + test_excluded_site: + description: test excluded site + latitude (deg): .na + longitude (deg): .na contexts: - context_property: plant sex category: entity_context @@ -551,5 +556,14 @@ taxonomic_updates: exclude_observations: - variable: taxon_name find: Syzygium gustavioides - reason: Test exclusion + reason: Test taxon_name exclusion +- variable: location_name + find: test_excluded_site + reason: Test location_name +- variable: flowering_time + find: test excluded observation + reason: Test trait_name exclusion +- variable: flowering_time + find: test excluded observation 2 + reason: Test trait_name exclusion 2 questions: .na diff --git a/tests/testthat/examples/Test_2023_1/output/excluded_data.csv b/tests/testthat/examples/Test_2023_1/output/excluded_data.csv index 99e3217e..61e393ca 100644 --- a/tests/testthat/examples/Test_2023_1/output/excluded_data.csv +++ b/tests/testthat/examples/Test_2023_1/output/excluded_data.csv @@ -56,9 +56,11 @@ Missing unit conversion,Test_2023_1,Alstonia scholaris,042,seed_dry_mass,2,mass, Missing unit conversion,Test_2023_1,Alstonia scholaris,042,seed_dry_mass,2,mass,species,mean,measurement,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,03,,Alstonia scholaris Trait name not in trait dictionary,Test_2023_1,Alstonia scholaris,042,wrong_trait_name,test,,species,mode,expert_score,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,01,,Alstonia scholaris Trait name not in trait dictionary,Test_2023_1,Alstonia scholaris,042,wrong_trait_name,test,,species,mode,expert_score,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,01,,Alstonia scholaris +Observation excluded in metadata,Test_2023_1,Argyrodendron peralatum,045,flowering_time,test excluded observation,,individual,mode,expert_score,3,field,adult,10,01,,,,02,12,,01,,from Falster_2005_1,01,,Argyrodendron peralatum Missing unit conversion,Test_2023_1,Argyrodendron peralatum,047,seed_dry_mass,2,mass,species,mean,measurement,3,field,adult,,,,,,,12,,01,2004/2004,from Falster_2005_1,03,,Argyrodendron peralatum Missing unit conversion,Test_2023_1,Argyrodendron peralatum,047,wood_density,0.726,,species,mean,measurement,3,field,adult,,,,,,,12,,01,2004/2004,from Falster_2005_1,02,,Argyrodendron peralatum Trait name not in trait dictionary,Test_2023_1,Argyrodendron peralatum,047,wrong_trait_name,test,,species,mode,expert_score,3,field,adult,,,,,,,12,,01,2004/2004,from Falster_2005_1,01,,Argyrodendron peralatum +Observation excluded in metadata,Test_2023_1,Atractocarpus hirtus,050,flowering_time,test excluded observation 2,,individual,mode,expert_score,3,field,adult,10,01,,,,02,13,,01,,from Falster_2005_1,01,,Atractocarpus hirtus Missing unit conversion,Test_2023_1,Atractocarpus hirtus,052,seed_dry_mass,2,mass,species,mean,measurement,3,field,adult,,,,,,,13,,01,2004/2004,from Falster_2005_1,03,,Atractocarpus hirtus Missing unit conversion,Test_2023_1,Atractocarpus hirtus,052,wood_density,0.804,,species,mean,measurement,3,field,adult,,,,,,,13,,01,2004/2004,from Falster_2005_1,02,,Atractocarpus hirtus Trait name not in trait dictionary,Test_2023_1,Atractocarpus hirtus,052,wrong_trait_name,test,,species,mode,expert_score,3,field,adult,,,,,,,13,,01,2004/2004,from Falster_2005_1,01,,Atractocarpus hirtus @@ -95,9 +97,20 @@ Trait name not in trait dictionary,Test_2023_1,Cryptocarya murrayi,089,wrong_tra Missing unit conversion,Test_2023_1,Dendrocnide moroides,094,seed_dry_mass,2,mass,species,mean,measurement,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,03,,Dendrocnide moroides Missing unit conversion,Test_2023_1,Dendrocnide moroides,094,wood_density,0.23,,species,mean,measurement,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,02,,Dendrocnide moroides Trait name not in trait dictionary,Test_2023_1,Dendrocnide moroides,094,wrong_trait_name,test,,species,mode,expert_score,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,01,,Dendrocnide moroides -Missing unit conversion,Test_2023_1,Elaeocarpus grandis,099,seed_dry_mass,2,mass,species,mean,measurement,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,03,,Elaeocarpus grandis -Missing unit conversion,Test_2023_1,Elaeocarpus grandis,099,wood_density,0.499,,species,mean,measurement,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,02,,Elaeocarpus grandis -Trait name not in trait dictionary,Test_2023_1,Elaeocarpus grandis,099,wrong_trait_name,test,,species,mode,expert_score,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,01,,Elaeocarpus grandis +Observation excluded in metadata,Test_2023_1,Elaeocarpus grandis,095,huber_value,4635,mm2{leaf}/mm2{sapwood},individual,mean,model_derived,5,field,adult,13,01,,,,03,,,,2002/2002,made-up measurement remarks,05,,Elaeocarpus grandis +Observation excluded in metadata,Test_2023_1,Elaeocarpus grandis,096,leaf_length,40,mm,individual,mean,measurement,3,field,adult,13,01,,,,03,,,,2004/2004,from Falster_2005_1,01,,Elaeocarpus grandis +Observation excluded in metadata,Test_2023_1,Elaeocarpus grandis,097,huber_value,4635,mm2{leaf}/mm2{sapwood},individual,raw,model_derived,5,field,adult,13,01,,,,03,,,,,made-up measurement remarks,04,01,Elaeocarpus grandis +Observation excluded in metadata,Test_2023_1,Elaeocarpus grandis,098,huber_value,2598,mm2{leaf}/mm2{sapwood},population,mean,measurement,3,field,adult,13,,,,,03,,,,2004/2004,from Falster_2005_1,02,02,Elaeocarpus grandis +Observation excluded in metadata,Test_2023_1,Elaeocarpus grandis,098,huber_value,1748,mm2{leaf}/mm2{sapwood},population,mean,measurement,3,field,adult,13,,,,,03,,,,2004/2004,from Falster_2005_1,03,03,Elaeocarpus grandis +Observation excluded in metadata,Test_2023_1,Elaeocarpus grandis,098,huber_value,1748,mm2{leaf}/mm2{sapwood},population,mean,measurement,3,field,adult,13,,,,,03,,,,2004/2004,from Falster_2005_1,03,,Elaeocarpus grandis +Observation excluded in metadata,Test_2023_1,Elaeocarpus grandis,098,leaf_N_per_dry_mass,0.0187,mg/mg,population,mean,measurement,3,field,adult,13,,,,,03,,,,2004/2004,from Falster_2005_1,01,,Elaeocarpus grandis +Observation excluded in metadata,Test_2023_1,Elaeocarpus grandis,098,leaf_area,2762,mm2,population,mean,measurement,3,field,adult,13,,,,,03,,,,2004/2004,from Falster_2005_1,01,,Elaeocarpus grandis +Observation excluded in metadata,Test_2023_1,Elaeocarpus grandis,098,leaf_mass_per_area,0.122,mg/mm2,population,mean,measurement,3,field,adult,13,,,,,03,,,,2004/2004,from Falster_2005_1,01,,Elaeocarpus grandis +Observation excluded in metadata,Test_2023_1,Elaeocarpus grandis,098,seed_dry_mass,3699,mg,population,mean,measurement,3,field,adult,13,,,,,03,,,,2004/2004,from Falster_2005_1,01,,Elaeocarpus grandis +Observation excluded in metadata,Test_2023_1,Elaeocarpus grandis,098,wood_density,0.499,mg/mm3,population,mean,measurement,3,field,adult,13,,,,,03,,,,2004/2004,from Falster_2005_1,01,,Elaeocarpus grandis +Observation excluded in metadata,Test_2023_1,Elaeocarpus grandis,099,seed_dry_mass,2,mass,species,mean,measurement,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,03,,Elaeocarpus grandis +Observation excluded in metadata,Test_2023_1,Elaeocarpus grandis,099,wood_density,0.499,,species,mean,measurement,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,02,,Elaeocarpus grandis +Observation excluded in metadata,Test_2023_1,Elaeocarpus grandis,099,wrong_trait_name,test,,species,mode,expert_score,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,01,,Elaeocarpus grandis Missing unit conversion,Test_2023_1,Endiandra leptodendron,104,seed_dry_mass,2,mass,species,mean,measurement,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,03,,Endiandra leptodendron Missing unit conversion,Test_2023_1,Endiandra leptodendron,104,wood_density,0.611,,species,mean,measurement,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,02,,Endiandra leptodendron Trait name not in trait dictionary,Test_2023_1,Endiandra leptodendron,104,wrong_trait_name,test,,species,mode,expert_score,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,01,,Endiandra leptodendron @@ -195,4 +208,4 @@ Missing unit conversion,Test_2023_1,Syzygium sayeri,234,wood_density,0.485,,spec Trait name not in trait dictionary,Test_2023_1,Syzygium sayeri,234,wrong_trait_name,test,,species,mode,expert_score,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,01,,Syzygium sayeri Missing unit conversion,Test_2023_1,Trema aspera,239,seed_dry_mass,2,mass,species,mean,measurement,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,03,,Trema aspera Missing unit conversion,Test_2023_1,Trema aspera,239,wood_density,0.357,,species,mean,measurement,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,02,,Trema aspera -Trait name not in trait dictionary,Test_2023_1,Trema aspera,239,wrong_trait_name,test,,species,mode,expert_score,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,01,,Trema aspera +Trait name not in trait dictionary,Test_2023_1,Trema aspera,239,wrong_trait_name,test excluded observation,,species,mode,expert_score,3,field,adult,,,,,,,,,,2004/2004,from Falster_2005_1,01,,Trema aspera diff --git a/tests/testthat/examples/Test_2023_1/output/locations.csv b/tests/testthat/examples/Test_2023_1/output/locations.csv index f9758d10..1a20c324 100644 --- a/tests/testthat/examples/Test_2023_1/output/locations.csv +++ b/tests/testthat/examples/Test_2023_1/output/locations.csv @@ -7,3 +7,6 @@ Test_2023_1,02,Cape Tribulation,latitude (deg), Test_2023_1,02,Cape Tribulation,longitude (deg), Test_2023_1,02,Cape Tribulation,elevation (m),25 Test_2023_1,02,Cape Tribulation,rainfall (mm),3500 +Test_2023_1,03,test_excluded_site,description,test excluded site +Test_2023_1,03,test_excluded_site,latitude (deg), +Test_2023_1,03,test_excluded_site,longitude (deg), diff --git a/tests/testthat/examples/Test_2023_1/output/metadata.yml b/tests/testthat/examples/Test_2023_1/output/metadata.yml index a38d6462..5dde7c3a 100644 --- a/tests/testthat/examples/Test_2023_1/output/metadata.yml +++ b/tests/testthat/examples/Test_2023_1/output/metadata.yml @@ -5,7 +5,7 @@ description: AusTraits is a transformative database, containing measurements on used to build the resource are also available on the project's GitHub repository,http://traitecoevo.github.io/traits.build. Further information on the project is available in the associated publication and at the project website https://austraits.org. -version: 4.0.0 +version: 5.0.0 doi: 10.5281/zenodo.5112001 structure_URI: https://github.com/traitecoevo/traits.build geo_location: diff --git a/tests/testthat/examples/Test_2023_1/output/taxa.csv b/tests/testthat/examples/Test_2023_1/output/taxa.csv index 74892a9c..f7e063c1 100644 --- a/tests/testthat/examples/Test_2023_1/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_1/output/taxa.csv @@ -1,45 +1,44 @@ -taxon_name,taxonomic_dataset,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution -Acacia celsa,APC,species,accepted,Acacia,Acacia celsa,,Fabaceae,https://id.biodiversity.org.au/taxon/apni/51436506,Qld -Acmena graveolens,,,,,,,,, -Acronychia acidula,APC,species,accepted,Acronychia,Acronychia acidula,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913200,Qld -Aleurites rockinghamensis,,,,,,,,, -Alphitonia petriei,APC,species,accepted,Alphitonia,Alphitonia petriei,,Rhamnaceae,https://id.biodiversity.org.au/node/apni/2887911,"Qld, NSW" -Alstonia scholaris,,,,,,,,, -Argyrodendron peralatum,,,,,,,,, -Atractocarpus hirtus,,,,,,,,, -Brombya platynema,,,,,,,,, -Cardwellia sublimis,,,,,,,,, -Castanospermum australe,,,,,,,,, -Cleistanthus myrianthus,,,,,,,,, -Cryptocarya laevigata,,,,,,,,, -Cryptocarya mackinnoniana,,,,,,,,, -Cryptocarya murrayi,,,,,,,,, -Dendrocnide moroides,,,,,,,,, -Elaeocarpus grandis,,,,,,,,, -Endiandra leptodendron,,,,,,,,, -Endiandra microneura,,,,,,,,, -Gillbeea adenopetala,,,,,,,,, -Glochidion hylandii,APC,species,accepted,Glochidion,Glochidion hylandii,,Phyllanthaceae,https://id.biodiversity.org.au/node/apni/2889113,Qld -Haplostichanthus submontanus,,,,,,,,, -Harpullia rhyticarpa,,,,,,,,, -Hernandia albiflora,,,,,,,,, -Homalanthus novo-guineensis,,,,,,,,, -Ixora biflora,,,,,,,,, -Lasianthus strigosus,,,,,,,,, -Litsea leefeana,,,,,,,,, -Macaranga tanarius,,,,,,,,, -Mallotus mollissimus,,,,,,,,, -Medicosma sessiliflora,,,,,,,,, -Melastoma cyanoides,,,,,,,,, -Melicope elleryana,APC,species,accepted,Melicope,Melicope elleryana,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913641,"WA, NT, Qld, NSW" -Myristica insipida,,,,,,,,, -Neolitsea dealbata,,,,,,,,, -Pittosporum rubiginosum,,,,,,,,, -Polyscias australiana,,,,,,,,, -Psychotria dallachiana,,,,,,,,, -Psychotria sp. Utchee Creek (H.Flecker NQNC5313),,,,,,,,, -Quassia baileyana,,,,,,,,, -Rhodomyrtus trineura,,,,,,,,, -Rockinghamia angustifolia,,,,,,,,, -Syzygium sayeri,,,,,,,,, -Trema aspera,,,,,,,,, +original_name,taxon_name,taxon_name_alternatives,genus,family,taxon_rank,taxonomic_dataset,taxonomic_status,subclass,taxon_distribution,scientific_name,taxon_id,taxon_ID_genus,scientific_name_id,canonical_name,cleaned_scientific_name_id,taxon_id_family,trinomial,binomial,establishment_means +Acacia celsa,Acacia celsa,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,Qld,Acacia celsa Tindale,https://id.biodiversity.org.au/taxon/apni/51436506,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/154988,Acacia celsa,https://id.biodiversity.org.au/name/apni/154988,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia celsa,native +Acronychia acidula,Acronychia acidula,,Acronychia,Rutaceae,species,APC,accepted,Magnoliidae,Qld,Acronychia acidula F.Muell.,https://id.biodiversity.org.au/node/apni/2913200,https://id.biodiversity.org.au/taxon/apni/51446847,https://id.biodiversity.org.au/name/apni/73794,Acronychia acidula,https://id.biodiversity.org.au/name/apni/73794,https://id.biodiversity.org.au/taxon/apni/51461748,,Acronychia acidula,native +Aleurites rockinghamensis,Aleurites rockinghamensis,,Aleurites,Euphorbiaceae,species,APC,accepted,Magnoliidae,Qld,Aleurites rockinghamensis (Baill.) P.I.Forst.,https://id.biodiversity.org.au/node/apni/2916622,https://id.biodiversity.org.au/node/apni/2900410,https://id.biodiversity.org.au/name/apni/171057,Aleurites rockinghamensis,https://id.biodiversity.org.au/name/apni/171057,https://id.biodiversity.org.au/taxon/apni/51442249,,Aleurites rockinghamensis,native +Alphitonia petriei,Alphitonia petriei,,Alphitonia,Rhamnaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Alphitonia petriei Braid & C.T.White,https://id.biodiversity.org.au/node/apni/2887911,https://id.biodiversity.org.au/taxon/apni/51446205,https://id.biodiversity.org.au/name/apni/82935,Alphitonia petriei,https://id.biodiversity.org.au/name/apni/82935,https://id.biodiversity.org.au/taxon/apni/51446206,,Alphitonia petriei,native +Alstonia scholaris,Alstonia scholaris,,Alstonia,Apocynaceae,species,APC,accepted,Magnoliidae,Qld,Alstonia scholaris (L.) R.Br.,https://id.biodiversity.org.au/node/apni/2916809,https://id.biodiversity.org.au/node/apni/6684160,https://id.biodiversity.org.au/name/apni/83915,Alstonia scholaris,https://id.biodiversity.org.au/name/apni/83915,https://id.biodiversity.org.au/taxon/apni/51700686,,Alstonia scholaris,native +Argyrodendron peralatum,Argyrodendron peralatum,,Argyrodendron,Malvaceae,species,APC,accepted,Magnoliidae,Qld,Argyrodendron peralatum (F.M.Bailey) Edlin ex I.H.Boas,https://id.biodiversity.org.au/node/apni/2915243,https://id.biodiversity.org.au/taxon/apni/51288410,https://id.biodiversity.org.au/name/apni/100216,Argyrodendron peralatum,https://id.biodiversity.org.au/name/apni/100216,https://id.biodiversity.org.au/taxon/apni/51439248,,Argyrodendron peralatum,native +Atractocarpus hirtus,Atractocarpus hirtus,,Atractocarpus,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Atractocarpus hirtus (F.Muell.) Puttock,https://id.biodiversity.org.au/node/apni/2910460,https://id.biodiversity.org.au/taxon/apni/51446611,https://id.biodiversity.org.au/name/apni/146883,Atractocarpus hirtus,https://id.biodiversity.org.au/name/apni/146883,https://id.biodiversity.org.au/taxon/apni/51446612,,Atractocarpus hirtus,native +Brombya platynema,Brombya platynema,,Brombya,Rutaceae,species,APC,accepted,Magnoliidae,Qld,Brombya platynema F.Muell.,https://id.biodiversity.org.au/node/apni/2890280,https://id.biodiversity.org.au/node/apni/7937668,https://id.biodiversity.org.au/name/apni/67607,Brombya platynema,https://id.biodiversity.org.au/name/apni/67607,https://id.biodiversity.org.au/taxon/apni/51461748,,Brombya platynema,native +Cardwellia sublimis,Cardwellia sublimis,,Cardwellia,Proteaceae,species,APC,accepted,Magnoliidae,Qld,Cardwellia sublimis F.Muell.,https://id.biodiversity.org.au/node/apni/2899253,https://id.biodiversity.org.au/node/apni/2908094,https://id.biodiversity.org.au/name/apni/109268,Cardwellia sublimis,https://id.biodiversity.org.au/name/apni/109268,https://id.biodiversity.org.au/taxon/apni/51614274,,Cardwellia sublimis,native +Castanospermum australe,Castanospermum australe,,Castanospermum,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, NI (doubtfully naturalised)",Castanospermum australe A.Cunn. ex Mudie,https://id.biodiversity.org.au/node/apni/2894943,https://id.biodiversity.org.au/node/apni/7226268,https://id.biodiversity.org.au/name/apni/196675,Castanospermum australe,https://id.biodiversity.org.au/name/apni/196675,https://id.biodiversity.org.au/taxon/apni/51702961,,Castanospermum australe,native and naturalised +Cleistanthus myrianthus,Cleistanthus myrianthus,,Cleistanthus,Phyllanthaceae,species,APC,accepted,Magnoliidae,Qld,Cleistanthus myrianthus (Hassk.) Kurz,https://id.biodiversity.org.au/node/apni/2897700,https://id.biodiversity.org.au/node/apni/2914326,https://id.biodiversity.org.au/name/apni/71354,Cleistanthus myrianthus,https://id.biodiversity.org.au/name/apni/71354,https://id.biodiversity.org.au/taxon/apni/51442162,,Cleistanthus myrianthus,native +Cryptocarya laevigata,Cryptocarya laevigata,,Cryptocarya,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Cryptocarya laevigata Blume,https://id.biodiversity.org.au/node/apni/2903400,https://id.biodiversity.org.au/taxon/apni/51438401,https://id.biodiversity.org.au/name/apni/88410,Cryptocarya laevigata,https://id.biodiversity.org.au/name/apni/88410,https://id.biodiversity.org.au/taxon/apni/51438397,,Cryptocarya laevigata,native +Cryptocarya mackinnoniana,Cryptocarya mackinnoniana,,Cryptocarya,Lauraceae,species,APC,accepted,Magnoliidae,Qld,Cryptocarya mackinnoniana F.Muell.,https://id.biodiversity.org.au/node/apni/2914946,https://id.biodiversity.org.au/taxon/apni/51438401,https://id.biodiversity.org.au/name/apni/88421,Cryptocarya mackinnoniana,https://id.biodiversity.org.au/name/apni/88421,https://id.biodiversity.org.au/taxon/apni/51438397,,Cryptocarya mackinnoniana,native +Cryptocarya murrayi,Cryptocarya murrayi,,Cryptocarya,Lauraceae,species,APC,accepted,Magnoliidae,Qld,Cryptocarya murrayi F.Muell.,https://id.biodiversity.org.au/node/apni/2910393,https://id.biodiversity.org.au/taxon/apni/51438401,https://id.biodiversity.org.au/name/apni/88472,Cryptocarya murrayi,https://id.biodiversity.org.au/name/apni/88472,https://id.biodiversity.org.au/taxon/apni/51438397,,Cryptocarya murrayi,native +Dendrocnide moroides,Dendrocnide moroides,,Dendrocnide,Urticaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Dendrocnide moroides (Wedd.) Chew,https://id.biodiversity.org.au/node/apni/2904177,https://id.biodiversity.org.au/taxon/apni/51448284,https://id.biodiversity.org.au/name/apni/86919,Dendrocnide moroides,https://id.biodiversity.org.au/name/apni/86919,https://id.biodiversity.org.au/taxon/apni/51662052,,Dendrocnide moroides,native +Endiandra leptodendron,Endiandra leptodendron,,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,Qld,Endiandra leptodendron B.Hyland,https://id.biodiversity.org.au/node/apni/2910725,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111888,Endiandra leptodendron,https://id.biodiversity.org.au/name/apni/111888,https://id.biodiversity.org.au/taxon/apni/51438397,,Endiandra leptodendron,native +Endiandra microneura,Endiandra microneura,,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,Qld,Endiandra microneura C.T.White,https://id.biodiversity.org.au/node/apni/2899314,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111949,Endiandra microneura,https://id.biodiversity.org.au/name/apni/111949,https://id.biodiversity.org.au/taxon/apni/51438397,,Endiandra microneura,native +Gillbeea adenopetala,Gillbeea adenopetala,,Gillbeea,Cunoniaceae,species,APC,accepted,Magnoliidae,Qld,Gillbeea adenopetala F.Muell.,https://id.biodiversity.org.au/node/apni/2913815,https://id.biodiversity.org.au/node/apni/2918249,https://id.biodiversity.org.au/name/apni/98098,Gillbeea adenopetala,https://id.biodiversity.org.au/name/apni/98098,https://id.biodiversity.org.au/taxon/apni/51434138,,Gillbeea adenopetala,native +Glochidion hylandii,Glochidion hylandii,,Glochidion,Phyllanthaceae,species,APC,accepted,Magnoliidae,Qld,Glochidion hylandii Airy Shaw,https://id.biodiversity.org.au/node/apni/2889113,https://id.biodiversity.org.au/node/apni/8387508,https://id.biodiversity.org.au/name/apni/78303,Glochidion hylandii,https://id.biodiversity.org.au/name/apni/78303,https://id.biodiversity.org.au/taxon/apni/51442162,,Glochidion hylandii,native +Harpullia rhyticarpa,Harpullia rhyticarpa,,Harpullia,Sapindaceae,species,APC,accepted,Magnoliidae,Qld,Harpullia rhyticarpa C.T.White & W.D.Francis,https://id.biodiversity.org.au/node/apni/2910766,https://id.biodiversity.org.au/taxon/apni/51447330,https://id.biodiversity.org.au/name/apni/108928,Harpullia rhyticarpa,https://id.biodiversity.org.au/name/apni/108928,https://id.biodiversity.org.au/taxon/apni/51447212,,Harpullia rhyticarpa,native +Hernandia albiflora,Hernandia albiflora,,Hernandia,Hernandiaceae,species,APC,accepted,Magnoliidae,Qld,Hernandia albiflora (C.T.White) Kubitzki,https://id.biodiversity.org.au/node/apni/2911354,https://id.biodiversity.org.au/taxon/apni/51437691,https://id.biodiversity.org.au/name/apni/92773,Hernandia albiflora,https://id.biodiversity.org.au/name/apni/92773,https://id.biodiversity.org.au/taxon/apni/51437692,,Hernandia albiflora,native +Homalanthus novoguineensis,Homalanthus novo-guineensis,,Homalanthus,Euphorbiaceae,species,APC,accepted,Magnoliidae,"WA (native and naturalised), NT, Qld",Homalanthus novo-guineensis (Warb.) Lauterb. & K.Schum.,https://id.biodiversity.org.au/node/apni/2888327,https://id.biodiversity.org.au/node/apni/4932846,https://id.biodiversity.org.au/name/apni/130383,Homalanthus novo-guineensis,https://id.biodiversity.org.au/name/apni/130383,https://id.biodiversity.org.au/taxon/apni/51442249,,Homalanthus novo-guineensis,native and naturalised +Ixora biflora,Ixora biflora,,Ixora,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Ixora biflora Fosberg,https://id.biodiversity.org.au/node/apni/2915627,https://id.biodiversity.org.au/taxon/apni/51446659,https://id.biodiversity.org.au/name/apni/90479,Ixora biflora,https://id.biodiversity.org.au/name/apni/90479,https://id.biodiversity.org.au/taxon/apni/51446612,,Ixora biflora,native +Lasianthus strigosus,Lasianthus chlorocarpus,,Lasianthus,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Lasianthus chlorocarpus K.Schum.,https://id.biodiversity.org.au/node/apni/7839740,https://id.biodiversity.org.au/node/apni/8136656,https://id.biodiversity.org.au/name/apni/219373,Lasianthus chlorocarpus,https://id.biodiversity.org.au/name/apni/71294,https://id.biodiversity.org.au/taxon/apni/51446612,,Lasianthus chlorocarpus,native +Litsea leefeana,Litsea leefeana,,Litsea,Lauraceae,species,APC,accepted,Magnoliidae,Qld,Litsea leefeana (F.Muell.) Merr.,https://id.biodiversity.org.au/node/apni/2921063,https://id.biodiversity.org.au/taxon/apni/51438430,https://id.biodiversity.org.au/name/apni/81094,Litsea leefeana,https://id.biodiversity.org.au/name/apni/81094,https://id.biodiversity.org.au/taxon/apni/51438397,,Litsea leefeana,native +Macaranga tanarius,Macaranga tanarius,,Macaranga,Euphorbiaceae,species,APC,accepted,Magnoliidae,"ChI, NT, Qld, NSW",Macaranga tanarius (L.) Müll.Arg.,https://id.biodiversity.org.au/node/apni/2902044,https://id.biodiversity.org.au/node/apni/2900788,https://id.biodiversity.org.au/name/apni/57015,Macaranga tanarius,https://id.biodiversity.org.au/name/apni/57015,https://id.biodiversity.org.au/taxon/apni/51442249,,Macaranga tanarius,native +Mallotus mollissimus,Mallotus mollissimus,,Mallotus,Euphorbiaceae,species,APC,accepted,Magnoliidae,Qld,Mallotus mollissimus (Geiseler) Airy Shaw,https://id.biodiversity.org.au/node/apni/2904445,https://id.biodiversity.org.au/taxon/apni/51284195,https://id.biodiversity.org.au/name/apni/59376,Mallotus mollissimus,https://id.biodiversity.org.au/name/apni/59376,https://id.biodiversity.org.au/taxon/apni/51442249,,Mallotus mollissimus,native +Medicosma sessiliflora,Medicosma sessiliflora,,Medicosma,Rutaceae,species,APC,accepted,Magnoliidae,Qld,Medicosma sessiliflora (C.T.White) T.G.Hartley,https://id.biodiversity.org.au/node/apni/2914896,https://id.biodiversity.org.au/taxon/apni/51446918,https://id.biodiversity.org.au/name/apni/73658,Medicosma sessiliflora,https://id.biodiversity.org.au/name/apni/73658,https://id.biodiversity.org.au/taxon/apni/51461748,,Medicosma sessiliflora,native +Melastoma cyanoides,Melastoma cyanoides,,Melastoma,Melastomataceae,species,APC,accepted,Magnoliidae,Qld,Melastoma cyanoides Sm.,https://id.biodiversity.org.au/node/apni/2895184,https://id.biodiversity.org.au/taxon/apni/51439399,https://id.biodiversity.org.au/name/apni/172752,Melastoma cyanoides,https://id.biodiversity.org.au/name/apni/172752,https://id.biodiversity.org.au/taxon/apni/51439392,,Melastoma cyanoides,native +Melicope elleryana,Melicope elleryana,,Melicope,Rutaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Melicope elleryana (F.Muell.) T.G.Hartley,https://id.biodiversity.org.au/node/apni/2913641,https://id.biodiversity.org.au/node/apni/2918609,https://id.biodiversity.org.au/name/apni/118560,Melicope elleryana,https://id.biodiversity.org.au/name/apni/118560,https://id.biodiversity.org.au/taxon/apni/51461748,,Melicope elleryana,native +Myristica insipida,Myristica insipida,,Myristica,Myristicaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Myristica insipida R.Br.,https://id.biodiversity.org.au/node/apni/2902429,https://id.biodiversity.org.au/node/apni/2895962,https://id.biodiversity.org.au/name/apni/86064,Myristica insipida,https://id.biodiversity.org.au/name/apni/86064,https://id.biodiversity.org.au/node/apni/2903136,,Myristica insipida,native +Neolitsea dealbata,Neolitsea dealbata,,Neolitsea,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Neolitsea dealbata (R.Br.) Merr.,https://id.biodiversity.org.au/node/apni/2910025,https://id.biodiversity.org.au/node/apni/2914447,https://id.biodiversity.org.au/name/apni/79589,Neolitsea dealbata,https://id.biodiversity.org.au/name/apni/79589,https://id.biodiversity.org.au/taxon/apni/51438397,,Neolitsea dealbata,native +Pittosporum rubiginosum,Pittosporum rubiginosum,,Pittosporum,Pittosporaceae,species,APC,accepted,Magnoliidae,Qld,Pittosporum rubiginosum A.Cunn.,https://id.biodiversity.org.au/node/apni/2887772,https://id.biodiversity.org.au/taxon/apni/51442349,https://id.biodiversity.org.au/name/apni/100119,Pittosporum rubiginosum,https://id.biodiversity.org.au/name/apni/100119,https://id.biodiversity.org.au/taxon/apni/51442315,,Pittosporum rubiginosum,native +Haplostichanthus sp Coop. Ck,Polyalthia submontana,,Polyalthia,Annonaceae,species,APC,accepted,Magnoliidae,Qld,Polyalthia submontana (Jessup) B.Xue & R.M.K.Saunders,https://id.biodiversity.org.au/taxon/apni/51613975,https://id.biodiversity.org.au/taxon/apni/51613976,https://id.biodiversity.org.au/name/apni/246294,Polyalthia submontana,https://id.biodiversity.org.au/name/apni/191525,https://id.biodiversity.org.au/taxon/apni/51613977,,Polyalthia submontana,native +Polyscias australiana,Polyscias australiana,,Polyscias,Araliaceae,species,APC,accepted,Magnoliidae,"NT, Qld",Polyscias australiana (F.Muell.) Philipson,https://id.biodiversity.org.au/node/apni/7223338,https://id.biodiversity.org.au/taxon/apni/51292784,https://id.biodiversity.org.au/name/apni/84802,Polyscias australiana,https://id.biodiversity.org.au/name/apni/84787,https://id.biodiversity.org.au/taxon/apni/51632289,,Polyscias australiana,native +Psychotria dallachiana,Psychotria dallachiana,,Psychotria,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Psychotria dallachiana Benth.,https://id.biodiversity.org.au/node/apni/2890013,https://id.biodiversity.org.au/taxon/apni/51446698,https://id.biodiversity.org.au/name/apni/89074,Psychotria dallachiana,https://id.biodiversity.org.au/name/apni/89074,https://id.biodiversity.org.au/taxon/apni/51446612,,Psychotria dallachiana,native +Psychotria sp Utchee Creek,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),,Psychotria,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Psychotria sp. Utchee Creek (H.Flecker NQNC5313) Qld Herbarium,https://id.biodiversity.org.au/taxon/apni/51446727,https://id.biodiversity.org.au/taxon/apni/51446698,https://id.biodiversity.org.au/name/apni/218829,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),https://id.biodiversity.org.au/name/apni/218829,https://id.biodiversity.org.au/taxon/apni/51446612,,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),native +Rhodomyrtus trineura,Rhodomyrtus trineura,,Rhodomyrtus,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Rhodomyrtus trineura (F.Muell.) Benth.,https://id.biodiversity.org.au/taxon/apni/51441176,https://id.biodiversity.org.au/taxon/apni/51441177,https://id.biodiversity.org.au/name/apni/69289,Rhodomyrtus trineura,https://id.biodiversity.org.au/name/apni/69289,https://id.biodiversity.org.au/taxon/apni/51702983,,Rhodomyrtus trineura,native +Rockinghamia angustifolia,Rockinghamia angustifolia,,Rockinghamia,Euphorbiaceae,species,APC,accepted,Magnoliidae,Qld,Rockinghamia angustifolia (Benth.) Airy Shaw,https://id.biodiversity.org.au/node/apni/2921179,https://id.biodiversity.org.au/node/apni/2892697,https://id.biodiversity.org.au/name/apni/61487,Rockinghamia angustifolia,https://id.biodiversity.org.au/name/apni/61487,https://id.biodiversity.org.au/taxon/apni/51442249,,Rockinghamia angustifolia,native +Quassia baileyana,Samadera baileyana,,Samadera,Simaroubaceae,species,APC,accepted,Magnoliidae,Qld,Samadera baileyana Oliv.,https://id.biodiversity.org.au/node/apni/2891526,https://id.biodiversity.org.au/node/apni/2900441,https://id.biodiversity.org.au/name/apni/60763,Samadera baileyana,https://id.biodiversity.org.au/name/apni/70084,https://id.biodiversity.org.au/taxon/apni/51316490,,Samadera baileyana,native +Acmena graveolens,Syzygium graveolens,,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium graveolens (F.M.Bailey) Craven & Biffin,https://id.biodiversity.org.au/node/apni/2920364,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/202985,Syzygium graveolens,https://id.biodiversity.org.au/name/apni/73535,https://id.biodiversity.org.au/taxon/apni/51702983,,Syzygium graveolens,native +Syzygium sayeri,Syzygium sayeri,,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium sayeri (F.Muell.) B.Hyland,https://id.biodiversity.org.au/node/apni/2888968,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/64837,Syzygium sayeri,https://id.biodiversity.org.au/name/apni/64837,https://id.biodiversity.org.au/taxon/apni/51702983,,Syzygium sayeri,native +Trema aspera,Trema tomentosa var. aspera,,Trema,Cannabaceae,variety,APC,accepted,Magnoliidae,"WA, Qld, NSW, Vic (presumed extinct)",Trema tomentosa var. aspera (Brongn.) Hewson,https://id.biodiversity.org.au/node/apni/2917190,https://id.biodiversity.org.au/node/apni/2913617,https://id.biodiversity.org.au/name/apni/206199,Trema tomentosa var. aspera,https://id.biodiversity.org.au/name/apni/101838,https://id.biodiversity.org.au/taxon/apni/51269919,Trema tomentosa var. aspera,Trema tomentosa,native diff --git a/tests/testthat/examples/Test_2023_1/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_1/output/taxonomic_updates.csv index 8a92fb23..8c885759 100644 --- a/tests/testthat/examples/Test_2023_1/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_1/output/taxonomic_updates.csv @@ -1,45 +1,45 @@ dataset_id,original_name,aligned_name,taxonomic_resolution,taxon_name Test_2023_1,Acacia celsa,Acacia celsa,,Acacia celsa -Test_2023_1,Acmena graveolens,Acmena graveolens,, +Test_2023_1,Acmena graveolens,Acmena graveolens,,Syzygium graveolens Test_2023_1,Acronychia acidula,Acronychia acidula,,Acronychia acidula -Test_2023_1,Aleurites rockinghamensis,Aleurites rockinghamensis,, +Test_2023_1,Aleurites rockinghamensis,Aleurites rockinghamensis,,Aleurites rockinghamensis Test_2023_1,Alphitonia petriei,Alphitonia petriei,,Alphitonia petriei -Test_2023_1,Alstonia scholaris,Alstonia scholaris,, -Test_2023_1,Argyrodendron peralatum,Argyrodendron peralatum,, -Test_2023_1,Atractocarpus hirtus,Atractocarpus hirtus,, -Test_2023_1,Brombya platynema,Brombya platynema,, -Test_2023_1,Cardwellia sublimis,Cardwellia sublimis,, -Test_2023_1,Castanospermum australe,Castanospermum australe,, -Test_2023_1,Cleistanthus myrianthus,Cleistanthus myrianthus,, -Test_2023_1,Cryptocarya laevigata,Cryptocarya laevigata,, -Test_2023_1,Cryptocarya mackinnoniana,Cryptocarya mackinnoniana,, -Test_2023_1,Cryptocarya murrayi,Cryptocarya murrayi,, -Test_2023_1,Dendrocnide moroides,Dendrocnide moroides,, -Test_2023_1,Elaeocarpus grandis,Elaeocarpus grandis,, -Test_2023_1,Endiandra leptodendron,Endiandra leptodendron,, -Test_2023_1,Endiandra microneura,Endiandra microneura,, -Test_2023_1,Gillbeea adenopetala,Gillbeea adenopetala,, +Test_2023_1,Alstonia scholaris,Alstonia scholaris,,Alstonia scholaris +Test_2023_1,Argyrodendron peralatum,Argyrodendron peralatum,,Argyrodendron peralatum +Test_2023_1,Atractocarpus hirtus,Atractocarpus hirtus,,Atractocarpus hirtus +Test_2023_1,Brombya platynema,Brombya platynema,,Brombya platynema +Test_2023_1,Cardwellia sublimis,Cardwellia sublimis,,Cardwellia sublimis +Test_2023_1,Castanospermum australe,Castanospermum australe,,Castanospermum australe +Test_2023_1,Cleistanthus myrianthus,Cleistanthus myrianthus,,Cleistanthus myrianthus +Test_2023_1,Cryptocarya laevigata,Cryptocarya laevigata,,Cryptocarya laevigata +Test_2023_1,Cryptocarya mackinnoniana,Cryptocarya mackinnoniana,,Cryptocarya mackinnoniana +Test_2023_1,Cryptocarya murrayi,Cryptocarya murrayi,,Cryptocarya murrayi +Test_2023_1,Dendrocnide moroides,Dendrocnide moroides,,Dendrocnide moroides +Test_2023_1,Elaeocarpus grandis,Elaeocarpus grandis,,Elaeocarpus grandis +Test_2023_1,Endiandra leptodendron,Endiandra leptodendron,,Endiandra leptodendron +Test_2023_1,Endiandra microneura,Endiandra microneura,,Endiandra microneura +Test_2023_1,Gillbeea adenopetala,Gillbeea adenopetala,,Gillbeea adenopetala Test_2023_1,Glochidion hylandii,Glochidion hylandii,,Glochidion hylandii -Test_2023_1,Haplostichanthus sp Coop. Ck,Haplostichanthus submontanus,species, -Test_2023_1,Harpullia rhyticarpa,Harpullia rhyticarpa,, -Test_2023_1,Hernandia albiflora,Hernandia albiflora,, -Test_2023_1,Homalanthus novoguineensis,Homalanthus novo-guineensis,species, -Test_2023_1,Ixora biflora,Ixora biflora,, -Test_2023_1,Lasianthus strigosus,Lasianthus strigosus,, -Test_2023_1,Litsea leefeana,Litsea leefeana,, -Test_2023_1,Macaranga tanarius,Macaranga tanarius,, -Test_2023_1,Mallotus mollissimus,Mallotus mollissimus,, -Test_2023_1,Medicosma sessiliflora,Medicosma sessiliflora,, -Test_2023_1,Melastoma cyanoides,Melastoma cyanoides,, +Test_2023_1,Haplostichanthus sp Coop. Ck,Haplostichanthus submontanus,species,Polyalthia submontana +Test_2023_1,Harpullia rhyticarpa,Harpullia rhyticarpa,,Harpullia rhyticarpa +Test_2023_1,Hernandia albiflora,Hernandia albiflora,,Hernandia albiflora +Test_2023_1,Homalanthus novoguineensis,Homalanthus novo-guineensis,species,Homalanthus novo-guineensis +Test_2023_1,Ixora biflora,Ixora biflora,,Ixora biflora +Test_2023_1,Lasianthus strigosus,Lasianthus strigosus,,Lasianthus chlorocarpus +Test_2023_1,Litsea leefeana,Litsea leefeana,,Litsea leefeana +Test_2023_1,Macaranga tanarius,Macaranga tanarius,,Macaranga tanarius +Test_2023_1,Mallotus mollissimus,Mallotus mollissimus,,Mallotus mollissimus +Test_2023_1,Medicosma sessiliflora,Medicosma sessiliflora,,Medicosma sessiliflora +Test_2023_1,Melastoma cyanoides,Melastoma cyanoides,,Melastoma cyanoides Test_2023_1,Melicope elleryana,Melicope elleryana,,Melicope elleryana -Test_2023_1,Myristica insipida,Myristica insipida,, -Test_2023_1,Neolitsea dealbata,Neolitsea dealbata,, -Test_2023_1,Pittosporum rubiginosum,Pittosporum rubiginosum,, -Test_2023_1,Polyscias australiana,Polyscias australiana,, -Test_2023_1,Psychotria dallachiana,Psychotria dallachiana,, -Test_2023_1,Psychotria sp Utchee Creek,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),species, -Test_2023_1,Quassia baileyana,Quassia baileyana,, -Test_2023_1,Rhodomyrtus trineura,Rhodomyrtus trineura,, -Test_2023_1,Rockinghamia angustifolia,Rockinghamia angustifolia,, -Test_2023_1,Syzygium sayeri,Syzygium sayeri,, -Test_2023_1,Trema aspera,Trema aspera,, +Test_2023_1,Myristica insipida,Myristica insipida,,Myristica insipida +Test_2023_1,Neolitsea dealbata,Neolitsea dealbata,,Neolitsea dealbata +Test_2023_1,Pittosporum rubiginosum,Pittosporum rubiginosum,,Pittosporum rubiginosum +Test_2023_1,Polyscias australiana,Polyscias australiana,,Polyscias australiana +Test_2023_1,Psychotria dallachiana,Psychotria dallachiana,,Psychotria dallachiana +Test_2023_1,Psychotria sp Utchee Creek,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),species,Psychotria sp. Utchee Creek (H.Flecker NQNC5313) +Test_2023_1,Quassia baileyana,Quassia baileyana,,Samadera baileyana +Test_2023_1,Rhodomyrtus trineura,Rhodomyrtus trineura,,Rhodomyrtus trineura +Test_2023_1,Rockinghamia angustifolia,Rockinghamia angustifolia,,Rockinghamia angustifolia +Test_2023_1,Syzygium sayeri,Syzygium sayeri,,Syzygium sayeri +Test_2023_1,Trema aspera,Trema aspera,,Trema tomentosa var. aspera diff --git a/tests/testthat/examples/Test_2023_1/output/traits.csv b/tests/testthat/examples/Test_2023_1/output/traits.csv index 3a32e6e7..908540f3 100644 --- a/tests/testthat/examples/Test_2023_1/output/traits.csv +++ b/tests/testthat/examples/Test_2023_1/output/traits.csv @@ -24,16 +24,16 @@ Test_2023_1,Acacia celsa,007,leaf_stomatal_conductance,0.7,mol{H2O}/m2/s,populat Test_2023_1,Acacia celsa,007,leaf_stomatal_conductance,0.66,mol{H2O}/m2/s,population,raw,measurement,1,field,adult,04,,04,,,02,,,,2004/2004,from Falster_2005_1,01,,Acacia celsa Test_2023_1,Acacia celsa,007,leaf_stomatal_conductance,0.3,mol{H2O}/m2/s,population,raw,measurement,1,field,adult,04,,05,,,02,,,,2004/2004,from Falster_2005_1,01,,Acacia celsa Test_2023_1,Acacia celsa,008,plant_growth_form,herb,,species,mode,expert_score,3,field,adult,,,,02,,,04,01,01,2004/2004,from Falster_2005_1,01,07,Acacia celsa -Test_2023_1,Acmena graveolens,010,huber_value,0.000139742873113471,mm2{sapwood}/mm2{leaf},individual,mean,model_derived,5,field,adult,04,01,,,,02,10,,,2002/2002,made-up measurement remarks,05,,Acmena graveolens -Test_2023_1,Acmena graveolens,011,leaf_length,40,mm,individual,mean,measurement,3,field,adult,04,01,,,,02,10,,,2004/2004,from Falster_2005_1,01,,Acmena graveolens -Test_2023_1,Acmena graveolens,012,huber_value,0.000139742873113471,mm2{sapwood}/mm2{leaf},individual,raw,model_derived,5,field,adult,04,01,,,,02,10,,,,made-up measurement remarks,04,01,Acmena graveolens -Test_2023_1,Acmena graveolens,013,huber_value,0.000327118089630357,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,10,,,2004/2004,from Falster_2005_1,02,02,Acmena graveolens -Test_2023_1,Acmena graveolens,013,huber_value,0.000374953130858643,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,10,,,2004/2004,from Falster_2005_1,03,03,Acmena graveolens -Test_2023_1,Acmena graveolens,013,huber_value,0.000374953130858643,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,10,,,2004/2004,from Falster_2005_1,03,,Acmena graveolens -Test_2023_1,Acmena graveolens,013,leaf_N_per_dry_mass,15.5,mg/g,population,mean,measurement,3,field,adult,04,,,,,02,10,,,2004/2004,from Falster_2005_1,01,,Acmena graveolens -Test_2023_1,Acmena graveolens,013,leaf_area,5246,mm2,population,mean,measurement,3,field,adult,04,,,,,02,10,,,2004/2004,from Falster_2005_1,01,,Acmena graveolens -Test_2023_1,Acmena graveolens,013,leaf_mass_per_area,151,g/m2,population,mean,measurement,3,field,adult,04,,,,,02,10,,,2004/2004,from Falster_2005_1,01,,Acmena graveolens -Test_2023_1,Acmena graveolens,013,wood_density,0.599,mg/mm3,population,mean,measurement,3,field,adult,04,,,,,02,10,,,2004/2004,from Falster_2005_1,01,,Acmena graveolens +Test_2023_1,Syzygium graveolens,010,huber_value,0.000139742873113471,mm2{sapwood}/mm2{leaf},individual,mean,model_derived,5,field,adult,04,01,,,,02,10,,,2002/2002,made-up measurement remarks,05,,Acmena graveolens +Test_2023_1,Syzygium graveolens,011,leaf_length,40,mm,individual,mean,measurement,3,field,adult,04,01,,,,02,10,,,2004/2004,from Falster_2005_1,01,,Acmena graveolens +Test_2023_1,Syzygium graveolens,012,huber_value,0.000139742873113471,mm2{sapwood}/mm2{leaf},individual,raw,model_derived,5,field,adult,04,01,,,,02,10,,,,made-up measurement remarks,04,01,Acmena graveolens +Test_2023_1,Syzygium graveolens,013,huber_value,0.000327118089630357,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,10,,,2004/2004,from Falster_2005_1,02,02,Acmena graveolens +Test_2023_1,Syzygium graveolens,013,huber_value,0.000374953130858643,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,10,,,2004/2004,from Falster_2005_1,03,03,Acmena graveolens +Test_2023_1,Syzygium graveolens,013,huber_value,0.000374953130858643,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,10,,,2004/2004,from Falster_2005_1,03,,Acmena graveolens +Test_2023_1,Syzygium graveolens,013,leaf_N_per_dry_mass,15.5,mg/g,population,mean,measurement,3,field,adult,04,,,,,02,10,,,2004/2004,from Falster_2005_1,01,,Acmena graveolens +Test_2023_1,Syzygium graveolens,013,leaf_area,5246,mm2,population,mean,measurement,3,field,adult,04,,,,,02,10,,,2004/2004,from Falster_2005_1,01,,Acmena graveolens +Test_2023_1,Syzygium graveolens,013,leaf_mass_per_area,151,g/m2,population,mean,measurement,3,field,adult,04,,,,,02,10,,,2004/2004,from Falster_2005_1,01,,Acmena graveolens +Test_2023_1,Syzygium graveolens,013,wood_density,0.599,mg/mm3,population,mean,measurement,3,field,adult,04,,,,,02,10,,,2004/2004,from Falster_2005_1,01,,Acmena graveolens Test_2023_1,Acronychia acidula,015,leaf_photosynthesis,5,umol/m2/s,individual,raw,measurement,1,field,adult,02,01,01,,,01,09,,,2004/2004,from Falster_2005_1,01,,Acronychia acidula Test_2023_1,Acronychia acidula,015,leaf_photosynthesis,3,umol/m2/s,individual,raw,measurement,1,field,adult,02,01,02,,,01,09,,,2004/2004,from Falster_2005_1,01,,Acronychia acidula Test_2023_1,Acronychia acidula,015,leaf_photosynthesis,2,umol/m2/s,individual,raw,measurement,1,field,adult,02,01,03,,,01,09,,,2004/2004,from Falster_2005_1,01,,Acronychia acidula @@ -214,17 +214,6 @@ Test_2023_1,Dendrocnide moroides,093,leaf_area,26454,mm2,population,mean,measure Test_2023_1,Dendrocnide moroides,093,leaf_mass_per_area,52,g/m2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Dendrocnide moroides Test_2023_1,Dendrocnide moroides,093,seed_dry_mass,0.71,mg,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Dendrocnide moroides Test_2023_1,Dendrocnide moroides,093,wood_density,0.23,mg/mm3,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Dendrocnide moroides -Test_2023_1,Elaeocarpus grandis,095,huber_value,0.000215749730312837,mm2{sapwood}/mm2{leaf},individual,mean,model_derived,5,field,adult,04,01,,,,02,,,,2002/2002,made-up measurement remarks,05,,Elaeocarpus grandis -Test_2023_1,Elaeocarpus grandis,096,leaf_length,40,mm,individual,mean,measurement,3,field,adult,04,01,,,,02,,,,2004/2004,from Falster_2005_1,01,,Elaeocarpus grandis -Test_2023_1,Elaeocarpus grandis,097,huber_value,0.000215749730312837,mm2{sapwood}/mm2{leaf},individual,raw,model_derived,5,field,adult,04,01,,,,02,,,,,made-up measurement remarks,04,01,Elaeocarpus grandis -Test_2023_1,Elaeocarpus grandis,098,huber_value,0.000384911470361817,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,02,02,Elaeocarpus grandis -Test_2023_1,Elaeocarpus grandis,098,huber_value,0.0005720823798627,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,03,Elaeocarpus grandis -Test_2023_1,Elaeocarpus grandis,098,huber_value,0.0005720823798627,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,,Elaeocarpus grandis -Test_2023_1,Elaeocarpus grandis,098,leaf_N_per_dry_mass,18.7,mg/g,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Elaeocarpus grandis -Test_2023_1,Elaeocarpus grandis,098,leaf_area,2762,mm2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Elaeocarpus grandis -Test_2023_1,Elaeocarpus grandis,098,leaf_mass_per_area,122,g/m2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Elaeocarpus grandis -Test_2023_1,Elaeocarpus grandis,098,seed_dry_mass,3699,mg,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Elaeocarpus grandis -Test_2023_1,Elaeocarpus grandis,098,wood_density,0.499,mg/mm3,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Elaeocarpus grandis Test_2023_1,Endiandra leptodendron,100,huber_value,0.00013374348000535,mm2{sapwood}/mm2{leaf},individual,mean,model_derived,5,field,adult,04,01,,,,02,,,,2002/2002,made-up measurement remarks,05,,Endiandra leptodendron Test_2023_1,Endiandra leptodendron,101,leaf_length,40,mm,individual,mean,measurement,3,field,adult,04,01,,,,02,,,,2004/2004,from Falster_2005_1,01,,Endiandra leptodendron Test_2023_1,Endiandra leptodendron,102,huber_value,0.00013374348000535,mm2{sapwood}/mm2{leaf},individual,raw,model_derived,5,field,adult,04,01,,,,02,,,,,made-up measurement remarks,04,01,Endiandra leptodendron @@ -271,17 +260,17 @@ Test_2023_1,Glochidion hylandii,118,leaf_area,3209,mm2,population,mean,measureme Test_2023_1,Glochidion hylandii,118,leaf_mass_per_area,106,g/m2,population,mean,measurement,3,field,adult,06,,,,,01,05,,02,2004/2004,from Falster_2005_1,01,11,Glochidion hylandii Test_2023_1,Glochidion hylandii,118,seed_dry_mass,10.41,mg,population,mean,measurement,3,field,adult,06,,,,,01,05,,02,2004/2004,from Falster_2005_1,01,11,Glochidion hylandii Test_2023_1,Glochidion hylandii,118,wood_density,0.566,mg/mm3,population,mean,measurement,3,field,adult,06,,,,,01,05,,02,2004/2004,from Falster_2005_1,01,11,Glochidion hylandii -Test_2023_1,Haplostichanthus submontanus,120,huber_value,0.000334224598930481,mm2{sapwood}/mm2{leaf},individual,mean,model_derived,5,field,adult,04,01,,,,02,,,,2002/2002,made-up measurement remarks,05,,Haplostichanthus sp Coop. Ck -Test_2023_1,Haplostichanthus submontanus,121,leaf_length,40,mm,individual,mean,measurement,3,field,adult,04,01,,,,02,,,,2004/2004,from Falster_2005_1,01,,Haplostichanthus sp Coop. Ck -Test_2023_1,Haplostichanthus submontanus,122,huber_value,0.000334224598930481,mm2{sapwood}/mm2{leaf},individual,raw,model_derived,5,field,adult,04,01,,,,02,,,,,made-up measurement remarks,04,01,Haplostichanthus sp Coop. Ck -Test_2023_1,Haplostichanthus submontanus,123,huber_value,0.000411522633744856,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Haplostichanthus sp Coop. Ck -Test_2023_1,Haplostichanthus submontanus,123,huber_value,8.12743823146944e-05,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,02,02,Haplostichanthus sp Coop. Ck -Test_2023_1,Haplostichanthus submontanus,123,huber_value,0.000304692260816575,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,03,Haplostichanthus sp Coop. Ck -Test_2023_1,Haplostichanthus submontanus,123,huber_value,0.000304692260816575,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,,Haplostichanthus sp Coop. Ck -Test_2023_1,Haplostichanthus submontanus,123,leaf_N_per_dry_mass,22,mg/g,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Haplostichanthus sp Coop. Ck -Test_2023_1,Haplostichanthus submontanus,123,leaf_area,4685,mm2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Haplostichanthus sp Coop. Ck -Test_2023_1,Haplostichanthus submontanus,123,leaf_mass_per_area,72,g/m2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Haplostichanthus sp Coop. Ck -Test_2023_1,Haplostichanthus submontanus,123,wood_density,0.668,mg/mm3,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Haplostichanthus sp Coop. Ck +Test_2023_1,Polyalthia submontana,120,huber_value,0.000334224598930481,mm2{sapwood}/mm2{leaf},individual,mean,model_derived,5,field,adult,04,01,,,,02,,,,2002/2002,made-up measurement remarks,05,,Haplostichanthus sp Coop. Ck +Test_2023_1,Polyalthia submontana,121,leaf_length,40,mm,individual,mean,measurement,3,field,adult,04,01,,,,02,,,,2004/2004,from Falster_2005_1,01,,Haplostichanthus sp Coop. Ck +Test_2023_1,Polyalthia submontana,122,huber_value,0.000334224598930481,mm2{sapwood}/mm2{leaf},individual,raw,model_derived,5,field,adult,04,01,,,,02,,,,,made-up measurement remarks,04,01,Haplostichanthus sp Coop. Ck +Test_2023_1,Polyalthia submontana,123,huber_value,0.000411522633744856,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Haplostichanthus sp Coop. Ck +Test_2023_1,Polyalthia submontana,123,huber_value,8.12743823146944e-05,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,02,02,Haplostichanthus sp Coop. Ck +Test_2023_1,Polyalthia submontana,123,huber_value,0.000304692260816575,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,03,Haplostichanthus sp Coop. Ck +Test_2023_1,Polyalthia submontana,123,huber_value,0.000304692260816575,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,,Haplostichanthus sp Coop. Ck +Test_2023_1,Polyalthia submontana,123,leaf_N_per_dry_mass,22,mg/g,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Haplostichanthus sp Coop. Ck +Test_2023_1,Polyalthia submontana,123,leaf_area,4685,mm2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Haplostichanthus sp Coop. Ck +Test_2023_1,Polyalthia submontana,123,leaf_mass_per_area,72,g/m2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Haplostichanthus sp Coop. Ck +Test_2023_1,Polyalthia submontana,123,wood_density,0.668,mg/mm3,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Haplostichanthus sp Coop. Ck Test_2023_1,Harpullia rhyticarpa,125,huber_value,0.000214178624973228,mm2{sapwood}/mm2{leaf},individual,mean,model_derived,5,field,adult,04,01,,,,02,,,,2002/2002,made-up measurement remarks,05,,Harpullia rhyticarpa Test_2023_1,Harpullia rhyticarpa,126,leaf_length,40,mm,individual,mean,measurement,3,field,adult,04,01,,,,02,,,,2004/2004,from Falster_2005_1,01,,Harpullia rhyticarpa Test_2023_1,Harpullia rhyticarpa,127,huber_value,0.000214178624973228,mm2{sapwood}/mm2{leaf},individual,raw,model_derived,5,field,adult,04,01,,,,02,,,,,made-up measurement remarks,04,01,Harpullia rhyticarpa @@ -328,18 +317,18 @@ Test_2023_1,Ixora biflora,143,leaf_area,2760,mm2,population,mean,measurement,3,f Test_2023_1,Ixora biflora,143,leaf_mass_per_area,81,g/m2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Ixora biflora Test_2023_1,Ixora biflora,143,seed_dry_mass,41.5,mg,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Ixora biflora Test_2023_1,Ixora biflora,143,wood_density,0.843,mg/mm3,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Ixora biflora -Test_2023_1,Lasianthus strigosus,145,huber_value,0.000366166239472721,mm2{sapwood}/mm2{leaf},individual,mean,model_derived,5,field,adult,04,01,,,,02,,,,2002/2002,made-up measurement remarks,05,,Lasianthus strigosus -Test_2023_1,Lasianthus strigosus,146,leaf_length,40,mm,individual,mean,measurement,3,field,adult,04,01,,,,02,,,,2004/2004,from Falster_2005_1,01,,Lasianthus strigosus -Test_2023_1,Lasianthus strigosus,147,huber_value,0.000366166239472721,mm2{sapwood}/mm2{leaf},individual,raw,model_derived,5,field,adult,04,01,,,,02,,,,,made-up measurement remarks,04,01,Lasianthus strigosus -Test_2023_1,Lasianthus strigosus,148,huber_value,0.000543183052688756,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Lasianthus strigosus -Test_2023_1,Lasianthus strigosus,148,huber_value,0.000196078431372549,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,02,02,Lasianthus strigosus -Test_2023_1,Lasianthus strigosus,148,huber_value,0.000420344682639765,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,03,Lasianthus strigosus -Test_2023_1,Lasianthus strigosus,148,huber_value,0.000420344682639765,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,,Lasianthus strigosus -Test_2023_1,Lasianthus strigosus,148,leaf_N_per_dry_mass,15.8,mg/g,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Lasianthus strigosus -Test_2023_1,Lasianthus strigosus,148,leaf_area,3313,mm2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Lasianthus strigosus -Test_2023_1,Lasianthus strigosus,148,leaf_mass_per_area,55,g/m2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Lasianthus strigosus -Test_2023_1,Lasianthus strigosus,148,seed_dry_mass,7,mg,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Lasianthus strigosus -Test_2023_1,Lasianthus strigosus,148,wood_density,0.684,mg/mm3,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Lasianthus strigosus +Test_2023_1,Lasianthus chlorocarpus,145,huber_value,0.000366166239472721,mm2{sapwood}/mm2{leaf},individual,mean,model_derived,5,field,adult,04,01,,,,02,,,,2002/2002,made-up measurement remarks,05,,Lasianthus strigosus +Test_2023_1,Lasianthus chlorocarpus,146,leaf_length,40,mm,individual,mean,measurement,3,field,adult,04,01,,,,02,,,,2004/2004,from Falster_2005_1,01,,Lasianthus strigosus +Test_2023_1,Lasianthus chlorocarpus,147,huber_value,0.000366166239472721,mm2{sapwood}/mm2{leaf},individual,raw,model_derived,5,field,adult,04,01,,,,02,,,,,made-up measurement remarks,04,01,Lasianthus strigosus +Test_2023_1,Lasianthus chlorocarpus,148,huber_value,0.000543183052688756,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Lasianthus strigosus +Test_2023_1,Lasianthus chlorocarpus,148,huber_value,0.000196078431372549,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,02,02,Lasianthus strigosus +Test_2023_1,Lasianthus chlorocarpus,148,huber_value,0.000420344682639765,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,03,Lasianthus strigosus +Test_2023_1,Lasianthus chlorocarpus,148,huber_value,0.000420344682639765,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,,Lasianthus strigosus +Test_2023_1,Lasianthus chlorocarpus,148,leaf_N_per_dry_mass,15.8,mg/g,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Lasianthus strigosus +Test_2023_1,Lasianthus chlorocarpus,148,leaf_area,3313,mm2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Lasianthus strigosus +Test_2023_1,Lasianthus chlorocarpus,148,leaf_mass_per_area,55,g/m2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Lasianthus strigosus +Test_2023_1,Lasianthus chlorocarpus,148,seed_dry_mass,7,mg,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Lasianthus strigosus +Test_2023_1,Lasianthus chlorocarpus,148,wood_density,0.684,mg/mm3,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Lasianthus strigosus Test_2023_1,Litsea leefeana,150,huber_value,0.000103680663556247,mm2{sapwood}/mm2{leaf},individual,mean,model_derived,5,field,adult,04,01,,,,02,,,,2002/2002,made-up measurement remarks,05,,Litsea leefeana Test_2023_1,Litsea leefeana,151,leaf_length,40,mm,individual,mean,measurement,3,field,adult,04,01,,,,02,,,,2004/2004,from Falster_2005_1,01,,Litsea leefeana Test_2023_1,Litsea leefeana,152,huber_value,0.000103680663556247,mm2{sapwood}/mm2{leaf},individual,raw,model_derived,5,field,adult,04,01,,,,02,,,,,made-up measurement remarks,04,01,Litsea leefeana @@ -476,16 +465,16 @@ Test_2023_1,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),208,leaf_area,11157 Test_2023_1,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),208,leaf_mass_per_area,108,g/m2,population,mean,measurement,3,field,adult,09,,,,,01,02,02,,2004/2004,from Falster_2005_1,01,,Psychotria sp Utchee Creek Test_2023_1,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),208,seed_dry_mass,23.09,mg,population,mean,measurement,3,field,adult,09,,,,,01,02,02,,2004/2004,from Falster_2005_1,01,,Psychotria sp Utchee Creek Test_2023_1,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),208,wood_density,0.582,mg/mm3,population,mean,measurement,3,field,adult,09,,,,,01,02,02,,2004/2004,from Falster_2005_1,01,,Psychotria sp Utchee Creek -Test_2023_1,Quassia baileyana,210,huber_value,0.000174855744011191,mm2{sapwood}/mm2{leaf},individual,mean,model_derived,5,field,adult,04,01,,,,02,,,,2002/2002,made-up measurement remarks,05,,Quassia baileyana -Test_2023_1,Quassia baileyana,211,leaf_length,40,mm,individual,mean,measurement,3,field,adult,04,01,,,,02,,,,2004/2004,from Falster_2005_1,01,,Quassia baileyana -Test_2023_1,Quassia baileyana,212,huber_value,0.000174855744011191,mm2{sapwood}/mm2{leaf},individual,raw,model_derived,5,field,adult,04,01,,,,02,,,,,made-up measurement remarks,04,01,Quassia baileyana -Test_2023_1,Quassia baileyana,213,huber_value,0.000170444861087438,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,02,02,Quassia baileyana -Test_2023_1,Quassia baileyana,213,huber_value,0.000310945273631841,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,03,Quassia baileyana -Test_2023_1,Quassia baileyana,213,huber_value,0.000310945273631841,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,,Quassia baileyana -Test_2023_1,Quassia baileyana,213,leaf_N_per_dry_mass,23,mg/g,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Quassia baileyana -Test_2023_1,Quassia baileyana,213,leaf_area,9624,mm2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Quassia baileyana -Test_2023_1,Quassia baileyana,213,leaf_mass_per_area,86,g/m2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Quassia baileyana -Test_2023_1,Quassia baileyana,213,wood_density,0.501,mg/mm3,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Quassia baileyana +Test_2023_1,Samadera baileyana,210,huber_value,0.000174855744011191,mm2{sapwood}/mm2{leaf},individual,mean,model_derived,5,field,adult,04,01,,,,02,,,,2002/2002,made-up measurement remarks,05,,Quassia baileyana +Test_2023_1,Samadera baileyana,211,leaf_length,40,mm,individual,mean,measurement,3,field,adult,04,01,,,,02,,,,2004/2004,from Falster_2005_1,01,,Quassia baileyana +Test_2023_1,Samadera baileyana,212,huber_value,0.000174855744011191,mm2{sapwood}/mm2{leaf},individual,raw,model_derived,5,field,adult,04,01,,,,02,,,,,made-up measurement remarks,04,01,Quassia baileyana +Test_2023_1,Samadera baileyana,213,huber_value,0.000170444861087438,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,02,02,Quassia baileyana +Test_2023_1,Samadera baileyana,213,huber_value,0.000310945273631841,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,03,Quassia baileyana +Test_2023_1,Samadera baileyana,213,huber_value,0.000310945273631841,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,,Quassia baileyana +Test_2023_1,Samadera baileyana,213,leaf_N_per_dry_mass,23,mg/g,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Quassia baileyana +Test_2023_1,Samadera baileyana,213,leaf_area,9624,mm2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Quassia baileyana +Test_2023_1,Samadera baileyana,213,leaf_mass_per_area,86,g/m2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Quassia baileyana +Test_2023_1,Samadera baileyana,213,wood_density,0.501,mg/mm3,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Quassia baileyana Test_2023_1,Rhodomyrtus trineura,215,huber_value,0.00014541224371092,mm2{sapwood}/mm2{leaf},individual,mean,model_derived,5,field,adult,02,01,,,,01,15,,,2002/2002,made-up measurement remarks,05,,Rhodomyrtus trineura Test_2023_1,Rhodomyrtus trineura,216,leaf_length,40,mm,individual,mean,measurement,3,field,adult,02,01,,,,01,15,,,2004/2004,from Falster_2005_1,01,,Rhodomyrtus trineura Test_2023_1,Rhodomyrtus trineura,217,flowering_time,nnnnnnnnnnny,,individual,mode,expert_score,3,field,adult,02,01,,,,01,15,,,,from Falster_2005_1,01,,Rhodomyrtus trineura @@ -522,15 +511,15 @@ Test_2023_1,Syzygium sayeri,233,leaf_area,2645,mm2,population,mean,measurement,3 Test_2023_1,Syzygium sayeri,233,leaf_mass_per_area,131,g/m2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Syzygium sayeri Test_2023_1,Syzygium sayeri,233,seed_dry_mass,841,mg,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Syzygium sayeri Test_2023_1,Syzygium sayeri,233,wood_density,0.485,mg/mm3,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Syzygium sayeri -Test_2023_1,Trema aspera,235,huber_value,0.000149365197908887,mm2{sapwood}/mm2{leaf},individual,mean,model_derived,5,field,adult,04,01,,,,02,,,,2002/2002,made-up measurement remarks,05,,Trema aspera -Test_2023_1,Trema aspera,236,leaf_length,40,mm,individual,mean,measurement,3,field,adult,04,01,,,,02,,,,2004/2004,from Falster_2005_1,01,,Trema aspera -Test_2023_1,Trema aspera,237,huber_value,0.000149365197908887,mm2{sapwood}/mm2{leaf},individual,raw,model_derived,5,field,adult,04,01,,,,02,,,,,made-up measurement remarks,04,01,Trema aspera -Test_2023_1,Trema aspera,238,huber_value,0.000279485746226942,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Trema aspera -Test_2023_1,Trema aspera,238,huber_value,0.000189000189000189,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,02,02,Trema aspera -Test_2023_1,Trema aspera,238,huber_value,0.000183823529411765,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,03,Trema aspera -Test_2023_1,Trema aspera,238,huber_value,0.000183823529411765,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,,Trema aspera -Test_2023_1,Trema aspera,238,leaf_N_per_dry_mass,29.9,mg/g,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Trema aspera -Test_2023_1,Trema aspera,238,leaf_area,2071,mm2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Trema aspera -Test_2023_1,Trema aspera,238,leaf_mass_per_area,53,g/m2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Trema aspera -Test_2023_1,Trema aspera,238,seed_dry_mass,5.12,mg,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Trema aspera -Test_2023_1,Trema aspera,238,wood_density,0.357,mg/mm3,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Trema aspera +Test_2023_1,Trema tomentosa var. aspera,235,huber_value,0.000149365197908887,mm2{sapwood}/mm2{leaf},individual,mean,model_derived,5,field,adult,04,01,,,,02,,,,2002/2002,made-up measurement remarks,05,,Trema aspera +Test_2023_1,Trema tomentosa var. aspera,236,leaf_length,40,mm,individual,mean,measurement,3,field,adult,04,01,,,,02,,,,2004/2004,from Falster_2005_1,01,,Trema aspera +Test_2023_1,Trema tomentosa var. aspera,237,huber_value,0.000149365197908887,mm2{sapwood}/mm2{leaf},individual,raw,model_derived,5,field,adult,04,01,,,,02,,,,,made-up measurement remarks,04,01,Trema aspera +Test_2023_1,Trema tomentosa var. aspera,238,huber_value,0.000279485746226942,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Trema aspera +Test_2023_1,Trema tomentosa var. aspera,238,huber_value,0.000189000189000189,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,02,02,Trema aspera +Test_2023_1,Trema tomentosa var. aspera,238,huber_value,0.000183823529411765,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,03,Trema aspera +Test_2023_1,Trema tomentosa var. aspera,238,huber_value,0.000183823529411765,mm2{sapwood}/mm2{leaf},population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,03,,Trema aspera +Test_2023_1,Trema tomentosa var. aspera,238,leaf_N_per_dry_mass,29.9,mg/g,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Trema aspera +Test_2023_1,Trema tomentosa var. aspera,238,leaf_area,2071,mm2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Trema aspera +Test_2023_1,Trema tomentosa var. aspera,238,leaf_mass_per_area,53,g/m2,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Trema aspera +Test_2023_1,Trema tomentosa var. aspera,238,seed_dry_mass,5.12,mg,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Trema aspera +Test_2023_1,Trema tomentosa var. aspera,238,wood_density,0.357,mg/mm3,population,mean,measurement,3,field,adult,04,,,,,02,,,,2004/2004,from Falster_2005_1,01,,Trema aspera diff --git a/tests/testthat/examples/Test_2023_2/output/metadata.yml b/tests/testthat/examples/Test_2023_2/output/metadata.yml index a38d6462..5dde7c3a 100644 --- a/tests/testthat/examples/Test_2023_2/output/metadata.yml +++ b/tests/testthat/examples/Test_2023_2/output/metadata.yml @@ -5,7 +5,7 @@ description: AusTraits is a transformative database, containing measurements on used to build the resource are also available on the project's GitHub repository,http://traitecoevo.github.io/traits.build. Further information on the project is available in the associated publication and at the project website https://austraits.org. -version: 4.0.0 +version: 5.0.0 doi: 10.5281/zenodo.5112001 structure_URI: https://github.com/traitecoevo/traits.build geo_location: diff --git a/tests/testthat/examples/Test_2023_2/output/taxa.csv b/tests/testthat/examples/Test_2023_2/output/taxa.csv index 84196068..19bec5a5 100644 --- a/tests/testthat/examples/Test_2023_2/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_2/output/taxa.csv @@ -1,46 +1,46 @@ -taxon_name,taxonomic_dataset,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution -Acacia celsa,APC,species,accepted,Acacia,Acacia celsa,,Fabaceae,https://id.biodiversity.org.au/taxon/apni/51436506,Qld -Acmena graveolens,,,,,,,,, -Acronychia acidula,APC,species,accepted,Acronychia,Acronychia acidula,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913200,Qld -Aleurites rockinghamensis,,,,,,,,, -Alphitonia petriei,APC,species,accepted,Alphitonia,Alphitonia petriei,,Rhamnaceae,https://id.biodiversity.org.au/node/apni/2887911,"Qld, NSW" -Alstonia scholaris,,,,,,,,, -Argyrodendron peralatum,,,,,,,,, -Atractocarpus hirtus,,,,,,,,, -Brombya platynema,,,,,,,,, -Cardwellia sublimis,,,,,,,,, -Castanospermum australe,,,,,,,,, -Cleistanthus myrianthus,,,,,,,,, -Cryptocarya laevigata,,,,,,,,, -Cryptocarya mackinnoniana,,,,,,,,, -Cryptocarya murrayi,,,,,,,,, -Dendrocnide moroides,,,,,,,,, -Elaeocarpus grandis,,,,,,,,, -Endiandra leptodendron,,,,,,,,, -Endiandra microneura,,,,,,,,, -Gillbeea adenopetala,,,,,,,,, -Glochidion hylandii,APC,species,accepted,Glochidion,Glochidion hylandii,,Phyllanthaceae,https://id.biodiversity.org.au/node/apni/2889113,Qld -Haplostichanthus submontanus,,,,,,,,, -Harpullia rhyticarpa,,,,,,,,, -Hernandia albiflora,,,,,,,,, -Homalanthus novo-guineensis,,,,,,,,, -Ixora biflora,,,,,,,,, -Lasianthus strigosus,,,,,,,,, -Litsea leefeana,,,,,,,,, -Macaranga tanarius,,,,,,,,, -Mallotus mollissimus,,,,,,,,, -Medicosma sessiliflora,,,,,,,,, -Melastoma cyanoides,,,,,,,,, -Melicope elleryana,APC,species,accepted,Melicope,Melicope elleryana,,Rutaceae,https://id.biodiversity.org.au/node/apni/2913641,"WA, NT, Qld, NSW" -Myristica insipida,,,,,,,,, -Neolitsea dealbata,,,,,,,,, -Pittosporum rubiginosum,,,,,,,,, -Polyscias australiana,,,,,,,,, -Psychotria dallachiana,,,,,,,,, -Psychotria sp. Utchee Creek (H.Flecker NQNC5313),,,,,,,,, -Quassia baileyana,,,,,,,,, -Rhodomyrtus trineura,,,,,,,,, -Rockinghamia angustifolia,,,,,,,,, -Syzygium gustavioides,,,,,,,,, -Syzygium sayeri,,,,,,,,, -Trema aspera,,,,,,,,, +original_name,taxon_name,taxon_name_alternatives,genus,family,taxon_rank,taxonomic_dataset,taxonomic_status,subclass,taxon_distribution,scientific_name,taxon_id,taxon_ID_genus,scientific_name_id,canonical_name,cleaned_scientific_name_id,taxon_id_family,trinomial,binomial,establishment_means +Acacia celsa,Acacia celsa,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,Qld,Acacia celsa Tindale,https://id.biodiversity.org.au/taxon/apni/51436506,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/154988,Acacia celsa,https://id.biodiversity.org.au/name/apni/154988,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia celsa,native +Acronychia acidula,Acronychia acidula,,Acronychia,Rutaceae,species,APC,accepted,Magnoliidae,Qld,Acronychia acidula F.Muell.,https://id.biodiversity.org.au/node/apni/2913200,https://id.biodiversity.org.au/taxon/apni/51446847,https://id.biodiversity.org.au/name/apni/73794,Acronychia acidula,https://id.biodiversity.org.au/name/apni/73794,https://id.biodiversity.org.au/taxon/apni/51461748,,Acronychia acidula,native +Aleurites rockinghamensis,Aleurites rockinghamensis,,Aleurites,Euphorbiaceae,species,APC,accepted,Magnoliidae,Qld,Aleurites rockinghamensis (Baill.) P.I.Forst.,https://id.biodiversity.org.au/node/apni/2916622,https://id.biodiversity.org.au/node/apni/2900410,https://id.biodiversity.org.au/name/apni/171057,Aleurites rockinghamensis,https://id.biodiversity.org.au/name/apni/171057,https://id.biodiversity.org.au/taxon/apni/51442249,,Aleurites rockinghamensis,native +Alphitonia petriei,Alphitonia petriei,,Alphitonia,Rhamnaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Alphitonia petriei Braid & C.T.White,https://id.biodiversity.org.au/node/apni/2887911,https://id.biodiversity.org.au/taxon/apni/51446205,https://id.biodiversity.org.au/name/apni/82935,Alphitonia petriei,https://id.biodiversity.org.au/name/apni/82935,https://id.biodiversity.org.au/taxon/apni/51446206,,Alphitonia petriei,native +Alstonia scholaris,Alstonia scholaris,,Alstonia,Apocynaceae,species,APC,accepted,Magnoliidae,Qld,Alstonia scholaris (L.) R.Br.,https://id.biodiversity.org.au/node/apni/2916809,https://id.biodiversity.org.au/node/apni/6684160,https://id.biodiversity.org.au/name/apni/83915,Alstonia scholaris,https://id.biodiversity.org.au/name/apni/83915,https://id.biodiversity.org.au/taxon/apni/51700686,,Alstonia scholaris,native +Argyrodendron peralatum,Argyrodendron peralatum,,Argyrodendron,Malvaceae,species,APC,accepted,Magnoliidae,Qld,Argyrodendron peralatum (F.M.Bailey) Edlin ex I.H.Boas,https://id.biodiversity.org.au/node/apni/2915243,https://id.biodiversity.org.au/taxon/apni/51288410,https://id.biodiversity.org.au/name/apni/100216,Argyrodendron peralatum,https://id.biodiversity.org.au/name/apni/100216,https://id.biodiversity.org.au/taxon/apni/51439248,,Argyrodendron peralatum,native +Atractocarpus hirtus,Atractocarpus hirtus,,Atractocarpus,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Atractocarpus hirtus (F.Muell.) Puttock,https://id.biodiversity.org.au/node/apni/2910460,https://id.biodiversity.org.au/taxon/apni/51446611,https://id.biodiversity.org.au/name/apni/146883,Atractocarpus hirtus,https://id.biodiversity.org.au/name/apni/146883,https://id.biodiversity.org.au/taxon/apni/51446612,,Atractocarpus hirtus,native +Brombya platynema,Brombya platynema,,Brombya,Rutaceae,species,APC,accepted,Magnoliidae,Qld,Brombya platynema F.Muell.,https://id.biodiversity.org.au/node/apni/2890280,https://id.biodiversity.org.au/node/apni/7937668,https://id.biodiversity.org.au/name/apni/67607,Brombya platynema,https://id.biodiversity.org.au/name/apni/67607,https://id.biodiversity.org.au/taxon/apni/51461748,,Brombya platynema,native +Cardwellia sublimis,Cardwellia sublimis,,Cardwellia,Proteaceae,species,APC,accepted,Magnoliidae,Qld,Cardwellia sublimis F.Muell.,https://id.biodiversity.org.au/node/apni/2899253,https://id.biodiversity.org.au/node/apni/2908094,https://id.biodiversity.org.au/name/apni/109268,Cardwellia sublimis,https://id.biodiversity.org.au/name/apni/109268,https://id.biodiversity.org.au/taxon/apni/51614274,,Cardwellia sublimis,native +Castanospermum australe,Castanospermum australe,,Castanospermum,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, NI (doubtfully naturalised)",Castanospermum australe A.Cunn. ex Mudie,https://id.biodiversity.org.au/node/apni/2894943,https://id.biodiversity.org.au/node/apni/7226268,https://id.biodiversity.org.au/name/apni/196675,Castanospermum australe,https://id.biodiversity.org.au/name/apni/196675,https://id.biodiversity.org.au/taxon/apni/51702961,,Castanospermum australe,native and naturalised +Cleistanthus myrianthus,Cleistanthus myrianthus,,Cleistanthus,Phyllanthaceae,species,APC,accepted,Magnoliidae,Qld,Cleistanthus myrianthus (Hassk.) Kurz,https://id.biodiversity.org.au/node/apni/2897700,https://id.biodiversity.org.au/node/apni/2914326,https://id.biodiversity.org.au/name/apni/71354,Cleistanthus myrianthus,https://id.biodiversity.org.au/name/apni/71354,https://id.biodiversity.org.au/taxon/apni/51442162,,Cleistanthus myrianthus,native +Cryptocarya laevigata,Cryptocarya laevigata,,Cryptocarya,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Cryptocarya laevigata Blume,https://id.biodiversity.org.au/node/apni/2903400,https://id.biodiversity.org.au/taxon/apni/51438401,https://id.biodiversity.org.au/name/apni/88410,Cryptocarya laevigata,https://id.biodiversity.org.au/name/apni/88410,https://id.biodiversity.org.au/taxon/apni/51438397,,Cryptocarya laevigata,native +Cryptocarya mackinnoniana,Cryptocarya mackinnoniana,,Cryptocarya,Lauraceae,species,APC,accepted,Magnoliidae,Qld,Cryptocarya mackinnoniana F.Muell.,https://id.biodiversity.org.au/node/apni/2914946,https://id.biodiversity.org.au/taxon/apni/51438401,https://id.biodiversity.org.au/name/apni/88421,Cryptocarya mackinnoniana,https://id.biodiversity.org.au/name/apni/88421,https://id.biodiversity.org.au/taxon/apni/51438397,,Cryptocarya mackinnoniana,native +Cryptocarya murrayi,Cryptocarya murrayi,,Cryptocarya,Lauraceae,species,APC,accepted,Magnoliidae,Qld,Cryptocarya murrayi F.Muell.,https://id.biodiversity.org.au/node/apni/2910393,https://id.biodiversity.org.au/taxon/apni/51438401,https://id.biodiversity.org.au/name/apni/88472,Cryptocarya murrayi,https://id.biodiversity.org.au/name/apni/88472,https://id.biodiversity.org.au/taxon/apni/51438397,,Cryptocarya murrayi,native +Dendrocnide moroides,Dendrocnide moroides,,Dendrocnide,Urticaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Dendrocnide moroides (Wedd.) Chew,https://id.biodiversity.org.au/node/apni/2904177,https://id.biodiversity.org.au/taxon/apni/51448284,https://id.biodiversity.org.au/name/apni/86919,Dendrocnide moroides,https://id.biodiversity.org.au/name/apni/86919,https://id.biodiversity.org.au/taxon/apni/51662052,,Dendrocnide moroides,native +Elaeocarpus grandis,Elaeocarpus grandis,,Elaeocarpus,Elaeocarpaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Elaeocarpus grandis F.Muell.,https://id.biodiversity.org.au/node/apni/2895259,https://id.biodiversity.org.au/taxon/apni/51435153,https://id.biodiversity.org.au/name/apni/115772,Elaeocarpus grandis,https://id.biodiversity.org.au/name/apni/115772,https://id.biodiversity.org.au/taxon/apni/51632282,,Elaeocarpus grandis,native +Endiandra leptodendron,Endiandra leptodendron,,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,Qld,Endiandra leptodendron B.Hyland,https://id.biodiversity.org.au/node/apni/2910725,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111888,Endiandra leptodendron,https://id.biodiversity.org.au/name/apni/111888,https://id.biodiversity.org.au/taxon/apni/51438397,,Endiandra leptodendron,native +Endiandra microneura,Endiandra microneura,,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,Qld,Endiandra microneura C.T.White,https://id.biodiversity.org.au/node/apni/2899314,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111949,Endiandra microneura,https://id.biodiversity.org.au/name/apni/111949,https://id.biodiversity.org.au/taxon/apni/51438397,,Endiandra microneura,native +Gillbeea adenopetala,Gillbeea adenopetala,,Gillbeea,Cunoniaceae,species,APC,accepted,Magnoliidae,Qld,Gillbeea adenopetala F.Muell.,https://id.biodiversity.org.au/node/apni/2913815,https://id.biodiversity.org.au/node/apni/2918249,https://id.biodiversity.org.au/name/apni/98098,Gillbeea adenopetala,https://id.biodiversity.org.au/name/apni/98098,https://id.biodiversity.org.au/taxon/apni/51434138,,Gillbeea adenopetala,native +Glochidion hylandii,Glochidion hylandii,,Glochidion,Phyllanthaceae,species,APC,accepted,Magnoliidae,Qld,Glochidion hylandii Airy Shaw,https://id.biodiversity.org.au/node/apni/2889113,https://id.biodiversity.org.au/node/apni/8387508,https://id.biodiversity.org.au/name/apni/78303,Glochidion hylandii,https://id.biodiversity.org.au/name/apni/78303,https://id.biodiversity.org.au/taxon/apni/51442162,,Glochidion hylandii,native +Harpullia rhyticarpa,Harpullia rhyticarpa,,Harpullia,Sapindaceae,species,APC,accepted,Magnoliidae,Qld,Harpullia rhyticarpa C.T.White & W.D.Francis,https://id.biodiversity.org.au/node/apni/2910766,https://id.biodiversity.org.au/taxon/apni/51447330,https://id.biodiversity.org.au/name/apni/108928,Harpullia rhyticarpa,https://id.biodiversity.org.au/name/apni/108928,https://id.biodiversity.org.au/taxon/apni/51447212,,Harpullia rhyticarpa,native +Hernandia albiflora,Hernandia albiflora,,Hernandia,Hernandiaceae,species,APC,accepted,Magnoliidae,Qld,Hernandia albiflora (C.T.White) Kubitzki,https://id.biodiversity.org.au/node/apni/2911354,https://id.biodiversity.org.au/taxon/apni/51437691,https://id.biodiversity.org.au/name/apni/92773,Hernandia albiflora,https://id.biodiversity.org.au/name/apni/92773,https://id.biodiversity.org.au/taxon/apni/51437692,,Hernandia albiflora,native +Homalanthus novoguineensis,Homalanthus novo-guineensis,,Homalanthus,Euphorbiaceae,species,APC,accepted,Magnoliidae,"WA (native and naturalised), NT, Qld",Homalanthus novo-guineensis (Warb.) Lauterb. & K.Schum.,https://id.biodiversity.org.au/node/apni/2888327,https://id.biodiversity.org.au/node/apni/4932846,https://id.biodiversity.org.au/name/apni/130383,Homalanthus novo-guineensis,https://id.biodiversity.org.au/name/apni/130383,https://id.biodiversity.org.au/taxon/apni/51442249,,Homalanthus novo-guineensis,native and naturalised +Ixora biflora,Ixora biflora,,Ixora,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Ixora biflora Fosberg,https://id.biodiversity.org.au/node/apni/2915627,https://id.biodiversity.org.au/taxon/apni/51446659,https://id.biodiversity.org.au/name/apni/90479,Ixora biflora,https://id.biodiversity.org.au/name/apni/90479,https://id.biodiversity.org.au/taxon/apni/51446612,,Ixora biflora,native +Lasianthus strigosus,Lasianthus chlorocarpus,,Lasianthus,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Lasianthus chlorocarpus K.Schum.,https://id.biodiversity.org.au/node/apni/7839740,https://id.biodiversity.org.au/node/apni/8136656,https://id.biodiversity.org.au/name/apni/219373,Lasianthus chlorocarpus,https://id.biodiversity.org.au/name/apni/71294,https://id.biodiversity.org.au/taxon/apni/51446612,,Lasianthus chlorocarpus,native +Litsea leefeana,Litsea leefeana,,Litsea,Lauraceae,species,APC,accepted,Magnoliidae,Qld,Litsea leefeana (F.Muell.) Merr.,https://id.biodiversity.org.au/node/apni/2921063,https://id.biodiversity.org.au/taxon/apni/51438430,https://id.biodiversity.org.au/name/apni/81094,Litsea leefeana,https://id.biodiversity.org.au/name/apni/81094,https://id.biodiversity.org.au/taxon/apni/51438397,,Litsea leefeana,native +Macaranga tanarius,Macaranga tanarius,,Macaranga,Euphorbiaceae,species,APC,accepted,Magnoliidae,"ChI, NT, Qld, NSW",Macaranga tanarius (L.) Müll.Arg.,https://id.biodiversity.org.au/node/apni/2902044,https://id.biodiversity.org.au/node/apni/2900788,https://id.biodiversity.org.au/name/apni/57015,Macaranga tanarius,https://id.biodiversity.org.au/name/apni/57015,https://id.biodiversity.org.au/taxon/apni/51442249,,Macaranga tanarius,native +Mallotus mollissimus,Mallotus mollissimus,,Mallotus,Euphorbiaceae,species,APC,accepted,Magnoliidae,Qld,Mallotus mollissimus (Geiseler) Airy Shaw,https://id.biodiversity.org.au/node/apni/2904445,https://id.biodiversity.org.au/taxon/apni/51284195,https://id.biodiversity.org.au/name/apni/59376,Mallotus mollissimus,https://id.biodiversity.org.au/name/apni/59376,https://id.biodiversity.org.au/taxon/apni/51442249,,Mallotus mollissimus,native +Medicosma sessiliflora,Medicosma sessiliflora,,Medicosma,Rutaceae,species,APC,accepted,Magnoliidae,Qld,Medicosma sessiliflora (C.T.White) T.G.Hartley,https://id.biodiversity.org.au/node/apni/2914896,https://id.biodiversity.org.au/taxon/apni/51446918,https://id.biodiversity.org.au/name/apni/73658,Medicosma sessiliflora,https://id.biodiversity.org.au/name/apni/73658,https://id.biodiversity.org.au/taxon/apni/51461748,,Medicosma sessiliflora,native +Melastoma cyanoides,Melastoma cyanoides,,Melastoma,Melastomataceae,species,APC,accepted,Magnoliidae,Qld,Melastoma cyanoides Sm.,https://id.biodiversity.org.au/node/apni/2895184,https://id.biodiversity.org.au/taxon/apni/51439399,https://id.biodiversity.org.au/name/apni/172752,Melastoma cyanoides,https://id.biodiversity.org.au/name/apni/172752,https://id.biodiversity.org.au/taxon/apni/51439392,,Melastoma cyanoides,native +Melicope elleryana,Melicope elleryana,,Melicope,Rutaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Melicope elleryana (F.Muell.) T.G.Hartley,https://id.biodiversity.org.au/node/apni/2913641,https://id.biodiversity.org.au/node/apni/2918609,https://id.biodiversity.org.au/name/apni/118560,Melicope elleryana,https://id.biodiversity.org.au/name/apni/118560,https://id.biodiversity.org.au/taxon/apni/51461748,,Melicope elleryana,native +Myristica insipida,Myristica insipida,,Myristica,Myristicaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Myristica insipida R.Br.,https://id.biodiversity.org.au/node/apni/2902429,https://id.biodiversity.org.au/node/apni/2895962,https://id.biodiversity.org.au/name/apni/86064,Myristica insipida,https://id.biodiversity.org.au/name/apni/86064,https://id.biodiversity.org.au/node/apni/2903136,,Myristica insipida,native +Neolitsea dealbata,Neolitsea dealbata,,Neolitsea,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Neolitsea dealbata (R.Br.) Merr.,https://id.biodiversity.org.au/node/apni/2910025,https://id.biodiversity.org.au/node/apni/2914447,https://id.biodiversity.org.au/name/apni/79589,Neolitsea dealbata,https://id.biodiversity.org.au/name/apni/79589,https://id.biodiversity.org.au/taxon/apni/51438397,,Neolitsea dealbata,native +Pittosporum rubiginosum,Pittosporum rubiginosum,,Pittosporum,Pittosporaceae,species,APC,accepted,Magnoliidae,Qld,Pittosporum rubiginosum A.Cunn.,https://id.biodiversity.org.au/node/apni/2887772,https://id.biodiversity.org.au/taxon/apni/51442349,https://id.biodiversity.org.au/name/apni/100119,Pittosporum rubiginosum,https://id.biodiversity.org.au/name/apni/100119,https://id.biodiversity.org.au/taxon/apni/51442315,,Pittosporum rubiginosum,native +Haplostichanthus sp Coop. Ck,Polyalthia submontana,,Polyalthia,Annonaceae,species,APC,accepted,Magnoliidae,Qld,Polyalthia submontana (Jessup) B.Xue & R.M.K.Saunders,https://id.biodiversity.org.au/taxon/apni/51613975,https://id.biodiversity.org.au/taxon/apni/51613976,https://id.biodiversity.org.au/name/apni/246294,Polyalthia submontana,https://id.biodiversity.org.au/name/apni/191525,https://id.biodiversity.org.au/taxon/apni/51613977,,Polyalthia submontana,native +Polyscias australiana,Polyscias australiana,,Polyscias,Araliaceae,species,APC,accepted,Magnoliidae,"NT, Qld",Polyscias australiana (F.Muell.) Philipson,https://id.biodiversity.org.au/node/apni/7223338,https://id.biodiversity.org.au/taxon/apni/51292784,https://id.biodiversity.org.au/name/apni/84802,Polyscias australiana,https://id.biodiversity.org.au/name/apni/84787,https://id.biodiversity.org.au/taxon/apni/51632289,,Polyscias australiana,native +Psychotria dallachiana,Psychotria dallachiana,,Psychotria,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Psychotria dallachiana Benth.,https://id.biodiversity.org.au/node/apni/2890013,https://id.biodiversity.org.au/taxon/apni/51446698,https://id.biodiversity.org.au/name/apni/89074,Psychotria dallachiana,https://id.biodiversity.org.au/name/apni/89074,https://id.biodiversity.org.au/taxon/apni/51446612,,Psychotria dallachiana,native +Psychotria sp Utchee Creek,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),,Psychotria,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Psychotria sp. Utchee Creek (H.Flecker NQNC5313) Qld Herbarium,https://id.biodiversity.org.au/taxon/apni/51446727,https://id.biodiversity.org.au/taxon/apni/51446698,https://id.biodiversity.org.au/name/apni/218829,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),https://id.biodiversity.org.au/name/apni/218829,https://id.biodiversity.org.au/taxon/apni/51446612,,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),native +Rhodomyrtus trineura,Rhodomyrtus trineura,,Rhodomyrtus,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Rhodomyrtus trineura (F.Muell.) Benth.,https://id.biodiversity.org.au/taxon/apni/51441176,https://id.biodiversity.org.au/taxon/apni/51441177,https://id.biodiversity.org.au/name/apni/69289,Rhodomyrtus trineura,https://id.biodiversity.org.au/name/apni/69289,https://id.biodiversity.org.au/taxon/apni/51702983,,Rhodomyrtus trineura,native +Rockinghamia angustifolia,Rockinghamia angustifolia,,Rockinghamia,Euphorbiaceae,species,APC,accepted,Magnoliidae,Qld,Rockinghamia angustifolia (Benth.) Airy Shaw,https://id.biodiversity.org.au/node/apni/2921179,https://id.biodiversity.org.au/node/apni/2892697,https://id.biodiversity.org.au/name/apni/61487,Rockinghamia angustifolia,https://id.biodiversity.org.au/name/apni/61487,https://id.biodiversity.org.au/taxon/apni/51442249,,Rockinghamia angustifolia,native +Quassia baileyana,Samadera baileyana,,Samadera,Simaroubaceae,species,APC,accepted,Magnoliidae,Qld,Samadera baileyana Oliv.,https://id.biodiversity.org.au/node/apni/2891526,https://id.biodiversity.org.au/node/apni/2900441,https://id.biodiversity.org.au/name/apni/60763,Samadera baileyana,https://id.biodiversity.org.au/name/apni/70084,https://id.biodiversity.org.au/taxon/apni/51316490,,Samadera baileyana,native +Acmena graveolens,Syzygium graveolens,,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium graveolens (F.M.Bailey) Craven & Biffin,https://id.biodiversity.org.au/node/apni/2920364,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/202985,Syzygium graveolens,https://id.biodiversity.org.au/name/apni/73535,https://id.biodiversity.org.au/taxon/apni/51702983,,Syzygium graveolens,native +Syzygium gustavioides,Syzygium gustavioides,,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium gustavioides (F.M.Bailey) B.Hyland,https://id.biodiversity.org.au/taxon/apni/51429676,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/64722,Syzygium gustavioides,https://id.biodiversity.org.au/name/apni/64722,https://id.biodiversity.org.au/taxon/apni/51702983,,Syzygium gustavioides,native +Syzygium sayeri,Syzygium sayeri,,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium sayeri (F.Muell.) B.Hyland,https://id.biodiversity.org.au/node/apni/2888968,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/64837,Syzygium sayeri,https://id.biodiversity.org.au/name/apni/64837,https://id.biodiversity.org.au/taxon/apni/51702983,,Syzygium sayeri,native +Trema aspera,Trema tomentosa var. aspera,,Trema,Cannabaceae,variety,APC,accepted,Magnoliidae,"WA, Qld, NSW, Vic (presumed extinct)",Trema tomentosa var. aspera (Brongn.) Hewson,https://id.biodiversity.org.au/node/apni/2917190,https://id.biodiversity.org.au/node/apni/2913617,https://id.biodiversity.org.au/name/apni/206199,Trema tomentosa var. aspera,https://id.biodiversity.org.au/name/apni/101838,https://id.biodiversity.org.au/taxon/apni/51269919,Trema tomentosa var. aspera,Trema tomentosa,native diff --git a/tests/testthat/examples/Test_2023_2/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_2/output/taxonomic_updates.csv index 35d71e1c..25fc280d 100644 --- a/tests/testthat/examples/Test_2023_2/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_2/output/taxonomic_updates.csv @@ -1,46 +1,46 @@ dataset_id,original_name,aligned_name,taxonomic_resolution,taxon_name Test_2023_2,Acacia celsa,Acacia celsa,,Acacia celsa -Test_2023_2,Acmena graveolens,Acmena graveolens,, +Test_2023_2,Acmena graveolens,Acmena graveolens,,Syzygium graveolens Test_2023_2,Acronychia acidula,Acronychia acidula,,Acronychia acidula -Test_2023_2,Aleurites rockinghamensis,Aleurites rockinghamensis,, +Test_2023_2,Aleurites rockinghamensis,Aleurites rockinghamensis,,Aleurites rockinghamensis Test_2023_2,Alphitonia petriei,Alphitonia petriei,,Alphitonia petriei -Test_2023_2,Alstonia scholaris,Alstonia scholaris,, -Test_2023_2,Argyrodendron peralatum,Argyrodendron peralatum,, -Test_2023_2,Atractocarpus hirtus,Atractocarpus hirtus,, -Test_2023_2,Brombya platynema,Brombya platynema,, -Test_2023_2,Cardwellia sublimis,Cardwellia sublimis,, -Test_2023_2,Castanospermum australe,Castanospermum australe,, -Test_2023_2,Cleistanthus myrianthus,Cleistanthus myrianthus,, -Test_2023_2,Cryptocarya laevigata,Cryptocarya laevigata,, -Test_2023_2,Cryptocarya mackinnoniana,Cryptocarya mackinnoniana,, -Test_2023_2,Cryptocarya murrayi,Cryptocarya murrayi,, -Test_2023_2,Dendrocnide moroides,Dendrocnide moroides,, -Test_2023_2,Elaeocarpus grandis,Elaeocarpus grandis,, -Test_2023_2,Endiandra leptodendron,Endiandra leptodendron,, -Test_2023_2,Endiandra microneura,Endiandra microneura,, -Test_2023_2,Gillbeea adenopetala,Gillbeea adenopetala,, +Test_2023_2,Alstonia scholaris,Alstonia scholaris,,Alstonia scholaris +Test_2023_2,Argyrodendron peralatum,Argyrodendron peralatum,,Argyrodendron peralatum +Test_2023_2,Atractocarpus hirtus,Atractocarpus hirtus,,Atractocarpus hirtus +Test_2023_2,Brombya platynema,Brombya platynema,,Brombya platynema +Test_2023_2,Cardwellia sublimis,Cardwellia sublimis,,Cardwellia sublimis +Test_2023_2,Castanospermum australe,Castanospermum australe,,Castanospermum australe +Test_2023_2,Cleistanthus myrianthus,Cleistanthus myrianthus,,Cleistanthus myrianthus +Test_2023_2,Cryptocarya laevigata,Cryptocarya laevigata,,Cryptocarya laevigata +Test_2023_2,Cryptocarya mackinnoniana,Cryptocarya mackinnoniana,,Cryptocarya mackinnoniana +Test_2023_2,Cryptocarya murrayi,Cryptocarya murrayi,,Cryptocarya murrayi +Test_2023_2,Dendrocnide moroides,Dendrocnide moroides,,Dendrocnide moroides +Test_2023_2,Elaeocarpus grandis,Elaeocarpus grandis,,Elaeocarpus grandis +Test_2023_2,Endiandra leptodendron,Endiandra leptodendron,,Endiandra leptodendron +Test_2023_2,Endiandra microneura,Endiandra microneura,,Endiandra microneura +Test_2023_2,Gillbeea adenopetala,Gillbeea adenopetala,,Gillbeea adenopetala Test_2023_2,Glochidion hylandii,Glochidion hylandii,,Glochidion hylandii -Test_2023_2,Haplostichanthus sp Coop. Ck,Haplostichanthus submontanus,species, -Test_2023_2,Harpullia rhyticarpa,Harpullia rhyticarpa,, -Test_2023_2,Hernandia albiflora,Hernandia albiflora,, -Test_2023_2,Homalanthus novoguineensis,Homalanthus novo-guineensis,species, -Test_2023_2,Ixora biflora,Ixora biflora,, -Test_2023_2,Lasianthus strigosus,Lasianthus strigosus,, -Test_2023_2,Litsea leefeana,Litsea leefeana,, -Test_2023_2,Macaranga tanarius,Macaranga tanarius,, -Test_2023_2,Mallotus mollissimus,Mallotus mollissimus,, -Test_2023_2,Medicosma sessiliflora,Medicosma sessiliflora,, -Test_2023_2,Melastoma cyanoides,Melastoma cyanoides,, +Test_2023_2,Haplostichanthus sp Coop. Ck,Haplostichanthus submontanus,species,Polyalthia submontana +Test_2023_2,Harpullia rhyticarpa,Harpullia rhyticarpa,,Harpullia rhyticarpa +Test_2023_2,Hernandia albiflora,Hernandia albiflora,,Hernandia albiflora +Test_2023_2,Homalanthus novoguineensis,Homalanthus novo-guineensis,species,Homalanthus novo-guineensis +Test_2023_2,Ixora biflora,Ixora biflora,,Ixora biflora +Test_2023_2,Lasianthus strigosus,Lasianthus strigosus,,Lasianthus chlorocarpus +Test_2023_2,Litsea leefeana,Litsea leefeana,,Litsea leefeana +Test_2023_2,Macaranga tanarius,Macaranga tanarius,,Macaranga tanarius +Test_2023_2,Mallotus mollissimus,Mallotus mollissimus,,Mallotus mollissimus +Test_2023_2,Medicosma sessiliflora,Medicosma sessiliflora,,Medicosma sessiliflora +Test_2023_2,Melastoma cyanoides,Melastoma cyanoides,,Melastoma cyanoides Test_2023_2,Melicope elleryana,Melicope elleryana,,Melicope elleryana -Test_2023_2,Myristica insipida,Myristica insipida,, -Test_2023_2,Neolitsea dealbata,Neolitsea dealbata,, -Test_2023_2,Pittosporum rubiginosum,Pittosporum rubiginosum,, -Test_2023_2,Polyscias australiana,Polyscias australiana,, -Test_2023_2,Psychotria dallachiana,Psychotria dallachiana,, -Test_2023_2,Psychotria sp Utchee Creek,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),species, -Test_2023_2,Quassia baileyana,Quassia baileyana,, -Test_2023_2,Rhodomyrtus trineura,Rhodomyrtus trineura,, -Test_2023_2,Rockinghamia angustifolia,Rockinghamia angustifolia,, -Test_2023_2,Syzygium gustavioides,Syzygium gustavioides,, -Test_2023_2,Syzygium sayeri,Syzygium sayeri,, -Test_2023_2,Trema aspera,Trema aspera,, +Test_2023_2,Myristica insipida,Myristica insipida,,Myristica insipida +Test_2023_2,Neolitsea dealbata,Neolitsea dealbata,,Neolitsea dealbata +Test_2023_2,Pittosporum rubiginosum,Pittosporum rubiginosum,,Pittosporum rubiginosum +Test_2023_2,Polyscias australiana,Polyscias australiana,,Polyscias australiana +Test_2023_2,Psychotria dallachiana,Psychotria dallachiana,,Psychotria dallachiana +Test_2023_2,Psychotria sp Utchee Creek,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),species,Psychotria sp. Utchee Creek (H.Flecker NQNC5313) +Test_2023_2,Quassia baileyana,Quassia baileyana,,Samadera baileyana +Test_2023_2,Rhodomyrtus trineura,Rhodomyrtus trineura,,Rhodomyrtus trineura +Test_2023_2,Rockinghamia angustifolia,Rockinghamia angustifolia,,Rockinghamia angustifolia +Test_2023_2,Syzygium gustavioides,Syzygium gustavioides,,Syzygium gustavioides +Test_2023_2,Syzygium sayeri,Syzygium sayeri,,Syzygium sayeri +Test_2023_2,Trema aspera,Trema aspera,,Trema tomentosa var. aspera diff --git a/tests/testthat/examples/Test_2023_2/output/traits.csv b/tests/testthat/examples/Test_2023_2/output/traits.csv index 3b955ce4..1911c42e 100644 --- a/tests/testthat/examples/Test_2023_2/output/traits.csv +++ b/tests/testthat/examples/Test_2023_2/output/traits.csv @@ -21,15 +21,15 @@ Test_2023_2,Acacia celsa,006,leaf_N_per_dry_mass,21.4,mg/g,species,raw,measureme Test_2023_2,Acacia celsa,006,leaf_area,2786,mm2,species,raw,measurement,1,field,adult,,,,,Test_2022,,,,,2004-03,,01,,Acacia celsa Test_2023_2,Acacia celsa,006,leaf_mass_per_area,145,g/m2,species,raw,measurement,1,field,adult,,,,,Test_2022,,,,,2004-03,,01,,Acacia celsa Test_2023_2,Acacia celsa,006,wood_density,0.498,mg/mm3,species,raw,measurement,1,field,adult,,,,,Test_2022,,,,,2004-03,,01,,Acacia celsa -Test_2023_2,Acmena graveolens,007,branch_mass_fraction,0.67,mg/mg,population,,,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Acmena graveolens -Test_2023_2,Acmena graveolens,007,huber_value,0.000139742873113471,mm2{sapwood}/mm2{leaf},population,mean,,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Acmena graveolens -Test_2023_2,Acmena graveolens,007,huber_value,0.000139742873113471,mm2{sapwood}/mm2{leaf},population,maximum,,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Acmena graveolens -Test_2023_2,Acmena graveolens,007,huber_value,0.000327118089630357,mm2{sapwood}/mm2{leaf},population,,,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Acmena graveolens -Test_2023_2,Acmena graveolens,007,huber_value,0.000374953130858643,mm2{sapwood}/mm2{leaf},population,,,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Acmena graveolens -Test_2023_2,Acmena graveolens,008,leaf_N_per_dry_mass,15.5,mg/g,species,,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Acmena graveolens -Test_2023_2,Acmena graveolens,008,leaf_area,5246,mm2,species,,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Acmena graveolens -Test_2023_2,Acmena graveolens,008,leaf_mass_per_area,151,g/m2,species,,measurement,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Acmena graveolens -Test_2023_2,Acmena graveolens,008,wood_density,0.599,mg/mm3,species,,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Acmena graveolens +Test_2023_2,Syzygium graveolens,007,branch_mass_fraction,0.67,mg/mg,population,,,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Acmena graveolens +Test_2023_2,Syzygium graveolens,007,huber_value,0.000139742873113471,mm2{sapwood}/mm2{leaf},population,mean,,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Acmena graveolens +Test_2023_2,Syzygium graveolens,007,huber_value,0.000139742873113471,mm2{sapwood}/mm2{leaf},population,maximum,,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Acmena graveolens +Test_2023_2,Syzygium graveolens,007,huber_value,0.000327118089630357,mm2{sapwood}/mm2{leaf},population,,,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Acmena graveolens +Test_2023_2,Syzygium graveolens,007,huber_value,0.000374953130858643,mm2{sapwood}/mm2{leaf},population,,,,field_experiment,juvenile,02,,,,Test_2002,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Acmena graveolens +Test_2023_2,Syzygium graveolens,008,leaf_N_per_dry_mass,15.5,mg/g,species,,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Acmena graveolens +Test_2023_2,Syzygium graveolens,008,leaf_area,5246,mm2,species,,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Acmena graveolens +Test_2023_2,Syzygium graveolens,008,leaf_mass_per_area,151,g/m2,species,,measurement,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Acmena graveolens +Test_2023_2,Syzygium graveolens,008,wood_density,0.599,mg/mm3,species,,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Acmena graveolens Test_2023_2,Acronychia acidula,009,branch_mass_fraction,0.48,mg/mg,population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,,Made-up remarks for `branch_mass_fraction`,01,,Acronychia acidula Test_2023_2,Acronychia acidula,009,huber_value,0.000132275132275132,mm2{sapwood}/mm2{leaf},population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,,,02,,Acronychia acidula Test_2023_2,Acronychia acidula,009,huber_value,0.000180472838837755,mm2{sapwood}/mm2{leaf},population,raw,measurement,1,field,adult,01,,,,Test_2022,01,,,,,,03,,Acronychia acidula @@ -216,16 +216,16 @@ Test_2023_2,Glochidion hylandii,048,leaf_N_per_dry_mass,13.7,mg/g,species,mean,m Test_2023_2,Glochidion hylandii,048,leaf_area,3209,mm2,species,mean,measurement,3,field,adult,,,,,Test_2002,,,,,,,01,,Glochidion hylandii Test_2023_2,Glochidion hylandii,048,leaf_mass_per_area,106,g/m2,species,mean,measurement,3,field,adult,,,,,Test_2002,,,,,,,01,,Glochidion hylandii Test_2023_2,Glochidion hylandii,048,wood_density,0.566,mg/mm3,species,mean,measurement,3,field,adult,,,,,Test_2002,,,,,,,01,,Glochidion hylandii -Test_2023_2,Haplostichanthus submontanus,049,branch_mass_fraction,0.36,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Haplostichanthus sp Coop. Ck -Test_2023_2,Haplostichanthus submontanus,049,huber_value,0.000411522633744856,mm2{sapwood}/mm2{leaf},population,mean,unknown,7,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Haplostichanthus sp Coop. Ck -Test_2023_2,Haplostichanthus submontanus,049,huber_value,8.12743823146944e-05,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Haplostichanthus sp Coop. Ck -Test_2023_2,Haplostichanthus submontanus,049,huber_value,0.000304692260816575,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Haplostichanthus sp Coop. Ck -Test_2023_2,Haplostichanthus submontanus,049,huber_value,0.000334224598930481,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Haplostichanthus sp Coop. Ck -Test_2023_2,Haplostichanthus submontanus,049,huber_value,0.000334224598930481,mm2{sapwood}/mm2{leaf},population,maximum,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Haplostichanthus sp Coop. Ck -Test_2023_2,Haplostichanthus submontanus,050,leaf_N_per_dry_mass,22,mg/g,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Haplostichanthus sp Coop. Ck -Test_2023_2,Haplostichanthus submontanus,050,leaf_area,4685,mm2,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Haplostichanthus sp Coop. Ck -Test_2023_2,Haplostichanthus submontanus,050,leaf_mass_per_area,72,g/m2,species,mean,measurement,2,field,,,,,,Test_2022,,,,,,,01,,Haplostichanthus sp Coop. Ck -Test_2023_2,Haplostichanthus submontanus,050,wood_density,0.668,mg/mm3,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Haplostichanthus sp Coop. Ck +Test_2023_2,Polyalthia submontana,049,branch_mass_fraction,0.36,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Haplostichanthus sp Coop. Ck +Test_2023_2,Polyalthia submontana,049,huber_value,0.000411522633744856,mm2{sapwood}/mm2{leaf},population,mean,unknown,7,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Haplostichanthus sp Coop. Ck +Test_2023_2,Polyalthia submontana,049,huber_value,8.12743823146944e-05,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Haplostichanthus sp Coop. Ck +Test_2023_2,Polyalthia submontana,049,huber_value,0.000304692260816575,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Haplostichanthus sp Coop. Ck +Test_2023_2,Polyalthia submontana,049,huber_value,0.000334224598930481,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Haplostichanthus sp Coop. Ck +Test_2023_2,Polyalthia submontana,049,huber_value,0.000334224598930481,mm2{sapwood}/mm2{leaf},population,maximum,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Haplostichanthus sp Coop. Ck +Test_2023_2,Polyalthia submontana,050,leaf_N_per_dry_mass,22,mg/g,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Haplostichanthus sp Coop. Ck +Test_2023_2,Polyalthia submontana,050,leaf_area,4685,mm2,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Haplostichanthus sp Coop. Ck +Test_2023_2,Polyalthia submontana,050,leaf_mass_per_area,72,g/m2,species,mean,measurement,2,field,,,,,,Test_2022,,,,,,,01,,Haplostichanthus sp Coop. Ck +Test_2023_2,Polyalthia submontana,050,wood_density,0.668,mg/mm3,species,mean,unknown,2,field,,,,,,Test_2022,,,,,,,01,,Haplostichanthus sp Coop. Ck Test_2023_2,Harpullia rhyticarpa,051,branch_mass_fraction,0.01,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Harpullia rhyticarpa Test_2023_2,Harpullia rhyticarpa,051,huber_value,0.000111470293166871,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Harpullia rhyticarpa Test_2023_2,Harpullia rhyticarpa,051,huber_value,0.000168861870989531,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Harpullia rhyticarpa @@ -266,17 +266,17 @@ Test_2023_2,Ixora biflora,059,leaf_N_per_dry_mass,10,mg/g,species,mean,unknown,2 Test_2023_2,Ixora biflora,059,leaf_area,2760,mm2,species,mean,unknown,2,field,adult,,,,,,,,,,,,01,,Ixora biflora Test_2023_2,Ixora biflora,059,leaf_mass_per_area,81,g/m2,species,mean,measurement,2,field,adult,,,,,,,,,,,,01,,Ixora biflora Test_2023_2,Ixora biflora,059,wood_density,0.843,mg/mm3,species,mean,unknown,2,field,adult,,,,,,,,,,,,01,,Ixora biflora -Test_2023_2,Lasianthus strigosus,060,branch_mass_fraction,0.15,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Lasianthus strigosus -Test_2023_2,Lasianthus strigosus,060,huber_value,0.000543183052688756,mm2{sapwood}/mm2{leaf},population,mean,unknown,7,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Lasianthus strigosus -Test_2023_2,Lasianthus strigosus,060,huber_value,0.000196078431372549,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Lasianthus strigosus -Test_2023_2,Lasianthus strigosus,060,huber_value,0.000420344682639765,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Lasianthus strigosus -Test_2023_2,Lasianthus strigosus,060,huber_value,0.000366166239472721,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Lasianthus strigosus -Test_2023_2,Lasianthus strigosus,060,huber_value,0.000366166239472721,mm2{sapwood}/mm2{leaf},population,maximum,unknown,2,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Lasianthus strigosus -Test_2023_2,Lasianthus strigosus,060,seed_dry_mass,7,mg,population,mean,unknown,unknown,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Lasianthus strigosus -Test_2023_2,Lasianthus strigosus,061,leaf_N_per_dry_mass,15.8,mg/g,species,mean,unknown,2,field,adult,,,,,,,,,,,,01,,Lasianthus strigosus -Test_2023_2,Lasianthus strigosus,061,leaf_area,3313,mm2,species,mean,unknown,2,field,adult,,,,,,,,,,,,01,,Lasianthus strigosus -Test_2023_2,Lasianthus strigosus,061,leaf_mass_per_area,55,g/m2,species,mean,measurement,2,field,adult,,,,,,,,,,,,01,,Lasianthus strigosus -Test_2023_2,Lasianthus strigosus,061,wood_density,0.684,mg/mm3,species,mean,unknown,2,field,adult,,,,,,,,,,,,01,,Lasianthus strigosus +Test_2023_2,Lasianthus chlorocarpus,060,branch_mass_fraction,0.15,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Lasianthus strigosus +Test_2023_2,Lasianthus chlorocarpus,060,huber_value,0.000543183052688756,mm2{sapwood}/mm2{leaf},population,mean,unknown,7,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Lasianthus strigosus +Test_2023_2,Lasianthus chlorocarpus,060,huber_value,0.000196078431372549,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Lasianthus strigosus +Test_2023_2,Lasianthus chlorocarpus,060,huber_value,0.000420344682639765,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Lasianthus strigosus +Test_2023_2,Lasianthus chlorocarpus,060,huber_value,0.000366166239472721,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Lasianthus strigosus +Test_2023_2,Lasianthus chlorocarpus,060,huber_value,0.000366166239472721,mm2{sapwood}/mm2{leaf},population,maximum,unknown,2,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Lasianthus strigosus +Test_2023_2,Lasianthus chlorocarpus,060,seed_dry_mass,7,mg,population,mean,unknown,unknown,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Lasianthus strigosus +Test_2023_2,Lasianthus chlorocarpus,061,leaf_N_per_dry_mass,15.8,mg/g,species,mean,unknown,2,field,adult,,,,,,,,,,,,01,,Lasianthus strigosus +Test_2023_2,Lasianthus chlorocarpus,061,leaf_area,3313,mm2,species,mean,unknown,2,field,adult,,,,,,,,,,,,01,,Lasianthus strigosus +Test_2023_2,Lasianthus chlorocarpus,061,leaf_mass_per_area,55,g/m2,species,mean,measurement,2,field,adult,,,,,,,,,,,,01,,Lasianthus strigosus +Test_2023_2,Lasianthus chlorocarpus,061,wood_density,0.684,mg/mm3,species,mean,unknown,2,field,adult,,,,,,,,,,,,01,,Lasianthus strigosus Test_2023_2,Litsea leefeana,062,branch_mass_fraction,0.68,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Litsea leefeana Test_2023_2,Litsea leefeana,062,huber_value,0.000251004016064257,mm2{sapwood}/mm2{leaf},population,mean,unknown,7,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Litsea leefeana Test_2023_2,Litsea leefeana,062,huber_value,0.000241487563390485,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Litsea leefeana @@ -399,15 +399,15 @@ Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),089,leaf_N_per_dry_ Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),089,leaf_area,11157,mm2,species,mean,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Psychotria sp Utchee Creek Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),089,leaf_mass_per_area,108,g/m2,species,mean,measurement,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Psychotria sp Utchee Creek Test_2023_2,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),089,wood_density,0.582,mg/mm3,species,mean,,,field,,,,,,Test_2002,,,,,,Test dataset-level measurement_remarks,01,,Psychotria sp Utchee Creek -Test_2023_2,Quassia baileyana,090,branch_mass_fraction,0.42,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Quassia baileyana -Test_2023_2,Quassia baileyana,090,huber_value,0.000170444861087438,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Quassia baileyana -Test_2023_2,Quassia baileyana,090,huber_value,0.000310945273631841,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Quassia baileyana -Test_2023_2,Quassia baileyana,090,huber_value,0.000174855744011191,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Quassia baileyana -Test_2023_2,Quassia baileyana,090,huber_value,0.000174855744011191,mm2{sapwood}/mm2{leaf},population,maximum,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Quassia baileyana -Test_2023_2,Quassia baileyana,091,leaf_N_per_dry_mass,23,mg/g,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Quassia baileyana -Test_2023_2,Quassia baileyana,091,leaf_area,9624,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Quassia baileyana -Test_2023_2,Quassia baileyana,091,leaf_mass_per_area,86,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Quassia baileyana -Test_2023_2,Quassia baileyana,091,wood_density,0.501,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Quassia baileyana +Test_2023_2,Samadera baileyana,090,branch_mass_fraction,0.42,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Quassia baileyana +Test_2023_2,Samadera baileyana,090,huber_value,0.000170444861087438,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Quassia baileyana +Test_2023_2,Samadera baileyana,090,huber_value,0.000310945273631841,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Quassia baileyana +Test_2023_2,Samadera baileyana,090,huber_value,0.000174855744011191,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Quassia baileyana +Test_2023_2,Samadera baileyana,090,huber_value,0.000174855744011191,mm2{sapwood}/mm2{leaf},population,maximum,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Quassia baileyana +Test_2023_2,Samadera baileyana,091,leaf_N_per_dry_mass,23,mg/g,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Quassia baileyana +Test_2023_2,Samadera baileyana,091,leaf_area,9624,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Quassia baileyana +Test_2023_2,Samadera baileyana,091,leaf_mass_per_area,86,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Quassia baileyana +Test_2023_2,Samadera baileyana,091,wood_density,0.501,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Quassia baileyana Test_2023_2,Rhodomyrtus trineura,092,branch_mass_fraction,0.34,mg/mg,population,mean,,,field,,01,,,,Test_2002,01,,,,,Made-up remarks for `branch_mass_fraction`,01,,Rhodomyrtus trineura Test_2023_2,Rhodomyrtus trineura,092,huber_value,0.000231427910205971,mm2{sapwood}/mm2{leaf},population,mean,,7,field,,01,,,,Test_2002,01,,,,,Test dataset-level measurement_remarks,01,,Rhodomyrtus trineura Test_2023_2,Rhodomyrtus trineura,092,huber_value,0.000262950302392848,mm2{sapwood}/mm2{leaf},population,mean,,,field,,01,,,,Test_2002,01,,,,,Test dataset-level measurement_remarks,02,,Rhodomyrtus trineura @@ -450,14 +450,14 @@ Test_2023_2,Syzygium sayeri,099,leaf_N_per_dry_mass,13.7,mg/g,species,mean,unkno Test_2023_2,Syzygium sayeri,099,leaf_area,2645,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Syzygium sayeri Test_2023_2,Syzygium sayeri,099,leaf_mass_per_area,131,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Syzygium sayeri Test_2023_2,Syzygium sayeri,099,wood_density,0.485,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Syzygium sayeri -Test_2023_2,Trema aspera,100,branch_mass_fraction,0.53,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Trema aspera -Test_2023_2,Trema aspera,100,huber_value,0.000279485746226942,mm2{sapwood}/mm2{leaf},population,mean,unknown,7,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Trema aspera -Test_2023_2,Trema aspera,100,huber_value,0.000189000189000189,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Trema aspera -Test_2023_2,Trema aspera,100,huber_value,0.000183823529411765,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Trema aspera -Test_2023_2,Trema aspera,100,huber_value,0.000149365197908887,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Trema aspera -Test_2023_2,Trema aspera,100,huber_value,0.000149365197908887,mm2{sapwood}/mm2{leaf},population,maximum,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Trema aspera -Test_2023_2,Trema aspera,100,seed_dry_mass,5.12,mg,population,mean,unknown,unknown,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Trema aspera -Test_2023_2,Trema aspera,101,leaf_N_per_dry_mass,29.9,mg/g,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Trema aspera -Test_2023_2,Trema aspera,101,leaf_area,2071,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Trema aspera -Test_2023_2,Trema aspera,101,leaf_mass_per_area,53,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Trema aspera -Test_2023_2,Trema aspera,101,wood_density,0.357,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Trema aspera +Test_2023_2,Trema tomentosa var. aspera,100,branch_mass_fraction,0.53,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Trema aspera +Test_2023_2,Trema tomentosa var. aspera,100,huber_value,0.000279485746226942,mm2{sapwood}/mm2{leaf},population,mean,unknown,7,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Trema aspera +Test_2023_2,Trema tomentosa var. aspera,100,huber_value,0.000189000189000189,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Trema aspera +Test_2023_2,Trema tomentosa var. aspera,100,huber_value,0.000183823529411765,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Trema aspera +Test_2023_2,Trema tomentosa var. aspera,100,huber_value,0.000149365197908887,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Trema aspera +Test_2023_2,Trema tomentosa var. aspera,100,huber_value,0.000149365197908887,mm2{sapwood}/mm2{leaf},population,maximum,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Trema aspera +Test_2023_2,Trema tomentosa var. aspera,100,seed_dry_mass,5.12,mg,population,mean,unknown,unknown,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Trema aspera +Test_2023_2,Trema tomentosa var. aspera,101,leaf_N_per_dry_mass,29.9,mg/g,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Trema aspera +Test_2023_2,Trema tomentosa var. aspera,101,leaf_area,2071,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Trema aspera +Test_2023_2,Trema tomentosa var. aspera,101,leaf_mass_per_area,53,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Trema aspera +Test_2023_2,Trema tomentosa var. aspera,101,wood_density,0.357,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Trema aspera diff --git a/tests/testthat/examples/Test_2023_3/output/metadata.yml b/tests/testthat/examples/Test_2023_3/output/metadata.yml index a38d6462..5dde7c3a 100644 --- a/tests/testthat/examples/Test_2023_3/output/metadata.yml +++ b/tests/testthat/examples/Test_2023_3/output/metadata.yml @@ -5,7 +5,7 @@ description: AusTraits is a transformative database, containing measurements on used to build the resource are also available on the project's GitHub repository,http://traitecoevo.github.io/traits.build. Further information on the project is available in the associated publication and at the project website https://austraits.org. -version: 4.0.0 +version: 5.0.0 doi: 10.5281/zenodo.5112001 structure_URI: https://github.com/traitecoevo/traits.build geo_location: diff --git a/tests/testthat/examples/Test_2023_3/output/taxa.csv b/tests/testthat/examples/Test_2023_3/output/taxa.csv index 29fddfe3..fbbc4378 100644 --- a/tests/testthat/examples/Test_2023_3/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_3/output/taxa.csv @@ -1,186 +1,185 @@ -taxon_name,taxonomic_dataset,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution -Abildgaardia ovata,,,,,,,,, -Acacia alpina,,,,,,,,, -Acacia beadleana,,,,,,,,, -Acacia bulgaensis,,,,,,,,, -Acacia caroleae,,,,,,,,, -Acacia crassa,,,,,,,,, -Acacia flexifolia,,,,,,,,, -Acacia gladiiformis,,,,,,,,, -Acacia havilandiorum,,,,,,,,, -Acacia leiocalyx subsp. leiocalyx,,,,,,,,, -Acacia myrtifolia,,,,,,,,, -Acacia ramulosa var. ramulosa,,,,,,,,, -Acacia spectabilis,,,,,,,,, -Acacia terminalis subsp. Glabrous form (M.Hancock 94),,,,,,,,, -Acronychia littoralis,,,,,,,,, -Adriana tomentosa,,,,,,,,, -Alectryon coriaceus,,,,,,,,, -Alectryon oleifolius,,,,,,,,, -Alectryon subdentatus,,,,,,,,, -Amyema preissii,,,,,,,,, -Angophora leiocarpa,,,,,,,,, -Apophyllum anomalum,,,,,,,,, -Arbutus unedo,,,,,,,,, -Australina pusilla,,,,,,,,, -Burmannia disticha,,,,,,,,, -Bursaria spinosa subsp. spinosa,,,,,,,,, -Calendula arvensis,,,,,,,,, -Callistemon purpurascens,,,,,,,,, -Carex cephalotes,,,,,,,,, -Carex leporina,,,,,,,,, -Carex raleighii,,,,,,,,, -Carmichaelia exsul,,,,,,,,, -Cassinia compacta,,,,,,,,, -Castanospermum australe,,,,,,,,, -Centaurium tenuiflorum,,,,,,,,, -Cestrum nocturnum,,,,,,,,, -Chthonocephalus pseudevax,,,,,,,,, -Claoxylon australe,,,,,,,,, -Commersonia amystia,,,,,,,,, -Commersonia salviifolia,,,,,,,,, -Convolvulus farinosus,,,,,,,,, -Coprosma niphophila,,,,,,,,, -Coprosma nivalis,,,,,,,,, -Correa alba,,,,,,,,, -Corymbia citriodora,,,,,,,,, -Corymbia eximia,,,,,,,,, -Crassula decumbens,,,,,,,,, -Crassula peduncularis,,,,,,,,, -Crotalaria brevis,,,,,,,,, -Crotalaria grahamiana,,,,,,,,, -Crotalaria lanceolata,,,,,,,,, -Cylindropuntia kleiniae,,,,,,,,, -Cyperus albostriatus,,,,,,,,, -Cyperus betchei,,,,,,,,, -Cyperus bulbosus,,,,,,,,, -Cyperus laevigatus,,,,,,,,, -Cyperus sculptus,,,,,,,,, -Dampiera fusca,,,,,,,,, -Davidsonia johnsonii,,,,,,,,, -Daviesia arenaria,,,,,,,,, -Derris involuta,,,,,,,,, -Dichromochlamys dentatifolia,,,,,,,,, -Dillwynia cinerascens,,,,,,,,, -Dillwynia floribunda,,,,,,,,, -Dinosperma erythrococcum,,,,,,,,, -Dodonaea petiolaris,,,,,,,,, -Dodonaea truncatiales,,,,,,,,, -Dovyalis caffra,,,,,,,,, -Elaeocarpus grandis,,,,,,,,, -Eleocharis pallens,,,,,,,,, -Endiandra globosa,,,,,,,,, -Endiandra muelleri,,,,,,,,, -Epilobium gunnianum,,,,,,,,, -Eremophila deserti,,,,,,,,, -Eremophila oppositifolia,,,,,,,,, -Erigeron conyzoides,,,,,,,,, -Erythroxylum australe,,,,,,,,, -Escallonia bifida,,,,,,,,, -Eucalyptus badjensis,,,,,,,,, -Eucalyptus camphora,,,,,,,,, -Eucalyptus dorrigoensis,,,,,,,,, -Eucalyptus leucoxylon subsp. pruinosa,,,,,,,,, -Eucalyptus muelleriana,,,,,,,,, -Eucalyptus nandewarica,,,,,,,,, -Eucalyptus oblonga,,,,,,,,, -Eucalyptus olida,,,,,,,,, -Eucalyptus pulverulenta,,,,,,,,, -Eucalyptus recurva,,,,,,,,, -Eucalyptus rossii,,,,,,,,, -Eucalyptus scias,,,,,,,,, -Eucalyptus viminalis,,,,,,,,, -Eucalyptus yangoura,,,,,,,,, -Eucalyptus youmanii,,,,,,,,, -Euphorbia inappendiculata var. queenslandica,,,,,,,,, -Exocarpos homalocladus,,,,,,,,, -Exocarpos sparteus,,,,,,,,, -Ficus henneana,,,,,,,,, -Freesia hybrid,,,,,,,,, -Freesia laxa,,,,,,,,, -Geijera salicifolia,,,,,,,,, -Gentiana wingecarribiensis,,,,,,,,, -Geranium obtusisepalum,,,,,,,,, -Geranium purpureum subsp. purpureum,,,,,,,,, -Gompholobium grandiflorum,,,,,,,,, -Goodenia varia,,,,,,,,, -Gossia bidwillii,,,,,,,,, -Grevillea scortechinii,,,,,,,,, -Hakea macraeana,,,,,,,,, -Hemisteptia lyrata,,,,,,,,, -Hibbertia crinita,,,,,,,,, -Hibiscus brachysiphonius,,,,,,,,, -Hibiscus sturtii,,,,,,,,, -Hypericum elodes,,,,,,,,, -Hypoxis glabella var. glabella,,,,,,,,, -Imperata cylindrica,,,,,,,,, -Indigofera triflora,,,,,,,,, -Ipomoea cairica,,,,,,,,, -Isolepis montivaga,,,,,,,,, -Isotoma axillaris,,,,,,,,, -Isotoma fluviatilis subsp. fluviatilis,,,,,,,,, -Juncus acutus subsp. acutus,,,,,,,,, -Juncus kraussii,,,,,,,,, -Lantana montevidensis,,,,,,,,, -Lepidium africanum,,,,,,,,, -Lepidium foliosum,,,,,,,,, -Lepidium oxytrichum,,,,,,,,, -Leptomeria drupacea,,,,,,,,, -Leptospermum continentale,,,,,,,,, -Leptospermum obovatum,,,,,,,,, -Leucopogon amplexicaulis,,,,,,,,, -Lobelia pedunculata,,,,,,,,, -Lobelia trigonocaulis,,,,,,,,, -Lotononis bainesii,,,,,,,,, -Lotus corniculatus,,,,,,,,, -Lupinus polyphyllus,,,,,,,,, -Medicago orbicularis,,,,,,,,, -Melichrus procumbens,,,,,,,,, -Mischocarpus australis,,,,,,,,, -Muehlenbeckia adpressa,,,,,,,,, -Myoporum boninense subsp. australe,,,,,,,,, -Nicotiana glauca,,,,,,,,, -Nicotiana goodspeedii,,,,,,,,, -Oxalis corniculata,,,,,,,,, -Pandorea pandorana subsp. austrocaledonica,,,,,,,,, -Paraserianthes lophantha,,,,,,,,, -Parentucellia latifolia,,,,,,,,, -Phlegmatospermum cochlearinum,,,,,,,,, -Phyla nodiflora,,,,,,,,, -Picris barbarorum,,,,,,,,, -Pimelea ligustrina subsp. ligustrina,,,,,,,,, -Pinus pinea,,,,,,,,, -Pisum sativum var. arvense,,,,,,,,, -Pittosporum erioloma,,,,,,,,, -Plantago turrifera,,,,,,,,, -Polycarpon tetraphyllum,,,,,,,,, -Potamogeton australiensis,,,,,,,,, -Psoralea pinnata,,,,,,,,, -Pultenaea ferruginea,,,,,,,,, -Rhodamnia argentea,,,,,,,,, -Rorippa gigantea,,,,,,,,, -Rubus parvifolius,,,,,,,,, -Salix alba,,,,,,,,, -Schenkia australis,,,,,,,,, -Schoenus apogon,,,,,,,,, -Schoenus brevifolius,,,,,,,,, -Schoenus lepidosperma,,,,,,,,, -Schoenus vaginatus,,,,,,,,, -Scleria rugosa,,,,,,,,, -Senecio longipilus,,,,,,,,, -Sida goniocarpa,,,,,,,,, -Sigesbeckia orientalis,,,,,,,,, -Sisymbrium irio,,,,,,,,, -Sparaxis bulbifera,,,,,,,,, -Spergularia diandra,,,,,,,,, -Sphaeromorphaea littoralis,,,,,,,,, -Stellaria angustifolia subsp. angustifolia,,,,,,,,, -Styphelia viridis,,,,,,,,, -Swainsona cadellii,,,,,,,,, -Teucrium puberulum,,,,,,,,, -Thelymitra kangaloonica,,,,,,,,, -Thesium australe,,,,,,,,, -Trifolium dubium,,,,,,,,, -Veronica catenata,,,,,,,,, -Veronica derwentiana,,,,,,,,, -Wahlenbergia luteola,,,,,,,,, +original_name,taxon_name,taxon_name_alternatives,genus,family,taxon_rank,taxonomic_dataset,taxonomic_status,subclass,taxon_distribution,scientific_name,taxon_id,taxon_ID_genus,scientific_name_id,canonical_name,cleaned_scientific_name_id,taxon_id_family,trinomial,binomial,establishment_means +Abildgaardia ovata,Abildgaardia ovata,,Abildgaardia,Cyperaceae,species,APC,accepted,Magnoliidae,"NT, Qld, NSW",Abildgaardia ovata (Burm.f.) Kral,https://id.biodiversity.org.au/node/apni/2919627,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/150737,Abildgaardia ovata,https://id.biodiversity.org.au/name/apni/150737,https://id.biodiversity.org.au/taxon/apni/51460154,,Abildgaardia ovata,native +Acacia alpina,Acacia alpina,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Acacia alpina F.Muell.,https://id.biodiversity.org.au/node/apni/2907301,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/58263,Acacia alpina,https://id.biodiversity.org.au/name/apni/58263,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia alpina,native +Acacia beadleana,Acacia beadleana,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Acacia beadleana R.H.Jones & J.J.Bruhl,https://id.biodiversity.org.au/node/apni/2902581,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/198624,Acacia beadleana,https://id.biodiversity.org.au/name/apni/165277,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia beadleana,native +Acacia bulgaensis,Acacia bulgaensis,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Acacia bulgaensis Tindale & S.J.Davies,https://id.biodiversity.org.au/node/apni/2889179,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/117995,Acacia bulgaensis,https://id.biodiversity.org.au/name/apni/117995,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia bulgaensis,native +Acacia caroleae,Acacia caroleae,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acacia caroleae Pedley,https://id.biodiversity.org.au/node/apni/2894332,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/60225,Acacia caroleae,https://id.biodiversity.org.au/name/apni/60225,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia caroleae,native +Acacia crassa,Acacia crassa,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acacia crassa Pedley,https://id.biodiversity.org.au/node/apni/2919707,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/60887,Acacia crassa,https://id.biodiversity.org.au/name/apni/60887,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia crassa,native +Acacia flexifolia,Acacia flexifolia,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic",Acacia flexifolia A.Cunn. ex Benth.,https://id.biodiversity.org.au/node/apni/2914740,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/63146,Acacia flexifolia,https://id.biodiversity.org.au/name/apni/63146,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia flexifolia,native +Acacia gladiiformis,Acacia gladiiformis,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acacia gladiiformis A.Cunn. ex Benth.,https://id.biodiversity.org.au/node/apni/2887779,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/63580,Acacia gladiiformis,https://id.biodiversity.org.au/name/apni/63580,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia gladiiformis,native +Acacia havilandiorum,Acacia havilandiorum,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic",Acacia havilandiorum Maiden,https://id.biodiversity.org.au/node/apni/2897713,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/135274,Acacia havilandiorum,https://id.biodiversity.org.au/name/apni/135274,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia havilandiorum,native +Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx subsp. leiocalyx,,Acacia,Fabaceae,subspecies,APC,accepted,Magnoliidae,"Qld, NSW",Acacia leiocalyx (Domin) Pedley subsp. leiocalyx,https://id.biodiversity.org.au/node/apni/2894438,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/65375,Acacia leiocalyx subsp. leiocalyx,https://id.biodiversity.org.au/name/apni/65375,https://id.biodiversity.org.au/taxon/apni/51702961,Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx,native +Acacia myrtifolia,Acacia myrtifolia,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic, Tas",Acacia myrtifolia (Sm.) Willd.,https://id.biodiversity.org.au/node/apni/2901160,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/162110,Acacia myrtifolia,https://id.biodiversity.org.au/name/apni/162110,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia myrtifolia,native +Acacia ramulosa var. ramulosa,Acacia ramulosa var. ramulosa,,Acacia,Fabaceae,variety,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Acacia ramulosa W.Fitzg. var. ramulosa,https://id.biodiversity.org.au/node/apni/2915768,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/168882,Acacia ramulosa var. ramulosa,https://id.biodiversity.org.au/name/apni/168882,https://id.biodiversity.org.au/taxon/apni/51702961,Acacia ramulosa var. ramulosa,Acacia ramulosa,native +Acacia spectabilis,Acacia spectabilis,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW (native and naturalised)",Acacia spectabilis A.Cunn. ex Benth.,https://id.biodiversity.org.au/node/apni/2918795,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/70543,Acacia spectabilis,https://id.biodiversity.org.au/name/apni/70543,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia spectabilis,native and naturalised +Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis subsp. Glabrous form (M.Hancock 94),,Acacia,Fabaceae,subspecies,APC,accepted,Magnoliidae,"NSW, Vic, Tas",Acacia terminalis subsp. Glabrous form (M.Hancock 94) NSW Herbarium,https://id.biodiversity.org.au/node/apni/2886403,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/199841,Acacia terminalis subsp. Glabrous form (M.Hancock 94),https://id.biodiversity.org.au/name/apni/199841,https://id.biodiversity.org.au/taxon/apni/51702961,Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis,native +Acronychia littoralis,Acronychia littoralis,,Acronychia,Rutaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acronychia littoralis T.G.Hartley & J.B.Williams,https://id.biodiversity.org.au/node/apni/2907701,https://id.biodiversity.org.au/taxon/apni/51446847,https://id.biodiversity.org.au/name/apni/73953,Acronychia littoralis,https://id.biodiversity.org.au/name/apni/73953,https://id.biodiversity.org.au/taxon/apni/51461748,,Acronychia littoralis,native +Adriana tomentosa,Adriana tomentosa,,Adriana,Euphorbiaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, ACT, Vic",Adriana tomentosa Gaudich.,https://id.biodiversity.org.au/node/apni/2898187,https://id.biodiversity.org.au/node/apni/8408111,https://id.biodiversity.org.au/name/apni/77104,Adriana tomentosa,https://id.biodiversity.org.au/name/apni/77104,https://id.biodiversity.org.au/taxon/apni/51442249,,Adriana tomentosa,native +Alectryon coriaceus,Alectryon coriaceus,,Alectryon,Sapindaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Alectryon coriaceus (Benth.) Radlk.,https://id.biodiversity.org.au/node/apni/2891604,https://id.biodiversity.org.au/taxon/apni/51299789,https://id.biodiversity.org.au/name/apni/81043,Alectryon coriaceus,https://id.biodiversity.org.au/name/apni/81043,https://id.biodiversity.org.au/taxon/apni/51447212,,Alectryon coriaceus,native +Alectryon oleifolius,Alectryon oleifolius,,Alectryon,Sapindaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Alectryon oleifolius (Desf.) S.T.Reynolds,https://id.biodiversity.org.au/node/apni/2900874,https://id.biodiversity.org.au/taxon/apni/51299789,https://id.biodiversity.org.au/name/apni/81066,Alectryon oleifolius,https://id.biodiversity.org.au/name/apni/81066,https://id.biodiversity.org.au/taxon/apni/51447212,,Alectryon oleifolius,native +Alectryon subdentatus,Alectryon subdentatus,,Alectryon,Sapindaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Alectryon subdentatus (F.Muell. ex Benth.) Radlk.,https://id.biodiversity.org.au/node/apni/2890534,https://id.biodiversity.org.au/taxon/apni/51299789,https://id.biodiversity.org.au/name/apni/81114,Alectryon subdentatus,https://id.biodiversity.org.au/name/apni/81114,https://id.biodiversity.org.au/taxon/apni/51447212,,Alectryon subdentatus,native +Amyema preissii,Amyema preissii,,Amyema,Loranthaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Amyema preissii (Miq.) Tiegh.,https://id.biodiversity.org.au/node/apni/2888430,https://id.biodiversity.org.au/taxon/apni/51438795,https://id.biodiversity.org.au/name/apni/87461,Amyema preissii,https://id.biodiversity.org.au/name/apni/87461,https://id.biodiversity.org.au/taxon/apni/51438796,,Amyema preissii,native +Angophora leiocarpa,Angophora leiocarpa,,Angophora,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Angophora leiocarpa (L.A.S.Johnson ex G.J.Leach) K.R.Thiele & Ladiges,https://id.biodiversity.org.au/node/apni/2894339,https://id.biodiversity.org.au/taxon/apni/51439560,https://id.biodiversity.org.au/name/apni/123435,Angophora leiocarpa,https://id.biodiversity.org.au/name/apni/123435,https://id.biodiversity.org.au/taxon/apni/51702983,,Angophora leiocarpa,native +Arbutus unedo,Arbutus unedo,,Arbutus,Ericaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (doubtfully naturalised), NSW (doubtfully naturalised), ACT (doubtfully naturalised), Vic (naturalised), Tas (doubtfully naturalised)",Arbutus unedo L.,https://id.biodiversity.org.au/node/apni/2904939,https://id.biodiversity.org.au/node/apni/2892910,https://id.biodiversity.org.au/name/apni/98540,Arbutus unedo,https://id.biodiversity.org.au/name/apni/98540,https://id.biodiversity.org.au/taxon/apni/51436079,,Arbutus unedo,naturalised +Australina pusilla,Australina pusilla,,Australina,Urticaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic, Tas",Australina pusilla (Poir.) Gaudich.,https://id.biodiversity.org.au/node/apni/2913845,https://id.biodiversity.org.au/node/apni/2907879,https://id.biodiversity.org.au/name/apni/113875,Australina pusilla,https://id.biodiversity.org.au/name/apni/113875,https://id.biodiversity.org.au/taxon/apni/51662052,,Australina pusilla,native +Burmannia disticha,Burmannia disticha,,Burmannia,Burmanniaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Burmannia disticha L.,https://id.biodiversity.org.au/node/apni/2900088,https://id.biodiversity.org.au/node/apni/2915743,https://id.biodiversity.org.au/name/apni/70173,Burmannia disticha,https://id.biodiversity.org.au/name/apni/70173,https://id.biodiversity.org.au/node/apni/2887196,,Burmannia disticha,native +Bursaria spinosa subsp. spinosa,Bursaria spinosa subsp. spinosa,,Bursaria,Pittosporaceae,subspecies,APC,accepted,Magnoliidae,"SA, Qld, NSW, Vic, Tas",Bursaria spinosa Cav. subsp. spinosa,https://id.biodiversity.org.au/taxon/apni/51442337,https://id.biodiversity.org.au/taxon/apni/51442339,https://id.biodiversity.org.au/name/apni/142036,Bursaria spinosa subsp. spinosa,https://id.biodiversity.org.au/name/apni/142036,https://id.biodiversity.org.au/taxon/apni/51442315,Bursaria spinosa subsp. spinosa,Bursaria spinosa,native +Calendula arvensis,Calendula arvensis,,Calendula,Asteraceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (naturalised), Tas (naturalised)",Calendula arvensis L.,https://id.biodiversity.org.au/node/apni/2891878,https://id.biodiversity.org.au/node/apni/2893748,https://id.biodiversity.org.au/name/apni/95042,Calendula arvensis,https://id.biodiversity.org.au/name/apni/95042,https://id.biodiversity.org.au/taxon/apni/51695393,,Calendula arvensis,naturalised +Callistemon purpurascens,Callistemon purpurascens,,Callistemon,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Callistemon purpurascens S.M.Douglas & S.David,https://id.biodiversity.org.au/taxon/apni/51288952,https://id.biodiversity.org.au/taxon/apni/51439657,https://id.biodiversity.org.au/name/apni/4630985,Callistemon purpurascens,https://id.biodiversity.org.au/name/apni/4630985,https://id.biodiversity.org.au/taxon/apni/51702983,,Callistemon purpurascens,native +Apophyllum anomalum,Capparis anomala,,Capparis,Capparaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Capparis anomala (F.Muell.) Byng & Christenh.,https://id.biodiversity.org.au/taxon/apni/51432888,https://id.biodiversity.org.au/taxon/apni/51432886,https://id.biodiversity.org.au/name/apni/50561973,Capparis anomala,https://id.biodiversity.org.au/name/apni/97697,https://id.biodiversity.org.au/taxon/apni/51433682,,Capparis anomala,native +Carex leporina,Carex leporina,,Carex,Cyperaceae,species,APC,accepted,Magnoliidae,"NSW (naturalised), NI (naturalised), Vic (naturalised), Tas (naturalised)",Carex leporina L.,https://id.biodiversity.org.au/node/apni/2902492,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/135236,Carex leporina,https://id.biodiversity.org.au/name/apni/135236,https://id.biodiversity.org.au/taxon/apni/51460154,,Carex leporina,naturalised +Carex cephalotes,Carex pyrenaica var. cephalotes,,Carex,Cyperaceae,variety,APC,accepted,Magnoliidae,"NSW, Vic, Tas",Carex pyrenaica var. cephalotes (F.Muell.) Kük.,https://id.biodiversity.org.au/node/apni/2892693,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/111655,Carex pyrenaica var. cephalotes,https://id.biodiversity.org.au/name/apni/110600,https://id.biodiversity.org.au/taxon/apni/51460154,Carex pyrenaica var. cephalotes,Carex pyrenaica,native +Carex raleighii,Carex raleighii,,Carex,Cyperaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic, Tas",Carex raleighii Nelmes,https://id.biodiversity.org.au/node/apni/2910405,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/111690,Carex raleighii,https://id.biodiversity.org.au/name/apni/111690,https://id.biodiversity.org.au/taxon/apni/51460154,,Carex raleighii,native +Carmichaelia exsul,Carmichaelia exsul,,Carmichaelia,Fabaceae,species,APC,accepted,Magnoliidae,LHI,Carmichaelia exsul F.Muell.,https://id.biodiversity.org.au/node/apni/2915240,https://id.biodiversity.org.au/node/apni/8138105,https://id.biodiversity.org.au/name/apni/112335,Carmichaelia exsul,https://id.biodiversity.org.au/name/apni/112335,https://id.biodiversity.org.au/taxon/apni/51702961,,Carmichaelia exsul,native +Cassinia compacta,Cassinia compacta,Cassinia accipitrum (pro parte misapplied) | Cassinia straminea (pro parte misapplied) | Cassinia telfordii (pro parte misapplied) | Cassinia accipitrum (misapplied),Cassinia,Asteraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Cassinia compacta F.Muell.,https://id.biodiversity.org.au/node/apni/2909860,https://id.biodiversity.org.au/taxon/apni/51431788,https://id.biodiversity.org.au/name/apni/54723,Cassinia compacta [alternative possible names: Cassinia accipitrum (pro parte misapplied) | Cassinia straminea (pro parte misapplied) | Cassinia telfordii (pro parte misapplied) | Cassinia accipitrum (misapplied)],,https://id.biodiversity.org.au/taxon/apni/51695393,,Cassinia compacta,native +Castanospermum australe,Castanospermum australe,,Castanospermum,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, NI (doubtfully naturalised)",Castanospermum australe A.Cunn. ex Mudie,https://id.biodiversity.org.au/node/apni/2894943,https://id.biodiversity.org.au/node/apni/7226268,https://id.biodiversity.org.au/name/apni/196675,Castanospermum australe,https://id.biodiversity.org.au/name/apni/196675,https://id.biodiversity.org.au/taxon/apni/51702961,,Castanospermum australe,native and naturalised +Centaurium tenuiflorum,Centaurium tenuiflorum,,Centaurium,Gentianaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Centaurium tenuiflorum (Hoffmanns. & Link) Fritsch,https://id.biodiversity.org.au/node/apni/7385749,https://id.biodiversity.org.au/node/apni/7385753,https://id.biodiversity.org.au/name/apni/58491,Centaurium tenuiflorum,https://id.biodiversity.org.au/name/apni/58491,https://id.biodiversity.org.au/taxon/apni/51436871,,Centaurium tenuiflorum,naturalised +Cestrum nocturnum,Cestrum nocturnum,,Cestrum,Solanaceae,species,APC,accepted,Magnoliidae,"Qld (doubtfully naturalised), NSW (naturalised), NI (naturalised)",Cestrum nocturnum L.,https://id.biodiversity.org.au/node/apni/2911237,https://id.biodiversity.org.au/node/apni/2889884,https://id.biodiversity.org.au/name/apni/60565,Cestrum nocturnum,https://id.biodiversity.org.au/name/apni/60565,https://id.biodiversity.org.au/taxon/apni/51447684,,Cestrum nocturnum,naturalised +Chthonocephalus pseudevax,Chthonocephalus pseudevax,,Chthonocephalus,Asteraceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Chthonocephalus pseudevax Steetz,https://id.biodiversity.org.au/node/apni/2917443,https://id.biodiversity.org.au/node/apni/2892496,https://id.biodiversity.org.au/name/apni/68863,Chthonocephalus pseudevax,https://id.biodiversity.org.au/name/apni/68863,https://id.biodiversity.org.au/taxon/apni/51695393,,Chthonocephalus pseudevax,native +Claoxylon australe,Claoxylon australe,,Claoxylon,Euphorbiaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Claoxylon australe Baill.,https://id.biodiversity.org.au/node/apni/2887203,https://id.biodiversity.org.au/node/apni/2920593,https://id.biodiversity.org.au/name/apni/70907,Claoxylon australe,https://id.biodiversity.org.au/name/apni/70907,https://id.biodiversity.org.au/taxon/apni/51442249,,Claoxylon australe,native +Commersonia amystia,Commersonia amystia,,Commersonia,Malvaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Commersonia amystia C.F.Wilkins & L.M.Copel.,https://id.biodiversity.org.au/node/apni/2904387,https://id.biodiversity.org.au/taxon/apni/51438976,https://id.biodiversity.org.au/name/apni/214136,Commersonia amystia,https://id.biodiversity.org.au/name/apni/214136,https://id.biodiversity.org.au/taxon/apni/51439248,,Commersonia amystia,native +Commersonia salviifolia,Commersonia salviifolia,,Commersonia,Malvaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Commersonia salviifolia (Hook. ex Steetz) F.Muell.,https://id.biodiversity.org.au/node/apni/2901795,https://id.biodiversity.org.au/taxon/apni/51438976,https://id.biodiversity.org.au/name/apni/75211,Commersonia salviifolia,https://id.biodiversity.org.au/name/apni/75211,https://id.biodiversity.org.au/taxon/apni/51439248,,Commersonia salviifolia,native +Convolvulus farinosus,Convolvulus farinosus,,Convolvulus,Convolvulaceae,species,APC,accepted,Magnoliidae,NSW (naturalised),Convolvulus farinosus L.,https://id.biodiversity.org.au/node/apni/2895672,https://id.biodiversity.org.au/taxon/apni/51298269,https://id.biodiversity.org.au/name/apni/206071,Convolvulus farinosus,https://id.biodiversity.org.au/name/apni/206071,https://id.biodiversity.org.au/taxon/apni/51695210,,Convolvulus farinosus,naturalised +Coprosma niphophila,Coprosma niphophila,,Coprosma,Rubiaceae,species,APC,accepted,Magnoliidae,NSW,Coprosma niphophila Orchard,https://id.biodiversity.org.au/node/apni/2910618,https://id.biodiversity.org.au/node/apni/8135850,https://id.biodiversity.org.au/name/apni/78856,Coprosma niphophila,https://id.biodiversity.org.au/name/apni/78856,https://id.biodiversity.org.au/taxon/apni/51446612,,Coprosma niphophila,native +Coprosma nivalis,Coprosma nivalis,,Coprosma,Rubiaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Coprosma nivalis W.R.B.Oliv.,https://id.biodiversity.org.au/node/apni/2915002,https://id.biodiversity.org.au/node/apni/8135850,https://id.biodiversity.org.au/name/apni/78866,Coprosma nivalis,https://id.biodiversity.org.au/name/apni/78866,https://id.biodiversity.org.au/taxon/apni/51446612,,Coprosma nivalis,native +Correa alba,Correa alba,,Correa,Rutaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Correa alba Andrews,https://id.biodiversity.org.au/node/apni/2906721,https://id.biodiversity.org.au/taxon/apni/51447015,https://id.biodiversity.org.au/name/apni/80283,Correa alba,https://id.biodiversity.org.au/name/apni/80283,https://id.biodiversity.org.au/taxon/apni/51461748,,Correa alba,native +Corymbia citriodora,Corymbia citriodora,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (doubtfully naturalised), Qld, NSW (native and naturalised), Vic (naturalised)",Corymbia citriodora (Hook.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2912509,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119387,Corymbia citriodora,https://id.biodiversity.org.au/name/apni/119387,https://id.biodiversity.org.au/taxon/apni/51702983,,Corymbia citriodora,native and naturalised +Corymbia eximia,Corymbia eximia,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Corymbia eximia (Schauer) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2909833,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119402,Corymbia eximia,https://id.biodiversity.org.au/name/apni/119402,https://id.biodiversity.org.au/taxon/apni/51702983,,Corymbia eximia,native +Crassula decumbens,Crassula decumbens,,Crassula,Crassulaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, ACT, Vic, Tas",Crassula decumbens Thunb.,https://id.biodiversity.org.au/node/apni/2889646,https://id.biodiversity.org.au/node/apni/2903354,https://id.biodiversity.org.au/name/apni/83855,Crassula decumbens,https://id.biodiversity.org.au/name/apni/83855,https://id.biodiversity.org.au/taxon/apni/51270792,,Crassula decumbens,native +Crassula peduncularis,Crassula peduncularis,,Crassula,Crassulaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, ACT, Vic, Tas",Crassula peduncularis (Sm.) F.Meigen,https://id.biodiversity.org.au/node/apni/2895654,https://id.biodiversity.org.au/node/apni/2903354,https://id.biodiversity.org.au/name/apni/84005,Crassula peduncularis,https://id.biodiversity.org.au/name/apni/84005,https://id.biodiversity.org.au/taxon/apni/51270792,,Crassula peduncularis,native +Crotalaria brevis,Crotalaria brevis,,Crotalaria,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Crotalaria brevis Domin,https://id.biodiversity.org.au/node/apni/2906180,https://id.biodiversity.org.au/taxon/apni/51300011,https://id.biodiversity.org.au/name/apni/85578,Crotalaria brevis,https://id.biodiversity.org.au/name/apni/85578,https://id.biodiversity.org.au/taxon/apni/51702961,,Crotalaria brevis,native +Crotalaria grahamiana,Crotalaria grahamiana,,Crotalaria,Fabaceae,species,APC,accepted,Magnoliidae,"Qld (naturalised), NSW (naturalised)",Crotalaria grahamiana Wight & Arn.,https://id.biodiversity.org.au/node/apni/2917131,https://id.biodiversity.org.au/taxon/apni/51300011,https://id.biodiversity.org.au/name/apni/85770,Crotalaria grahamiana,https://id.biodiversity.org.au/name/apni/85770,https://id.biodiversity.org.au/taxon/apni/51702961,,Crotalaria grahamiana,naturalised +Crotalaria lanceolata,Crotalaria lanceolata,,Crotalaria,Fabaceae,species,APC,accepted,Magnoliidae,"NT (naturalised), Qld (naturalised), NSW (naturalised), NI (naturalised)",Crotalaria lanceolata E.Mey.,https://id.biodiversity.org.au/node/apni/2887683,https://id.biodiversity.org.au/taxon/apni/51300011,https://id.biodiversity.org.au/name/apni/85830,Crotalaria lanceolata,https://id.biodiversity.org.au/name/apni/85830,https://id.biodiversity.org.au/taxon/apni/51702961,,Crotalaria lanceolata,naturalised +Cylindropuntia kleiniae,Cylindropuntia kleiniae,,Cylindropuntia,Cactaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised)",Cylindropuntia kleiniae (DC.) F.M.Knuth,https://id.biodiversity.org.au/taxon/apni/51432847,https://id.biodiversity.org.au/taxon/apni/51432841,https://id.biodiversity.org.au/name/apni/191050,Cylindropuntia kleiniae,https://id.biodiversity.org.au/name/apni/191050,https://id.biodiversity.org.au/taxon/apni/51432828,,Cylindropuntia kleiniae,naturalised +Cyperus albostriatus,Cyperus albostriatus,,Cyperus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised), NI (naturalised)",Cyperus albostriatus Schrad.,https://id.biodiversity.org.au/node/apni/2893623,https://id.biodiversity.org.au/taxon/apni/51434383,https://id.biodiversity.org.au/name/apni/96258,Cyperus albostriatus,https://id.biodiversity.org.au/name/apni/96258,https://id.biodiversity.org.au/taxon/apni/51460154,,Cyperus albostriatus,naturalised +Cyperus betchei,Cyperus betchei,,Cyperus,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Cyperus betchei (Kük.) S.T.Blake,https://id.biodiversity.org.au/node/apni/2888104,https://id.biodiversity.org.au/taxon/apni/51434383,https://id.biodiversity.org.au/name/apni/96480,Cyperus betchei,https://id.biodiversity.org.au/name/apni/96480,https://id.biodiversity.org.au/taxon/apni/51460154,,Cyperus betchei,native +Cyperus bulbosus,Cyperus bulbosus,,Cyperus,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Cyperus bulbosus Vahl,https://id.biodiversity.org.au/node/apni/2902422,https://id.biodiversity.org.au/taxon/apni/51434383,https://id.biodiversity.org.au/name/apni/96591,Cyperus bulbosus,https://id.biodiversity.org.au/name/apni/96591,https://id.biodiversity.org.au/taxon/apni/51460154,,Cyperus bulbosus,native +Cyperus laevigatus,Cyperus laevigatus,,Cyperus,Cyperaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT, SA, Qld, NSW",Cyperus laevigatus L.,https://id.biodiversity.org.au/node/apni/2916573,https://id.biodiversity.org.au/taxon/apni/51434383,https://id.biodiversity.org.au/name/apni/97862,Cyperus laevigatus,https://id.biodiversity.org.au/name/apni/97862,https://id.biodiversity.org.au/taxon/apni/51460154,,Cyperus laevigatus,native and naturalised +Cyperus sculptus,Cyperus sculptus,,Cyperus,Cyperaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Cyperus sculptus S.T.Blake,https://id.biodiversity.org.au/node/apni/2902340,https://id.biodiversity.org.au/taxon/apni/51434383,https://id.biodiversity.org.au/name/apni/98972,Cyperus sculptus,https://id.biodiversity.org.au/name/apni/98972,https://id.biodiversity.org.au/taxon/apni/51460154,,Cyperus sculptus,native +Dampiera fusca,Dampiera fusca,,Dampiera,Goodeniaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Dampiera fusca Rajput & Carolin,https://id.biodiversity.org.au/node/apni/2908327,https://id.biodiversity.org.au/taxon/apni/51437007,https://id.biodiversity.org.au/name/apni/78388,Dampiera fusca,https://id.biodiversity.org.au/name/apni/78388,https://id.biodiversity.org.au/taxon/apni/51462931,,Dampiera fusca,native +Davidsonia johnsonii,Davidsonia johnsonii,,Davidsonia,Cunoniaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Davidsonia johnsonii J.B.Williams & G.Harden,https://id.biodiversity.org.au/taxon/apni/51434155,https://id.biodiversity.org.au/taxon/apni/51434156,https://id.biodiversity.org.au/name/apni/166907,Davidsonia johnsonii,https://id.biodiversity.org.au/name/apni/166907,https://id.biodiversity.org.au/taxon/apni/51434138,,Davidsonia johnsonii,native +Daviesia arenaria,Daviesia arenaria,,Daviesia,Fabaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic",Daviesia arenaria Crisp,https://id.biodiversity.org.au/taxon/apni/51435880,https://id.biodiversity.org.au/taxon/apni/51461520,https://id.biodiversity.org.au/name/apni/82236,Daviesia arenaria,https://id.biodiversity.org.au/name/apni/82236,https://id.biodiversity.org.au/taxon/apni/51702961,,Daviesia arenaria,native +Dichromochlamys dentatifolia,Dichromochlamys dentatifolia,,Dichromochlamys,Asteraceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Dichromochlamys dentatifolia (F.Muell.) Dunlop,https://id.biodiversity.org.au/node/apni/2888915,https://id.biodiversity.org.au/node/apni/2894601,https://id.biodiversity.org.au/name/apni/102074,Dichromochlamys dentatifolia,https://id.biodiversity.org.au/name/apni/102074,https://id.biodiversity.org.au/taxon/apni/51695393,,Dichromochlamys dentatifolia,native +Dillwynia cinerascens,Dillwynia cinerascens,,Dillwynia,Fabaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Dillwynia cinerascens R.Br.,https://id.biodiversity.org.au/node/apni/2920072,https://id.biodiversity.org.au/taxon/apni/51285570,https://id.biodiversity.org.au/name/apni/105476,Dillwynia cinerascens,https://id.biodiversity.org.au/name/apni/105476,https://id.biodiversity.org.au/taxon/apni/51702961,,Dillwynia cinerascens,native +Dillwynia floribunda,Dillwynia floribunda,,Dillwynia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Dillwynia floribunda Sm.,https://id.biodiversity.org.au/node/apni/2892820,https://id.biodiversity.org.au/taxon/apni/51285570,https://id.biodiversity.org.au/name/apni/105728,Dillwynia floribunda,https://id.biodiversity.org.au/name/apni/105728,https://id.biodiversity.org.au/taxon/apni/51702961,,Dillwynia floribunda,native +Dinosperma erythrococcum,Dinosperma erythrococcum,,Dinosperma,Rutaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Dinosperma erythrococcum (F.Muell.) T.G.Hartley,https://id.biodiversity.org.au/node/apni/2897246,https://id.biodiversity.org.au/node/apni/2900591,https://id.biodiversity.org.au/name/apni/157718,Dinosperma erythrococcum,https://id.biodiversity.org.au/name/apni/157718,https://id.biodiversity.org.au/taxon/apni/51461748,,Dinosperma erythrococcum,native +Dodonaea petiolaris,Dodonaea petiolaris,Dodonaea viscosa subsp. mucronata (pro parte misapplied),Dodonaea,Sapindaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Dodonaea petiolaris F.Muell.,https://id.biodiversity.org.au/node/apni/2921131,https://id.biodiversity.org.au/taxon/apni/51447268,https://id.biodiversity.org.au/name/apni/72184,Dodonaea petiolaris [alternative possible names: Dodonaea viscosa subsp. mucronata (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51447212,,Dodonaea petiolaris,native +Dodonaea truncatiales,Dodonaea truncatiales,Dodonaea heteromorpha (pro parte misapplied) | Dodonaea heteromorpha (misapplied),Dodonaea,Sapindaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Dodonaea truncatiales F.Muell.,https://id.biodiversity.org.au/node/apni/7870563,https://id.biodiversity.org.au/taxon/apni/51447268,https://id.biodiversity.org.au/name/apni/72648,Dodonaea truncatiales [alternative possible names: Dodonaea heteromorpha (pro parte misapplied) | Dodonaea heteromorpha (misapplied)],,https://id.biodiversity.org.au/taxon/apni/51447212,,Dodonaea truncatiales,native +Dovyalis caffra,Dovyalis caffra,,Dovyalis,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised)",Dovyalis caffra (Hook.f. & Harv.) Hook.f.,https://id.biodiversity.org.au/node/apni/2888866,https://id.biodiversity.org.au/node/apni/2897632,https://id.biodiversity.org.au/name/apni/199157,Dovyalis caffra,https://id.biodiversity.org.au/name/apni/86110,https://id.biodiversity.org.au/taxon/apni/51436847,,Dovyalis caffra,naturalised +Elaeocarpus grandis,Elaeocarpus grandis,,Elaeocarpus,Elaeocarpaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Elaeocarpus grandis F.Muell.,https://id.biodiversity.org.au/node/apni/2895259,https://id.biodiversity.org.au/taxon/apni/51435153,https://id.biodiversity.org.au/name/apni/115772,Elaeocarpus grandis,https://id.biodiversity.org.au/name/apni/115772,https://id.biodiversity.org.au/taxon/apni/51632282,,Elaeocarpus grandis,native +Eleocharis pallens,Eleocharis pallens,,Eleocharis,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Eleocharis pallens S.T.Blake,https://id.biodiversity.org.au/node/apni/2899827,https://id.biodiversity.org.au/taxon/apni/51434435,https://id.biodiversity.org.au/name/apni/67140,Eleocharis pallens,https://id.biodiversity.org.au/name/apni/67140,https://id.biodiversity.org.au/taxon/apni/51460154,,Eleocharis pallens,native +Endiandra globosa,Endiandra globosa,,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Endiandra globosa Maiden & Betche,https://id.biodiversity.org.au/node/apni/2901094,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111780,Endiandra globosa,https://id.biodiversity.org.au/name/apni/111780,https://id.biodiversity.org.au/taxon/apni/51438397,,Endiandra globosa,native +Endiandra muelleri,Endiandra muelleri,,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Endiandra muelleri Meisn.,https://id.biodiversity.org.au/node/apni/2903619,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111996,Endiandra muelleri,https://id.biodiversity.org.au/name/apni/111996,https://id.biodiversity.org.au/taxon/apni/51438397,,Endiandra muelleri,native +Epilobium gunnianum,Epilobium gunnianum,,Epilobium,Onagraceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic, Tas",Epilobium gunnianum Hausskn.,https://id.biodiversity.org.au/node/apni/2903068,https://id.biodiversity.org.au/taxon/apni/51440863,https://id.biodiversity.org.au/name/apni/105579,Epilobium gunnianum,https://id.biodiversity.org.au/name/apni/105579,https://id.biodiversity.org.au/taxon/apni/51440864,,Epilobium gunnianum,native +Eremophila deserti,Eremophila deserti,,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila deserti (A.Cunn. ex Benth.) Chinnock,https://id.biodiversity.org.au/node/apni/2897363,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/123426,Eremophila deserti,https://id.biodiversity.org.au/name/apni/123426,https://id.biodiversity.org.au/taxon/apni/51461527,,Eremophila deserti,native +Eremophila oppositifolia,Eremophila oppositifolia,,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila oppositifolia R.Br.,https://id.biodiversity.org.au/node/apni/7951462,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/114575,Eremophila oppositifolia,https://id.biodiversity.org.au/name/apni/114575,https://id.biodiversity.org.au/taxon/apni/51461527,,Eremophila oppositifolia,native +Erigeron conyzoides,Erigeron conyzoides,,Erigeron,Asteraceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Erigeron conyzoides F.Muell.,https://id.biodiversity.org.au/node/apni/2913579,https://id.biodiversity.org.au/taxon/apni/51432118,https://id.biodiversity.org.au/name/apni/73195,Erigeron conyzoides,https://id.biodiversity.org.au/name/apni/239637,https://id.biodiversity.org.au/taxon/apni/51695393,,Erigeron conyzoides,native +Erythroxylum australe,Erythroxylum australe,Erythroxylum sp. Splityard Creek (L.Pedley 5360) (pro parte misapplied),Erythroxylum,Erythroxylaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Erythroxylum australe F.Muell.,https://id.biodiversity.org.au/node/apni/2912212,https://id.biodiversity.org.au/node/apni/2919669,https://id.biodiversity.org.au/name/apni/75959,Erythroxylum australe [alternative possible names: Erythroxylum sp. Splityard Creek (L.Pedley 5360) (pro parte misapplied)],,https://id.biodiversity.org.au/node/apni/2893375,,Erythroxylum australe,native +Escallonia bifida,Escallonia bifida,,Escallonia,Escalloniaceae,species,APC,accepted,Magnoliidae,NSW (naturalised),Escallonia bifida Link & Otto,https://id.biodiversity.org.au/taxon/apni/51435441,https://id.biodiversity.org.au/taxon/apni/51435442,https://id.biodiversity.org.au/name/apni/116602,Escallonia bifida,https://id.biodiversity.org.au/name/apni/116602,https://id.biodiversity.org.au/taxon/apni/51435443,,Escallonia bifida,naturalised +Eucalyptus badjensis,Eucalyptus badjensis,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus badjensis Beuzev. & M.B.Welch,https://id.biodiversity.org.au/node/apni/2912724,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/57323,Eucalyptus badjensis,https://id.biodiversity.org.au/name/apni/57323,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus badjensis,native +Eucalyptus camphora,Eucalyptus camphora,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic",Eucalyptus camphora R.T.Baker,https://id.biodiversity.org.au/node/apni/2891665,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/94439,Eucalyptus camphora,https://id.biodiversity.org.au/name/apni/94439,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus camphora,native +Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus dorrigoensis (Blakely) L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2903351,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118668,Eucalyptus dorrigoensis,https://id.biodiversity.org.au/name/apni/118668,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus dorrigoensis,native +Eucalyptus yangoura,Eucalyptus globoidea,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus globoidea Blakely,https://id.biodiversity.org.au/node/apni/5270850,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/61141,Eucalyptus globoidea,https://id.biodiversity.org.au/name/apni/92470,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus globoidea,native +Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,,Eucalyptus,Myrtaceae,subspecies,APC,accepted,Magnoliidae,"SA, NSW, Vic",Eucalyptus leucoxylon subsp. pruinosa (F.Muell. ex Miq.) Boland,https://id.biodiversity.org.au/node/apni/2908258,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/77407,Eucalyptus leucoxylon subsp. pruinosa,https://id.biodiversity.org.au/name/apni/77407,https://id.biodiversity.org.au/taxon/apni/51702983,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon,native +Eucalyptus muelleriana,Eucalyptus muelleriana,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus muelleriana A.W.Howitt,https://id.biodiversity.org.au/node/apni/2888508,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/56840,Eucalyptus muelleriana,https://id.biodiversity.org.au/name/apni/56840,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus muelleriana,native +Eucalyptus nandewarica,Eucalyptus nandewarica,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus nandewarica L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2897688,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118852,Eucalyptus nandewarica,https://id.biodiversity.org.au/name/apni/118852,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus nandewarica,native +Eucalyptus olida,Eucalyptus olida,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus olida L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2914019,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118797,Eucalyptus olida,https://id.biodiversity.org.au/name/apni/118797,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus olida,native +Eucalyptus pulverulenta,Eucalyptus pulverulenta,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus pulverulenta Sims,https://id.biodiversity.org.au/taxon/apni/51440675,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/106609,Eucalyptus pulverulenta,https://id.biodiversity.org.au/name/apni/106609,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus pulverulenta,native +Eucalyptus recurva,Eucalyptus recurva,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus recurva Crisp,https://id.biodiversity.org.au/node/apni/2892273,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/101532,Eucalyptus recurva,https://id.biodiversity.org.au/name/apni/101532,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus recurva,native +Eucalyptus rossii,Eucalyptus rossii,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus rossii R.T.Baker & H.G.Sm.,https://id.biodiversity.org.au/node/apni/2900822,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/58182,Eucalyptus rossii,https://id.biodiversity.org.au/name/apni/58182,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus rossii,native +Eucalyptus scias,Eucalyptus scias,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus scias L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2893839,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118833,Eucalyptus scias,https://id.biodiversity.org.au/name/apni/118833,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus scias,native +Eucalyptus viminalis,Eucalyptus viminalis,Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied),Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic, Tas",Eucalyptus viminalis Labill.,https://id.biodiversity.org.au/taxon/apni/51290421,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/65838,Eucalyptus viminalis [alternative possible names: Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus viminalis,native +Eucalyptus youmanii,Eucalyptus youmanii,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Eucalyptus youmanii Blakely & McKie,https://id.biodiversity.org.au/node/apni/2916227,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/92496,Eucalyptus youmanii,https://id.biodiversity.org.au/name/apni/92496,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus youmanii,native +Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata var. queenslandica,,Euphorbia,Euphorbiaceae,variety,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Euphorbia inappendiculata var. queenslandica Domin,https://id.biodiversity.org.au/node/apni/7200245,https://id.biodiversity.org.au/taxon/apni/51435529,https://id.biodiversity.org.au/name/apni/92612,Euphorbia inappendiculata var. queenslandica,https://id.biodiversity.org.au/name/apni/92612,https://id.biodiversity.org.au/taxon/apni/51442249,Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata,native +Exocarpos homalocladus,Exocarpos homalocladus,,Exocarpos,Santalaceae,species,APC,accepted,Magnoliidae,LHI,Exocarpos homalocladus C.Moore & F.Muell.,https://id.biodiversity.org.au/node/apni/2898548,https://id.biodiversity.org.au/taxon/apni/51447153,https://id.biodiversity.org.au/name/apni/58158,Exocarpos homalocladus,https://id.biodiversity.org.au/name/apni/58158,https://id.biodiversity.org.au/taxon/apni/51447154,,Exocarpos homalocladus,native +Exocarpos sparteus,Exocarpos sparteus,,Exocarpos,Santalaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Exocarpos sparteus R.Br.,https://id.biodiversity.org.au/node/apni/2898676,https://id.biodiversity.org.au/taxon/apni/51447153,https://id.biodiversity.org.au/name/apni/58330,Exocarpos sparteus,https://id.biodiversity.org.au/name/apni/58330,https://id.biodiversity.org.au/taxon/apni/51447154,,Exocarpos sparteus,native +Ficus henneana,Ficus henneana,,Ficus,Moraceae,species,APC,accepted,Magnoliidae,"NT, Qld, NSW",Ficus henneana Miq.,https://id.biodiversity.org.au/node/apni/2903067,https://id.biodiversity.org.au/taxon/apni/51439476,https://id.biodiversity.org.au/name/apni/91212,Ficus henneana,https://id.biodiversity.org.au/name/apni/91212,https://id.biodiversity.org.au/taxon/apni/51439463,,Ficus henneana,native +Freesia laxa,Freesia laxa,,Freesia,Iridaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), Qld (naturalised), NSW (naturalised), NI (naturalised), Vic (naturalised)",Freesia laxa (Thunb.) Goldblatt & J.C.Manning,https://id.biodiversity.org.au/node/apni/2886987,https://id.biodiversity.org.au/node/apni/2913899,https://id.biodiversity.org.au/name/apni/200132,Freesia laxa,https://id.biodiversity.org.au/name/apni/200132,https://id.biodiversity.org.au/taxon/apni/51438006,,Freesia laxa,naturalised +Freesia hybrid,Freesia leichtlinii subsp. leichtlinii x Freesia leichtlinii subsp. alba,,Freesia,Iridaceae,subspecies,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised)",Freesia leichtlinii Klatt subsp. leichtlinii x Freesia leichtlinii subsp. alba (G.L.Mey.) J.C.Manning & Goldblatt,https://id.biodiversity.org.au/node/apni/2908401,https://id.biodiversity.org.au/node/apni/2913899,https://id.biodiversity.org.au/name/apni/241787,Freesia leichtlinii subsp. leichtlinii x Freesia leichtlinii subsp. alba,https://id.biodiversity.org.au/name/apni/171901,https://id.biodiversity.org.au/taxon/apni/51438006,Freesia leichtlinii subsp. leichtlinii x Freesia leichtlinii subsp. alba,Freesia leichtlinii,naturalised +Geijera salicifolia,Geijera salicifolia,,Geijera,Rutaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Geijera salicifolia Schott,https://id.biodiversity.org.au/node/apni/2901807,https://id.biodiversity.org.au/node/apni/2905474,https://id.biodiversity.org.au/name/apni/101381,Geijera salicifolia,https://id.biodiversity.org.au/name/apni/101381,https://id.biodiversity.org.au/taxon/apni/51461748,,Geijera salicifolia,native +Gentiana wingecarribiensis,Gentiana wingecarribiensis,,Gentiana,Gentianaceae,species,APC,accepted,Magnoliidae,NSW,Gentiana wingecarribiensis L.G.Adams,https://id.biodiversity.org.au/node/apni/2915610,https://id.biodiversity.org.au/taxon/apni/51436928,https://id.biodiversity.org.au/name/apni/80378,Gentiana wingecarribiensis,https://id.biodiversity.org.au/name/apni/80378,https://id.biodiversity.org.au/taxon/apni/51436871,,Gentiana wingecarribiensis,native +Geranium obtusisepalum,Geranium obtusisepalum,,Geranium,Geraniaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Geranium obtusisepalum Carolin,https://id.biodiversity.org.au/node/apni/2910251,https://id.biodiversity.org.au/taxon/apni/51436946,https://id.biodiversity.org.au/name/apni/82004,Geranium obtusisepalum,https://id.biodiversity.org.au/name/apni/82004,https://id.biodiversity.org.au/taxon/apni/51436947,,Geranium obtusisepalum,native +Geranium purpureum subsp. purpureum,Geranium purpureum,,Geranium,Geraniaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised)",Geranium purpureum Vill.,https://id.biodiversity.org.au/node/apni/2919721,https://id.biodiversity.org.au/taxon/apni/51436946,https://id.biodiversity.org.au/name/apni/82353,Geranium purpureum,https://id.biodiversity.org.au/name/apni/82382,https://id.biodiversity.org.au/taxon/apni/51436947,,Geranium purpureum,naturalised +Gompholobium grandiflorum,Gompholobium grandiflorum,,Gompholobium,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Gompholobium grandiflorum Sm.,https://id.biodiversity.org.au/node/apni/2909013,https://id.biodiversity.org.au/taxon/apni/51436123,https://id.biodiversity.org.au/name/apni/65291,Gompholobium grandiflorum,https://id.biodiversity.org.au/name/apni/65291,https://id.biodiversity.org.au/taxon/apni/51702961,,Gompholobium grandiflorum,native +Goodenia varia,Goodenia varia,,Goodenia,Goodeniaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic",Goodenia varia R.Br.,https://id.biodiversity.org.au/node/apni/2910439,https://id.biodiversity.org.au/taxon/apni/51437012,https://id.biodiversity.org.au/name/apni/92079,Goodenia varia,https://id.biodiversity.org.au/name/apni/92079,https://id.biodiversity.org.au/taxon/apni/51462931,,Goodenia varia,native +Gossia bidwillii,Gossia bidwillii,,Gossia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Gossia bidwillii (Benth.) N.Snow & Guymer,https://id.biodiversity.org.au/taxon/apni/51439972,https://id.biodiversity.org.au/taxon/apni/51439958,https://id.biodiversity.org.au/name/apni/180918,Gossia bidwillii,https://id.biodiversity.org.au/name/apni/180918,https://id.biodiversity.org.au/taxon/apni/51702983,,Gossia bidwillii,native +Grevillea scortechinii,Grevillea scortechinii,,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Grevillea scortechinii (F.Muell. ex Scort.) F.Muell.,https://id.biodiversity.org.au/node/apni/2918803,https://id.biodiversity.org.au/taxon/apni/51445337,https://id.biodiversity.org.au/name/apni/63322,Grevillea scortechinii,https://id.biodiversity.org.au/name/apni/63322,https://id.biodiversity.org.au/taxon/apni/51614274,,Grevillea scortechinii,native +Hakea macraeana,Hakea macraeana,Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied),Hakea,Proteaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Hakea macraeana F.Muell.,https://id.biodiversity.org.au/node/apni/2895080,https://id.biodiversity.org.au/taxon/apni/51445456,https://id.biodiversity.org.au/name/apni/94862,Hakea macraeana [alternative possible names: Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied)],,https://id.biodiversity.org.au/taxon/apni/51614274,,Hakea macraeana,native +Hemisteptia lyrata,Hemisteptia lyrata,,Hemisteptia,Asteraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Hemisteptia lyrata (Bunge) Fisch. & C.A.Mey.,https://id.biodiversity.org.au/taxon/apni/51268530,https://id.biodiversity.org.au/taxon/apni/51268531,https://id.biodiversity.org.au/name/apni/230066,Hemisteptia lyrata,https://id.biodiversity.org.au/name/apni/230066,https://id.biodiversity.org.au/taxon/apni/51695393,,Hemisteptia lyrata,native +Hibbertia crinita,Hibbertia crinita,,Hibbertia,Dilleniaceae,species,APC,accepted,Magnoliidae,"SA, Vic",Hibbertia crinita Toelken,https://id.biodiversity.org.au/node/apni/2899370,https://id.biodiversity.org.au/taxon/apni/51434912,https://id.biodiversity.org.au/name/apni/170069,Hibbertia crinita,https://id.biodiversity.org.au/name/apni/170069,https://id.biodiversity.org.au/taxon/apni/51434913,,Hibbertia crinita,native +Hibiscus brachysiphonius,Hibiscus brachysiphonius,,Hibiscus,Malvaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Hibiscus brachysiphonius F.Muell.,https://id.biodiversity.org.au/node/apni/2891329,https://id.biodiversity.org.au/taxon/apni/51439316,https://id.biodiversity.org.au/name/apni/91736,Hibiscus brachysiphonius,https://id.biodiversity.org.au/name/apni/91736,https://id.biodiversity.org.au/taxon/apni/51439248,,Hibiscus brachysiphonius,native +Hibiscus sturtii,Hibiscus sturtii,,Hibiscus,Malvaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Hibiscus sturtii Hook.,https://id.biodiversity.org.au/taxon/apni/51439064,https://id.biodiversity.org.au/taxon/apni/51439316,https://id.biodiversity.org.au/name/apni/63902,Hibiscus sturtii,https://id.biodiversity.org.au/name/apni/63902,https://id.biodiversity.org.au/taxon/apni/51439248,,Hibiscus sturtii,native +Hypericum elodes,Hypericum elodes,,Hypericum,Hypericaceae,species,APC,accepted,Magnoliidae,NSW (naturalised),Hypericum elodes L.,https://id.biodiversity.org.au/node/apni/2909044,https://id.biodiversity.org.au/taxon/apni/51433733,https://id.biodiversity.org.au/name/apni/136721,Hypericum elodes,https://id.biodiversity.org.au/name/apni/136721,https://id.biodiversity.org.au/taxon/apni/51433734,,Hypericum elodes,naturalised +Imperata cylindrica,Imperata cylindrica,,Imperata,Poaceae,species,APC,accepted,Magnoliidae,"WA, CoI (naturalised), ChI (naturalised), NT, SA, Qld, NSW, LHI (naturalised), ACT, Vic, Tas",Imperata cylindrica (L.) P.Beauv.,https://id.biodiversity.org.au/node/apni/2920993,https://id.biodiversity.org.au/node/apni/2905343,https://id.biodiversity.org.au/name/apni/71806,Imperata cylindrica,https://id.biodiversity.org.au/name/apni/179218,https://id.biodiversity.org.au/taxon/apni/51644646,,Imperata cylindrica,native and naturalised +Indigofera triflora,Indigofera triflora,,Indigofera,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Indigofera triflora Peter G.Wilson & Rowe,https://id.biodiversity.org.au/node/apni/2905193,https://id.biodiversity.org.au/taxon/apni/51436152,https://id.biodiversity.org.au/name/apni/189510,Indigofera triflora,https://id.biodiversity.org.au/name/apni/189510,https://id.biodiversity.org.au/taxon/apni/51702961,,Indigofera triflora,native +Ipomoea cairica,Ipomoea cairica,,Ipomoea,Convolvulaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), ChI (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), NI (naturalised)",Ipomoea cairica (L.) Sweet,https://id.biodiversity.org.au/node/apni/2897935,https://id.biodiversity.org.au/taxon/apni/51433921,https://id.biodiversity.org.au/name/apni/93713,Ipomoea cairica,https://id.biodiversity.org.au/name/apni/93713,https://id.biodiversity.org.au/taxon/apni/51695210,,Ipomoea cairica,naturalised +Isolepis montivaga,Isolepis montivaga,,Isolepis,Cyperaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic, Tas",Isolepis montivaga (S.T.Blake) K.L.Wilson,https://id.biodiversity.org.au/node/apni/2921053,https://id.biodiversity.org.au/taxon/apni/51336324,https://id.biodiversity.org.au/name/apni/74456,Isolepis montivaga,https://id.biodiversity.org.au/name/apni/74456,https://id.biodiversity.org.au/taxon/apni/51460154,,Isolepis montivaga,native +Isotoma axillaris,Isotoma axillaris,,Isotoma,Campanulaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic",Isotoma axillaris Lindl.,https://id.biodiversity.org.au/node/apni/2902056,https://id.biodiversity.org.au/node/apni/2892848,https://id.biodiversity.org.au/name/apni/102004,Isotoma axillaris,https://id.biodiversity.org.au/name/apni/102004,https://id.biodiversity.org.au/taxon/apni/51432853,,Isotoma axillaris,native +Isotoma fluviatilis subsp. fluviatilis,Isotoma fluviatilis subsp. fluviatilis,,Isotoma,Campanulaceae,subspecies,APC,accepted,Magnoliidae,NSW,Isotoma fluviatilis (R.Br.) F.Muell. ex Benth. subsp. fluviatilis,https://id.biodiversity.org.au/node/apni/2897543,https://id.biodiversity.org.au/node/apni/2892848,https://id.biodiversity.org.au/name/apni/102114,Isotoma fluviatilis subsp. fluviatilis,https://id.biodiversity.org.au/name/apni/102114,https://id.biodiversity.org.au/taxon/apni/51432853,Isotoma fluviatilis subsp. fluviatilis,Isotoma fluviatilis,native +Juncus acutus subsp. acutus,Juncus acutus subsp. acutus,,Juncus,Juncaceae,subspecies,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), Qld (naturalised), NSW (naturalised), Vic (naturalised)",Juncus acutus L. subsp. acutus,https://id.biodiversity.org.au/node/apni/2887983,https://id.biodiversity.org.au/taxon/apni/51438170,https://id.biodiversity.org.au/name/apni/182490,Juncus acutus subsp. acutus,https://id.biodiversity.org.au/name/apni/182490,https://id.biodiversity.org.au/taxon/apni/51438171,Juncus acutus subsp. acutus,Juncus acutus,naturalised +Juncus kraussii,Juncus kraussii,,Juncus,Juncaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic, Tas",Juncus kraussii Hochst.,https://id.biodiversity.org.au/node/apni/2900900,https://id.biodiversity.org.au/taxon/apni/51438170,https://id.biodiversity.org.au/name/apni/55859,Juncus kraussii,https://id.biodiversity.org.au/name/apni/55859,https://id.biodiversity.org.au/taxon/apni/51438171,,Juncus kraussii,native +Lantana montevidensis,Lantana montevidensis,,Lantana,Verbenaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), Qld (naturalised), NSW (naturalised), NI (doubtfully naturalised)",Lantana montevidensis (Spreng.) Briq.,https://id.biodiversity.org.au/node/apni/2894994,https://id.biodiversity.org.au/taxon/apni/51448661,https://id.biodiversity.org.au/name/apni/70044,Lantana montevidensis,https://id.biodiversity.org.au/name/apni/70044,https://id.biodiversity.org.au/taxon/apni/51448662,,Lantana montevidensis,naturalised +Lepidium africanum,Lepidium africanum,,Lepidium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Lepidium africanum (Burm.f.) DC.,https://id.biodiversity.org.au/node/apni/2887818,https://id.biodiversity.org.au/taxon/apni/51612686,https://id.biodiversity.org.au/name/apni/68961,Lepidium africanum,https://id.biodiversity.org.au/name/apni/68961,https://id.biodiversity.org.au/taxon/apni/51612687,,Lepidium africanum,naturalised +Lepidium foliosum,Lepidium foliosum,,Lepidium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Lepidium foliosum Desv.,https://id.biodiversity.org.au/node/apni/2908453,https://id.biodiversity.org.au/taxon/apni/51612686,https://id.biodiversity.org.au/name/apni/69389,Lepidium foliosum,https://id.biodiversity.org.au/name/apni/69389,https://id.biodiversity.org.au/taxon/apni/51612687,,Lepidium foliosum,native +Lepidium oxytrichum,Lepidium oxytrichum,,Lepidium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Lepidium oxytrichum Sprague,https://id.biodiversity.org.au/node/apni/2915883,https://id.biodiversity.org.au/taxon/apni/51612686,https://id.biodiversity.org.au/name/apni/84027,Lepidium oxytrichum,https://id.biodiversity.org.au/name/apni/84027,https://id.biodiversity.org.au/taxon/apni/51612687,,Lepidium oxytrichum,native +Leptomeria drupacea,Leptomeria drupacea,,Leptomeria,Santalaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic, Tas",Leptomeria drupacea (Labill.) Druce,https://id.biodiversity.org.au/node/apni/2892780,https://id.biodiversity.org.au/node/apni/2897704,https://id.biodiversity.org.au/name/apni/61625,Leptomeria drupacea,https://id.biodiversity.org.au/name/apni/61625,https://id.biodiversity.org.au/taxon/apni/51447154,,Leptomeria drupacea,native +Leptospermum continentale,Leptospermum continentale,,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic",Leptospermum continentale Joy Thomps.,https://id.biodiversity.org.au/node/apni/2917147,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/81291,Leptospermum continentale,https://id.biodiversity.org.au/name/apni/81291,https://id.biodiversity.org.au/taxon/apni/51702983,,Leptospermum continentale,native +Leptospermum obovatum,Leptospermum obovatum,,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Leptospermum obovatum Sweet,https://id.biodiversity.org.au/node/apni/2891711,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/99608,Leptospermum obovatum,https://id.biodiversity.org.au/name/apni/99608,https://id.biodiversity.org.au/taxon/apni/51702983,,Leptospermum obovatum,native +Leucopogon amplexicaulis,Leucopogon amplexicaulis,,Leucopogon,Ericaceae,species,APC,accepted,Magnoliidae,NSW,Leucopogon amplexicaulis (Rudge) R.Br.,https://id.biodiversity.org.au/node/apni/2896081,https://id.biodiversity.org.au/taxon/apni/51435325,https://id.biodiversity.org.au/name/apni/106715,Leucopogon amplexicaulis,https://id.biodiversity.org.au/name/apni/106715,https://id.biodiversity.org.au/taxon/apni/51436079,,Leucopogon amplexicaulis,native +Lobelia pedunculata,Lobelia pedunculata,,Lobelia,Campanulaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic, Tas",Lobelia pedunculata R.Br.,https://id.biodiversity.org.au/node/apni/2901444,https://id.biodiversity.org.au/taxon/apni/51432852,https://id.biodiversity.org.au/name/apni/106999,Lobelia pedunculata,https://id.biodiversity.org.au/name/apni/106999,https://id.biodiversity.org.au/taxon/apni/51432853,,Lobelia pedunculata,native +Lobelia trigonocaulis,Lobelia trigonocaulis,,Lobelia,Campanulaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Lobelia trigonocaulis F.Muell.,https://id.biodiversity.org.au/node/apni/2901863,https://id.biodiversity.org.au/taxon/apni/51432852,https://id.biodiversity.org.au/name/apni/107808,Lobelia trigonocaulis,https://id.biodiversity.org.au/name/apni/107808,https://id.biodiversity.org.au/taxon/apni/51432853,,Lobelia trigonocaulis,native +Lotononis bainesii,Lotononis bainesii,,Lotononis,Fabaceae,species,APC,accepted,Magnoliidae,"Qld (naturalised), NSW (naturalised)",Lotononis bainesii Baker,https://id.biodiversity.org.au/node/apni/2904277,https://id.biodiversity.org.au/node/apni/2898035,https://id.biodiversity.org.au/name/apni/109834,Lotononis bainesii,https://id.biodiversity.org.au/name/apni/109834,https://id.biodiversity.org.au/taxon/apni/51702961,,Lotononis bainesii,naturalised +Lotus corniculatus,Lotus corniculatus,Lotus preslii (pro parte misapplied) | Lotus uliginosus (pro parte misapplied),Lotus,Fabaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (formerly naturalised), NSW (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Lotus corniculatus L.,https://id.biodiversity.org.au/node/apni/2921302,https://id.biodiversity.org.au/taxon/apni/51436215,https://id.biodiversity.org.au/name/apni/110319,Lotus corniculatus [alternative possible names: Lotus preslii (pro parte misapplied) | Lotus uliginosus (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51702961,,Lotus corniculatus,naturalised +Lupinus polyphyllus,Lupinus polyphyllus,,Lupinus,Fabaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), Vic (naturalised)",Lupinus polyphyllus Lindl.,https://id.biodiversity.org.au/node/apni/2917429,https://id.biodiversity.org.au/node/apni/2918316,https://id.biodiversity.org.au/name/apni/100609,Lupinus polyphyllus,https://id.biodiversity.org.au/name/apni/100609,https://id.biodiversity.org.au/taxon/apni/51702961,,Lupinus polyphyllus,naturalised +Medicago orbicularis,Medicago orbicularis,,Medicago,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (formerly naturalised)",Medicago orbicularis (L.) Bartal.,https://id.biodiversity.org.au/node/apni/2901771,https://id.biodiversity.org.au/taxon/apni/51285690,https://id.biodiversity.org.au/name/apni/59568,Medicago orbicularis,https://id.biodiversity.org.au/name/apni/59568,https://id.biodiversity.org.au/taxon/apni/51702961,,Medicago orbicularis,naturalised +Melichrus procumbens,Melichrus procumbens,,Melichrus,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Melichrus procumbens (Cav.) Druce,https://id.biodiversity.org.au/node/apni/2905836,https://id.biodiversity.org.au/node/apni/2914566,https://id.biodiversity.org.au/name/apni/114051,Melichrus procumbens,https://id.biodiversity.org.au/name/apni/114051,https://id.biodiversity.org.au/taxon/apni/51436079,,Melichrus procumbens,native +Mischocarpus australis,Mischocarpus australis,,Mischocarpus,Sapindaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Mischocarpus australis S.T.Reynolds,https://id.biodiversity.org.au/node/apni/2893744,https://id.biodiversity.org.au/taxon/apni/51389373,https://id.biodiversity.org.au/name/apni/115917,Mischocarpus australis,https://id.biodiversity.org.au/name/apni/115917,https://id.biodiversity.org.au/taxon/apni/51447212,,Mischocarpus australis,native +Muehlenbeckia adpressa,Muehlenbeckia adpressa,,Muehlenbeckia,Polygonaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Muehlenbeckia adpressa (Labill.) Meisn.,https://id.biodiversity.org.au/node/apni/4750977,https://id.biodiversity.org.au/taxon/apni/51291654,https://id.biodiversity.org.au/name/apni/107852,Muehlenbeckia adpressa,https://id.biodiversity.org.au/name/apni/107852,https://id.biodiversity.org.au/taxon/apni/51444856,,Muehlenbeckia adpressa,native +Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,,Myoporum,Scrophulariaceae,subspecies,APC,accepted,Magnoliidae,"Qld, NSW",Myoporum boninense subsp. australe Chinnock,https://id.biodiversity.org.au/node/apni/7957248,https://id.biodiversity.org.au/taxon/apni/51447443,https://id.biodiversity.org.au/name/apni/117892,Myoporum boninense subsp. australe,https://id.biodiversity.org.au/name/apni/117892,https://id.biodiversity.org.au/taxon/apni/51461527,Myoporum boninense subsp. australe,Myoporum boninense,native +Nicotiana glauca,Nicotiana glauca,,Nicotiana,Solanaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (naturalised)",Nicotiana glauca Graham,https://id.biodiversity.org.au/node/apni/2887606,https://id.biodiversity.org.au/taxon/apni/51447689,https://id.biodiversity.org.au/name/apni/77368,Nicotiana glauca,https://id.biodiversity.org.au/name/apni/77368,https://id.biodiversity.org.au/taxon/apni/51447684,,Nicotiana glauca,naturalised +Nicotiana goodspeedii,Nicotiana goodspeedii,,Nicotiana,Solanaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic",Nicotiana goodspeedii H.-M.Wheeler,https://id.biodiversity.org.au/node/apni/2908652,https://id.biodiversity.org.au/taxon/apni/51447689,https://id.biodiversity.org.au/name/apni/77381,Nicotiana goodspeedii,https://id.biodiversity.org.au/name/apni/77381,https://id.biodiversity.org.au/taxon/apni/51447684,,Nicotiana goodspeedii,native +Oxalis corniculata,Oxalis corniculata,,Oxalis,Oxalidaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), ChI (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Oxalis corniculata L.,https://id.biodiversity.org.au/node/apni/2909588,https://id.biodiversity.org.au/taxon/apni/51442068,https://id.biodiversity.org.au/name/apni/89460,Oxalis corniculata,https://id.biodiversity.org.au/name/apni/89460,https://id.biodiversity.org.au/taxon/apni/51442069,,Oxalis corniculata,naturalised +Pandorea pandorana subsp. austrocaledonica,Pandorea pandorana,,Pandorea,Bignoniaceae,species,APC,accepted,Magnoliidae,"WA, SA (native and naturalised), Qld, NSW, LHI, NI (presumed extinct), Vic (native and naturalised), Tas",Pandorea pandorana (Andrews) Steenis,https://id.biodiversity.org.au/taxon/apni/51269199,https://id.biodiversity.org.au/taxon/apni/51269200,https://id.biodiversity.org.au/name/apni/91117,Pandorea pandorana,https://id.biodiversity.org.au/name/apni/141640,https://id.biodiversity.org.au/taxon/apni/51439229,,Pandorea pandorana,native and naturalised +Paraserianthes lophantha,Paraserianthes lophantha,,Paraserianthes,Fabaceae,species,APC,accepted,Magnoliidae,"WA (native and naturalised), SA (naturalised), NSW (naturalised), NI (naturalised), Vic (naturalised), Tas (naturalised)",Paraserianthes lophantha (Willd.) I.C.Nielsen,https://id.biodiversity.org.au/taxon/apni/51286820,https://id.biodiversity.org.au/taxon/apni/51286819,https://id.biodiversity.org.au/name/apni/116755,Paraserianthes lophantha,https://id.biodiversity.org.au/name/apni/116755,https://id.biodiversity.org.au/taxon/apni/51702961,,Paraserianthes lophantha,native and naturalised +Parentucellia latifolia,Parentucellia latifolia,,Parentucellia,Orobanchaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Parentucellia latifolia (L.) Caruel,https://id.biodiversity.org.au/taxon/apni/51291069,https://id.biodiversity.org.au/taxon/apni/51291062,https://id.biodiversity.org.au/name/apni/96753,Parentucellia latifolia,https://id.biodiversity.org.au/name/apni/96753,https://id.biodiversity.org.au/taxon/apni/51291037,,Parentucellia latifolia,naturalised +Hypoxis glabella var. glabella,Pauridia glabella var. glabella,,Pauridia,Hypoxidaceae,variety,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Pauridia glabella (R.Br.) Snijman & Kocyan var. glabella,https://id.biodiversity.org.au/node/apni/7455351,https://id.biodiversity.org.au/taxon/apni/51437983,https://id.biodiversity.org.au/name/apni/244102,Pauridia glabella var. glabella,https://id.biodiversity.org.au/name/apni/81442,https://id.biodiversity.org.au/taxon/apni/51437984,Pauridia glabella var. glabella,Pauridia glabella,native +Phlegmatospermum cochlearinum,Phlegmatospermum cochlearinum,,Phlegmatospermum,Brassicaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic",Phlegmatospermum cochlearinum (F.Muell.) O.E.Schulz,https://id.biodiversity.org.au/node/apni/2915554,https://id.biodiversity.org.au/node/apni/2897988,https://id.biodiversity.org.au/name/apni/81861,Phlegmatospermum cochlearinum,https://id.biodiversity.org.au/name/apni/81861,https://id.biodiversity.org.au/taxon/apni/51612687,,Phlegmatospermum cochlearinum,native +Phyla nodiflora,Phyla nodiflora,,Phyla,Verbenaceae,species,APC,accepted,Magnoliidae,"WA (native and naturalised), CoI (naturalised), NT, Qld, NSW (naturalised)",Phyla nodiflora (L.) Greene,https://id.biodiversity.org.au/node/apni/2907374,https://id.biodiversity.org.au/node/apni/2892182,https://id.biodiversity.org.au/name/apni/74617,Phyla nodiflora,https://id.biodiversity.org.au/name/apni/74617,https://id.biodiversity.org.au/taxon/apni/51448662,,Phyla nodiflora,native and naturalised +Picris barbarorum,Picris barbarorum,,Picris,Asteraceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic (presumed extinct)",Picris barbarorum Lindl.,https://id.biodiversity.org.au/node/apni/2916052,https://id.biodiversity.org.au/node/apni/7890078,https://id.biodiversity.org.au/name/apni/110349,Picris barbarorum,https://id.biodiversity.org.au/name/apni/110349,https://id.biodiversity.org.au/taxon/apni/51695393,,Picris barbarorum,native +Pimelea ligustrina subsp. ligustrina,Pimelea ligustrina subsp. ligustrina,,Pimelea,Thymelaeaceae,subspecies,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Pimelea ligustrina Labill. subsp. ligustrina,https://id.biodiversity.org.au/node/apni/2889686,https://id.biodiversity.org.au/taxon/apni/51449000,https://id.biodiversity.org.au/name/apni/69062,Pimelea ligustrina subsp. ligustrina,https://id.biodiversity.org.au/name/apni/69062,https://id.biodiversity.org.au/taxon/apni/51449001,Pimelea ligustrina subsp. ligustrina,Pimelea ligustrina,native +Pinus pinea,Pinus pinea,,Pinus,Pinaceae,species,APC,accepted,Pinidae,"WA (naturalised), NSW (naturalised), Vic (naturalised)",Pinus pinea L.,https://id.biodiversity.org.au/node/apni/2904478,https://id.biodiversity.org.au/node/apni/2902806,https://id.biodiversity.org.au/name/apni/171468,Pinus pinea,https://id.biodiversity.org.au/name/apni/171468,https://id.biodiversity.org.au/node/apni/7742574,,Pinus pinea,naturalised +Pisum sativum var. arvense,Pisum sativum var. arvense,,Pisum,Fabaceae,variety,APC,accepted,Magnoliidae,NSW (naturalised),Pisum sativum var. arvense (L.) Poir.,https://id.biodiversity.org.au/node/apni/2920606,https://id.biodiversity.org.au/node/apni/2898529,https://id.biodiversity.org.au/name/apni/153418,Pisum sativum var. arvense,https://id.biodiversity.org.au/name/apni/153418,https://id.biodiversity.org.au/taxon/apni/51702961,Pisum sativum var. arvense,Pisum sativum,naturalised +Pittosporum erioloma,Pittosporum erioloma,,Pittosporum,Pittosporaceae,species,APC,accepted,Magnoliidae,LHI,Pittosporum erioloma C.Moore & F.Muell.,https://id.biodiversity.org.au/node/apni/2891204,https://id.biodiversity.org.au/taxon/apni/51442349,https://id.biodiversity.org.au/name/apni/99523,Pittosporum erioloma,https://id.biodiversity.org.au/name/apni/99523,https://id.biodiversity.org.au/taxon/apni/51442315,,Pittosporum erioloma,native +Plantago turrifera,Plantago turrifera,,Plantago,Plantaginaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW (native and naturalised), Vic","Plantago turrifera B.G.Briggs, Carolin & Pulley",https://id.biodiversity.org.au/node/apni/2895983,https://id.biodiversity.org.au/node/apni/7745425,https://id.biodiversity.org.au/name/apni/79077,Plantago turrifera,https://id.biodiversity.org.au/name/apni/79077,https://id.biodiversity.org.au/taxon/apni/51699383,,Plantago turrifera,native and naturalised +Polycarpon tetraphyllum,Polycarpon tetraphyllum,,Polycarpon,Caryophyllaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Polycarpon tetraphyllum (L.) L.,https://id.biodiversity.org.au/taxon/apni/51270276,https://id.biodiversity.org.au/taxon/apni/51270277,https://id.biodiversity.org.au/name/apni/107982,Polycarpon tetraphyllum,https://id.biodiversity.org.au/name/apni/107982,https://id.biodiversity.org.au/taxon/apni/51432987,,Polycarpon tetraphyllum,naturalised +Potamogeton australiensis,Potamogeton australiensis,,Potamogeton,Potamogetonaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Potamogeton australiensis A.Benn.,https://id.biodiversity.org.au/node/apni/7808489,https://id.biodiversity.org.au/node/apni/8770682,https://id.biodiversity.org.au/name/apni/65827,Potamogeton australiensis,https://id.biodiversity.org.au/name/apni/65827,https://id.biodiversity.org.au/taxon/apni/51353530,,Potamogeton australiensis,native +Psoralea pinnata,Psoralea pinnata,,Psoralea,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised), Tas (naturalised)",Psoralea pinnata L.,https://id.biodiversity.org.au/node/apni/2887023,https://id.biodiversity.org.au/node/apni/8771698,https://id.biodiversity.org.au/name/apni/88820,Psoralea pinnata,https://id.biodiversity.org.au/name/apni/88820,https://id.biodiversity.org.au/taxon/apni/51702961,,Psoralea pinnata,naturalised +Pultenaea ferruginea,Pultenaea ferruginea,,Pultenaea,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Pultenaea ferruginea Rudge,https://id.biodiversity.org.au/node/apni/2906803,https://id.biodiversity.org.au/taxon/apni/51436286,https://id.biodiversity.org.au/name/apni/59158,Pultenaea ferruginea,https://id.biodiversity.org.au/name/apni/59158,https://id.biodiversity.org.au/taxon/apni/51702961,,Pultenaea ferruginea,native +Rhodamnia argentea,Rhodamnia argentea,,Rhodamnia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Rhodamnia argentea Benth.,https://id.biodiversity.org.au/node/apni/2919069,https://id.biodiversity.org.au/taxon/apni/51440311,https://id.biodiversity.org.au/name/apni/68532,Rhodamnia argentea,https://id.biodiversity.org.au/name/apni/68532,https://id.biodiversity.org.au/taxon/apni/51702983,,Rhodamnia argentea,native +Rorippa gigantea,Rorippa gigantea,,Rorippa,Brassicaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Rorippa gigantea (Hook.) Garn.-Jones,https://id.biodiversity.org.au/node/apni/2920330,https://id.biodiversity.org.au/node/apni/8442201,https://id.biodiversity.org.au/name/apni/75950,Rorippa gigantea,https://id.biodiversity.org.au/name/apni/75950,https://id.biodiversity.org.au/taxon/apni/51612687,,Rorippa gigantea,native +Rubus parvifolius,Rubus parvifolius,,Rubus,Rosaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Rubus parvifolius L.,https://id.biodiversity.org.au/node/apni/2901867,https://id.biodiversity.org.au/taxon/apni/51446575,https://id.biodiversity.org.au/name/apni/85986,Rubus parvifolius,https://id.biodiversity.org.au/name/apni/85986,https://id.biodiversity.org.au/taxon/apni/51446278,,Rubus parvifolius,native +Salix alba,Salix alba,,Salix,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised)",Salix alba L.,https://id.biodiversity.org.au/node/apni/2896377,https://id.biodiversity.org.au/node/apni/8905801,https://id.biodiversity.org.au/name/apni/59687,Salix alba [alternative possible names: NA],,https://id.biodiversity.org.au/taxon/apni/51436847,,Salix alba,naturalised +Schenkia australis,Schenkia australis,,Schenkia,Gentianaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic, Tas",Schenkia australis (R.Br.) G.Mans.,https://id.biodiversity.org.au/taxon/apni/51436897,https://id.biodiversity.org.au/taxon/apni/51436898,https://id.biodiversity.org.au/name/apni/200895,Schenkia australis,https://id.biodiversity.org.au/name/apni/200895,https://id.biodiversity.org.au/taxon/apni/51436871,,Schenkia australis,native +Schoenus apogon,Schoenus apogon,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Schoenus apogon Roem. & Schult.,https://id.biodiversity.org.au/node/apni/2908439,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/109452,Schoenus apogon,https://id.biodiversity.org.au/name/apni/109452,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus apogon,native +Schoenus brevifolius,Schoenus brevifolius,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic, Tas",Schoenus brevifolius R.Br.,https://id.biodiversity.org.au/node/apni/2904000,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/109778,Schoenus brevifolius,https://id.biodiversity.org.au/name/apni/109778,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus brevifolius,native +Schoenus lepidosperma,Schoenus lepidosperma,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Schoenus lepidosperma (F.Muell.) K.L.Wilson,https://id.biodiversity.org.au/node/apni/2893030,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/141376,Schoenus lepidosperma,https://id.biodiversity.org.au/name/apni/243667,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus lepidosperma,native +Schoenus vaginatus,Schoenus vaginatus,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Schoenus vaginatus F.Muell. ex Benth.,https://id.biodiversity.org.au/node/apni/2896591,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/113246,Schoenus vaginatus,https://id.biodiversity.org.au/name/apni/113246,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus vaginatus,native +Scleria rugosa,Scleria rugosa,,Scleria,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Scleria rugosa R.Br.,https://id.biodiversity.org.au/node/apni/2892143,https://id.biodiversity.org.au/taxon/apni/51434752,https://id.biodiversity.org.au/name/apni/64346,Scleria rugosa,https://id.biodiversity.org.au/name/apni/64346,https://id.biodiversity.org.au/taxon/apni/51460154,,Scleria rugosa,native +Senecio longipilus,Senecio longipilus,,Senecio,Asteraceae,species,APC,accepted,Magnoliidae,"NSW, Tas",Senecio longipilus I.Thomps.,https://id.biodiversity.org.au/node/apni/2907653,https://id.biodiversity.org.au/taxon/apni/51614245,https://id.biodiversity.org.au/name/apni/189666,Senecio longipilus,https://id.biodiversity.org.au/name/apni/189666,https://id.biodiversity.org.au/taxon/apni/51695393,,Senecio longipilus,native +Sida goniocarpa,Sida goniocarpa,,Sida,Malvaceae,species,APC,accepted,Magnoliidae,"NT, SA, Qld, NSW",Sida goniocarpa (Benth.) Domin,https://id.biodiversity.org.au/node/apni/2893354,https://id.biodiversity.org.au/taxon/apni/51439283,https://id.biodiversity.org.au/name/apni/73352,Sida goniocarpa,https://id.biodiversity.org.au/name/apni/73352,https://id.biodiversity.org.au/taxon/apni/51439248,,Sida goniocarpa,native +Sigesbeckia orientalis,Sigesbeckia orientalis,,Sigesbeckia,Asteraceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT, SA, Qld, NSW, NI (naturalised), ACT, Vic, Tas (doubtfully naturalised)",Sigesbeckia orientalis L.,https://id.biodiversity.org.au/node/apni/2920819,https://id.biodiversity.org.au/taxon/apni/51432306,https://id.biodiversity.org.au/name/apni/75539,Sigesbeckia orientalis,https://id.biodiversity.org.au/name/apni/75539,https://id.biodiversity.org.au/taxon/apni/51695393,,Sigesbeckia orientalis,native and naturalised +Sisymbrium irio,Sisymbrium irio,,Sisymbrium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Sisymbrium irio L.,https://id.biodiversity.org.au/node/apni/2887936,https://id.biodiversity.org.au/node/apni/2921080,https://id.biodiversity.org.au/name/apni/78148,Sisymbrium irio,https://id.biodiversity.org.au/name/apni/78148,https://id.biodiversity.org.au/taxon/apni/51612687,,Sisymbrium irio,naturalised +Derris involuta,Solori involuta,,Solori,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Solori involuta (Sprague) Sirich. & Adema,https://id.biodiversity.org.au/taxon/apni/51311103,https://id.biodiversity.org.au/taxon/apni/51311094,https://id.biodiversity.org.au/name/apni/4447863,Solori involuta,https://id.biodiversity.org.au/name/apni/87525,https://id.biodiversity.org.au/taxon/apni/51702961,,Solori involuta,native +Sparaxis bulbifera,Sparaxis bulbifera,,Sparaxis,Iridaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised), Tas (naturalised)",Sparaxis bulbifera (L.) Ker Gawl.,https://id.biodiversity.org.au/node/apni/2894715,https://id.biodiversity.org.au/taxon/apni/51438097,https://id.biodiversity.org.au/name/apni/68699,Sparaxis bulbifera,https://id.biodiversity.org.au/name/apni/68699,https://id.biodiversity.org.au/taxon/apni/51438006,,Sparaxis bulbifera,naturalised +Spergularia diandra,Spergularia diandra,,Spergularia,Caryophyllaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised)",Spergularia diandra (Guss.) Heldr.,https://id.biodiversity.org.au/node/apni/2886696,https://id.biodiversity.org.au/taxon/apni/51295406,https://id.biodiversity.org.au/name/apni/83464,Spergularia diandra,https://id.biodiversity.org.au/name/apni/83464,https://id.biodiversity.org.au/taxon/apni/51432987,,Spergularia diandra,naturalised +Sphaeromorphaea littoralis,Sphaeromorphaea littoralis,,Sphaeromorphaea,Asteraceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Sphaeromorphaea littoralis (Retz.) A.R.Bean,https://id.biodiversity.org.au/node/apni/7069871,https://id.biodiversity.org.au/node/apni/7071683,https://id.biodiversity.org.au/name/apni/246779,Sphaeromorphaea littoralis,https://id.biodiversity.org.au/name/apni/246779,https://id.biodiversity.org.au/taxon/apni/51695393,,Sphaeromorphaea littoralis,native +Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia subsp. angustifolia,,Stellaria,Caryophyllaceae,subspecies,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Stellaria angustifolia Hook. subsp. angustifolia,https://id.biodiversity.org.au/node/apni/2890520,https://id.biodiversity.org.au/taxon/apni/51433015,https://id.biodiversity.org.au/name/apni/240421,Stellaria angustifolia subsp. angustifolia,https://id.biodiversity.org.au/name/apni/240421,https://id.biodiversity.org.au/taxon/apni/51432987,Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia,native +Styphelia viridis,Styphelia viridis,,Styphelia,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Styphelia viridis Andrews,https://id.biodiversity.org.au/node/apni/2912747,https://id.biodiversity.org.au/taxon/apni/51435346,https://id.biodiversity.org.au/name/apni/109318,Styphelia viridis,https://id.biodiversity.org.au/name/apni/109318,https://id.biodiversity.org.au/taxon/apni/51436079,,Styphelia viridis,native +Swainsona cadellii,Swainsona cadellii,,Swainsona,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Swainsona cadellii F.Muell. ex C.Moore,https://id.biodiversity.org.au/node/apni/2904099,https://id.biodiversity.org.au/taxon/apni/51436313,https://id.biodiversity.org.au/name/apni/76870,Swainsona cadellii,https://id.biodiversity.org.au/name/apni/76870,https://id.biodiversity.org.au/taxon/apni/51702961,,Swainsona cadellii,native +Teucrium puberulum,Teucrium puberulum,,Teucrium,Lamiaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Teucrium puberulum (F.Muell.) Kattari & Bräuchler,https://id.biodiversity.org.au/taxon/apni/51288087,https://id.biodiversity.org.au/taxon/apni/51438311,https://id.biodiversity.org.au/name/apni/7660439,Teucrium puberulum,https://id.biodiversity.org.au/name/apni/7660439,https://id.biodiversity.org.au/taxon/apni/51696573,,Teucrium puberulum,native +Thelymitra kangaloonica,Thelymitra kangaloonica,,Thelymitra,Orchidaceae,species,APC,accepted,Magnoliidae,NSW,Thelymitra kangaloonica Jeanes,https://id.biodiversity.org.au/taxon/apni/51414328,https://id.biodiversity.org.au/taxon/apni/51631246,https://id.biodiversity.org.au/name/apni/233692,Thelymitra kangaloonica,https://id.biodiversity.org.au/name/apni/233692,https://id.biodiversity.org.au/taxon/apni/51697009,,Thelymitra kangaloonica,native +Thesium australe,Thesium australe,,Thesium,Santalaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic, Tas (presumed extinct)",Thesium australe R.Br.,https://id.biodiversity.org.au/node/apni/2891975,https://id.biodiversity.org.au/node/apni/2913858,https://id.biodiversity.org.au/name/apni/56224,Thesium australe,https://id.biodiversity.org.au/name/apni/56224,https://id.biodiversity.org.au/taxon/apni/51447154,,Thesium australe,native +Trifolium dubium,Trifolium dubium,,Trifolium,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Trifolium dubium Sibth.,https://id.biodiversity.org.au/taxon/apni/51436351,https://id.biodiversity.org.au/taxon/apni/51436341,https://id.biodiversity.org.au/name/apni/115704,Trifolium dubium,https://id.biodiversity.org.au/name/apni/115704,https://id.biodiversity.org.au/taxon/apni/51702961,,Trifolium dubium,naturalised +Veronica catenata,Veronica catenata,,Veronica,Plantaginaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), Vic (naturalised)",Veronica catenata Pennell,https://id.biodiversity.org.au/node/apni/2897164,https://id.biodiversity.org.au/taxon/apni/51632390,https://id.biodiversity.org.au/name/apni/67965,Veronica catenata,https://id.biodiversity.org.au/name/apni/67965,https://id.biodiversity.org.au/taxon/apni/51699383,,Veronica catenata,naturalised +Veronica derwentiana,Veronica derwentiana,,Veronica,Plantaginaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Veronica derwentiana Andrews,https://id.biodiversity.org.au/node/apni/2917078,https://id.biodiversity.org.au/taxon/apni/51632390,https://id.biodiversity.org.au/name/apni/68107,Veronica derwentiana,https://id.biodiversity.org.au/name/apni/68107,https://id.biodiversity.org.au/taxon/apni/51699383,,Veronica derwentiana,native +Wahlenbergia luteola,Wahlenbergia luteola,,Wahlenbergia,Campanulaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic",Wahlenbergia luteola P.J.Sm.,https://id.biodiversity.org.au/node/apni/2916523,https://id.biodiversity.org.au/taxon/apni/51432869,https://id.biodiversity.org.au/name/apni/73194,Wahlenbergia luteola,https://id.biodiversity.org.au/name/apni/73194,https://id.biodiversity.org.au/taxon/apni/51432853,,Wahlenbergia luteola,native diff --git a/tests/testthat/examples/Test_2023_3/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_3/output/taxonomic_updates.csv index c1f14ddf..1b88236f 100644 --- a/tests/testthat/examples/Test_2023_3/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_3/output/taxonomic_updates.csv @@ -1,188 +1,188 @@ dataset_id,original_name,aligned_name,taxonomic_resolution,taxon_name -Test_2023_3,Abildgaardia ovata,Abildgaardia ovata,, -Test_2023_3,Acacia alpina,Acacia alpina,, -Test_2023_3,Acacia beadleana,Acacia beadleana,, -Test_2023_3,Acacia bulgaensis,Acacia bulgaensis,, -Test_2023_3,Acacia caroleae,Acacia caroleae,, -Test_2023_3,Acacia crassa,Acacia crassa,, -Test_2023_3,Acacia flexifolia,Acacia flexifolia,, -Test_2023_3,Acacia gladiiformis,Acacia gladiiformis,, -Test_2023_3,Acacia havilandiorum,Acacia havilandiorum,, -Test_2023_3,Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx subsp. leiocalyx,, -Test_2023_3,Acacia myrtifolia,Acacia myrtifolia,, -Test_2023_3,Acacia ramulosa var. ramulosa,Acacia ramulosa var. ramulosa,, -Test_2023_3,Acacia spectabilis,Acacia spectabilis,, -Test_2023_3,Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis subsp. Glabrous form (M.Hancock 94),, -Test_2023_3,Acronychia littoralis,Acronychia littoralis,, -Test_2023_3,Adriana tomentosa,Adriana tomentosa,, -Test_2023_3,Alectryon coriaceus,Alectryon coriaceus,, -Test_2023_3,Alectryon oleifolius,Alectryon oleifolius,, -Test_2023_3,Alectryon subdentatus,Alectryon subdentatus,, -Test_2023_3,Amyema preissii,Amyema preissii,, -Test_2023_3,Angophora leiocarpa,Angophora leiocarpa,, -Test_2023_3,Apophyllum anomalum,Apophyllum anomalum,, -Test_2023_3,Arbutus unedo,Arbutus unedo,, -Test_2023_3,Australina pusilla,Australina pusilla,, -Test_2023_3,Burmannia disticha,Burmannia disticha,, -Test_2023_3,Bursaria spinosa subsp. spinosa,Bursaria spinosa subsp. spinosa,, -Test_2023_3,Calendula arvensis,Calendula arvensis,, -Test_2023_3,Callistemon purpurascens,Callistemon purpurascens,, -Test_2023_3,Carex cephalotes,Carex cephalotes,, -Test_2023_3,Carex leporina,Carex leporina,, -Test_2023_3,Carex raleighii,Carex raleighii,, -Test_2023_3,Carmichaelia exsul,Carmichaelia exsul,, -Test_2023_3,Cassinia compacta,Cassinia compacta,, -Test_2023_3,Castanospermum australe,Castanospermum australe,, -Test_2023_3,Centaurium tenuiflorum,Centaurium tenuiflorum,, -Test_2023_3,Cestrum nocturnum,Cestrum nocturnum,, -Test_2023_3,Chthonocephalus pseudevax,Chthonocephalus pseudevax,, -Test_2023_3,Claoxylon australe,Claoxylon australe,, -Test_2023_3,Commersonia amystia,Commersonia amystia,, -Test_2023_3,Commersonia salviifolia,Commersonia salviifolia,, -Test_2023_3,Convolvulus farinosus,Convolvulus farinosus,, -Test_2023_3,Coprosma niphophila,Coprosma niphophila,, -Test_2023_3,Coprosma nivalis,Coprosma nivalis,, -Test_2023_3,Correa alba,Correa alba,, -Test_2023_3,Corymbia citriodora,Corymbia citriodora,, -Test_2023_3,Corymbia eximia,Corymbia eximia,, -Test_2023_3,Crassula decumbens,Crassula decumbens,, -Test_2023_3,Crassula peduncularis,Crassula peduncularis,, -Test_2023_3,Crotalaria brevis,Crotalaria brevis,, -Test_2023_3,Crotalaria grahamiana,Crotalaria grahamiana,, -Test_2023_3,Crotalaria lanceolata,Crotalaria lanceolata,, -Test_2023_3,Cylindropuntia kleiniae,Cylindropuntia kleiniae,, -Test_2023_3,Cyperus albostriatus,Cyperus albostriatus,, -Test_2023_3,Cyperus betchei,Cyperus betchei,, -Test_2023_3,Cyperus bulbosus,Cyperus bulbosus,, -Test_2023_3,Cyperus laevigatus,Cyperus laevigatus,, -Test_2023_3,Cyperus sculptus,Cyperus sculptus,, -Test_2023_3,Dampiera fusca,Dampiera fusca,, -Test_2023_3,Davidsonia johnsonii,Davidsonia johnsonii,, -Test_2023_3,Daviesia arenaria,Daviesia arenaria,, -Test_2023_3,Derris involuta,Derris involuta,, -Test_2023_3,Dichromochlamys dentatifolia,Dichromochlamys dentatifolia,, -Test_2023_3,Dillwynia cinerascens,Dillwynia cinerascens,, -Test_2023_3,Dillwynia floribunda,Dillwynia floribunda,, -Test_2023_3,Dinosperma erythrococcum,Dinosperma erythrococcum,, -Test_2023_3,Dodonaea petiolaris,Dodonaea petiolaris,, -Test_2023_3,Dodonaea truncatiales,Dodonaea truncatiales,, -Test_2023_3,Dovyalis caffra,Dovyalis caffra,, -Test_2023_3,Elaeocarpus grandis,Elaeocarpus grandis,, -Test_2023_3,Eleocharis pallens,Eleocharis pallens,, -Test_2023_3,Endiandra globosa,Endiandra globosa,, -Test_2023_3,Endiandra muelleri,Endiandra muelleri,, -Test_2023_3,Epilobium gunnianum,Epilobium gunnianum,, -Test_2023_3,Eremophila deserti,Eremophila deserti,, -Test_2023_3,Eremophila oppositifolia,Eremophila oppositifolia,, -Test_2023_3,Erigeron conyzoides,Erigeron conyzoides,, -Test_2023_3,Erythroxylum australe,Erythroxylum australe,, -Test_2023_3,Escallonia bifida,Escallonia bifida,, -Test_2023_3,Eucalyptus badjensis,Eucalyptus badjensis,, -Test_2023_3,Eucalyptus camphora,Eucalyptus camphora,, -Test_2023_3,Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,, -Test_2023_3,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,, -Test_2023_3,Eucalyptus muelleriana,Eucalyptus muelleriana,, -Test_2023_3,Eucalyptus nandewarica,Eucalyptus nandewarica,, -Test_2023_3,Eucalyptus oblonga,Eucalyptus oblonga,, -Test_2023_3,Eucalyptus olida,Eucalyptus olida,, -Test_2023_3,Eucalyptus pulverulenta,Eucalyptus pulverulenta,, -Test_2023_3,Eucalyptus recurva,Eucalyptus recurva,, -Test_2023_3,Eucalyptus rossii,Eucalyptus rossii,, -Test_2023_3,Eucalyptus scias,Eucalyptus scias,, -Test_2023_3,Eucalyptus viminalis,Eucalyptus viminalis,, -Test_2023_3,Eucalyptus yangoura,Eucalyptus yangoura,, -Test_2023_3,Eucalyptus youmanii,Eucalyptus youmanii,, -Test_2023_3,Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata var. queenslandica,, -Test_2023_3,Exocarpos homalocladus,Exocarpos homalocladus,, -Test_2023_3,Exocarpos sparteus,Exocarpos sparteus,, -Test_2023_3,Ficus henneana,Ficus henneana,, -Test_2023_3,Freesia hybrid,Freesia hybrid,, -Test_2023_3,Freesia laxa,Freesia laxa,, -Test_2023_3,Geijera salicifolia,Geijera salicifolia,, -Test_2023_3,Gentiana wingecarribiensis,Gentiana wingecarribiensis,, -Test_2023_3,Gentianella barringtonensis,Gentianella barringtonensis,, -Test_2023_3,Geranium obtusisepalum,Geranium obtusisepalum,, -Test_2023_3,Geranium purpureum subsp. purpureum,Geranium purpureum subsp. purpureum,, -Test_2023_3,Gompholobium grandiflorum,Gompholobium grandiflorum,, -Test_2023_3,Goodenia varia,Goodenia varia,, -Test_2023_3,Gossia bidwillii,Gossia bidwillii,, -Test_2023_3,Grevillea scortechinii,Grevillea scortechinii,, -Test_2023_3,Hakea macraeana,Hakea macraeana,, -Test_2023_3,Hemisteptia lyrata,Hemisteptia lyrata,, -Test_2023_3,Hibbertia crinita,Hibbertia crinita,, -Test_2023_3,Hibiscus brachysiphonius,Hibiscus brachysiphonius,, -Test_2023_3,Hibiscus sturtii,Hibiscus sturtii,, -Test_2023_3,Hypericum elodes,Hypericum elodes,, -Test_2023_3,Hypoxis glabella var. glabella,Hypoxis glabella var. glabella,, -Test_2023_3,Imperata cylindrica,Imperata cylindrica,, -Test_2023_3,Indigofera triflora,Indigofera triflora,, -Test_2023_3,Ipomoea cairica,Ipomoea cairica,, -Test_2023_3,Isolepis montivaga,Isolepis montivaga,, -Test_2023_3,Isotoma axillaris,Isotoma axillaris,, -Test_2023_3,Isotoma fluviatilis subsp. fluviatilis,Isotoma fluviatilis subsp. fluviatilis,, -Test_2023_3,Juncus acutus subsp. acutus,Juncus acutus subsp. acutus,, -Test_2023_3,Juncus kraussii,Juncus kraussii,, -Test_2023_3,Lantana montevidensis,Lantana montevidensis,, -Test_2023_3,Lepidium africanum,Lepidium africanum,, -Test_2023_3,Lepidium foliosum,Lepidium foliosum,, -Test_2023_3,Lepidium oxytrichum,Lepidium oxytrichum,, -Test_2023_3,Lepidosperma gladiatum,Lepidosperma gladiatum,, -Test_2023_3,Leptomeria drupacea,Leptomeria drupacea,, -Test_2023_3,Leptospermum continentale,Leptospermum continentale,, -Test_2023_3,Leptospermum obovatum,Leptospermum obovatum,, -Test_2023_3,Leucopogon amplexicaulis,Leucopogon amplexicaulis,, -Test_2023_3,Lobelia pedunculata,Lobelia pedunculata,, -Test_2023_3,Lobelia trigonocaulis,Lobelia trigonocaulis,, -Test_2023_3,Lotononis bainesii,Lotononis bainesii,, -Test_2023_3,Lotus corniculatus,Lotus corniculatus,, -Test_2023_3,Lupinus polyphyllus,Lupinus polyphyllus,, -Test_2023_3,Medicago orbicularis,Medicago orbicularis,, -Test_2023_3,Melichrus procumbens,Melichrus procumbens,, -Test_2023_3,Mischocarpus australis,Mischocarpus australis,, -Test_2023_3,Muehlenbeckia adpressa,Muehlenbeckia adpressa,, -Test_2023_3,Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,, -Test_2023_3,Nicotiana glauca,Nicotiana glauca,, -Test_2023_3,Nicotiana goodspeedii,Nicotiana goodspeedii,, -Test_2023_3,Oxalis corniculata,Oxalis corniculata,, -Test_2023_3,Pandorea pandorana subsp. austrocaledonica,Pandorea pandorana subsp. austrocaledonica,, -Test_2023_3,Paraserianthes lophantha,Paraserianthes lophantha,, -Test_2023_3,Parentucellia latifolia,Parentucellia latifolia,, -Test_2023_3,Phlegmatospermum cochlearinum,Phlegmatospermum cochlearinum,, -Test_2023_3,Phyla nodiflora,Phyla nodiflora,, -Test_2023_3,Picris barbarorum,Picris barbarorum,, -Test_2023_3,Pimelea ligustrina subsp. ligustrina,Pimelea ligustrina subsp. ligustrina,, -Test_2023_3,Pinus pinea,Pinus pinea,, -Test_2023_3,Pisum sativum var. arvense,Pisum sativum var. arvense,, -Test_2023_3,Pittosporum erioloma,Pittosporum erioloma,, -Test_2023_3,Plantago turrifera,Plantago turrifera,, -Test_2023_3,Polycarpon tetraphyllum,Polycarpon tetraphyllum,, -Test_2023_3,Potamogeton australiensis,Potamogeton australiensis,, -Test_2023_3,Psoralea pinnata,Psoralea pinnata,, -Test_2023_3,Pultenaea ferruginea,Pultenaea ferruginea,, -Test_2023_3,Rhodamnia argentea,Rhodamnia argentea,, -Test_2023_3,Rorippa gigantea,Rorippa gigantea,, -Test_2023_3,Rubus parvifolius,Rubus parvifolius,, -Test_2023_3,Salix alba,Salix alba,, -Test_2023_3,Schenkia australis,Schenkia australis,, -Test_2023_3,Schoenus apogon,Schoenus apogon,, -Test_2023_3,Schoenus brevifolius,Schoenus brevifolius,, -Test_2023_3,Schoenus lepidosperma,Schoenus lepidosperma,, -Test_2023_3,Schoenus vaginatus,Schoenus vaginatus,, -Test_2023_3,Scleria rugosa,Scleria rugosa,, -Test_2023_3,Senecio longipilus,Senecio longipilus,, -Test_2023_3,Sida goniocarpa,Sida goniocarpa,, -Test_2023_3,Sigesbeckia orientalis,Sigesbeckia orientalis,, -Test_2023_3,Sisymbrium irio,Sisymbrium irio,, -Test_2023_3,Sparaxis bulbifera,Sparaxis bulbifera,, -Test_2023_3,Spergularia diandra,Spergularia diandra,, -Test_2023_3,Sphaeromorphaea littoralis,Sphaeromorphaea littoralis,, -Test_2023_3,Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia subsp. angustifolia,, -Test_2023_3,Styphelia viridis,Styphelia viridis,, -Test_2023_3,Swainsona cadellii,Swainsona cadellii,, -Test_2023_3,Teucrium puberulum,Teucrium puberulum,, -Test_2023_3,Thelymitra kangaloonica,Thelymitra kangaloonica,, -Test_2023_3,Thesium australe,Thesium australe,, -Test_2023_3,Trifolium dubium,Trifolium dubium,, -Test_2023_3,Veronica catenata,Veronica catenata,, -Test_2023_3,Veronica derwentiana,Veronica derwentiana,, -Test_2023_3,Wahlenbergia luteola,Wahlenbergia luteola,, +Test_2023_3,Abildgaardia ovata,Abildgaardia ovata,,Abildgaardia ovata +Test_2023_3,Acacia alpina,Acacia alpina,,Acacia alpina +Test_2023_3,Acacia beadleana,Acacia beadleana,,Acacia beadleana +Test_2023_3,Acacia bulgaensis,Acacia bulgaensis,,Acacia bulgaensis +Test_2023_3,Acacia caroleae,Acacia caroleae,,Acacia caroleae +Test_2023_3,Acacia crassa,Acacia crassa,,Acacia crassa +Test_2023_3,Acacia flexifolia,Acacia flexifolia,,Acacia flexifolia +Test_2023_3,Acacia gladiiformis,Acacia gladiiformis,,Acacia gladiiformis +Test_2023_3,Acacia havilandiorum,Acacia havilandiorum,,Acacia havilandiorum +Test_2023_3,Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx subsp. leiocalyx,,Acacia leiocalyx subsp. leiocalyx +Test_2023_3,Acacia myrtifolia,Acacia myrtifolia,,Acacia myrtifolia +Test_2023_3,Acacia ramulosa var. ramulosa,Acacia ramulosa var. ramulosa,,Acacia ramulosa var. ramulosa +Test_2023_3,Acacia spectabilis,Acacia spectabilis,,Acacia spectabilis +Test_2023_3,Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis subsp. Glabrous form (M.Hancock 94),,Acacia terminalis subsp. Glabrous form (M.Hancock 94) +Test_2023_3,Acronychia littoralis,Acronychia littoralis,,Acronychia littoralis +Test_2023_3,Adriana tomentosa,Adriana tomentosa,,Adriana tomentosa +Test_2023_3,Alectryon coriaceus,Alectryon coriaceus,,Alectryon coriaceus +Test_2023_3,Alectryon oleifolius,Alectryon oleifolius,,Alectryon oleifolius +Test_2023_3,Alectryon subdentatus,Alectryon subdentatus,,Alectryon subdentatus +Test_2023_3,Amyema preissii,Amyema preissii,,Amyema preissii +Test_2023_3,Angophora leiocarpa,Angophora leiocarpa,,Angophora leiocarpa +Test_2023_3,Apophyllum anomalum,Apophyllum anomalum,,Capparis anomala +Test_2023_3,Arbutus unedo,Arbutus unedo,,Arbutus unedo +Test_2023_3,Australina pusilla,Australina pusilla,,Australina pusilla +Test_2023_3,Burmannia disticha,Burmannia disticha,,Burmannia disticha +Test_2023_3,Bursaria spinosa subsp. spinosa,Bursaria spinosa subsp. spinosa,,Bursaria spinosa subsp. spinosa +Test_2023_3,Calendula arvensis,Calendula arvensis,,Calendula arvensis +Test_2023_3,Callistemon purpurascens,Callistemon purpurascens,,Callistemon purpurascens +Test_2023_3,Carex cephalotes,Carex cephalotes,,Carex pyrenaica var. cephalotes +Test_2023_3,Carex leporina,Carex leporina,,Carex leporina +Test_2023_3,Carex raleighii,Carex raleighii,,Carex raleighii +Test_2023_3,Carmichaelia exsul,Carmichaelia exsul,,Carmichaelia exsul +Test_2023_3,Cassinia compacta,Cassinia compacta,,Cassinia compacta +Test_2023_3,Castanospermum australe,Castanospermum australe,,Castanospermum australe +Test_2023_3,Centaurium tenuiflorum,Centaurium tenuiflorum,,Centaurium tenuiflorum +Test_2023_3,Cestrum nocturnum,Cestrum nocturnum,,Cestrum nocturnum +Test_2023_3,Chthonocephalus pseudevax,Chthonocephalus pseudevax,,Chthonocephalus pseudevax +Test_2023_3,Claoxylon australe,Claoxylon australe,,Claoxylon australe +Test_2023_3,Commersonia amystia,Commersonia amystia,,Commersonia amystia +Test_2023_3,Commersonia salviifolia,Commersonia salviifolia,,Commersonia salviifolia +Test_2023_3,Convolvulus farinosus,Convolvulus farinosus,,Convolvulus farinosus +Test_2023_3,Coprosma niphophila,Coprosma niphophila,,Coprosma niphophila +Test_2023_3,Coprosma nivalis,Coprosma nivalis,,Coprosma nivalis +Test_2023_3,Correa alba,Correa alba,,Correa alba +Test_2023_3,Corymbia citriodora,Corymbia citriodora,,Corymbia citriodora +Test_2023_3,Corymbia eximia,Corymbia eximia,,Corymbia eximia +Test_2023_3,Crassula decumbens,Crassula decumbens,,Crassula decumbens +Test_2023_3,Crassula peduncularis,Crassula peduncularis,,Crassula peduncularis +Test_2023_3,Crotalaria brevis,Crotalaria brevis,,Crotalaria brevis +Test_2023_3,Crotalaria grahamiana,Crotalaria grahamiana,,Crotalaria grahamiana +Test_2023_3,Crotalaria lanceolata,Crotalaria lanceolata,,Crotalaria lanceolata +Test_2023_3,Cylindropuntia kleiniae,Cylindropuntia kleiniae,,Cylindropuntia kleiniae +Test_2023_3,Cyperus albostriatus,Cyperus albostriatus,,Cyperus albostriatus +Test_2023_3,Cyperus betchei,Cyperus betchei,,Cyperus betchei +Test_2023_3,Cyperus bulbosus,Cyperus bulbosus,,Cyperus bulbosus +Test_2023_3,Cyperus laevigatus,Cyperus laevigatus,,Cyperus laevigatus +Test_2023_3,Cyperus sculptus,Cyperus sculptus,,Cyperus sculptus +Test_2023_3,Dampiera fusca,Dampiera fusca,,Dampiera fusca +Test_2023_3,Davidsonia johnsonii,Davidsonia johnsonii,,Davidsonia johnsonii +Test_2023_3,Daviesia arenaria,Daviesia arenaria,,Daviesia arenaria +Test_2023_3,Derris involuta,Derris involuta,,Solori involuta +Test_2023_3,Dichromochlamys dentatifolia,Dichromochlamys dentatifolia,,Dichromochlamys dentatifolia +Test_2023_3,Dillwynia cinerascens,Dillwynia cinerascens,,Dillwynia cinerascens +Test_2023_3,Dillwynia floribunda,Dillwynia floribunda,,Dillwynia floribunda +Test_2023_3,Dinosperma erythrococcum,Dinosperma erythrococcum,,Dinosperma erythrococcum +Test_2023_3,Dodonaea petiolaris,Dodonaea petiolaris,,Dodonaea petiolaris +Test_2023_3,Dodonaea truncatiales,Dodonaea truncatiales,,Dodonaea truncatiales +Test_2023_3,Dovyalis caffra,Dovyalis caffra,,Dovyalis caffra +Test_2023_3,Elaeocarpus grandis,Elaeocarpus grandis,,Elaeocarpus grandis +Test_2023_3,Eleocharis pallens,Eleocharis pallens,,Eleocharis pallens +Test_2023_3,Endiandra globosa,Endiandra globosa,,Endiandra globosa +Test_2023_3,Endiandra muelleri,Endiandra muelleri,,Endiandra muelleri +Test_2023_3,Epilobium gunnianum,Epilobium gunnianum,,Epilobium gunnianum +Test_2023_3,Eremophila deserti,Eremophila deserti,,Eremophila deserti +Test_2023_3,Eremophila oppositifolia,Eremophila oppositifolia,,Eremophila oppositifolia +Test_2023_3,Erigeron conyzoides,Erigeron conyzoides,,Erigeron conyzoides +Test_2023_3,Erythroxylum australe,Erythroxylum australe,,Erythroxylum australe +Test_2023_3,Escallonia bifida,Escallonia bifida,,Escallonia bifida +Test_2023_3,Eucalyptus badjensis,Eucalyptus badjensis,,Eucalyptus badjensis +Test_2023_3,Eucalyptus camphora,Eucalyptus camphora,,Eucalyptus camphora +Test_2023_3,Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,,Eucalyptus dorrigoensis +Test_2023_3,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,,Eucalyptus leucoxylon subsp. pruinosa +Test_2023_3,Eucalyptus muelleriana,Eucalyptus muelleriana,,Eucalyptus muelleriana +Test_2023_3,Eucalyptus nandewarica,Eucalyptus nandewarica,,Eucalyptus nandewarica +Test_2023_3,Eucalyptus oblonga,Eucalyptus oblonga,,Eucalyptus globoidea +Test_2023_3,Eucalyptus olida,Eucalyptus olida,,Eucalyptus olida +Test_2023_3,Eucalyptus pulverulenta,Eucalyptus pulverulenta,,Eucalyptus pulverulenta +Test_2023_3,Eucalyptus recurva,Eucalyptus recurva,,Eucalyptus recurva +Test_2023_3,Eucalyptus rossii,Eucalyptus rossii,,Eucalyptus rossii +Test_2023_3,Eucalyptus scias,Eucalyptus scias,,Eucalyptus scias +Test_2023_3,Eucalyptus viminalis,Eucalyptus viminalis,,Eucalyptus viminalis +Test_2023_3,Eucalyptus yangoura,Eucalyptus yangoura,,Eucalyptus globoidea +Test_2023_3,Eucalyptus youmanii,Eucalyptus youmanii,,Eucalyptus youmanii +Test_2023_3,Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata var. queenslandica,,Euphorbia inappendiculata var. queenslandica +Test_2023_3,Exocarpos homalocladus,Exocarpos homalocladus,,Exocarpos homalocladus +Test_2023_3,Exocarpos sparteus,Exocarpos sparteus,,Exocarpos sparteus +Test_2023_3,Ficus henneana,Ficus henneana,,Ficus henneana +Test_2023_3,Freesia hybrid,Freesia hybrid,,Freesia leichtlinii subsp. leichtlinii x Freesia leichtlinii subsp. alba +Test_2023_3,Freesia laxa,Freesia laxa,,Freesia laxa +Test_2023_3,Geijera salicifolia,Geijera salicifolia,,Geijera salicifolia +Test_2023_3,Gentiana wingecarribiensis,Gentiana wingecarribiensis,,Gentiana wingecarribiensis +Test_2023_3,Gentianella barringtonensis,Gentianella barringtonensis,,Gentianella barringtonensis +Test_2023_3,Geranium obtusisepalum,Geranium obtusisepalum,,Geranium obtusisepalum +Test_2023_3,Geranium purpureum subsp. purpureum,Geranium purpureum subsp. purpureum,,Geranium purpureum +Test_2023_3,Gompholobium grandiflorum,Gompholobium grandiflorum,,Gompholobium grandiflorum +Test_2023_3,Goodenia varia,Goodenia varia,,Goodenia varia +Test_2023_3,Gossia bidwillii,Gossia bidwillii,,Gossia bidwillii +Test_2023_3,Grevillea scortechinii,Grevillea scortechinii,,Grevillea scortechinii +Test_2023_3,Hakea macraeana,Hakea macraeana,,Hakea macraeana +Test_2023_3,Hemisteptia lyrata,Hemisteptia lyrata,,Hemisteptia lyrata +Test_2023_3,Hibbertia crinita,Hibbertia crinita,,Hibbertia crinita +Test_2023_3,Hibiscus brachysiphonius,Hibiscus brachysiphonius,,Hibiscus brachysiphonius +Test_2023_3,Hibiscus sturtii,Hibiscus sturtii,,Hibiscus sturtii +Test_2023_3,Hypericum elodes,Hypericum elodes,,Hypericum elodes +Test_2023_3,Hypoxis glabella var. glabella,Hypoxis glabella var. glabella,,Pauridia glabella var. glabella +Test_2023_3,Imperata cylindrica,Imperata cylindrica,,Imperata cylindrica +Test_2023_3,Indigofera triflora,Indigofera triflora,,Indigofera triflora +Test_2023_3,Ipomoea cairica,Ipomoea cairica,,Ipomoea cairica +Test_2023_3,Isolepis montivaga,Isolepis montivaga,,Isolepis montivaga +Test_2023_3,Isotoma axillaris,Isotoma axillaris,,Isotoma axillaris +Test_2023_3,Isotoma fluviatilis subsp. fluviatilis,Isotoma fluviatilis subsp. fluviatilis,,Isotoma fluviatilis subsp. fluviatilis +Test_2023_3,Juncus acutus subsp. acutus,Juncus acutus subsp. acutus,,Juncus acutus subsp. acutus +Test_2023_3,Juncus kraussii,Juncus kraussii,,Juncus kraussii +Test_2023_3,Lantana montevidensis,Lantana montevidensis,,Lantana montevidensis +Test_2023_3,Lepidium africanum,Lepidium africanum,,Lepidium africanum +Test_2023_3,Lepidium foliosum,Lepidium foliosum,,Lepidium foliosum +Test_2023_3,Lepidium oxytrichum,Lepidium oxytrichum,,Lepidium oxytrichum +Test_2023_3,Lepidosperma gladiatum,Lepidosperma gladiatum,,Lepidosperma gladiatum +Test_2023_3,Leptomeria drupacea,Leptomeria drupacea,,Leptomeria drupacea +Test_2023_3,Leptospermum continentale,Leptospermum continentale,,Leptospermum continentale +Test_2023_3,Leptospermum obovatum,Leptospermum obovatum,,Leptospermum obovatum +Test_2023_3,Leucopogon amplexicaulis,Leucopogon amplexicaulis,,Leucopogon amplexicaulis +Test_2023_3,Lobelia pedunculata,Lobelia pedunculata,,Lobelia pedunculata +Test_2023_3,Lobelia trigonocaulis,Lobelia trigonocaulis,,Lobelia trigonocaulis +Test_2023_3,Lotononis bainesii,Lotononis bainesii,,Lotononis bainesii +Test_2023_3,Lotus corniculatus,Lotus corniculatus,,Lotus corniculatus +Test_2023_3,Lupinus polyphyllus,Lupinus polyphyllus,,Lupinus polyphyllus +Test_2023_3,Medicago orbicularis,Medicago orbicularis,,Medicago orbicularis +Test_2023_3,Melichrus procumbens,Melichrus procumbens,,Melichrus procumbens +Test_2023_3,Mischocarpus australis,Mischocarpus australis,,Mischocarpus australis +Test_2023_3,Muehlenbeckia adpressa,Muehlenbeckia adpressa,,Muehlenbeckia adpressa +Test_2023_3,Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,,Myoporum boninense subsp. australe +Test_2023_3,Nicotiana glauca,Nicotiana glauca,,Nicotiana glauca +Test_2023_3,Nicotiana goodspeedii,Nicotiana goodspeedii,,Nicotiana goodspeedii +Test_2023_3,Oxalis corniculata,Oxalis corniculata,,Oxalis corniculata +Test_2023_3,Pandorea pandorana subsp. austrocaledonica,Pandorea pandorana subsp. austrocaledonica,,Pandorea pandorana +Test_2023_3,Paraserianthes lophantha,Paraserianthes lophantha,,Paraserianthes lophantha +Test_2023_3,Parentucellia latifolia,Parentucellia latifolia,,Parentucellia latifolia +Test_2023_3,Phlegmatospermum cochlearinum,Phlegmatospermum cochlearinum,,Phlegmatospermum cochlearinum +Test_2023_3,Phyla nodiflora,Phyla nodiflora,,Phyla nodiflora +Test_2023_3,Picris barbarorum,Picris barbarorum,,Picris barbarorum +Test_2023_3,Pimelea ligustrina subsp. ligustrina,Pimelea ligustrina subsp. ligustrina,,Pimelea ligustrina subsp. ligustrina +Test_2023_3,Pinus pinea,Pinus pinea,,Pinus pinea +Test_2023_3,Pisum sativum var. arvense,Pisum sativum var. arvense,,Pisum sativum var. arvense +Test_2023_3,Pittosporum erioloma,Pittosporum erioloma,,Pittosporum erioloma +Test_2023_3,Plantago turrifera,Plantago turrifera,,Plantago turrifera +Test_2023_3,Polycarpon tetraphyllum,Polycarpon tetraphyllum,,Polycarpon tetraphyllum +Test_2023_3,Potamogeton australiensis,Potamogeton australiensis,,Potamogeton australiensis +Test_2023_3,Psoralea pinnata,Psoralea pinnata,,Psoralea pinnata +Test_2023_3,Pultenaea ferruginea,Pultenaea ferruginea,,Pultenaea ferruginea +Test_2023_3,Rhodamnia argentea,Rhodamnia argentea,,Rhodamnia argentea +Test_2023_3,Rorippa gigantea,Rorippa gigantea,,Rorippa gigantea +Test_2023_3,Rubus parvifolius,Rubus parvifolius,,Rubus parvifolius +Test_2023_3,Salix alba,Salix alba,,Salix alba +Test_2023_3,Schenkia australis,Schenkia australis,,Schenkia australis +Test_2023_3,Schoenus apogon,Schoenus apogon,,Schoenus apogon +Test_2023_3,Schoenus brevifolius,Schoenus brevifolius,,Schoenus brevifolius +Test_2023_3,Schoenus lepidosperma,Schoenus lepidosperma,,Schoenus lepidosperma +Test_2023_3,Schoenus vaginatus,Schoenus vaginatus,,Schoenus vaginatus +Test_2023_3,Scleria rugosa,Scleria rugosa,,Scleria rugosa +Test_2023_3,Senecio longipilus,Senecio longipilus,,Senecio longipilus +Test_2023_3,Sida goniocarpa,Sida goniocarpa,,Sida goniocarpa +Test_2023_3,Sigesbeckia orientalis,Sigesbeckia orientalis,,Sigesbeckia orientalis +Test_2023_3,Sisymbrium irio,Sisymbrium irio,,Sisymbrium irio +Test_2023_3,Sparaxis bulbifera,Sparaxis bulbifera,,Sparaxis bulbifera +Test_2023_3,Spergularia diandra,Spergularia diandra,,Spergularia diandra +Test_2023_3,Sphaeromorphaea littoralis,Sphaeromorphaea littoralis,,Sphaeromorphaea littoralis +Test_2023_3,Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia subsp. angustifolia,,Stellaria angustifolia subsp. angustifolia +Test_2023_3,Styphelia viridis,Styphelia viridis,,Styphelia viridis +Test_2023_3,Swainsona cadellii,Swainsona cadellii,,Swainsona cadellii +Test_2023_3,Teucrium puberulum,Teucrium puberulum,,Teucrium puberulum +Test_2023_3,Thelymitra kangaloonica,Thelymitra kangaloonica,,Thelymitra kangaloonica +Test_2023_3,Thesium australe,Thesium australe,,Thesium australe +Test_2023_3,Trifolium dubium,Trifolium dubium,,Trifolium dubium +Test_2023_3,Veronica catenata,Veronica catenata,,Veronica catenata +Test_2023_3,Veronica derwentiana,Veronica derwentiana,,Veronica derwentiana +Test_2023_3,Wahlenbergia luteola,Wahlenbergia luteola,,Wahlenbergia luteola diff --git a/tests/testthat/examples/Test_2023_3/output/traits.csv b/tests/testthat/examples/Test_2023_3/output/traits.csv index 3cd2b0a0..34e43781 100644 --- a/tests/testthat/examples/Test_2023_3/output/traits.csv +++ b/tests/testthat/examples/Test_2023_3/output/traits.csv @@ -20,15 +20,15 @@ Test_2023_3,Alectryon oleifolius,018,fruit_width,10,mm,species,minimum,measureme Test_2023_3,Alectryon subdentatus,019,fruit_length,8,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to capsule,01,04,Alectryon subdentatus Test_2023_3,Amyema preissii,020,fruit_colour,pink white,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,04,Amyema preissii Test_2023_3,Angophora leiocarpa,021,fruit_width,11,mm,species,maximum,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to fruit,02,04,Angophora leiocarpa -Test_2023_3,Apophyllum anomalum,022,fruit_colour,purple,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,04,Apophyllum anomalum +Test_2023_3,Capparis anomala,022,fruit_colour,purple,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,04,Apophyllum anomalum Test_2023_3,Arbutus unedo,023,fruit_colour,red,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,04,Arbutus unedo Test_2023_3,Australina pusilla,024,fruit_length,1,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to achene,01,04,Australina pusilla Test_2023_3,Burmannia disticha,025,fruit_dehiscence,dehiscent,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,02,Burmannia disticha Test_2023_3,Bursaria spinosa subsp. spinosa,026,fruit_width,9,mm,species,maximum,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to capsules,02,04,Bursaria spinosa subsp. spinosa Test_2023_3,Calendula arvensis,027,fruit_length,15,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to achenes,01,04,Calendula arvensis Test_2023_3,Callistemon purpurascens,028,fruit_dehiscence,dehiscent,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,02,Callistemon purpurascens -Test_2023_3,Carex cephalotes,029,fruit_width,1,mm,species,minimum,measurement,3,literature,adult,,,,,,,01,,,,Trait value refers to utricles,01,04,Carex cephalotes -Test_2023_3,Carex cephalotes,030,fruit_length,2.5,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to utricles,01,04,Carex cephalotes +Test_2023_3,Carex pyrenaica var. cephalotes,029,fruit_width,1,mm,species,minimum,measurement,3,literature,adult,,,,,,,01,,,,Trait value refers to utricles,01,04,Carex cephalotes +Test_2023_3,Carex pyrenaica var. cephalotes,030,fruit_length,2.5,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to utricles,01,04,Carex cephalotes Test_2023_3,Carex leporina,031,fruit_length,3.5,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to utricles,01,04,Carex leporina Test_2023_3,Carex raleighii,032,fruit_length,2.5,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to utricles,01,04,Carex raleighii Test_2023_3,Carmichaelia exsul,033,fruit_length,10,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to pods,01,04,Carmichaelia exsul @@ -61,7 +61,7 @@ Test_2023_3,Cyperus sculptus,058,fruit_length,1,mm,species,mean,measurement,3,li Test_2023_3,Dampiera fusca,059,fruit_colour,brown,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,04,Dampiera fusca Test_2023_3,Davidsonia johnsonii,060,fruit_length,30,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to fruit,01,04,Davidsonia johnsonii Test_2023_3,Daviesia arenaria,061,fruit_length,7,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to pod,01,04,Daviesia arenaria -Test_2023_3,Derris involuta,062,fruit_dehiscence,indehiscent,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,02,Derris involuta +Test_2023_3,Solori involuta,062,fruit_dehiscence,indehiscent,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,02,Derris involuta Test_2023_3,Dichromochlamys dentatifolia,063,fruit_length,1.8,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to achenes,01,04,Dichromochlamys dentatifolia Test_2023_3,Dillwynia cinerascens,064,fruit_length,5,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to pod,01,04,Dillwynia cinerascens Test_2023_3,Dillwynia floribunda,065,fruit_length,4,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to pod,01,04,Dillwynia floribunda @@ -85,26 +85,26 @@ Test_2023_3,Eucalyptus dorrigoensis,082,fruit_length,5,mm,species,mean,measureme Test_2023_3,Eucalyptus leucoxylon subsp. pruinosa,083,fruit_dehiscence,dehiscent,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,04,Eucalyptus leucoxylon subsp. pruinosa Test_2023_3,Eucalyptus muelleriana,084,fruit_dehiscence,dehiscent,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,04,Eucalyptus muelleriana Test_2023_3,Eucalyptus nandewarica,085,fruit_length,3,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to fruit,01,04,Eucalyptus nandewarica -Test_2023_3,Eucalyptus oblonga,086,fruit_length,8,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to fruit,01,04,Eucalyptus oblonga +Test_2023_3,Eucalyptus globoidea,086,fruit_length,8,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to fruit,01,04,Eucalyptus oblonga Test_2023_3,Eucalyptus olida,087,fruit_length,5,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to fruit,01,04,Eucalyptus olida Test_2023_3,Eucalyptus pulverulenta,088,fruit_width,6,mm,species,minimum,measurement,3,literature,adult,,,,,,,01,,,,Trait value refers to fruit,01,04,Eucalyptus pulverulenta Test_2023_3,Eucalyptus recurva,089,fruit_length,4,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to fruit,01,04,Eucalyptus recurva Test_2023_3,Eucalyptus rossii,090,fruit_width,6,mm,species,maximum,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to fruit,02,04,Eucalyptus rossii Test_2023_3,Eucalyptus scias,091,fruit_dehiscence,dehiscent,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,04,Eucalyptus scias Test_2023_3,Eucalyptus viminalis,092,fruit_width,4,mm,species,minimum,measurement,3,literature,adult,,,,,,,01,,,,Trait value refers to fruit,01,04,Eucalyptus viminalis -Test_2023_3,Eucalyptus yangoura,093,fruit_width,6,mm,species,minimum,measurement,3,literature,adult,,,,,,,01,,,,Trait value refers to fruit,01,04,Eucalyptus yangoura +Test_2023_3,Eucalyptus globoidea,093,fruit_width,6,mm,species,minimum,measurement,3,literature,adult,,,,,,,01,,,,Trait value refers to fruit,01,04,Eucalyptus yangoura Test_2023_3,Eucalyptus youmanii,094,fruit_width,9,mm,species,minimum,measurement,3,literature,adult,,,,,,,01,,,,Trait value refers to fruit,01,04,Eucalyptus youmanii Test_2023_3,Eucalyptus youmanii,095,fruit_length,12,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to fruit,01,04,Eucalyptus youmanii Test_2023_3,Euphorbia inappendiculata var. queenslandica,096,fruit_length,1.5,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to capsule,01,04,Euphorbia inappendiculata var. queenslandica Test_2023_3,Exocarpos homalocladus,097,fruit_width,8,mm,species,maximum,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to drupe,02,04,Exocarpos homalocladus Test_2023_3,Exocarpos sparteus,098,fruit_length,5,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to drupe,01,04,Exocarpos sparteus Test_2023_3,Ficus henneana,099,fruit_length,15,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to figs,01,04,Ficus henneana -Test_2023_3,Freesia hybrid,100,fruit_colour,green,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,04,Freesia hybrid +Test_2023_3,Freesia leichtlinii subsp. leichtlinii x Freesia leichtlinii subsp. alba,100,fruit_colour,green,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,04,Freesia hybrid Test_2023_3,Freesia laxa,101,fruit_length,12,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to capsule,01,04,Freesia laxa Test_2023_3,Geijera salicifolia,102,fruit_width,6,mm,species,maximum,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to fruit,02,04,Geijera salicifolia Test_2023_3,Gentiana wingecarribiensis,103,fruit_dehiscence,dehiscent,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,02,Gentiana wingecarribiensis Test_2023_3,Geranium obtusisepalum,105,fruit_length,17,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to fruit,01,04,Geranium obtusisepalum -Test_2023_3,Geranium purpureum subsp. purpureum,106,fruit_length,12,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to fruit,01,04,Geranium purpureum subsp. purpureum +Test_2023_3,Geranium purpureum,106,fruit_length,12,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to fruit,01,04,Geranium purpureum subsp. purpureum Test_2023_3,Gompholobium grandiflorum,107,fruit_length,15,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to pod,01,04,Gompholobium grandiflorum Test_2023_3,Goodenia varia,108,fruit_length,10,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to fruit,01,04,Goodenia varia Test_2023_3,Gossia bidwillii,109,fruit_colour,black,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,04,Gossia bidwillii @@ -117,7 +117,7 @@ Test_2023_3,Hibbertia crinita,115,fruit_dehiscence,dehiscent,,species,mean,exper Test_2023_3,Hibiscus brachysiphonius,116,fruit_length,15,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to capsule,01,04,Hibiscus brachysiphonius Test_2023_3,Hibiscus sturtii,117,fruit_dehiscence,dehiscent,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,02,Hibiscus sturtii Test_2023_3,Hypericum elodes,118,fruit_length,4,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to capsule,01,04,Hypericum elodes -Test_2023_3,Hypoxis glabella var. glabella,119,fruit_dehiscence,dehiscent,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,02,Hypoxis glabella var. glabella +Test_2023_3,Pauridia glabella var. glabella,119,fruit_dehiscence,dehiscent,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,02,Hypoxis glabella var. glabella Test_2023_3,Imperata cylindrica,120,fruit_length,1,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to caryopsis,01,04,Imperata cylindrica Test_2023_3,Indigofera triflora,121,fruit_length,30,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to pods,01,04,Indigofera triflora Test_2023_3,Ipomoea cairica,122,fruit_length,11,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to capsule,01,04,Ipomoea cairica @@ -147,7 +147,7 @@ Test_2023_3,Myoporum boninense subsp. australe,146,fruit_length,10,mm,species,me Test_2023_3,Nicotiana glauca,147,fruit_length,13,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to capsule,01,04,Nicotiana glauca Test_2023_3,Nicotiana goodspeedii,148,fruit_length,5,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to capsule,01,04,Nicotiana goodspeedii Test_2023_3,Oxalis corniculata,149,fruit_width,1.5,mm,species,minimum,measurement,3,literature,adult,,,,,,,01,,,,Trait value refers to fruit,01,04,Oxalis corniculata -Test_2023_3,Pandorea pandorana subsp. austrocaledonica,150,fruit_dehiscence,dehiscent,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,04,Pandorea pandorana subsp. austrocaledonica +Test_2023_3,Pandorea pandorana,150,fruit_dehiscence,dehiscent,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,04,Pandorea pandorana subsp. austrocaledonica Test_2023_3,Paraserianthes lophantha,151,fruit_width,25,mm,species,maximum,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to pod,02,04,Paraserianthes lophantha Test_2023_3,Parentucellia latifolia,152,fruit_dehiscence,dehiscent,,species,mean,expert_score,,literature,adult,,,,,,,01,,,unknown/2022,,01,02,Parentucellia latifolia Test_2023_3,Phlegmatospermum cochlearinum,153,fruit_length,10,mm,species,mean,measurement,3,literature,adult,,,,,,,01,,,unknown/2022,Trait value refers to silicula,01,04,Phlegmatospermum cochlearinum diff --git a/tests/testthat/examples/Test_2023_4/output/metadata.yml b/tests/testthat/examples/Test_2023_4/output/metadata.yml index a38d6462..5dde7c3a 100644 --- a/tests/testthat/examples/Test_2023_4/output/metadata.yml +++ b/tests/testthat/examples/Test_2023_4/output/metadata.yml @@ -5,7 +5,7 @@ description: AusTraits is a transformative database, containing measurements on used to build the resource are also available on the project's GitHub repository,http://traitecoevo.github.io/traits.build. Further information on the project is available in the associated publication and at the project website https://austraits.org. -version: 4.0.0 +version: 5.0.0 doi: 10.5281/zenodo.5112001 structure_URI: https://github.com/traitecoevo/traits.build geo_location: diff --git a/tests/testthat/examples/Test_2023_4/output/taxa.csv b/tests/testthat/examples/Test_2023_4/output/taxa.csv index 6f392a80..7e850333 100644 --- a/tests/testthat/examples/Test_2023_4/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_4/output/taxa.csv @@ -1,188 +1,187 @@ -taxon_name,taxonomic_dataset,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution -Abildgaardia ovata,,,,,,,,, -Acacia alpina,,,,,,,,, -Acacia beadleana,,,,,,,,, -Acacia bulgaensis,,,,,,,,, -Acacia caroleae,,,,,,,,, -Acacia crassa,,,,,,,,, -Acacia flexifolia,,,,,,,,, -Acacia gladiiformis,,,,,,,,, -Acacia havilandiorum,,,,,,,,, -Acacia leiocalyx subsp. leiocalyx,,,,,,,,, -Acacia myrtifolia,,,,,,,,, -Acacia ramulosa var. ramulosa,,,,,,,,, -Acacia spectabilis,,,,,,,,, -Acacia terminalis subsp. Glabrous form (M.Hancock 94),,,,,,,,, -Acronychia littoralis,,,,,,,,, -Adriana tomentosa,,,,,,,,, -Alectryon coriaceus,,,,,,,,, -Alectryon oleifolius,,,,,,,,, -Alectryon subdentatus,,,,,,,,, -Amyema preissii,,,,,,,,, -Angophora leiocarpa,,,,,,,,, -Apophyllum anomalum,,,,,,,,, -Arbutus unedo,,,,,,,,, -Australina pusilla,,,,,,,,, -Burmannia disticha,,,,,,,,, -Bursaria spinosa subsp. spinosa,,,,,,,,, -Calendula arvensis,,,,,,,,, -Callistemon purpurascens,,,,,,,,, -Carex cephalotes,,,,,,,,, -Carex leporina,,,,,,,,, -Carex raleighii,,,,,,,,, -Carmichaelia exsul,,,,,,,,, -Cassinia compacta,,,,,,,,, -Castanospermum australe,,,,,,,,, -Centaurium tenuiflorum,,,,,,,,, -Cestrum nocturnum,,,,,,,,, -Chthonocephalus pseudevax,,,,,,,,, -Claoxylon australe,,,,,,,,, -Commersonia amystia,,,,,,,,, -Commersonia salviifolia,,,,,,,,, -Convolvulus farinosus,,,,,,,,, -Coprosma niphophila,,,,,,,,, -Coprosma nivalis,,,,,,,,, -Correa alba,,,,,,,,, -Corymbia citriodora,,,,,,,,, -Corymbia eximia,,,,,,,,, -Crassula decumbens,,,,,,,,, -Crassula peduncularis,,,,,,,,, -Crotalaria brevis,,,,,,,,, -Crotalaria grahamiana,,,,,,,,, -Crotalaria lanceolata,,,,,,,,, -Cylindropuntia kleiniae,,,,,,,,, -Cyperus albostriatus,,,,,,,,, -Cyperus betchei,,,,,,,,, -Cyperus bulbosus,,,,,,,,, -Cyperus laevigatus,,,,,,,,, -Cyperus sculptus,,,,,,,,, -Dampiera fusca,,,,,,,,, -Davidsonia johnsonii,,,,,,,,, -Daviesia arenaria,,,,,,,,, -Derris involuta,,,,,,,,, -Dichromochlamys dentatifolia,,,,,,,,, -Dillwynia cinerascens,,,,,,,,, -Dillwynia floribunda,,,,,,,,, -Dinosperma erythrococcum,,,,,,,,, -Dodonaea petiolaris,,,,,,,,, -Dodonaea truncatiales,,,,,,,,, -Dovyalis caffra,,,,,,,,, -Elaeocarpus grandis,,,,,,,,, -Eleocharis pallens,,,,,,,,, -Endiandra globosa,,,,,,,,, -Endiandra muelleri,,,,,,,,, -Epilobium gunnianum,,,,,,,,, -Eremophila deserti,,,,,,,,, -Eremophila oppositifolia,,,,,,,,, -Erigeron conyzoides,,,,,,,,, -Erythroxylum australe,,,,,,,,, -Escallonia bifida,,,,,,,,, -Eucalyptus badjensis,,,,,,,,, -Eucalyptus camphora,,,,,,,,, -Eucalyptus dorrigoensis,,,,,,,,, -Eucalyptus leucoxylon subsp. pruinosa,,,,,,,,, -Eucalyptus muelleriana,,,,,,,,, -Eucalyptus nandewarica,,,,,,,,, -Eucalyptus oblonga,,,,,,,,, -Eucalyptus olida,,,,,,,,, -Eucalyptus pulverulenta,,,,,,,,, -Eucalyptus recurva,,,,,,,,, -Eucalyptus rossii,,,,,,,,, -Eucalyptus scias,,,,,,,,, -Eucalyptus viminalis,,,,,,,,, -Eucalyptus yangoura,,,,,,,,, -Eucalyptus youmanii,,,,,,,,, -Euphorbia inappendiculata var. queenslandica,,,,,,,,, -Exocarpos homalocladus,,,,,,,,, -Exocarpos sparteus,,,,,,,,, -Ficus henneana,,,,,,,,, -Freesia hybrid,,,,,,,,, -Freesia laxa,,,,,,,,, -Geijera salicifolia,,,,,,,,, -Gentiana wingecarribiensis,,,,,,,,, -Gentianella barringtonensis,,,,,,,,, -Geranium obtusisepalum,,,,,,,,, -Geranium purpureum subsp. purpureum,,,,,,,,, -Gompholobium grandiflorum,,,,,,,,, -Goodenia varia,,,,,,,,, -Gossia bidwillii,,,,,,,,, -Grevillea scortechinii,,,,,,,,, -Hakea macraeana,,,,,,,,, -Hemisteptia lyrata,,,,,,,,, -Hibbertia crinita,,,,,,,,, -Hibiscus brachysiphonius,,,,,,,,, -Hibiscus sturtii,,,,,,,,, -Hypericum elodes,,,,,,,,, -Hypoxis glabella var. glabella,,,,,,,,, -Imperata cylindrica,,,,,,,,, -Indigofera triflora,,,,,,,,, -Ipomoea cairica,,,,,,,,, -Isolepis montivaga,,,,,,,,, -Isotoma axillaris,,,,,,,,, -Isotoma fluviatilis subsp. fluviatilis,,,,,,,,, -Juncus acutus subsp. acutus,,,,,,,,, -Juncus kraussii,,,,,,,,, -Lantana montevidensis,,,,,,,,, -Lepidium africanum,,,,,,,,, -Lepidium foliosum,,,,,,,,, -Lepidium oxytrichum,,,,,,,,, -Lepidosperma gladiatum,,,,,,,,, -Leptomeria drupacea,,,,,,,,, -Leptospermum continentale,,,,,,,,, -Leptospermum obovatum,,,,,,,,, -Leucopogon amplexicaulis,,,,,,,,, -Lobelia pedunculata,,,,,,,,, -Lobelia trigonocaulis,,,,,,,,, -Lotononis bainesii,,,,,,,,, -Lotus corniculatus,,,,,,,,, -Lupinus polyphyllus,,,,,,,,, -Medicago orbicularis,,,,,,,,, -Melichrus procumbens,,,,,,,,, -Mischocarpus australis,,,,,,,,, -Muehlenbeckia adpressa,,,,,,,,, -Myoporum boninense subsp. australe,,,,,,,,, -Nicotiana glauca,,,,,,,,, -Nicotiana goodspeedii,,,,,,,,, -Oxalis corniculata,,,,,,,,, -Pandorea pandorana subsp. austrocaledonica,,,,,,,,, -Paraserianthes lophantha,,,,,,,,, -Parentucellia latifolia,,,,,,,,, -Phlegmatospermum cochlearinum,,,,,,,,, -Phyla nodiflora,,,,,,,,, -Picris barbarorum,,,,,,,,, -Pimelea ligustrina subsp. ligustrina,,,,,,,,, -Pinus pinea,,,,,,,,, -Pisum sativum var. arvense,,,,,,,,, -Pittosporum erioloma,,,,,,,,, -Plantago turrifera,,,,,,,,, -Polycarpon tetraphyllum,,,,,,,,, -Potamogeton australiensis,,,,,,,,, -Psoralea pinnata,,,,,,,,, -Pultenaea ferruginea,,,,,,,,, -Rhodamnia argentea,,,,,,,,, -Rorippa gigantea,,,,,,,,, -Rubus parvifolius,,,,,,,,, -Salix alba,,,,,,,,, -Schenkia australis,,,,,,,,, -Schoenus apogon,,,,,,,,, -Schoenus brevifolius,,,,,,,,, -Schoenus lepidosperma,,,,,,,,, -Schoenus vaginatus,,,,,,,,, -Scleria rugosa,,,,,,,,, -Senecio longipilus,,,,,,,,, -Sida goniocarpa,,,,,,,,, -Sigesbeckia orientalis,,,,,,,,, -Sisymbrium irio,,,,,,,,, -Sparaxis bulbifera,,,,,,,,, -Spergularia diandra,,,,,,,,, -Sphaeromorphaea littoralis,,,,,,,,, -Stellaria angustifolia subsp. angustifolia,,,,,,,,, -Styphelia viridis,,,,,,,,, -Swainsona cadellii,,,,,,,,, -Teucrium puberulum,,,,,,,,, -Thelymitra kangaloonica,,,,,,,,, -Thesium australe,,,,,,,,, -Trifolium dubium,,,,,,,,, -Veronica catenata,,,,,,,,, -Veronica derwentiana,,,,,,,,, -Wahlenbergia luteola,,,,,,,,, +original_name,taxon_name,taxon_name_alternatives,genus,family,taxon_rank,taxonomic_dataset,taxonomic_status,subclass,taxon_distribution,scientific_name,taxon_id,taxon_ID_genus,scientific_name_id,canonical_name,cleaned_scientific_name_id,taxon_id_family,trinomial,binomial,establishment_means +Abildgaardia ovata,Abildgaardia ovata,,Abildgaardia,Cyperaceae,species,APC,accepted,Magnoliidae,"NT, Qld, NSW",Abildgaardia ovata (Burm.f.) Kral,https://id.biodiversity.org.au/node/apni/2919627,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/150737,Abildgaardia ovata,https://id.biodiversity.org.au/name/apni/150737,https://id.biodiversity.org.au/taxon/apni/51460154,,Abildgaardia ovata,native +Acacia alpina,Acacia alpina,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Acacia alpina F.Muell.,https://id.biodiversity.org.au/node/apni/2907301,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/58263,Acacia alpina,https://id.biodiversity.org.au/name/apni/58263,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia alpina,native +Acacia beadleana,Acacia beadleana,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Acacia beadleana R.H.Jones & J.J.Bruhl,https://id.biodiversity.org.au/node/apni/2902581,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/198624,Acacia beadleana,https://id.biodiversity.org.au/name/apni/165277,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia beadleana,native +Acacia bulgaensis,Acacia bulgaensis,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Acacia bulgaensis Tindale & S.J.Davies,https://id.biodiversity.org.au/node/apni/2889179,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/117995,Acacia bulgaensis,https://id.biodiversity.org.au/name/apni/117995,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia bulgaensis,native +Acacia caroleae,Acacia caroleae,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acacia caroleae Pedley,https://id.biodiversity.org.au/node/apni/2894332,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/60225,Acacia caroleae,https://id.biodiversity.org.au/name/apni/60225,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia caroleae,native +Acacia crassa,Acacia crassa,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acacia crassa Pedley,https://id.biodiversity.org.au/node/apni/2919707,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/60887,Acacia crassa,https://id.biodiversity.org.au/name/apni/60887,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia crassa,native +Acacia flexifolia,Acacia flexifolia,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic",Acacia flexifolia A.Cunn. ex Benth.,https://id.biodiversity.org.au/node/apni/2914740,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/63146,Acacia flexifolia,https://id.biodiversity.org.au/name/apni/63146,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia flexifolia,native +Acacia gladiiformis,Acacia gladiiformis,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acacia gladiiformis A.Cunn. ex Benth.,https://id.biodiversity.org.au/node/apni/2887779,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/63580,Acacia gladiiformis,https://id.biodiversity.org.au/name/apni/63580,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia gladiiformis,native +Acacia havilandiorum,Acacia havilandiorum,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic",Acacia havilandiorum Maiden,https://id.biodiversity.org.au/node/apni/2897713,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/135274,Acacia havilandiorum,https://id.biodiversity.org.au/name/apni/135274,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia havilandiorum,native +Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx subsp. leiocalyx,,Acacia,Fabaceae,subspecies,APC,accepted,Magnoliidae,"Qld, NSW",Acacia leiocalyx (Domin) Pedley subsp. leiocalyx,https://id.biodiversity.org.au/node/apni/2894438,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/65375,Acacia leiocalyx subsp. leiocalyx,https://id.biodiversity.org.au/name/apni/65375,https://id.biodiversity.org.au/taxon/apni/51702961,Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx,native +Acacia myrtifolia,Acacia myrtifolia,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic, Tas",Acacia myrtifolia (Sm.) Willd.,https://id.biodiversity.org.au/node/apni/2901160,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/162110,Acacia myrtifolia,https://id.biodiversity.org.au/name/apni/162110,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia myrtifolia,native +Acacia ramulosa var. ramulosa,Acacia ramulosa var. ramulosa,,Acacia,Fabaceae,variety,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Acacia ramulosa W.Fitzg. var. ramulosa,https://id.biodiversity.org.au/node/apni/2915768,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/168882,Acacia ramulosa var. ramulosa,https://id.biodiversity.org.au/name/apni/168882,https://id.biodiversity.org.au/taxon/apni/51702961,Acacia ramulosa var. ramulosa,Acacia ramulosa,native +Acacia spectabilis,Acacia spectabilis,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW (native and naturalised)",Acacia spectabilis A.Cunn. ex Benth.,https://id.biodiversity.org.au/node/apni/2918795,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/70543,Acacia spectabilis,https://id.biodiversity.org.au/name/apni/70543,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia spectabilis,native and naturalised +Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis subsp. Glabrous form (M.Hancock 94),,Acacia,Fabaceae,subspecies,APC,accepted,Magnoliidae,"NSW, Vic, Tas",Acacia terminalis subsp. Glabrous form (M.Hancock 94) NSW Herbarium,https://id.biodiversity.org.au/node/apni/2886403,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/199841,Acacia terminalis subsp. Glabrous form (M.Hancock 94),https://id.biodiversity.org.au/name/apni/199841,https://id.biodiversity.org.au/taxon/apni/51702961,Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis,native +Acronychia littoralis,Acronychia littoralis,,Acronychia,Rutaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acronychia littoralis T.G.Hartley & J.B.Williams,https://id.biodiversity.org.au/node/apni/2907701,https://id.biodiversity.org.au/taxon/apni/51446847,https://id.biodiversity.org.au/name/apni/73953,Acronychia littoralis,https://id.biodiversity.org.au/name/apni/73953,https://id.biodiversity.org.au/taxon/apni/51461748,,Acronychia littoralis,native +Adriana tomentosa,Adriana tomentosa,,Adriana,Euphorbiaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, ACT, Vic",Adriana tomentosa Gaudich.,https://id.biodiversity.org.au/node/apni/2898187,https://id.biodiversity.org.au/node/apni/8408111,https://id.biodiversity.org.au/name/apni/77104,Adriana tomentosa,https://id.biodiversity.org.au/name/apni/77104,https://id.biodiversity.org.au/taxon/apni/51442249,,Adriana tomentosa,native +Alectryon coriaceus,Alectryon coriaceus,,Alectryon,Sapindaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Alectryon coriaceus (Benth.) Radlk.,https://id.biodiversity.org.au/node/apni/2891604,https://id.biodiversity.org.au/taxon/apni/51299789,https://id.biodiversity.org.au/name/apni/81043,Alectryon coriaceus,https://id.biodiversity.org.au/name/apni/81043,https://id.biodiversity.org.au/taxon/apni/51447212,,Alectryon coriaceus,native +Alectryon oleifolius,Alectryon oleifolius,,Alectryon,Sapindaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Alectryon oleifolius (Desf.) S.T.Reynolds,https://id.biodiversity.org.au/node/apni/2900874,https://id.biodiversity.org.au/taxon/apni/51299789,https://id.biodiversity.org.au/name/apni/81066,Alectryon oleifolius,https://id.biodiversity.org.au/name/apni/81066,https://id.biodiversity.org.au/taxon/apni/51447212,,Alectryon oleifolius,native +Alectryon subdentatus,Alectryon subdentatus,,Alectryon,Sapindaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Alectryon subdentatus (F.Muell. ex Benth.) Radlk.,https://id.biodiversity.org.au/node/apni/2890534,https://id.biodiversity.org.au/taxon/apni/51299789,https://id.biodiversity.org.au/name/apni/81114,Alectryon subdentatus,https://id.biodiversity.org.au/name/apni/81114,https://id.biodiversity.org.au/taxon/apni/51447212,,Alectryon subdentatus,native +Amyema preissii,Amyema preissii,,Amyema,Loranthaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Amyema preissii (Miq.) Tiegh.,https://id.biodiversity.org.au/node/apni/2888430,https://id.biodiversity.org.au/taxon/apni/51438795,https://id.biodiversity.org.au/name/apni/87461,Amyema preissii,https://id.biodiversity.org.au/name/apni/87461,https://id.biodiversity.org.au/taxon/apni/51438796,,Amyema preissii,native +Angophora leiocarpa,Angophora leiocarpa,,Angophora,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Angophora leiocarpa (L.A.S.Johnson ex G.J.Leach) K.R.Thiele & Ladiges,https://id.biodiversity.org.au/node/apni/2894339,https://id.biodiversity.org.au/taxon/apni/51439560,https://id.biodiversity.org.au/name/apni/123435,Angophora leiocarpa,https://id.biodiversity.org.au/name/apni/123435,https://id.biodiversity.org.au/taxon/apni/51702983,,Angophora leiocarpa,native +Arbutus unedo,Arbutus unedo,,Arbutus,Ericaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (doubtfully naturalised), NSW (doubtfully naturalised), ACT (doubtfully naturalised), Vic (naturalised), Tas (doubtfully naturalised)",Arbutus unedo L.,https://id.biodiversity.org.au/node/apni/2904939,https://id.biodiversity.org.au/node/apni/2892910,https://id.biodiversity.org.au/name/apni/98540,Arbutus unedo,https://id.biodiversity.org.au/name/apni/98540,https://id.biodiversity.org.au/taxon/apni/51436079,,Arbutus unedo,naturalised +Australina pusilla,Australina pusilla,,Australina,Urticaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic, Tas",Australina pusilla (Poir.) Gaudich.,https://id.biodiversity.org.au/node/apni/2913845,https://id.biodiversity.org.au/node/apni/2907879,https://id.biodiversity.org.au/name/apni/113875,Australina pusilla,https://id.biodiversity.org.au/name/apni/113875,https://id.biodiversity.org.au/taxon/apni/51662052,,Australina pusilla,native +Burmannia disticha,Burmannia disticha,,Burmannia,Burmanniaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Burmannia disticha L.,https://id.biodiversity.org.au/node/apni/2900088,https://id.biodiversity.org.au/node/apni/2915743,https://id.biodiversity.org.au/name/apni/70173,Burmannia disticha,https://id.biodiversity.org.au/name/apni/70173,https://id.biodiversity.org.au/node/apni/2887196,,Burmannia disticha,native +Bursaria spinosa subsp. spinosa,Bursaria spinosa subsp. spinosa,,Bursaria,Pittosporaceae,subspecies,APC,accepted,Magnoliidae,"SA, Qld, NSW, Vic, Tas",Bursaria spinosa Cav. subsp. spinosa,https://id.biodiversity.org.au/taxon/apni/51442337,https://id.biodiversity.org.au/taxon/apni/51442339,https://id.biodiversity.org.au/name/apni/142036,Bursaria spinosa subsp. spinosa,https://id.biodiversity.org.au/name/apni/142036,https://id.biodiversity.org.au/taxon/apni/51442315,Bursaria spinosa subsp. spinosa,Bursaria spinosa,native +Calendula arvensis,Calendula arvensis,,Calendula,Asteraceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (naturalised), Tas (naturalised)",Calendula arvensis L.,https://id.biodiversity.org.au/node/apni/2891878,https://id.biodiversity.org.au/node/apni/2893748,https://id.biodiversity.org.au/name/apni/95042,Calendula arvensis,https://id.biodiversity.org.au/name/apni/95042,https://id.biodiversity.org.au/taxon/apni/51695393,,Calendula arvensis,naturalised +Callistemon purpurascens,Callistemon purpurascens,,Callistemon,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Callistemon purpurascens S.M.Douglas & S.David,https://id.biodiversity.org.au/taxon/apni/51288952,https://id.biodiversity.org.au/taxon/apni/51439657,https://id.biodiversity.org.au/name/apni/4630985,Callistemon purpurascens,https://id.biodiversity.org.au/name/apni/4630985,https://id.biodiversity.org.au/taxon/apni/51702983,,Callistemon purpurascens,native +Apophyllum anomalum,Capparis anomala,,Capparis,Capparaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Capparis anomala (F.Muell.) Byng & Christenh.,https://id.biodiversity.org.au/taxon/apni/51432888,https://id.biodiversity.org.au/taxon/apni/51432886,https://id.biodiversity.org.au/name/apni/50561973,Capparis anomala,https://id.biodiversity.org.au/name/apni/97697,https://id.biodiversity.org.au/taxon/apni/51433682,,Capparis anomala,native +Carex leporina,Carex leporina,,Carex,Cyperaceae,species,APC,accepted,Magnoliidae,"NSW (naturalised), NI (naturalised), Vic (naturalised), Tas (naturalised)",Carex leporina L.,https://id.biodiversity.org.au/node/apni/2902492,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/135236,Carex leporina,https://id.biodiversity.org.au/name/apni/135236,https://id.biodiversity.org.au/taxon/apni/51460154,,Carex leporina,naturalised +Carex cephalotes,Carex pyrenaica var. cephalotes,,Carex,Cyperaceae,variety,APC,accepted,Magnoliidae,"NSW, Vic, Tas",Carex pyrenaica var. cephalotes (F.Muell.) Kük.,https://id.biodiversity.org.au/node/apni/2892693,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/111655,Carex pyrenaica var. cephalotes,https://id.biodiversity.org.au/name/apni/110600,https://id.biodiversity.org.au/taxon/apni/51460154,Carex pyrenaica var. cephalotes,Carex pyrenaica,native +Carex raleighii,Carex raleighii,,Carex,Cyperaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic, Tas",Carex raleighii Nelmes,https://id.biodiversity.org.au/node/apni/2910405,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/111690,Carex raleighii,https://id.biodiversity.org.au/name/apni/111690,https://id.biodiversity.org.au/taxon/apni/51460154,,Carex raleighii,native +Carmichaelia exsul,Carmichaelia exsul,,Carmichaelia,Fabaceae,species,APC,accepted,Magnoliidae,LHI,Carmichaelia exsul F.Muell.,https://id.biodiversity.org.au/node/apni/2915240,https://id.biodiversity.org.au/node/apni/8138105,https://id.biodiversity.org.au/name/apni/112335,Carmichaelia exsul,https://id.biodiversity.org.au/name/apni/112335,https://id.biodiversity.org.au/taxon/apni/51702961,,Carmichaelia exsul,native +Cassinia compacta,Cassinia compacta,Cassinia accipitrum (pro parte misapplied) | Cassinia straminea (pro parte misapplied) | Cassinia telfordii (pro parte misapplied) | Cassinia accipitrum (misapplied),Cassinia,Asteraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Cassinia compacta F.Muell.,https://id.biodiversity.org.au/node/apni/2909860,https://id.biodiversity.org.au/taxon/apni/51431788,https://id.biodiversity.org.au/name/apni/54723,Cassinia compacta [alternative possible names: Cassinia accipitrum (pro parte misapplied) | Cassinia straminea (pro parte misapplied) | Cassinia telfordii (pro parte misapplied) | Cassinia accipitrum (misapplied)],,https://id.biodiversity.org.au/taxon/apni/51695393,,Cassinia compacta,native +Castanospermum australe,Castanospermum australe,,Castanospermum,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, NI (doubtfully naturalised)",Castanospermum australe A.Cunn. ex Mudie,https://id.biodiversity.org.au/node/apni/2894943,https://id.biodiversity.org.au/node/apni/7226268,https://id.biodiversity.org.au/name/apni/196675,Castanospermum australe,https://id.biodiversity.org.au/name/apni/196675,https://id.biodiversity.org.au/taxon/apni/51702961,,Castanospermum australe,native and naturalised +Centaurium tenuiflorum,Centaurium tenuiflorum,,Centaurium,Gentianaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Centaurium tenuiflorum (Hoffmanns. & Link) Fritsch,https://id.biodiversity.org.au/node/apni/7385749,https://id.biodiversity.org.au/node/apni/7385753,https://id.biodiversity.org.au/name/apni/58491,Centaurium tenuiflorum,https://id.biodiversity.org.au/name/apni/58491,https://id.biodiversity.org.au/taxon/apni/51436871,,Centaurium tenuiflorum,naturalised +Cestrum nocturnum,Cestrum nocturnum,,Cestrum,Solanaceae,species,APC,accepted,Magnoliidae,"Qld (doubtfully naturalised), NSW (naturalised), NI (naturalised)",Cestrum nocturnum L.,https://id.biodiversity.org.au/node/apni/2911237,https://id.biodiversity.org.au/node/apni/2889884,https://id.biodiversity.org.au/name/apni/60565,Cestrum nocturnum,https://id.biodiversity.org.au/name/apni/60565,https://id.biodiversity.org.au/taxon/apni/51447684,,Cestrum nocturnum,naturalised +Chthonocephalus pseudevax,Chthonocephalus pseudevax,,Chthonocephalus,Asteraceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Chthonocephalus pseudevax Steetz,https://id.biodiversity.org.au/node/apni/2917443,https://id.biodiversity.org.au/node/apni/2892496,https://id.biodiversity.org.au/name/apni/68863,Chthonocephalus pseudevax,https://id.biodiversity.org.au/name/apni/68863,https://id.biodiversity.org.au/taxon/apni/51695393,,Chthonocephalus pseudevax,native +Claoxylon australe,Claoxylon australe,,Claoxylon,Euphorbiaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Claoxylon australe Baill.,https://id.biodiversity.org.au/node/apni/2887203,https://id.biodiversity.org.au/node/apni/2920593,https://id.biodiversity.org.au/name/apni/70907,Claoxylon australe,https://id.biodiversity.org.au/name/apni/70907,https://id.biodiversity.org.au/taxon/apni/51442249,,Claoxylon australe,native +Commersonia amystia,Commersonia amystia,,Commersonia,Malvaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Commersonia amystia C.F.Wilkins & L.M.Copel.,https://id.biodiversity.org.au/node/apni/2904387,https://id.biodiversity.org.au/taxon/apni/51438976,https://id.biodiversity.org.au/name/apni/214136,Commersonia amystia,https://id.biodiversity.org.au/name/apni/214136,https://id.biodiversity.org.au/taxon/apni/51439248,,Commersonia amystia,native +Commersonia salviifolia,Commersonia salviifolia,,Commersonia,Malvaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Commersonia salviifolia (Hook. ex Steetz) F.Muell.,https://id.biodiversity.org.au/node/apni/2901795,https://id.biodiversity.org.au/taxon/apni/51438976,https://id.biodiversity.org.au/name/apni/75211,Commersonia salviifolia,https://id.biodiversity.org.au/name/apni/75211,https://id.biodiversity.org.au/taxon/apni/51439248,,Commersonia salviifolia,native +Convolvulus farinosus,Convolvulus farinosus,,Convolvulus,Convolvulaceae,species,APC,accepted,Magnoliidae,NSW (naturalised),Convolvulus farinosus L.,https://id.biodiversity.org.au/node/apni/2895672,https://id.biodiversity.org.au/taxon/apni/51298269,https://id.biodiversity.org.au/name/apni/206071,Convolvulus farinosus,https://id.biodiversity.org.au/name/apni/206071,https://id.biodiversity.org.au/taxon/apni/51695210,,Convolvulus farinosus,naturalised +Coprosma niphophila,Coprosma niphophila,,Coprosma,Rubiaceae,species,APC,accepted,Magnoliidae,NSW,Coprosma niphophila Orchard,https://id.biodiversity.org.au/node/apni/2910618,https://id.biodiversity.org.au/node/apni/8135850,https://id.biodiversity.org.au/name/apni/78856,Coprosma niphophila,https://id.biodiversity.org.au/name/apni/78856,https://id.biodiversity.org.au/taxon/apni/51446612,,Coprosma niphophila,native +Coprosma nivalis,Coprosma nivalis,,Coprosma,Rubiaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Coprosma nivalis W.R.B.Oliv.,https://id.biodiversity.org.au/node/apni/2915002,https://id.biodiversity.org.au/node/apni/8135850,https://id.biodiversity.org.au/name/apni/78866,Coprosma nivalis,https://id.biodiversity.org.au/name/apni/78866,https://id.biodiversity.org.au/taxon/apni/51446612,,Coprosma nivalis,native +Correa alba,Correa alba,,Correa,Rutaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Correa alba Andrews,https://id.biodiversity.org.au/node/apni/2906721,https://id.biodiversity.org.au/taxon/apni/51447015,https://id.biodiversity.org.au/name/apni/80283,Correa alba,https://id.biodiversity.org.au/name/apni/80283,https://id.biodiversity.org.au/taxon/apni/51461748,,Correa alba,native +Corymbia citriodora,Corymbia citriodora,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (doubtfully naturalised), Qld, NSW (native and naturalised), Vic (naturalised)",Corymbia citriodora (Hook.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2912509,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119387,Corymbia citriodora,https://id.biodiversity.org.au/name/apni/119387,https://id.biodiversity.org.au/taxon/apni/51702983,,Corymbia citriodora,native and naturalised +Corymbia eximia,Corymbia eximia,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Corymbia eximia (Schauer) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2909833,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119402,Corymbia eximia,https://id.biodiversity.org.au/name/apni/119402,https://id.biodiversity.org.au/taxon/apni/51702983,,Corymbia eximia,native +Crassula decumbens,Crassula decumbens,,Crassula,Crassulaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, ACT, Vic, Tas",Crassula decumbens Thunb.,https://id.biodiversity.org.au/node/apni/2889646,https://id.biodiversity.org.au/node/apni/2903354,https://id.biodiversity.org.au/name/apni/83855,Crassula decumbens,https://id.biodiversity.org.au/name/apni/83855,https://id.biodiversity.org.au/taxon/apni/51270792,,Crassula decumbens,native +Crassula peduncularis,Crassula peduncularis,,Crassula,Crassulaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, ACT, Vic, Tas",Crassula peduncularis (Sm.) F.Meigen,https://id.biodiversity.org.au/node/apni/2895654,https://id.biodiversity.org.au/node/apni/2903354,https://id.biodiversity.org.au/name/apni/84005,Crassula peduncularis,https://id.biodiversity.org.au/name/apni/84005,https://id.biodiversity.org.au/taxon/apni/51270792,,Crassula peduncularis,native +Crotalaria brevis,Crotalaria brevis,,Crotalaria,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Crotalaria brevis Domin,https://id.biodiversity.org.au/node/apni/2906180,https://id.biodiversity.org.au/taxon/apni/51300011,https://id.biodiversity.org.au/name/apni/85578,Crotalaria brevis,https://id.biodiversity.org.au/name/apni/85578,https://id.biodiversity.org.au/taxon/apni/51702961,,Crotalaria brevis,native +Crotalaria grahamiana,Crotalaria grahamiana,,Crotalaria,Fabaceae,species,APC,accepted,Magnoliidae,"Qld (naturalised), NSW (naturalised)",Crotalaria grahamiana Wight & Arn.,https://id.biodiversity.org.au/node/apni/2917131,https://id.biodiversity.org.au/taxon/apni/51300011,https://id.biodiversity.org.au/name/apni/85770,Crotalaria grahamiana,https://id.biodiversity.org.au/name/apni/85770,https://id.biodiversity.org.au/taxon/apni/51702961,,Crotalaria grahamiana,naturalised +Crotalaria lanceolata,Crotalaria lanceolata,,Crotalaria,Fabaceae,species,APC,accepted,Magnoliidae,"NT (naturalised), Qld (naturalised), NSW (naturalised), NI (naturalised)",Crotalaria lanceolata E.Mey.,https://id.biodiversity.org.au/node/apni/2887683,https://id.biodiversity.org.au/taxon/apni/51300011,https://id.biodiversity.org.au/name/apni/85830,Crotalaria lanceolata,https://id.biodiversity.org.au/name/apni/85830,https://id.biodiversity.org.au/taxon/apni/51702961,,Crotalaria lanceolata,naturalised +Cylindropuntia kleiniae,Cylindropuntia kleiniae,,Cylindropuntia,Cactaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised)",Cylindropuntia kleiniae (DC.) F.M.Knuth,https://id.biodiversity.org.au/taxon/apni/51432847,https://id.biodiversity.org.au/taxon/apni/51432841,https://id.biodiversity.org.au/name/apni/191050,Cylindropuntia kleiniae,https://id.biodiversity.org.au/name/apni/191050,https://id.biodiversity.org.au/taxon/apni/51432828,,Cylindropuntia kleiniae,naturalised +Cyperus albostriatus,Cyperus albostriatus,,Cyperus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised), NI (naturalised)",Cyperus albostriatus Schrad.,https://id.biodiversity.org.au/node/apni/2893623,https://id.biodiversity.org.au/taxon/apni/51434383,https://id.biodiversity.org.au/name/apni/96258,Cyperus albostriatus,https://id.biodiversity.org.au/name/apni/96258,https://id.biodiversity.org.au/taxon/apni/51460154,,Cyperus albostriatus,naturalised +Cyperus betchei,Cyperus betchei,,Cyperus,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Cyperus betchei (Kük.) S.T.Blake,https://id.biodiversity.org.au/node/apni/2888104,https://id.biodiversity.org.au/taxon/apni/51434383,https://id.biodiversity.org.au/name/apni/96480,Cyperus betchei,https://id.biodiversity.org.au/name/apni/96480,https://id.biodiversity.org.au/taxon/apni/51460154,,Cyperus betchei,native +Cyperus bulbosus,Cyperus bulbosus,,Cyperus,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Cyperus bulbosus Vahl,https://id.biodiversity.org.au/node/apni/2902422,https://id.biodiversity.org.au/taxon/apni/51434383,https://id.biodiversity.org.au/name/apni/96591,Cyperus bulbosus,https://id.biodiversity.org.au/name/apni/96591,https://id.biodiversity.org.au/taxon/apni/51460154,,Cyperus bulbosus,native +Cyperus laevigatus,Cyperus laevigatus,,Cyperus,Cyperaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT, SA, Qld, NSW",Cyperus laevigatus L.,https://id.biodiversity.org.au/node/apni/2916573,https://id.biodiversity.org.au/taxon/apni/51434383,https://id.biodiversity.org.au/name/apni/97862,Cyperus laevigatus,https://id.biodiversity.org.au/name/apni/97862,https://id.biodiversity.org.au/taxon/apni/51460154,,Cyperus laevigatus,native and naturalised +Cyperus sculptus,Cyperus sculptus,,Cyperus,Cyperaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Cyperus sculptus S.T.Blake,https://id.biodiversity.org.au/node/apni/2902340,https://id.biodiversity.org.au/taxon/apni/51434383,https://id.biodiversity.org.au/name/apni/98972,Cyperus sculptus,https://id.biodiversity.org.au/name/apni/98972,https://id.biodiversity.org.au/taxon/apni/51460154,,Cyperus sculptus,native +Dampiera fusca,Dampiera fusca,,Dampiera,Goodeniaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Dampiera fusca Rajput & Carolin,https://id.biodiversity.org.au/node/apni/2908327,https://id.biodiversity.org.au/taxon/apni/51437007,https://id.biodiversity.org.au/name/apni/78388,Dampiera fusca,https://id.biodiversity.org.au/name/apni/78388,https://id.biodiversity.org.au/taxon/apni/51462931,,Dampiera fusca,native +Davidsonia johnsonii,Davidsonia johnsonii,,Davidsonia,Cunoniaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Davidsonia johnsonii J.B.Williams & G.Harden,https://id.biodiversity.org.au/taxon/apni/51434155,https://id.biodiversity.org.au/taxon/apni/51434156,https://id.biodiversity.org.au/name/apni/166907,Davidsonia johnsonii,https://id.biodiversity.org.au/name/apni/166907,https://id.biodiversity.org.au/taxon/apni/51434138,,Davidsonia johnsonii,native +Daviesia arenaria,Daviesia arenaria,,Daviesia,Fabaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic",Daviesia arenaria Crisp,https://id.biodiversity.org.au/taxon/apni/51435880,https://id.biodiversity.org.au/taxon/apni/51461520,https://id.biodiversity.org.au/name/apni/82236,Daviesia arenaria,https://id.biodiversity.org.au/name/apni/82236,https://id.biodiversity.org.au/taxon/apni/51702961,,Daviesia arenaria,native +Dichromochlamys dentatifolia,Dichromochlamys dentatifolia,,Dichromochlamys,Asteraceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Dichromochlamys dentatifolia (F.Muell.) Dunlop,https://id.biodiversity.org.au/node/apni/2888915,https://id.biodiversity.org.au/node/apni/2894601,https://id.biodiversity.org.au/name/apni/102074,Dichromochlamys dentatifolia,https://id.biodiversity.org.au/name/apni/102074,https://id.biodiversity.org.au/taxon/apni/51695393,,Dichromochlamys dentatifolia,native +Dillwynia cinerascens,Dillwynia cinerascens,,Dillwynia,Fabaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Dillwynia cinerascens R.Br.,https://id.biodiversity.org.au/node/apni/2920072,https://id.biodiversity.org.au/taxon/apni/51285570,https://id.biodiversity.org.au/name/apni/105476,Dillwynia cinerascens,https://id.biodiversity.org.au/name/apni/105476,https://id.biodiversity.org.au/taxon/apni/51702961,,Dillwynia cinerascens,native +Dillwynia floribunda,Dillwynia floribunda,,Dillwynia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Dillwynia floribunda Sm.,https://id.biodiversity.org.au/node/apni/2892820,https://id.biodiversity.org.au/taxon/apni/51285570,https://id.biodiversity.org.au/name/apni/105728,Dillwynia floribunda,https://id.biodiversity.org.au/name/apni/105728,https://id.biodiversity.org.au/taxon/apni/51702961,,Dillwynia floribunda,native +Dinosperma erythrococcum,Dinosperma erythrococcum,,Dinosperma,Rutaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Dinosperma erythrococcum (F.Muell.) T.G.Hartley,https://id.biodiversity.org.au/node/apni/2897246,https://id.biodiversity.org.au/node/apni/2900591,https://id.biodiversity.org.au/name/apni/157718,Dinosperma erythrococcum,https://id.biodiversity.org.au/name/apni/157718,https://id.biodiversity.org.au/taxon/apni/51461748,,Dinosperma erythrococcum,native +Dodonaea petiolaris,Dodonaea petiolaris,Dodonaea viscosa subsp. mucronata (pro parte misapplied),Dodonaea,Sapindaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Dodonaea petiolaris F.Muell.,https://id.biodiversity.org.au/node/apni/2921131,https://id.biodiversity.org.au/taxon/apni/51447268,https://id.biodiversity.org.au/name/apni/72184,Dodonaea petiolaris [alternative possible names: Dodonaea viscosa subsp. mucronata (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51447212,,Dodonaea petiolaris,native +Dodonaea truncatiales,Dodonaea truncatiales,Dodonaea heteromorpha (pro parte misapplied) | Dodonaea heteromorpha (misapplied),Dodonaea,Sapindaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Dodonaea truncatiales F.Muell.,https://id.biodiversity.org.au/node/apni/7870563,https://id.biodiversity.org.au/taxon/apni/51447268,https://id.biodiversity.org.au/name/apni/72648,Dodonaea truncatiales [alternative possible names: Dodonaea heteromorpha (pro parte misapplied) | Dodonaea heteromorpha (misapplied)],,https://id.biodiversity.org.au/taxon/apni/51447212,,Dodonaea truncatiales,native +Dovyalis caffra,Dovyalis caffra,,Dovyalis,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised)",Dovyalis caffra (Hook.f. & Harv.) Hook.f.,https://id.biodiversity.org.au/node/apni/2888866,https://id.biodiversity.org.au/node/apni/2897632,https://id.biodiversity.org.au/name/apni/199157,Dovyalis caffra,https://id.biodiversity.org.au/name/apni/86110,https://id.biodiversity.org.au/taxon/apni/51436847,,Dovyalis caffra,naturalised +Elaeocarpus grandis,Elaeocarpus grandis,,Elaeocarpus,Elaeocarpaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Elaeocarpus grandis F.Muell.,https://id.biodiversity.org.au/node/apni/2895259,https://id.biodiversity.org.au/taxon/apni/51435153,https://id.biodiversity.org.au/name/apni/115772,Elaeocarpus grandis,https://id.biodiversity.org.au/name/apni/115772,https://id.biodiversity.org.au/taxon/apni/51632282,,Elaeocarpus grandis,native +Eleocharis pallens,Eleocharis pallens,,Eleocharis,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Eleocharis pallens S.T.Blake,https://id.biodiversity.org.au/node/apni/2899827,https://id.biodiversity.org.au/taxon/apni/51434435,https://id.biodiversity.org.au/name/apni/67140,Eleocharis pallens,https://id.biodiversity.org.au/name/apni/67140,https://id.biodiversity.org.au/taxon/apni/51460154,,Eleocharis pallens,native +Endiandra globosa,Endiandra globosa,,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Endiandra globosa Maiden & Betche,https://id.biodiversity.org.au/node/apni/2901094,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111780,Endiandra globosa,https://id.biodiversity.org.au/name/apni/111780,https://id.biodiversity.org.au/taxon/apni/51438397,,Endiandra globosa,native +Endiandra muelleri,Endiandra muelleri,,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Endiandra muelleri Meisn.,https://id.biodiversity.org.au/node/apni/2903619,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111996,Endiandra muelleri,https://id.biodiversity.org.au/name/apni/111996,https://id.biodiversity.org.au/taxon/apni/51438397,,Endiandra muelleri,native +Epilobium gunnianum,Epilobium gunnianum,,Epilobium,Onagraceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic, Tas",Epilobium gunnianum Hausskn.,https://id.biodiversity.org.au/node/apni/2903068,https://id.biodiversity.org.au/taxon/apni/51440863,https://id.biodiversity.org.au/name/apni/105579,Epilobium gunnianum,https://id.biodiversity.org.au/name/apni/105579,https://id.biodiversity.org.au/taxon/apni/51440864,,Epilobium gunnianum,native +Eremophila deserti,Eremophila deserti,,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila deserti (A.Cunn. ex Benth.) Chinnock,https://id.biodiversity.org.au/node/apni/2897363,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/123426,Eremophila deserti,https://id.biodiversity.org.au/name/apni/123426,https://id.biodiversity.org.au/taxon/apni/51461527,,Eremophila deserti,native +Eremophila oppositifolia,Eremophila oppositifolia,,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila oppositifolia R.Br.,https://id.biodiversity.org.au/node/apni/7951462,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/114575,Eremophila oppositifolia,https://id.biodiversity.org.au/name/apni/114575,https://id.biodiversity.org.au/taxon/apni/51461527,,Eremophila oppositifolia,native +Erigeron conyzoides,Erigeron conyzoides,,Erigeron,Asteraceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Erigeron conyzoides F.Muell.,https://id.biodiversity.org.au/node/apni/2913579,https://id.biodiversity.org.au/taxon/apni/51432118,https://id.biodiversity.org.au/name/apni/73195,Erigeron conyzoides,https://id.biodiversity.org.au/name/apni/239637,https://id.biodiversity.org.au/taxon/apni/51695393,,Erigeron conyzoides,native +Erythroxylum australe,Erythroxylum australe,Erythroxylum sp. Splityard Creek (L.Pedley 5360) (pro parte misapplied),Erythroxylum,Erythroxylaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Erythroxylum australe F.Muell.,https://id.biodiversity.org.au/node/apni/2912212,https://id.biodiversity.org.au/node/apni/2919669,https://id.biodiversity.org.au/name/apni/75959,Erythroxylum australe [alternative possible names: Erythroxylum sp. Splityard Creek (L.Pedley 5360) (pro parte misapplied)],,https://id.biodiversity.org.au/node/apni/2893375,,Erythroxylum australe,native +Escallonia bifida,Escallonia bifida,,Escallonia,Escalloniaceae,species,APC,accepted,Magnoliidae,NSW (naturalised),Escallonia bifida Link & Otto,https://id.biodiversity.org.au/taxon/apni/51435441,https://id.biodiversity.org.au/taxon/apni/51435442,https://id.biodiversity.org.au/name/apni/116602,Escallonia bifida,https://id.biodiversity.org.au/name/apni/116602,https://id.biodiversity.org.au/taxon/apni/51435443,,Escallonia bifida,naturalised +Eucalyptus badjensis,Eucalyptus badjensis,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus badjensis Beuzev. & M.B.Welch,https://id.biodiversity.org.au/node/apni/2912724,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/57323,Eucalyptus badjensis,https://id.biodiversity.org.au/name/apni/57323,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus badjensis,native +Eucalyptus camphora,Eucalyptus camphora,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic",Eucalyptus camphora R.T.Baker,https://id.biodiversity.org.au/node/apni/2891665,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/94439,Eucalyptus camphora,https://id.biodiversity.org.au/name/apni/94439,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus camphora,native +Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus dorrigoensis (Blakely) L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2903351,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118668,Eucalyptus dorrigoensis,https://id.biodiversity.org.au/name/apni/118668,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus dorrigoensis,native +Eucalyptus yangoura,Eucalyptus globoidea,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus globoidea Blakely,https://id.biodiversity.org.au/node/apni/5270850,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/61141,Eucalyptus globoidea,https://id.biodiversity.org.au/name/apni/92470,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus globoidea,native +Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,,Eucalyptus,Myrtaceae,subspecies,APC,accepted,Magnoliidae,"SA, NSW, Vic",Eucalyptus leucoxylon subsp. pruinosa (F.Muell. ex Miq.) Boland,https://id.biodiversity.org.au/node/apni/2908258,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/77407,Eucalyptus leucoxylon subsp. pruinosa,https://id.biodiversity.org.au/name/apni/77407,https://id.biodiversity.org.au/taxon/apni/51702983,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon,native +Eucalyptus muelleriana,Eucalyptus muelleriana,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus muelleriana A.W.Howitt,https://id.biodiversity.org.au/node/apni/2888508,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/56840,Eucalyptus muelleriana,https://id.biodiversity.org.au/name/apni/56840,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus muelleriana,native +Eucalyptus nandewarica,Eucalyptus nandewarica,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus nandewarica L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2897688,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118852,Eucalyptus nandewarica,https://id.biodiversity.org.au/name/apni/118852,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus nandewarica,native +Eucalyptus olida,Eucalyptus olida,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus olida L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2914019,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118797,Eucalyptus olida,https://id.biodiversity.org.au/name/apni/118797,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus olida,native +Eucalyptus pulverulenta,Eucalyptus pulverulenta,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus pulverulenta Sims,https://id.biodiversity.org.au/taxon/apni/51440675,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/106609,Eucalyptus pulverulenta,https://id.biodiversity.org.au/name/apni/106609,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus pulverulenta,native +Eucalyptus recurva,Eucalyptus recurva,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus recurva Crisp,https://id.biodiversity.org.au/node/apni/2892273,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/101532,Eucalyptus recurva,https://id.biodiversity.org.au/name/apni/101532,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus recurva,native +Eucalyptus rossii,Eucalyptus rossii,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus rossii R.T.Baker & H.G.Sm.,https://id.biodiversity.org.au/node/apni/2900822,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/58182,Eucalyptus rossii,https://id.biodiversity.org.au/name/apni/58182,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus rossii,native +Eucalyptus scias,Eucalyptus scias,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus scias L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2893839,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118833,Eucalyptus scias,https://id.biodiversity.org.au/name/apni/118833,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus scias,native +Eucalyptus viminalis,Eucalyptus viminalis,Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied),Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic, Tas",Eucalyptus viminalis Labill.,https://id.biodiversity.org.au/taxon/apni/51290421,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/65838,Eucalyptus viminalis [alternative possible names: Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus viminalis,native +Eucalyptus youmanii,Eucalyptus youmanii,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Eucalyptus youmanii Blakely & McKie,https://id.biodiversity.org.au/node/apni/2916227,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/92496,Eucalyptus youmanii,https://id.biodiversity.org.au/name/apni/92496,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus youmanii,native +Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata var. queenslandica,,Euphorbia,Euphorbiaceae,variety,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Euphorbia inappendiculata var. queenslandica Domin,https://id.biodiversity.org.au/node/apni/7200245,https://id.biodiversity.org.au/taxon/apni/51435529,https://id.biodiversity.org.au/name/apni/92612,Euphorbia inappendiculata var. queenslandica,https://id.biodiversity.org.au/name/apni/92612,https://id.biodiversity.org.au/taxon/apni/51442249,Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata,native +Exocarpos homalocladus,Exocarpos homalocladus,,Exocarpos,Santalaceae,species,APC,accepted,Magnoliidae,LHI,Exocarpos homalocladus C.Moore & F.Muell.,https://id.biodiversity.org.au/node/apni/2898548,https://id.biodiversity.org.au/taxon/apni/51447153,https://id.biodiversity.org.au/name/apni/58158,Exocarpos homalocladus,https://id.biodiversity.org.au/name/apni/58158,https://id.biodiversity.org.au/taxon/apni/51447154,,Exocarpos homalocladus,native +Exocarpos sparteus,Exocarpos sparteus,,Exocarpos,Santalaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Exocarpos sparteus R.Br.,https://id.biodiversity.org.au/node/apni/2898676,https://id.biodiversity.org.au/taxon/apni/51447153,https://id.biodiversity.org.au/name/apni/58330,Exocarpos sparteus,https://id.biodiversity.org.au/name/apni/58330,https://id.biodiversity.org.au/taxon/apni/51447154,,Exocarpos sparteus,native +Ficus henneana,Ficus henneana,,Ficus,Moraceae,species,APC,accepted,Magnoliidae,"NT, Qld, NSW",Ficus henneana Miq.,https://id.biodiversity.org.au/node/apni/2903067,https://id.biodiversity.org.au/taxon/apni/51439476,https://id.biodiversity.org.au/name/apni/91212,Ficus henneana,https://id.biodiversity.org.au/name/apni/91212,https://id.biodiversity.org.au/taxon/apni/51439463,,Ficus henneana,native +Freesia laxa,Freesia laxa,,Freesia,Iridaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), Qld (naturalised), NSW (naturalised), NI (naturalised), Vic (naturalised)",Freesia laxa (Thunb.) Goldblatt & J.C.Manning,https://id.biodiversity.org.au/node/apni/2886987,https://id.biodiversity.org.au/node/apni/2913899,https://id.biodiversity.org.au/name/apni/200132,Freesia laxa,https://id.biodiversity.org.au/name/apni/200132,https://id.biodiversity.org.au/taxon/apni/51438006,,Freesia laxa,naturalised +Freesia hybrid,Freesia leichtlinii subsp. leichtlinii x Freesia leichtlinii subsp. alba,,Freesia,Iridaceae,subspecies,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised)",Freesia leichtlinii Klatt subsp. leichtlinii x Freesia leichtlinii subsp. alba (G.L.Mey.) J.C.Manning & Goldblatt,https://id.biodiversity.org.au/node/apni/2908401,https://id.biodiversity.org.au/node/apni/2913899,https://id.biodiversity.org.au/name/apni/241787,Freesia leichtlinii subsp. leichtlinii x Freesia leichtlinii subsp. alba,https://id.biodiversity.org.au/name/apni/171901,https://id.biodiversity.org.au/taxon/apni/51438006,Freesia leichtlinii subsp. leichtlinii x Freesia leichtlinii subsp. alba,Freesia leichtlinii,naturalised +Geijera salicifolia,Geijera salicifolia,,Geijera,Rutaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Geijera salicifolia Schott,https://id.biodiversity.org.au/node/apni/2901807,https://id.biodiversity.org.au/node/apni/2905474,https://id.biodiversity.org.au/name/apni/101381,Geijera salicifolia,https://id.biodiversity.org.au/name/apni/101381,https://id.biodiversity.org.au/taxon/apni/51461748,,Geijera salicifolia,native +Gentiana wingecarribiensis,Gentiana wingecarribiensis,,Gentiana,Gentianaceae,species,APC,accepted,Magnoliidae,NSW,Gentiana wingecarribiensis L.G.Adams,https://id.biodiversity.org.au/node/apni/2915610,https://id.biodiversity.org.au/taxon/apni/51436928,https://id.biodiversity.org.au/name/apni/80378,Gentiana wingecarribiensis,https://id.biodiversity.org.au/name/apni/80378,https://id.biodiversity.org.au/taxon/apni/51436871,,Gentiana wingecarribiensis,native +Gentianella barringtonensis,Gentianella barringtonensis,,Gentianella,Gentianaceae,species,APC,accepted,Magnoliidae,NSW,Gentianella barringtonensis (L.G.Adams) Glenny,https://id.biodiversity.org.au/taxon/apni/51301045,https://id.biodiversity.org.au/taxon/apni/51301038,https://id.biodiversity.org.au/name/apni/192277,Gentianella barringtonensis,https://id.biodiversity.org.au/name/apni/192277,https://id.biodiversity.org.au/taxon/apni/51436871,,Gentianella barringtonensis,native +Geranium obtusisepalum,Geranium obtusisepalum,,Geranium,Geraniaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Geranium obtusisepalum Carolin,https://id.biodiversity.org.au/node/apni/2910251,https://id.biodiversity.org.au/taxon/apni/51436946,https://id.biodiversity.org.au/name/apni/82004,Geranium obtusisepalum,https://id.biodiversity.org.au/name/apni/82004,https://id.biodiversity.org.au/taxon/apni/51436947,,Geranium obtusisepalum,native +Geranium purpureum subsp. purpureum,Geranium purpureum,,Geranium,Geraniaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised)",Geranium purpureum Vill.,https://id.biodiversity.org.au/node/apni/2919721,https://id.biodiversity.org.au/taxon/apni/51436946,https://id.biodiversity.org.au/name/apni/82353,Geranium purpureum,https://id.biodiversity.org.au/name/apni/82382,https://id.biodiversity.org.au/taxon/apni/51436947,,Geranium purpureum,naturalised +Gompholobium grandiflorum,Gompholobium grandiflorum,,Gompholobium,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Gompholobium grandiflorum Sm.,https://id.biodiversity.org.au/node/apni/2909013,https://id.biodiversity.org.au/taxon/apni/51436123,https://id.biodiversity.org.au/name/apni/65291,Gompholobium grandiflorum,https://id.biodiversity.org.au/name/apni/65291,https://id.biodiversity.org.au/taxon/apni/51702961,,Gompholobium grandiflorum,native +Goodenia varia,Goodenia varia,,Goodenia,Goodeniaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic",Goodenia varia R.Br.,https://id.biodiversity.org.au/node/apni/2910439,https://id.biodiversity.org.au/taxon/apni/51437012,https://id.biodiversity.org.au/name/apni/92079,Goodenia varia,https://id.biodiversity.org.au/name/apni/92079,https://id.biodiversity.org.au/taxon/apni/51462931,,Goodenia varia,native +Gossia bidwillii,Gossia bidwillii,,Gossia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Gossia bidwillii (Benth.) N.Snow & Guymer,https://id.biodiversity.org.au/taxon/apni/51439972,https://id.biodiversity.org.au/taxon/apni/51439958,https://id.biodiversity.org.au/name/apni/180918,Gossia bidwillii,https://id.biodiversity.org.au/name/apni/180918,https://id.biodiversity.org.au/taxon/apni/51702983,,Gossia bidwillii,native +Grevillea scortechinii,Grevillea scortechinii,,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Grevillea scortechinii (F.Muell. ex Scort.) F.Muell.,https://id.biodiversity.org.au/node/apni/2918803,https://id.biodiversity.org.au/taxon/apni/51445337,https://id.biodiversity.org.au/name/apni/63322,Grevillea scortechinii,https://id.biodiversity.org.au/name/apni/63322,https://id.biodiversity.org.au/taxon/apni/51614274,,Grevillea scortechinii,native +Hakea macraeana,Hakea macraeana,Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied),Hakea,Proteaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Hakea macraeana F.Muell.,https://id.biodiversity.org.au/node/apni/2895080,https://id.biodiversity.org.au/taxon/apni/51445456,https://id.biodiversity.org.au/name/apni/94862,Hakea macraeana [alternative possible names: Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied)],,https://id.biodiversity.org.au/taxon/apni/51614274,,Hakea macraeana,native +Hemisteptia lyrata,Hemisteptia lyrata,,Hemisteptia,Asteraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Hemisteptia lyrata (Bunge) Fisch. & C.A.Mey.,https://id.biodiversity.org.au/taxon/apni/51268530,https://id.biodiversity.org.au/taxon/apni/51268531,https://id.biodiversity.org.au/name/apni/230066,Hemisteptia lyrata,https://id.biodiversity.org.au/name/apni/230066,https://id.biodiversity.org.au/taxon/apni/51695393,,Hemisteptia lyrata,native +Hibbertia crinita,Hibbertia crinita,,Hibbertia,Dilleniaceae,species,APC,accepted,Magnoliidae,"SA, Vic",Hibbertia crinita Toelken,https://id.biodiversity.org.au/node/apni/2899370,https://id.biodiversity.org.au/taxon/apni/51434912,https://id.biodiversity.org.au/name/apni/170069,Hibbertia crinita,https://id.biodiversity.org.au/name/apni/170069,https://id.biodiversity.org.au/taxon/apni/51434913,,Hibbertia crinita,native +Hibiscus brachysiphonius,Hibiscus brachysiphonius,,Hibiscus,Malvaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Hibiscus brachysiphonius F.Muell.,https://id.biodiversity.org.au/node/apni/2891329,https://id.biodiversity.org.au/taxon/apni/51439316,https://id.biodiversity.org.au/name/apni/91736,Hibiscus brachysiphonius,https://id.biodiversity.org.au/name/apni/91736,https://id.biodiversity.org.au/taxon/apni/51439248,,Hibiscus brachysiphonius,native +Hibiscus sturtii,Hibiscus sturtii,,Hibiscus,Malvaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Hibiscus sturtii Hook.,https://id.biodiversity.org.au/taxon/apni/51439064,https://id.biodiversity.org.au/taxon/apni/51439316,https://id.biodiversity.org.au/name/apni/63902,Hibiscus sturtii,https://id.biodiversity.org.au/name/apni/63902,https://id.biodiversity.org.au/taxon/apni/51439248,,Hibiscus sturtii,native +Hypericum elodes,Hypericum elodes,,Hypericum,Hypericaceae,species,APC,accepted,Magnoliidae,NSW (naturalised),Hypericum elodes L.,https://id.biodiversity.org.au/node/apni/2909044,https://id.biodiversity.org.au/taxon/apni/51433733,https://id.biodiversity.org.au/name/apni/136721,Hypericum elodes,https://id.biodiversity.org.au/name/apni/136721,https://id.biodiversity.org.au/taxon/apni/51433734,,Hypericum elodes,naturalised +Imperata cylindrica,Imperata cylindrica,,Imperata,Poaceae,species,APC,accepted,Magnoliidae,"WA, CoI (naturalised), ChI (naturalised), NT, SA, Qld, NSW, LHI (naturalised), ACT, Vic, Tas",Imperata cylindrica (L.) P.Beauv.,https://id.biodiversity.org.au/node/apni/2920993,https://id.biodiversity.org.au/node/apni/2905343,https://id.biodiversity.org.au/name/apni/71806,Imperata cylindrica,https://id.biodiversity.org.au/name/apni/179218,https://id.biodiversity.org.au/taxon/apni/51644646,,Imperata cylindrica,native and naturalised +Indigofera triflora,Indigofera triflora,,Indigofera,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Indigofera triflora Peter G.Wilson & Rowe,https://id.biodiversity.org.au/node/apni/2905193,https://id.biodiversity.org.au/taxon/apni/51436152,https://id.biodiversity.org.au/name/apni/189510,Indigofera triflora,https://id.biodiversity.org.au/name/apni/189510,https://id.biodiversity.org.au/taxon/apni/51702961,,Indigofera triflora,native +Ipomoea cairica,Ipomoea cairica,,Ipomoea,Convolvulaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), ChI (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), NI (naturalised)",Ipomoea cairica (L.) Sweet,https://id.biodiversity.org.au/node/apni/2897935,https://id.biodiversity.org.au/taxon/apni/51433921,https://id.biodiversity.org.au/name/apni/93713,Ipomoea cairica,https://id.biodiversity.org.au/name/apni/93713,https://id.biodiversity.org.au/taxon/apni/51695210,,Ipomoea cairica,naturalised +Isolepis montivaga,Isolepis montivaga,,Isolepis,Cyperaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic, Tas",Isolepis montivaga (S.T.Blake) K.L.Wilson,https://id.biodiversity.org.au/node/apni/2921053,https://id.biodiversity.org.au/taxon/apni/51336324,https://id.biodiversity.org.au/name/apni/74456,Isolepis montivaga,https://id.biodiversity.org.au/name/apni/74456,https://id.biodiversity.org.au/taxon/apni/51460154,,Isolepis montivaga,native +Isotoma axillaris,Isotoma axillaris,,Isotoma,Campanulaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic",Isotoma axillaris Lindl.,https://id.biodiversity.org.au/node/apni/2902056,https://id.biodiversity.org.au/node/apni/2892848,https://id.biodiversity.org.au/name/apni/102004,Isotoma axillaris,https://id.biodiversity.org.au/name/apni/102004,https://id.biodiversity.org.au/taxon/apni/51432853,,Isotoma axillaris,native +Isotoma fluviatilis subsp. fluviatilis,Isotoma fluviatilis subsp. fluviatilis,,Isotoma,Campanulaceae,subspecies,APC,accepted,Magnoliidae,NSW,Isotoma fluviatilis (R.Br.) F.Muell. ex Benth. subsp. fluviatilis,https://id.biodiversity.org.au/node/apni/2897543,https://id.biodiversity.org.au/node/apni/2892848,https://id.biodiversity.org.au/name/apni/102114,Isotoma fluviatilis subsp. fluviatilis,https://id.biodiversity.org.au/name/apni/102114,https://id.biodiversity.org.au/taxon/apni/51432853,Isotoma fluviatilis subsp. fluviatilis,Isotoma fluviatilis,native +Juncus acutus subsp. acutus,Juncus acutus subsp. acutus,,Juncus,Juncaceae,subspecies,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), Qld (naturalised), NSW (naturalised), Vic (naturalised)",Juncus acutus L. subsp. acutus,https://id.biodiversity.org.au/node/apni/2887983,https://id.biodiversity.org.au/taxon/apni/51438170,https://id.biodiversity.org.au/name/apni/182490,Juncus acutus subsp. acutus,https://id.biodiversity.org.au/name/apni/182490,https://id.biodiversity.org.au/taxon/apni/51438171,Juncus acutus subsp. acutus,Juncus acutus,naturalised +Juncus kraussii,Juncus kraussii,,Juncus,Juncaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic, Tas",Juncus kraussii Hochst.,https://id.biodiversity.org.au/node/apni/2900900,https://id.biodiversity.org.au/taxon/apni/51438170,https://id.biodiversity.org.au/name/apni/55859,Juncus kraussii,https://id.biodiversity.org.au/name/apni/55859,https://id.biodiversity.org.au/taxon/apni/51438171,,Juncus kraussii,native +Lantana montevidensis,Lantana montevidensis,,Lantana,Verbenaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), Qld (naturalised), NSW (naturalised), NI (doubtfully naturalised)",Lantana montevidensis (Spreng.) Briq.,https://id.biodiversity.org.au/node/apni/2894994,https://id.biodiversity.org.au/taxon/apni/51448661,https://id.biodiversity.org.au/name/apni/70044,Lantana montevidensis,https://id.biodiversity.org.au/name/apni/70044,https://id.biodiversity.org.au/taxon/apni/51448662,,Lantana montevidensis,naturalised +Lepidium africanum,Lepidium africanum,,Lepidium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Lepidium africanum (Burm.f.) DC.,https://id.biodiversity.org.au/node/apni/2887818,https://id.biodiversity.org.au/taxon/apni/51612686,https://id.biodiversity.org.au/name/apni/68961,Lepidium africanum,https://id.biodiversity.org.au/name/apni/68961,https://id.biodiversity.org.au/taxon/apni/51612687,,Lepidium africanum,naturalised +Lepidium foliosum,Lepidium foliosum,,Lepidium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Lepidium foliosum Desv.,https://id.biodiversity.org.au/node/apni/2908453,https://id.biodiversity.org.au/taxon/apni/51612686,https://id.biodiversity.org.au/name/apni/69389,Lepidium foliosum,https://id.biodiversity.org.au/name/apni/69389,https://id.biodiversity.org.au/taxon/apni/51612687,,Lepidium foliosum,native +Lepidium oxytrichum,Lepidium oxytrichum,,Lepidium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Lepidium oxytrichum Sprague,https://id.biodiversity.org.au/node/apni/2915883,https://id.biodiversity.org.au/taxon/apni/51612686,https://id.biodiversity.org.au/name/apni/84027,Lepidium oxytrichum,https://id.biodiversity.org.au/name/apni/84027,https://id.biodiversity.org.au/taxon/apni/51612687,,Lepidium oxytrichum,native +Lepidosperma gladiatum,Lepidosperma gladiatum,,Lepidosperma,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Lepidosperma gladiatum Labill.,https://id.biodiversity.org.au/node/apni/2896726,https://id.biodiversity.org.au/taxon/apni/51434499,https://id.biodiversity.org.au/name/apni/85937,Lepidosperma gladiatum,https://id.biodiversity.org.au/name/apni/85937,https://id.biodiversity.org.au/taxon/apni/51460154,,Lepidosperma gladiatum,native +Leptomeria drupacea,Leptomeria drupacea,,Leptomeria,Santalaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic, Tas",Leptomeria drupacea (Labill.) Druce,https://id.biodiversity.org.au/node/apni/2892780,https://id.biodiversity.org.au/node/apni/2897704,https://id.biodiversity.org.au/name/apni/61625,Leptomeria drupacea,https://id.biodiversity.org.au/name/apni/61625,https://id.biodiversity.org.au/taxon/apni/51447154,,Leptomeria drupacea,native +Leptospermum continentale,Leptospermum continentale,,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic",Leptospermum continentale Joy Thomps.,https://id.biodiversity.org.au/node/apni/2917147,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/81291,Leptospermum continentale,https://id.biodiversity.org.au/name/apni/81291,https://id.biodiversity.org.au/taxon/apni/51702983,,Leptospermum continentale,native +Leptospermum obovatum,Leptospermum obovatum,,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Leptospermum obovatum Sweet,https://id.biodiversity.org.au/node/apni/2891711,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/99608,Leptospermum obovatum,https://id.biodiversity.org.au/name/apni/99608,https://id.biodiversity.org.au/taxon/apni/51702983,,Leptospermum obovatum,native +Leucopogon amplexicaulis,Leucopogon amplexicaulis,,Leucopogon,Ericaceae,species,APC,accepted,Magnoliidae,NSW,Leucopogon amplexicaulis (Rudge) R.Br.,https://id.biodiversity.org.au/node/apni/2896081,https://id.biodiversity.org.au/taxon/apni/51435325,https://id.biodiversity.org.au/name/apni/106715,Leucopogon amplexicaulis,https://id.biodiversity.org.au/name/apni/106715,https://id.biodiversity.org.au/taxon/apni/51436079,,Leucopogon amplexicaulis,native +Lobelia pedunculata,Lobelia pedunculata,,Lobelia,Campanulaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic, Tas",Lobelia pedunculata R.Br.,https://id.biodiversity.org.au/node/apni/2901444,https://id.biodiversity.org.au/taxon/apni/51432852,https://id.biodiversity.org.au/name/apni/106999,Lobelia pedunculata,https://id.biodiversity.org.au/name/apni/106999,https://id.biodiversity.org.au/taxon/apni/51432853,,Lobelia pedunculata,native +Lobelia trigonocaulis,Lobelia trigonocaulis,,Lobelia,Campanulaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Lobelia trigonocaulis F.Muell.,https://id.biodiversity.org.au/node/apni/2901863,https://id.biodiversity.org.au/taxon/apni/51432852,https://id.biodiversity.org.au/name/apni/107808,Lobelia trigonocaulis,https://id.biodiversity.org.au/name/apni/107808,https://id.biodiversity.org.au/taxon/apni/51432853,,Lobelia trigonocaulis,native +Lotononis bainesii,Lotononis bainesii,,Lotononis,Fabaceae,species,APC,accepted,Magnoliidae,"Qld (naturalised), NSW (naturalised)",Lotononis bainesii Baker,https://id.biodiversity.org.au/node/apni/2904277,https://id.biodiversity.org.au/node/apni/2898035,https://id.biodiversity.org.au/name/apni/109834,Lotononis bainesii,https://id.biodiversity.org.au/name/apni/109834,https://id.biodiversity.org.au/taxon/apni/51702961,,Lotononis bainesii,naturalised +Lotus corniculatus,Lotus corniculatus,Lotus preslii (pro parte misapplied) | Lotus uliginosus (pro parte misapplied),Lotus,Fabaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (formerly naturalised), NSW (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Lotus corniculatus L.,https://id.biodiversity.org.au/node/apni/2921302,https://id.biodiversity.org.au/taxon/apni/51436215,https://id.biodiversity.org.au/name/apni/110319,Lotus corniculatus [alternative possible names: Lotus preslii (pro parte misapplied) | Lotus uliginosus (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51702961,,Lotus corniculatus,naturalised +Lupinus polyphyllus,Lupinus polyphyllus,,Lupinus,Fabaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), Vic (naturalised)",Lupinus polyphyllus Lindl.,https://id.biodiversity.org.au/node/apni/2917429,https://id.biodiversity.org.au/node/apni/2918316,https://id.biodiversity.org.au/name/apni/100609,Lupinus polyphyllus,https://id.biodiversity.org.au/name/apni/100609,https://id.biodiversity.org.au/taxon/apni/51702961,,Lupinus polyphyllus,naturalised +Medicago orbicularis,Medicago orbicularis,,Medicago,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (formerly naturalised)",Medicago orbicularis (L.) Bartal.,https://id.biodiversity.org.au/node/apni/2901771,https://id.biodiversity.org.au/taxon/apni/51285690,https://id.biodiversity.org.au/name/apni/59568,Medicago orbicularis,https://id.biodiversity.org.au/name/apni/59568,https://id.biodiversity.org.au/taxon/apni/51702961,,Medicago orbicularis,naturalised +Melichrus procumbens,Melichrus procumbens,,Melichrus,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Melichrus procumbens (Cav.) Druce,https://id.biodiversity.org.au/node/apni/2905836,https://id.biodiversity.org.au/node/apni/2914566,https://id.biodiversity.org.au/name/apni/114051,Melichrus procumbens,https://id.biodiversity.org.au/name/apni/114051,https://id.biodiversity.org.au/taxon/apni/51436079,,Melichrus procumbens,native +Mischocarpus australis,Mischocarpus australis,,Mischocarpus,Sapindaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Mischocarpus australis S.T.Reynolds,https://id.biodiversity.org.au/node/apni/2893744,https://id.biodiversity.org.au/taxon/apni/51389373,https://id.biodiversity.org.au/name/apni/115917,Mischocarpus australis,https://id.biodiversity.org.au/name/apni/115917,https://id.biodiversity.org.au/taxon/apni/51447212,,Mischocarpus australis,native +Muehlenbeckia adpressa,Muehlenbeckia adpressa,,Muehlenbeckia,Polygonaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Muehlenbeckia adpressa (Labill.) Meisn.,https://id.biodiversity.org.au/node/apni/4750977,https://id.biodiversity.org.au/taxon/apni/51291654,https://id.biodiversity.org.au/name/apni/107852,Muehlenbeckia adpressa,https://id.biodiversity.org.au/name/apni/107852,https://id.biodiversity.org.au/taxon/apni/51444856,,Muehlenbeckia adpressa,native +Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,,Myoporum,Scrophulariaceae,subspecies,APC,accepted,Magnoliidae,"Qld, NSW",Myoporum boninense subsp. australe Chinnock,https://id.biodiversity.org.au/node/apni/7957248,https://id.biodiversity.org.au/taxon/apni/51447443,https://id.biodiversity.org.au/name/apni/117892,Myoporum boninense subsp. australe,https://id.biodiversity.org.au/name/apni/117892,https://id.biodiversity.org.au/taxon/apni/51461527,Myoporum boninense subsp. australe,Myoporum boninense,native +Nicotiana glauca,Nicotiana glauca,,Nicotiana,Solanaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (naturalised)",Nicotiana glauca Graham,https://id.biodiversity.org.au/node/apni/2887606,https://id.biodiversity.org.au/taxon/apni/51447689,https://id.biodiversity.org.au/name/apni/77368,Nicotiana glauca,https://id.biodiversity.org.au/name/apni/77368,https://id.biodiversity.org.au/taxon/apni/51447684,,Nicotiana glauca,naturalised +Nicotiana goodspeedii,Nicotiana goodspeedii,,Nicotiana,Solanaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic",Nicotiana goodspeedii H.-M.Wheeler,https://id.biodiversity.org.au/node/apni/2908652,https://id.biodiversity.org.au/taxon/apni/51447689,https://id.biodiversity.org.au/name/apni/77381,Nicotiana goodspeedii,https://id.biodiversity.org.au/name/apni/77381,https://id.biodiversity.org.au/taxon/apni/51447684,,Nicotiana goodspeedii,native +Oxalis corniculata,Oxalis corniculata,,Oxalis,Oxalidaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), ChI (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Oxalis corniculata L.,https://id.biodiversity.org.au/node/apni/2909588,https://id.biodiversity.org.au/taxon/apni/51442068,https://id.biodiversity.org.au/name/apni/89460,Oxalis corniculata,https://id.biodiversity.org.au/name/apni/89460,https://id.biodiversity.org.au/taxon/apni/51442069,,Oxalis corniculata,naturalised +Pandorea pandorana subsp. austrocaledonica,Pandorea pandorana,,Pandorea,Bignoniaceae,species,APC,accepted,Magnoliidae,"WA, SA (native and naturalised), Qld, NSW, LHI, NI (presumed extinct), Vic (native and naturalised), Tas",Pandorea pandorana (Andrews) Steenis,https://id.biodiversity.org.au/taxon/apni/51269199,https://id.biodiversity.org.au/taxon/apni/51269200,https://id.biodiversity.org.au/name/apni/91117,Pandorea pandorana,https://id.biodiversity.org.au/name/apni/141640,https://id.biodiversity.org.au/taxon/apni/51439229,,Pandorea pandorana,native and naturalised +Paraserianthes lophantha,Paraserianthes lophantha,,Paraserianthes,Fabaceae,species,APC,accepted,Magnoliidae,"WA (native and naturalised), SA (naturalised), NSW (naturalised), NI (naturalised), Vic (naturalised), Tas (naturalised)",Paraserianthes lophantha (Willd.) I.C.Nielsen,https://id.biodiversity.org.au/taxon/apni/51286820,https://id.biodiversity.org.au/taxon/apni/51286819,https://id.biodiversity.org.au/name/apni/116755,Paraserianthes lophantha,https://id.biodiversity.org.au/name/apni/116755,https://id.biodiversity.org.au/taxon/apni/51702961,,Paraserianthes lophantha,native and naturalised +Parentucellia latifolia,Parentucellia latifolia,,Parentucellia,Orobanchaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Parentucellia latifolia (L.) Caruel,https://id.biodiversity.org.au/taxon/apni/51291069,https://id.biodiversity.org.au/taxon/apni/51291062,https://id.biodiversity.org.au/name/apni/96753,Parentucellia latifolia,https://id.biodiversity.org.au/name/apni/96753,https://id.biodiversity.org.au/taxon/apni/51291037,,Parentucellia latifolia,naturalised +Hypoxis glabella var. glabella,Pauridia glabella var. glabella,,Pauridia,Hypoxidaceae,variety,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Pauridia glabella (R.Br.) Snijman & Kocyan var. glabella,https://id.biodiversity.org.au/node/apni/7455351,https://id.biodiversity.org.au/taxon/apni/51437983,https://id.biodiversity.org.au/name/apni/244102,Pauridia glabella var. glabella,https://id.biodiversity.org.au/name/apni/81442,https://id.biodiversity.org.au/taxon/apni/51437984,Pauridia glabella var. glabella,Pauridia glabella,native +Phlegmatospermum cochlearinum,Phlegmatospermum cochlearinum,,Phlegmatospermum,Brassicaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic",Phlegmatospermum cochlearinum (F.Muell.) O.E.Schulz,https://id.biodiversity.org.au/node/apni/2915554,https://id.biodiversity.org.au/node/apni/2897988,https://id.biodiversity.org.au/name/apni/81861,Phlegmatospermum cochlearinum,https://id.biodiversity.org.au/name/apni/81861,https://id.biodiversity.org.au/taxon/apni/51612687,,Phlegmatospermum cochlearinum,native +Phyla nodiflora,Phyla nodiflora,,Phyla,Verbenaceae,species,APC,accepted,Magnoliidae,"WA (native and naturalised), CoI (naturalised), NT, Qld, NSW (naturalised)",Phyla nodiflora (L.) Greene,https://id.biodiversity.org.au/node/apni/2907374,https://id.biodiversity.org.au/node/apni/2892182,https://id.biodiversity.org.au/name/apni/74617,Phyla nodiflora,https://id.biodiversity.org.au/name/apni/74617,https://id.biodiversity.org.au/taxon/apni/51448662,,Phyla nodiflora,native and naturalised +Picris barbarorum,Picris barbarorum,,Picris,Asteraceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic (presumed extinct)",Picris barbarorum Lindl.,https://id.biodiversity.org.au/node/apni/2916052,https://id.biodiversity.org.au/node/apni/7890078,https://id.biodiversity.org.au/name/apni/110349,Picris barbarorum,https://id.biodiversity.org.au/name/apni/110349,https://id.biodiversity.org.au/taxon/apni/51695393,,Picris barbarorum,native +Pimelea ligustrina subsp. ligustrina,Pimelea ligustrina subsp. ligustrina,,Pimelea,Thymelaeaceae,subspecies,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Pimelea ligustrina Labill. subsp. ligustrina,https://id.biodiversity.org.au/node/apni/2889686,https://id.biodiversity.org.au/taxon/apni/51449000,https://id.biodiversity.org.au/name/apni/69062,Pimelea ligustrina subsp. ligustrina,https://id.biodiversity.org.au/name/apni/69062,https://id.biodiversity.org.au/taxon/apni/51449001,Pimelea ligustrina subsp. ligustrina,Pimelea ligustrina,native +Pinus pinea,Pinus pinea,,Pinus,Pinaceae,species,APC,accepted,Pinidae,"WA (naturalised), NSW (naturalised), Vic (naturalised)",Pinus pinea L.,https://id.biodiversity.org.au/node/apni/2904478,https://id.biodiversity.org.au/node/apni/2902806,https://id.biodiversity.org.au/name/apni/171468,Pinus pinea,https://id.biodiversity.org.au/name/apni/171468,https://id.biodiversity.org.au/node/apni/7742574,,Pinus pinea,naturalised +Pisum sativum var. arvense,Pisum sativum var. arvense,,Pisum,Fabaceae,variety,APC,accepted,Magnoliidae,NSW (naturalised),Pisum sativum var. arvense (L.) Poir.,https://id.biodiversity.org.au/node/apni/2920606,https://id.biodiversity.org.au/node/apni/2898529,https://id.biodiversity.org.au/name/apni/153418,Pisum sativum var. arvense,https://id.biodiversity.org.au/name/apni/153418,https://id.biodiversity.org.au/taxon/apni/51702961,Pisum sativum var. arvense,Pisum sativum,naturalised +Pittosporum erioloma,Pittosporum erioloma,,Pittosporum,Pittosporaceae,species,APC,accepted,Magnoliidae,LHI,Pittosporum erioloma C.Moore & F.Muell.,https://id.biodiversity.org.au/node/apni/2891204,https://id.biodiversity.org.au/taxon/apni/51442349,https://id.biodiversity.org.au/name/apni/99523,Pittosporum erioloma,https://id.biodiversity.org.au/name/apni/99523,https://id.biodiversity.org.au/taxon/apni/51442315,,Pittosporum erioloma,native +Plantago turrifera,Plantago turrifera,,Plantago,Plantaginaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW (native and naturalised), Vic","Plantago turrifera B.G.Briggs, Carolin & Pulley",https://id.biodiversity.org.au/node/apni/2895983,https://id.biodiversity.org.au/node/apni/7745425,https://id.biodiversity.org.au/name/apni/79077,Plantago turrifera,https://id.biodiversity.org.au/name/apni/79077,https://id.biodiversity.org.au/taxon/apni/51699383,,Plantago turrifera,native and naturalised +Polycarpon tetraphyllum,Polycarpon tetraphyllum,,Polycarpon,Caryophyllaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Polycarpon tetraphyllum (L.) L.,https://id.biodiversity.org.au/taxon/apni/51270276,https://id.biodiversity.org.au/taxon/apni/51270277,https://id.biodiversity.org.au/name/apni/107982,Polycarpon tetraphyllum,https://id.biodiversity.org.au/name/apni/107982,https://id.biodiversity.org.au/taxon/apni/51432987,,Polycarpon tetraphyllum,naturalised +Potamogeton australiensis,Potamogeton australiensis,,Potamogeton,Potamogetonaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Potamogeton australiensis A.Benn.,https://id.biodiversity.org.au/node/apni/7808489,https://id.biodiversity.org.au/node/apni/8770682,https://id.biodiversity.org.au/name/apni/65827,Potamogeton australiensis,https://id.biodiversity.org.au/name/apni/65827,https://id.biodiversity.org.au/taxon/apni/51353530,,Potamogeton australiensis,native +Psoralea pinnata,Psoralea pinnata,,Psoralea,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised), Tas (naturalised)",Psoralea pinnata L.,https://id.biodiversity.org.au/node/apni/2887023,https://id.biodiversity.org.au/node/apni/8771698,https://id.biodiversity.org.au/name/apni/88820,Psoralea pinnata,https://id.biodiversity.org.au/name/apni/88820,https://id.biodiversity.org.au/taxon/apni/51702961,,Psoralea pinnata,naturalised +Pultenaea ferruginea,Pultenaea ferruginea,,Pultenaea,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Pultenaea ferruginea Rudge,https://id.biodiversity.org.au/node/apni/2906803,https://id.biodiversity.org.au/taxon/apni/51436286,https://id.biodiversity.org.au/name/apni/59158,Pultenaea ferruginea,https://id.biodiversity.org.au/name/apni/59158,https://id.biodiversity.org.au/taxon/apni/51702961,,Pultenaea ferruginea,native +Rhodamnia argentea,Rhodamnia argentea,,Rhodamnia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Rhodamnia argentea Benth.,https://id.biodiversity.org.au/node/apni/2919069,https://id.biodiversity.org.au/taxon/apni/51440311,https://id.biodiversity.org.au/name/apni/68532,Rhodamnia argentea,https://id.biodiversity.org.au/name/apni/68532,https://id.biodiversity.org.au/taxon/apni/51702983,,Rhodamnia argentea,native +Rorippa gigantea,Rorippa gigantea,,Rorippa,Brassicaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Rorippa gigantea (Hook.) Garn.-Jones,https://id.biodiversity.org.au/node/apni/2920330,https://id.biodiversity.org.au/node/apni/8442201,https://id.biodiversity.org.au/name/apni/75950,Rorippa gigantea,https://id.biodiversity.org.au/name/apni/75950,https://id.biodiversity.org.au/taxon/apni/51612687,,Rorippa gigantea,native +Rubus parvifolius,Rubus parvifolius,,Rubus,Rosaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Rubus parvifolius L.,https://id.biodiversity.org.au/node/apni/2901867,https://id.biodiversity.org.au/taxon/apni/51446575,https://id.biodiversity.org.au/name/apni/85986,Rubus parvifolius,https://id.biodiversity.org.au/name/apni/85986,https://id.biodiversity.org.au/taxon/apni/51446278,,Rubus parvifolius,native +Salix alba,Salix alba,,Salix,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised)",Salix alba L.,https://id.biodiversity.org.au/node/apni/2896377,https://id.biodiversity.org.au/node/apni/8905801,https://id.biodiversity.org.au/name/apni/59687,Salix alba [alternative possible names: NA],,https://id.biodiversity.org.au/taxon/apni/51436847,,Salix alba,naturalised +Schenkia australis,Schenkia australis,,Schenkia,Gentianaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic, Tas",Schenkia australis (R.Br.) G.Mans.,https://id.biodiversity.org.au/taxon/apni/51436897,https://id.biodiversity.org.au/taxon/apni/51436898,https://id.biodiversity.org.au/name/apni/200895,Schenkia australis,https://id.biodiversity.org.au/name/apni/200895,https://id.biodiversity.org.au/taxon/apni/51436871,,Schenkia australis,native +Schoenus apogon,Schoenus apogon,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Schoenus apogon Roem. & Schult.,https://id.biodiversity.org.au/node/apni/2908439,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/109452,Schoenus apogon,https://id.biodiversity.org.au/name/apni/109452,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus apogon,native +Schoenus brevifolius,Schoenus brevifolius,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic, Tas",Schoenus brevifolius R.Br.,https://id.biodiversity.org.au/node/apni/2904000,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/109778,Schoenus brevifolius,https://id.biodiversity.org.au/name/apni/109778,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus brevifolius,native +Schoenus lepidosperma,Schoenus lepidosperma,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Schoenus lepidosperma (F.Muell.) K.L.Wilson,https://id.biodiversity.org.au/node/apni/2893030,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/141376,Schoenus lepidosperma,https://id.biodiversity.org.au/name/apni/243667,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus lepidosperma,native +Schoenus vaginatus,Schoenus vaginatus,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Schoenus vaginatus F.Muell. ex Benth.,https://id.biodiversity.org.au/node/apni/2896591,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/113246,Schoenus vaginatus,https://id.biodiversity.org.au/name/apni/113246,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus vaginatus,native +Scleria rugosa,Scleria rugosa,,Scleria,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Scleria rugosa R.Br.,https://id.biodiversity.org.au/node/apni/2892143,https://id.biodiversity.org.au/taxon/apni/51434752,https://id.biodiversity.org.au/name/apni/64346,Scleria rugosa,https://id.biodiversity.org.au/name/apni/64346,https://id.biodiversity.org.au/taxon/apni/51460154,,Scleria rugosa,native +Senecio longipilus,Senecio longipilus,,Senecio,Asteraceae,species,APC,accepted,Magnoliidae,"NSW, Tas",Senecio longipilus I.Thomps.,https://id.biodiversity.org.au/node/apni/2907653,https://id.biodiversity.org.au/taxon/apni/51614245,https://id.biodiversity.org.au/name/apni/189666,Senecio longipilus,https://id.biodiversity.org.au/name/apni/189666,https://id.biodiversity.org.au/taxon/apni/51695393,,Senecio longipilus,native +Sida goniocarpa,Sida goniocarpa,,Sida,Malvaceae,species,APC,accepted,Magnoliidae,"NT, SA, Qld, NSW",Sida goniocarpa (Benth.) Domin,https://id.biodiversity.org.au/node/apni/2893354,https://id.biodiversity.org.au/taxon/apni/51439283,https://id.biodiversity.org.au/name/apni/73352,Sida goniocarpa,https://id.biodiversity.org.au/name/apni/73352,https://id.biodiversity.org.au/taxon/apni/51439248,,Sida goniocarpa,native +Sigesbeckia orientalis,Sigesbeckia orientalis,,Sigesbeckia,Asteraceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT, SA, Qld, NSW, NI (naturalised), ACT, Vic, Tas (doubtfully naturalised)",Sigesbeckia orientalis L.,https://id.biodiversity.org.au/node/apni/2920819,https://id.biodiversity.org.au/taxon/apni/51432306,https://id.biodiversity.org.au/name/apni/75539,Sigesbeckia orientalis,https://id.biodiversity.org.au/name/apni/75539,https://id.biodiversity.org.au/taxon/apni/51695393,,Sigesbeckia orientalis,native and naturalised +Sisymbrium irio,Sisymbrium irio,,Sisymbrium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Sisymbrium irio L.,https://id.biodiversity.org.au/node/apni/2887936,https://id.biodiversity.org.au/node/apni/2921080,https://id.biodiversity.org.au/name/apni/78148,Sisymbrium irio,https://id.biodiversity.org.au/name/apni/78148,https://id.biodiversity.org.au/taxon/apni/51612687,,Sisymbrium irio,naturalised +Derris involuta,Solori involuta,,Solori,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Solori involuta (Sprague) Sirich. & Adema,https://id.biodiversity.org.au/taxon/apni/51311103,https://id.biodiversity.org.au/taxon/apni/51311094,https://id.biodiversity.org.au/name/apni/4447863,Solori involuta,https://id.biodiversity.org.au/name/apni/87525,https://id.biodiversity.org.au/taxon/apni/51702961,,Solori involuta,native +Sparaxis bulbifera,Sparaxis bulbifera,,Sparaxis,Iridaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised), Tas (naturalised)",Sparaxis bulbifera (L.) Ker Gawl.,https://id.biodiversity.org.au/node/apni/2894715,https://id.biodiversity.org.au/taxon/apni/51438097,https://id.biodiversity.org.au/name/apni/68699,Sparaxis bulbifera,https://id.biodiversity.org.au/name/apni/68699,https://id.biodiversity.org.au/taxon/apni/51438006,,Sparaxis bulbifera,naturalised +Spergularia diandra,Spergularia diandra,,Spergularia,Caryophyllaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised)",Spergularia diandra (Guss.) Heldr.,https://id.biodiversity.org.au/node/apni/2886696,https://id.biodiversity.org.au/taxon/apni/51295406,https://id.biodiversity.org.au/name/apni/83464,Spergularia diandra,https://id.biodiversity.org.au/name/apni/83464,https://id.biodiversity.org.au/taxon/apni/51432987,,Spergularia diandra,naturalised +Sphaeromorphaea littoralis,Sphaeromorphaea littoralis,,Sphaeromorphaea,Asteraceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Sphaeromorphaea littoralis (Retz.) A.R.Bean,https://id.biodiversity.org.au/node/apni/7069871,https://id.biodiversity.org.au/node/apni/7071683,https://id.biodiversity.org.au/name/apni/246779,Sphaeromorphaea littoralis,https://id.biodiversity.org.au/name/apni/246779,https://id.biodiversity.org.au/taxon/apni/51695393,,Sphaeromorphaea littoralis,native +Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia subsp. angustifolia,,Stellaria,Caryophyllaceae,subspecies,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Stellaria angustifolia Hook. subsp. angustifolia,https://id.biodiversity.org.au/node/apni/2890520,https://id.biodiversity.org.au/taxon/apni/51433015,https://id.biodiversity.org.au/name/apni/240421,Stellaria angustifolia subsp. angustifolia,https://id.biodiversity.org.au/name/apni/240421,https://id.biodiversity.org.au/taxon/apni/51432987,Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia,native +Styphelia viridis,Styphelia viridis,,Styphelia,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Styphelia viridis Andrews,https://id.biodiversity.org.au/node/apni/2912747,https://id.biodiversity.org.au/taxon/apni/51435346,https://id.biodiversity.org.au/name/apni/109318,Styphelia viridis,https://id.biodiversity.org.au/name/apni/109318,https://id.biodiversity.org.au/taxon/apni/51436079,,Styphelia viridis,native +Swainsona cadellii,Swainsona cadellii,,Swainsona,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Swainsona cadellii F.Muell. ex C.Moore,https://id.biodiversity.org.au/node/apni/2904099,https://id.biodiversity.org.au/taxon/apni/51436313,https://id.biodiversity.org.au/name/apni/76870,Swainsona cadellii,https://id.biodiversity.org.au/name/apni/76870,https://id.biodiversity.org.au/taxon/apni/51702961,,Swainsona cadellii,native +Teucrium puberulum,Teucrium puberulum,,Teucrium,Lamiaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Teucrium puberulum (F.Muell.) Kattari & Bräuchler,https://id.biodiversity.org.au/taxon/apni/51288087,https://id.biodiversity.org.au/taxon/apni/51438311,https://id.biodiversity.org.au/name/apni/7660439,Teucrium puberulum,https://id.biodiversity.org.au/name/apni/7660439,https://id.biodiversity.org.au/taxon/apni/51696573,,Teucrium puberulum,native +Thelymitra kangaloonica,Thelymitra kangaloonica,,Thelymitra,Orchidaceae,species,APC,accepted,Magnoliidae,NSW,Thelymitra kangaloonica Jeanes,https://id.biodiversity.org.au/taxon/apni/51414328,https://id.biodiversity.org.au/taxon/apni/51631246,https://id.biodiversity.org.au/name/apni/233692,Thelymitra kangaloonica,https://id.biodiversity.org.au/name/apni/233692,https://id.biodiversity.org.au/taxon/apni/51697009,,Thelymitra kangaloonica,native +Thesium australe,Thesium australe,,Thesium,Santalaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic, Tas (presumed extinct)",Thesium australe R.Br.,https://id.biodiversity.org.au/node/apni/2891975,https://id.biodiversity.org.au/node/apni/2913858,https://id.biodiversity.org.au/name/apni/56224,Thesium australe,https://id.biodiversity.org.au/name/apni/56224,https://id.biodiversity.org.au/taxon/apni/51447154,,Thesium australe,native +Trifolium dubium,Trifolium dubium,,Trifolium,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Trifolium dubium Sibth.,https://id.biodiversity.org.au/taxon/apni/51436351,https://id.biodiversity.org.au/taxon/apni/51436341,https://id.biodiversity.org.au/name/apni/115704,Trifolium dubium,https://id.biodiversity.org.au/name/apni/115704,https://id.biodiversity.org.au/taxon/apni/51702961,,Trifolium dubium,naturalised +Veronica catenata,Veronica catenata,,Veronica,Plantaginaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), Vic (naturalised)",Veronica catenata Pennell,https://id.biodiversity.org.au/node/apni/2897164,https://id.biodiversity.org.au/taxon/apni/51632390,https://id.biodiversity.org.au/name/apni/67965,Veronica catenata,https://id.biodiversity.org.au/name/apni/67965,https://id.biodiversity.org.au/taxon/apni/51699383,,Veronica catenata,naturalised +Veronica derwentiana,Veronica derwentiana,,Veronica,Plantaginaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Veronica derwentiana Andrews,https://id.biodiversity.org.au/node/apni/2917078,https://id.biodiversity.org.au/taxon/apni/51632390,https://id.biodiversity.org.au/name/apni/68107,Veronica derwentiana,https://id.biodiversity.org.au/name/apni/68107,https://id.biodiversity.org.au/taxon/apni/51699383,,Veronica derwentiana,native +Wahlenbergia luteola,Wahlenbergia luteola,,Wahlenbergia,Campanulaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic",Wahlenbergia luteola P.J.Sm.,https://id.biodiversity.org.au/node/apni/2916523,https://id.biodiversity.org.au/taxon/apni/51432869,https://id.biodiversity.org.au/name/apni/73194,Wahlenbergia luteola,https://id.biodiversity.org.au/name/apni/73194,https://id.biodiversity.org.au/taxon/apni/51432853,,Wahlenbergia luteola,native diff --git a/tests/testthat/examples/Test_2023_4/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_4/output/taxonomic_updates.csv index a9c0b2f7..f5a8f979 100644 --- a/tests/testthat/examples/Test_2023_4/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_4/output/taxonomic_updates.csv @@ -1,188 +1,188 @@ dataset_id,original_name,aligned_name,taxonomic_resolution,taxon_name -Test_2023_4,Abildgaardia ovata,Abildgaardia ovata,, -Test_2023_4,Acacia alpina,Acacia alpina,, -Test_2023_4,Acacia beadleana,Acacia beadleana,, -Test_2023_4,Acacia bulgaensis,Acacia bulgaensis,, -Test_2023_4,Acacia caroleae,Acacia caroleae,, -Test_2023_4,Acacia crassa,Acacia crassa,, -Test_2023_4,Acacia flexifolia,Acacia flexifolia,, -Test_2023_4,Acacia gladiiformis,Acacia gladiiformis,, -Test_2023_4,Acacia havilandiorum,Acacia havilandiorum,, -Test_2023_4,Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx subsp. leiocalyx,, -Test_2023_4,Acacia myrtifolia,Acacia myrtifolia,, -Test_2023_4,Acacia ramulosa var. ramulosa,Acacia ramulosa var. ramulosa,, -Test_2023_4,Acacia spectabilis,Acacia spectabilis,, -Test_2023_4,Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis subsp. Glabrous form (M.Hancock 94),, -Test_2023_4,Acronychia littoralis,Acronychia littoralis,, -Test_2023_4,Adriana tomentosa,Adriana tomentosa,, -Test_2023_4,Alectryon coriaceus,Alectryon coriaceus,, -Test_2023_4,Alectryon oleifolius,Alectryon oleifolius,, -Test_2023_4,Alectryon subdentatus,Alectryon subdentatus,, -Test_2023_4,Amyema preissii,Amyema preissii,, -Test_2023_4,Angophora leiocarpa,Angophora leiocarpa,, -Test_2023_4,Apophyllum anomalum,Apophyllum anomalum,, -Test_2023_4,Arbutus unedo,Arbutus unedo,, -Test_2023_4,Australina pusilla,Australina pusilla,, -Test_2023_4,Burmannia disticha,Burmannia disticha,, -Test_2023_4,Bursaria spinosa subsp. spinosa,Bursaria spinosa subsp. spinosa,, -Test_2023_4,Calendula arvensis,Calendula arvensis,, -Test_2023_4,Callistemon purpurascens,Callistemon purpurascens,, -Test_2023_4,Carex cephalotes,Carex cephalotes,, -Test_2023_4,Carex leporina,Carex leporina,, -Test_2023_4,Carex raleighii,Carex raleighii,, -Test_2023_4,Carmichaelia exsul,Carmichaelia exsul,, -Test_2023_4,Cassinia compacta,Cassinia compacta,, -Test_2023_4,Castanospermum australe,Castanospermum australe,, -Test_2023_4,Centaurium tenuiflorum,Centaurium tenuiflorum,, -Test_2023_4,Cestrum nocturnum,Cestrum nocturnum,, -Test_2023_4,Chthonocephalus pseudevax,Chthonocephalus pseudevax,, -Test_2023_4,Claoxylon australe,Claoxylon australe,, -Test_2023_4,Commersonia amystia,Commersonia amystia,, -Test_2023_4,Commersonia salviifolia,Commersonia salviifolia,, -Test_2023_4,Convolvulus farinosus,Convolvulus farinosus,, -Test_2023_4,Coprosma niphophila,Coprosma niphophila,, -Test_2023_4,Coprosma nivalis,Coprosma nivalis,, -Test_2023_4,Correa alba,Correa alba,, -Test_2023_4,Corymbia citriodora,Corymbia citriodora,, -Test_2023_4,Corymbia eximia,Corymbia eximia,, -Test_2023_4,Crassula decumbens,Crassula decumbens,, -Test_2023_4,Crassula peduncularis,Crassula peduncularis,, -Test_2023_4,Crotalaria brevis,Crotalaria brevis,, -Test_2023_4,Crotalaria grahamiana,Crotalaria grahamiana,, -Test_2023_4,Crotalaria lanceolata,Crotalaria lanceolata,, -Test_2023_4,Cylindropuntia kleiniae,Cylindropuntia kleiniae,, -Test_2023_4,Cyperus albostriatus,Cyperus albostriatus,, -Test_2023_4,Cyperus betchei,Cyperus betchei,, -Test_2023_4,Cyperus bulbosus,Cyperus bulbosus,, -Test_2023_4,Cyperus laevigatus,Cyperus laevigatus,, -Test_2023_4,Cyperus sculptus,Cyperus sculptus,, -Test_2023_4,Dampiera fusca,Dampiera fusca,, -Test_2023_4,Davidsonia johnsonii,Davidsonia johnsonii,, -Test_2023_4,Daviesia arenaria,Daviesia arenaria,, -Test_2023_4,Derris involuta,Derris involuta,, -Test_2023_4,Dichromochlamys dentatifolia,Dichromochlamys dentatifolia,, -Test_2023_4,Dillwynia cinerascens,Dillwynia cinerascens,, -Test_2023_4,Dillwynia floribunda,Dillwynia floribunda,, -Test_2023_4,Dinosperma erythrococcum,Dinosperma erythrococcum,, -Test_2023_4,Dodonaea petiolaris,Dodonaea petiolaris,, -Test_2023_4,Dodonaea truncatiales,Dodonaea truncatiales,, -Test_2023_4,Dovyalis caffra,Dovyalis caffra,, -Test_2023_4,Elaeocarpus grandis,Elaeocarpus grandis,, -Test_2023_4,Eleocharis pallens,Eleocharis pallens,, -Test_2023_4,Endiandra globosa,Endiandra globosa,, -Test_2023_4,Endiandra muelleri,Endiandra muelleri,, -Test_2023_4,Epilobium gunnianum,Epilobium gunnianum,, -Test_2023_4,Eremophila deserti,Eremophila deserti,, -Test_2023_4,Eremophila oppositifolia,Eremophila oppositifolia,, -Test_2023_4,Erigeron conyzoides,Erigeron conyzoides,, -Test_2023_4,Erythroxylum australe,Erythroxylum australe,, -Test_2023_4,Escallonia bifida,Escallonia bifida,, -Test_2023_4,Eucalyptus badjensis,Eucalyptus badjensis,, -Test_2023_4,Eucalyptus camphora,Eucalyptus camphora,, -Test_2023_4,Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,, -Test_2023_4,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,, -Test_2023_4,Eucalyptus muelleriana,Eucalyptus muelleriana,, -Test_2023_4,Eucalyptus nandewarica,Eucalyptus nandewarica,, -Test_2023_4,Eucalyptus oblonga,Eucalyptus oblonga,, -Test_2023_4,Eucalyptus olida,Eucalyptus olida,, -Test_2023_4,Eucalyptus pulverulenta,Eucalyptus pulverulenta,, -Test_2023_4,Eucalyptus recurva,Eucalyptus recurva,, -Test_2023_4,Eucalyptus rossii,Eucalyptus rossii,, -Test_2023_4,Eucalyptus scias,Eucalyptus scias,, -Test_2023_4,Eucalyptus viminalis,Eucalyptus viminalis,, -Test_2023_4,Eucalyptus yangoura,Eucalyptus yangoura,, -Test_2023_4,Eucalyptus youmanii,Eucalyptus youmanii,, -Test_2023_4,Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata var. queenslandica,, -Test_2023_4,Exocarpos homalocladus,Exocarpos homalocladus,, -Test_2023_4,Exocarpos sparteus,Exocarpos sparteus,, -Test_2023_4,Ficus henneana,Ficus henneana,, -Test_2023_4,Freesia hybrid,Freesia hybrid,, -Test_2023_4,Freesia laxa,Freesia laxa,, -Test_2023_4,Geijera salicifolia,Geijera salicifolia,, -Test_2023_4,Gentiana wingecarribiensis,Gentiana wingecarribiensis,, -Test_2023_4,Gentianella barringtonensis,Gentianella barringtonensis,, -Test_2023_4,Geranium obtusisepalum,Geranium obtusisepalum,, -Test_2023_4,Geranium purpureum subsp. purpureum,Geranium purpureum subsp. purpureum,, -Test_2023_4,Gompholobium grandiflorum,Gompholobium grandiflorum,, -Test_2023_4,Goodenia varia,Goodenia varia,, -Test_2023_4,Gossia bidwillii,Gossia bidwillii,, -Test_2023_4,Grevillea scortechinii,Grevillea scortechinii,, -Test_2023_4,Hakea macraeana,Hakea macraeana,, -Test_2023_4,Hemisteptia lyrata,Hemisteptia lyrata,, -Test_2023_4,Hibbertia crinita,Hibbertia crinita,, -Test_2023_4,Hibiscus brachysiphonius,Hibiscus brachysiphonius,, -Test_2023_4,Hibiscus sturtii,Hibiscus sturtii,, -Test_2023_4,Hypericum elodes,Hypericum elodes,, -Test_2023_4,Hypoxis glabella var. glabella,Hypoxis glabella var. glabella,, -Test_2023_4,Imperata cylindrica,Imperata cylindrica,, -Test_2023_4,Indigofera triflora,Indigofera triflora,, -Test_2023_4,Ipomoea cairica,Ipomoea cairica,, -Test_2023_4,Isolepis montivaga,Isolepis montivaga,, -Test_2023_4,Isotoma axillaris,Isotoma axillaris,, -Test_2023_4,Isotoma fluviatilis subsp. fluviatilis,Isotoma fluviatilis subsp. fluviatilis,, -Test_2023_4,Juncus acutus subsp. acutus,Juncus acutus subsp. acutus,, -Test_2023_4,Juncus kraussii,Juncus kraussii,, -Test_2023_4,Lantana montevidensis,Lantana montevidensis,, -Test_2023_4,Lepidium africanum,Lepidium africanum,, -Test_2023_4,Lepidium foliosum,Lepidium foliosum,, -Test_2023_4,Lepidium oxytrichum,Lepidium oxytrichum,, -Test_2023_4,Lepidosperma gladiatum,Lepidosperma gladiatum,, -Test_2023_4,Leptomeria drupacea,Leptomeria drupacea,, -Test_2023_4,Leptospermum continentale,Leptospermum continentale,, -Test_2023_4,Leptospermum obovatum,Leptospermum obovatum,, -Test_2023_4,Leucopogon amplexicaulis,Leucopogon amplexicaulis,, -Test_2023_4,Lobelia pedunculata,Lobelia pedunculata,, -Test_2023_4,Lobelia trigonocaulis,Lobelia trigonocaulis,, -Test_2023_4,Lotononis bainesii,Lotononis bainesii,, -Test_2023_4,Lotus corniculatus,Lotus corniculatus,, -Test_2023_4,Lupinus polyphyllus,Lupinus polyphyllus,, -Test_2023_4,Medicago orbicularis,Medicago orbicularis,, -Test_2023_4,Melichrus procumbens,Melichrus procumbens,, -Test_2023_4,Mischocarpus australis,Mischocarpus australis,, -Test_2023_4,Muehlenbeckia adpressa,Muehlenbeckia adpressa,, -Test_2023_4,Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,, -Test_2023_4,Nicotiana glauca,Nicotiana glauca,, -Test_2023_4,Nicotiana goodspeedii,Nicotiana goodspeedii,, -Test_2023_4,Oxalis corniculata,Oxalis corniculata,, -Test_2023_4,Pandorea pandorana subsp. austrocaledonica,Pandorea pandorana subsp. austrocaledonica,, -Test_2023_4,Paraserianthes lophantha,Paraserianthes lophantha,, -Test_2023_4,Parentucellia latifolia,Parentucellia latifolia,, -Test_2023_4,Phlegmatospermum cochlearinum,Phlegmatospermum cochlearinum,, -Test_2023_4,Phyla nodiflora,Phyla nodiflora,, -Test_2023_4,Picris barbarorum,Picris barbarorum,, -Test_2023_4,Pimelea ligustrina subsp. ligustrina,Pimelea ligustrina subsp. ligustrina,, -Test_2023_4,Pinus pinea,Pinus pinea,, -Test_2023_4,Pisum sativum var. arvense,Pisum sativum var. arvense,, -Test_2023_4,Pittosporum erioloma,Pittosporum erioloma,, -Test_2023_4,Plantago turrifera,Plantago turrifera,, -Test_2023_4,Polycarpon tetraphyllum,Polycarpon tetraphyllum,, -Test_2023_4,Potamogeton australiensis,Potamogeton australiensis,, -Test_2023_4,Psoralea pinnata,Psoralea pinnata,, -Test_2023_4,Pultenaea ferruginea,Pultenaea ferruginea,, -Test_2023_4,Rhodamnia argentea,Rhodamnia argentea,, -Test_2023_4,Rorippa gigantea,Rorippa gigantea,, -Test_2023_4,Rubus parvifolius,Rubus parvifolius,, -Test_2023_4,Salix alba,Salix alba,, -Test_2023_4,Schenkia australis,Schenkia australis,, -Test_2023_4,Schoenus apogon,Schoenus apogon,, -Test_2023_4,Schoenus brevifolius,Schoenus brevifolius,, -Test_2023_4,Schoenus lepidosperma,Schoenus lepidosperma,, -Test_2023_4,Schoenus vaginatus,Schoenus vaginatus,, -Test_2023_4,Scleria rugosa,Scleria rugosa,, -Test_2023_4,Senecio longipilus,Senecio longipilus,, -Test_2023_4,Sida goniocarpa,Sida goniocarpa,, -Test_2023_4,Sigesbeckia orientalis,Sigesbeckia orientalis,, -Test_2023_4,Sisymbrium irio,Sisymbrium irio,, -Test_2023_4,Sparaxis bulbifera,Sparaxis bulbifera,, -Test_2023_4,Spergularia diandra,Spergularia diandra,, -Test_2023_4,Sphaeromorphaea littoralis,Sphaeromorphaea littoralis,, -Test_2023_4,Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia subsp. angustifolia,, -Test_2023_4,Styphelia viridis,Styphelia viridis,, -Test_2023_4,Swainsona cadellii,Swainsona cadellii,, -Test_2023_4,Teucrium puberulum,Teucrium puberulum,, -Test_2023_4,Thelymitra kangaloonica,Thelymitra kangaloonica,, -Test_2023_4,Thesium australe,Thesium australe,, -Test_2023_4,Trifolium dubium,Trifolium dubium,, -Test_2023_4,Veronica catenata,Veronica catenata,, -Test_2023_4,Veronica derwentiana,Veronica derwentiana,, -Test_2023_4,Wahlenbergia luteola,Wahlenbergia luteola,, +Test_2023_4,Abildgaardia ovata,Abildgaardia ovata,,Abildgaardia ovata +Test_2023_4,Acacia alpina,Acacia alpina,,Acacia alpina +Test_2023_4,Acacia beadleana,Acacia beadleana,,Acacia beadleana +Test_2023_4,Acacia bulgaensis,Acacia bulgaensis,,Acacia bulgaensis +Test_2023_4,Acacia caroleae,Acacia caroleae,,Acacia caroleae +Test_2023_4,Acacia crassa,Acacia crassa,,Acacia crassa +Test_2023_4,Acacia flexifolia,Acacia flexifolia,,Acacia flexifolia +Test_2023_4,Acacia gladiiformis,Acacia gladiiformis,,Acacia gladiiformis +Test_2023_4,Acacia havilandiorum,Acacia havilandiorum,,Acacia havilandiorum +Test_2023_4,Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx subsp. leiocalyx,,Acacia leiocalyx subsp. leiocalyx +Test_2023_4,Acacia myrtifolia,Acacia myrtifolia,,Acacia myrtifolia +Test_2023_4,Acacia ramulosa var. ramulosa,Acacia ramulosa var. ramulosa,,Acacia ramulosa var. ramulosa +Test_2023_4,Acacia spectabilis,Acacia spectabilis,,Acacia spectabilis +Test_2023_4,Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis subsp. Glabrous form (M.Hancock 94),,Acacia terminalis subsp. Glabrous form (M.Hancock 94) +Test_2023_4,Acronychia littoralis,Acronychia littoralis,,Acronychia littoralis +Test_2023_4,Adriana tomentosa,Adriana tomentosa,,Adriana tomentosa +Test_2023_4,Alectryon coriaceus,Alectryon coriaceus,,Alectryon coriaceus +Test_2023_4,Alectryon oleifolius,Alectryon oleifolius,,Alectryon oleifolius +Test_2023_4,Alectryon subdentatus,Alectryon subdentatus,,Alectryon subdentatus +Test_2023_4,Amyema preissii,Amyema preissii,,Amyema preissii +Test_2023_4,Angophora leiocarpa,Angophora leiocarpa,,Angophora leiocarpa +Test_2023_4,Apophyllum anomalum,Apophyllum anomalum,,Capparis anomala +Test_2023_4,Arbutus unedo,Arbutus unedo,,Arbutus unedo +Test_2023_4,Australina pusilla,Australina pusilla,,Australina pusilla +Test_2023_4,Burmannia disticha,Burmannia disticha,,Burmannia disticha +Test_2023_4,Bursaria spinosa subsp. spinosa,Bursaria spinosa subsp. spinosa,,Bursaria spinosa subsp. spinosa +Test_2023_4,Calendula arvensis,Calendula arvensis,,Calendula arvensis +Test_2023_4,Callistemon purpurascens,Callistemon purpurascens,,Callistemon purpurascens +Test_2023_4,Carex cephalotes,Carex cephalotes,,Carex pyrenaica var. cephalotes +Test_2023_4,Carex leporina,Carex leporina,,Carex leporina +Test_2023_4,Carex raleighii,Carex raleighii,,Carex raleighii +Test_2023_4,Carmichaelia exsul,Carmichaelia exsul,,Carmichaelia exsul +Test_2023_4,Cassinia compacta,Cassinia compacta,,Cassinia compacta +Test_2023_4,Castanospermum australe,Castanospermum australe,,Castanospermum australe +Test_2023_4,Centaurium tenuiflorum,Centaurium tenuiflorum,,Centaurium tenuiflorum +Test_2023_4,Cestrum nocturnum,Cestrum nocturnum,,Cestrum nocturnum +Test_2023_4,Chthonocephalus pseudevax,Chthonocephalus pseudevax,,Chthonocephalus pseudevax +Test_2023_4,Claoxylon australe,Claoxylon australe,,Claoxylon australe +Test_2023_4,Commersonia amystia,Commersonia amystia,,Commersonia amystia +Test_2023_4,Commersonia salviifolia,Commersonia salviifolia,,Commersonia salviifolia +Test_2023_4,Convolvulus farinosus,Convolvulus farinosus,,Convolvulus farinosus +Test_2023_4,Coprosma niphophila,Coprosma niphophila,,Coprosma niphophila +Test_2023_4,Coprosma nivalis,Coprosma nivalis,,Coprosma nivalis +Test_2023_4,Correa alba,Correa alba,,Correa alba +Test_2023_4,Corymbia citriodora,Corymbia citriodora,,Corymbia citriodora +Test_2023_4,Corymbia eximia,Corymbia eximia,,Corymbia eximia +Test_2023_4,Crassula decumbens,Crassula decumbens,,Crassula decumbens +Test_2023_4,Crassula peduncularis,Crassula peduncularis,,Crassula peduncularis +Test_2023_4,Crotalaria brevis,Crotalaria brevis,,Crotalaria brevis +Test_2023_4,Crotalaria grahamiana,Crotalaria grahamiana,,Crotalaria grahamiana +Test_2023_4,Crotalaria lanceolata,Crotalaria lanceolata,,Crotalaria lanceolata +Test_2023_4,Cylindropuntia kleiniae,Cylindropuntia kleiniae,,Cylindropuntia kleiniae +Test_2023_4,Cyperus albostriatus,Cyperus albostriatus,,Cyperus albostriatus +Test_2023_4,Cyperus betchei,Cyperus betchei,,Cyperus betchei +Test_2023_4,Cyperus bulbosus,Cyperus bulbosus,,Cyperus bulbosus +Test_2023_4,Cyperus laevigatus,Cyperus laevigatus,,Cyperus laevigatus +Test_2023_4,Cyperus sculptus,Cyperus sculptus,,Cyperus sculptus +Test_2023_4,Dampiera fusca,Dampiera fusca,,Dampiera fusca +Test_2023_4,Davidsonia johnsonii,Davidsonia johnsonii,,Davidsonia johnsonii +Test_2023_4,Daviesia arenaria,Daviesia arenaria,,Daviesia arenaria +Test_2023_4,Derris involuta,Derris involuta,,Solori involuta +Test_2023_4,Dichromochlamys dentatifolia,Dichromochlamys dentatifolia,,Dichromochlamys dentatifolia +Test_2023_4,Dillwynia cinerascens,Dillwynia cinerascens,,Dillwynia cinerascens +Test_2023_4,Dillwynia floribunda,Dillwynia floribunda,,Dillwynia floribunda +Test_2023_4,Dinosperma erythrococcum,Dinosperma erythrococcum,,Dinosperma erythrococcum +Test_2023_4,Dodonaea petiolaris,Dodonaea petiolaris,,Dodonaea petiolaris +Test_2023_4,Dodonaea truncatiales,Dodonaea truncatiales,,Dodonaea truncatiales +Test_2023_4,Dovyalis caffra,Dovyalis caffra,,Dovyalis caffra +Test_2023_4,Elaeocarpus grandis,Elaeocarpus grandis,,Elaeocarpus grandis +Test_2023_4,Eleocharis pallens,Eleocharis pallens,,Eleocharis pallens +Test_2023_4,Endiandra globosa,Endiandra globosa,,Endiandra globosa +Test_2023_4,Endiandra muelleri,Endiandra muelleri,,Endiandra muelleri +Test_2023_4,Epilobium gunnianum,Epilobium gunnianum,,Epilobium gunnianum +Test_2023_4,Eremophila deserti,Eremophila deserti,,Eremophila deserti +Test_2023_4,Eremophila oppositifolia,Eremophila oppositifolia,,Eremophila oppositifolia +Test_2023_4,Erigeron conyzoides,Erigeron conyzoides,,Erigeron conyzoides +Test_2023_4,Erythroxylum australe,Erythroxylum australe,,Erythroxylum australe +Test_2023_4,Escallonia bifida,Escallonia bifida,,Escallonia bifida +Test_2023_4,Eucalyptus badjensis,Eucalyptus badjensis,,Eucalyptus badjensis +Test_2023_4,Eucalyptus camphora,Eucalyptus camphora,,Eucalyptus camphora +Test_2023_4,Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,,Eucalyptus dorrigoensis +Test_2023_4,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,,Eucalyptus leucoxylon subsp. pruinosa +Test_2023_4,Eucalyptus muelleriana,Eucalyptus muelleriana,,Eucalyptus muelleriana +Test_2023_4,Eucalyptus nandewarica,Eucalyptus nandewarica,,Eucalyptus nandewarica +Test_2023_4,Eucalyptus oblonga,Eucalyptus oblonga,,Eucalyptus globoidea +Test_2023_4,Eucalyptus olida,Eucalyptus olida,,Eucalyptus olida +Test_2023_4,Eucalyptus pulverulenta,Eucalyptus pulverulenta,,Eucalyptus pulverulenta +Test_2023_4,Eucalyptus recurva,Eucalyptus recurva,,Eucalyptus recurva +Test_2023_4,Eucalyptus rossii,Eucalyptus rossii,,Eucalyptus rossii +Test_2023_4,Eucalyptus scias,Eucalyptus scias,,Eucalyptus scias +Test_2023_4,Eucalyptus viminalis,Eucalyptus viminalis,,Eucalyptus viminalis +Test_2023_4,Eucalyptus yangoura,Eucalyptus yangoura,,Eucalyptus globoidea +Test_2023_4,Eucalyptus youmanii,Eucalyptus youmanii,,Eucalyptus youmanii +Test_2023_4,Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata var. queenslandica,,Euphorbia inappendiculata var. queenslandica +Test_2023_4,Exocarpos homalocladus,Exocarpos homalocladus,,Exocarpos homalocladus +Test_2023_4,Exocarpos sparteus,Exocarpos sparteus,,Exocarpos sparteus +Test_2023_4,Ficus henneana,Ficus henneana,,Ficus henneana +Test_2023_4,Freesia hybrid,Freesia hybrid,,Freesia leichtlinii subsp. leichtlinii x Freesia leichtlinii subsp. alba +Test_2023_4,Freesia laxa,Freesia laxa,,Freesia laxa +Test_2023_4,Geijera salicifolia,Geijera salicifolia,,Geijera salicifolia +Test_2023_4,Gentiana wingecarribiensis,Gentiana wingecarribiensis,,Gentiana wingecarribiensis +Test_2023_4,Gentianella barringtonensis,Gentianella barringtonensis,,Gentianella barringtonensis +Test_2023_4,Geranium obtusisepalum,Geranium obtusisepalum,,Geranium obtusisepalum +Test_2023_4,Geranium purpureum subsp. purpureum,Geranium purpureum subsp. purpureum,,Geranium purpureum +Test_2023_4,Gompholobium grandiflorum,Gompholobium grandiflorum,,Gompholobium grandiflorum +Test_2023_4,Goodenia varia,Goodenia varia,,Goodenia varia +Test_2023_4,Gossia bidwillii,Gossia bidwillii,,Gossia bidwillii +Test_2023_4,Grevillea scortechinii,Grevillea scortechinii,,Grevillea scortechinii +Test_2023_4,Hakea macraeana,Hakea macraeana,,Hakea macraeana +Test_2023_4,Hemisteptia lyrata,Hemisteptia lyrata,,Hemisteptia lyrata +Test_2023_4,Hibbertia crinita,Hibbertia crinita,,Hibbertia crinita +Test_2023_4,Hibiscus brachysiphonius,Hibiscus brachysiphonius,,Hibiscus brachysiphonius +Test_2023_4,Hibiscus sturtii,Hibiscus sturtii,,Hibiscus sturtii +Test_2023_4,Hypericum elodes,Hypericum elodes,,Hypericum elodes +Test_2023_4,Hypoxis glabella var. glabella,Hypoxis glabella var. glabella,,Pauridia glabella var. glabella +Test_2023_4,Imperata cylindrica,Imperata cylindrica,,Imperata cylindrica +Test_2023_4,Indigofera triflora,Indigofera triflora,,Indigofera triflora +Test_2023_4,Ipomoea cairica,Ipomoea cairica,,Ipomoea cairica +Test_2023_4,Isolepis montivaga,Isolepis montivaga,,Isolepis montivaga +Test_2023_4,Isotoma axillaris,Isotoma axillaris,,Isotoma axillaris +Test_2023_4,Isotoma fluviatilis subsp. fluviatilis,Isotoma fluviatilis subsp. fluviatilis,,Isotoma fluviatilis subsp. fluviatilis +Test_2023_4,Juncus acutus subsp. acutus,Juncus acutus subsp. acutus,,Juncus acutus subsp. acutus +Test_2023_4,Juncus kraussii,Juncus kraussii,,Juncus kraussii +Test_2023_4,Lantana montevidensis,Lantana montevidensis,,Lantana montevidensis +Test_2023_4,Lepidium africanum,Lepidium africanum,,Lepidium africanum +Test_2023_4,Lepidium foliosum,Lepidium foliosum,,Lepidium foliosum +Test_2023_4,Lepidium oxytrichum,Lepidium oxytrichum,,Lepidium oxytrichum +Test_2023_4,Lepidosperma gladiatum,Lepidosperma gladiatum,,Lepidosperma gladiatum +Test_2023_4,Leptomeria drupacea,Leptomeria drupacea,,Leptomeria drupacea +Test_2023_4,Leptospermum continentale,Leptospermum continentale,,Leptospermum continentale +Test_2023_4,Leptospermum obovatum,Leptospermum obovatum,,Leptospermum obovatum +Test_2023_4,Leucopogon amplexicaulis,Leucopogon amplexicaulis,,Leucopogon amplexicaulis +Test_2023_4,Lobelia pedunculata,Lobelia pedunculata,,Lobelia pedunculata +Test_2023_4,Lobelia trigonocaulis,Lobelia trigonocaulis,,Lobelia trigonocaulis +Test_2023_4,Lotononis bainesii,Lotononis bainesii,,Lotononis bainesii +Test_2023_4,Lotus corniculatus,Lotus corniculatus,,Lotus corniculatus +Test_2023_4,Lupinus polyphyllus,Lupinus polyphyllus,,Lupinus polyphyllus +Test_2023_4,Medicago orbicularis,Medicago orbicularis,,Medicago orbicularis +Test_2023_4,Melichrus procumbens,Melichrus procumbens,,Melichrus procumbens +Test_2023_4,Mischocarpus australis,Mischocarpus australis,,Mischocarpus australis +Test_2023_4,Muehlenbeckia adpressa,Muehlenbeckia adpressa,,Muehlenbeckia adpressa +Test_2023_4,Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,,Myoporum boninense subsp. australe +Test_2023_4,Nicotiana glauca,Nicotiana glauca,,Nicotiana glauca +Test_2023_4,Nicotiana goodspeedii,Nicotiana goodspeedii,,Nicotiana goodspeedii +Test_2023_4,Oxalis corniculata,Oxalis corniculata,,Oxalis corniculata +Test_2023_4,Pandorea pandorana subsp. austrocaledonica,Pandorea pandorana subsp. austrocaledonica,,Pandorea pandorana +Test_2023_4,Paraserianthes lophantha,Paraserianthes lophantha,,Paraserianthes lophantha +Test_2023_4,Parentucellia latifolia,Parentucellia latifolia,,Parentucellia latifolia +Test_2023_4,Phlegmatospermum cochlearinum,Phlegmatospermum cochlearinum,,Phlegmatospermum cochlearinum +Test_2023_4,Phyla nodiflora,Phyla nodiflora,,Phyla nodiflora +Test_2023_4,Picris barbarorum,Picris barbarorum,,Picris barbarorum +Test_2023_4,Pimelea ligustrina subsp. ligustrina,Pimelea ligustrina subsp. ligustrina,,Pimelea ligustrina subsp. ligustrina +Test_2023_4,Pinus pinea,Pinus pinea,,Pinus pinea +Test_2023_4,Pisum sativum var. arvense,Pisum sativum var. arvense,,Pisum sativum var. arvense +Test_2023_4,Pittosporum erioloma,Pittosporum erioloma,,Pittosporum erioloma +Test_2023_4,Plantago turrifera,Plantago turrifera,,Plantago turrifera +Test_2023_4,Polycarpon tetraphyllum,Polycarpon tetraphyllum,,Polycarpon tetraphyllum +Test_2023_4,Potamogeton australiensis,Potamogeton australiensis,,Potamogeton australiensis +Test_2023_4,Psoralea pinnata,Psoralea pinnata,,Psoralea pinnata +Test_2023_4,Pultenaea ferruginea,Pultenaea ferruginea,,Pultenaea ferruginea +Test_2023_4,Rhodamnia argentea,Rhodamnia argentea,,Rhodamnia argentea +Test_2023_4,Rorippa gigantea,Rorippa gigantea,,Rorippa gigantea +Test_2023_4,Rubus parvifolius,Rubus parvifolius,,Rubus parvifolius +Test_2023_4,Salix alba,Salix alba,,Salix alba +Test_2023_4,Schenkia australis,Schenkia australis,,Schenkia australis +Test_2023_4,Schoenus apogon,Schoenus apogon,,Schoenus apogon +Test_2023_4,Schoenus brevifolius,Schoenus brevifolius,,Schoenus brevifolius +Test_2023_4,Schoenus lepidosperma,Schoenus lepidosperma,,Schoenus lepidosperma +Test_2023_4,Schoenus vaginatus,Schoenus vaginatus,,Schoenus vaginatus +Test_2023_4,Scleria rugosa,Scleria rugosa,,Scleria rugosa +Test_2023_4,Senecio longipilus,Senecio longipilus,,Senecio longipilus +Test_2023_4,Sida goniocarpa,Sida goniocarpa,,Sida goniocarpa +Test_2023_4,Sigesbeckia orientalis,Sigesbeckia orientalis,,Sigesbeckia orientalis +Test_2023_4,Sisymbrium irio,Sisymbrium irio,,Sisymbrium irio +Test_2023_4,Sparaxis bulbifera,Sparaxis bulbifera,,Sparaxis bulbifera +Test_2023_4,Spergularia diandra,Spergularia diandra,,Spergularia diandra +Test_2023_4,Sphaeromorphaea littoralis,Sphaeromorphaea littoralis,,Sphaeromorphaea littoralis +Test_2023_4,Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia subsp. angustifolia,,Stellaria angustifolia subsp. angustifolia +Test_2023_4,Styphelia viridis,Styphelia viridis,,Styphelia viridis +Test_2023_4,Swainsona cadellii,Swainsona cadellii,,Swainsona cadellii +Test_2023_4,Teucrium puberulum,Teucrium puberulum,,Teucrium puberulum +Test_2023_4,Thelymitra kangaloonica,Thelymitra kangaloonica,,Thelymitra kangaloonica +Test_2023_4,Thesium australe,Thesium australe,,Thesium australe +Test_2023_4,Trifolium dubium,Trifolium dubium,,Trifolium dubium +Test_2023_4,Veronica catenata,Veronica catenata,,Veronica catenata +Test_2023_4,Veronica derwentiana,Veronica derwentiana,,Veronica derwentiana +Test_2023_4,Wahlenbergia luteola,Wahlenbergia luteola,,Wahlenbergia luteola diff --git a/tests/testthat/examples/Test_2023_4/output/traits.csv b/tests/testthat/examples/Test_2023_4/output/traits.csv index ac42b70c..be35a67d 100644 --- a/tests/testthat/examples/Test_2023_4/output/traits.csv +++ b/tests/testthat/examples/Test_2023_4/output/traits.csv @@ -21,15 +21,15 @@ Test_2023_4,Alectryon subdentatus,019,fruit_length,8,mm,species,minimum,measurem Test_2023_4,Alectryon subdentatus,020,fruit_length,8,mm,species,minimum,measurement,1,,seedling,,,,,Test_2003,,01,,,2009-01,Part of Test Dataset 4,01,04,Alectryon subdentatus Test_2023_4,Amyema preissii,021,fruit_colour,pink white,,,mode,,1,,seedling,,,,,Test_2003,,02,,,,Part of Test Dataset 4,01,04,Amyema preissii Test_2023_4,Angophora leiocarpa,022,fruit_width,11,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Angophora leiocarpa -Test_2023_4,Apophyllum anomalum,023,fruit_colour,purple,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Apophyllum anomalum +Test_2023_4,Capparis anomala,023,fruit_colour,purple,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Apophyllum anomalum Test_2023_4,Arbutus unedo,024,fruit_colour,red,,metapopulation,mode,,1,,seedling,03,,,,,02,02,,,,From `australia_2` site,01,04,Arbutus unedo Test_2023_4,Australina pusilla,025,fruit_length,1,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Australina pusilla Test_2023_4,Burmannia disticha,026,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Burmannia disticha Test_2023_4,Bursaria spinosa subsp. spinosa,027,fruit_width,9,mm,species,mode,,1,field_experiment,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Bursaria spinosa subsp. spinosa Test_2023_4,Calendula arvensis,028,fruit_length,15,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Calendula arvensis Test_2023_4,Callistemon purpurascens,029,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Callistemon purpurascens -Test_2023_4,Carex cephalotes,030,fruit_length,2.5,mm,species,,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Carex cephalotes -Test_2023_4,Carex cephalotes,031,fruit_width,1,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Carex cephalotes +Test_2023_4,Carex pyrenaica var. cephalotes,030,fruit_length,2.5,mm,species,,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Carex cephalotes +Test_2023_4,Carex pyrenaica var. cephalotes,031,fruit_width,1,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Carex cephalotes Test_2023_4,Carex leporina,032,fruit_length,3.5,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Carex leporina Test_2023_4,Carex raleighii,033,fruit_length,2.5,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Carex raleighii Test_2023_4,Carmichaelia exsul,034,fruit_length,10,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Carmichaelia exsul @@ -63,7 +63,7 @@ Test_2023_4,Cyperus sculptus,060,fruit_length,1,mm,species,mode,,1,,seedling,,,, Test_2023_4,Dampiera fusca,061,fruit_colour,brown,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Dampiera fusca Test_2023_4,Davidsonia johnsonii,062,fruit_length,30,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Davidsonia johnsonii Test_2023_4,Daviesia arenaria,063,fruit_length,7,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Daviesia arenaria -Test_2023_4,Derris involuta,064,fruit_dehiscence,indehiscent,,population,mode,,1,literature,adult,03,,,,Test_2003,02,02,,,,From `australia_2` site,01,02,Derris involuta +Test_2023_4,Solori involuta,064,fruit_dehiscence,indehiscent,,population,mode,,1,literature,adult,03,,,,Test_2003,02,02,,,,From `australia_2` site,01,02,Derris involuta Test_2023_4,Dichromochlamys dentatifolia,065,fruit_length,1.8,mm,,mode,,1,field_experiment,seedling,,,,,Test_2003,,01,,,,Part of Test Dataset 4,01,04,Dichromochlamys dentatifolia Test_2023_4,Dillwynia cinerascens,066,fruit_length,5,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Dillwynia cinerascens Test_2023_4,Dillwynia floribunda,067,fruit_length,4,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Dillwynia floribunda @@ -88,7 +88,7 @@ Test_2023_4,Eucalyptus dorrigoensis,085,fruit_length,5,mm,species,minimum,measur Test_2023_4,Eucalyptus leucoxylon subsp. pruinosa,086,fruit_dehiscence,dehiscent,,species,,,1,,adult,,,,,,,02,,,,,01,04,Eucalyptus leucoxylon subsp. pruinosa Test_2023_4,Eucalyptus muelleriana,087,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,04,Eucalyptus muelleriana Test_2023_4,Eucalyptus nandewarica,088,fruit_length,3,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus nandewarica -Test_2023_4,Eucalyptus oblonga,089,fruit_length,8,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus oblonga +Test_2023_4,Eucalyptus globoidea,089,fruit_length,8,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus oblonga Test_2023_4,Eucalyptus olida,090,fruit_length,5,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus olida Test_2023_4,Eucalyptus pulverulenta,091,fruit_width,6,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus pulverulenta Test_2023_4,Eucalyptus pulverulenta,092,leaf_stomatal_conductance,0.3,mol{H2O}/m2/s,species,raw,measurement,5,field_experiment,seedling,,,01,,,,02,,,,Part of Test Dataset 4,01,04,Eucalyptus pulverulenta @@ -99,20 +99,20 @@ Test_2023_4,Eucalyptus recurva,093,fruit_length,4,mm,metapopulation,mode,,1,,see Test_2023_4,Eucalyptus rossii,094,fruit_width,6,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus rossii Test_2023_4,Eucalyptus scias,095,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,04,Eucalyptus scias Test_2023_4,Eucalyptus viminalis,096,fruit_width,4,mm,species,,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus viminalis -Test_2023_4,Eucalyptus yangoura,097,fruit_width,6,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus yangoura +Test_2023_4,Eucalyptus globoidea,097,fruit_width,6,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus yangoura Test_2023_4,Eucalyptus youmanii,098,fruit_length,12,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus youmanii Test_2023_4,Eucalyptus youmanii,099,fruit_width,9,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus youmanii Test_2023_4,Euphorbia inappendiculata var. queenslandica,100,fruit_length,1.5,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Euphorbia inappendiculata var. queenslandica Test_2023_4,Exocarpos homalocladus,101,fruit_width,8,mm,species,maximum,,1,field_experiment,seedling,,,,,Test_2000,,02,,,,Part of Test Dataset 4,01,04,Exocarpos homalocladus Test_2023_4,Exocarpos sparteus,102,fruit_length,5,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Exocarpos sparteus Test_2023_4,Ficus henneana,103,fruit_length,15,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Ficus henneana -Test_2023_4,Freesia hybrid,104,fruit_colour,green,,metapopulation,mode,,1,,seedling,03,,,,,02,02,,,,From `australia_2` site,01,04,Freesia hybrid +Test_2023_4,Freesia leichtlinii subsp. leichtlinii x Freesia leichtlinii subsp. alba,104,fruit_colour,green,,metapopulation,mode,,1,,seedling,03,,,,,02,02,,,,From `australia_2` site,01,04,Freesia hybrid Test_2023_4,Freesia laxa,105,fruit_length,12,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Freesia laxa Test_2023_4,Geijera salicifolia,106,fruit_width,6,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Geijera salicifolia Test_2023_4,Gentiana wingecarribiensis,107,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Gentiana wingecarribiensis Test_2023_4,Gentianella barringtonensis,108,fruit_colour,brown,,species,minimum,,1,literature,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,02,Gentianella barringtonensis Test_2023_4,Geranium obtusisepalum,109,fruit_length,17,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Geranium obtusisepalum -Test_2023_4,Geranium purpureum subsp. purpureum,110,fruit_length,12,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Geranium purpureum subsp. purpureum +Test_2023_4,Geranium purpureum,110,fruit_length,12,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Geranium purpureum subsp. purpureum Test_2023_4,Gompholobium grandiflorum,111,fruit_length,15,mm,species,maximum,,1,,seedling,,,,,Test_2003,,02,,,,Part of Test Dataset 4,01,04,Gompholobium grandiflorum Test_2023_4,Goodenia varia,112,fruit_length,10,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Goodenia varia Test_2023_4,Gossia bidwillii,113,fruit_colour,black,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Gossia bidwillii @@ -124,7 +124,7 @@ Test_2023_4,Hibbertia crinita,118,fruit_dehiscence,dehiscent,,species,,,1,,adult Test_2023_4,Hibiscus brachysiphonius,119,fruit_length,15,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Hibiscus brachysiphonius Test_2023_4,Hibiscus sturtii,120,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Hibiscus sturtii Test_2023_4,Hypericum elodes,121,fruit_length,4,mm,species,mean,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Hypericum elodes -Test_2023_4,Hypoxis glabella var. glabella,122,fruit_dehiscence,dehiscent,,population,mode,,1,literature,adult,03,,,,Test_2003,02,02,,,,From `australia_2` site,01,02,Hypoxis glabella var. glabella +Test_2023_4,Pauridia glabella var. glabella,122,fruit_dehiscence,dehiscent,,population,mode,,1,literature,adult,03,,,,Test_2003,02,02,,,,From `australia_2` site,01,02,Hypoxis glabella var. glabella Test_2023_4,Imperata cylindrica,123,fruit_length,1,mm,species,minimum,measurement,1,literature,seedling,,,,,Test_2000,,02,,,2006-03,Part of Test Dataset 4,01,04,Imperata cylindrica Test_2023_4,Imperata cylindrica,124,fruit_length,1,mm,species,minimum,measurement,1,literature,seedling,,,,,Test_2000,,02,,,2007-03,Part of Test Dataset 4,01,04,Imperata cylindrica Test_2023_4,Indigofera triflora,125,fruit_length,30,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Indigofera triflora @@ -171,7 +171,7 @@ Test_2023_4,Nicotiana glauca,156,leaf_photosynthesis,3.7,umol/m2/s,individual,ra Test_2023_4,Nicotiana glauca,157,fruit_length,13,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Nicotiana glauca Test_2023_4,Nicotiana goodspeedii,158,fruit_length,5,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Nicotiana goodspeedii Test_2023_4,Oxalis corniculata,159,fruit_width,1.5,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Oxalis corniculata -Test_2023_4,Pandorea pandorana subsp. austrocaledonica,160,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,04,Pandorea pandorana subsp. austrocaledonica +Test_2023_4,Pandorea pandorana,160,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,04,Pandorea pandorana subsp. austrocaledonica Test_2023_4,Paraserianthes lophantha,161,fruit_width,25,mm,species,mode,,1,field_experiment,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Paraserianthes lophantha Test_2023_4,Parentucellia latifolia,162,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Parentucellia latifolia Test_2023_4,Phlegmatospermum cochlearinum,163,fruit_length,10,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Phlegmatospermum cochlearinum diff --git a/tests/testthat/examples/Test_2023_7/output/metadata.yml b/tests/testthat/examples/Test_2023_7/output/metadata.yml index a38d6462..5dde7c3a 100644 --- a/tests/testthat/examples/Test_2023_7/output/metadata.yml +++ b/tests/testthat/examples/Test_2023_7/output/metadata.yml @@ -5,7 +5,7 @@ description: AusTraits is a transformative database, containing measurements on used to build the resource are also available on the project's GitHub repository,http://traitecoevo.github.io/traits.build. Further information on the project is available in the associated publication and at the project website https://austraits.org. -version: 4.0.0 +version: 5.0.0 doi: 10.5281/zenodo.5112001 structure_URI: https://github.com/traitecoevo/traits.build geo_location: diff --git a/tests/testthat/examples/Test_2023_7/output/taxa.csv b/tests/testthat/examples/Test_2023_7/output/taxa.csv index 2af805f4..1eeab5bc 100644 --- a/tests/testthat/examples/Test_2023_7/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_7/output/taxa.csv @@ -1,3 +1,3 @@ -taxon_name,taxonomic_dataset,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution -Eucalyptus miniata,,,,,,,,, -Eucalyptus tetrodonta,,,,,,,,, +original_name,taxon_name,taxon_name_alternatives,genus,family,taxon_rank,taxonomic_dataset,taxonomic_status,subclass,taxon_distribution,scientific_name,taxon_id,taxon_ID_genus,scientific_name_id,canonical_name,cleaned_scientific_name_id,taxon_id_family,trinomial,binomial,establishment_means +Eucalyptus miniata,Eucalyptus miniata,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus miniata A.Cunn. ex Schauer,https://id.biodiversity.org.au/node/apni/2889426,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/56460,Eucalyptus miniata,https://id.biodiversity.org.au/name/apni/56460,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus miniata,native +Eucalyptus tetrodonta,Eucalyptus tetrodonta,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus tetrodonta F.Muell.,https://id.biodiversity.org.au/node/apni/2905964,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/55572,Eucalyptus tetrodonta,https://id.biodiversity.org.au/name/apni/55572,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus tetrodonta,native diff --git a/tests/testthat/examples/Test_2023_7/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_7/output/taxonomic_updates.csv index 90f4fda9..f37e1485 100644 --- a/tests/testthat/examples/Test_2023_7/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_7/output/taxonomic_updates.csv @@ -1,3 +1,3 @@ dataset_id,original_name,aligned_name,taxonomic_resolution,taxon_name -Test_2023_7,Eucalyptus miniata,Eucalyptus miniata,, -Test_2023_7,Eucalyptus tetrodonta,Eucalyptus tetrodonta,, +Test_2023_7,Eucalyptus miniata,Eucalyptus miniata,,Eucalyptus miniata +Test_2023_7,Eucalyptus tetrodonta,Eucalyptus tetrodonta,,Eucalyptus tetrodonta diff --git a/tests/testthat/examples/Test_2023_8/output/metadata.yml b/tests/testthat/examples/Test_2023_8/output/metadata.yml index a38d6462..5dde7c3a 100644 --- a/tests/testthat/examples/Test_2023_8/output/metadata.yml +++ b/tests/testthat/examples/Test_2023_8/output/metadata.yml @@ -5,7 +5,7 @@ description: AusTraits is a transformative database, containing measurements on used to build the resource are also available on the project's GitHub repository,http://traitecoevo.github.io/traits.build. Further information on the project is available in the associated publication and at the project website https://austraits.org. -version: 4.0.0 +version: 5.0.0 doi: 10.5281/zenodo.5112001 structure_URI: https://github.com/traitecoevo/traits.build geo_location: diff --git a/tests/testthat/examples/Test_2023_8/output/taxa.csv b/tests/testthat/examples/Test_2023_8/output/taxa.csv index 2af805f4..1eeab5bc 100644 --- a/tests/testthat/examples/Test_2023_8/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_8/output/taxa.csv @@ -1,3 +1,3 @@ -taxon_name,taxonomic_dataset,taxon_rank,taxonomic_status,genus,binomial,trinomial,family,taxon_id,taxon_distribution -Eucalyptus miniata,,,,,,,,, -Eucalyptus tetrodonta,,,,,,,,, +original_name,taxon_name,taxon_name_alternatives,genus,family,taxon_rank,taxonomic_dataset,taxonomic_status,subclass,taxon_distribution,scientific_name,taxon_id,taxon_ID_genus,scientific_name_id,canonical_name,cleaned_scientific_name_id,taxon_id_family,trinomial,binomial,establishment_means +Eucalyptus miniata,Eucalyptus miniata,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus miniata A.Cunn. ex Schauer,https://id.biodiversity.org.au/node/apni/2889426,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/56460,Eucalyptus miniata,https://id.biodiversity.org.au/name/apni/56460,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus miniata,native +Eucalyptus tetrodonta,Eucalyptus tetrodonta,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus tetrodonta F.Muell.,https://id.biodiversity.org.au/node/apni/2905964,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/55572,Eucalyptus tetrodonta,https://id.biodiversity.org.au/name/apni/55572,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus tetrodonta,native diff --git a/tests/testthat/examples/Test_2023_8/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_8/output/taxonomic_updates.csv index 99b177ae..016fabeb 100644 --- a/tests/testthat/examples/Test_2023_8/output/taxonomic_updates.csv +++ b/tests/testthat/examples/Test_2023_8/output/taxonomic_updates.csv @@ -1,3 +1,3 @@ dataset_id,original_name,aligned_name,taxonomic_resolution,taxon_name -Test_2023_8,Eucalyptus miniata,Eucalyptus miniata,, -Test_2023_8,Eucalyptus tetrodonta,Eucalyptus tetrodonta,, +Test_2023_8,Eucalyptus miniata,Eucalyptus miniata,,Eucalyptus miniata +Test_2023_8,Eucalyptus tetrodonta,Eucalyptus tetrodonta,,Eucalyptus tetrodonta diff --git a/tests/testthat/test-setup.R b/tests/testthat/test-setup.R index d5550862..2ad85ea5 100644 --- a/tests/testthat/test-setup.R +++ b/tests/testthat/test-setup.R @@ -616,7 +616,7 @@ test_that("`build_setup_pipeline` is working", { expect_silent(taxa2 <- read_csv_char("config/taxon_list.csv")) expect_contains(names(taxa2), vars) expect_true(length(names(taxa2)) > 2) - expect_true(nrow(taxa2) == 7) + expect_true(nrow(taxa2) == 232) ## Now try building in a controlled env, using base method base_tmp_env <- new.env() @@ -661,7 +661,7 @@ test_that("`build_setup_pipeline` is working", { expect_null(austraits_raw$build_info$version) expect_null(austraits_raw$build_info$git_SHA) # Test that austraits has version and git_SHA from testgit folder - expect_equal(austraits$build_info$version, "4.0.0") + expect_equal(austraits$build_info$version, "5.0.0") expect_type(austraits$build_info$git_SHA, "character") expect_equal(austraits$build_info$git_SHA, sha) expect_equal(austraits$build_info$git_SHA, "6c73238d8d048781d9a4f5239a03813be313f0dd") From b5e96964caa70e64812229c51f9343c54450c0b1 Mon Sep 17 00:00:00 2001 From: Daniel Falster Date: Thu, 16 Nov 2023 15:31:05 +1100 Subject: [PATCH 19/31] Add more version info on build, assign class traits.build (#126) * Ensure call for SHA works when not in a git repo * Add traits.build version into main metadata (for #124) * Add tests for util_get_SHA and adding `resource_type` to main metadata * Assign output as class traits.build --------- Co-authored-by: yangsophieee --- R/get.R | 5 ++++- R/process.R | 31 ++++++++++++++++++++++++++++--- R/testdata.R | 2 +- tests/testthat/functions.R | 2 +- tests/testthat/test-process.R | 1 + tests/testthat/test-setup.R | 25 ++++++++++++++++++++++++- 6 files changed, 59 insertions(+), 7 deletions(-) diff --git a/R/get.R b/R/get.R index dad8a940..789a17b9 100644 --- a/R/get.R +++ b/R/get.R @@ -47,5 +47,8 @@ util_get_version <- function(path = "config/metadata.yml") { #' @return 40-digit SHA character string for the latest commit to the repository #' @export util_get_SHA <- function(path = ".") { - git2r::sha(git2r::last_commit(git2r::repository(path))) + sha <- tryCatch({ + git2r::sha(git2r::last_commit(git2r::repository(path))) + }, error = function(cond) {NA}) + sha } diff --git a/R/process.R b/R/process.R index 40463096..e7b79b0c 100644 --- a/R/process.R +++ b/R/process.R @@ -249,10 +249,28 @@ dataset_process <- function(filename_data_raw, traits %>% dplyr::filter(!(!is.na(.data$error) & (.data$error == "Missing value"))) } - # Todo - resource_metadata - # - Add contributors + # Update metadata + metadata <- resource_metadata + + if (is.null(metadata[["related_identifiers"]][1])) { + metadata[["related_identifiers"]] <- list() + } + + metadata[["related_identifiers"]] <- + util_append_to_list( + metadata[["related_identifiers"]], + list( + related_identifier_type = "url", + identifier = "https://github.com/traitecoevo/traits.build", + relation_type = "isCompiledBy", + resource_type = "software", + version = as.character(packageVersion("traits.build")) + ) + ) + # Combine for final output + ret <- list( traits = traits %>% dplyr::filter(is.na(.data$error)) %>% dplyr::select(-dplyr::all_of(c("error", "unit_in"))), locations = locations, @@ -271,9 +289,13 @@ dataset_process <- function(filename_data_raw, sources = sources, definitions = definitions, schema = schema, - metadata = resource_metadata, + metadata = metadata, build_info = list(session_info = utils::sessionInfo()) ) + + class(ret) <- c("list", "traits.build") + + ret } #' Build dataset @@ -1858,6 +1880,9 @@ build_combine <- function(..., d = list(...)) { session_info = utils::sessionInfo() ) ) + + class(ret) <- c("list", "traits.build") + ret } diff --git a/R/testdata.R b/R/testdata.R index b378a467..421ae712 100644 --- a/R/testdata.R +++ b/R/testdata.R @@ -304,7 +304,7 @@ dataset_test_worker <- } expect_list <- function(data, info) { - expect_true(class(data) == "list", info = sprintf("%s - is not a list", info)) + expect_true("list" %in% class(data), info = sprintf("%s - is not a list", info)) } expect_list_names_valid <- function(data, info, label) { diff --git a/tests/testthat/functions.R b/tests/testthat/functions.R index 53dd8428..3b821b4c 100644 --- a/tests/testthat/functions.R +++ b/tests/testthat/functions.R @@ -54,7 +54,7 @@ expect_not_NA <- function(object, info = NULL, label = NULL) { expect_list <- function(data, info) { - expect_true(class(data) == "list", info = info) + expect_true("list" %in% class(data), info = info) } diff --git a/tests/testthat/test-process.R b/tests/testthat/test-process.R index d483b1c9..16d763ad 100644 --- a/tests/testthat/test-process.R +++ b/tests/testthat/test-process.R @@ -24,6 +24,7 @@ test_that("`dataset_process` is working", { expect_no_error(austraits_names <- schema$austraits$elements %>% names()) expect_no_error(x <- dataset_process(test_data, test_config, schema, resource_metadata, unit_conversions)) expect_type(x, "list") + expect_equal(class(x), c("list", "traits.build")) expect_length(x, 13) expect_named(x, austraits_names) expect_equal(nrow(x$excluded_data), 0) diff --git a/tests/testthat/test-setup.R b/tests/testthat/test-setup.R index 2ad85ea5..3c10cf1c 100644 --- a/tests/testthat/test-setup.R +++ b/tests/testthat/test-setup.R @@ -594,7 +594,9 @@ test_that("`build_setup_pipeline` is working", { expect_true(file.copy("data/Test_2022/test-metadata.yml", "data/Test_2022/metadata.yml", overwrite = TRUE)) expect_no_error(zip::unzip("config/testgit.zip")) - expect_no_error(sha <- git2r::sha(git2r::last_commit())) + # Expect no error if not within a git repo + expect_no_error(sha <- util_get_SHA("../../..")) + expect_no_error(sha <- util_get_SHA()) # Expect error if path or method is wrong expect_error(build_setup_pipeline(path = "Datas")) expect_error(build_setup_pipeline(method = "grrrr")) @@ -666,8 +668,29 @@ test_that("`build_setup_pipeline` is working", { expect_equal(austraits$build_info$git_SHA, sha) expect_equal(austraits$build_info$git_SHA, "6c73238d8d048781d9a4f5239a03813be313f0dd") + # Check output lists have required parts + ## Todo add mode here + + ## sources + + ## metadata + + ## schema + expect_equal(austraits$schema, get_schema()) + + ## Compiled by traits.build + traits.build_tag <- last(austraits$metadata$related_identifiers) + expected_output <- list( + related_identifier_type = "url", + identifier = "https://github.com/traitecoevo/traits.build", + relation_type = "isCompiledBy", + resource_type = "software", + version = as.character(packageVersion("traits.build")) + ) + expect_equal(traits.build_tag, expected_output) #expect_length(austraits_raw$taxa, 14) #not valid test with new `dataset_update_taxonomy setup` #expect_length(austraits$taxa, 14) #not valid test with new `dataset_update_taxonomy setup` + expect_equal(nrow(austraits$taxa), nrow(austraits_raw$taxa)) # Compare products from three methods, except `build_info` From 256ab7abeea79ff2fafb7d10b9786cd2e4cd60aa Mon Sep 17 00:00:00 2001 From: Sophie Yang <78716301+yangsophieee@users.noreply.github.com> Date: Thu, 16 Nov 2023 15:32:02 +1100 Subject: [PATCH 20/31] Fix `plot_trait_distribution_beeswarm` error (#130) * Try fix error * Remove browsers * Fix error with `plot_trait_distribution_beeswarm` * Rename file to plot.R * Update documentation --- R/{plot_trait_beeswarm.R => plot.R} | 79 +++++++++++++------------ inst/support/report_dataset.Rmd | 2 +- man/plot_trait_distribution_beeswarm.Rd | 6 +- tests/testthat/test-setup.R | 2 +- tests/testthat/test-usage.R | 4 +- 5 files changed, 48 insertions(+), 45 deletions(-) rename R/{plot_trait_beeswarm.R => plot.R} (63%) diff --git a/R/plot_trait_beeswarm.R b/R/plot.R similarity index 63% rename from R/plot_trait_beeswarm.R rename to R/plot.R index 2153e8cd..f9d72bda 100644 --- a/R/plot_trait_beeswarm.R +++ b/R/plot.R @@ -2,7 +2,7 @@ #' @description Plots distribution of trait values by a grouping variable using ggbeeswarm package #' #' @param austraits austraits data object -#' @param trait_name Name of trait to plot +#' @param trait Name of trait to plot #' @param y_axis_category One of `dataset_id`, `family` #' @param highlight specify a group to highlight #' @param hide_ids add label on y_axis? @@ -17,14 +17,14 @@ #' @export # -plot_trait_distribution_beeswarm <- function(austraits, trait_name, y_axis_category, highlight=NA, hide_ids = FALSE) { +plot_trait_distribution_beeswarm <- function(austraits, trait, y_axis_category, highlight = NA, hide_ids = FALSE) { # Subset data to this trait austraits_trait <- - austraits$traits %>% filter(trait_name == trait_name) %>% - mutate(value = as.numeric(.data$value)) + austraits$traits %>% dplyr::filter(.data$trait_name == trait) %>% + dplyr::mutate(value = as.numeric(.data$value)) - my_shapes = c("_min" = 60, "_mean" = 16, "_max" =62, "unknown" = 18) + my_shapes <- c("_min" = 60, "_mean" = 16, "_max" = 62, "unknown" = 18) as_shape <- function(value_type) { p <- rep("unknown", length(value_type)) @@ -32,7 +32,7 @@ plot_trait_distribution_beeswarm <- function(austraits, trait_name, y_axis_categ p[grepl("mean", value_type)] <- "_mean" #16 p[grepl("min", value_type)] <- "_min" #60 p[grepl("max", value_type)] <- "_max" #62 - factor(p, levels=names(my_shapes)) + factor(p, levels = names(my_shapes)) } tax_info <- austraits$taxa @@ -43,57 +43,58 @@ plot_trait_distribution_beeswarm <- function(austraits, trait_name, y_axis_categ dplyr::left_join(by = "taxon_name", tax_info) # Define grouping variables and derivatives - if(!y_axis_category %in% names(data)){ + if (!y_axis_category %in% names(data)) { stop("Incorrect grouping variable! Currently implemented for `family` or `dataset_id`") } # define grouping variable, ordered by group-level by mean values # use log_value where possible - if(min(data$value, na.rm=TRUE) > 0 ) { + if (min(data$value, na.rm = TRUE) > 0) { data$value2 <- log10(data$value) } else { data$value2 <- data$value } - data$Group = forcats::fct_reorder(data[[y_axis_category]], data$value2, na.rm=TRUE) + + data$Group <- forcats::fct_reorder(data[[y_axis_category]], data$value2, na.rm = TRUE) n_group <- levels(data$Group) %>% length() - # set colour to be alternating - data$colour = ifelse(data$Group %in% levels(data$Group)[seq(1, n_group, by=2)], + # Set colour to be alternating + data$colour <- ifelse(data$Group %in% levels(data$Group)[seq(1, n_group, by = 2)], "a", "b") - # set colour of group to highlight - if(!is.na(highlight) & highlight %in% data$Group) { + # Set colour of group to highlight + if (!is.na(highlight) && highlight %in% data$Group) { data <- dplyr::mutate(data, colour = ifelse(.data$Group %in% highlight, "c", .data$colour)) } - vals <- list(minimum = purrr::pluck(austraits, "definitions", trait_name, "allowed_values_min"), - maximum = purrr::pluck(austraits, "definitions", trait_name, "allowed_values_max")) + vals <- list(minimum = purrr::pluck(austraits, "definitions", trait, "allowed_values_min"), + maximum = purrr::pluck(austraits, "definitions", trait, "allowed_values_max")) range <- (vals$maximum/vals$minimum) # Check range on y-axis y.text <- ifelse(n_group > 20, 0.75, 1) - heights = c(1, max(1, n_group/7)) + heights <- c(1, max(1, n_group / 7)) # Top plot - plain histogram of data p1 <- - ggplot2::ggplot(data, ggplot2::aes(x=.data$value)) + - ggplot2::geom_histogram(ggplot2::aes(y = ..density..), color="darkgrey", fill="darkgrey", bins=50) + - ggplot2::geom_density(color="black") + + ggplot2::ggplot(data, ggplot2::aes(x = .data$value)) + + ggplot2::geom_histogram(ggplot2::aes(y = ..density..), color = "darkgrey", fill = "darkgrey", bins = 50) + + ggplot2::geom_density(color = "black") + ggplot2::xlab("") + ggplot2::ylab("All data") + ggplot2::theme_bw() + ggplot2::theme(legend.position = "none", panel.grid.minor = ggplot2::element_blank(), panel.grid.major = ggplot2::element_blank(), - axis.ticks.y= ggplot2::element_blank(), - axis.text= ggplot2::element_blank(), + axis.ticks.y = ggplot2::element_blank(), + axis.text = ggplot2::element_blank(), panel.background = ggplot2::element_blank() ) # Second plot -- dots by groups, using ggbeeswarm package p2 <- ggplot2::ggplot(data, ggplot2::aes(x = .data$value, y = .data$Group, colour = .data$colour, shape = .data$shapes)) + - ggbeeswarm::geom_quasirandom(groupOnX=FALSE) + + ggbeeswarm::geom_quasirandom(groupOnX = FALSE) + ggplot2::ylab(paste("By ", y_axis_category)) + # inclusion of custom shapes: for min, mean, unknown # NB: this single line of code makes function about 4-5 slower for some reason @@ -102,45 +103,45 @@ plot_trait_distribution_beeswarm <- function(austraits, trait_name, y_axis_categ ggplot2::theme(legend.position = "none", panel.grid.major.x = ggplot2::element_blank(), panel.grid.minor.x = ggplot2::element_blank(), - axis.text.x = ggplot2::element_text(size=ggplot2::rel(1.25)), - axis.text.y = ggplot2::element_text(size=ggplot2::rel(y.text)) + axis.text.x = ggplot2::element_text(size = ggplot2::rel(1.25)), + axis.text.y = ggplot2::element_text(size = ggplot2::rel(y.text)) ) #+ # guides(colour=FALSE) - if(hide_ids) { + if (hide_ids) { p2 <- p2 + ggplot2::theme(axis.text.y = ggplot2::element_blank()) } #Sourced from https://gist.github.com/bbolker/5ba6a37d64b06a176e320b2b696b6733 - scientific_10 <- function(x,suppress_ones=TRUE) { + scientific_10 <- function(x, suppress_ones = TRUE) { s <- scales::scientific_format()(x) ## substitute for exact zeros - s[s=="0e+00"] <- "0" + s[s == "0e+00"] <- "0" ## regex: [+]? = "zero or one occurrences of '+'" - s2 <- gsub("e[+]?", " %*% 10^", s ) + s2 <- gsub("e[+]?", " %*% 10^", s) ## suppress 1 x - if (suppress_ones) s2 <- gsub("1 %\\*% +","",s2) - parse(text=s2) + if (suppress_ones) s2 <- gsub("1 %\\*% +", "", s2) + parse(text = s2) } # Define scale on x-axis and transform to log if required - if(vals$minimum !=0 & range > 20) { + if (vals$minimum != 0 && range > 20) { #log transformation p1 <- p1 + - ggplot2::scale_x_log10(name="", + ggplot2::scale_x_log10(name = "", breaks = scales::breaks_log(), labels = scientific_10, - limits=c(vals$minimum, vals$maximum)) + limits = c(vals$minimum, vals$maximum)) p2 <- p2 + - ggplot2::scale_x_log10(name=paste(trait_name, ' (', data$unit[1], ')'), + ggplot2::scale_x_log10(name = paste(trait, " (", data$unit[1], ")"), breaks = scales::breaks_log(), labels = scientific_10, - limits=c(vals$minimum, vals$maximum)) + limits = c(vals$minimum, vals$maximum)) } else { - p1 <- p1 + ggplot2::scale_x_continuous(limits=c(vals$minimum, vals$maximum)) - p2 <- p2 + ggplot2::scale_x_continuous(limits=c(vals$minimum, vals$maximum)) + - ggplot2::xlab(paste(trait_name, ' (', data$unit[1], ')')) + p1 <- p1 + ggplot2::scale_x_continuous(limits = c(vals$minimum, vals$maximum)) + p2 <- p2 + ggplot2::scale_x_continuous(limits = c(vals$minimum, vals$maximum)) + + ggplot2::xlab(paste(trait, " (", data$unit[1], ")")) } @@ -152,5 +153,5 @@ plot_trait_distribution_beeswarm <- function(austraits, trait_name, y_axis_categ p2 <- f(p2) # Fix width of second plot to be same as bottom using ggplot_table p1$widths[2:3] <- p2$widths[2:3] - gridExtra::grid.arrange(p1, p2, nrow=2, widths=c(1), heights=heights) + gridExtra::grid.arrange(p1, p2, nrow = 2, widths = c(1), heights = heights) } diff --git a/inst/support/report_dataset.Rmd b/inst/support/report_dataset.Rmd index e38efc2d..9fee1b83 100644 --- a/inst/support/report_dataset.Rmd +++ b/inst/support/report_dataset.Rmd @@ -567,7 +567,7 @@ if (nrow(filter(data_study$excluded_data, error == "Value out of allowable range writeLines() } - plot_trait_distribution_beeswarm(austraits, trait, "dataset_id", highlight = dataset_id, hide_ids = TRUE) + traits.build::plot_trait_distribution_beeswarm(austraits, trait, "dataset_id", highlight = dataset_id, hide_ids = TRUE) writeLines(c("")) diff --git a/man/plot_trait_distribution_beeswarm.Rd b/man/plot_trait_distribution_beeswarm.Rd index fe8d83cb..930bd69d 100644 --- a/man/plot_trait_distribution_beeswarm.Rd +++ b/man/plot_trait_distribution_beeswarm.Rd @@ -1,12 +1,12 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/plot_trait_beeswarm.R +% Please edit documentation in R/plot.R \name{plot_trait_distribution_beeswarm} \alias{plot_trait_distribution_beeswarm} \title{Beeswarm Trait distribution} \usage{ plot_trait_distribution_beeswarm( austraits, - trait_name, + trait, y_axis_category, highlight = NA, hide_ids = FALSE @@ -15,7 +15,7 @@ plot_trait_distribution_beeswarm( \arguments{ \item{austraits}{austraits data object} -\item{trait_name}{Name of trait to plot} +\item{trait}{Name of trait to plot} \item{y_axis_category}{One of `dataset_id`, `family`} diff --git a/tests/testthat/test-setup.R b/tests/testthat/test-setup.R index 3c10cf1c..2b885c3a 100644 --- a/tests/testthat/test-setup.R +++ b/tests/testthat/test-setup.R @@ -731,7 +731,7 @@ test_that("reports and plots are produced", { # Not testing right now #expect_no_error( #p <- - #plot_trait_distribution_beeswarm( + #traits.build::plot_trait_distribution_beeswarm( #austraits, "huber_value", "dataset_id", highlight = "Test_2022", hide_ids = TRUE) #) expect_silent( diff --git a/tests/testthat/test-usage.R b/tests/testthat/test-usage.R index 1b198830..8f152b28 100644 --- a/tests/testthat/test-usage.R +++ b/tests/testthat/test-usage.R @@ -5,5 +5,7 @@ austraits <- readRDS("test_austraits.rds") # Note, requires existnec of "test_austraits.rds", generated from `test-process.R` test_that("plots", { - expect_invisible(suppressMessages(austraits %>% plot_trait_distribution_beeswarm("wood_density", "dataset_id", "Test_2022"))) + expect_invisible(suppressMessages( + austraits %>% traits.build::plot_trait_distribution_beeswarm("wood_density", "dataset_id", "Test_2022") + )) }) From c7068042507b471e494cc90f232973d678405a03 Mon Sep 17 00:00:00 2001 From: Sophie Yang <78716301+yangsophieee@users.noreply.github.com> Date: Thu, 16 Nov 2023 15:41:29 +1100 Subject: [PATCH 21/31] More dataset tests (#132) - Fixes #118 - Rename check_duplicates to check_pivot_duplicates - Add option in metadata_check_custom_R_code path_data to allow easier testing in tests/testthat - Add Test Datasets 5 and 6 - Update taxon_list-orig.csv - Clean existing test metadata files --- NAMESPACE | 3 +- R/pivot.R | 3 +- R/process.R | 20 +- R/setup.R | 11 +- R/testdata.R | 349 +++++++++----- R/utils.R | 4 +- inst/support/traits.build_schema.yml | 4 +- ...uplicates.Rd => check_pivot_duplicates.Rd} | 6 +- man/metadata_check_custom_R_code.Rd | 4 +- man/metadata_path_dataset_id.Rd | 4 +- man/read_metadata_dataset.Rd | 4 +- tests/testthat/config/taxon_list-orig.R | 1 + tests/testthat/config/taxon_list-orig.csv | 130 +++--- tests/testthat/config/traits.yml | 16 + tests/testthat/config/unit_conversions.csv | 2 + .../examples/Test_2023_1/output/taxa.csv | 14 +- .../examples/Test_2023_2/output/taxa.csv | 16 +- .../examples/Test_2023_3/metadata.yml | 391 +--------------- .../examples/Test_2023_3/output/taxa.csv | 80 ++-- .../examples/Test_2023_4/metadata.yml | 425 +----------------- .../examples/Test_2023_4/output/contexts.csv | 28 -- .../examples/Test_2023_4/output/taxa.csv | 80 ++-- .../examples/Test_2023_4/output/traits.csv | 16 +- tests/testthat/examples/Test_2023_5/README.md | 12 +- tests/testthat/examples/Test_2023_5/data.csv | 80 ++-- .../examples/Test_2023_5/metadata.yml | 387 ++++------------ .../examples/Test_2023_5/output/contexts.csv | 1 + .../Test_2023_5/output/contributors.csv | 2 + .../Test_2023_5/output/definitions.yml | 34 ++ .../Test_2023_5/output/excluded_data.csv | 1 + .../examples/Test_2023_5/output/locations.csv | 1 + .../examples/Test_2023_5/output/metadata.yml | 86 ++++ .../examples/Test_2023_5/output/methods.csv | 3 + .../examples/Test_2023_5/output/sources.bib | 46 ++ .../examples/Test_2023_5/output/taxa.csv | 31 ++ .../Test_2023_5/output/taxonomic_updates.csv | 31 ++ .../examples/Test_2023_5/output/traits.csv | 37 ++ tests/testthat/examples/Test_2023_6/README.md | 8 +- tests/testthat/examples/Test_2023_6/data.csv | 37 ++ .../examples/Test_2023_6/metadata.yml | 120 +++++ .../examples/Test_2023_6/output/contexts.csv | 1 + .../Test_2023_6/output/contributors.csv | 2 + .../Test_2023_6/output/definitions.yml | 34 ++ .../Test_2023_6/output/excluded_data.csv | 1 + .../examples/Test_2023_6/output/locations.csv | 7 + .../examples/Test_2023_6/output/metadata.yml | 86 ++++ .../examples/Test_2023_6/output/methods.csv | 3 + .../examples/Test_2023_6/output/sources.bib | 46 ++ .../examples/Test_2023_6/output/taxa.csv | 31 ++ .../Test_2023_6/output/taxonomic_updates.csv | 31 ++ .../examples/Test_2023_6/output/traits.csv | 37 ++ .../examples/Test_2023_7/output/taxa.csv | 4 +- .../examples/Test_2023_8/output/taxa.csv | 4 +- tests/testthat/test-setup.R | 2 +- tests/testthat/test-xamples.R | 69 +++ 55 files changed, 1391 insertions(+), 1495 deletions(-) rename man/{check_duplicates.Rd => check_pivot_duplicates.Rd} (85%) create mode 100644 tests/testthat/examples/Test_2023_5/output/contexts.csv create mode 100644 tests/testthat/examples/Test_2023_5/output/contributors.csv create mode 100644 tests/testthat/examples/Test_2023_5/output/definitions.yml create mode 100644 tests/testthat/examples/Test_2023_5/output/excluded_data.csv create mode 100644 tests/testthat/examples/Test_2023_5/output/locations.csv create mode 100644 tests/testthat/examples/Test_2023_5/output/metadata.yml create mode 100644 tests/testthat/examples/Test_2023_5/output/methods.csv create mode 100644 tests/testthat/examples/Test_2023_5/output/sources.bib create mode 100644 tests/testthat/examples/Test_2023_5/output/taxa.csv create mode 100644 tests/testthat/examples/Test_2023_5/output/taxonomic_updates.csv create mode 100644 tests/testthat/examples/Test_2023_5/output/traits.csv create mode 100644 tests/testthat/examples/Test_2023_6/data.csv create mode 100644 tests/testthat/examples/Test_2023_6/metadata.yml create mode 100644 tests/testthat/examples/Test_2023_6/output/contexts.csv create mode 100644 tests/testthat/examples/Test_2023_6/output/contributors.csv create mode 100644 tests/testthat/examples/Test_2023_6/output/definitions.yml create mode 100644 tests/testthat/examples/Test_2023_6/output/excluded_data.csv create mode 100644 tests/testthat/examples/Test_2023_6/output/locations.csv create mode 100644 tests/testthat/examples/Test_2023_6/output/metadata.yml create mode 100644 tests/testthat/examples/Test_2023_6/output/methods.csv create mode 100644 tests/testthat/examples/Test_2023_6/output/sources.bib create mode 100644 tests/testthat/examples/Test_2023_6/output/taxa.csv create mode 100644 tests/testthat/examples/Test_2023_6/output/taxonomic_updates.csv create mode 100644 tests/testthat/examples/Test_2023_6/output/traits.csv diff --git a/NAMESPACE b/NAMESPACE index e0602133..4ab6a394 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -4,8 +4,7 @@ export("%>%") export(build_add_version) export(build_combine) export(build_setup_pipeline) -export(check_duplicates) -export(check_pivot_wider) +export(check_pivot_duplicates) export(dataset_build) export(dataset_configure) export(dataset_find_taxon) diff --git a/R/pivot.R b/R/pivot.R index 7ebf0f18..cd742750 100644 --- a/R/pivot.R +++ b/R/pivot.R @@ -5,7 +5,6 @@ #' @param dataset Built dataset with `test_build_dataset` #' #' @return Number of rows with duplicates preventing pivoting wider -#' @export check_pivot_wider <- function(dataset) { @@ -27,7 +26,7 @@ check_pivot_wider <- function(dataset) { if (duplicates == 0) { invisible(TRUE) } else { - invisible(FALSE) + invisible(FALSE) } } diff --git a/R/process.R b/R/process.R index e7b79b0c..5608b120 100644 --- a/R/process.R +++ b/R/process.R @@ -191,6 +191,7 @@ dataset_process <- function(filename_data_raw, # Record methods methods <- process_format_methods(metadata, dataset_id, sources, contributors) + # Retrieve taxonomic details for known species taxonomic_updates <- traits %>% @@ -1902,7 +1903,7 @@ dataset_update_taxonomy <- function(austraits_raw, taxa) { columns_in_taxon_list <- names(taxa) - # incoming table from austraits_raw is a list of all taxa for the study + # Incoming table from `austraits_raw` is a list of all taxa for the study # `original_name` and `aligned_name` will be different if # there were taxonomic_updates specified in metadata file austraits_raw$taxonomic_updates <- @@ -1922,7 +1923,8 @@ dataset_update_taxonomy <- function(austraits_raw, taxa) { taxa %>% dplyr::select(dplyr::all_of(c("aligned_name", "taxon_name"))) ) %>% dplyr::select(dplyr::all_of(c("dataset_id", "taxon_name")), dplyr::everything()) %>% - # for taxa where there is no taxon_name to matched to a "aligned_name", maintain the "aligned_name" as the "taxon_name" + # For taxa where there is no `taxon_name` to matched to a `aligned_name`, + # maintain the `aligned_name` as the `taxon_name` dplyr::mutate( taxon_name = ifelse(is.na(.data$taxon_name), .data$aligned_name, .data$taxon_name)#, ) %>% @@ -1942,13 +1944,13 @@ dataset_update_taxonomy <- function(austraits_raw, taxa) { .data$taxonomic_resolution), taxon_rank = .data$taxonomic_resolution, name_to_match_to = .data$taxon_name, - # Create variable `name_to_match_to` which specifies the part of the taxon name to which matches can be made. - # This step requires taxon_rank. - name_to_match_to = stringr::str_replace(.data$taxon_name, " \\[.+",""), + # Create variable `name_to_match_to` which specifies the part of the taxon name to which matches can be made + # This step requires `taxon_rank` + name_to_match_to = stringr::str_replace(.data$taxon_name, " \\[.+", ""), name_to_match_to = ifelse(!.data$taxon_rank %in% c("species", "subspecies", "series", "variety", "form"), - stringr::word(.data$taxon_name,1), .data$name_to_match_to) + stringr::word(.data$taxon_name, 1), .data$name_to_match_to) ) %>% - # Remove taxon_rank, as it is about to be merged back in, but matches will now be possible to more rows. + # Remove `taxon_rank`, as it is about to be merged back in, but matches will now be possible to more rows select(-dplyr::any_of(c("taxon_rank", "taxonomic_resolution"))) %>% util_df_convert_character() %>% # Merge in all data from taxa. @@ -1967,7 +1969,7 @@ dataset_update_taxonomy <- function(austraits_raw, taxa) { dplyr::distinct(.data$taxon_name, .keep_all = TRUE) %>% dplyr::select(dplyr::any_of(columns_in_taxon_list)) - # Now `taxonomic_resolution` be removed from the traits table. + # Now `taxonomic_resolution` be removed from the traits table austraits_raw$traits <- austraits_raw$traits %>% dplyr::select(-dplyr::all_of(c("taxonomic_resolution"))) @@ -2038,7 +2040,7 @@ write_plaintext <- function(austraits, path) { #' #' @return Tibble with duplicates and pivot columns #' @export -check_duplicates <- function( +check_pivot_duplicates <- function( database_object, dataset_ids = unique(database_object$traits$dataset_id) ) { diff --git a/R/setup.R b/R/setup.R index 1d6accf8..0786365b 100644 --- a/R/setup.R +++ b/R/setup.R @@ -1,10 +1,11 @@ #' Path to the `metadata.yml` file for specified `dataset_id` #' #' @param dataset_id Identifier for a particular study in the database +#' @param path_data Path to folder with data #' #' @return A string -metadata_path_dataset_id <- function(dataset_id) { - file.path("data", dataset_id, "metadata.yml") +metadata_path_dataset_id <- function(dataset_id, path_data = "data") { + file.path(path_data, dataset_id, "metadata.yml") } #' Create a template of file `metadata.yml` for specified `dataset_id` @@ -223,13 +224,13 @@ metadata_user_select_names <- function(title, vars) { #' @inheritParams metadata_path_dataset_id #' #' @export -metadata_check_custom_R_code <- function(dataset_id) { +metadata_check_custom_R_code <- function(dataset_id, path_data = "data") { # Read metadata - metadata <- read_metadata_dataset(dataset_id) + metadata <- read_metadata_dataset(dataset_id, path_data) # Load trait data and run `custom_R_code` - readr::read_csv(file.path("data", dataset_id, "data.csv"), col_types = cols(), guess_max = 100000) %>% + readr::read_csv(file.path(path_data, dataset_id, "data.csv"), col_types = cols(), guess_max = 100000) %>% process_custom_code(metadata[["dataset"]][["custom_R_code"]])() } diff --git a/R/testdata.R b/R/testdata.R index 421ae712..b12ddb1d 100644 --- a/R/testdata.R +++ b/R/testdata.R @@ -68,9 +68,9 @@ dataset_test_worker <- expect( comp$equal, sprintf( - "%s - %s should not contain: %s", + "%s - %s should not contain: '%s'", info, label, - paste(object[!i], collapse = ", ") + paste(object[!i], collapse = "', '") )) invisible(object) @@ -83,7 +83,7 @@ dataset_test_worker <- comp <- compare(all(i), TRUE, ...) expect( comp$equal, - sprintf("%s - does not contain: %s", info, paste(expected[!i], collapse = ", ")) + sprintf("%s - does not contain: '%s'", info, paste(expected[!i], collapse = "', '")) ) invisible(object) @@ -97,9 +97,9 @@ dataset_test_worker <- expect( comp$equal, sprintf( - "%s - %s include(s) invalid terms: %s", + "%s - %s include(s) invalid terms: '%s'", info, label, - paste(object[!i], collapse = ", ") + paste(object[!i], collapse = "', '") )) invisible(object) @@ -167,7 +167,7 @@ dataset_test_worker <- x <- table(unlist(object)) i <- x == 1 comp <- compare(all(i), TRUE) - expect(comp$equal, sprintf("%s - %s not unique: %s", info, label, paste(names(x)[!i], collapse = ", "))) + expect(comp$equal, sprintf("%s - %s not unique: '%s'", info, label, paste(names(x)[!i], collapse = "', '"))) invisible(object) } @@ -279,9 +279,10 @@ dataset_test_worker <- } expect_list_elements_exact_names <- function(object, expected, info) { - for (i in seq_along(object)) + for (i in seq_along(object)) { expect_contains(names(object[[i]]), expected, info = paste(info, i)) expect_allowed(names(object[[i]]), expected, info = paste(info, i), label = "field names") + } invisible(object) } @@ -360,13 +361,13 @@ dataset_test_worker <- context(sprintf("%s", dataset_id)) - # Exists + ## Files exist files <- file.path(s, c("data.csv", "metadata.yml")) for (f in files) { expect_true(file.exists(f), info = sprintf("%s" %+% "\tfile does not exist", red(f))) } - # Check for other files + ## Check for other files vals <- c("data.csv", "metadata.yml", "raw") expect_is_in( dir(s), vals, @@ -374,13 +375,13 @@ dataset_test_worker <- label = "folder" ) - # `data.csv` + ## `data.csv` f <- files[1] expect_silent( data <- read_csv(f, col_types = cols(), guess_max = 1e5, progress = FALSE) # Time columns get reformatted ) - # Check no issues flagged when parsing file + ## Check no issues flagged when parsing file expect_no_error( readr::stop_for_problems(data), info = sprintf(red("`read_csv(%s)`"), f) @@ -388,7 +389,7 @@ dataset_test_worker <- expect_dataframe_valid(data, info = paste0(red(f), "\tdata"), label = "column names") - # Metadata + ## Metadata f <- files[2] expect_allowed_text(readLines(f, encoding = "UTF-8"), info = paste0(red(f), "\tmetadata"), label = "metadata") expect_silent(metadata <- yaml::read_yaml(f)) @@ -397,7 +398,7 @@ dataset_test_worker <- info = red(f), label = "metadata sections" ) - # Custom R code + ## Custom R code txt <- metadata[["dataset"]][["custom_R_code"]] # Check that `custom_R_code` is immediately followed by `collection_date` expect_equal( @@ -408,7 +409,7 @@ dataset_test_worker <- # Apply custom manipulations expect_no_error(data <- process_custom_code(txt)(data), info = paste0(red(f), "\t`custom_R_code`")) - # Source + ## Source expect_list_names_valid(metadata[["source"]], info = sprintf("%s\tsource", red(f)), label = "field names") v <- names(metadata[["source"]]) @@ -443,7 +444,7 @@ dataset_test_worker <- label = "keys" ) - # People + ## People expect_list(metadata[["contributors"]], info = paste0(red(f), "\tcontributors")) expect_list_names_allowed( @@ -452,7 +453,7 @@ dataset_test_worker <- info = paste0(red(f), "\tcontributors"), label = "contributor type fields" ) - # Data collectors + ## Data collectors if (!is.na(metadata[["contributors"]][["data_collectors"]][1])) { expect_list(metadata[["contributors"]][["data_collectors"]], info = paste0(red(f), "\tdata_collectors")) @@ -472,7 +473,7 @@ dataset_test_worker <- } } - # Dataset curators + ## Dataset curators expect_true( !is.null(metadata[["contributors"]][["dataset_curators"]]), info = sprintf("%s\tcontributors - `dataset_curators` is missing", red(f)) @@ -482,14 +483,14 @@ dataset_test_worker <- info = paste0(red(f), "\tcontributors"), label = "`dataset_curators`" ) - # Assistants + ## Assistants if (!is.null(metadata[["contributors"]][["assistants"]][1])) expect_type( metadata[["contributors"]][["assistants"]], "character", info = paste0(red(f), "\tcontributors"), label = "`assistants`" ) - # Dataset + ## Dataset expect_list_names_allowed( metadata[["dataset"]], schema$metadata$elements$dataset$values %>% names(), @@ -506,17 +507,19 @@ dataset_test_worker <- info = paste0(red(f), "\tdataset"), label = "metadata" ) - # Locations - if (length(unlist(metadata[["locations"]])) > 1) { - expect_list(metadata[["locations"]], info = paste0(red(f), "\tlocations")) + ## Locations - expect_silent( - locations <- - metadata$locations %>% - process_format_locations(dataset_id, schema) %>% - process_add_all_columns(names(schema[["austraits"]][["elements"]][["locations"]][["elements"]])) + expect_silent( + locations <- + metadata$locations %>% + process_format_locations(dataset_id, schema) %>% + process_add_all_columns(names(schema[["austraits"]][["elements"]][["locations"]][["elements"]])) ) + if (length(unlist(metadata[["locations"]])) > 1) { + + expect_list(metadata[["locations"]], info = paste0(red(f), "\tlocations")) + expect_dataframe_names_contain( locations, c("dataset_id", "location_name", "location_property", "value"), @@ -524,30 +527,63 @@ dataset_test_worker <- ) for (v in names(metadata$locations)) { + expect_list(metadata[["locations"]][[v]], info = paste0(red(f), "\tlocation ", v)) - expect_contains( - names(metadata[["locations"]][[v]]), - c("latitude (deg)", "longitude (deg)"), - info = paste0(red(f), "\tlocation '", v, "'") - ) + + # If fields do not contain both 'latitude range (deg)' and 'longitude range (deg)' + if (!(all(c("latitude range (deg)", "longitude range (deg)") %in% names(metadata[["locations"]][[v]])))) { + + # Check that it contains 'latitude (deg)' and 'longitude (deg)' + expect_contains( + names(metadata[["locations"]][[v]]), + c("latitude (deg)", "longitude (deg)"), + info = paste0(red(f), "\tlocation '", v, "'") + ) + } } - } - # Contexts - filename_data <- paste0(path_data, "/", dataset_id, "/data.csv") + # Check `location_name`'s from metadata are in dataset and vice versa + expect_true( + !is.null(metadata[["dataset"]][["location_name"]]), + info = paste0(red(files[2]), "\tdataset - `location_name` is missing") + ) + + expect_contains( + names(data), + metadata[["dataset"]][["location_name"]], + info = paste0( + red(files[2]), + "\tdataset - `location_name` column not found in data") + ) + + v <- data[[metadata[["dataset"]][["location_name"]]]] %>% unique %>% na.omit + i <- v %in% names(metadata$locations) + expect_true( + all(i), + info = paste0( + red(f), + "\tlocations - location names from data file not present in metadata: ", + v[!i]) + ) - traits <- - # Read all columns as character type to prevent time data types from being reformatted - readr::read_csv(filename_data, col_types = cols(), guess_max = 100000, progress = FALSE) %>% - process_custom_code(metadata[["dataset"]][["custom_R_code"]])() + i <- names(metadata$locations) %in% v + expect_true( + all(i), + info = paste0( + red(f), + "\tlocations - location names from metadata not present in data file: ", + names(metadata$locations)[!i]) + ) + } + ## Contexts expect_silent( contexts <- metadata$contexts %>% - process_format_contexts(dataset_id, traits) + process_format_contexts(dataset_id, data) ) - ## Check context details load + # Check context details load if (nrow(contexts) > 0) { expect_dataframe_names_contain( @@ -556,6 +592,34 @@ dataset_test_worker <- info = paste0(red(f), "\tcontexts"), label = "field names" ) + # Check that unique context `value`'s only have one unique description + expect_equal( + contexts %>% dplyr::group_by(.data$context_property, .data$value) %>% dplyr::summarise(n = dplyr::n_distinct(.data$description)) %>% + filter(.data$n > 1) %>% nrow(), + 0, info = sprintf( + "%s\tcontexts - `value`'s should only have one unique description each: '%s'", + red(f), + paste( + contexts %>% dplyr::group_by(.data$context_property, .data$value) %>% dplyr::summarise(n = dplyr::n_distinct(.data$description)) %>% + filter(.data$n > 1) %>% dplyr::pull(.data$value) %>% unique(), + collapse = "', '") + ) + ) + + # Check that there are no duplicate `find` fields + expect_equal( + contexts %>% dplyr::group_by(.data$context_property, .data$find) %>% dplyr::summarise(n = dplyr::n()) %>% filter(.data$n > 1) %>% + nrow(), + 0, info = sprintf( + "%s\tcontexts - duplicate `find` values detected: '%s'", + red(f), + paste( + contexts %>% dplyr::group_by(.data$context_property, .data$find) %>% dplyr::summarise(n = dplyr::n()) %>% filter(.data$n > 1) %>% + dplyr::pull(.data$find) %>% unique(), + collapse = "', '") + ) + ) + for (i in seq_along(metadata$contexts)) { vals <- metadata$contexts[[i]][["values"]] @@ -610,10 +674,10 @@ dataset_test_worker <- } } - # Traits + ## Traits expect_list_elements_contains_names( metadata[["traits"]], - schema$metadata$elements$traits$elements[1:3] %>% names(), # Add `value_type` and `basis_of_value` + c("var_in", "unit_in", "trait_name", "value_type", "basis_of_value"), info = paste0(red(f), "\ttrait") ) @@ -636,7 +700,9 @@ dataset_test_worker <- label = "`trait_name`'s" ) - # Now that traits loaded, check details of context match + # Check no duplicate `var_in`'s + + # Now that traits loaded, check details of contexts match if (nrow(contexts > 0)) { # Check they are in context dataset @@ -646,11 +712,12 @@ dataset_test_worker <- info = paste0(red(files[1]), red(", "), red(files[2]), "\tdata and/or traits metadata") ) + unique2 <- function(x) unique(x[!is.na(x)]) + for (j in unique(contexts[["var_in"]])) { contextsub <- contexts %>% filter(var_in == j) - unique2 <- function(x) unique(x[!is.na(x)]) # Context values align either with a column of data or a column of traits table if (is.null(data[[j]])) { v <- traits[[j]] %>% unique2() @@ -668,11 +735,11 @@ dataset_test_worker <- info = ifelse( "hms" %in% class(v), sprintf( - "%s\tcontexts - context values of '%s' from data file not present in metadata contexts: %s\n\n'%s' has been detected as a time data type and reformatted\n\t-> Please make sure context metadata matches reformatting", - red(f), j, v[!i], j), + "%s\tcontexts - context values of '%s' from data file not present in metadata contexts: '%s'\n\n'%s' has been detected as a time data type and reformatted\n\t-> Please make sure context metadata matches reformatting", + red(f), j, paste(as.character(v)[!i], collapse = "', '"), j), sprintf( - "%s\tcontexts - context values of '%s' from data file not present in metadata: %s", - red(f), j, v[!i])) + "%s\tcontexts - context values of '%s' from data file not present in metadata: '%s'", + red(f), j, paste(v[!i], collapse = "', '"))) ) i <- contextsub[["find"]] %in% v @@ -682,46 +749,70 @@ dataset_test_worker <- info = ifelse( !is.null(data[[j]]), sprintf( - "%s\tcontexts - values of '%s' in metadata not detected in context values from data file: %s", - red(f), j, contextsub[["find"]][!i]), + "%s\tcontexts - values of '%s' in metadata not detected in context values from data file: '%s'", + red(f), j, paste(contextsub[["find"]][!i], collapse = "', '")), sprintf( - "%s\tcontexts - values of '%s' in metadata not detected in context values from traits metadata: %s", - red(f), j, contextsub[["find"]][!i]) + "%s\tcontexts - values of '%s' in metadata not detected in context values from traits metadata: '%s'", + red(f), j, paste(contextsub[["find"]][!i], collapse = "', '")) ) ) } } - # Check value types in metadata and any columns of data + ## Check metadata values are allowed for fields specified in traits metadata + metadata_fields <- c("entity_type", "value_type", "basis_of_value", "basis_of_record") - # XXXX TODO -- also check for entity type, basis of value and any other columns - # Note this only checks for `value_type` at the trait metadata level, which is appropriate for `value_type` - # but may not be appropriate for other fields on the TODO list + for (field in metadata_fields) { - if ("value_type" %in% names(traits)) { + if (field %in% names(traits)) { - i <- traits$value_type %in% names(data) + not_allowed <- schema[[field]][["values"]] %>% names() + i <- traits[[field]] %in% names(data) & !(traits[[field]] %in% not_allowed) + fixed <- traits[[field]][!i] %>% unique() + cols <- traits[[field]][i] %>% unique() - value_type_fixed <- traits$value_type[!i] %>% unique() - value_type_cols <- traits$value_type[i] %>% unique() + # Check fixed values in metadata are allowed + expect_is_in( + fixed, schema[[field]][["values"]] %>% names, + info = paste0(red(f), "\ttraits"), label = sprintf("`%s`", field) + ) - expect_is_in( - value_type_fixed, - schema$value_type$values %>% names, - info = paste0(red(f), "\ttraits"), label = "value types" - ) + # Check column values are allowed + if (length(cols) > 0) { + for (c in cols) { + expect_is_in( + data[[c]] %>% unique(), schema[[field]][["values"]] %>% names, + info = sprintf("%s\t'%s'", red(files[1]), c), + label = sprintf("`%s` column", field) + ) + } + } + } + + ## Check metadata values are allowed for fields specified in dataset metadata + if (field %in% names(metadata[["dataset"]])) { - if (length(value_type_cols) > 0) { - for (v in value_type_cols) + not_allowed <- schema[[field]][["values"]] %>% names() + + # If the metadata field is a column in the data (and not an accepted value of the field) + if (metadata[["dataset"]][[field]] %in% names(data) & !(metadata[["dataset"]][[field]] %in% not_allowed)) { + expect_is_in( + data[[metadata[["dataset"]][[field]]]] %>% unique(), schema[[field]][["values"]] %>% names, + info = sprintf("%s\t'%s'", red(files[1]), metadata[["dataset"]][[field]]), + label = sprintf("`%s` column", field) + ) + # Otherwise check fixed value + } else { expect_is_in( - data[[v]] %>% unique(), - schema$value_type$values %>% names, - info = sprintf("%s\t%s", red(files[1]), v), label = "value type column" + metadata[["dataset"]][[field]], schema[[field]][["values"]] %>% names, + info = paste0(red(f), "\tdataset"), label = sprintf("`%s`", field) ) + } } } - # Substitutions + ## Substitutions + if (!is.na(metadata[["substitutions"]][1])) { expect_list_elements_exact_names( @@ -729,7 +820,6 @@ dataset_test_worker <- schema$metadata$elements$substitutions$values %>% names(), info = paste0(red(f), "\tsubstitution") ) - trait_names <- sapply(metadata[["substitutions"]], "[[", "trait_name") expect_is_in( unique(trait_names), definitions$elements %>% names(), @@ -740,18 +830,33 @@ dataset_test_worker <- info = paste0(red(f), "\tsubstitutions"), label = "`trait_name`'s" ) - # Check for allowable values of categorical variables expect_no_error( x <- metadata[["substitutions"]] %>% util_list_to_df2() %>% split(.$trait_name), info = paste0(red(f), "\tconverting substitutions to a dataframe and splitting by `trait_name`") ) + # Check for allowable values of categorical variables for (trait in names(x)) { - if (!is.null(definitions$elements[[trait]]) && - definitions$elements[[trait]]$type == "categorical") { + # First check no duplicate combinations of `find` + expect_equal( + x[[trait]] %>% dplyr::group_by(.data$find) %>% dplyr::summarise(n = dplyr::n()) %>% filter(.data$n > 1) %>% nrow(), + 0, info = sprintf( + "%s\tsubstitutions - duplicate `find` values detected: '%s'", + red(f), + paste( + x[[trait]] %>% dplyr::group_by(.data$find) %>% dplyr::summarise(n = dplyr::n()) %>% filter(.data$n > 1) %>% + dplyr::pull(.data$find) %>% unique(), + collapse = "', '") + ) + ) + + # If trait is categorical + if (!is.null(definitions$elements[[trait]]) && definitions$elements[[trait]]$type == "categorical") { + # Check replacement values to_check <- x[[trait]]$replace %>% unique() + # Filter out `flowering_time` values from to-check list to_check <- to_check[!(grepl("^[YyNn]+$", to_check) & stringr::str_length(to_check) == 12)] allowable <- c(definitions$elements[[trait]]$allowed_values_levels %>% names(), NA) failing <- to_check[!( @@ -764,15 +869,34 @@ dataset_test_worker <- info = sprintf( "%s\tsubstitutions - `%s` has invalid replacement values", red(f), trait), - label = failing %>% paste(collapse = ", ") + label = failing %>% paste(collapse = "', '") ) } } } - # Taxonomic updates + ## Taxonomic updates + if (!is.na(metadata[["taxonomic_updates"]][1])) { + expect_no_error( + x <- metadata[["taxonomic_updates"]] %>% util_list_to_df2(), + info = paste0(red(f), "\tconverting `taxonomic_updates` to a dataframe") + ) + + # Check no duplicate `find` values + expect_equal( + x %>% dplyr::group_by(.data$find) %>% dplyr::summarise(n = dplyr::n()) %>% filter(.data$n > 1) %>% nrow(), + 0, info = sprintf( + "%s\ttaxonomic_updates - duplicate `find` values detected: '%s'", + red(f), + paste( + x %>% dplyr::group_by(.data$find) %>% dplyr::summarise(n = dplyr::n()) %>% filter(.data$n > 1) %>% + dplyr::pull(.data$find) %>% unique(), + collapse = "', '") + ) + ) + expect_list_elements_exact_names( metadata[["taxonomic_updates"]], schema$metadata$elements$taxonomic_updates$values %>% names(), @@ -786,7 +910,7 @@ dataset_test_worker <- } - # Check that special characters do not make it into the data + ## Check that special characters do not make it into the data expect_no_error( parsed_data <- data %>% process_parse_data(dataset_id, metadata, contexts, schema), @@ -797,7 +921,7 @@ dataset_test_worker <- info = sprintf("%s", red(files[1])) ) - # Process data so that you can check excluded observations + ## Process data so that you can check excluded observations parsed_data <- parsed_data$traits %>% process_add_all_columns( @@ -805,7 +929,7 @@ dataset_test_worker <- "parsing_id", "location_name", "taxonomic_resolution", "methods", "unit_in") ) - # Replace original `location_id` with a new `location_id` + ## Replace original `location_id` with a new `location_id` if (nrow(locations) > 0) { parsed_data <- parsed_data %>% @@ -821,7 +945,7 @@ dataset_test_worker <- ) } - # Where missing, fill variables in traits table with values from locations + ## Where missing, fill variables in traits table with values from locations # Trait metadata should probably have precedence -- right now trait metadata # is being read in during `process_parse_data` and getting overwritten here #TODO # If process.R changes, this needs to be updated @@ -847,9 +971,28 @@ dataset_test_worker <- } } - # Excluded observations + ## Excluded observations + if (!is.na(metadata[["exclude_observations"]][1])) { + expect_no_error( + x <- metadata[["exclude_observations"]] %>% util_list_to_df2(), + info = paste0(red(f), "\tconverting `exclude_observations` to a dataframe") + ) + + # Check no duplicate `find` values + expect_equal( + x %>% dplyr::group_by(.data$variable, .data$find) %>% dplyr::summarise(n = dplyr::n()) %>% filter(.data$n > 1) %>% nrow(), + 0, info = sprintf( + "%s\texclude_observations - duplicate `find` values detected: '%s'", + red(f), + paste( + x %>% dplyr::group_by(.data$variable, .data$find) %>% dplyr::summarise(n = dplyr::n()) %>% filter(.data$n > 1) %>% + dplyr::pull(.data$find) %>% unique(), + collapse = "', '") + ) + ) + expect_list_elements_exact_names( metadata[["exclude_observations"]], schema$metadata$elements$exclude_observations$values %>% names(), @@ -918,43 +1061,9 @@ dataset_test_worker <- ## For numeric trait data, check it looks reasonable & converts properly - ## Check `location_name`'s are in locations dataset - if (length(unlist(metadata[["locations"]])) > 1) { - - expect_true( - !is.null(metadata[["dataset"]][["location_name"]]), - info = paste0(red(files[2]), "\tdataset - `location_name` is missing") - ) - - expect_contains( - names(data), - metadata[["dataset"]][["location_name"]], - info = paste0( - red(files[2]), - "\tdataset - `location_name` column not found in data") - ) - - v <- data[[metadata[["dataset"]][["location_name"]]]] %>% unique %>% na.omit - i <- v %in% names(metadata$locations) - expect_true( - all(i), - info = paste0( - red(f), - "\tlocations - location names from data file not present in metadata: ", - v[!i]) - ) - - i <- names(metadata$locations) %in% v - expect_true( - all(i), - info = paste0( - red(f), - "\tlocations - location names from metadata not present in data file: ", - names(metadata$locations)[!i]) - ) - } + ## Check traits are not only NAs expect_false( nrow(metadata[["traits"]] %>% util_list_to_df2() %>% dplyr::filter(!is.na(.data$trait_name))) == 0, info = paste0(red(f), "\ttraits - only contain NA `trait_name`'s")) @@ -975,10 +1084,10 @@ dataset_test_worker <- ), info = sprintf("%s\tbuilding dataset", red(dataset_id))) - # Check that traits table is not empty + ## Check that traits table is not empty expect_false(nrow(dataset$traits) == 0, info = sprintf("%s\t`traits` table is empty", red(dataset_id))) - # Check that dataset can pivot wider + ## Check that dataset can pivot wider if (nrow(dataset$traits) > 0) { expect_true( dataset %>% check_pivot_wider(), diff --git a/R/utils.R b/R/utils.R index c953ae43..819b000a 100644 --- a/R/utils.R +++ b/R/utils.R @@ -231,9 +231,9 @@ read_metadata <- function(path) { #' @inheritParams metadata_path_dataset_id #' #' @return A list with contents of metadata for specified `dataset_id` -read_metadata_dataset <- function(dataset_id) { +read_metadata_dataset <- function(dataset_id, path_data = "data") { dataset_id %>% - metadata_path_dataset_id() %>% + metadata_path_dataset_id(path_data = path_data) %>% read_metadata() } diff --git a/inst/support/traits.build_schema.yml b/inst/support/traits.build_schema.yml index 70f70809..74d2cffc 100644 --- a/inst/support/traits.build_schema.yml +++ b/inst/support/traits.build_schema.yml @@ -417,8 +417,8 @@ metadata: values: find: *original_name replace: *taxon_name - reason: Records why the change was implemented, e.g. `typos`, `taxonomic synonyms`, and `standardising spellings`. - taxonomic_resolution: The taxonomic rank of the most specific name that can be aligned. + reason: Records why the change was implemented, e.g. `typos`, `taxonomic synonyms`, and `standardising spellings` + taxonomic_resolution: *taxonomic_resolution exclude_observations: description: A table of observations to remove from the compilation. type: array diff --git a/man/check_duplicates.Rd b/man/check_pivot_duplicates.Rd similarity index 85% rename from man/check_duplicates.Rd rename to man/check_pivot_duplicates.Rd index adbdc869..c26004c9 100644 --- a/man/check_duplicates.Rd +++ b/man/check_pivot_duplicates.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/process.R -\name{check_duplicates} -\alias{check_duplicates} +\name{check_pivot_duplicates} +\alias{check_pivot_duplicates} \title{Identify duplicates preventing pivoting wider} \usage{ -check_duplicates( +check_pivot_duplicates( database_object, dataset_ids = unique(database_object$traits$dataset_id) ) diff --git a/man/metadata_check_custom_R_code.Rd b/man/metadata_check_custom_R_code.Rd index 9be03c54..f47d6aad 100644 --- a/man/metadata_check_custom_R_code.Rd +++ b/man/metadata_check_custom_R_code.Rd @@ -5,10 +5,12 @@ \title{Check the output of running `custom_R_code` specified in the metadata for specified `dataset_id`} \usage{ -metadata_check_custom_R_code(dataset_id) +metadata_check_custom_R_code(dataset_id, path_data = "data") } \arguments{ \item{dataset_id}{Identifier for a particular study in the database} + +\item{path_data}{Path to folder with data} } \description{ Function to check the output of running `custom_R_code` specified in diff --git a/man/metadata_path_dataset_id.Rd b/man/metadata_path_dataset_id.Rd index d499a39b..c0058d24 100644 --- a/man/metadata_path_dataset_id.Rd +++ b/man/metadata_path_dataset_id.Rd @@ -4,10 +4,12 @@ \alias{metadata_path_dataset_id} \title{Path to the `metadata.yml` file for specified `dataset_id`} \usage{ -metadata_path_dataset_id(dataset_id) +metadata_path_dataset_id(dataset_id, path_data = "data") } \arguments{ \item{dataset_id}{Identifier for a particular study in the database} + +\item{path_data}{Path to folder with data} } \value{ A string diff --git a/man/read_metadata_dataset.Rd b/man/read_metadata_dataset.Rd index 85146463..c28e4101 100644 --- a/man/read_metadata_dataset.Rd +++ b/man/read_metadata_dataset.Rd @@ -4,10 +4,12 @@ \alias{read_metadata_dataset} \title{Read the `metadata.yml` file for specified `dataset_id`} \usage{ -read_metadata_dataset(dataset_id) +read_metadata_dataset(dataset_id, path_data = "data") } \arguments{ \item{dataset_id}{Identifier for a particular study in the database} + +\item{path_data}{Path to folder with data} } \value{ A list with contents of metadata for specified `dataset_id` diff --git a/tests/testthat/config/taxon_list-orig.R b/tests/testthat/config/taxon_list-orig.R index 29876ad3..c870283a 100644 --- a/tests/testthat/config/taxon_list-orig.R +++ b/tests/testthat/config/taxon_list-orig.R @@ -7,5 +7,6 @@ # Then source "build.R" and "R/build_update_taxon_list.R" in "tests/testthat" # Run the function on the built test database with `replace = TRUE` # (Remove the tests from the data folder afterwards) +# Replace config/taxon_list-orig.csv with config/taxon_list.csv build_update_taxon_list(database, read_csv("config/taxon_list.csv"), replace = TRUE) diff --git a/tests/testthat/config/taxon_list-orig.csv b/tests/testthat/config/taxon_list-orig.csv index 764bc6b7..935e7923 100644 --- a/tests/testthat/config/taxon_list-orig.csv +++ b/tests/testthat/config/taxon_list-orig.csv @@ -1,7 +1,9 @@ original_name,aligned_name,taxon_name,taxon_name_alternatives,genus,family,taxon_rank,taxonomic_dataset,taxonomic_status,subclass,taxon_distribution,scientific_name,taxon_id,taxon_ID_genus,scientific_name_id,canonical_name,cleaned_scientific_name_id,aligned_name_taxonomic_status,aligned_name_taxon_id,taxon_id_family,trinomial,binomial,establishment_means Abildgaardia ovata,Abildgaardia ovata,Abildgaardia ovata,NA,Abildgaardia,Cyperaceae,species,APC,accepted,Magnoliidae,"NT, Qld, NSW",Abildgaardia ovata (Burm.f.) Kral,https://id.biodiversity.org.au/node/apni/2919627,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/150737,Abildgaardia ovata,https://id.biodiversity.org.au/name/apni/150737,accepted,https://id.biodiversity.org.au/node/apni/2919627,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Abildgaardia ovata,native Acacia alpina,Acacia alpina,Acacia alpina,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Acacia alpina F.Muell.,https://id.biodiversity.org.au/node/apni/2907301,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/58263,Acacia alpina,https://id.biodiversity.org.au/name/apni/58263,accepted,https://id.biodiversity.org.au/node/apni/2907301,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia alpina,native -Acacia beadleana,Acacia beadleana,Acacia beadleana,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Acacia beadleana R.H.Jones & J.J.Bruhl,https://id.biodiversity.org.au/node/apni/2902581,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/198624,Acacia beadleana,https://id.biodiversity.org.au/name/apni/165277,taxonomic synonym,https://id.biodiversity.org.au/instance/apni/949589,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia beadleana,native +Acacia aneura var. major,Acacia aneura var. major,Acacia aneura var. major,NA,Acacia,Fabaceae,variety,APC,accepted,Magnoliidae,"NT, SA, Qld, NSW",Acacia aneura var. major Pedley,https://id.biodiversity.org.au/node/apni/2888234,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/169532,Acacia aneura var. major,https://id.biodiversity.org.au/name/apni/230757,taxonomic synonym,https://id.biodiversity.org.au/instance/apni/914729,https://id.biodiversity.org.au/taxon/apni/51702961,Acacia aneura var. major,Acacia aneura,native +Acacia auriculiformis,Acacia auriculiformis,Acacia auriculiformis,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT, Qld",Acacia auriculiformis A.Cunn. ex Benth.,https://id.biodiversity.org.au/node/apni/2900508,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/58974,Acacia auriculiformis,https://id.biodiversity.org.au/name/apni/58974,accepted,https://id.biodiversity.org.au/node/apni/2900508,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia auriculiformis,native and naturalised +Acacia beadleana,Acacia beadleana,Acacia beadleana,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Acacia beadleana R.H.Jones & J.J.Bruhl,https://id.biodiversity.org.au/node/apni/2902581,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/198624,Acacia beadleana,https://id.biodiversity.org.au/name/apni/244690,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/842202,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia beadleana,native Acacia bulgaensis,Acacia bulgaensis,Acacia bulgaensis,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Acacia bulgaensis Tindale & S.J.Davies,https://id.biodiversity.org.au/node/apni/2889179,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/117995,Acacia bulgaensis,https://id.biodiversity.org.au/name/apni/117995,accepted,https://id.biodiversity.org.au/node/apni/2889179,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia bulgaensis,native Acacia caroleae,Acacia caroleae,Acacia caroleae,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acacia caroleae Pedley,https://id.biodiversity.org.au/node/apni/2894332,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/60225,Acacia caroleae,https://id.biodiversity.org.au/name/apni/60225,accepted,https://id.biodiversity.org.au/node/apni/2894332,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia caroleae,native Acacia celsa,Acacia celsa,Acacia celsa,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,Qld,Acacia celsa Tindale,https://id.biodiversity.org.au/taxon/apni/51436506,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/154988,Acacia celsa,https://id.biodiversity.org.au/name/apni/154988,accepted,https://id.biodiversity.org.au/taxon/apni/51436506,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia celsa,native @@ -9,9 +11,14 @@ Acacia crassa,Acacia crassa,Acacia crassa,NA,Acacia,Fabaceae,species,APC,accepte Acacia flexifolia,Acacia flexifolia,Acacia flexifolia,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic",Acacia flexifolia A.Cunn. ex Benth.,https://id.biodiversity.org.au/node/apni/2914740,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/63146,Acacia flexifolia,https://id.biodiversity.org.au/name/apni/63146,accepted,https://id.biodiversity.org.au/node/apni/2914740,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia flexifolia,native Acacia gladiiformis,Acacia gladiiformis,Acacia gladiiformis,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acacia gladiiformis A.Cunn. ex Benth.,https://id.biodiversity.org.au/node/apni/2887779,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/63580,Acacia gladiiformis,https://id.biodiversity.org.au/name/apni/63580,accepted,https://id.biodiversity.org.au/node/apni/2887779,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia gladiiformis,native Acacia havilandiorum,Acacia havilandiorum,Acacia havilandiorum,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic",Acacia havilandiorum Maiden,https://id.biodiversity.org.au/node/apni/2897713,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/135274,Acacia havilandiorum,https://id.biodiversity.org.au/name/apni/135274,accepted,https://id.biodiversity.org.au/node/apni/2897713,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia havilandiorum,native +Acacia holosericea,Acacia holosericea,Acacia holosericea , Acacia colei (pro parte misapplied) | Acacia colei (misapplied),Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Acacia holosericea A.Cunn. ex G.Don,https://id.biodiversity.org.au/node/apni/2908330,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/64393,Acacia holosericea [alternative possible names: Acacia colei (pro parte misapplied) | Acacia colei (misapplied)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia holosericea,native +Acacia kempeana,Acacia kempeana,Acacia kempeana , Acacia sibirica (pro parte misapplied),Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA",Acacia kempeana F.Muell.,https://id.biodiversity.org.au/taxon/apni/51436560,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/65035,Acacia kempeana [alternative possible names: Acacia sibirica (pro parte misapplied)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia kempeana,native Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx subsp. leiocalyx,NA,Acacia,Fabaceae,subspecies,APC,accepted,Magnoliidae,"Qld, NSW",Acacia leiocalyx (Domin) Pedley subsp. leiocalyx,https://id.biodiversity.org.au/node/apni/2894438,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/65375,Acacia leiocalyx subsp. leiocalyx,https://id.biodiversity.org.au/name/apni/65375,accepted,https://id.biodiversity.org.au/node/apni/2894438,https://id.biodiversity.org.au/taxon/apni/51702961,Acacia leiocalyx subsp. leiocalyx,Acacia leiocalyx,native +Acacia lysiphloia,Acacia lysiphloia,Acacia lysiphloia,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Acacia lysiphloia F.Muell.,https://id.biodiversity.org.au/node/apni/2898828,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/66472,Acacia lysiphloia,https://id.biodiversity.org.au/name/apni/66472,accepted,https://id.biodiversity.org.au/node/apni/2898828,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia lysiphloia,native Acacia myrtifolia,Acacia myrtifolia,Acacia myrtifolia,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic, Tas",Acacia myrtifolia (Sm.) Willd.,https://id.biodiversity.org.au/node/apni/2901160,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/162110,Acacia myrtifolia,https://id.biodiversity.org.au/name/apni/162110,accepted,https://id.biodiversity.org.au/node/apni/2901160,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia myrtifolia,native +Acacia neurocarpa,Acacia neurocarpa,Acacia neurocarpa,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT",Acacia neurocarpa A.Cunn. ex Hook.,https://id.biodiversity.org.au/taxon/apni/51286994,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/67333,Acacia neurocarpa,https://id.biodiversity.org.au/name/apni/67333,accepted,https://id.biodiversity.org.au/taxon/apni/51286994,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia neurocarpa,native Acacia ramulosa var. ramulosa,Acacia ramulosa var. ramulosa,Acacia ramulosa var. ramulosa,NA,Acacia,Fabaceae,variety,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Acacia ramulosa W.Fitzg. var. ramulosa,https://id.biodiversity.org.au/node/apni/2915768,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/168882,Acacia ramulosa var. ramulosa,https://id.biodiversity.org.au/name/apni/168882,accepted,https://id.biodiversity.org.au/node/apni/2915768,https://id.biodiversity.org.au/taxon/apni/51702961,Acacia ramulosa var. ramulosa,Acacia ramulosa,native +Acacia shirleyi,Acacia shirleyi,Acacia shirleyi,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"NT, Qld",Acacia shirleyi Maiden,https://id.biodiversity.org.au/node/apni/2897282,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/70301,Acacia shirleyi,https://id.biodiversity.org.au/name/apni/70301,accepted,https://id.biodiversity.org.au/node/apni/2897282,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia shirleyi,native Acacia spectabilis,Acacia spectabilis,Acacia spectabilis,NA,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW (native and naturalised)",Acacia spectabilis A.Cunn. ex Benth.,https://id.biodiversity.org.au/node/apni/2918795,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/70543,Acacia spectabilis,https://id.biodiversity.org.au/name/apni/70543,accepted,https://id.biodiversity.org.au/node/apni/2918795,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Acacia spectabilis,native and naturalised Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis subsp. Glabrous form (M.Hancock 94),NA,Acacia,Fabaceae,subspecies,APC,accepted,Magnoliidae,"NSW, Vic, Tas",Acacia terminalis subsp. Glabrous form (M.Hancock 94) NSW Herbarium,https://id.biodiversity.org.au/node/apni/2886403,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/199841,Acacia terminalis subsp. Glabrous form (M.Hancock 94),https://id.biodiversity.org.au/name/apni/199841,accepted,https://id.biodiversity.org.au/node/apni/2886403,https://id.biodiversity.org.au/taxon/apni/51702961,Acacia terminalis subsp. Glabrous form (M.Hancock 94),Acacia terminalis,native Acronychia acidula,Acronychia acidula,Acronychia acidula,NA,Acronychia,Rutaceae,species,APC,accepted,Magnoliidae,Qld,Acronychia acidula F.Muell.,https://id.biodiversity.org.au/node/apni/2913200,https://id.biodiversity.org.au/taxon/apni/51446847,https://id.biodiversity.org.au/name/apni/73794,Acronychia acidula,https://id.biodiversity.org.au/name/apni/73794,accepted,https://id.biodiversity.org.au/node/apni/2913200,https://id.biodiversity.org.au/taxon/apni/51461748,NA,Acronychia acidula,native @@ -22,10 +29,12 @@ Alectryon oleifolius,Alectryon oleifolius,Alectryon oleifolius,NA,Alectryon,Sapi Alectryon subdentatus,Alectryon subdentatus,Alectryon subdentatus,NA,Alectryon,Sapindaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Alectryon subdentatus (F.Muell. ex Benth.) Radlk.,https://id.biodiversity.org.au/node/apni/2890534,https://id.biodiversity.org.au/taxon/apni/51299789,https://id.biodiversity.org.au/name/apni/81114,Alectryon subdentatus,https://id.biodiversity.org.au/name/apni/81114,accepted,https://id.biodiversity.org.au/node/apni/2890534,https://id.biodiversity.org.au/taxon/apni/51447212,NA,Alectryon subdentatus,native Aleurites rockinghamensis,Aleurites rockinghamensis,Aleurites rockinghamensis,NA,Aleurites,Euphorbiaceae,species,APC,accepted,Magnoliidae,Qld,Aleurites rockinghamensis (Baill.) P.I.Forst.,https://id.biodiversity.org.au/node/apni/2916622,https://id.biodiversity.org.au/node/apni/2900410,https://id.biodiversity.org.au/name/apni/171057,Aleurites rockinghamensis,https://id.biodiversity.org.au/name/apni/171057,accepted,https://id.biodiversity.org.au/node/apni/2916622,https://id.biodiversity.org.au/taxon/apni/51442249,NA,Aleurites rockinghamensis,native Alphitonia petriei,Alphitonia petriei,Alphitonia petriei,NA,Alphitonia,Rhamnaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Alphitonia petriei Braid & C.T.White,https://id.biodiversity.org.au/node/apni/2887911,https://id.biodiversity.org.au/taxon/apni/51446205,https://id.biodiversity.org.au/name/apni/82935,Alphitonia petriei,https://id.biodiversity.org.au/name/apni/82935,accepted,https://id.biodiversity.org.au/node/apni/2887911,https://id.biodiversity.org.au/taxon/apni/51446206,NA,Alphitonia petriei,native -Alstonia scholaris,Alstonia scholaris,Alstonia scholaris,NA,Alstonia,Apocynaceae,species,APC,accepted,Magnoliidae,Qld,Alstonia scholaris (L.) R.Br.,https://id.biodiversity.org.au/node/apni/2916809,https://id.biodiversity.org.au/node/apni/6684160,https://id.biodiversity.org.au/name/apni/83915,Alstonia scholaris,https://id.biodiversity.org.au/name/apni/83915,accepted,https://id.biodiversity.org.au/node/apni/2916809,https://id.biodiversity.org.au/taxon/apni/51700686,NA,Alstonia scholaris,native +Alstonia scholaris,Alstonia scholaris,Alstonia scholaris,NA,Alstonia,Apocynaceae,species,APC,accepted,Magnoliidae,Qld,Alstonia scholaris (L.) R.Br.,https://id.biodiversity.org.au/node/apni/2916809,https://id.biodiversity.org.au/node/apni/6684160,https://id.biodiversity.org.au/name/apni/83915,Alstonia scholaris,https://id.biodiversity.org.au/name/apni/83915,accepted,https://id.biodiversity.org.au/node/apni/2916809,https://id.biodiversity.org.au/taxon/apni/51736528,NA,Alstonia scholaris,native Amyema preissii,Amyema preissii,Amyema preissii,NA,Amyema,Loranthaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Amyema preissii (Miq.) Tiegh.,https://id.biodiversity.org.au/node/apni/2888430,https://id.biodiversity.org.au/taxon/apni/51438795,https://id.biodiversity.org.au/name/apni/87461,Amyema preissii,https://id.biodiversity.org.au/name/apni/87461,accepted,https://id.biodiversity.org.au/node/apni/2888430,https://id.biodiversity.org.au/taxon/apni/51438796,NA,Amyema preissii,native -Angophora leiocarpa,Angophora leiocarpa,Angophora leiocarpa,NA,Angophora,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Angophora leiocarpa (L.A.S.Johnson ex G.J.Leach) K.R.Thiele & Ladiges,https://id.biodiversity.org.au/node/apni/2894339,https://id.biodiversity.org.au/taxon/apni/51439560,https://id.biodiversity.org.au/name/apni/123435,Angophora leiocarpa,https://id.biodiversity.org.au/name/apni/123435,accepted,https://id.biodiversity.org.au/node/apni/2894339,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Angophora leiocarpa,native -Arbutus unedo,Arbutus unedo,Arbutus unedo,NA,Arbutus,Ericaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (doubtfully naturalised), NSW (doubtfully naturalised), ACT (doubtfully naturalised), Vic (naturalised), Tas (doubtfully naturalised)",Arbutus unedo L.,https://id.biodiversity.org.au/node/apni/2904939,https://id.biodiversity.org.au/node/apni/2892910,https://id.biodiversity.org.au/name/apni/98540,Arbutus unedo,https://id.biodiversity.org.au/name/apni/98540,accepted,https://id.biodiversity.org.au/node/apni/2904939,https://id.biodiversity.org.au/taxon/apni/51436079,NA,Arbutus unedo,naturalised +Angophora leiocarpa,Angophora leiocarpa,Angophora leiocarpa,NA,Angophora,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Angophora leiocarpa (L.A.S.Johnson ex G.J.Leach) K.R.Thiele & Ladiges,https://id.biodiversity.org.au/node/apni/2894339,https://id.biodiversity.org.au/taxon/apni/51439560,https://id.biodiversity.org.au/name/apni/123435,Angophora leiocarpa,https://id.biodiversity.org.au/name/apni/123435,accepted,https://id.biodiversity.org.au/node/apni/2894339,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Angophora leiocarpa,native +Arbutus unedo,Arbutus unedo,Arbutus unedo,NA,Arbutus,Ericaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (doubtfully naturalised), NSW (doubtfully naturalised), ACT (doubtfully naturalised), Vic (naturalised), Tas (doubtfully naturalised)",Arbutus unedo L.,https://id.biodiversity.org.au/node/apni/2904939,https://id.biodiversity.org.au/node/apni/2892910,https://id.biodiversity.org.au/name/apni/98540,Arbutus unedo,https://id.biodiversity.org.au/name/apni/98540,accepted,https://id.biodiversity.org.au/node/apni/2904939,https://id.biodiversity.org.au/taxon/apni/51738121,NA,Arbutus unedo,naturalised +Archidendron kanisii,Archidendron kanisii,Archidendron kanisii,NA,Archidendron,Fabaceae,species,APC,accepted,Magnoliidae,Qld,Archidendron kanisii R.S.Cowan,https://id.biodiversity.org.au/node/apni/2910703,https://id.biodiversity.org.au/taxon/apni/51299843,https://id.biodiversity.org.au/name/apni/154409,Archidendron kanisii,https://id.biodiversity.org.au/name/apni/154409,accepted,https://id.biodiversity.org.au/node/apni/2910703,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Archidendron kanisii,native +Archidendron whitei,Archidendron whitei,Archidendron whitei,NA,Archidendron,Fabaceae,species,APC,accepted,Magnoliidae,Qld,Archidendron whitei I.C.Nielsen,https://id.biodiversity.org.au/node/apni/2895435,https://id.biodiversity.org.au/taxon/apni/51299843,https://id.biodiversity.org.au/name/apni/116851,Archidendron whitei,https://id.biodiversity.org.au/name/apni/116851,accepted,https://id.biodiversity.org.au/node/apni/2895435,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Archidendron whitei,native Argyrodendron peralatum,Argyrodendron peralatum,Argyrodendron peralatum,NA,Argyrodendron,Malvaceae,species,APC,accepted,Magnoliidae,Qld,Argyrodendron peralatum (F.M.Bailey) Edlin ex I.H.Boas,https://id.biodiversity.org.au/node/apni/2915243,https://id.biodiversity.org.au/taxon/apni/51288410,https://id.biodiversity.org.au/name/apni/100216,Argyrodendron peralatum,https://id.biodiversity.org.au/name/apni/100216,accepted,https://id.biodiversity.org.au/node/apni/2915243,https://id.biodiversity.org.au/taxon/apni/51439248,NA,Argyrodendron peralatum,native Atractocarpus hirtus,Atractocarpus hirtus,Atractocarpus hirtus,NA,Atractocarpus,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Atractocarpus hirtus (F.Muell.) Puttock,https://id.biodiversity.org.au/node/apni/2910460,https://id.biodiversity.org.au/taxon/apni/51446611,https://id.biodiversity.org.au/name/apni/146883,Atractocarpus hirtus,https://id.biodiversity.org.au/name/apni/146883,accepted,https://id.biodiversity.org.au/node/apni/2910460,https://id.biodiversity.org.au/taxon/apni/51446612,NA,Atractocarpus hirtus,native Australina pusilla,Australina pusilla,Australina pusilla,NA,Australina,Urticaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic, Tas",Australina pusilla (Poir.) Gaudich.,https://id.biodiversity.org.au/node/apni/2913845,https://id.biodiversity.org.au/node/apni/2907879,https://id.biodiversity.org.au/name/apni/113875,Australina pusilla,https://id.biodiversity.org.au/name/apni/113875,accepted,https://id.biodiversity.org.au/node/apni/2913845,https://id.biodiversity.org.au/taxon/apni/51662052,NA,Australina pusilla,native @@ -33,11 +42,11 @@ Brombya platynema,Brombya platynema,Brombya platynema,NA,Brombya,Rutaceae,specie Burmannia disticha,Burmannia disticha,Burmannia disticha,NA,Burmannia,Burmanniaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Burmannia disticha L.,https://id.biodiversity.org.au/node/apni/2900088,https://id.biodiversity.org.au/node/apni/2915743,https://id.biodiversity.org.au/name/apni/70173,Burmannia disticha,https://id.biodiversity.org.au/name/apni/70173,accepted,https://id.biodiversity.org.au/node/apni/2900088,https://id.biodiversity.org.au/node/apni/2887196,NA,Burmannia disticha,native Bursaria spinosa subsp. spinosa,Bursaria spinosa subsp. spinosa,Bursaria spinosa subsp. spinosa,NA,Bursaria,Pittosporaceae,subspecies,APC,accepted,Magnoliidae,"SA, Qld, NSW, Vic, Tas",Bursaria spinosa Cav. subsp. spinosa,https://id.biodiversity.org.au/taxon/apni/51442337,https://id.biodiversity.org.au/taxon/apni/51442339,https://id.biodiversity.org.au/name/apni/142036,Bursaria spinosa subsp. spinosa,https://id.biodiversity.org.au/name/apni/142036,accepted,https://id.biodiversity.org.au/taxon/apni/51442337,https://id.biodiversity.org.au/taxon/apni/51442315,Bursaria spinosa subsp. spinosa,Bursaria spinosa,native Calendula arvensis,Calendula arvensis,Calendula arvensis,NA,Calendula,Asteraceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (naturalised), Tas (naturalised)",Calendula arvensis L.,https://id.biodiversity.org.au/node/apni/2891878,https://id.biodiversity.org.au/node/apni/2893748,https://id.biodiversity.org.au/name/apni/95042,Calendula arvensis,https://id.biodiversity.org.au/name/apni/95042,accepted,https://id.biodiversity.org.au/node/apni/2891878,https://id.biodiversity.org.au/taxon/apni/51695393,NA,Calendula arvensis,naturalised -Callistemon purpurascens,Callistemon purpurascens,Callistemon purpurascens,NA,Callistemon,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Callistemon purpurascens S.M.Douglas & S.David,https://id.biodiversity.org.au/taxon/apni/51288952,https://id.biodiversity.org.au/taxon/apni/51439657,https://id.biodiversity.org.au/name/apni/4630985,Callistemon purpurascens,https://id.biodiversity.org.au/name/apni/4630985,accepted,https://id.biodiversity.org.au/taxon/apni/51288952,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Callistemon purpurascens,native +Callistemon purpurascens,Callistemon purpurascens,Callistemon purpurascens,NA,Callistemon,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Callistemon purpurascens S.M.Douglas & S.David,https://id.biodiversity.org.au/taxon/apni/51288952,https://id.biodiversity.org.au/taxon/apni/51439657,https://id.biodiversity.org.au/name/apni/4630985,Callistemon purpurascens,https://id.biodiversity.org.au/name/apni/4630985,accepted,https://id.biodiversity.org.au/taxon/apni/51288952,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Callistemon purpurascens,native Apophyllum anomalum,Apophyllum anomalum,Capparis anomala,NA,Capparis,Capparaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Capparis anomala (F.Muell.) Byng & Christenh.,https://id.biodiversity.org.au/taxon/apni/51432888,https://id.biodiversity.org.au/taxon/apni/51432886,https://id.biodiversity.org.au/name/apni/50561973,Capparis anomala,https://id.biodiversity.org.au/name/apni/97697,basionym,https://id.biodiversity.org.au/instance/apni/50562214,https://id.biodiversity.org.au/taxon/apni/51433682,NA,Capparis anomala,native -Cardwellia sublimis,Cardwellia sublimis,Cardwellia sublimis,NA,Cardwellia,Proteaceae,species,APC,accepted,Magnoliidae,Qld,Cardwellia sublimis F.Muell.,https://id.biodiversity.org.au/node/apni/2899253,https://id.biodiversity.org.au/node/apni/2908094,https://id.biodiversity.org.au/name/apni/109268,Cardwellia sublimis,https://id.biodiversity.org.au/name/apni/109268,accepted,https://id.biodiversity.org.au/node/apni/2899253,https://id.biodiversity.org.au/taxon/apni/51614274,NA,Cardwellia sublimis,native +Cardwellia sublimis,Cardwellia sublimis,Cardwellia sublimis,NA,Cardwellia,Proteaceae,species,APC,accepted,Magnoliidae,Qld,Cardwellia sublimis F.Muell.,https://id.biodiversity.org.au/node/apni/2899253,https://id.biodiversity.org.au/node/apni/2908094,https://id.biodiversity.org.au/name/apni/109268,Cardwellia sublimis,https://id.biodiversity.org.au/name/apni/109268,accepted,https://id.biodiversity.org.au/node/apni/2899253,https://id.biodiversity.org.au/taxon/apni/51732901,NA,Cardwellia sublimis,native Carex leporina,Carex leporina,Carex leporina,NA,Carex,Cyperaceae,species,APC,accepted,Magnoliidae,"NSW (naturalised), NI (naturalised), Vic (naturalised), Tas (naturalised)",Carex leporina L.,https://id.biodiversity.org.au/node/apni/2902492,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/135236,Carex leporina,https://id.biodiversity.org.au/name/apni/135236,accepted,https://id.biodiversity.org.au/node/apni/2902492,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Carex leporina,naturalised -Carex cephalotes,Carex cephalotes,Carex pyrenaica var. cephalotes,NA,Carex,Cyperaceae,variety,APC,accepted,Magnoliidae,"NSW, Vic, Tas",Carex pyrenaica var. cephalotes (F.Muell.) Kük.,https://id.biodiversity.org.au/node/apni/2892693,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/111655,Carex pyrenaica var. cephalotes,https://id.biodiversity.org.au/name/apni/110600,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/946222,https://id.biodiversity.org.au/taxon/apni/51460154,Carex pyrenaica var. cephalotes,Carex pyrenaica,native +Carex cephalotes,Carex cephalotes,Carex pyrenaica var. cephalotes,NA,Carex,Cyperaceae,variety,APC,accepted,Magnoliidae,"NSW, Vic, Tas",Carex pyrenaica var. cephalotes (F.Muell.) Kük.,https://id.biodiversity.org.au/node/apni/2892693,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/111655,Carex pyrenaica var. cephalotes,https://id.biodiversity.org.au/name/apni/235569,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/946223,https://id.biodiversity.org.au/taxon/apni/51460154,Carex pyrenaica var. cephalotes,Carex pyrenaica,native Carex raleighii,Carex raleighii,Carex raleighii,NA,Carex,Cyperaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic, Tas",Carex raleighii Nelmes,https://id.biodiversity.org.au/node/apni/2910405,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/111690,Carex raleighii,https://id.biodiversity.org.au/name/apni/111690,accepted,https://id.biodiversity.org.au/node/apni/2910405,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Carex raleighii,native Carmichaelia exsul,Carmichaelia exsul,Carmichaelia exsul,NA,Carmichaelia,Fabaceae,species,APC,accepted,Magnoliidae,LHI,Carmichaelia exsul F.Muell.,https://id.biodiversity.org.au/node/apni/2915240,https://id.biodiversity.org.au/node/apni/8138105,https://id.biodiversity.org.au/name/apni/112335,Carmichaelia exsul,https://id.biodiversity.org.au/name/apni/112335,accepted,https://id.biodiversity.org.au/node/apni/2915240,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Carmichaelia exsul,native Cassinia compacta,Cassinia compacta,Cassinia compacta , Cassinia accipitrum (pro parte misapplied) | Cassinia straminea (pro parte misapplied) | Cassinia telfordii (pro parte misapplied) | Cassinia accipitrum (misapplied),Cassinia,Asteraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Cassinia compacta F.Muell.,https://id.biodiversity.org.au/node/apni/2909860,https://id.biodiversity.org.au/taxon/apni/51431788,https://id.biodiversity.org.au/name/apni/54723,Cassinia compacta [alternative possible names: Cassinia accipitrum (pro parte misapplied) | Cassinia straminea (pro parte misapplied) | Cassinia telfordii (pro parte misapplied) | Cassinia accipitrum (misapplied)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51695393,NA,Cassinia compacta,native @@ -53,8 +62,11 @@ Convolvulus farinosus,Convolvulus farinosus,Convolvulus farinosus,NA,Convolvulus Coprosma niphophila,Coprosma niphophila,Coprosma niphophila,NA,Coprosma,Rubiaceae,species,APC,accepted,Magnoliidae,NSW,Coprosma niphophila Orchard,https://id.biodiversity.org.au/node/apni/2910618,https://id.biodiversity.org.au/node/apni/8135850,https://id.biodiversity.org.au/name/apni/78856,Coprosma niphophila,https://id.biodiversity.org.au/name/apni/78856,accepted,https://id.biodiversity.org.au/node/apni/2910618,https://id.biodiversity.org.au/taxon/apni/51446612,NA,Coprosma niphophila,native Coprosma nivalis,Coprosma nivalis,Coprosma nivalis,NA,Coprosma,Rubiaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Coprosma nivalis W.R.B.Oliv.,https://id.biodiversity.org.au/node/apni/2915002,https://id.biodiversity.org.au/node/apni/8135850,https://id.biodiversity.org.au/name/apni/78866,Coprosma nivalis,https://id.biodiversity.org.au/name/apni/78866,accepted,https://id.biodiversity.org.au/node/apni/2915002,https://id.biodiversity.org.au/taxon/apni/51446612,NA,Coprosma nivalis,native Correa alba,Correa alba,Correa alba,NA,Correa,Rutaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Correa alba Andrews,https://id.biodiversity.org.au/node/apni/2906721,https://id.biodiversity.org.au/taxon/apni/51447015,https://id.biodiversity.org.au/name/apni/80283,Correa alba,https://id.biodiversity.org.au/name/apni/80283,accepted,https://id.biodiversity.org.au/node/apni/2906721,https://id.biodiversity.org.au/taxon/apni/51461748,NA,Correa alba,native -Corymbia citriodora,Corymbia citriodora,Corymbia citriodora,NA,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (doubtfully naturalised), Qld, NSW (native and naturalised), Vic (naturalised)",Corymbia citriodora (Hook.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2912509,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119387,Corymbia citriodora,https://id.biodiversity.org.au/name/apni/119387,accepted,https://id.biodiversity.org.au/node/apni/2912509,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Corymbia citriodora,native and naturalised -Corymbia eximia,Corymbia eximia,Corymbia eximia,NA,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Corymbia eximia (Schauer) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2909833,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119402,Corymbia eximia,https://id.biodiversity.org.au/name/apni/119402,accepted,https://id.biodiversity.org.au/node/apni/2909833,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Corymbia eximia,native +Corymbia citriodora,Corymbia citriodora,Corymbia citriodora,NA,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (doubtfully naturalised), Qld, NSW (native and naturalised), Vic (naturalised)",Corymbia citriodora (Hook.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2912509,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119387,Corymbia citriodora,https://id.biodiversity.org.au/name/apni/119387,accepted,https://id.biodiversity.org.au/node/apni/2912509,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Corymbia citriodora,native and naturalised +Corymbia dichromophloia,Corymbia dichromophloia,Corymbia dichromophloia,NA,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Corymbia dichromophloia (F.Muell.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2902117,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119396,Corymbia dichromophloia,https://id.biodiversity.org.au/name/apni/119396,accepted,https://id.biodiversity.org.au/node/apni/2902117,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Corymbia dichromophloia,native +Corymbia eximia,Corymbia eximia,Corymbia eximia,NA,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Corymbia eximia (Schauer) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2909833,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119402,Corymbia eximia,https://id.biodiversity.org.au/name/apni/119402,accepted,https://id.biodiversity.org.au/node/apni/2909833,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Corymbia eximia,native +Corymbia foelscheana,Corymbia foelscheana,Corymbia foelscheana,NA,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT",Corymbia foelscheana (F.Muell.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2892950,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119404,Corymbia foelscheana,https://id.biodiversity.org.au/name/apni/119404,accepted,https://id.biodiversity.org.au/node/apni/2892950,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Corymbia foelscheana,native +Corymbia terminalis,Corymbia terminalis,Corymbia terminalis,NA,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"NT, SA, Qld, NSW",Corymbia terminalis (F.Muell.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/7549846,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119435,Corymbia terminalis,https://id.biodiversity.org.au/name/apni/119435,accepted,https://id.biodiversity.org.au/node/apni/7549846,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Corymbia terminalis,native Crassula decumbens,Crassula decumbens,Crassula decumbens,NA,Crassula,Crassulaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, ACT, Vic, Tas",Crassula decumbens Thunb.,https://id.biodiversity.org.au/node/apni/2889646,https://id.biodiversity.org.au/node/apni/2903354,https://id.biodiversity.org.au/name/apni/83855,Crassula decumbens,https://id.biodiversity.org.au/name/apni/83855,accepted,https://id.biodiversity.org.au/node/apni/2889646,https://id.biodiversity.org.au/taxon/apni/51270792,NA,Crassula decumbens,native Crassula peduncularis,Crassula peduncularis,Crassula peduncularis,NA,Crassula,Crassulaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, ACT, Vic, Tas",Crassula peduncularis (Sm.) F.Meigen,https://id.biodiversity.org.au/node/apni/2895654,https://id.biodiversity.org.au/node/apni/2903354,https://id.biodiversity.org.au/name/apni/84005,Crassula peduncularis,https://id.biodiversity.org.au/name/apni/84005,accepted,https://id.biodiversity.org.au/node/apni/2895654,https://id.biodiversity.org.au/taxon/apni/51270792,NA,Crassula peduncularis,native Crotalaria brevis,Crotalaria brevis,Crotalaria brevis,NA,Crotalaria,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Crotalaria brevis Domin,https://id.biodiversity.org.au/node/apni/2906180,https://id.biodiversity.org.au/taxon/apni/51300011,https://id.biodiversity.org.au/name/apni/85578,Crotalaria brevis,https://id.biodiversity.org.au/name/apni/85578,accepted,https://id.biodiversity.org.au/node/apni/2906180,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Crotalaria brevis,native @@ -79,7 +91,8 @@ Dillwynia floribunda,Dillwynia floribunda,Dillwynia floribunda,NA,Dillwynia,Faba Dinosperma erythrococcum,Dinosperma erythrococcum,Dinosperma erythrococcum,NA,Dinosperma,Rutaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Dinosperma erythrococcum (F.Muell.) T.G.Hartley,https://id.biodiversity.org.au/node/apni/2897246,https://id.biodiversity.org.au/node/apni/2900591,https://id.biodiversity.org.au/name/apni/157718,Dinosperma erythrococcum,https://id.biodiversity.org.au/name/apni/157718,accepted,https://id.biodiversity.org.au/node/apni/2897246,https://id.biodiversity.org.au/taxon/apni/51461748,NA,Dinosperma erythrococcum,native Dodonaea petiolaris,Dodonaea petiolaris,Dodonaea petiolaris , Dodonaea viscosa subsp. mucronata (pro parte misapplied),Dodonaea,Sapindaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Dodonaea petiolaris F.Muell.,https://id.biodiversity.org.au/node/apni/2921131,https://id.biodiversity.org.au/taxon/apni/51447268,https://id.biodiversity.org.au/name/apni/72184,Dodonaea petiolaris [alternative possible names: Dodonaea viscosa subsp. mucronata (pro parte misapplied)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51447212,NA,Dodonaea petiolaris,native Dodonaea truncatiales,Dodonaea truncatiales,Dodonaea truncatiales , Dodonaea heteromorpha (pro parte misapplied) | Dodonaea heteromorpha (misapplied),Dodonaea,Sapindaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Dodonaea truncatiales F.Muell.,https://id.biodiversity.org.au/node/apni/7870563,https://id.biodiversity.org.au/taxon/apni/51447268,https://id.biodiversity.org.au/name/apni/72648,Dodonaea truncatiales [alternative possible names: Dodonaea heteromorpha (pro parte misapplied) | Dodonaea heteromorpha (misapplied)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51447212,NA,Dodonaea truncatiales,native -Dovyalis caffra,Dovyalis caffra,Dovyalis caffra,NA,Dovyalis,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised)",Dovyalis caffra (Hook.f. & Harv.) Hook.f.,https://id.biodiversity.org.au/node/apni/2888866,https://id.biodiversity.org.au/node/apni/2897632,https://id.biodiversity.org.au/name/apni/199157,Dovyalis caffra,https://id.biodiversity.org.au/name/apni/86110,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/841664,https://id.biodiversity.org.au/taxon/apni/51436847,NA,Dovyalis caffra,naturalised +Dovyalis caffra,Dovyalis caffra,Dovyalis caffra,NA,Dovyalis,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised)",Dovyalis caffra (Hook.f. & Harv.) Hook.f.,https://id.biodiversity.org.au/node/apni/2888866,https://id.biodiversity.org.au/node/apni/2897632,https://id.biodiversity.org.au/name/apni/199157,Dovyalis caffra,https://id.biodiversity.org.au/name/apni/199157,accepted,https://id.biodiversity.org.au/node/apni/2888866,https://id.biodiversity.org.au/taxon/apni/51436847,NA,Dovyalis caffra,naturalised +Elaeocarpus angustifolius,Elaeocarpus angustifolius,Elaeocarpus angustifolius , Elaeocarpus grandis (pro parte misapplied),Elaeocarpus,Elaeocarpaceae,species,APC,accepted,Magnoliidae,NT,Elaeocarpus angustifolius Blume,https://id.biodiversity.org.au/node/apni/2909850,https://id.biodiversity.org.au/taxon/apni/51435153,https://id.biodiversity.org.au/name/apni/115318,Elaeocarpus angustifolius [alternative possible names: Elaeocarpus grandis (pro parte misapplied)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51632282,NA,Elaeocarpus angustifolius,native Elaeocarpus grandis,Elaeocarpus grandis,Elaeocarpus grandis,NA,Elaeocarpus,Elaeocarpaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Elaeocarpus grandis F.Muell.,https://id.biodiversity.org.au/node/apni/2895259,https://id.biodiversity.org.au/taxon/apni/51435153,https://id.biodiversity.org.au/name/apni/115772,Elaeocarpus grandis,https://id.biodiversity.org.au/name/apni/115772,accepted,https://id.biodiversity.org.au/node/apni/2895259,https://id.biodiversity.org.au/taxon/apni/51632282,NA,Elaeocarpus grandis,native Eleocharis pallens,Eleocharis pallens,Eleocharis pallens,NA,Eleocharis,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Eleocharis pallens S.T.Blake,https://id.biodiversity.org.au/node/apni/2899827,https://id.biodiversity.org.au/taxon/apni/51434435,https://id.biodiversity.org.au/name/apni/67140,Eleocharis pallens,https://id.biodiversity.org.au/name/apni/67140,accepted,https://id.biodiversity.org.au/node/apni/2899827,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Eleocharis pallens,native Endiandra globosa,Endiandra globosa,Endiandra globosa,NA,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Endiandra globosa Maiden & Betche,https://id.biodiversity.org.au/node/apni/2901094,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111780,Endiandra globosa,https://id.biodiversity.org.au/name/apni/111780,accepted,https://id.biodiversity.org.au/node/apni/2901094,https://id.biodiversity.org.au/taxon/apni/51438397,NA,Endiandra globosa,native @@ -87,34 +100,39 @@ Endiandra leptodendron,Endiandra leptodendron,Endiandra leptodendron,NA,Endiandr Endiandra microneura,Endiandra microneura,Endiandra microneura,NA,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,Qld,Endiandra microneura C.T.White,https://id.biodiversity.org.au/node/apni/2899314,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111949,Endiandra microneura,https://id.biodiversity.org.au/name/apni/111949,accepted,https://id.biodiversity.org.au/node/apni/2899314,https://id.biodiversity.org.au/taxon/apni/51438397,NA,Endiandra microneura,native Endiandra muelleri,Endiandra muelleri,Endiandra muelleri,NA,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Endiandra muelleri Meisn.,https://id.biodiversity.org.au/node/apni/2903619,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111996,Endiandra muelleri,https://id.biodiversity.org.au/name/apni/111996,accepted,https://id.biodiversity.org.au/node/apni/2903619,https://id.biodiversity.org.au/taxon/apni/51438397,NA,Endiandra muelleri,native Epilobium gunnianum,Epilobium gunnianum,Epilobium gunnianum,NA,Epilobium,Onagraceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic, Tas",Epilobium gunnianum Hausskn.,https://id.biodiversity.org.au/node/apni/2903068,https://id.biodiversity.org.au/taxon/apni/51440863,https://id.biodiversity.org.au/name/apni/105579,Epilobium gunnianum,https://id.biodiversity.org.au/name/apni/105579,accepted,https://id.biodiversity.org.au/node/apni/2903068,https://id.biodiversity.org.au/taxon/apni/51440864,NA,Epilobium gunnianum,native -Eremophila deserti,Eremophila deserti,Eremophila deserti,NA,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila deserti (A.Cunn. ex Benth.) Chinnock,https://id.biodiversity.org.au/node/apni/2897363,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/123426,Eremophila deserti,https://id.biodiversity.org.au/name/apni/123426,accepted,https://id.biodiversity.org.au/node/apni/2897363,https://id.biodiversity.org.au/taxon/apni/51461527,NA,Eremophila deserti,native -Eremophila oppositifolia,Eremophila oppositifolia,Eremophila oppositifolia,NA,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila oppositifolia R.Br.,https://id.biodiversity.org.au/node/apni/7951462,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/114575,Eremophila oppositifolia,https://id.biodiversity.org.au/name/apni/114575,accepted,https://id.biodiversity.org.au/node/apni/7951462,https://id.biodiversity.org.au/taxon/apni/51461527,NA,Eremophila oppositifolia,native +Eremophila deserti,Eremophila deserti,Eremophila deserti,NA,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila deserti (A.Cunn. ex Benth.) Chinnock,https://id.biodiversity.org.au/node/apni/2897363,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/123426,Eremophila deserti,https://id.biodiversity.org.au/name/apni/123426,accepted,https://id.biodiversity.org.au/node/apni/2897363,https://id.biodiversity.org.au/taxon/apni/51734003,NA,Eremophila deserti,native +Eremophila oppositifolia,Eremophila oppositifolia,Eremophila oppositifolia,NA,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila oppositifolia R.Br.,https://id.biodiversity.org.au/node/apni/7951462,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/114575,Eremophila oppositifolia,https://id.biodiversity.org.au/name/apni/114575,accepted,https://id.biodiversity.org.au/node/apni/7951462,https://id.biodiversity.org.au/taxon/apni/51734003,NA,Eremophila oppositifolia,native Erigeron conyzoides,Erigeron conyzoides,Erigeron conyzoides,NA,Erigeron,Asteraceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Erigeron conyzoides F.Muell.,https://id.biodiversity.org.au/node/apni/2913579,https://id.biodiversity.org.au/taxon/apni/51432118,https://id.biodiversity.org.au/name/apni/73195,Erigeron conyzoides,https://id.biodiversity.org.au/name/apni/239637,taxonomic synonym,https://id.biodiversity.org.au/instance/apni/6407754,https://id.biodiversity.org.au/taxon/apni/51695393,NA,Erigeron conyzoides,native Erythroxylum australe,Erythroxylum australe,Erythroxylum australe , Erythroxylum sp. Splityard Creek (L.Pedley 5360) (pro parte misapplied),Erythroxylum,Erythroxylaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Erythroxylum australe F.Muell.,https://id.biodiversity.org.au/node/apni/2912212,https://id.biodiversity.org.au/node/apni/2919669,https://id.biodiversity.org.au/name/apni/75959,Erythroxylum australe [alternative possible names: Erythroxylum sp. Splityard Creek (L.Pedley 5360) (pro parte misapplied)],NA,NA,NA,https://id.biodiversity.org.au/node/apni/2893375,NA,Erythroxylum australe,native Escallonia bifida,Escallonia bifida,Escallonia bifida,NA,Escallonia,Escalloniaceae,species,APC,accepted,Magnoliidae,NSW (naturalised),Escallonia bifida Link & Otto,https://id.biodiversity.org.au/taxon/apni/51435441,https://id.biodiversity.org.au/taxon/apni/51435442,https://id.biodiversity.org.au/name/apni/116602,Escallonia bifida,https://id.biodiversity.org.au/name/apni/116602,accepted,https://id.biodiversity.org.au/taxon/apni/51435441,https://id.biodiversity.org.au/taxon/apni/51435443,NA,Escallonia bifida,naturalised -Eucalyptus badjensis,Eucalyptus badjensis,Eucalyptus badjensis,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus badjensis Beuzev. & M.B.Welch,https://id.biodiversity.org.au/node/apni/2912724,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/57323,Eucalyptus badjensis,https://id.biodiversity.org.au/name/apni/57323,accepted,https://id.biodiversity.org.au/node/apni/2912724,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus badjensis,native -Eucalyptus camphora,Eucalyptus camphora,Eucalyptus camphora,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic",Eucalyptus camphora R.T.Baker,https://id.biodiversity.org.au/node/apni/2891665,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/94439,Eucalyptus camphora,https://id.biodiversity.org.au/name/apni/94439,accepted,https://id.biodiversity.org.au/node/apni/2891665,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus camphora,native -Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus dorrigoensis (Blakely) L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2903351,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118668,Eucalyptus dorrigoensis,https://id.biodiversity.org.au/name/apni/118668,accepted,https://id.biodiversity.org.au/node/apni/2903351,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus dorrigoensis,native -Eucalyptus yangoura,Eucalyptus yangoura,Eucalyptus globoidea,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus globoidea Blakely,https://id.biodiversity.org.au/node/apni/5270850,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/61141,Eucalyptus globoidea,https://id.biodiversity.org.au/name/apni/92470,taxonomic synonym,https://id.biodiversity.org.au/instance/apni/853397,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus globoidea,native -Eucalyptus oblonga,Eucalyptus oblonga,Eucalyptus globoidea , Eucalyptus sparsifolia (pro parte taxonomic synonym),Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus globoidea Blakely,https://id.biodiversity.org.au/node/apni/5270850,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/61141,Eucalyptus globoidea [alternative possible names: Eucalyptus sparsifolia (pro parte taxonomic synonym)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus globoidea,native -Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,NA,Eucalyptus,Myrtaceae,subspecies,APC,accepted,Magnoliidae,"SA, NSW, Vic",Eucalyptus leucoxylon subsp. pruinosa (F.Muell. ex Miq.) Boland,https://id.biodiversity.org.au/node/apni/2908258,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/77407,Eucalyptus leucoxylon subsp. pruinosa,https://id.biodiversity.org.au/name/apni/77407,accepted,https://id.biodiversity.org.au/node/apni/2908258,https://id.biodiversity.org.au/taxon/apni/51702983,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon,native -Eucalyptus miniata,Eucalyptus miniata,Eucalyptus miniata,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus miniata A.Cunn. ex Schauer,https://id.biodiversity.org.au/node/apni/2889426,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/56460,Eucalyptus miniata,https://id.biodiversity.org.au/name/apni/56460,accepted,https://id.biodiversity.org.au/node/apni/2889426,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus miniata,native -Eucalyptus muelleriana,Eucalyptus muelleriana,Eucalyptus muelleriana,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus muelleriana A.W.Howitt,https://id.biodiversity.org.au/node/apni/2888508,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/56840,Eucalyptus muelleriana,https://id.biodiversity.org.au/name/apni/56840,accepted,https://id.biodiversity.org.au/node/apni/2888508,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus muelleriana,native -Eucalyptus nandewarica,Eucalyptus nandewarica,Eucalyptus nandewarica,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus nandewarica L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2897688,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118852,Eucalyptus nandewarica,https://id.biodiversity.org.au/name/apni/118852,accepted,https://id.biodiversity.org.au/node/apni/2897688,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus nandewarica,native -Eucalyptus olida,Eucalyptus olida,Eucalyptus olida,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus olida L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2914019,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118797,Eucalyptus olida,https://id.biodiversity.org.au/name/apni/118797,accepted,https://id.biodiversity.org.au/node/apni/2914019,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus olida,native -Eucalyptus pulverulenta,Eucalyptus pulverulenta,Eucalyptus pulverulenta,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus pulverulenta Sims,https://id.biodiversity.org.au/taxon/apni/51440675,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/106609,Eucalyptus pulverulenta,https://id.biodiversity.org.au/name/apni/106609,accepted,https://id.biodiversity.org.au/taxon/apni/51440675,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus pulverulenta,native -Eucalyptus recurva,Eucalyptus recurva,Eucalyptus recurva,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus recurva Crisp,https://id.biodiversity.org.au/node/apni/2892273,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/101532,Eucalyptus recurva,https://id.biodiversity.org.au/name/apni/101532,accepted,https://id.biodiversity.org.au/node/apni/2892273,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus recurva,native -Eucalyptus rossii,Eucalyptus rossii,Eucalyptus rossii,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus rossii R.T.Baker & H.G.Sm.,https://id.biodiversity.org.au/node/apni/2900822,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/58182,Eucalyptus rossii,https://id.biodiversity.org.au/name/apni/58182,accepted,https://id.biodiversity.org.au/node/apni/2900822,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus rossii,native -Eucalyptus scias,Eucalyptus scias,Eucalyptus scias,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus scias L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2893839,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118833,Eucalyptus scias,https://id.biodiversity.org.au/name/apni/118833,accepted,https://id.biodiversity.org.au/node/apni/2893839,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus scias,native -Eucalyptus tetrodonta,Eucalyptus tetrodonta,Eucalyptus tetrodonta,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus tetrodonta F.Muell.,https://id.biodiversity.org.au/node/apni/2905964,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/55572,Eucalyptus tetrodonta,https://id.biodiversity.org.au/name/apni/55572,accepted,https://id.biodiversity.org.au/node/apni/2905964,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus tetrodonta,native -Eucalyptus viminalis,Eucalyptus viminalis,Eucalyptus viminalis , Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied),Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic, Tas",Eucalyptus viminalis Labill.,https://id.biodiversity.org.au/taxon/apni/51290421,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/65838,Eucalyptus viminalis [alternative possible names: Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus viminalis,native -Eucalyptus youmanii,Eucalyptus youmanii,Eucalyptus youmanii,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Eucalyptus youmanii Blakely & McKie,https://id.biodiversity.org.au/node/apni/2916227,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/92496,Eucalyptus youmanii,https://id.biodiversity.org.au/name/apni/92496,accepted,https://id.biodiversity.org.au/node/apni/2916227,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Eucalyptus youmanii,native +Eucalyptus badjensis,Eucalyptus badjensis,Eucalyptus badjensis,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus badjensis Beuzev. & M.B.Welch,https://id.biodiversity.org.au/node/apni/2912724,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/57323,Eucalyptus badjensis,https://id.biodiversity.org.au/name/apni/57323,accepted,https://id.biodiversity.org.au/node/apni/2912724,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus badjensis,native +Eucalyptus camphora,Eucalyptus camphora,Eucalyptus camphora,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic",Eucalyptus camphora R.T.Baker,https://id.biodiversity.org.au/taxon/apni/51738742,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/94439,Eucalyptus camphora,https://id.biodiversity.org.au/name/apni/94439,accepted,https://id.biodiversity.org.au/taxon/apni/51738742,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus camphora,native +Eucalyptus chlorophylla,Eucalyptus chlorophylla,Eucalyptus chlorophylla,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus chlorophylla Brooker & Done,https://id.biodiversity.org.au/node/apni/2893400,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/112391,Eucalyptus chlorophylla,https://id.biodiversity.org.au/name/apni/112391,accepted,https://id.biodiversity.org.au/node/apni/2893400,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus chlorophylla,native +Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus dorrigoensis (Blakely) L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2903351,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/118668,Eucalyptus dorrigoensis,https://id.biodiversity.org.au/name/apni/118668,accepted,https://id.biodiversity.org.au/node/apni/2903351,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus dorrigoensis,native +Eucalyptus yangoura,Eucalyptus yangoura,Eucalyptus globoidea,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus globoidea Blakely,https://id.biodiversity.org.au/node/apni/5270850,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/61141,Eucalyptus globoidea,https://id.biodiversity.org.au/name/apni/92470,taxonomic synonym,https://id.biodiversity.org.au/instance/apni/853397,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus globoidea,native +Eucalyptus oblonga,Eucalyptus oblonga,Eucalyptus globoidea , Eucalyptus sparsifolia (pro parte taxonomic synonym),Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus globoidea Blakely,https://id.biodiversity.org.au/node/apni/5270850,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/61141,Eucalyptus globoidea [alternative possible names: Eucalyptus sparsifolia (pro parte taxonomic synonym)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus globoidea,native +Eucalyptus grandis,Eucalyptus grandis,Eucalyptus grandis,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), Qld, NSW",Eucalyptus grandis W.Hill,https://id.biodiversity.org.au/taxon/apni/51439812,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/75405,Eucalyptus grandis,https://id.biodiversity.org.au/name/apni/75405,accepted,https://id.biodiversity.org.au/taxon/apni/51439812,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus grandis,native and naturalised +Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,NA,Eucalyptus,Myrtaceae,subspecies,APC,accepted,Magnoliidae,"SA, NSW, Vic",Eucalyptus leucoxylon subsp. pruinosa (F.Muell. ex Miq.) Boland,https://id.biodiversity.org.au/node/apni/2908258,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/77407,Eucalyptus leucoxylon subsp. pruinosa,https://id.biodiversity.org.au/name/apni/77407,accepted,https://id.biodiversity.org.au/node/apni/2908258,https://id.biodiversity.org.au/taxon/apni/51738744,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon,native +Eucalyptus miniata,Eucalyptus miniata,Eucalyptus miniata,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus miniata A.Cunn. ex Schauer,https://id.biodiversity.org.au/node/apni/2889426,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/56460,Eucalyptus miniata,https://id.biodiversity.org.au/name/apni/56460,accepted,https://id.biodiversity.org.au/node/apni/2889426,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus miniata,native +Eucalyptus muelleriana,Eucalyptus muelleriana,Eucalyptus muelleriana,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus muelleriana A.W.Howitt,https://id.biodiversity.org.au/node/apni/2888508,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/56840,Eucalyptus muelleriana,https://id.biodiversity.org.au/name/apni/56840,accepted,https://id.biodiversity.org.au/node/apni/2888508,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus muelleriana,native +Eucalyptus nandewarica,Eucalyptus nandewarica,Eucalyptus nandewarica,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus nandewarica L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2897688,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/118852,Eucalyptus nandewarica,https://id.biodiversity.org.au/name/apni/118852,accepted,https://id.biodiversity.org.au/node/apni/2897688,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus nandewarica,native +Eucalyptus olida,Eucalyptus olida,Eucalyptus olida,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus olida L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2914019,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/118797,Eucalyptus olida,https://id.biodiversity.org.au/name/apni/118797,accepted,https://id.biodiversity.org.au/node/apni/2914019,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus olida,native +Eucalyptus patellaris,Eucalyptus patellaris,Eucalyptus patellaris,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NT,Eucalyptus patellaris F.Muell.,https://id.biodiversity.org.au/node/apni/2906207,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/87496,Eucalyptus patellaris,https://id.biodiversity.org.au/name/apni/87496,accepted,https://id.biodiversity.org.au/node/apni/2906207,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus patellaris,native +Eucalyptus pulverulenta,Eucalyptus pulverulenta,Eucalyptus pulverulenta,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus pulverulenta Sims,https://id.biodiversity.org.au/taxon/apni/51440675,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/106609,Eucalyptus pulverulenta,https://id.biodiversity.org.au/name/apni/106609,accepted,https://id.biodiversity.org.au/taxon/apni/51440675,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus pulverulenta,native +Eucalyptus recurva,Eucalyptus recurva,Eucalyptus recurva,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus recurva Crisp,https://id.biodiversity.org.au/node/apni/2892273,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/101532,Eucalyptus recurva,https://id.biodiversity.org.au/name/apni/101532,accepted,https://id.biodiversity.org.au/node/apni/2892273,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus recurva,native +Eucalyptus rossii,Eucalyptus rossii,Eucalyptus rossii,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus rossii R.T.Baker & H.G.Sm.,https://id.biodiversity.org.au/node/apni/2900822,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/58182,Eucalyptus rossii,https://id.biodiversity.org.au/name/apni/58182,accepted,https://id.biodiversity.org.au/node/apni/2900822,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus rossii,native +Eucalyptus scias,Eucalyptus scias,Eucalyptus scias,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus scias L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2893839,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/118833,Eucalyptus scias,https://id.biodiversity.org.au/name/apni/118833,accepted,https://id.biodiversity.org.au/node/apni/2893839,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus scias,native +Eucalyptus tetrodonta,Eucalyptus tetrodonta,Eucalyptus tetrodonta,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus tetrodonta F.Muell.,https://id.biodiversity.org.au/node/apni/2905964,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/55572,Eucalyptus tetrodonta,https://id.biodiversity.org.au/name/apni/55572,accepted,https://id.biodiversity.org.au/node/apni/2905964,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus tetrodonta,native +Eucalyptus viminalis,Eucalyptus viminalis,Eucalyptus viminalis , Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied),Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic, Tas",Eucalyptus viminalis Labill.,https://id.biodiversity.org.au/taxon/apni/51290421,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/65838,Eucalyptus viminalis [alternative possible names: Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus viminalis,native +Eucalyptus youmanii,Eucalyptus youmanii,Eucalyptus youmanii,NA,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Eucalyptus youmanii Blakely & McKie,https://id.biodiversity.org.au/node/apni/2916227,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/92496,Eucalyptus youmanii,https://id.biodiversity.org.au/name/apni/92496,accepted,https://id.biodiversity.org.au/node/apni/2916227,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Eucalyptus youmanii,native Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata var. queenslandica,NA,Euphorbia,Euphorbiaceae,variety,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Euphorbia inappendiculata var. queenslandica Domin,https://id.biodiversity.org.au/node/apni/7200245,https://id.biodiversity.org.au/taxon/apni/51435529,https://id.biodiversity.org.au/name/apni/92612,Euphorbia inappendiculata var. queenslandica,https://id.biodiversity.org.au/name/apni/92612,accepted,https://id.biodiversity.org.au/node/apni/7200245,https://id.biodiversity.org.au/taxon/apni/51442249,Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata,native Exocarpos homalocladus,Exocarpos homalocladus,Exocarpos homalocladus,NA,Exocarpos,Santalaceae,species,APC,accepted,Magnoliidae,LHI,Exocarpos homalocladus C.Moore & F.Muell.,https://id.biodiversity.org.au/node/apni/2898548,https://id.biodiversity.org.au/taxon/apni/51447153,https://id.biodiversity.org.au/name/apni/58158,Exocarpos homalocladus,https://id.biodiversity.org.au/name/apni/58158,accepted,https://id.biodiversity.org.au/node/apni/2898548,https://id.biodiversity.org.au/taxon/apni/51447154,NA,Exocarpos homalocladus,native Exocarpos sparteus,Exocarpos sparteus,Exocarpos sparteus,NA,Exocarpos,Santalaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Exocarpos sparteus R.Br.,https://id.biodiversity.org.au/node/apni/2898676,https://id.biodiversity.org.au/taxon/apni/51447153,https://id.biodiversity.org.au/name/apni/58330,Exocarpos sparteus,https://id.biodiversity.org.au/name/apni/58330,accepted,https://id.biodiversity.org.au/node/apni/2898676,https://id.biodiversity.org.au/taxon/apni/51447154,NA,Exocarpos sparteus,native Ficus henneana,Ficus henneana,Ficus henneana,NA,Ficus,Moraceae,species,APC,accepted,Magnoliidae,"NT, Qld, NSW",Ficus henneana Miq.,https://id.biodiversity.org.au/node/apni/2903067,https://id.biodiversity.org.au/taxon/apni/51439476,https://id.biodiversity.org.au/name/apni/91212,Ficus henneana,https://id.biodiversity.org.au/name/apni/91212,accepted,https://id.biodiversity.org.au/node/apni/2903067,https://id.biodiversity.org.au/taxon/apni/51439463,NA,Ficus henneana,native Freesia laxa,Freesia laxa,Freesia laxa,NA,Freesia,Iridaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), Qld (naturalised), NSW (naturalised), NI (naturalised), Vic (naturalised)",Freesia laxa (Thunb.) Goldblatt & J.C.Manning,https://id.biodiversity.org.au/node/apni/2886987,https://id.biodiversity.org.au/node/apni/2913899,https://id.biodiversity.org.au/name/apni/200132,Freesia laxa,https://id.biodiversity.org.au/name/apni/200132,accepted,https://id.biodiversity.org.au/node/apni/2886987,https://id.biodiversity.org.au/taxon/apni/51438006,NA,Freesia laxa,naturalised Freesia hybrid,Freesia hybrid,Freesia leichtlinii subsp. leichtlinii x Freesia leichtlinii subsp. alba,NA,Freesia,Iridaceae,subspecies,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised)",Freesia leichtlinii Klatt subsp. leichtlinii x Freesia leichtlinii subsp. alba (G.L.Mey.) J.C.Manning & Goldblatt,https://id.biodiversity.org.au/node/apni/2908401,https://id.biodiversity.org.au/node/apni/2913899,https://id.biodiversity.org.au/name/apni/241787,Freesia leichtlinii subsp. leichtlinii x Freesia leichtlinii subsp. alba,https://id.biodiversity.org.au/name/apni/171901,taxonomic synonym,https://id.biodiversity.org.au/instance/apni/953836,https://id.biodiversity.org.au/taxon/apni/51438006,Freesia leichtlinii subsp. leichtlinii x Freesia leichtlinii subsp. alba,Freesia leichtlinii,naturalised +Gardenia actinocarpa,Gardenia actinocarpa,Gardenia actinocarpa,NA,Gardenia,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Gardenia actinocarpa Puttock,https://id.biodiversity.org.au/taxon/apni/51293926,https://id.biodiversity.org.au/taxon/apni/51293927,https://id.biodiversity.org.au/name/apni/74954,Gardenia actinocarpa,https://id.biodiversity.org.au/name/apni/74954,accepted,https://id.biodiversity.org.au/taxon/apni/51293926,https://id.biodiversity.org.au/taxon/apni/51446612,NA,Gardenia actinocarpa,native +Gardenia ovularis,Gardenia ovularis,Gardenia ovularis,NA,Gardenia,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Gardenia ovularis F.M.Bailey,https://id.biodiversity.org.au/node/apni/2895410,https://id.biodiversity.org.au/taxon/apni/51293927,https://id.biodiversity.org.au/name/apni/75259,Gardenia ovularis,https://id.biodiversity.org.au/name/apni/75259,accepted,https://id.biodiversity.org.au/node/apni/2895410,https://id.biodiversity.org.au/taxon/apni/51446612,NA,Gardenia ovularis,native Geijera salicifolia,Geijera salicifolia,Geijera salicifolia,NA,Geijera,Rutaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Geijera salicifolia Schott,https://id.biodiversity.org.au/node/apni/2901807,https://id.biodiversity.org.au/node/apni/2905474,https://id.biodiversity.org.au/name/apni/101381,Geijera salicifolia,https://id.biodiversity.org.au/name/apni/101381,accepted,https://id.biodiversity.org.au/node/apni/2901807,https://id.biodiversity.org.au/taxon/apni/51461748,NA,Geijera salicifolia,native Gentiana wingecarribiensis,Gentiana wingecarribiensis,Gentiana wingecarribiensis,NA,Gentiana,Gentianaceae,species,APC,accepted,Magnoliidae,NSW,Gentiana wingecarribiensis L.G.Adams,https://id.biodiversity.org.au/node/apni/2915610,https://id.biodiversity.org.au/taxon/apni/51436928,https://id.biodiversity.org.au/name/apni/80378,Gentiana wingecarribiensis,https://id.biodiversity.org.au/name/apni/80378,accepted,https://id.biodiversity.org.au/node/apni/2915610,https://id.biodiversity.org.au/taxon/apni/51436871,NA,Gentiana wingecarribiensis,native Gentianella barringtonensis,Gentianella barringtonensis,Gentianella barringtonensis,NA,Gentianella,Gentianaceae,species,APC,accepted,Magnoliidae,NSW,Gentianella barringtonensis (L.G.Adams) Glenny,https://id.biodiversity.org.au/taxon/apni/51301045,https://id.biodiversity.org.au/taxon/apni/51301038,https://id.biodiversity.org.au/name/apni/192277,Gentianella barringtonensis,https://id.biodiversity.org.au/name/apni/192277,accepted,https://id.biodiversity.org.au/taxon/apni/51301045,https://id.biodiversity.org.au/taxon/apni/51436871,NA,Gentianella barringtonensis,native @@ -122,11 +140,16 @@ Geranium obtusisepalum,Geranium obtusisepalum,Geranium obtusisepalum,NA,Geranium Geranium purpureum subsp. purpureum,Geranium purpureum subsp. purpureum,Geranium purpureum,NA,Geranium,Geraniaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised)",Geranium purpureum Vill.,https://id.biodiversity.org.au/node/apni/2919721,https://id.biodiversity.org.au/taxon/apni/51436946,https://id.biodiversity.org.au/name/apni/82353,Geranium purpureum,https://id.biodiversity.org.au/name/apni/82382,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/895632,https://id.biodiversity.org.au/taxon/apni/51436947,NA,Geranium purpureum,naturalised Gillbeea adenopetala,Gillbeea adenopetala,Gillbeea adenopetala,NA,Gillbeea,Cunoniaceae,species,APC,accepted,Magnoliidae,Qld,Gillbeea adenopetala F.Muell.,https://id.biodiversity.org.au/node/apni/2913815,https://id.biodiversity.org.au/node/apni/2918249,https://id.biodiversity.org.au/name/apni/98098,Gillbeea adenopetala,https://id.biodiversity.org.au/name/apni/98098,accepted,https://id.biodiversity.org.au/node/apni/2913815,https://id.biodiversity.org.au/taxon/apni/51434138,NA,Gillbeea adenopetala,native Glochidion hylandii,Glochidion hylandii,Glochidion hylandii,NA,Glochidion,Phyllanthaceae,species,APC,accepted,Magnoliidae,Qld,Glochidion hylandii Airy Shaw,https://id.biodiversity.org.au/node/apni/2889113,https://id.biodiversity.org.au/node/apni/8387508,https://id.biodiversity.org.au/name/apni/78303,Glochidion hylandii,https://id.biodiversity.org.au/name/apni/78303,accepted,https://id.biodiversity.org.au/node/apni/2889113,https://id.biodiversity.org.au/taxon/apni/51442162,NA,Glochidion hylandii,native -Gompholobium grandiflorum,Gompholobium grandiflorum,Gompholobium grandiflorum,NA,Gompholobium,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Gompholobium grandiflorum Sm.,https://id.biodiversity.org.au/node/apni/2909013,https://id.biodiversity.org.au/taxon/apni/51436123,https://id.biodiversity.org.au/name/apni/65291,Gompholobium grandiflorum,https://id.biodiversity.org.au/name/apni/65291,accepted,https://id.biodiversity.org.au/node/apni/2909013,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Gompholobium grandiflorum,native +Gompholobium grandiflorum,Gompholobium grandiflorum,Gompholobium grandiflorum,NA,Gompholobium,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Gompholobium grandiflorum Sm.,https://id.biodiversity.org.au/node/apni/2909013,https://id.biodiversity.org.au/taxon/apni/51436123,https://id.biodiversity.org.au/name/apni/65291,Gompholobium grandiflorum,https://id.biodiversity.org.au/name/apni/65305,taxonomic synonym,https://id.biodiversity.org.au/instance/apni/934224,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Gompholobium grandiflorum,native Goodenia varia,Goodenia varia,Goodenia varia,NA,Goodenia,Goodeniaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic",Goodenia varia R.Br.,https://id.biodiversity.org.au/node/apni/2910439,https://id.biodiversity.org.au/taxon/apni/51437012,https://id.biodiversity.org.au/name/apni/92079,Goodenia varia,https://id.biodiversity.org.au/name/apni/92079,accepted,https://id.biodiversity.org.au/node/apni/2910439,https://id.biodiversity.org.au/taxon/apni/51462931,NA,Goodenia varia,native -Gossia bidwillii,Gossia bidwillii,Gossia bidwillii,NA,Gossia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Gossia bidwillii (Benth.) N.Snow & Guymer,https://id.biodiversity.org.au/taxon/apni/51439972,https://id.biodiversity.org.au/taxon/apni/51439958,https://id.biodiversity.org.au/name/apni/180918,Gossia bidwillii,https://id.biodiversity.org.au/name/apni/180918,accepted,https://id.biodiversity.org.au/taxon/apni/51439972,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Gossia bidwillii,native -Grevillea scortechinii,Grevillea scortechinii,Grevillea scortechinii,NA,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Grevillea scortechinii (F.Muell. ex Scort.) F.Muell.,https://id.biodiversity.org.au/node/apni/2918803,https://id.biodiversity.org.au/taxon/apni/51445337,https://id.biodiversity.org.au/name/apni/63322,Grevillea scortechinii,https://id.biodiversity.org.au/name/apni/63322,accepted,https://id.biodiversity.org.au/node/apni/2918803,https://id.biodiversity.org.au/taxon/apni/51614274,NA,Grevillea scortechinii,native -Hakea macraeana,Hakea macraeana,Hakea macraeana , Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied),Hakea,Proteaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Hakea macraeana F.Muell.,https://id.biodiversity.org.au/node/apni/2895080,https://id.biodiversity.org.au/taxon/apni/51445456,https://id.biodiversity.org.au/name/apni/94862,Hakea macraeana [alternative possible names: Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51614274,NA,Hakea macraeana,native +Gossia bidwillii,Gossia bidwillii,Gossia bidwillii,NA,Gossia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Gossia bidwillii (Benth.) N.Snow & Guymer,https://id.biodiversity.org.au/taxon/apni/51439972,https://id.biodiversity.org.au/taxon/apni/51439958,https://id.biodiversity.org.au/name/apni/180918,Gossia bidwillii,https://id.biodiversity.org.au/name/apni/180918,accepted,https://id.biodiversity.org.au/taxon/apni/51439972,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Gossia bidwillii,native +Grevillea dimidiata,Grevillea dimidiata,Grevillea dimidiata,NA,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"WA, NT",Grevillea dimidiata F.Muell.,https://id.biodiversity.org.au/node/apni/2901789,https://id.biodiversity.org.au/taxon/apni/51726302,https://id.biodiversity.org.au/name/apni/61434,Grevillea dimidiata,https://id.biodiversity.org.au/name/apni/61434,accepted,https://id.biodiversity.org.au/node/apni/2901789,https://id.biodiversity.org.au/taxon/apni/51732901,NA,Grevillea dimidiata,native +Grevillea pteridifolia,Grevillea pteridifolia,Grevillea pteridifolia,NA,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Grevillea pteridifolia Knight,https://id.biodiversity.org.au/node/apni/2910744,https://id.biodiversity.org.au/taxon/apni/51726302,https://id.biodiversity.org.au/name/apni/111324,Grevillea pteridifolia,https://id.biodiversity.org.au/name/apni/111324,accepted,https://id.biodiversity.org.au/node/apni/2910744,https://id.biodiversity.org.au/taxon/apni/51732901,NA,Grevillea pteridifolia,native +Grevillea robusta,Grevillea robusta,Grevillea robusta,NA,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"Qld, NSW (native and naturalised), LHI (naturalised), NI (naturalised)",Grevillea robusta A.Cunn. ex R.Br.,https://id.biodiversity.org.au/node/apni/2918082,https://id.biodiversity.org.au/taxon/apni/51726302,https://id.biodiversity.org.au/name/apni/55137,Grevillea robusta,https://id.biodiversity.org.au/name/apni/55137,accepted,https://id.biodiversity.org.au/node/apni/2918082,https://id.biodiversity.org.au/taxon/apni/51732901,NA,Grevillea robusta,native and naturalised +Grevillea scortechinii,Grevillea scortechinii,Grevillea scortechinii,NA,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Grevillea scortechinii (F.Muell. ex Scort.) F.Muell.,https://id.biodiversity.org.au/node/apni/2918803,https://id.biodiversity.org.au/taxon/apni/51726302,https://id.biodiversity.org.au/name/apni/63322,Grevillea scortechinii,https://id.biodiversity.org.au/name/apni/63322,accepted,https://id.biodiversity.org.au/node/apni/2918803,https://id.biodiversity.org.au/taxon/apni/51732901,NA,Grevillea scortechinii,native +Hakea arborescens,Hakea arborescens,Hakea arborescens,NA,Hakea,Proteaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Hakea arborescens R.Br.,https://id.biodiversity.org.au/node/apni/2897149,https://id.biodiversity.org.au/taxon/apni/51445456,https://id.biodiversity.org.au/name/apni/76681,Hakea arborescens,https://id.biodiversity.org.au/name/apni/76681,accepted,https://id.biodiversity.org.au/node/apni/2897149,https://id.biodiversity.org.au/taxon/apni/51732901,NA,Hakea arborescens,native +Hakea suberea,Hakea suberea,Hakea lorea subsp. lorea,NA,Hakea,Proteaceae,subspecies,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Hakea lorea (R.Br.) R.Br. subsp. lorea,https://id.biodiversity.org.au/node/apni/2918427,https://id.biodiversity.org.au/taxon/apni/51445456,https://id.biodiversity.org.au/name/apni/162920,Hakea lorea subsp. lorea,https://id.biodiversity.org.au/name/apni/99787,taxonomic synonym,https://id.biodiversity.org.au/instance/apni/838725,https://id.biodiversity.org.au/taxon/apni/51732901,Hakea lorea subsp. lorea,Hakea lorea,native +Hakea macraeana,Hakea macraeana,Hakea macraeana , Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied),Hakea,Proteaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Hakea macraeana F.Muell.,https://id.biodiversity.org.au/node/apni/2895080,https://id.biodiversity.org.au/taxon/apni/51445456,https://id.biodiversity.org.au/name/apni/94862,Hakea macraeana [alternative possible names: Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51732901,NA,Hakea macraeana,native Harpullia rhyticarpa,Harpullia rhyticarpa,Harpullia rhyticarpa,NA,Harpullia,Sapindaceae,species,APC,accepted,Magnoliidae,Qld,Harpullia rhyticarpa C.T.White & W.D.Francis,https://id.biodiversity.org.au/node/apni/2910766,https://id.biodiversity.org.au/taxon/apni/51447330,https://id.biodiversity.org.au/name/apni/108928,Harpullia rhyticarpa,https://id.biodiversity.org.au/name/apni/108928,accepted,https://id.biodiversity.org.au/node/apni/2910766,https://id.biodiversity.org.au/taxon/apni/51447212,NA,Harpullia rhyticarpa,native Hemisteptia lyrata,Hemisteptia lyrata,Hemisteptia lyrata,NA,Hemisteptia,Asteraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Hemisteptia lyrata (Bunge) Fisch. & C.A.Mey.,https://id.biodiversity.org.au/taxon/apni/51268530,https://id.biodiversity.org.au/taxon/apni/51268531,https://id.biodiversity.org.au/name/apni/230066,Hemisteptia lyrata,https://id.biodiversity.org.au/name/apni/230066,accepted,https://id.biodiversity.org.au/taxon/apni/51268530,https://id.biodiversity.org.au/taxon/apni/51695393,NA,Hemisteptia lyrata,native Hernandia albiflora,Hernandia albiflora,Hernandia albiflora,NA,Hernandia,Hernandiaceae,species,APC,accepted,Magnoliidae,Qld,Hernandia albiflora (C.T.White) Kubitzki,https://id.biodiversity.org.au/node/apni/2911354,https://id.biodiversity.org.au/taxon/apni/51437691,https://id.biodiversity.org.au/name/apni/92773,Hernandia albiflora,https://id.biodiversity.org.au/name/apni/92773,accepted,https://id.biodiversity.org.au/node/apni/2911354,https://id.biodiversity.org.au/taxon/apni/51437692,NA,Hernandia albiflora,native @@ -145,15 +168,15 @@ Ixora biflora,Ixora biflora,Ixora biflora,NA,Ixora,Rubiaceae,species,APC,accepte Juncus acutus subsp. acutus,Juncus acutus subsp. acutus,Juncus acutus subsp. acutus,NA,Juncus,Juncaceae,subspecies,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), Qld (naturalised), NSW (naturalised), Vic (naturalised)",Juncus acutus L. subsp. acutus,https://id.biodiversity.org.au/node/apni/2887983,https://id.biodiversity.org.au/taxon/apni/51438170,https://id.biodiversity.org.au/name/apni/182490,Juncus acutus subsp. acutus,https://id.biodiversity.org.au/name/apni/182490,accepted,https://id.biodiversity.org.au/node/apni/2887983,https://id.biodiversity.org.au/taxon/apni/51438171,Juncus acutus subsp. acutus,Juncus acutus,naturalised Juncus kraussii,Juncus kraussii,Juncus kraussii,NA,Juncus,Juncaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic, Tas",Juncus kraussii Hochst.,https://id.biodiversity.org.au/node/apni/2900900,https://id.biodiversity.org.au/taxon/apni/51438170,https://id.biodiversity.org.au/name/apni/55859,Juncus kraussii,https://id.biodiversity.org.au/name/apni/55859,accepted,https://id.biodiversity.org.au/node/apni/2900900,https://id.biodiversity.org.au/taxon/apni/51438171,NA,Juncus kraussii,native Lantana montevidensis,Lantana montevidensis,Lantana montevidensis,NA,Lantana,Verbenaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), Qld (naturalised), NSW (naturalised), NI (doubtfully naturalised)",Lantana montevidensis (Spreng.) Briq.,https://id.biodiversity.org.au/node/apni/2894994,https://id.biodiversity.org.au/taxon/apni/51448661,https://id.biodiversity.org.au/name/apni/70044,Lantana montevidensis,https://id.biodiversity.org.au/name/apni/70044,accepted,https://id.biodiversity.org.au/node/apni/2894994,https://id.biodiversity.org.au/taxon/apni/51448662,NA,Lantana montevidensis,naturalised -Lasianthus strigosus,Lasianthus strigosus,Lasianthus chlorocarpus,NA,Lasianthus,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Lasianthus chlorocarpus K.Schum.,https://id.biodiversity.org.au/node/apni/7839740,https://id.biodiversity.org.au/node/apni/8136656,https://id.biodiversity.org.au/name/apni/219373,Lasianthus chlorocarpus,https://id.biodiversity.org.au/name/apni/71294,misapplied,https://id.biodiversity.org.au/instance/apni/7839725,https://id.biodiversity.org.au/taxon/apni/51446612,NA,Lasianthus chlorocarpus,native +Lasianthus strigosus,Lasianthus strigosus,Lasianthus chlorocarpus,NA,Lasianthus,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Lasianthus chlorocarpus K.Schum.,https://id.biodiversity.org.au/node/apni/7839740,https://id.biodiversity.org.au/node/apni/8136656,https://id.biodiversity.org.au/name/apni/219373,Lasianthus chlorocarpus,https://id.biodiversity.org.au/name/apni/71294,misapplied,https://id.biodiversity.org.au/instance/apni/7839722,https://id.biodiversity.org.au/taxon/apni/51446612,NA,Lasianthus chlorocarpus,native Lepidium africanum,Lepidium africanum,Lepidium africanum,NA,Lepidium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Lepidium africanum (Burm.f.) DC.,https://id.biodiversity.org.au/node/apni/2887818,https://id.biodiversity.org.au/taxon/apni/51612686,https://id.biodiversity.org.au/name/apni/68961,Lepidium africanum,https://id.biodiversity.org.au/name/apni/68961,accepted,https://id.biodiversity.org.au/node/apni/2887818,https://id.biodiversity.org.au/taxon/apni/51612687,NA,Lepidium africanum,naturalised Lepidium foliosum,Lepidium foliosum,Lepidium foliosum,NA,Lepidium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Lepidium foliosum Desv.,https://id.biodiversity.org.au/node/apni/2908453,https://id.biodiversity.org.au/taxon/apni/51612686,https://id.biodiversity.org.au/name/apni/69389,Lepidium foliosum,https://id.biodiversity.org.au/name/apni/69389,accepted,https://id.biodiversity.org.au/node/apni/2908453,https://id.biodiversity.org.au/taxon/apni/51612687,NA,Lepidium foliosum,native Lepidium oxytrichum,Lepidium oxytrichum,Lepidium oxytrichum,NA,Lepidium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Lepidium oxytrichum Sprague,https://id.biodiversity.org.au/node/apni/2915883,https://id.biodiversity.org.au/taxon/apni/51612686,https://id.biodiversity.org.au/name/apni/84027,Lepidium oxytrichum,https://id.biodiversity.org.au/name/apni/84027,accepted,https://id.biodiversity.org.au/node/apni/2915883,https://id.biodiversity.org.au/taxon/apni/51612687,NA,Lepidium oxytrichum,native Lepidosperma gladiatum,Lepidosperma gladiatum,Lepidosperma gladiatum,NA,Lepidosperma,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Lepidosperma gladiatum Labill.,https://id.biodiversity.org.au/node/apni/2896726,https://id.biodiversity.org.au/taxon/apni/51434499,https://id.biodiversity.org.au/name/apni/85937,Lepidosperma gladiatum,https://id.biodiversity.org.au/name/apni/85937,accepted,https://id.biodiversity.org.au/node/apni/2896726,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Lepidosperma gladiatum,native Leptomeria drupacea,Leptomeria drupacea,Leptomeria drupacea,NA,Leptomeria,Santalaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic, Tas",Leptomeria drupacea (Labill.) Druce,https://id.biodiversity.org.au/node/apni/2892780,https://id.biodiversity.org.au/node/apni/2897704,https://id.biodiversity.org.au/name/apni/61625,Leptomeria drupacea,https://id.biodiversity.org.au/name/apni/61625,accepted,https://id.biodiversity.org.au/node/apni/2892780,https://id.biodiversity.org.au/taxon/apni/51447154,NA,Leptomeria drupacea,native -Leptospermum continentale,Leptospermum continentale,Leptospermum continentale,NA,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic",Leptospermum continentale Joy Thomps.,https://id.biodiversity.org.au/node/apni/2917147,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/81291,Leptospermum continentale,https://id.biodiversity.org.au/name/apni/81291,accepted,https://id.biodiversity.org.au/node/apni/2917147,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Leptospermum continentale,native -Leptospermum obovatum,Leptospermum obovatum,Leptospermum obovatum,NA,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Leptospermum obovatum Sweet,https://id.biodiversity.org.au/node/apni/2891711,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/99608,Leptospermum obovatum,https://id.biodiversity.org.au/name/apni/99608,accepted,https://id.biodiversity.org.au/node/apni/2891711,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Leptospermum obovatum,native -Leucopogon amplexicaulis,Leucopogon amplexicaulis,Leucopogon amplexicaulis,NA,Leucopogon,Ericaceae,species,APC,accepted,Magnoliidae,NSW,Leucopogon amplexicaulis (Rudge) R.Br.,https://id.biodiversity.org.au/node/apni/2896081,https://id.biodiversity.org.au/taxon/apni/51435325,https://id.biodiversity.org.au/name/apni/106715,Leucopogon amplexicaulis,https://id.biodiversity.org.au/name/apni/106715,accepted,https://id.biodiversity.org.au/node/apni/2896081,https://id.biodiversity.org.au/taxon/apni/51436079,NA,Leucopogon amplexicaulis,native +Leptospermum continentale,Leptospermum continentale,Leptospermum continentale,NA,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic",Leptospermum continentale Joy Thomps.,https://id.biodiversity.org.au/node/apni/2917147,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/81291,Leptospermum continentale,https://id.biodiversity.org.au/name/apni/81291,accepted,https://id.biodiversity.org.au/node/apni/2917147,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Leptospermum continentale,native +Leptospermum obovatum,Leptospermum obovatum,Leptospermum obovatum,NA,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Leptospermum obovatum Sweet,https://id.biodiversity.org.au/node/apni/2891711,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/99608,Leptospermum obovatum,https://id.biodiversity.org.au/name/apni/99608,accepted,https://id.biodiversity.org.au/node/apni/2891711,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Leptospermum obovatum,native +Leucopogon amplexicaulis,Leucopogon amplexicaulis,Leucopogon amplexicaulis,NA,Leucopogon,Ericaceae,species,APC,accepted,Magnoliidae,NSW,Leucopogon amplexicaulis (Rudge) R.Br.,https://id.biodiversity.org.au/node/apni/2896081,https://id.biodiversity.org.au/taxon/apni/51435325,https://id.biodiversity.org.au/name/apni/106715,Leucopogon amplexicaulis,https://id.biodiversity.org.au/name/apni/106715,accepted,https://id.biodiversity.org.au/node/apni/2896081,https://id.biodiversity.org.au/taxon/apni/51738121,NA,Leucopogon amplexicaulis,native Litsea leefeana,Litsea leefeana,Litsea leefeana,NA,Litsea,Lauraceae,species,APC,accepted,Magnoliidae,Qld,Litsea leefeana (F.Muell.) Merr.,https://id.biodiversity.org.au/node/apni/2921063,https://id.biodiversity.org.au/taxon/apni/51438430,https://id.biodiversity.org.au/name/apni/81094,Litsea leefeana,https://id.biodiversity.org.au/name/apni/81094,accepted,https://id.biodiversity.org.au/node/apni/2921063,https://id.biodiversity.org.au/taxon/apni/51438397,NA,Litsea leefeana,native Lobelia pedunculata,Lobelia pedunculata,Lobelia pedunculata,NA,Lobelia,Campanulaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic, Tas",Lobelia pedunculata R.Br.,https://id.biodiversity.org.au/node/apni/2901444,https://id.biodiversity.org.au/taxon/apni/51432852,https://id.biodiversity.org.au/name/apni/106999,Lobelia pedunculata,https://id.biodiversity.org.au/name/apni/106999,accepted,https://id.biodiversity.org.au/node/apni/2901444,https://id.biodiversity.org.au/taxon/apni/51432853,NA,Lobelia pedunculata,native Lobelia trigonocaulis,Lobelia trigonocaulis,Lobelia trigonocaulis,NA,Lobelia,Campanulaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Lobelia trigonocaulis F.Muell.,https://id.biodiversity.org.au/node/apni/2901863,https://id.biodiversity.org.au/taxon/apni/51432852,https://id.biodiversity.org.au/name/apni/107808,Lobelia trigonocaulis,https://id.biodiversity.org.au/name/apni/107808,accepted,https://id.biodiversity.org.au/node/apni/2901863,https://id.biodiversity.org.au/taxon/apni/51432853,NA,Lobelia trigonocaulis,native @@ -165,11 +188,11 @@ Mallotus mollissimus,Mallotus mollissimus,Mallotus mollissimus,NA,Mallotus,Eupho Medicago orbicularis,Medicago orbicularis,Medicago orbicularis,NA,Medicago,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (formerly naturalised)",Medicago orbicularis (L.) Bartal.,https://id.biodiversity.org.au/node/apni/2901771,https://id.biodiversity.org.au/taxon/apni/51285690,https://id.biodiversity.org.au/name/apni/59568,Medicago orbicularis,https://id.biodiversity.org.au/name/apni/59568,accepted,https://id.biodiversity.org.au/node/apni/2901771,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Medicago orbicularis,naturalised Medicosma sessiliflora,Medicosma sessiliflora,Medicosma sessiliflora,NA,Medicosma,Rutaceae,species,APC,accepted,Magnoliidae,Qld,Medicosma sessiliflora (C.T.White) T.G.Hartley,https://id.biodiversity.org.au/node/apni/2914896,https://id.biodiversity.org.au/taxon/apni/51446918,https://id.biodiversity.org.au/name/apni/73658,Medicosma sessiliflora,https://id.biodiversity.org.au/name/apni/73658,accepted,https://id.biodiversity.org.au/node/apni/2914896,https://id.biodiversity.org.au/taxon/apni/51461748,NA,Medicosma sessiliflora,native Melastoma cyanoides,Melastoma cyanoides,Melastoma cyanoides,NA,Melastoma,Melastomataceae,species,APC,accepted,Magnoliidae,Qld,Melastoma cyanoides Sm.,https://id.biodiversity.org.au/node/apni/2895184,https://id.biodiversity.org.au/taxon/apni/51439399,https://id.biodiversity.org.au/name/apni/172752,Melastoma cyanoides,https://id.biodiversity.org.au/name/apni/172752,accepted,https://id.biodiversity.org.au/node/apni/2895184,https://id.biodiversity.org.au/taxon/apni/51439392,NA,Melastoma cyanoides,native -Melichrus procumbens,Melichrus procumbens,Melichrus procumbens,NA,Melichrus,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Melichrus procumbens (Cav.) Druce,https://id.biodiversity.org.au/node/apni/2905836,https://id.biodiversity.org.au/node/apni/2914566,https://id.biodiversity.org.au/name/apni/114051,Melichrus procumbens,https://id.biodiversity.org.au/name/apni/114051,accepted,https://id.biodiversity.org.au/node/apni/2905836,https://id.biodiversity.org.au/taxon/apni/51436079,NA,Melichrus procumbens,native +Melichrus procumbens,Melichrus procumbens,Melichrus procumbens,NA,Melichrus,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Melichrus procumbens (Cav.) Druce,https://id.biodiversity.org.au/node/apni/2905836,https://id.biodiversity.org.au/node/apni/2914566,https://id.biodiversity.org.au/name/apni/114051,Melichrus procumbens,https://id.biodiversity.org.au/name/apni/114051,accepted,https://id.biodiversity.org.au/node/apni/2905836,https://id.biodiversity.org.au/taxon/apni/51738121,NA,Melichrus procumbens,native Melicope elleryana,Melicope elleryana,Melicope elleryana,NA,Melicope,Rutaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Melicope elleryana (F.Muell.) T.G.Hartley,https://id.biodiversity.org.au/node/apni/2913641,https://id.biodiversity.org.au/node/apni/2918609,https://id.biodiversity.org.au/name/apni/118560,Melicope elleryana,https://id.biodiversity.org.au/name/apni/118560,accepted,https://id.biodiversity.org.au/node/apni/2913641,https://id.biodiversity.org.au/taxon/apni/51461748,NA,Melicope elleryana,native Mischocarpus australis,Mischocarpus australis,Mischocarpus australis,NA,Mischocarpus,Sapindaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Mischocarpus australis S.T.Reynolds,https://id.biodiversity.org.au/node/apni/2893744,https://id.biodiversity.org.au/taxon/apni/51389373,https://id.biodiversity.org.au/name/apni/115917,Mischocarpus australis,https://id.biodiversity.org.au/name/apni/115917,accepted,https://id.biodiversity.org.au/node/apni/2893744,https://id.biodiversity.org.au/taxon/apni/51447212,NA,Mischocarpus australis,native Muehlenbeckia adpressa,Muehlenbeckia adpressa,Muehlenbeckia adpressa,NA,Muehlenbeckia,Polygonaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Muehlenbeckia adpressa (Labill.) Meisn.,https://id.biodiversity.org.au/node/apni/4750977,https://id.biodiversity.org.au/taxon/apni/51291654,https://id.biodiversity.org.au/name/apni/107852,Muehlenbeckia adpressa,https://id.biodiversity.org.au/name/apni/107852,accepted,https://id.biodiversity.org.au/node/apni/4750977,https://id.biodiversity.org.au/taxon/apni/51444856,NA,Muehlenbeckia adpressa,native -Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,NA,Myoporum,Scrophulariaceae,subspecies,APC,accepted,Magnoliidae,"Qld, NSW",Myoporum boninense subsp. australe Chinnock,https://id.biodiversity.org.au/node/apni/7957248,https://id.biodiversity.org.au/taxon/apni/51447443,https://id.biodiversity.org.au/name/apni/117892,Myoporum boninense subsp. australe,https://id.biodiversity.org.au/name/apni/117892,accepted,https://id.biodiversity.org.au/node/apni/7957248,https://id.biodiversity.org.au/taxon/apni/51461527,Myoporum boninense subsp. australe,Myoporum boninense,native +Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,NA,Myoporum,Scrophulariaceae,subspecies,APC,accepted,Magnoliidae,"Qld, NSW",Myoporum boninense subsp. australe Chinnock,https://id.biodiversity.org.au/node/apni/7957248,https://id.biodiversity.org.au/taxon/apni/51447443,https://id.biodiversity.org.au/name/apni/117892,Myoporum boninense subsp. australe,https://id.biodiversity.org.au/name/apni/117892,accepted,https://id.biodiversity.org.au/node/apni/7957248,https://id.biodiversity.org.au/taxon/apni/51734003,Myoporum boninense subsp. australe,Myoporum boninense,native Myristica insipida,Myristica insipida,Myristica insipida,NA,Myristica,Myristicaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Myristica insipida R.Br.,https://id.biodiversity.org.au/node/apni/2902429,https://id.biodiversity.org.au/node/apni/2895962,https://id.biodiversity.org.au/name/apni/86064,Myristica insipida,https://id.biodiversity.org.au/name/apni/86064,accepted,https://id.biodiversity.org.au/node/apni/2902429,https://id.biodiversity.org.au/node/apni/2903136,NA,Myristica insipida,native Neolitsea dealbata,Neolitsea dealbata,Neolitsea dealbata,NA,Neolitsea,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Neolitsea dealbata (R.Br.) Merr.,https://id.biodiversity.org.au/node/apni/2910025,https://id.biodiversity.org.au/node/apni/2914447,https://id.biodiversity.org.au/name/apni/79589,Neolitsea dealbata,https://id.biodiversity.org.au/name/apni/79589,accepted,https://id.biodiversity.org.au/node/apni/2910025,https://id.biodiversity.org.au/taxon/apni/51438397,NA,Neolitsea dealbata,native Nicotiana glauca,Nicotiana glauca,Nicotiana glauca,NA,Nicotiana,Solanaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (naturalised)",Nicotiana glauca Graham,https://id.biodiversity.org.au/node/apni/2887606,https://id.biodiversity.org.au/taxon/apni/51447689,https://id.biodiversity.org.au/name/apni/77368,Nicotiana glauca,https://id.biodiversity.org.au/name/apni/77368,accepted,https://id.biodiversity.org.au/node/apni/2887606,https://id.biodiversity.org.au/taxon/apni/51447684,NA,Nicotiana glauca,naturalised @@ -177,8 +200,9 @@ Nicotiana goodspeedii,Nicotiana goodspeedii,Nicotiana goodspeedii,NA,Nicotiana,S Oxalis corniculata,Oxalis corniculata,Oxalis corniculata,NA,Oxalis,Oxalidaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), ChI (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Oxalis corniculata L.,https://id.biodiversity.org.au/node/apni/2909588,https://id.biodiversity.org.au/taxon/apni/51442068,https://id.biodiversity.org.au/name/apni/89460,Oxalis corniculata,https://id.biodiversity.org.au/name/apni/89460,accepted,https://id.biodiversity.org.au/node/apni/2909588,https://id.biodiversity.org.au/taxon/apni/51442069,NA,Oxalis corniculata,naturalised Pandorea pandorana subsp. austrocaledonica,Pandorea pandorana subsp. austrocaledonica,Pandorea pandorana,NA,Pandorea,Bignoniaceae,species,APC,accepted,Magnoliidae,"WA, SA (native and naturalised), Qld, NSW, LHI, NI (presumed extinct), Vic (native and naturalised), Tas",Pandorea pandorana (Andrews) Steenis,https://id.biodiversity.org.au/taxon/apni/51269199,https://id.biodiversity.org.au/taxon/apni/51269200,https://id.biodiversity.org.au/name/apni/91117,Pandorea pandorana,https://id.biodiversity.org.au/name/apni/141640,misapplied,https://id.biodiversity.org.au/instance/apni/51269194,https://id.biodiversity.org.au/taxon/apni/51439229,NA,Pandorea pandorana,native and naturalised Paraserianthes lophantha,Paraserianthes lophantha,Paraserianthes lophantha,NA,Paraserianthes,Fabaceae,species,APC,accepted,Magnoliidae,"WA (native and naturalised), SA (naturalised), NSW (naturalised), NI (naturalised), Vic (naturalised), Tas (naturalised)",Paraserianthes lophantha (Willd.) I.C.Nielsen,https://id.biodiversity.org.au/taxon/apni/51286820,https://id.biodiversity.org.au/taxon/apni/51286819,https://id.biodiversity.org.au/name/apni/116755,Paraserianthes lophantha,https://id.biodiversity.org.au/name/apni/116755,accepted,https://id.biodiversity.org.au/taxon/apni/51286820,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Paraserianthes lophantha,native and naturalised -Parentucellia latifolia,Parentucellia latifolia,Parentucellia latifolia,NA,Parentucellia,Orobanchaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Parentucellia latifolia (L.) Caruel,https://id.biodiversity.org.au/taxon/apni/51291069,https://id.biodiversity.org.au/taxon/apni/51291062,https://id.biodiversity.org.au/name/apni/96753,Parentucellia latifolia,https://id.biodiversity.org.au/name/apni/96753,accepted,https://id.biodiversity.org.au/taxon/apni/51291069,https://id.biodiversity.org.au/taxon/apni/51291037,NA,Parentucellia latifolia,naturalised +Parentucellia latifolia,Parentucellia latifolia,Parentucellia latifolia,NA,Parentucellia,Orobanchaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Parentucellia latifolia (L.) Caruel,https://id.biodiversity.org.au/taxon/apni/51291069,https://id.biodiversity.org.au/taxon/apni/51291062,https://id.biodiversity.org.au/name/apni/96753,Parentucellia latifolia,https://id.biodiversity.org.au/name/apni/96753,accepted,https://id.biodiversity.org.au/taxon/apni/51291069,https://id.biodiversity.org.au/taxon/apni/51734010,NA,Parentucellia latifolia,naturalised Hypoxis glabella var. glabella,Hypoxis glabella var. glabella,Pauridia glabella var. glabella,NA,Pauridia,Hypoxidaceae,variety,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Pauridia glabella (R.Br.) Snijman & Kocyan var. glabella,https://id.biodiversity.org.au/node/apni/7455351,https://id.biodiversity.org.au/taxon/apni/51437983,https://id.biodiversity.org.au/name/apni/244102,Pauridia glabella var. glabella,https://id.biodiversity.org.au/name/apni/81442,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/7455341,https://id.biodiversity.org.au/taxon/apni/51437984,Pauridia glabella var. glabella,Pauridia glabella,native +Persoonia falcata,Persoonia falcata,Persoonia falcata,NA,Persoonia,Proteaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Persoonia falcata R.Br.,https://id.biodiversity.org.au/node/apni/2904820,https://id.biodiversity.org.au/taxon/apni/51429033,https://id.biodiversity.org.au/name/apni/112478,Persoonia falcata,https://id.biodiversity.org.au/name/apni/112478,accepted,https://id.biodiversity.org.au/node/apni/2904820,https://id.biodiversity.org.au/taxon/apni/51732901,NA,Persoonia falcata,native Phlegmatospermum cochlearinum,Phlegmatospermum cochlearinum,Phlegmatospermum cochlearinum,NA,Phlegmatospermum,Brassicaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic",Phlegmatospermum cochlearinum (F.Muell.) O.E.Schulz,https://id.biodiversity.org.au/node/apni/2915554,https://id.biodiversity.org.au/node/apni/2897988,https://id.biodiversity.org.au/name/apni/81861,Phlegmatospermum cochlearinum,https://id.biodiversity.org.au/name/apni/81861,accepted,https://id.biodiversity.org.au/node/apni/2915554,https://id.biodiversity.org.au/taxon/apni/51612687,NA,Phlegmatospermum cochlearinum,native Phyla nodiflora,Phyla nodiflora,Phyla nodiflora,NA,Phyla,Verbenaceae,species,APC,accepted,Magnoliidae,"WA (native and naturalised), CoI (naturalised), NT, Qld, NSW (naturalised)",Phyla nodiflora (L.) Greene,https://id.biodiversity.org.au/node/apni/2907374,https://id.biodiversity.org.au/node/apni/2892182,https://id.biodiversity.org.au/name/apni/74617,Phyla nodiflora,https://id.biodiversity.org.au/name/apni/74617,accepted,https://id.biodiversity.org.au/node/apni/2907374,https://id.biodiversity.org.au/taxon/apni/51448662,NA,Phyla nodiflora,native and naturalised Picris barbarorum,Picris barbarorum,Picris barbarorum,NA,Picris,Asteraceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic (presumed extinct)",Picris barbarorum Lindl.,https://id.biodiversity.org.au/node/apni/2916052,https://id.biodiversity.org.au/node/apni/7890078,https://id.biodiversity.org.au/name/apni/110349,Picris barbarorum,https://id.biodiversity.org.au/name/apni/110349,accepted,https://id.biodiversity.org.au/node/apni/2916052,https://id.biodiversity.org.au/taxon/apni/51695393,NA,Picris barbarorum,native @@ -188,25 +212,25 @@ Pisum sativum var. arvense,Pisum sativum var. arvense,Pisum sativum var. arvense Pittosporum erioloma,Pittosporum erioloma,Pittosporum erioloma,NA,Pittosporum,Pittosporaceae,species,APC,accepted,Magnoliidae,LHI,Pittosporum erioloma C.Moore & F.Muell.,https://id.biodiversity.org.au/node/apni/2891204,https://id.biodiversity.org.au/taxon/apni/51442349,https://id.biodiversity.org.au/name/apni/99523,Pittosporum erioloma,https://id.biodiversity.org.au/name/apni/99523,accepted,https://id.biodiversity.org.au/node/apni/2891204,https://id.biodiversity.org.au/taxon/apni/51442315,NA,Pittosporum erioloma,native Pittosporum rubiginosum,Pittosporum rubiginosum,Pittosporum rubiginosum,NA,Pittosporum,Pittosporaceae,species,APC,accepted,Magnoliidae,Qld,Pittosporum rubiginosum A.Cunn.,https://id.biodiversity.org.au/node/apni/2887772,https://id.biodiversity.org.au/taxon/apni/51442349,https://id.biodiversity.org.au/name/apni/100119,Pittosporum rubiginosum,https://id.biodiversity.org.au/name/apni/100119,accepted,https://id.biodiversity.org.au/node/apni/2887772,https://id.biodiversity.org.au/taxon/apni/51442315,NA,Pittosporum rubiginosum,native Plantago turrifera,Plantago turrifera,Plantago turrifera,NA,Plantago,Plantaginaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW (native and naturalised), Vic","Plantago turrifera B.G.Briggs, Carolin & Pulley",https://id.biodiversity.org.au/node/apni/2895983,https://id.biodiversity.org.au/node/apni/7745425,https://id.biodiversity.org.au/name/apni/79077,Plantago turrifera,https://id.biodiversity.org.au/name/apni/79077,accepted,https://id.biodiversity.org.au/node/apni/2895983,https://id.biodiversity.org.au/taxon/apni/51699383,NA,Plantago turrifera,native and naturalised -Haplostichanthus sp Coop. Ck,Haplostichanthus submontanus,Polyalthia submontana,NA,Polyalthia,Annonaceae,species,APC,accepted,Magnoliidae,Qld,Polyalthia submontana (Jessup) B.Xue & R.M.K.Saunders,https://id.biodiversity.org.au/taxon/apni/51613975,https://id.biodiversity.org.au/taxon/apni/51613976,https://id.biodiversity.org.au/name/apni/246294,Polyalthia submontana,https://id.biodiversity.org.au/name/apni/191525,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/51430810,https://id.biodiversity.org.au/taxon/apni/51613977,NA,Polyalthia submontana,native +Haplostichanthus sp Coop. Ck,Haplostichanthus submontanus,Polyalthia submontana,NA,Polyalthia,Annonaceae,species,APC,accepted,Magnoliidae,Qld,Polyalthia submontana (Jessup) B.Xue & R.M.K.Saunders,https://id.biodiversity.org.au/taxon/apni/51735993,https://id.biodiversity.org.au/taxon/apni/51735989,https://id.biodiversity.org.au/name/apni/246294,Polyalthia submontana,https://id.biodiversity.org.au/name/apni/191525,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/51430810,https://id.biodiversity.org.au/taxon/apni/51735960,NA,Polyalthia submontana,native Polycarpon tetraphyllum,Polycarpon tetraphyllum,Polycarpon tetraphyllum,NA,Polycarpon,Caryophyllaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Polycarpon tetraphyllum (L.) L.,https://id.biodiversity.org.au/taxon/apni/51270276,https://id.biodiversity.org.au/taxon/apni/51270277,https://id.biodiversity.org.au/name/apni/107982,Polycarpon tetraphyllum,https://id.biodiversity.org.au/name/apni/107982,accepted,https://id.biodiversity.org.au/taxon/apni/51270276,https://id.biodiversity.org.au/taxon/apni/51432987,NA,Polycarpon tetraphyllum,naturalised -Polyscias australiana,Polyscias australiana,Polyscias australiana,NA,Polyscias,Araliaceae,species,APC,accepted,Magnoliidae,"NT, Qld",Polyscias australiana (F.Muell.) Philipson,https://id.biodiversity.org.au/node/apni/7223338,https://id.biodiversity.org.au/taxon/apni/51292784,https://id.biodiversity.org.au/name/apni/84802,Polyscias australiana,https://id.biodiversity.org.au/name/apni/84787,taxonomic synonym,https://id.biodiversity.org.au/instance/apni/941828,https://id.biodiversity.org.au/taxon/apni/51632289,NA,Polyscias australiana,native +Polyscias australiana,Polyscias australiana,Polyscias australiana,NA,Polyscias,Araliaceae,species,APC,accepted,Magnoliidae,"NT, Qld",Polyscias australiana (F.Muell.) Philipson,https://id.biodiversity.org.au/node/apni/7223338,https://id.biodiversity.org.au/taxon/apni/51737050,https://id.biodiversity.org.au/name/apni/84802,Polyscias australiana,https://id.biodiversity.org.au/name/apni/84787,taxonomic synonym,https://id.biodiversity.org.au/instance/apni/941828,https://id.biodiversity.org.au/taxon/apni/51736765,NA,Polyscias australiana,native Potamogeton australiensis,Potamogeton australiensis,Potamogeton australiensis,NA,Potamogeton,Potamogetonaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Potamogeton australiensis A.Benn.,https://id.biodiversity.org.au/node/apni/7808489,https://id.biodiversity.org.au/node/apni/8770682,https://id.biodiversity.org.au/name/apni/65827,Potamogeton australiensis,https://id.biodiversity.org.au/name/apni/65827,accepted,https://id.biodiversity.org.au/node/apni/7808489,https://id.biodiversity.org.au/taxon/apni/51353530,NA,Potamogeton australiensis,native Psoralea pinnata,Psoralea pinnata,Psoralea pinnata,NA,Psoralea,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised), Tas (naturalised)",Psoralea pinnata L.,https://id.biodiversity.org.au/node/apni/2887023,https://id.biodiversity.org.au/node/apni/8771698,https://id.biodiversity.org.au/name/apni/88820,Psoralea pinnata,https://id.biodiversity.org.au/name/apni/88820,accepted,https://id.biodiversity.org.au/node/apni/2887023,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Psoralea pinnata,naturalised Psychotria dallachiana,Psychotria dallachiana,Psychotria dallachiana,NA,Psychotria,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Psychotria dallachiana Benth.,https://id.biodiversity.org.au/node/apni/2890013,https://id.biodiversity.org.au/taxon/apni/51446698,https://id.biodiversity.org.au/name/apni/89074,Psychotria dallachiana,https://id.biodiversity.org.au/name/apni/89074,accepted,https://id.biodiversity.org.au/node/apni/2890013,https://id.biodiversity.org.au/taxon/apni/51446612,NA,Psychotria dallachiana,native Psychotria sp Utchee Creek,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),Psychotria sp. Utchee Creek (H.Flecker NQNC5313),NA,Psychotria,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Psychotria sp. Utchee Creek (H.Flecker NQNC5313) Qld Herbarium,https://id.biodiversity.org.au/taxon/apni/51446727,https://id.biodiversity.org.au/taxon/apni/51446698,https://id.biodiversity.org.au/name/apni/218829,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),https://id.biodiversity.org.au/name/apni/218829,accepted,https://id.biodiversity.org.au/taxon/apni/51446727,https://id.biodiversity.org.au/taxon/apni/51446612,NA,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),native Pultenaea ferruginea,Pultenaea ferruginea,Pultenaea ferruginea,NA,Pultenaea,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Pultenaea ferruginea Rudge,https://id.biodiversity.org.au/node/apni/2906803,https://id.biodiversity.org.au/taxon/apni/51436286,https://id.biodiversity.org.au/name/apni/59158,Pultenaea ferruginea,https://id.biodiversity.org.au/name/apni/59158,accepted,https://id.biodiversity.org.au/node/apni/2906803,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Pultenaea ferruginea,native -Rhodamnia argentea,Rhodamnia argentea,Rhodamnia argentea,NA,Rhodamnia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Rhodamnia argentea Benth.,https://id.biodiversity.org.au/node/apni/2919069,https://id.biodiversity.org.au/taxon/apni/51440311,https://id.biodiversity.org.au/name/apni/68532,Rhodamnia argentea,https://id.biodiversity.org.au/name/apni/68532,accepted,https://id.biodiversity.org.au/node/apni/2919069,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Rhodamnia argentea,native -Rhodomyrtus trineura,Rhodomyrtus trineura,Rhodomyrtus trineura,NA,Rhodomyrtus,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Rhodomyrtus trineura (F.Muell.) Benth.,https://id.biodiversity.org.au/taxon/apni/51441176,https://id.biodiversity.org.au/taxon/apni/51441177,https://id.biodiversity.org.au/name/apni/69289,Rhodomyrtus trineura,https://id.biodiversity.org.au/name/apni/69289,accepted,https://id.biodiversity.org.au/taxon/apni/51441176,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Rhodomyrtus trineura,native +Rhodamnia argentea,Rhodamnia argentea,Rhodamnia argentea,NA,Rhodamnia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Rhodamnia argentea Benth.,https://id.biodiversity.org.au/node/apni/2919069,https://id.biodiversity.org.au/taxon/apni/51440311,https://id.biodiversity.org.au/name/apni/68532,Rhodamnia argentea,https://id.biodiversity.org.au/name/apni/68532,accepted,https://id.biodiversity.org.au/node/apni/2919069,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Rhodamnia argentea,native +Rhodomyrtus trineura,Rhodomyrtus trineura,Rhodomyrtus trineura,NA,Rhodomyrtus,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Rhodomyrtus trineura (F.Muell.) Benth.,https://id.biodiversity.org.au/taxon/apni/51441176,https://id.biodiversity.org.au/taxon/apni/51441177,https://id.biodiversity.org.au/name/apni/69289,Rhodomyrtus trineura,https://id.biodiversity.org.au/name/apni/69289,accepted,https://id.biodiversity.org.au/taxon/apni/51441176,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Rhodomyrtus trineura,native Rockinghamia angustifolia,Rockinghamia angustifolia,Rockinghamia angustifolia,NA,Rockinghamia,Euphorbiaceae,species,APC,accepted,Magnoliidae,Qld,Rockinghamia angustifolia (Benth.) Airy Shaw,https://id.biodiversity.org.au/node/apni/2921179,https://id.biodiversity.org.au/node/apni/2892697,https://id.biodiversity.org.au/name/apni/61487,Rockinghamia angustifolia,https://id.biodiversity.org.au/name/apni/61487,accepted,https://id.biodiversity.org.au/node/apni/2921179,https://id.biodiversity.org.au/taxon/apni/51442249,NA,Rockinghamia angustifolia,native Rorippa gigantea,Rorippa gigantea,Rorippa gigantea,NA,Rorippa,Brassicaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Rorippa gigantea (Hook.) Garn.-Jones,https://id.biodiversity.org.au/node/apni/2920330,https://id.biodiversity.org.au/node/apni/8442201,https://id.biodiversity.org.au/name/apni/75950,Rorippa gigantea,https://id.biodiversity.org.au/name/apni/75950,accepted,https://id.biodiversity.org.au/node/apni/2920330,https://id.biodiversity.org.au/taxon/apni/51612687,NA,Rorippa gigantea,native -Rubus parvifolius,Rubus parvifolius,Rubus parvifolius,NA,Rubus,Rosaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Rubus parvifolius L.,https://id.biodiversity.org.au/node/apni/2901867,https://id.biodiversity.org.au/taxon/apni/51446575,https://id.biodiversity.org.au/name/apni/85986,Rubus parvifolius,https://id.biodiversity.org.au/name/apni/85986,accepted,https://id.biodiversity.org.au/node/apni/2901867,https://id.biodiversity.org.au/taxon/apni/51446278,NA,Rubus parvifolius,native -Salix alba,Salix alba,Salix alba , NA,Salix,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised)",Salix alba L.,https://id.biodiversity.org.au/node/apni/2896377,https://id.biodiversity.org.au/node/apni/8905801,https://id.biodiversity.org.au/name/apni/59687,Salix alba [alternative possible names: NA],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51436847,NA,Salix alba,naturalised +Rubus parvifolius,Rubus parvifolius,Rubus parvifolius,NA,Rubus,Rosaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Rubus parvifolius L.,https://id.biodiversity.org.au/node/apni/2901867,https://id.biodiversity.org.au/taxon/apni/51446575,https://id.biodiversity.org.au/name/apni/85986,Rubus parvifolius,https://id.biodiversity.org.au/name/apni/85986,accepted,https://id.biodiversity.org.au/node/apni/2901867,https://id.biodiversity.org.au/taxon/apni/51737985,NA,Rubus parvifolius,native +Salix alba,Salix alba,Salix alba , Salix x fragilis nothovar. fragilis (pro parte misapplied),Salix,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised)",Salix alba L.,https://id.biodiversity.org.au/node/apni/2896377,https://id.biodiversity.org.au/node/apni/8905801,https://id.biodiversity.org.au/name/apni/59687,Salix alba [alternative possible names: Salix x fragilis nothovar. fragilis (pro parte misapplied)],NA,NA,NA,https://id.biodiversity.org.au/taxon/apni/51436847,NA,Salix alba,naturalised Quassia baileyana,Quassia baileyana,Samadera baileyana,NA,Samadera,Simaroubaceae,species,APC,accepted,Magnoliidae,Qld,Samadera baileyana Oliv.,https://id.biodiversity.org.au/node/apni/2891526,https://id.biodiversity.org.au/node/apni/2900441,https://id.biodiversity.org.au/name/apni/60763,Samadera baileyana,https://id.biodiversity.org.au/name/apni/70084,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/897542,https://id.biodiversity.org.au/taxon/apni/51316490,NA,Samadera baileyana,native Schenkia australis,Schenkia australis,Schenkia australis,NA,Schenkia,Gentianaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic, Tas",Schenkia australis (R.Br.) G.Mans.,https://id.biodiversity.org.au/taxon/apni/51436897,https://id.biodiversity.org.au/taxon/apni/51436898,https://id.biodiversity.org.au/name/apni/200895,Schenkia australis,https://id.biodiversity.org.au/name/apni/200895,accepted,https://id.biodiversity.org.au/taxon/apni/51436897,https://id.biodiversity.org.au/taxon/apni/51436871,NA,Schenkia australis,native Schoenus apogon,Schoenus apogon,Schoenus apogon,NA,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Schoenus apogon Roem. & Schult.,https://id.biodiversity.org.au/node/apni/2908439,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/109452,Schoenus apogon,https://id.biodiversity.org.au/name/apni/109452,accepted,https://id.biodiversity.org.au/node/apni/2908439,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Schoenus apogon,native Schoenus brevifolius,Schoenus brevifolius,Schoenus brevifolius,NA,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic, Tas",Schoenus brevifolius R.Br.,https://id.biodiversity.org.au/node/apni/2904000,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/109778,Schoenus brevifolius,https://id.biodiversity.org.au/name/apni/109778,accepted,https://id.biodiversity.org.au/node/apni/2904000,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Schoenus brevifolius,native -Schoenus lepidosperma,Schoenus lepidosperma,Schoenus lepidosperma,NA,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Schoenus lepidosperma (F.Muell.) K.L.Wilson,https://id.biodiversity.org.au/node/apni/2893030,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/141376,Schoenus lepidosperma,https://id.biodiversity.org.au/name/apni/243667,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/947513,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Schoenus lepidosperma,native +Schoenus lepidosperma,Schoenus lepidosperma,Schoenus lepidosperma,NA,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Schoenus lepidosperma (F.Muell.) K.L.Wilson,https://id.biodiversity.org.au/node/apni/2893030,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/141376,Schoenus lepidosperma,https://id.biodiversity.org.au/name/apni/141376,accepted,https://id.biodiversity.org.au/node/apni/2893030,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Schoenus lepidosperma,native Schoenus vaginatus,Schoenus vaginatus,Schoenus vaginatus,NA,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Schoenus vaginatus F.Muell. ex Benth.,https://id.biodiversity.org.au/node/apni/2896591,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/113246,Schoenus vaginatus,https://id.biodiversity.org.au/name/apni/113246,accepted,https://id.biodiversity.org.au/node/apni/2896591,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Schoenus vaginatus,native Scleria rugosa,Scleria rugosa,Scleria rugosa,NA,Scleria,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Scleria rugosa R.Br.,https://id.biodiversity.org.au/node/apni/2892143,https://id.biodiversity.org.au/taxon/apni/51434752,https://id.biodiversity.org.au/name/apni/64346,Scleria rugosa,https://id.biodiversity.org.au/name/apni/64346,accepted,https://id.biodiversity.org.au/node/apni/2892143,https://id.biodiversity.org.au/taxon/apni/51460154,NA,Scleria rugosa,native Senecio longipilus,Senecio longipilus,Senecio longipilus,NA,Senecio,Asteraceae,species,APC,accepted,Magnoliidae,"NSW, Tas",Senecio longipilus I.Thomps.,https://id.biodiversity.org.au/node/apni/2907653,https://id.biodiversity.org.au/taxon/apni/51614245,https://id.biodiversity.org.au/name/apni/189666,Senecio longipilus,https://id.biodiversity.org.au/name/apni/189666,accepted,https://id.biodiversity.org.au/node/apni/2907653,https://id.biodiversity.org.au/taxon/apni/51695393,NA,Senecio longipilus,native @@ -218,16 +242,18 @@ Sparaxis bulbifera,Sparaxis bulbifera,Sparaxis bulbifera,NA,Sparaxis,Iridaceae,s Spergularia diandra,Spergularia diandra,Spergularia diandra,NA,Spergularia,Caryophyllaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised)",Spergularia diandra (Guss.) Heldr.,https://id.biodiversity.org.au/node/apni/2886696,https://id.biodiversity.org.au/taxon/apni/51295406,https://id.biodiversity.org.au/name/apni/83464,Spergularia diandra,https://id.biodiversity.org.au/name/apni/83464,accepted,https://id.biodiversity.org.au/node/apni/2886696,https://id.biodiversity.org.au/taxon/apni/51432987,NA,Spergularia diandra,naturalised Sphaeromorphaea littoralis,Sphaeromorphaea littoralis,Sphaeromorphaea littoralis,NA,Sphaeromorphaea,Asteraceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Sphaeromorphaea littoralis (Retz.) A.R.Bean,https://id.biodiversity.org.au/node/apni/7069871,https://id.biodiversity.org.au/node/apni/7071683,https://id.biodiversity.org.au/name/apni/246779,Sphaeromorphaea littoralis,https://id.biodiversity.org.au/name/apni/246779,accepted,https://id.biodiversity.org.au/node/apni/7069871,https://id.biodiversity.org.au/taxon/apni/51695393,NA,Sphaeromorphaea littoralis,native Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia subsp. angustifolia,NA,Stellaria,Caryophyllaceae,subspecies,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Stellaria angustifolia Hook. subsp. angustifolia,https://id.biodiversity.org.au/node/apni/2890520,https://id.biodiversity.org.au/taxon/apni/51433015,https://id.biodiversity.org.au/name/apni/240421,Stellaria angustifolia subsp. angustifolia,https://id.biodiversity.org.au/name/apni/240421,accepted,https://id.biodiversity.org.au/node/apni/2890520,https://id.biodiversity.org.au/taxon/apni/51432987,Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia,native -Styphelia viridis,Styphelia viridis,Styphelia viridis,NA,Styphelia,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Styphelia viridis Andrews,https://id.biodiversity.org.au/node/apni/2912747,https://id.biodiversity.org.au/taxon/apni/51435346,https://id.biodiversity.org.au/name/apni/109318,Styphelia viridis,https://id.biodiversity.org.au/name/apni/109318,accepted,https://id.biodiversity.org.au/node/apni/2912747,https://id.biodiversity.org.au/taxon/apni/51436079,NA,Styphelia viridis,native +Styphelia viridis,Styphelia viridis,Styphelia viridis,NA,Styphelia,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Styphelia viridis Andrews,https://id.biodiversity.org.au/node/apni/2912747,https://id.biodiversity.org.au/taxon/apni/51435346,https://id.biodiversity.org.au/name/apni/109318,Styphelia viridis,https://id.biodiversity.org.au/name/apni/109318,accepted,https://id.biodiversity.org.au/node/apni/2912747,https://id.biodiversity.org.au/taxon/apni/51738121,NA,Styphelia viridis,native Swainsona cadellii,Swainsona cadellii,Swainsona cadellii,NA,Swainsona,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Swainsona cadellii F.Muell. ex C.Moore,https://id.biodiversity.org.au/node/apni/2904099,https://id.biodiversity.org.au/taxon/apni/51436313,https://id.biodiversity.org.au/name/apni/76870,Swainsona cadellii,https://id.biodiversity.org.au/name/apni/76870,accepted,https://id.biodiversity.org.au/node/apni/2904099,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Swainsona cadellii,native -Acmena graveolens,Acmena graveolens,Syzygium graveolens,NA,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium graveolens (F.M.Bailey) Craven & Biffin,https://id.biodiversity.org.au/node/apni/2920364,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/202985,Syzygium graveolens,https://id.biodiversity.org.au/name/apni/73535,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/891710,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Syzygium graveolens,native -Syzygium gustavioides,Syzygium gustavioides,Syzygium gustavioides,NA,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium gustavioides (F.M.Bailey) B.Hyland,https://id.biodiversity.org.au/taxon/apni/51429676,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/64722,Syzygium gustavioides,https://id.biodiversity.org.au/name/apni/64722,accepted,https://id.biodiversity.org.au/taxon/apni/51429676,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Syzygium gustavioides,native -Syzygium sayeri,Syzygium sayeri,Syzygium sayeri,NA,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium sayeri (F.Muell.) B.Hyland,https://id.biodiversity.org.au/node/apni/2888968,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/64837,Syzygium sayeri,https://id.biodiversity.org.au/name/apni/64837,accepted,https://id.biodiversity.org.au/node/apni/2888968,https://id.biodiversity.org.au/taxon/apni/51702983,NA,Syzygium sayeri,native +Acmena graveolens,Acmena graveolens,Syzygium graveolens,NA,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium graveolens (F.M.Bailey) Craven & Biffin,https://id.biodiversity.org.au/node/apni/2920364,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/202985,Syzygium graveolens,https://id.biodiversity.org.au/name/apni/73535,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/891710,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Syzygium graveolens,native +Syzygium gustavioides,Syzygium gustavioides,Syzygium gustavioides,NA,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium gustavioides (F.M.Bailey) B.Hyland,https://id.biodiversity.org.au/taxon/apni/51429676,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/64722,Syzygium gustavioides,https://id.biodiversity.org.au/name/apni/64722,accepted,https://id.biodiversity.org.au/taxon/apni/51429676,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Syzygium gustavioides,native +Syzygium sayeri,Syzygium sayeri,Syzygium sayeri,NA,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium sayeri (F.Muell.) B.Hyland,https://id.biodiversity.org.au/node/apni/2888968,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/64837,Syzygium sayeri,https://id.biodiversity.org.au/name/apni/64837,accepted,https://id.biodiversity.org.au/node/apni/2888968,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Syzygium sayeri,native Teucrium puberulum,Teucrium puberulum,Teucrium puberulum,NA,Teucrium,Lamiaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Teucrium puberulum (F.Muell.) Kattari & Bräuchler,https://id.biodiversity.org.au/taxon/apni/51288087,https://id.biodiversity.org.au/taxon/apni/51438311,https://id.biodiversity.org.au/name/apni/7660439,Teucrium puberulum,https://id.biodiversity.org.au/name/apni/7660439,accepted,https://id.biodiversity.org.au/taxon/apni/51288087,https://id.biodiversity.org.au/taxon/apni/51696573,NA,Teucrium puberulum,native -Thelymitra kangaloonica,Thelymitra kangaloonica,Thelymitra kangaloonica,NA,Thelymitra,Orchidaceae,species,APC,accepted,Magnoliidae,NSW,Thelymitra kangaloonica Jeanes,https://id.biodiversity.org.au/taxon/apni/51414328,https://id.biodiversity.org.au/taxon/apni/51631246,https://id.biodiversity.org.au/name/apni/233692,Thelymitra kangaloonica,https://id.biodiversity.org.au/name/apni/233692,accepted,https://id.biodiversity.org.au/taxon/apni/51414328,https://id.biodiversity.org.au/taxon/apni/51697009,NA,Thelymitra kangaloonica,native +Thelymitra kangaloonica,Thelymitra kangaloonica,Thelymitra kangaloonica,NA,Thelymitra,Orchidaceae,species,APC,accepted,Magnoliidae,NSW,Thelymitra kangaloonica Jeanes,https://id.biodiversity.org.au/taxon/apni/51414328,https://id.biodiversity.org.au/taxon/apni/51631246,https://id.biodiversity.org.au/name/apni/233692,Thelymitra kangaloonica,https://id.biodiversity.org.au/name/apni/233692,accepted,https://id.biodiversity.org.au/taxon/apni/51414328,https://id.biodiversity.org.au/taxon/apni/51727417,NA,Thelymitra kangaloonica,native Thesium australe,Thesium australe,Thesium australe,NA,Thesium,Santalaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic, Tas (presumed extinct)",Thesium australe R.Br.,https://id.biodiversity.org.au/node/apni/2891975,https://id.biodiversity.org.au/node/apni/2913858,https://id.biodiversity.org.au/name/apni/56224,Thesium australe,https://id.biodiversity.org.au/name/apni/56224,accepted,https://id.biodiversity.org.au/node/apni/2891975,https://id.biodiversity.org.au/taxon/apni/51447154,NA,Thesium australe,native Trema aspera,Trema aspera,Trema tomentosa var. aspera,NA,Trema,Cannabaceae,variety,APC,accepted,Magnoliidae,"WA, Qld, NSW, Vic (presumed extinct)",Trema tomentosa var. aspera (Brongn.) Hewson,https://id.biodiversity.org.au/node/apni/2917190,https://id.biodiversity.org.au/node/apni/2913617,https://id.biodiversity.org.au/name/apni/206199,Trema tomentosa var. aspera,https://id.biodiversity.org.au/name/apni/101838,nomenclatural synonym,https://id.biodiversity.org.au/instance/apni/856997,https://id.biodiversity.org.au/taxon/apni/51269919,Trema tomentosa var. aspera,Trema tomentosa,native Trifolium dubium,Trifolium dubium,Trifolium dubium,NA,Trifolium,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Trifolium dubium Sibth.,https://id.biodiversity.org.au/taxon/apni/51436351,https://id.biodiversity.org.au/taxon/apni/51436341,https://id.biodiversity.org.au/name/apni/115704,Trifolium dubium,https://id.biodiversity.org.au/name/apni/115704,accepted,https://id.biodiversity.org.au/taxon/apni/51436351,https://id.biodiversity.org.au/taxon/apni/51702961,NA,Trifolium dubium,naturalised Veronica catenata,Veronica catenata,Veronica catenata,NA,Veronica,Plantaginaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), Vic (naturalised)",Veronica catenata Pennell,https://id.biodiversity.org.au/node/apni/2897164,https://id.biodiversity.org.au/taxon/apni/51632390,https://id.biodiversity.org.au/name/apni/67965,Veronica catenata,https://id.biodiversity.org.au/name/apni/67965,accepted,https://id.biodiversity.org.au/node/apni/2897164,https://id.biodiversity.org.au/taxon/apni/51699383,NA,Veronica catenata,naturalised Veronica derwentiana,Veronica derwentiana,Veronica derwentiana,NA,Veronica,Plantaginaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Veronica derwentiana Andrews,https://id.biodiversity.org.au/node/apni/2917078,https://id.biodiversity.org.au/taxon/apni/51632390,https://id.biodiversity.org.au/name/apni/68107,Veronica derwentiana,https://id.biodiversity.org.au/name/apni/68107,accepted,https://id.biodiversity.org.au/node/apni/2917078,https://id.biodiversity.org.au/taxon/apni/51699383,NA,Veronica derwentiana,native Wahlenbergia luteola,Wahlenbergia luteola,Wahlenbergia luteola,NA,Wahlenbergia,Campanulaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic",Wahlenbergia luteola P.J.Sm.,https://id.biodiversity.org.au/node/apni/2916523,https://id.biodiversity.org.au/taxon/apni/51432869,https://id.biodiversity.org.au/name/apni/73194,Wahlenbergia luteola,https://id.biodiversity.org.au/name/apni/73194,accepted,https://id.biodiversity.org.au/node/apni/2916523,https://id.biodiversity.org.au/taxon/apni/51432853,NA,Wahlenbergia luteola,native +Xanthostemon chrysanthus,Xanthostemon chrysanthus,Xanthostemon chrysanthus,NA,Xanthostemon,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Xanthostemon chrysanthus (F.Muell.) Benth.,https://id.biodiversity.org.au/node/apni/2920567,https://id.biodiversity.org.au/taxon/apni/51440420,https://id.biodiversity.org.au/name/apni/55063,Xanthostemon chrysanthus,https://id.biodiversity.org.au/name/apni/55063,accepted,https://id.biodiversity.org.au/node/apni/2920567,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Xanthostemon chrysanthus,native +Xanthostemon formosus,Xanthostemon formosus,Xanthostemon formosus,NA,Xanthostemon,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Xanthostemon formosus Peter G.Wilson,https://id.biodiversity.org.au/taxon/apni/51440419,https://id.biodiversity.org.au/taxon/apni/51440420,https://id.biodiversity.org.au/name/apni/117195,Xanthostemon formosus,https://id.biodiversity.org.au/name/apni/117195,accepted,https://id.biodiversity.org.au/taxon/apni/51440419,https://id.biodiversity.org.au/taxon/apni/51738744,NA,Xanthostemon formosus,native diff --git a/tests/testthat/config/traits.yml b/tests/testthat/config/traits.yml index c9167825..66fa3932 100644 --- a/tests/testthat/config/traits.yml +++ b/tests/testthat/config/traits.yml @@ -277,6 +277,22 @@ traits: tussock: A subcategory of graminoid, which is a plant where many shoots from the basal meristem form prominent tufts. entity_URI: https://w3id.org/APD/traits/trait_0030010 + leaf_lifespan: + label: Leaf lifespan + description: The duration [PATO:0001309] that an individual leaf [PO:0025034] + is attached to the stem [PO:0009047] and is physiologically functional [PATO:0001510].;Duration + of time that an individual leaf is attached to the stem and physiologically + functional; leaf longevity. + comments: Leaf lifespan is the inverse of the rate of leaf turnover. For some + species, leaflets or other portions of a leaf may be censused rather than + the entire leaf lamina. Leaf lifespan can be censused as either the rate of + shedding leaves (leaf death) or the rate of formation of new leaves (leaf + birth). + type: numeric + units: mo + allowed_values_min: 1.0 + allowed_values_max: 1000.0 + entity_URI: https://w3id.org/APD/traits/trait_0030025 flowering_time: label: Flowering time, by month description: The months [UO:0000035] during which a plant [PO:0000003] has open diff --git a/tests/testthat/config/unit_conversions.csv b/tests/testthat/config/unit_conversions.csv index 58822eae..9f706fcb 100644 --- a/tests/testthat/config/unit_conversions.csv +++ b/tests/testthat/config/unit_conversions.csv @@ -10,6 +10,8 @@ mo,a,x*1/12 wk,mo,x*1/4.3 wk,a,x*1/52 wk,d,x*7 +d,mo,x*1/30.4167 +mo,d,x*30.4167 {count}/m2,{count}/mm2,x*1/1000000 {count}/cm2,{count}/mm2,x*1/100 cm,m,x*0.01 diff --git a/tests/testthat/examples/Test_2023_1/output/taxa.csv b/tests/testthat/examples/Test_2023_1/output/taxa.csv index f7e063c1..fc4b7652 100644 --- a/tests/testthat/examples/Test_2023_1/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_1/output/taxa.csv @@ -3,11 +3,11 @@ Acacia celsa,Acacia celsa,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,Qld, Acronychia acidula,Acronychia acidula,,Acronychia,Rutaceae,species,APC,accepted,Magnoliidae,Qld,Acronychia acidula F.Muell.,https://id.biodiversity.org.au/node/apni/2913200,https://id.biodiversity.org.au/taxon/apni/51446847,https://id.biodiversity.org.au/name/apni/73794,Acronychia acidula,https://id.biodiversity.org.au/name/apni/73794,https://id.biodiversity.org.au/taxon/apni/51461748,,Acronychia acidula,native Aleurites rockinghamensis,Aleurites rockinghamensis,,Aleurites,Euphorbiaceae,species,APC,accepted,Magnoliidae,Qld,Aleurites rockinghamensis (Baill.) P.I.Forst.,https://id.biodiversity.org.au/node/apni/2916622,https://id.biodiversity.org.au/node/apni/2900410,https://id.biodiversity.org.au/name/apni/171057,Aleurites rockinghamensis,https://id.biodiversity.org.au/name/apni/171057,https://id.biodiversity.org.au/taxon/apni/51442249,,Aleurites rockinghamensis,native Alphitonia petriei,Alphitonia petriei,,Alphitonia,Rhamnaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Alphitonia petriei Braid & C.T.White,https://id.biodiversity.org.au/node/apni/2887911,https://id.biodiversity.org.au/taxon/apni/51446205,https://id.biodiversity.org.au/name/apni/82935,Alphitonia petriei,https://id.biodiversity.org.au/name/apni/82935,https://id.biodiversity.org.au/taxon/apni/51446206,,Alphitonia petriei,native -Alstonia scholaris,Alstonia scholaris,,Alstonia,Apocynaceae,species,APC,accepted,Magnoliidae,Qld,Alstonia scholaris (L.) R.Br.,https://id.biodiversity.org.au/node/apni/2916809,https://id.biodiversity.org.au/node/apni/6684160,https://id.biodiversity.org.au/name/apni/83915,Alstonia scholaris,https://id.biodiversity.org.au/name/apni/83915,https://id.biodiversity.org.au/taxon/apni/51700686,,Alstonia scholaris,native +Alstonia scholaris,Alstonia scholaris,,Alstonia,Apocynaceae,species,APC,accepted,Magnoliidae,Qld,Alstonia scholaris (L.) R.Br.,https://id.biodiversity.org.au/node/apni/2916809,https://id.biodiversity.org.au/node/apni/6684160,https://id.biodiversity.org.au/name/apni/83915,Alstonia scholaris,https://id.biodiversity.org.au/name/apni/83915,https://id.biodiversity.org.au/taxon/apni/51736528,,Alstonia scholaris,native Argyrodendron peralatum,Argyrodendron peralatum,,Argyrodendron,Malvaceae,species,APC,accepted,Magnoliidae,Qld,Argyrodendron peralatum (F.M.Bailey) Edlin ex I.H.Boas,https://id.biodiversity.org.au/node/apni/2915243,https://id.biodiversity.org.au/taxon/apni/51288410,https://id.biodiversity.org.au/name/apni/100216,Argyrodendron peralatum,https://id.biodiversity.org.au/name/apni/100216,https://id.biodiversity.org.au/taxon/apni/51439248,,Argyrodendron peralatum,native Atractocarpus hirtus,Atractocarpus hirtus,,Atractocarpus,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Atractocarpus hirtus (F.Muell.) Puttock,https://id.biodiversity.org.au/node/apni/2910460,https://id.biodiversity.org.au/taxon/apni/51446611,https://id.biodiversity.org.au/name/apni/146883,Atractocarpus hirtus,https://id.biodiversity.org.au/name/apni/146883,https://id.biodiversity.org.au/taxon/apni/51446612,,Atractocarpus hirtus,native Brombya platynema,Brombya platynema,,Brombya,Rutaceae,species,APC,accepted,Magnoliidae,Qld,Brombya platynema F.Muell.,https://id.biodiversity.org.au/node/apni/2890280,https://id.biodiversity.org.au/node/apni/7937668,https://id.biodiversity.org.au/name/apni/67607,Brombya platynema,https://id.biodiversity.org.au/name/apni/67607,https://id.biodiversity.org.au/taxon/apni/51461748,,Brombya platynema,native -Cardwellia sublimis,Cardwellia sublimis,,Cardwellia,Proteaceae,species,APC,accepted,Magnoliidae,Qld,Cardwellia sublimis F.Muell.,https://id.biodiversity.org.au/node/apni/2899253,https://id.biodiversity.org.au/node/apni/2908094,https://id.biodiversity.org.au/name/apni/109268,Cardwellia sublimis,https://id.biodiversity.org.au/name/apni/109268,https://id.biodiversity.org.au/taxon/apni/51614274,,Cardwellia sublimis,native +Cardwellia sublimis,Cardwellia sublimis,,Cardwellia,Proteaceae,species,APC,accepted,Magnoliidae,Qld,Cardwellia sublimis F.Muell.,https://id.biodiversity.org.au/node/apni/2899253,https://id.biodiversity.org.au/node/apni/2908094,https://id.biodiversity.org.au/name/apni/109268,Cardwellia sublimis,https://id.biodiversity.org.au/name/apni/109268,https://id.biodiversity.org.au/taxon/apni/51732901,,Cardwellia sublimis,native Castanospermum australe,Castanospermum australe,,Castanospermum,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, NI (doubtfully naturalised)",Castanospermum australe A.Cunn. ex Mudie,https://id.biodiversity.org.au/node/apni/2894943,https://id.biodiversity.org.au/node/apni/7226268,https://id.biodiversity.org.au/name/apni/196675,Castanospermum australe,https://id.biodiversity.org.au/name/apni/196675,https://id.biodiversity.org.au/taxon/apni/51702961,,Castanospermum australe,native and naturalised Cleistanthus myrianthus,Cleistanthus myrianthus,,Cleistanthus,Phyllanthaceae,species,APC,accepted,Magnoliidae,Qld,Cleistanthus myrianthus (Hassk.) Kurz,https://id.biodiversity.org.au/node/apni/2897700,https://id.biodiversity.org.au/node/apni/2914326,https://id.biodiversity.org.au/name/apni/71354,Cleistanthus myrianthus,https://id.biodiversity.org.au/name/apni/71354,https://id.biodiversity.org.au/taxon/apni/51442162,,Cleistanthus myrianthus,native Cryptocarya laevigata,Cryptocarya laevigata,,Cryptocarya,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Cryptocarya laevigata Blume,https://id.biodiversity.org.au/node/apni/2903400,https://id.biodiversity.org.au/taxon/apni/51438401,https://id.biodiversity.org.au/name/apni/88410,Cryptocarya laevigata,https://id.biodiversity.org.au/name/apni/88410,https://id.biodiversity.org.au/taxon/apni/51438397,,Cryptocarya laevigata,native @@ -32,13 +32,13 @@ Melicope elleryana,Melicope elleryana,,Melicope,Rutaceae,species,APC,accepted,Ma Myristica insipida,Myristica insipida,,Myristica,Myristicaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Myristica insipida R.Br.,https://id.biodiversity.org.au/node/apni/2902429,https://id.biodiversity.org.au/node/apni/2895962,https://id.biodiversity.org.au/name/apni/86064,Myristica insipida,https://id.biodiversity.org.au/name/apni/86064,https://id.biodiversity.org.au/node/apni/2903136,,Myristica insipida,native Neolitsea dealbata,Neolitsea dealbata,,Neolitsea,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Neolitsea dealbata (R.Br.) Merr.,https://id.biodiversity.org.au/node/apni/2910025,https://id.biodiversity.org.au/node/apni/2914447,https://id.biodiversity.org.au/name/apni/79589,Neolitsea dealbata,https://id.biodiversity.org.au/name/apni/79589,https://id.biodiversity.org.au/taxon/apni/51438397,,Neolitsea dealbata,native Pittosporum rubiginosum,Pittosporum rubiginosum,,Pittosporum,Pittosporaceae,species,APC,accepted,Magnoliidae,Qld,Pittosporum rubiginosum A.Cunn.,https://id.biodiversity.org.au/node/apni/2887772,https://id.biodiversity.org.au/taxon/apni/51442349,https://id.biodiversity.org.au/name/apni/100119,Pittosporum rubiginosum,https://id.biodiversity.org.au/name/apni/100119,https://id.biodiversity.org.au/taxon/apni/51442315,,Pittosporum rubiginosum,native -Haplostichanthus sp Coop. Ck,Polyalthia submontana,,Polyalthia,Annonaceae,species,APC,accepted,Magnoliidae,Qld,Polyalthia submontana (Jessup) B.Xue & R.M.K.Saunders,https://id.biodiversity.org.au/taxon/apni/51613975,https://id.biodiversity.org.au/taxon/apni/51613976,https://id.biodiversity.org.au/name/apni/246294,Polyalthia submontana,https://id.biodiversity.org.au/name/apni/191525,https://id.biodiversity.org.au/taxon/apni/51613977,,Polyalthia submontana,native -Polyscias australiana,Polyscias australiana,,Polyscias,Araliaceae,species,APC,accepted,Magnoliidae,"NT, Qld",Polyscias australiana (F.Muell.) Philipson,https://id.biodiversity.org.au/node/apni/7223338,https://id.biodiversity.org.au/taxon/apni/51292784,https://id.biodiversity.org.au/name/apni/84802,Polyscias australiana,https://id.biodiversity.org.au/name/apni/84787,https://id.biodiversity.org.au/taxon/apni/51632289,,Polyscias australiana,native +Haplostichanthus sp Coop. Ck,Polyalthia submontana,,Polyalthia,Annonaceae,species,APC,accepted,Magnoliidae,Qld,Polyalthia submontana (Jessup) B.Xue & R.M.K.Saunders,https://id.biodiversity.org.au/taxon/apni/51735993,https://id.biodiversity.org.au/taxon/apni/51735989,https://id.biodiversity.org.au/name/apni/246294,Polyalthia submontana,https://id.biodiversity.org.au/name/apni/191525,https://id.biodiversity.org.au/taxon/apni/51735960,,Polyalthia submontana,native +Polyscias australiana,Polyscias australiana,,Polyscias,Araliaceae,species,APC,accepted,Magnoliidae,"NT, Qld",Polyscias australiana (F.Muell.) Philipson,https://id.biodiversity.org.au/node/apni/7223338,https://id.biodiversity.org.au/taxon/apni/51737050,https://id.biodiversity.org.au/name/apni/84802,Polyscias australiana,https://id.biodiversity.org.au/name/apni/84787,https://id.biodiversity.org.au/taxon/apni/51736765,,Polyscias australiana,native Psychotria dallachiana,Psychotria dallachiana,,Psychotria,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Psychotria dallachiana Benth.,https://id.biodiversity.org.au/node/apni/2890013,https://id.biodiversity.org.au/taxon/apni/51446698,https://id.biodiversity.org.au/name/apni/89074,Psychotria dallachiana,https://id.biodiversity.org.au/name/apni/89074,https://id.biodiversity.org.au/taxon/apni/51446612,,Psychotria dallachiana,native Psychotria sp Utchee Creek,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),,Psychotria,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Psychotria sp. Utchee Creek (H.Flecker NQNC5313) Qld Herbarium,https://id.biodiversity.org.au/taxon/apni/51446727,https://id.biodiversity.org.au/taxon/apni/51446698,https://id.biodiversity.org.au/name/apni/218829,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),https://id.biodiversity.org.au/name/apni/218829,https://id.biodiversity.org.au/taxon/apni/51446612,,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),native -Rhodomyrtus trineura,Rhodomyrtus trineura,,Rhodomyrtus,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Rhodomyrtus trineura (F.Muell.) Benth.,https://id.biodiversity.org.au/taxon/apni/51441176,https://id.biodiversity.org.au/taxon/apni/51441177,https://id.biodiversity.org.au/name/apni/69289,Rhodomyrtus trineura,https://id.biodiversity.org.au/name/apni/69289,https://id.biodiversity.org.au/taxon/apni/51702983,,Rhodomyrtus trineura,native +Rhodomyrtus trineura,Rhodomyrtus trineura,,Rhodomyrtus,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Rhodomyrtus trineura (F.Muell.) Benth.,https://id.biodiversity.org.au/taxon/apni/51441176,https://id.biodiversity.org.au/taxon/apni/51441177,https://id.biodiversity.org.au/name/apni/69289,Rhodomyrtus trineura,https://id.biodiversity.org.au/name/apni/69289,https://id.biodiversity.org.au/taxon/apni/51738744,,Rhodomyrtus trineura,native Rockinghamia angustifolia,Rockinghamia angustifolia,,Rockinghamia,Euphorbiaceae,species,APC,accepted,Magnoliidae,Qld,Rockinghamia angustifolia (Benth.) Airy Shaw,https://id.biodiversity.org.au/node/apni/2921179,https://id.biodiversity.org.au/node/apni/2892697,https://id.biodiversity.org.au/name/apni/61487,Rockinghamia angustifolia,https://id.biodiversity.org.au/name/apni/61487,https://id.biodiversity.org.au/taxon/apni/51442249,,Rockinghamia angustifolia,native Quassia baileyana,Samadera baileyana,,Samadera,Simaroubaceae,species,APC,accepted,Magnoliidae,Qld,Samadera baileyana Oliv.,https://id.biodiversity.org.au/node/apni/2891526,https://id.biodiversity.org.au/node/apni/2900441,https://id.biodiversity.org.au/name/apni/60763,Samadera baileyana,https://id.biodiversity.org.au/name/apni/70084,https://id.biodiversity.org.au/taxon/apni/51316490,,Samadera baileyana,native -Acmena graveolens,Syzygium graveolens,,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium graveolens (F.M.Bailey) Craven & Biffin,https://id.biodiversity.org.au/node/apni/2920364,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/202985,Syzygium graveolens,https://id.biodiversity.org.au/name/apni/73535,https://id.biodiversity.org.au/taxon/apni/51702983,,Syzygium graveolens,native -Syzygium sayeri,Syzygium sayeri,,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium sayeri (F.Muell.) B.Hyland,https://id.biodiversity.org.au/node/apni/2888968,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/64837,Syzygium sayeri,https://id.biodiversity.org.au/name/apni/64837,https://id.biodiversity.org.au/taxon/apni/51702983,,Syzygium sayeri,native +Acmena graveolens,Syzygium graveolens,,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium graveolens (F.M.Bailey) Craven & Biffin,https://id.biodiversity.org.au/node/apni/2920364,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/202985,Syzygium graveolens,https://id.biodiversity.org.au/name/apni/73535,https://id.biodiversity.org.au/taxon/apni/51738744,,Syzygium graveolens,native +Syzygium sayeri,Syzygium sayeri,,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium sayeri (F.Muell.) B.Hyland,https://id.biodiversity.org.au/node/apni/2888968,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/64837,Syzygium sayeri,https://id.biodiversity.org.au/name/apni/64837,https://id.biodiversity.org.au/taxon/apni/51738744,,Syzygium sayeri,native Trema aspera,Trema tomentosa var. aspera,,Trema,Cannabaceae,variety,APC,accepted,Magnoliidae,"WA, Qld, NSW, Vic (presumed extinct)",Trema tomentosa var. aspera (Brongn.) Hewson,https://id.biodiversity.org.au/node/apni/2917190,https://id.biodiversity.org.au/node/apni/2913617,https://id.biodiversity.org.au/name/apni/206199,Trema tomentosa var. aspera,https://id.biodiversity.org.au/name/apni/101838,https://id.biodiversity.org.au/taxon/apni/51269919,Trema tomentosa var. aspera,Trema tomentosa,native diff --git a/tests/testthat/examples/Test_2023_2/output/taxa.csv b/tests/testthat/examples/Test_2023_2/output/taxa.csv index 19bec5a5..f431ec7f 100644 --- a/tests/testthat/examples/Test_2023_2/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_2/output/taxa.csv @@ -3,11 +3,11 @@ Acacia celsa,Acacia celsa,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,Qld, Acronychia acidula,Acronychia acidula,,Acronychia,Rutaceae,species,APC,accepted,Magnoliidae,Qld,Acronychia acidula F.Muell.,https://id.biodiversity.org.au/node/apni/2913200,https://id.biodiversity.org.au/taxon/apni/51446847,https://id.biodiversity.org.au/name/apni/73794,Acronychia acidula,https://id.biodiversity.org.au/name/apni/73794,https://id.biodiversity.org.au/taxon/apni/51461748,,Acronychia acidula,native Aleurites rockinghamensis,Aleurites rockinghamensis,,Aleurites,Euphorbiaceae,species,APC,accepted,Magnoliidae,Qld,Aleurites rockinghamensis (Baill.) P.I.Forst.,https://id.biodiversity.org.au/node/apni/2916622,https://id.biodiversity.org.au/node/apni/2900410,https://id.biodiversity.org.au/name/apni/171057,Aleurites rockinghamensis,https://id.biodiversity.org.au/name/apni/171057,https://id.biodiversity.org.au/taxon/apni/51442249,,Aleurites rockinghamensis,native Alphitonia petriei,Alphitonia petriei,,Alphitonia,Rhamnaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Alphitonia petriei Braid & C.T.White,https://id.biodiversity.org.au/node/apni/2887911,https://id.biodiversity.org.au/taxon/apni/51446205,https://id.biodiversity.org.au/name/apni/82935,Alphitonia petriei,https://id.biodiversity.org.au/name/apni/82935,https://id.biodiversity.org.au/taxon/apni/51446206,,Alphitonia petriei,native -Alstonia scholaris,Alstonia scholaris,,Alstonia,Apocynaceae,species,APC,accepted,Magnoliidae,Qld,Alstonia scholaris (L.) R.Br.,https://id.biodiversity.org.au/node/apni/2916809,https://id.biodiversity.org.au/node/apni/6684160,https://id.biodiversity.org.au/name/apni/83915,Alstonia scholaris,https://id.biodiversity.org.au/name/apni/83915,https://id.biodiversity.org.au/taxon/apni/51700686,,Alstonia scholaris,native +Alstonia scholaris,Alstonia scholaris,,Alstonia,Apocynaceae,species,APC,accepted,Magnoliidae,Qld,Alstonia scholaris (L.) R.Br.,https://id.biodiversity.org.au/node/apni/2916809,https://id.biodiversity.org.au/node/apni/6684160,https://id.biodiversity.org.au/name/apni/83915,Alstonia scholaris,https://id.biodiversity.org.au/name/apni/83915,https://id.biodiversity.org.au/taxon/apni/51736528,,Alstonia scholaris,native Argyrodendron peralatum,Argyrodendron peralatum,,Argyrodendron,Malvaceae,species,APC,accepted,Magnoliidae,Qld,Argyrodendron peralatum (F.M.Bailey) Edlin ex I.H.Boas,https://id.biodiversity.org.au/node/apni/2915243,https://id.biodiversity.org.au/taxon/apni/51288410,https://id.biodiversity.org.au/name/apni/100216,Argyrodendron peralatum,https://id.biodiversity.org.au/name/apni/100216,https://id.biodiversity.org.au/taxon/apni/51439248,,Argyrodendron peralatum,native Atractocarpus hirtus,Atractocarpus hirtus,,Atractocarpus,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Atractocarpus hirtus (F.Muell.) Puttock,https://id.biodiversity.org.au/node/apni/2910460,https://id.biodiversity.org.au/taxon/apni/51446611,https://id.biodiversity.org.au/name/apni/146883,Atractocarpus hirtus,https://id.biodiversity.org.au/name/apni/146883,https://id.biodiversity.org.au/taxon/apni/51446612,,Atractocarpus hirtus,native Brombya platynema,Brombya platynema,,Brombya,Rutaceae,species,APC,accepted,Magnoliidae,Qld,Brombya platynema F.Muell.,https://id.biodiversity.org.au/node/apni/2890280,https://id.biodiversity.org.au/node/apni/7937668,https://id.biodiversity.org.au/name/apni/67607,Brombya platynema,https://id.biodiversity.org.au/name/apni/67607,https://id.biodiversity.org.au/taxon/apni/51461748,,Brombya platynema,native -Cardwellia sublimis,Cardwellia sublimis,,Cardwellia,Proteaceae,species,APC,accepted,Magnoliidae,Qld,Cardwellia sublimis F.Muell.,https://id.biodiversity.org.au/node/apni/2899253,https://id.biodiversity.org.au/node/apni/2908094,https://id.biodiversity.org.au/name/apni/109268,Cardwellia sublimis,https://id.biodiversity.org.au/name/apni/109268,https://id.biodiversity.org.au/taxon/apni/51614274,,Cardwellia sublimis,native +Cardwellia sublimis,Cardwellia sublimis,,Cardwellia,Proteaceae,species,APC,accepted,Magnoliidae,Qld,Cardwellia sublimis F.Muell.,https://id.biodiversity.org.au/node/apni/2899253,https://id.biodiversity.org.au/node/apni/2908094,https://id.biodiversity.org.au/name/apni/109268,Cardwellia sublimis,https://id.biodiversity.org.au/name/apni/109268,https://id.biodiversity.org.au/taxon/apni/51732901,,Cardwellia sublimis,native Castanospermum australe,Castanospermum australe,,Castanospermum,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, NI (doubtfully naturalised)",Castanospermum australe A.Cunn. ex Mudie,https://id.biodiversity.org.au/node/apni/2894943,https://id.biodiversity.org.au/node/apni/7226268,https://id.biodiversity.org.au/name/apni/196675,Castanospermum australe,https://id.biodiversity.org.au/name/apni/196675,https://id.biodiversity.org.au/taxon/apni/51702961,,Castanospermum australe,native and naturalised Cleistanthus myrianthus,Cleistanthus myrianthus,,Cleistanthus,Phyllanthaceae,species,APC,accepted,Magnoliidae,Qld,Cleistanthus myrianthus (Hassk.) Kurz,https://id.biodiversity.org.au/node/apni/2897700,https://id.biodiversity.org.au/node/apni/2914326,https://id.biodiversity.org.au/name/apni/71354,Cleistanthus myrianthus,https://id.biodiversity.org.au/name/apni/71354,https://id.biodiversity.org.au/taxon/apni/51442162,,Cleistanthus myrianthus,native Cryptocarya laevigata,Cryptocarya laevigata,,Cryptocarya,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Cryptocarya laevigata Blume,https://id.biodiversity.org.au/node/apni/2903400,https://id.biodiversity.org.au/taxon/apni/51438401,https://id.biodiversity.org.au/name/apni/88410,Cryptocarya laevigata,https://id.biodiversity.org.au/name/apni/88410,https://id.biodiversity.org.au/taxon/apni/51438397,,Cryptocarya laevigata,native @@ -33,14 +33,14 @@ Melicope elleryana,Melicope elleryana,,Melicope,Rutaceae,species,APC,accepted,Ma Myristica insipida,Myristica insipida,,Myristica,Myristicaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Myristica insipida R.Br.,https://id.biodiversity.org.au/node/apni/2902429,https://id.biodiversity.org.au/node/apni/2895962,https://id.biodiversity.org.au/name/apni/86064,Myristica insipida,https://id.biodiversity.org.au/name/apni/86064,https://id.biodiversity.org.au/node/apni/2903136,,Myristica insipida,native Neolitsea dealbata,Neolitsea dealbata,,Neolitsea,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Neolitsea dealbata (R.Br.) Merr.,https://id.biodiversity.org.au/node/apni/2910025,https://id.biodiversity.org.au/node/apni/2914447,https://id.biodiversity.org.au/name/apni/79589,Neolitsea dealbata,https://id.biodiversity.org.au/name/apni/79589,https://id.biodiversity.org.au/taxon/apni/51438397,,Neolitsea dealbata,native Pittosporum rubiginosum,Pittosporum rubiginosum,,Pittosporum,Pittosporaceae,species,APC,accepted,Magnoliidae,Qld,Pittosporum rubiginosum A.Cunn.,https://id.biodiversity.org.au/node/apni/2887772,https://id.biodiversity.org.au/taxon/apni/51442349,https://id.biodiversity.org.au/name/apni/100119,Pittosporum rubiginosum,https://id.biodiversity.org.au/name/apni/100119,https://id.biodiversity.org.au/taxon/apni/51442315,,Pittosporum rubiginosum,native -Haplostichanthus sp Coop. Ck,Polyalthia submontana,,Polyalthia,Annonaceae,species,APC,accepted,Magnoliidae,Qld,Polyalthia submontana (Jessup) B.Xue & R.M.K.Saunders,https://id.biodiversity.org.au/taxon/apni/51613975,https://id.biodiversity.org.au/taxon/apni/51613976,https://id.biodiversity.org.au/name/apni/246294,Polyalthia submontana,https://id.biodiversity.org.au/name/apni/191525,https://id.biodiversity.org.au/taxon/apni/51613977,,Polyalthia submontana,native -Polyscias australiana,Polyscias australiana,,Polyscias,Araliaceae,species,APC,accepted,Magnoliidae,"NT, Qld",Polyscias australiana (F.Muell.) Philipson,https://id.biodiversity.org.au/node/apni/7223338,https://id.biodiversity.org.au/taxon/apni/51292784,https://id.biodiversity.org.au/name/apni/84802,Polyscias australiana,https://id.biodiversity.org.au/name/apni/84787,https://id.biodiversity.org.au/taxon/apni/51632289,,Polyscias australiana,native +Haplostichanthus sp Coop. Ck,Polyalthia submontana,,Polyalthia,Annonaceae,species,APC,accepted,Magnoliidae,Qld,Polyalthia submontana (Jessup) B.Xue & R.M.K.Saunders,https://id.biodiversity.org.au/taxon/apni/51735993,https://id.biodiversity.org.au/taxon/apni/51735989,https://id.biodiversity.org.au/name/apni/246294,Polyalthia submontana,https://id.biodiversity.org.au/name/apni/191525,https://id.biodiversity.org.au/taxon/apni/51735960,,Polyalthia submontana,native +Polyscias australiana,Polyscias australiana,,Polyscias,Araliaceae,species,APC,accepted,Magnoliidae,"NT, Qld",Polyscias australiana (F.Muell.) Philipson,https://id.biodiversity.org.au/node/apni/7223338,https://id.biodiversity.org.au/taxon/apni/51737050,https://id.biodiversity.org.au/name/apni/84802,Polyscias australiana,https://id.biodiversity.org.au/name/apni/84787,https://id.biodiversity.org.au/taxon/apni/51736765,,Polyscias australiana,native Psychotria dallachiana,Psychotria dallachiana,,Psychotria,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Psychotria dallachiana Benth.,https://id.biodiversity.org.au/node/apni/2890013,https://id.biodiversity.org.au/taxon/apni/51446698,https://id.biodiversity.org.au/name/apni/89074,Psychotria dallachiana,https://id.biodiversity.org.au/name/apni/89074,https://id.biodiversity.org.au/taxon/apni/51446612,,Psychotria dallachiana,native Psychotria sp Utchee Creek,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),,Psychotria,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Psychotria sp. Utchee Creek (H.Flecker NQNC5313) Qld Herbarium,https://id.biodiversity.org.au/taxon/apni/51446727,https://id.biodiversity.org.au/taxon/apni/51446698,https://id.biodiversity.org.au/name/apni/218829,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),https://id.biodiversity.org.au/name/apni/218829,https://id.biodiversity.org.au/taxon/apni/51446612,,Psychotria sp. Utchee Creek (H.Flecker NQNC5313),native -Rhodomyrtus trineura,Rhodomyrtus trineura,,Rhodomyrtus,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Rhodomyrtus trineura (F.Muell.) Benth.,https://id.biodiversity.org.au/taxon/apni/51441176,https://id.biodiversity.org.au/taxon/apni/51441177,https://id.biodiversity.org.au/name/apni/69289,Rhodomyrtus trineura,https://id.biodiversity.org.au/name/apni/69289,https://id.biodiversity.org.au/taxon/apni/51702983,,Rhodomyrtus trineura,native +Rhodomyrtus trineura,Rhodomyrtus trineura,,Rhodomyrtus,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Rhodomyrtus trineura (F.Muell.) Benth.,https://id.biodiversity.org.au/taxon/apni/51441176,https://id.biodiversity.org.au/taxon/apni/51441177,https://id.biodiversity.org.au/name/apni/69289,Rhodomyrtus trineura,https://id.biodiversity.org.au/name/apni/69289,https://id.biodiversity.org.au/taxon/apni/51738744,,Rhodomyrtus trineura,native Rockinghamia angustifolia,Rockinghamia angustifolia,,Rockinghamia,Euphorbiaceae,species,APC,accepted,Magnoliidae,Qld,Rockinghamia angustifolia (Benth.) Airy Shaw,https://id.biodiversity.org.au/node/apni/2921179,https://id.biodiversity.org.au/node/apni/2892697,https://id.biodiversity.org.au/name/apni/61487,Rockinghamia angustifolia,https://id.biodiversity.org.au/name/apni/61487,https://id.biodiversity.org.au/taxon/apni/51442249,,Rockinghamia angustifolia,native Quassia baileyana,Samadera baileyana,,Samadera,Simaroubaceae,species,APC,accepted,Magnoliidae,Qld,Samadera baileyana Oliv.,https://id.biodiversity.org.au/node/apni/2891526,https://id.biodiversity.org.au/node/apni/2900441,https://id.biodiversity.org.au/name/apni/60763,Samadera baileyana,https://id.biodiversity.org.au/name/apni/70084,https://id.biodiversity.org.au/taxon/apni/51316490,,Samadera baileyana,native -Acmena graveolens,Syzygium graveolens,,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium graveolens (F.M.Bailey) Craven & Biffin,https://id.biodiversity.org.au/node/apni/2920364,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/202985,Syzygium graveolens,https://id.biodiversity.org.au/name/apni/73535,https://id.biodiversity.org.au/taxon/apni/51702983,,Syzygium graveolens,native -Syzygium gustavioides,Syzygium gustavioides,,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium gustavioides (F.M.Bailey) B.Hyland,https://id.biodiversity.org.au/taxon/apni/51429676,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/64722,Syzygium gustavioides,https://id.biodiversity.org.au/name/apni/64722,https://id.biodiversity.org.au/taxon/apni/51702983,,Syzygium gustavioides,native -Syzygium sayeri,Syzygium sayeri,,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium sayeri (F.Muell.) B.Hyland,https://id.biodiversity.org.au/node/apni/2888968,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/64837,Syzygium sayeri,https://id.biodiversity.org.au/name/apni/64837,https://id.biodiversity.org.au/taxon/apni/51702983,,Syzygium sayeri,native +Acmena graveolens,Syzygium graveolens,,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium graveolens (F.M.Bailey) Craven & Biffin,https://id.biodiversity.org.au/node/apni/2920364,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/202985,Syzygium graveolens,https://id.biodiversity.org.au/name/apni/73535,https://id.biodiversity.org.au/taxon/apni/51738744,,Syzygium graveolens,native +Syzygium gustavioides,Syzygium gustavioides,,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium gustavioides (F.M.Bailey) B.Hyland,https://id.biodiversity.org.au/taxon/apni/51429676,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/64722,Syzygium gustavioides,https://id.biodiversity.org.au/name/apni/64722,https://id.biodiversity.org.au/taxon/apni/51738744,,Syzygium gustavioides,native +Syzygium sayeri,Syzygium sayeri,,Syzygium,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Syzygium sayeri (F.Muell.) B.Hyland,https://id.biodiversity.org.au/node/apni/2888968,https://id.biodiversity.org.au/taxon/apni/51440383,https://id.biodiversity.org.au/name/apni/64837,Syzygium sayeri,https://id.biodiversity.org.au/name/apni/64837,https://id.biodiversity.org.au/taxon/apni/51738744,,Syzygium sayeri,native Trema aspera,Trema tomentosa var. aspera,,Trema,Cannabaceae,variety,APC,accepted,Magnoliidae,"WA, Qld, NSW, Vic (presumed extinct)",Trema tomentosa var. aspera (Brongn.) Hewson,https://id.biodiversity.org.au/node/apni/2917190,https://id.biodiversity.org.au/node/apni/2913617,https://id.biodiversity.org.au/name/apni/206199,Trema tomentosa var. aspera,https://id.biodiversity.org.au/name/apni/101838,https://id.biodiversity.org.au/taxon/apni/51269919,Trema tomentosa var. aspera,Trema tomentosa,native diff --git a/tests/testthat/examples/Test_2023_3/metadata.yml b/tests/testthat/examples/Test_2023_3/metadata.yml index 15313841..6211a1ff 100644 --- a/tests/testthat/examples/Test_2023_3/metadata.yml +++ b/tests/testthat/examples/Test_2023_3/metadata.yml @@ -227,393 +227,6 @@ substitutions: - trait_name: flowering_time find: not observed replace: .na -taxonomic_updates: -- find: Acaena anserovina - replace: Acaena x anserovina - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Acaena ovina - replace: Acaena x ovina - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Acaena sp. Thredbo River Gorge (L.A.S.Johnson ;amp; E.F.Constable s.n., 19 - Jan 1951) - replace: Acaena sp. Thredbo River Gorge (L.A.S.Johnson & E.F.Constable s.n., 19 - Jan 1951) - reason: match_10_fuzzy. Imprecise fuzzy alignment with accepted canonical name in - APC (2022-11-21) - taxonomic_resolution: species -- find: Alstonia constricta f. Pubescent form - replace: Alstonia constricta Pubescent form - reason: match_08. Automatic alignment with synonymous name in APNI (2022-11-21) - taxonomic_resolution: species -- find: Arthropteris beckleri x tenella - replace: Arthropteris x [Arthropteris beckleri x tenella; NHNSW_2022] - reason: match_11. Rewording hybrid species name not in APC or APNI to indicate a - genus-level alignment with APC accepted genus (2022-11-22) - taxonomic_resolution: genus -- find: Atriplex sp. B sensu Jacobs (1990) - replace: Atriplex sp. B - reason: match_19. Automatic alignment with species-level canonical name in APNI - when notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Banksia spinulosa var. collina-spinulosa intergrade - replace: Banksia spinulosa var. collina - reason: match_12. Automatic alignment with infraspecific canonical name in APC accepted - when notes are ignored (2022-11-22) - taxonomic_resolution: variety -- find: Bertya tasmanica variant ;qu;Glabrous ovary;qu; - replace: Bertya tasmanica var. Glabrous ovary (T.A.James 527 & M.J.Taylor) - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: variety -- find: Blechnum fullagarii - replace: Blechnum fullagari - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Caladenia sp. A sensu Harden (1993) - replace: Caladenia sp. A - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: species -- find: Centaurea sp. A sensu Murray (1992) - replace: Centaurea sp. A - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Cephalomanes atrovirens subsp. atrovirens - replace: Cephalomanes atrovirens - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Choretrum sp. Coxs Gap (B.J.Lepschi 4218 ;amp; T.R.Lally) - replace: Choretrum sp. Coxs Gap (B.J.Lepschi 4218 & T.R.Lally) - reason: match_10_fuzzy. Imprecise fuzzy alignment with accepted canonical name in - APC (2022-11-21) - taxonomic_resolution: species -- find: Cipadessa baccifera - replace: Cipadessa baccifera - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: species -- find: Crocosmia crocosmiiflora - replace: Crocosmia x crocosmiiflora - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Cyperus bowmannii - replace: Cyperus bowmanni - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Cyperus sp. Stockton (K.L.Wilson 10541) - replace: Cyperus sp. [Cyperus sp. Stockton (K.L.Wilson 10541); NHNSW_2022] - reason: match_20. Rewording name to be recognised as genus rank, with genus accepted - by APC (2022-11-22) - taxonomic_resolution: genus -- find: Dillwynia sp. Ebor (P.C.Jobson 5318 ;amp; S.A.Mills) - replace: Dillwynia sp. Ebor (P.C.Jobson 5318 & S.A.Mills) - reason: match_17_fuzzy. Imprecise fuzzy alignment with canonical name in APNI (2022-11-21) - taxonomic_resolution: species -- find: Epidendrum radicans x secundum hybrid complex - replace: Epidendrum radicans x Epidendrum secundum - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: species -- find: Eriochilus cucullatus complex - replace: Eriochilus cucullatus - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Eucalyptus conjuncta - replace: Eucalyptus x conjuncta - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Eucalyptus dealbata subsp. dealbata - replace: Eucalyptus dealbata var. dealbata - reason: match_06. Automatic alignment with synonymous term among known canonical - names APC (2022-11-21) - taxonomic_resolution: variety -- find: Flacourtia sp. shiptons flat l w jessup gj.d3200 - replace: Flacourtia sp. Shiptons Flat (L.W.Jessup+ GJD3200) - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Genoplesium cuspidatum - replace: Genoplesium sp. Cuspidata (L.M.Copeland 3858) - reason: match_15_fuzzy. Fuzzy match alignment with species-level canonical name - in `APC known` when everything except first 2 words ignored (2022-11-22) - taxonomic_resolution: species -- find: Genoplesium sp. Charmhaven (NSW896673) - replace: Genoplesium sp. Charmhaven (NSW 896673) - reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Glycine pacifica - replace: Glycine pacifica (Grace 946) - reason: match_19. Automatic alignment with species-level canonical name in APNI - when notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Hibbertia sp. B sensu Harden (1990) - replace: Hibbertia sp. B - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Hibbertia stricta subsp. stricta - replace: Hibbertia stricta var. stricta - reason: match_06. Automatic alignment with synonymous term among known canonical - names APC (2022-11-21) - taxonomic_resolution: variety -- find: Hoffmannseggia glauca - replace: Hoffmannseggia glauca - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: species -- find: Houttuynia cordata - replace: Houttuynia cordata - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: species -- find: Impatiens balfouri - replace: Impatiens balfourii - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Kunzea capitata subsp. capitata - replace: Kunzea capitata var. capitata - reason: match_06. Automatic alignment with synonymous term among known canonical - names APC (2022-11-21) - taxonomic_resolution: variety -- find: Lenwebbia sp. Main Range (P.R.Sharpe 4877) - replace: Lenwebbia sp. Main Range (P.R.Sharpe+ 4877) - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Lepidium sp. Cooma (J.H.Maiden NSW642748) - replace: Lepidium sp. [Lepidium sp. Cooma (J.H.Maiden NSW642748); NHNSW_2022] - reason: match_20. Rewording name to be recognised as genus rank, with genus accepted - by APC (2022-11-22) - taxonomic_resolution: genus -- find: Leucopogon lanceolatus var. lanceolatus - replace: Leucopogon lanceolatus - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Luzula densiflora subsp. densiflora - replace: Luzula densiflora - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Luzula flaccida subsp. flaccida - replace: Leucas flaccida var. flaccida - reason: match_10_fuzzy. Imprecise fuzzy alignment with known canonical name in APC - (2022-11-21) - taxonomic_resolution: variety -- find: Margyricarpus pinnatus - replace: Margyricarpus pinnatus - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: species -- find: Muehlenbeckia diclina subsp. Gippsland (R.O.Makinson 1007) Makinson - replace: Muehlenbeckia diclina subsp. Gippsland (R.O.Makinson 1007) - reason: match_05. Automatic alignment with scientific name in APC accepted list - (2022-11-21) - taxonomic_resolution: subspecies -- find: Muehlenbeckia diclina subsp. Pooncarie (W.E. Mulham W811) - replace: Muehlenbeckia diclina subsp. Pooncarie (W.E.Mulham W811) - reason: match_08. Automatic alignment with synonymous name in APNI (2022-11-21) - taxonomic_resolution: subspecies -- find: Myosotis laxa subsp. caespitosa - replace: Myosotis laxa subsp. cespitosa - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: subspecies -- find: Netrostylis sp. East Coast (D.E. Albrecht 597) - replace: Netrostylis sp. [Netrostylis sp. East Coast (D.E. Albrecht 597); NHNSW_2022] - reason: match_20. Rewording name to be recognised as genus rank, with genus in APNI - (2022-11-22) - taxonomic_resolution: genus -- find: Notelaea sp. A sensu Harden (1992) - replace: Notelaea sp. A - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Opuntia sp. sensu I.Telford (1984) - replace: Opuntia sp. [Opuntia sp. sensu I.Telford (1984); NHNSW_2022] - reason: match_20. Rewording name to be recognised as genus rank, with genus accepted - by APC (2022-11-22) - taxonomic_resolution: genus -- find: Owenia reliqua - replace: Owenia x reliqua - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Pelargonium asperum - replace: Pelargonium x asperum - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Pimelea neo-anglica - replace: Pimelea neoanglica - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-22) - taxonomic_resolution: species -- find: Polyscias sambucifolia subsp. Long leaflets (P.G.Neish 208) Vic. Herbarium - replace: Polyscias sambucifolia subsp. Long leaflets (P.G.Neish 208) - reason: match_05. Automatic alignment with scientific name in APC accepted list - (2022-11-21) - taxonomic_resolution: subspecies -- find: Pomaderris andromedifolia f. ;qu;andromedifolia;qu; - replace: Pomaderris andromedifolia subsp. andromedifolia - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: subspecies -- find: Pomaderris andromedifolia f. ;qu;narrow-leaved;qu; - replace: Pomaderris andromedifolia f. 'narrow-leaved' - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: form -- find: Pomaderris andromedifolia f. ;qu;small-leaved;qu; - replace: Pomaderris andromedifolia subsp. andromedifolia - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: subspecies -- find: Potamogeton tricarinatus auct. non F.Muell. ;amp; A.Benn. ex A.Benn. - replace: Potamogeton tricarinatus - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Prasophyllum sp. A sensu Harden (1993) - replace: Prasophyllum sp. A - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Pultenaea sp. Dingo Creek (M.A.M.Renner 9176 ;amp; J.M.Cohen) - replace: Pultenaea sp. Dingo Creek (M.A.M.Renner 9176 & J.M.Cohen) - reason: match_17_fuzzy. Imprecise fuzzy alignment with canonical name in APNI (2022-11-22) - taxonomic_resolution: species -- find: Pultenaea sp. Narrabri (R.G.Coveny 8811 ;amp; S.K.Roy) - replace: Pultenaea sp. (Narrabri R.G.Coveny+ 8811) - reason: match_12. Automatic alignment with infraspecific canonical name in APC known - names when notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Pultenaea sp. Newnes (I.R.Telford 5072 ;amp; M.D.Crisp) - replace: Pultenaea sp. Newnes (I.R.Telford 5072 & M.D.Crisp) - reason: match_17_fuzzy. Imprecise fuzzy alignment with canonical name in APNI (2022-11-22) - taxonomic_resolution: species -- find: Pultenaea sp. Shadowgraph Bluff (T. ;amp; J.Whaite 3455) - replace: Pultenaea sp. Shadowgraph Bluff (T. & J.Whaite 3455) - reason: match_17_fuzzy. Imprecise fuzzy alignment with canonical name in APNI (2022-11-22) - taxonomic_resolution: species -- find: Quassia sp. Moonee Creek (King s.n., Nov 1949) - replace: Quassia sp. 'Moonee Creek' (King s.n., Nov 1949) - reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Radermachera sinica - replace: Radermachera sinica - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: species -- find: Rotheca myricoides subsp. myricoides - replace: Rotheca myricoides - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Rubus loganobaccus - replace: Rubus loganubaccus - reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Salix matsudana x alba - replace: Salix matsudana x Salix alba - reason: Manual alignment with canonical hybrid species name in APC (Elizabeth Wenk, - 2022-11-21) - taxonomic_resolution: species -- find: Salix x fragilis var. fragilis - replace: Salix x fragilis - reason: Manual alignment with canonical hybrid species name in APC (Elizabeth Wenk, - 2022-11-21) - taxonomic_resolution: species -- find: Salix x sepulcralis var. chrysocoma - replace: Salix x sepulcralis - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: species -- find: Salix x sepulcralis var. sepulcralis - replace: Salix x sepulcralis - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: variety -- find: Salvinia molesta - replace: Salvinia x molesta - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Sarcocornia quinqueflora subsp. quinqueflora - replace: Salicornia quinqueflora subsp. quinqueflora - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: subspecies -- find: Scleranthus sp. Fitz;qu;s Hill (J.G.West 5342) - replace: Scleranthus sp. Fitz's Hill (J.G.West 5342) - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Sebaea zeyheri subsp. cleistantha - replace: Sebaea zeyheri - reason: match_19. Automatic alignment with species-level canonical name in APNI - when notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Sida sp. B sensu Harden (1990) - replace: Sida sp. B - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Sida sp. C sensu Harden (1990) - replace: Sida sp. C - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Sorghum almum - replace: Sorghum x almum - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Sorghum bicolor subsp. almum - replace: Sorghum bicolor subsp. x almum - reason: match_08. Automatic alignment with synonymous name in APNI (2022-11-22) - taxonomic_resolution: subspecies -- find: Sorghum bicolor subsp. drummondii - replace: Sorghum bicolor subsp. x drummondii - reason: match_12. Automatic alignment with infraspecific canonical name in APC known - names when notes are ignored (2022-11-22) - taxonomic_resolution: subspecies -- find: Spiraea x billiardii - replace: Spiraea x billardii - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Suaeda sp. A sensu Harden (1990) - replace: Suaeda sp. A - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Teucrium sp. D sensu Conn (1992) - replace: Teucrium sp. D Flora of New South Wales (S.A.Horton 4114) - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Thelymitra irregularis - replace: Thelymitra x irregularis - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Thelymitra merraniae - replace: Thelymitra merranae - reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Thelymitra truncata - replace: Thelymitra x truncata - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: X Triticosecale - replace: x Triticosecale - reason: Manual matched to genus for taxon that can't be matched to species (Elizabeth - Wenk, 2022-11-22) - taxonomic_resolution: genus -- find: Acacia melvillei-homalophylla - replace: Acacia sp. [Acacia melvillei-homalophylla; NHNSW_2023] - reason: Manual matched to genus for taxon that can't be matched to species (Elizabeth - Wenk, 2023-05-24) - taxonomic_resolution: genus -exclude_observations: -- variable: taxon_name - find: Salix humboldtiana cv. ;qu;Pyramidalis;qu;, Salix matsudana cv. ;qu;Tortuosa;qu;, - Cyrtomium falcatum ;qu;Rochfordii;qu; - reason: excluding cultivars -- variable: taxon_name - find: Cipadessa baccifera, Hoffmannseggia glauca, Houttuynia cordata, Margyricarpus - pinnatus, Radermachera sinica, x Triticosecale, Euryops virgineus, Fraxinus chinensis, - Ipomoea fimbriosepala, Persicaria chinensis, Pteris nipponica, Passiflora miniata - reason: non-native, non-naturalised species +taxonomic_updates: .na +exclude_observations: .na questions: .na diff --git a/tests/testthat/examples/Test_2023_3/output/taxa.csv b/tests/testthat/examples/Test_2023_3/output/taxa.csv index fbbc4378..7a90d716 100644 --- a/tests/testthat/examples/Test_2023_3/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_3/output/taxa.csv @@ -1,7 +1,7 @@ original_name,taxon_name,taxon_name_alternatives,genus,family,taxon_rank,taxonomic_dataset,taxonomic_status,subclass,taxon_distribution,scientific_name,taxon_id,taxon_ID_genus,scientific_name_id,canonical_name,cleaned_scientific_name_id,taxon_id_family,trinomial,binomial,establishment_means Abildgaardia ovata,Abildgaardia ovata,,Abildgaardia,Cyperaceae,species,APC,accepted,Magnoliidae,"NT, Qld, NSW",Abildgaardia ovata (Burm.f.) Kral,https://id.biodiversity.org.au/node/apni/2919627,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/150737,Abildgaardia ovata,https://id.biodiversity.org.au/name/apni/150737,https://id.biodiversity.org.au/taxon/apni/51460154,,Abildgaardia ovata,native Acacia alpina,Acacia alpina,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Acacia alpina F.Muell.,https://id.biodiversity.org.au/node/apni/2907301,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/58263,Acacia alpina,https://id.biodiversity.org.au/name/apni/58263,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia alpina,native -Acacia beadleana,Acacia beadleana,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Acacia beadleana R.H.Jones & J.J.Bruhl,https://id.biodiversity.org.au/node/apni/2902581,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/198624,Acacia beadleana,https://id.biodiversity.org.au/name/apni/165277,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia beadleana,native +Acacia beadleana,Acacia beadleana,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Acacia beadleana R.H.Jones & J.J.Bruhl,https://id.biodiversity.org.au/node/apni/2902581,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/198624,Acacia beadleana,https://id.biodiversity.org.au/name/apni/244690,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia beadleana,native Acacia bulgaensis,Acacia bulgaensis,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Acacia bulgaensis Tindale & S.J.Davies,https://id.biodiversity.org.au/node/apni/2889179,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/117995,Acacia bulgaensis,https://id.biodiversity.org.au/name/apni/117995,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia bulgaensis,native Acacia caroleae,Acacia caroleae,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acacia caroleae Pedley,https://id.biodiversity.org.au/node/apni/2894332,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/60225,Acacia caroleae,https://id.biodiversity.org.au/name/apni/60225,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia caroleae,native Acacia crassa,Acacia crassa,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acacia crassa Pedley,https://id.biodiversity.org.au/node/apni/2919707,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/60887,Acacia crassa,https://id.biodiversity.org.au/name/apni/60887,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia crassa,native @@ -19,16 +19,16 @@ Alectryon coriaceus,Alectryon coriaceus,,Alectryon,Sapindaceae,species,APC,accep Alectryon oleifolius,Alectryon oleifolius,,Alectryon,Sapindaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Alectryon oleifolius (Desf.) S.T.Reynolds,https://id.biodiversity.org.au/node/apni/2900874,https://id.biodiversity.org.au/taxon/apni/51299789,https://id.biodiversity.org.au/name/apni/81066,Alectryon oleifolius,https://id.biodiversity.org.au/name/apni/81066,https://id.biodiversity.org.au/taxon/apni/51447212,,Alectryon oleifolius,native Alectryon subdentatus,Alectryon subdentatus,,Alectryon,Sapindaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Alectryon subdentatus (F.Muell. ex Benth.) Radlk.,https://id.biodiversity.org.au/node/apni/2890534,https://id.biodiversity.org.au/taxon/apni/51299789,https://id.biodiversity.org.au/name/apni/81114,Alectryon subdentatus,https://id.biodiversity.org.au/name/apni/81114,https://id.biodiversity.org.au/taxon/apni/51447212,,Alectryon subdentatus,native Amyema preissii,Amyema preissii,,Amyema,Loranthaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Amyema preissii (Miq.) Tiegh.,https://id.biodiversity.org.au/node/apni/2888430,https://id.biodiversity.org.au/taxon/apni/51438795,https://id.biodiversity.org.au/name/apni/87461,Amyema preissii,https://id.biodiversity.org.au/name/apni/87461,https://id.biodiversity.org.au/taxon/apni/51438796,,Amyema preissii,native -Angophora leiocarpa,Angophora leiocarpa,,Angophora,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Angophora leiocarpa (L.A.S.Johnson ex G.J.Leach) K.R.Thiele & Ladiges,https://id.biodiversity.org.au/node/apni/2894339,https://id.biodiversity.org.au/taxon/apni/51439560,https://id.biodiversity.org.au/name/apni/123435,Angophora leiocarpa,https://id.biodiversity.org.au/name/apni/123435,https://id.biodiversity.org.au/taxon/apni/51702983,,Angophora leiocarpa,native -Arbutus unedo,Arbutus unedo,,Arbutus,Ericaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (doubtfully naturalised), NSW (doubtfully naturalised), ACT (doubtfully naturalised), Vic (naturalised), Tas (doubtfully naturalised)",Arbutus unedo L.,https://id.biodiversity.org.au/node/apni/2904939,https://id.biodiversity.org.au/node/apni/2892910,https://id.biodiversity.org.au/name/apni/98540,Arbutus unedo,https://id.biodiversity.org.au/name/apni/98540,https://id.biodiversity.org.au/taxon/apni/51436079,,Arbutus unedo,naturalised +Angophora leiocarpa,Angophora leiocarpa,,Angophora,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Angophora leiocarpa (L.A.S.Johnson ex G.J.Leach) K.R.Thiele & Ladiges,https://id.biodiversity.org.au/node/apni/2894339,https://id.biodiversity.org.au/taxon/apni/51439560,https://id.biodiversity.org.au/name/apni/123435,Angophora leiocarpa,https://id.biodiversity.org.au/name/apni/123435,https://id.biodiversity.org.au/taxon/apni/51738744,,Angophora leiocarpa,native +Arbutus unedo,Arbutus unedo,,Arbutus,Ericaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (doubtfully naturalised), NSW (doubtfully naturalised), ACT (doubtfully naturalised), Vic (naturalised), Tas (doubtfully naturalised)",Arbutus unedo L.,https://id.biodiversity.org.au/node/apni/2904939,https://id.biodiversity.org.au/node/apni/2892910,https://id.biodiversity.org.au/name/apni/98540,Arbutus unedo,https://id.biodiversity.org.au/name/apni/98540,https://id.biodiversity.org.au/taxon/apni/51738121,,Arbutus unedo,naturalised Australina pusilla,Australina pusilla,,Australina,Urticaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic, Tas",Australina pusilla (Poir.) Gaudich.,https://id.biodiversity.org.au/node/apni/2913845,https://id.biodiversity.org.au/node/apni/2907879,https://id.biodiversity.org.au/name/apni/113875,Australina pusilla,https://id.biodiversity.org.au/name/apni/113875,https://id.biodiversity.org.au/taxon/apni/51662052,,Australina pusilla,native Burmannia disticha,Burmannia disticha,,Burmannia,Burmanniaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Burmannia disticha L.,https://id.biodiversity.org.au/node/apni/2900088,https://id.biodiversity.org.au/node/apni/2915743,https://id.biodiversity.org.au/name/apni/70173,Burmannia disticha,https://id.biodiversity.org.au/name/apni/70173,https://id.biodiversity.org.au/node/apni/2887196,,Burmannia disticha,native Bursaria spinosa subsp. spinosa,Bursaria spinosa subsp. spinosa,,Bursaria,Pittosporaceae,subspecies,APC,accepted,Magnoliidae,"SA, Qld, NSW, Vic, Tas",Bursaria spinosa Cav. subsp. spinosa,https://id.biodiversity.org.au/taxon/apni/51442337,https://id.biodiversity.org.au/taxon/apni/51442339,https://id.biodiversity.org.au/name/apni/142036,Bursaria spinosa subsp. spinosa,https://id.biodiversity.org.au/name/apni/142036,https://id.biodiversity.org.au/taxon/apni/51442315,Bursaria spinosa subsp. spinosa,Bursaria spinosa,native Calendula arvensis,Calendula arvensis,,Calendula,Asteraceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (naturalised), Tas (naturalised)",Calendula arvensis L.,https://id.biodiversity.org.au/node/apni/2891878,https://id.biodiversity.org.au/node/apni/2893748,https://id.biodiversity.org.au/name/apni/95042,Calendula arvensis,https://id.biodiversity.org.au/name/apni/95042,https://id.biodiversity.org.au/taxon/apni/51695393,,Calendula arvensis,naturalised -Callistemon purpurascens,Callistemon purpurascens,,Callistemon,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Callistemon purpurascens S.M.Douglas & S.David,https://id.biodiversity.org.au/taxon/apni/51288952,https://id.biodiversity.org.au/taxon/apni/51439657,https://id.biodiversity.org.au/name/apni/4630985,Callistemon purpurascens,https://id.biodiversity.org.au/name/apni/4630985,https://id.biodiversity.org.au/taxon/apni/51702983,,Callistemon purpurascens,native +Callistemon purpurascens,Callistemon purpurascens,,Callistemon,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Callistemon purpurascens S.M.Douglas & S.David,https://id.biodiversity.org.au/taxon/apni/51288952,https://id.biodiversity.org.au/taxon/apni/51439657,https://id.biodiversity.org.au/name/apni/4630985,Callistemon purpurascens,https://id.biodiversity.org.au/name/apni/4630985,https://id.biodiversity.org.au/taxon/apni/51738744,,Callistemon purpurascens,native Apophyllum anomalum,Capparis anomala,,Capparis,Capparaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Capparis anomala (F.Muell.) Byng & Christenh.,https://id.biodiversity.org.au/taxon/apni/51432888,https://id.biodiversity.org.au/taxon/apni/51432886,https://id.biodiversity.org.au/name/apni/50561973,Capparis anomala,https://id.biodiversity.org.au/name/apni/97697,https://id.biodiversity.org.au/taxon/apni/51433682,,Capparis anomala,native Carex leporina,Carex leporina,,Carex,Cyperaceae,species,APC,accepted,Magnoliidae,"NSW (naturalised), NI (naturalised), Vic (naturalised), Tas (naturalised)",Carex leporina L.,https://id.biodiversity.org.au/node/apni/2902492,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/135236,Carex leporina,https://id.biodiversity.org.au/name/apni/135236,https://id.biodiversity.org.au/taxon/apni/51460154,,Carex leporina,naturalised -Carex cephalotes,Carex pyrenaica var. cephalotes,,Carex,Cyperaceae,variety,APC,accepted,Magnoliidae,"NSW, Vic, Tas",Carex pyrenaica var. cephalotes (F.Muell.) Kük.,https://id.biodiversity.org.au/node/apni/2892693,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/111655,Carex pyrenaica var. cephalotes,https://id.biodiversity.org.au/name/apni/110600,https://id.biodiversity.org.au/taxon/apni/51460154,Carex pyrenaica var. cephalotes,Carex pyrenaica,native +Carex cephalotes,Carex pyrenaica var. cephalotes,,Carex,Cyperaceae,variety,APC,accepted,Magnoliidae,"NSW, Vic, Tas",Carex pyrenaica var. cephalotes (F.Muell.) Kük.,https://id.biodiversity.org.au/node/apni/2892693,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/111655,Carex pyrenaica var. cephalotes,https://id.biodiversity.org.au/name/apni/235569,https://id.biodiversity.org.au/taxon/apni/51460154,Carex pyrenaica var. cephalotes,Carex pyrenaica,native Carex raleighii,Carex raleighii,,Carex,Cyperaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic, Tas",Carex raleighii Nelmes,https://id.biodiversity.org.au/node/apni/2910405,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/111690,Carex raleighii,https://id.biodiversity.org.au/name/apni/111690,https://id.biodiversity.org.au/taxon/apni/51460154,,Carex raleighii,native Carmichaelia exsul,Carmichaelia exsul,,Carmichaelia,Fabaceae,species,APC,accepted,Magnoliidae,LHI,Carmichaelia exsul F.Muell.,https://id.biodiversity.org.au/node/apni/2915240,https://id.biodiversity.org.au/node/apni/8138105,https://id.biodiversity.org.au/name/apni/112335,Carmichaelia exsul,https://id.biodiversity.org.au/name/apni/112335,https://id.biodiversity.org.au/taxon/apni/51702961,,Carmichaelia exsul,native Cassinia compacta,Cassinia compacta,Cassinia accipitrum (pro parte misapplied) | Cassinia straminea (pro parte misapplied) | Cassinia telfordii (pro parte misapplied) | Cassinia accipitrum (misapplied),Cassinia,Asteraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Cassinia compacta F.Muell.,https://id.biodiversity.org.au/node/apni/2909860,https://id.biodiversity.org.au/taxon/apni/51431788,https://id.biodiversity.org.au/name/apni/54723,Cassinia compacta [alternative possible names: Cassinia accipitrum (pro parte misapplied) | Cassinia straminea (pro parte misapplied) | Cassinia telfordii (pro parte misapplied) | Cassinia accipitrum (misapplied)],,https://id.biodiversity.org.au/taxon/apni/51695393,,Cassinia compacta,native @@ -43,8 +43,8 @@ Convolvulus farinosus,Convolvulus farinosus,,Convolvulus,Convolvulaceae,species, Coprosma niphophila,Coprosma niphophila,,Coprosma,Rubiaceae,species,APC,accepted,Magnoliidae,NSW,Coprosma niphophila Orchard,https://id.biodiversity.org.au/node/apni/2910618,https://id.biodiversity.org.au/node/apni/8135850,https://id.biodiversity.org.au/name/apni/78856,Coprosma niphophila,https://id.biodiversity.org.au/name/apni/78856,https://id.biodiversity.org.au/taxon/apni/51446612,,Coprosma niphophila,native Coprosma nivalis,Coprosma nivalis,,Coprosma,Rubiaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Coprosma nivalis W.R.B.Oliv.,https://id.biodiversity.org.au/node/apni/2915002,https://id.biodiversity.org.au/node/apni/8135850,https://id.biodiversity.org.au/name/apni/78866,Coprosma nivalis,https://id.biodiversity.org.au/name/apni/78866,https://id.biodiversity.org.au/taxon/apni/51446612,,Coprosma nivalis,native Correa alba,Correa alba,,Correa,Rutaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Correa alba Andrews,https://id.biodiversity.org.au/node/apni/2906721,https://id.biodiversity.org.au/taxon/apni/51447015,https://id.biodiversity.org.au/name/apni/80283,Correa alba,https://id.biodiversity.org.au/name/apni/80283,https://id.biodiversity.org.au/taxon/apni/51461748,,Correa alba,native -Corymbia citriodora,Corymbia citriodora,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (doubtfully naturalised), Qld, NSW (native and naturalised), Vic (naturalised)",Corymbia citriodora (Hook.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2912509,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119387,Corymbia citriodora,https://id.biodiversity.org.au/name/apni/119387,https://id.biodiversity.org.au/taxon/apni/51702983,,Corymbia citriodora,native and naturalised -Corymbia eximia,Corymbia eximia,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Corymbia eximia (Schauer) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2909833,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119402,Corymbia eximia,https://id.biodiversity.org.au/name/apni/119402,https://id.biodiversity.org.au/taxon/apni/51702983,,Corymbia eximia,native +Corymbia citriodora,Corymbia citriodora,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (doubtfully naturalised), Qld, NSW (native and naturalised), Vic (naturalised)",Corymbia citriodora (Hook.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2912509,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119387,Corymbia citriodora,https://id.biodiversity.org.au/name/apni/119387,https://id.biodiversity.org.au/taxon/apni/51738744,,Corymbia citriodora,native and naturalised +Corymbia eximia,Corymbia eximia,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Corymbia eximia (Schauer) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2909833,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119402,Corymbia eximia,https://id.biodiversity.org.au/name/apni/119402,https://id.biodiversity.org.au/taxon/apni/51738744,,Corymbia eximia,native Crassula decumbens,Crassula decumbens,,Crassula,Crassulaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, ACT, Vic, Tas",Crassula decumbens Thunb.,https://id.biodiversity.org.au/node/apni/2889646,https://id.biodiversity.org.au/node/apni/2903354,https://id.biodiversity.org.au/name/apni/83855,Crassula decumbens,https://id.biodiversity.org.au/name/apni/83855,https://id.biodiversity.org.au/taxon/apni/51270792,,Crassula decumbens,native Crassula peduncularis,Crassula peduncularis,,Crassula,Crassulaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, ACT, Vic, Tas",Crassula peduncularis (Sm.) F.Meigen,https://id.biodiversity.org.au/node/apni/2895654,https://id.biodiversity.org.au/node/apni/2903354,https://id.biodiversity.org.au/name/apni/84005,Crassula peduncularis,https://id.biodiversity.org.au/name/apni/84005,https://id.biodiversity.org.au/taxon/apni/51270792,,Crassula peduncularis,native Crotalaria brevis,Crotalaria brevis,,Crotalaria,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Crotalaria brevis Domin,https://id.biodiversity.org.au/node/apni/2906180,https://id.biodiversity.org.au/taxon/apni/51300011,https://id.biodiversity.org.au/name/apni/85578,Crotalaria brevis,https://id.biodiversity.org.au/name/apni/85578,https://id.biodiversity.org.au/taxon/apni/51702961,,Crotalaria brevis,native @@ -65,31 +65,31 @@ Dillwynia floribunda,Dillwynia floribunda,,Dillwynia,Fabaceae,species,APC,accept Dinosperma erythrococcum,Dinosperma erythrococcum,,Dinosperma,Rutaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Dinosperma erythrococcum (F.Muell.) T.G.Hartley,https://id.biodiversity.org.au/node/apni/2897246,https://id.biodiversity.org.au/node/apni/2900591,https://id.biodiversity.org.au/name/apni/157718,Dinosperma erythrococcum,https://id.biodiversity.org.au/name/apni/157718,https://id.biodiversity.org.au/taxon/apni/51461748,,Dinosperma erythrococcum,native Dodonaea petiolaris,Dodonaea petiolaris,Dodonaea viscosa subsp. mucronata (pro parte misapplied),Dodonaea,Sapindaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Dodonaea petiolaris F.Muell.,https://id.biodiversity.org.au/node/apni/2921131,https://id.biodiversity.org.au/taxon/apni/51447268,https://id.biodiversity.org.au/name/apni/72184,Dodonaea petiolaris [alternative possible names: Dodonaea viscosa subsp. mucronata (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51447212,,Dodonaea petiolaris,native Dodonaea truncatiales,Dodonaea truncatiales,Dodonaea heteromorpha (pro parte misapplied) | Dodonaea heteromorpha (misapplied),Dodonaea,Sapindaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Dodonaea truncatiales F.Muell.,https://id.biodiversity.org.au/node/apni/7870563,https://id.biodiversity.org.au/taxon/apni/51447268,https://id.biodiversity.org.au/name/apni/72648,Dodonaea truncatiales [alternative possible names: Dodonaea heteromorpha (pro parte misapplied) | Dodonaea heteromorpha (misapplied)],,https://id.biodiversity.org.au/taxon/apni/51447212,,Dodonaea truncatiales,native -Dovyalis caffra,Dovyalis caffra,,Dovyalis,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised)",Dovyalis caffra (Hook.f. & Harv.) Hook.f.,https://id.biodiversity.org.au/node/apni/2888866,https://id.biodiversity.org.au/node/apni/2897632,https://id.biodiversity.org.au/name/apni/199157,Dovyalis caffra,https://id.biodiversity.org.au/name/apni/86110,https://id.biodiversity.org.au/taxon/apni/51436847,,Dovyalis caffra,naturalised +Dovyalis caffra,Dovyalis caffra,,Dovyalis,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised)",Dovyalis caffra (Hook.f. & Harv.) Hook.f.,https://id.biodiversity.org.au/node/apni/2888866,https://id.biodiversity.org.au/node/apni/2897632,https://id.biodiversity.org.au/name/apni/199157,Dovyalis caffra,https://id.biodiversity.org.au/name/apni/199157,https://id.biodiversity.org.au/taxon/apni/51436847,,Dovyalis caffra,naturalised Elaeocarpus grandis,Elaeocarpus grandis,,Elaeocarpus,Elaeocarpaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Elaeocarpus grandis F.Muell.,https://id.biodiversity.org.au/node/apni/2895259,https://id.biodiversity.org.au/taxon/apni/51435153,https://id.biodiversity.org.au/name/apni/115772,Elaeocarpus grandis,https://id.biodiversity.org.au/name/apni/115772,https://id.biodiversity.org.au/taxon/apni/51632282,,Elaeocarpus grandis,native Eleocharis pallens,Eleocharis pallens,,Eleocharis,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Eleocharis pallens S.T.Blake,https://id.biodiversity.org.au/node/apni/2899827,https://id.biodiversity.org.au/taxon/apni/51434435,https://id.biodiversity.org.au/name/apni/67140,Eleocharis pallens,https://id.biodiversity.org.au/name/apni/67140,https://id.biodiversity.org.au/taxon/apni/51460154,,Eleocharis pallens,native Endiandra globosa,Endiandra globosa,,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Endiandra globosa Maiden & Betche,https://id.biodiversity.org.au/node/apni/2901094,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111780,Endiandra globosa,https://id.biodiversity.org.au/name/apni/111780,https://id.biodiversity.org.au/taxon/apni/51438397,,Endiandra globosa,native Endiandra muelleri,Endiandra muelleri,,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Endiandra muelleri Meisn.,https://id.biodiversity.org.au/node/apni/2903619,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111996,Endiandra muelleri,https://id.biodiversity.org.au/name/apni/111996,https://id.biodiversity.org.au/taxon/apni/51438397,,Endiandra muelleri,native Epilobium gunnianum,Epilobium gunnianum,,Epilobium,Onagraceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic, Tas",Epilobium gunnianum Hausskn.,https://id.biodiversity.org.au/node/apni/2903068,https://id.biodiversity.org.au/taxon/apni/51440863,https://id.biodiversity.org.au/name/apni/105579,Epilobium gunnianum,https://id.biodiversity.org.au/name/apni/105579,https://id.biodiversity.org.au/taxon/apni/51440864,,Epilobium gunnianum,native -Eremophila deserti,Eremophila deserti,,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila deserti (A.Cunn. ex Benth.) Chinnock,https://id.biodiversity.org.au/node/apni/2897363,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/123426,Eremophila deserti,https://id.biodiversity.org.au/name/apni/123426,https://id.biodiversity.org.au/taxon/apni/51461527,,Eremophila deserti,native -Eremophila oppositifolia,Eremophila oppositifolia,,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila oppositifolia R.Br.,https://id.biodiversity.org.au/node/apni/7951462,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/114575,Eremophila oppositifolia,https://id.biodiversity.org.au/name/apni/114575,https://id.biodiversity.org.au/taxon/apni/51461527,,Eremophila oppositifolia,native +Eremophila deserti,Eremophila deserti,,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila deserti (A.Cunn. ex Benth.) Chinnock,https://id.biodiversity.org.au/node/apni/2897363,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/123426,Eremophila deserti,https://id.biodiversity.org.au/name/apni/123426,https://id.biodiversity.org.au/taxon/apni/51734003,,Eremophila deserti,native +Eremophila oppositifolia,Eremophila oppositifolia,,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila oppositifolia R.Br.,https://id.biodiversity.org.au/node/apni/7951462,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/114575,Eremophila oppositifolia,https://id.biodiversity.org.au/name/apni/114575,https://id.biodiversity.org.au/taxon/apni/51734003,,Eremophila oppositifolia,native Erigeron conyzoides,Erigeron conyzoides,,Erigeron,Asteraceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Erigeron conyzoides F.Muell.,https://id.biodiversity.org.au/node/apni/2913579,https://id.biodiversity.org.au/taxon/apni/51432118,https://id.biodiversity.org.au/name/apni/73195,Erigeron conyzoides,https://id.biodiversity.org.au/name/apni/239637,https://id.biodiversity.org.au/taxon/apni/51695393,,Erigeron conyzoides,native Erythroxylum australe,Erythroxylum australe,Erythroxylum sp. Splityard Creek (L.Pedley 5360) (pro parte misapplied),Erythroxylum,Erythroxylaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Erythroxylum australe F.Muell.,https://id.biodiversity.org.au/node/apni/2912212,https://id.biodiversity.org.au/node/apni/2919669,https://id.biodiversity.org.au/name/apni/75959,Erythroxylum australe [alternative possible names: Erythroxylum sp. Splityard Creek (L.Pedley 5360) (pro parte misapplied)],,https://id.biodiversity.org.au/node/apni/2893375,,Erythroxylum australe,native Escallonia bifida,Escallonia bifida,,Escallonia,Escalloniaceae,species,APC,accepted,Magnoliidae,NSW (naturalised),Escallonia bifida Link & Otto,https://id.biodiversity.org.au/taxon/apni/51435441,https://id.biodiversity.org.au/taxon/apni/51435442,https://id.biodiversity.org.au/name/apni/116602,Escallonia bifida,https://id.biodiversity.org.au/name/apni/116602,https://id.biodiversity.org.au/taxon/apni/51435443,,Escallonia bifida,naturalised -Eucalyptus badjensis,Eucalyptus badjensis,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus badjensis Beuzev. & M.B.Welch,https://id.biodiversity.org.au/node/apni/2912724,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/57323,Eucalyptus badjensis,https://id.biodiversity.org.au/name/apni/57323,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus badjensis,native -Eucalyptus camphora,Eucalyptus camphora,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic",Eucalyptus camphora R.T.Baker,https://id.biodiversity.org.au/node/apni/2891665,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/94439,Eucalyptus camphora,https://id.biodiversity.org.au/name/apni/94439,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus camphora,native -Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus dorrigoensis (Blakely) L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2903351,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118668,Eucalyptus dorrigoensis,https://id.biodiversity.org.au/name/apni/118668,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus dorrigoensis,native -Eucalyptus yangoura,Eucalyptus globoidea,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus globoidea Blakely,https://id.biodiversity.org.au/node/apni/5270850,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/61141,Eucalyptus globoidea,https://id.biodiversity.org.au/name/apni/92470,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus globoidea,native -Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,,Eucalyptus,Myrtaceae,subspecies,APC,accepted,Magnoliidae,"SA, NSW, Vic",Eucalyptus leucoxylon subsp. pruinosa (F.Muell. ex Miq.) Boland,https://id.biodiversity.org.au/node/apni/2908258,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/77407,Eucalyptus leucoxylon subsp. pruinosa,https://id.biodiversity.org.au/name/apni/77407,https://id.biodiversity.org.au/taxon/apni/51702983,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon,native -Eucalyptus muelleriana,Eucalyptus muelleriana,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus muelleriana A.W.Howitt,https://id.biodiversity.org.au/node/apni/2888508,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/56840,Eucalyptus muelleriana,https://id.biodiversity.org.au/name/apni/56840,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus muelleriana,native -Eucalyptus nandewarica,Eucalyptus nandewarica,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus nandewarica L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2897688,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118852,Eucalyptus nandewarica,https://id.biodiversity.org.au/name/apni/118852,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus nandewarica,native -Eucalyptus olida,Eucalyptus olida,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus olida L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2914019,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118797,Eucalyptus olida,https://id.biodiversity.org.au/name/apni/118797,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus olida,native -Eucalyptus pulverulenta,Eucalyptus pulverulenta,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus pulverulenta Sims,https://id.biodiversity.org.au/taxon/apni/51440675,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/106609,Eucalyptus pulverulenta,https://id.biodiversity.org.au/name/apni/106609,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus pulverulenta,native -Eucalyptus recurva,Eucalyptus recurva,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus recurva Crisp,https://id.biodiversity.org.au/node/apni/2892273,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/101532,Eucalyptus recurva,https://id.biodiversity.org.au/name/apni/101532,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus recurva,native -Eucalyptus rossii,Eucalyptus rossii,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus rossii R.T.Baker & H.G.Sm.,https://id.biodiversity.org.au/node/apni/2900822,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/58182,Eucalyptus rossii,https://id.biodiversity.org.au/name/apni/58182,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus rossii,native -Eucalyptus scias,Eucalyptus scias,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus scias L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2893839,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118833,Eucalyptus scias,https://id.biodiversity.org.au/name/apni/118833,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus scias,native -Eucalyptus viminalis,Eucalyptus viminalis,Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied),Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic, Tas",Eucalyptus viminalis Labill.,https://id.biodiversity.org.au/taxon/apni/51290421,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/65838,Eucalyptus viminalis [alternative possible names: Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus viminalis,native -Eucalyptus youmanii,Eucalyptus youmanii,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Eucalyptus youmanii Blakely & McKie,https://id.biodiversity.org.au/node/apni/2916227,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/92496,Eucalyptus youmanii,https://id.biodiversity.org.au/name/apni/92496,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus youmanii,native +Eucalyptus badjensis,Eucalyptus badjensis,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus badjensis Beuzev. & M.B.Welch,https://id.biodiversity.org.au/node/apni/2912724,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/57323,Eucalyptus badjensis,https://id.biodiversity.org.au/name/apni/57323,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus badjensis,native +Eucalyptus camphora,Eucalyptus camphora,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic",Eucalyptus camphora R.T.Baker,https://id.biodiversity.org.au/taxon/apni/51738742,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/94439,Eucalyptus camphora,https://id.biodiversity.org.au/name/apni/94439,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus camphora,native +Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus dorrigoensis (Blakely) L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2903351,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/118668,Eucalyptus dorrigoensis,https://id.biodiversity.org.au/name/apni/118668,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus dorrigoensis,native +Eucalyptus yangoura,Eucalyptus globoidea,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus globoidea Blakely,https://id.biodiversity.org.au/node/apni/5270850,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/61141,Eucalyptus globoidea,https://id.biodiversity.org.au/name/apni/92470,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus globoidea,native +Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,,Eucalyptus,Myrtaceae,subspecies,APC,accepted,Magnoliidae,"SA, NSW, Vic",Eucalyptus leucoxylon subsp. pruinosa (F.Muell. ex Miq.) Boland,https://id.biodiversity.org.au/node/apni/2908258,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/77407,Eucalyptus leucoxylon subsp. pruinosa,https://id.biodiversity.org.au/name/apni/77407,https://id.biodiversity.org.au/taxon/apni/51738744,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon,native +Eucalyptus muelleriana,Eucalyptus muelleriana,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus muelleriana A.W.Howitt,https://id.biodiversity.org.au/node/apni/2888508,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/56840,Eucalyptus muelleriana,https://id.biodiversity.org.au/name/apni/56840,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus muelleriana,native +Eucalyptus nandewarica,Eucalyptus nandewarica,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus nandewarica L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2897688,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/118852,Eucalyptus nandewarica,https://id.biodiversity.org.au/name/apni/118852,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus nandewarica,native +Eucalyptus olida,Eucalyptus olida,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus olida L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2914019,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/118797,Eucalyptus olida,https://id.biodiversity.org.au/name/apni/118797,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus olida,native +Eucalyptus pulverulenta,Eucalyptus pulverulenta,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus pulverulenta Sims,https://id.biodiversity.org.au/taxon/apni/51440675,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/106609,Eucalyptus pulverulenta,https://id.biodiversity.org.au/name/apni/106609,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus pulverulenta,native +Eucalyptus recurva,Eucalyptus recurva,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus recurva Crisp,https://id.biodiversity.org.au/node/apni/2892273,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/101532,Eucalyptus recurva,https://id.biodiversity.org.au/name/apni/101532,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus recurva,native +Eucalyptus rossii,Eucalyptus rossii,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus rossii R.T.Baker & H.G.Sm.,https://id.biodiversity.org.au/node/apni/2900822,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/58182,Eucalyptus rossii,https://id.biodiversity.org.au/name/apni/58182,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus rossii,native +Eucalyptus scias,Eucalyptus scias,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus scias L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2893839,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/118833,Eucalyptus scias,https://id.biodiversity.org.au/name/apni/118833,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus scias,native +Eucalyptus viminalis,Eucalyptus viminalis,Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied),Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic, Tas",Eucalyptus viminalis Labill.,https://id.biodiversity.org.au/taxon/apni/51290421,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/65838,Eucalyptus viminalis [alternative possible names: Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus viminalis,native +Eucalyptus youmanii,Eucalyptus youmanii,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Eucalyptus youmanii Blakely & McKie,https://id.biodiversity.org.au/node/apni/2916227,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/92496,Eucalyptus youmanii,https://id.biodiversity.org.au/name/apni/92496,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus youmanii,native Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata var. queenslandica,,Euphorbia,Euphorbiaceae,variety,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Euphorbia inappendiculata var. queenslandica Domin,https://id.biodiversity.org.au/node/apni/7200245,https://id.biodiversity.org.au/taxon/apni/51435529,https://id.biodiversity.org.au/name/apni/92612,Euphorbia inappendiculata var. queenslandica,https://id.biodiversity.org.au/name/apni/92612,https://id.biodiversity.org.au/taxon/apni/51442249,Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata,native Exocarpos homalocladus,Exocarpos homalocladus,,Exocarpos,Santalaceae,species,APC,accepted,Magnoliidae,LHI,Exocarpos homalocladus C.Moore & F.Muell.,https://id.biodiversity.org.au/node/apni/2898548,https://id.biodiversity.org.au/taxon/apni/51447153,https://id.biodiversity.org.au/name/apni/58158,Exocarpos homalocladus,https://id.biodiversity.org.au/name/apni/58158,https://id.biodiversity.org.au/taxon/apni/51447154,,Exocarpos homalocladus,native Exocarpos sparteus,Exocarpos sparteus,,Exocarpos,Santalaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Exocarpos sparteus R.Br.,https://id.biodiversity.org.au/node/apni/2898676,https://id.biodiversity.org.au/taxon/apni/51447153,https://id.biodiversity.org.au/name/apni/58330,Exocarpos sparteus,https://id.biodiversity.org.au/name/apni/58330,https://id.biodiversity.org.au/taxon/apni/51447154,,Exocarpos sparteus,native @@ -100,11 +100,11 @@ Geijera salicifolia,Geijera salicifolia,,Geijera,Rutaceae,species,APC,accepted,M Gentiana wingecarribiensis,Gentiana wingecarribiensis,,Gentiana,Gentianaceae,species,APC,accepted,Magnoliidae,NSW,Gentiana wingecarribiensis L.G.Adams,https://id.biodiversity.org.au/node/apni/2915610,https://id.biodiversity.org.au/taxon/apni/51436928,https://id.biodiversity.org.au/name/apni/80378,Gentiana wingecarribiensis,https://id.biodiversity.org.au/name/apni/80378,https://id.biodiversity.org.au/taxon/apni/51436871,,Gentiana wingecarribiensis,native Geranium obtusisepalum,Geranium obtusisepalum,,Geranium,Geraniaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Geranium obtusisepalum Carolin,https://id.biodiversity.org.au/node/apni/2910251,https://id.biodiversity.org.au/taxon/apni/51436946,https://id.biodiversity.org.au/name/apni/82004,Geranium obtusisepalum,https://id.biodiversity.org.au/name/apni/82004,https://id.biodiversity.org.au/taxon/apni/51436947,,Geranium obtusisepalum,native Geranium purpureum subsp. purpureum,Geranium purpureum,,Geranium,Geraniaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised)",Geranium purpureum Vill.,https://id.biodiversity.org.au/node/apni/2919721,https://id.biodiversity.org.au/taxon/apni/51436946,https://id.biodiversity.org.au/name/apni/82353,Geranium purpureum,https://id.biodiversity.org.au/name/apni/82382,https://id.biodiversity.org.au/taxon/apni/51436947,,Geranium purpureum,naturalised -Gompholobium grandiflorum,Gompholobium grandiflorum,,Gompholobium,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Gompholobium grandiflorum Sm.,https://id.biodiversity.org.au/node/apni/2909013,https://id.biodiversity.org.au/taxon/apni/51436123,https://id.biodiversity.org.au/name/apni/65291,Gompholobium grandiflorum,https://id.biodiversity.org.au/name/apni/65291,https://id.biodiversity.org.au/taxon/apni/51702961,,Gompholobium grandiflorum,native +Gompholobium grandiflorum,Gompholobium grandiflorum,,Gompholobium,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Gompholobium grandiflorum Sm.,https://id.biodiversity.org.au/node/apni/2909013,https://id.biodiversity.org.au/taxon/apni/51436123,https://id.biodiversity.org.au/name/apni/65291,Gompholobium grandiflorum,https://id.biodiversity.org.au/name/apni/65305,https://id.biodiversity.org.au/taxon/apni/51702961,,Gompholobium grandiflorum,native Goodenia varia,Goodenia varia,,Goodenia,Goodeniaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic",Goodenia varia R.Br.,https://id.biodiversity.org.au/node/apni/2910439,https://id.biodiversity.org.au/taxon/apni/51437012,https://id.biodiversity.org.au/name/apni/92079,Goodenia varia,https://id.biodiversity.org.au/name/apni/92079,https://id.biodiversity.org.au/taxon/apni/51462931,,Goodenia varia,native -Gossia bidwillii,Gossia bidwillii,,Gossia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Gossia bidwillii (Benth.) N.Snow & Guymer,https://id.biodiversity.org.au/taxon/apni/51439972,https://id.biodiversity.org.au/taxon/apni/51439958,https://id.biodiversity.org.au/name/apni/180918,Gossia bidwillii,https://id.biodiversity.org.au/name/apni/180918,https://id.biodiversity.org.au/taxon/apni/51702983,,Gossia bidwillii,native -Grevillea scortechinii,Grevillea scortechinii,,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Grevillea scortechinii (F.Muell. ex Scort.) F.Muell.,https://id.biodiversity.org.au/node/apni/2918803,https://id.biodiversity.org.au/taxon/apni/51445337,https://id.biodiversity.org.au/name/apni/63322,Grevillea scortechinii,https://id.biodiversity.org.au/name/apni/63322,https://id.biodiversity.org.au/taxon/apni/51614274,,Grevillea scortechinii,native -Hakea macraeana,Hakea macraeana,Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied),Hakea,Proteaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Hakea macraeana F.Muell.,https://id.biodiversity.org.au/node/apni/2895080,https://id.biodiversity.org.au/taxon/apni/51445456,https://id.biodiversity.org.au/name/apni/94862,Hakea macraeana [alternative possible names: Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied)],,https://id.biodiversity.org.au/taxon/apni/51614274,,Hakea macraeana,native +Gossia bidwillii,Gossia bidwillii,,Gossia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Gossia bidwillii (Benth.) N.Snow & Guymer,https://id.biodiversity.org.au/taxon/apni/51439972,https://id.biodiversity.org.au/taxon/apni/51439958,https://id.biodiversity.org.au/name/apni/180918,Gossia bidwillii,https://id.biodiversity.org.au/name/apni/180918,https://id.biodiversity.org.au/taxon/apni/51738744,,Gossia bidwillii,native +Grevillea scortechinii,Grevillea scortechinii,,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Grevillea scortechinii (F.Muell. ex Scort.) F.Muell.,https://id.biodiversity.org.au/node/apni/2918803,https://id.biodiversity.org.au/taxon/apni/51726302,https://id.biodiversity.org.au/name/apni/63322,Grevillea scortechinii,https://id.biodiversity.org.au/name/apni/63322,https://id.biodiversity.org.au/taxon/apni/51732901,,Grevillea scortechinii,native +Hakea macraeana,Hakea macraeana,Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied),Hakea,Proteaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Hakea macraeana F.Muell.,https://id.biodiversity.org.au/node/apni/2895080,https://id.biodiversity.org.au/taxon/apni/51445456,https://id.biodiversity.org.au/name/apni/94862,Hakea macraeana [alternative possible names: Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied)],,https://id.biodiversity.org.au/taxon/apni/51732901,,Hakea macraeana,native Hemisteptia lyrata,Hemisteptia lyrata,,Hemisteptia,Asteraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Hemisteptia lyrata (Bunge) Fisch. & C.A.Mey.,https://id.biodiversity.org.au/taxon/apni/51268530,https://id.biodiversity.org.au/taxon/apni/51268531,https://id.biodiversity.org.au/name/apni/230066,Hemisteptia lyrata,https://id.biodiversity.org.au/name/apni/230066,https://id.biodiversity.org.au/taxon/apni/51695393,,Hemisteptia lyrata,native Hibbertia crinita,Hibbertia crinita,,Hibbertia,Dilleniaceae,species,APC,accepted,Magnoliidae,"SA, Vic",Hibbertia crinita Toelken,https://id.biodiversity.org.au/node/apni/2899370,https://id.biodiversity.org.au/taxon/apni/51434912,https://id.biodiversity.org.au/name/apni/170069,Hibbertia crinita,https://id.biodiversity.org.au/name/apni/170069,https://id.biodiversity.org.au/taxon/apni/51434913,,Hibbertia crinita,native Hibiscus brachysiphonius,Hibiscus brachysiphonius,,Hibiscus,Malvaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Hibiscus brachysiphonius F.Muell.,https://id.biodiversity.org.au/node/apni/2891329,https://id.biodiversity.org.au/taxon/apni/51439316,https://id.biodiversity.org.au/name/apni/91736,Hibiscus brachysiphonius,https://id.biodiversity.org.au/name/apni/91736,https://id.biodiversity.org.au/taxon/apni/51439248,,Hibiscus brachysiphonius,native @@ -123,25 +123,25 @@ Lepidium africanum,Lepidium africanum,,Lepidium,Brassicaceae,species,APC,accepte Lepidium foliosum,Lepidium foliosum,,Lepidium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Lepidium foliosum Desv.,https://id.biodiversity.org.au/node/apni/2908453,https://id.biodiversity.org.au/taxon/apni/51612686,https://id.biodiversity.org.au/name/apni/69389,Lepidium foliosum,https://id.biodiversity.org.au/name/apni/69389,https://id.biodiversity.org.au/taxon/apni/51612687,,Lepidium foliosum,native Lepidium oxytrichum,Lepidium oxytrichum,,Lepidium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Lepidium oxytrichum Sprague,https://id.biodiversity.org.au/node/apni/2915883,https://id.biodiversity.org.au/taxon/apni/51612686,https://id.biodiversity.org.au/name/apni/84027,Lepidium oxytrichum,https://id.biodiversity.org.au/name/apni/84027,https://id.biodiversity.org.au/taxon/apni/51612687,,Lepidium oxytrichum,native Leptomeria drupacea,Leptomeria drupacea,,Leptomeria,Santalaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic, Tas",Leptomeria drupacea (Labill.) Druce,https://id.biodiversity.org.au/node/apni/2892780,https://id.biodiversity.org.au/node/apni/2897704,https://id.biodiversity.org.au/name/apni/61625,Leptomeria drupacea,https://id.biodiversity.org.au/name/apni/61625,https://id.biodiversity.org.au/taxon/apni/51447154,,Leptomeria drupacea,native -Leptospermum continentale,Leptospermum continentale,,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic",Leptospermum continentale Joy Thomps.,https://id.biodiversity.org.au/node/apni/2917147,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/81291,Leptospermum continentale,https://id.biodiversity.org.au/name/apni/81291,https://id.biodiversity.org.au/taxon/apni/51702983,,Leptospermum continentale,native -Leptospermum obovatum,Leptospermum obovatum,,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Leptospermum obovatum Sweet,https://id.biodiversity.org.au/node/apni/2891711,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/99608,Leptospermum obovatum,https://id.biodiversity.org.au/name/apni/99608,https://id.biodiversity.org.au/taxon/apni/51702983,,Leptospermum obovatum,native -Leucopogon amplexicaulis,Leucopogon amplexicaulis,,Leucopogon,Ericaceae,species,APC,accepted,Magnoliidae,NSW,Leucopogon amplexicaulis (Rudge) R.Br.,https://id.biodiversity.org.au/node/apni/2896081,https://id.biodiversity.org.au/taxon/apni/51435325,https://id.biodiversity.org.au/name/apni/106715,Leucopogon amplexicaulis,https://id.biodiversity.org.au/name/apni/106715,https://id.biodiversity.org.au/taxon/apni/51436079,,Leucopogon amplexicaulis,native +Leptospermum continentale,Leptospermum continentale,,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic",Leptospermum continentale Joy Thomps.,https://id.biodiversity.org.au/node/apni/2917147,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/81291,Leptospermum continentale,https://id.biodiversity.org.au/name/apni/81291,https://id.biodiversity.org.au/taxon/apni/51738744,,Leptospermum continentale,native +Leptospermum obovatum,Leptospermum obovatum,,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Leptospermum obovatum Sweet,https://id.biodiversity.org.au/node/apni/2891711,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/99608,Leptospermum obovatum,https://id.biodiversity.org.au/name/apni/99608,https://id.biodiversity.org.au/taxon/apni/51738744,,Leptospermum obovatum,native +Leucopogon amplexicaulis,Leucopogon amplexicaulis,,Leucopogon,Ericaceae,species,APC,accepted,Magnoliidae,NSW,Leucopogon amplexicaulis (Rudge) R.Br.,https://id.biodiversity.org.au/node/apni/2896081,https://id.biodiversity.org.au/taxon/apni/51435325,https://id.biodiversity.org.au/name/apni/106715,Leucopogon amplexicaulis,https://id.biodiversity.org.au/name/apni/106715,https://id.biodiversity.org.au/taxon/apni/51738121,,Leucopogon amplexicaulis,native Lobelia pedunculata,Lobelia pedunculata,,Lobelia,Campanulaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic, Tas",Lobelia pedunculata R.Br.,https://id.biodiversity.org.au/node/apni/2901444,https://id.biodiversity.org.au/taxon/apni/51432852,https://id.biodiversity.org.au/name/apni/106999,Lobelia pedunculata,https://id.biodiversity.org.au/name/apni/106999,https://id.biodiversity.org.au/taxon/apni/51432853,,Lobelia pedunculata,native Lobelia trigonocaulis,Lobelia trigonocaulis,,Lobelia,Campanulaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Lobelia trigonocaulis F.Muell.,https://id.biodiversity.org.au/node/apni/2901863,https://id.biodiversity.org.au/taxon/apni/51432852,https://id.biodiversity.org.au/name/apni/107808,Lobelia trigonocaulis,https://id.biodiversity.org.au/name/apni/107808,https://id.biodiversity.org.au/taxon/apni/51432853,,Lobelia trigonocaulis,native Lotononis bainesii,Lotononis bainesii,,Lotononis,Fabaceae,species,APC,accepted,Magnoliidae,"Qld (naturalised), NSW (naturalised)",Lotononis bainesii Baker,https://id.biodiversity.org.au/node/apni/2904277,https://id.biodiversity.org.au/node/apni/2898035,https://id.biodiversity.org.au/name/apni/109834,Lotononis bainesii,https://id.biodiversity.org.au/name/apni/109834,https://id.biodiversity.org.au/taxon/apni/51702961,,Lotononis bainesii,naturalised Lotus corniculatus,Lotus corniculatus,Lotus preslii (pro parte misapplied) | Lotus uliginosus (pro parte misapplied),Lotus,Fabaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (formerly naturalised), NSW (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Lotus corniculatus L.,https://id.biodiversity.org.au/node/apni/2921302,https://id.biodiversity.org.au/taxon/apni/51436215,https://id.biodiversity.org.au/name/apni/110319,Lotus corniculatus [alternative possible names: Lotus preslii (pro parte misapplied) | Lotus uliginosus (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51702961,,Lotus corniculatus,naturalised Lupinus polyphyllus,Lupinus polyphyllus,,Lupinus,Fabaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), Vic (naturalised)",Lupinus polyphyllus Lindl.,https://id.biodiversity.org.au/node/apni/2917429,https://id.biodiversity.org.au/node/apni/2918316,https://id.biodiversity.org.au/name/apni/100609,Lupinus polyphyllus,https://id.biodiversity.org.au/name/apni/100609,https://id.biodiversity.org.au/taxon/apni/51702961,,Lupinus polyphyllus,naturalised Medicago orbicularis,Medicago orbicularis,,Medicago,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (formerly naturalised)",Medicago orbicularis (L.) Bartal.,https://id.biodiversity.org.au/node/apni/2901771,https://id.biodiversity.org.au/taxon/apni/51285690,https://id.biodiversity.org.au/name/apni/59568,Medicago orbicularis,https://id.biodiversity.org.au/name/apni/59568,https://id.biodiversity.org.au/taxon/apni/51702961,,Medicago orbicularis,naturalised -Melichrus procumbens,Melichrus procumbens,,Melichrus,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Melichrus procumbens (Cav.) Druce,https://id.biodiversity.org.au/node/apni/2905836,https://id.biodiversity.org.au/node/apni/2914566,https://id.biodiversity.org.au/name/apni/114051,Melichrus procumbens,https://id.biodiversity.org.au/name/apni/114051,https://id.biodiversity.org.au/taxon/apni/51436079,,Melichrus procumbens,native +Melichrus procumbens,Melichrus procumbens,,Melichrus,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Melichrus procumbens (Cav.) Druce,https://id.biodiversity.org.au/node/apni/2905836,https://id.biodiversity.org.au/node/apni/2914566,https://id.biodiversity.org.au/name/apni/114051,Melichrus procumbens,https://id.biodiversity.org.au/name/apni/114051,https://id.biodiversity.org.au/taxon/apni/51738121,,Melichrus procumbens,native Mischocarpus australis,Mischocarpus australis,,Mischocarpus,Sapindaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Mischocarpus australis S.T.Reynolds,https://id.biodiversity.org.au/node/apni/2893744,https://id.biodiversity.org.au/taxon/apni/51389373,https://id.biodiversity.org.au/name/apni/115917,Mischocarpus australis,https://id.biodiversity.org.au/name/apni/115917,https://id.biodiversity.org.au/taxon/apni/51447212,,Mischocarpus australis,native Muehlenbeckia adpressa,Muehlenbeckia adpressa,,Muehlenbeckia,Polygonaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Muehlenbeckia adpressa (Labill.) Meisn.,https://id.biodiversity.org.au/node/apni/4750977,https://id.biodiversity.org.au/taxon/apni/51291654,https://id.biodiversity.org.au/name/apni/107852,Muehlenbeckia adpressa,https://id.biodiversity.org.au/name/apni/107852,https://id.biodiversity.org.au/taxon/apni/51444856,,Muehlenbeckia adpressa,native -Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,,Myoporum,Scrophulariaceae,subspecies,APC,accepted,Magnoliidae,"Qld, NSW",Myoporum boninense subsp. australe Chinnock,https://id.biodiversity.org.au/node/apni/7957248,https://id.biodiversity.org.au/taxon/apni/51447443,https://id.biodiversity.org.au/name/apni/117892,Myoporum boninense subsp. australe,https://id.biodiversity.org.au/name/apni/117892,https://id.biodiversity.org.au/taxon/apni/51461527,Myoporum boninense subsp. australe,Myoporum boninense,native +Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,,Myoporum,Scrophulariaceae,subspecies,APC,accepted,Magnoliidae,"Qld, NSW",Myoporum boninense subsp. australe Chinnock,https://id.biodiversity.org.au/node/apni/7957248,https://id.biodiversity.org.au/taxon/apni/51447443,https://id.biodiversity.org.au/name/apni/117892,Myoporum boninense subsp. australe,https://id.biodiversity.org.au/name/apni/117892,https://id.biodiversity.org.au/taxon/apni/51734003,Myoporum boninense subsp. australe,Myoporum boninense,native Nicotiana glauca,Nicotiana glauca,,Nicotiana,Solanaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (naturalised)",Nicotiana glauca Graham,https://id.biodiversity.org.au/node/apni/2887606,https://id.biodiversity.org.au/taxon/apni/51447689,https://id.biodiversity.org.au/name/apni/77368,Nicotiana glauca,https://id.biodiversity.org.au/name/apni/77368,https://id.biodiversity.org.au/taxon/apni/51447684,,Nicotiana glauca,naturalised Nicotiana goodspeedii,Nicotiana goodspeedii,,Nicotiana,Solanaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic",Nicotiana goodspeedii H.-M.Wheeler,https://id.biodiversity.org.au/node/apni/2908652,https://id.biodiversity.org.au/taxon/apni/51447689,https://id.biodiversity.org.au/name/apni/77381,Nicotiana goodspeedii,https://id.biodiversity.org.au/name/apni/77381,https://id.biodiversity.org.au/taxon/apni/51447684,,Nicotiana goodspeedii,native Oxalis corniculata,Oxalis corniculata,,Oxalis,Oxalidaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), ChI (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Oxalis corniculata L.,https://id.biodiversity.org.au/node/apni/2909588,https://id.biodiversity.org.au/taxon/apni/51442068,https://id.biodiversity.org.au/name/apni/89460,Oxalis corniculata,https://id.biodiversity.org.au/name/apni/89460,https://id.biodiversity.org.au/taxon/apni/51442069,,Oxalis corniculata,naturalised Pandorea pandorana subsp. austrocaledonica,Pandorea pandorana,,Pandorea,Bignoniaceae,species,APC,accepted,Magnoliidae,"WA, SA (native and naturalised), Qld, NSW, LHI, NI (presumed extinct), Vic (native and naturalised), Tas",Pandorea pandorana (Andrews) Steenis,https://id.biodiversity.org.au/taxon/apni/51269199,https://id.biodiversity.org.au/taxon/apni/51269200,https://id.biodiversity.org.au/name/apni/91117,Pandorea pandorana,https://id.biodiversity.org.au/name/apni/141640,https://id.biodiversity.org.au/taxon/apni/51439229,,Pandorea pandorana,native and naturalised Paraserianthes lophantha,Paraserianthes lophantha,,Paraserianthes,Fabaceae,species,APC,accepted,Magnoliidae,"WA (native and naturalised), SA (naturalised), NSW (naturalised), NI (naturalised), Vic (naturalised), Tas (naturalised)",Paraserianthes lophantha (Willd.) I.C.Nielsen,https://id.biodiversity.org.au/taxon/apni/51286820,https://id.biodiversity.org.au/taxon/apni/51286819,https://id.biodiversity.org.au/name/apni/116755,Paraserianthes lophantha,https://id.biodiversity.org.au/name/apni/116755,https://id.biodiversity.org.au/taxon/apni/51702961,,Paraserianthes lophantha,native and naturalised -Parentucellia latifolia,Parentucellia latifolia,,Parentucellia,Orobanchaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Parentucellia latifolia (L.) Caruel,https://id.biodiversity.org.au/taxon/apni/51291069,https://id.biodiversity.org.au/taxon/apni/51291062,https://id.biodiversity.org.au/name/apni/96753,Parentucellia latifolia,https://id.biodiversity.org.au/name/apni/96753,https://id.biodiversity.org.au/taxon/apni/51291037,,Parentucellia latifolia,naturalised +Parentucellia latifolia,Parentucellia latifolia,,Parentucellia,Orobanchaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Parentucellia latifolia (L.) Caruel,https://id.biodiversity.org.au/taxon/apni/51291069,https://id.biodiversity.org.au/taxon/apni/51291062,https://id.biodiversity.org.au/name/apni/96753,Parentucellia latifolia,https://id.biodiversity.org.au/name/apni/96753,https://id.biodiversity.org.au/taxon/apni/51734010,,Parentucellia latifolia,naturalised Hypoxis glabella var. glabella,Pauridia glabella var. glabella,,Pauridia,Hypoxidaceae,variety,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Pauridia glabella (R.Br.) Snijman & Kocyan var. glabella,https://id.biodiversity.org.au/node/apni/7455351,https://id.biodiversity.org.au/taxon/apni/51437983,https://id.biodiversity.org.au/name/apni/244102,Pauridia glabella var. glabella,https://id.biodiversity.org.au/name/apni/81442,https://id.biodiversity.org.au/taxon/apni/51437984,Pauridia glabella var. glabella,Pauridia glabella,native Phlegmatospermum cochlearinum,Phlegmatospermum cochlearinum,,Phlegmatospermum,Brassicaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic",Phlegmatospermum cochlearinum (F.Muell.) O.E.Schulz,https://id.biodiversity.org.au/node/apni/2915554,https://id.biodiversity.org.au/node/apni/2897988,https://id.biodiversity.org.au/name/apni/81861,Phlegmatospermum cochlearinum,https://id.biodiversity.org.au/name/apni/81861,https://id.biodiversity.org.au/taxon/apni/51612687,,Phlegmatospermum cochlearinum,native Phyla nodiflora,Phyla nodiflora,,Phyla,Verbenaceae,species,APC,accepted,Magnoliidae,"WA (native and naturalised), CoI (naturalised), NT, Qld, NSW (naturalised)",Phyla nodiflora (L.) Greene,https://id.biodiversity.org.au/node/apni/2907374,https://id.biodiversity.org.au/node/apni/2892182,https://id.biodiversity.org.au/name/apni/74617,Phyla nodiflora,https://id.biodiversity.org.au/name/apni/74617,https://id.biodiversity.org.au/taxon/apni/51448662,,Phyla nodiflora,native and naturalised @@ -155,14 +155,14 @@ Polycarpon tetraphyllum,Polycarpon tetraphyllum,,Polycarpon,Caryophyllaceae,spec Potamogeton australiensis,Potamogeton australiensis,,Potamogeton,Potamogetonaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Potamogeton australiensis A.Benn.,https://id.biodiversity.org.au/node/apni/7808489,https://id.biodiversity.org.au/node/apni/8770682,https://id.biodiversity.org.au/name/apni/65827,Potamogeton australiensis,https://id.biodiversity.org.au/name/apni/65827,https://id.biodiversity.org.au/taxon/apni/51353530,,Potamogeton australiensis,native Psoralea pinnata,Psoralea pinnata,,Psoralea,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised), Tas (naturalised)",Psoralea pinnata L.,https://id.biodiversity.org.au/node/apni/2887023,https://id.biodiversity.org.au/node/apni/8771698,https://id.biodiversity.org.au/name/apni/88820,Psoralea pinnata,https://id.biodiversity.org.au/name/apni/88820,https://id.biodiversity.org.au/taxon/apni/51702961,,Psoralea pinnata,naturalised Pultenaea ferruginea,Pultenaea ferruginea,,Pultenaea,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Pultenaea ferruginea Rudge,https://id.biodiversity.org.au/node/apni/2906803,https://id.biodiversity.org.au/taxon/apni/51436286,https://id.biodiversity.org.au/name/apni/59158,Pultenaea ferruginea,https://id.biodiversity.org.au/name/apni/59158,https://id.biodiversity.org.au/taxon/apni/51702961,,Pultenaea ferruginea,native -Rhodamnia argentea,Rhodamnia argentea,,Rhodamnia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Rhodamnia argentea Benth.,https://id.biodiversity.org.au/node/apni/2919069,https://id.biodiversity.org.au/taxon/apni/51440311,https://id.biodiversity.org.au/name/apni/68532,Rhodamnia argentea,https://id.biodiversity.org.au/name/apni/68532,https://id.biodiversity.org.au/taxon/apni/51702983,,Rhodamnia argentea,native +Rhodamnia argentea,Rhodamnia argentea,,Rhodamnia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Rhodamnia argentea Benth.,https://id.biodiversity.org.au/node/apni/2919069,https://id.biodiversity.org.au/taxon/apni/51440311,https://id.biodiversity.org.au/name/apni/68532,Rhodamnia argentea,https://id.biodiversity.org.au/name/apni/68532,https://id.biodiversity.org.au/taxon/apni/51738744,,Rhodamnia argentea,native Rorippa gigantea,Rorippa gigantea,,Rorippa,Brassicaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Rorippa gigantea (Hook.) Garn.-Jones,https://id.biodiversity.org.au/node/apni/2920330,https://id.biodiversity.org.au/node/apni/8442201,https://id.biodiversity.org.au/name/apni/75950,Rorippa gigantea,https://id.biodiversity.org.au/name/apni/75950,https://id.biodiversity.org.au/taxon/apni/51612687,,Rorippa gigantea,native -Rubus parvifolius,Rubus parvifolius,,Rubus,Rosaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Rubus parvifolius L.,https://id.biodiversity.org.au/node/apni/2901867,https://id.biodiversity.org.au/taxon/apni/51446575,https://id.biodiversity.org.au/name/apni/85986,Rubus parvifolius,https://id.biodiversity.org.au/name/apni/85986,https://id.biodiversity.org.au/taxon/apni/51446278,,Rubus parvifolius,native -Salix alba,Salix alba,,Salix,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised)",Salix alba L.,https://id.biodiversity.org.au/node/apni/2896377,https://id.biodiversity.org.au/node/apni/8905801,https://id.biodiversity.org.au/name/apni/59687,Salix alba [alternative possible names: NA],,https://id.biodiversity.org.au/taxon/apni/51436847,,Salix alba,naturalised +Rubus parvifolius,Rubus parvifolius,,Rubus,Rosaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Rubus parvifolius L.,https://id.biodiversity.org.au/node/apni/2901867,https://id.biodiversity.org.au/taxon/apni/51446575,https://id.biodiversity.org.au/name/apni/85986,Rubus parvifolius,https://id.biodiversity.org.au/name/apni/85986,https://id.biodiversity.org.au/taxon/apni/51737985,,Rubus parvifolius,native +Salix alba,Salix alba,Salix x fragilis nothovar. fragilis (pro parte misapplied),Salix,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised)",Salix alba L.,https://id.biodiversity.org.au/node/apni/2896377,https://id.biodiversity.org.au/node/apni/8905801,https://id.biodiversity.org.au/name/apni/59687,Salix alba [alternative possible names: Salix x fragilis nothovar. fragilis (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51436847,,Salix alba,naturalised Schenkia australis,Schenkia australis,,Schenkia,Gentianaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic, Tas",Schenkia australis (R.Br.) G.Mans.,https://id.biodiversity.org.au/taxon/apni/51436897,https://id.biodiversity.org.au/taxon/apni/51436898,https://id.biodiversity.org.au/name/apni/200895,Schenkia australis,https://id.biodiversity.org.au/name/apni/200895,https://id.biodiversity.org.au/taxon/apni/51436871,,Schenkia australis,native Schoenus apogon,Schoenus apogon,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Schoenus apogon Roem. & Schult.,https://id.biodiversity.org.au/node/apni/2908439,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/109452,Schoenus apogon,https://id.biodiversity.org.au/name/apni/109452,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus apogon,native Schoenus brevifolius,Schoenus brevifolius,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic, Tas",Schoenus brevifolius R.Br.,https://id.biodiversity.org.au/node/apni/2904000,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/109778,Schoenus brevifolius,https://id.biodiversity.org.au/name/apni/109778,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus brevifolius,native -Schoenus lepidosperma,Schoenus lepidosperma,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Schoenus lepidosperma (F.Muell.) K.L.Wilson,https://id.biodiversity.org.au/node/apni/2893030,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/141376,Schoenus lepidosperma,https://id.biodiversity.org.au/name/apni/243667,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus lepidosperma,native +Schoenus lepidosperma,Schoenus lepidosperma,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Schoenus lepidosperma (F.Muell.) K.L.Wilson,https://id.biodiversity.org.au/node/apni/2893030,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/141376,Schoenus lepidosperma,https://id.biodiversity.org.au/name/apni/141376,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus lepidosperma,native Schoenus vaginatus,Schoenus vaginatus,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Schoenus vaginatus F.Muell. ex Benth.,https://id.biodiversity.org.au/node/apni/2896591,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/113246,Schoenus vaginatus,https://id.biodiversity.org.au/name/apni/113246,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus vaginatus,native Scleria rugosa,Scleria rugosa,,Scleria,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Scleria rugosa R.Br.,https://id.biodiversity.org.au/node/apni/2892143,https://id.biodiversity.org.au/taxon/apni/51434752,https://id.biodiversity.org.au/name/apni/64346,Scleria rugosa,https://id.biodiversity.org.au/name/apni/64346,https://id.biodiversity.org.au/taxon/apni/51460154,,Scleria rugosa,native Senecio longipilus,Senecio longipilus,,Senecio,Asteraceae,species,APC,accepted,Magnoliidae,"NSW, Tas",Senecio longipilus I.Thomps.,https://id.biodiversity.org.au/node/apni/2907653,https://id.biodiversity.org.au/taxon/apni/51614245,https://id.biodiversity.org.au/name/apni/189666,Senecio longipilus,https://id.biodiversity.org.au/name/apni/189666,https://id.biodiversity.org.au/taxon/apni/51695393,,Senecio longipilus,native @@ -174,10 +174,10 @@ Sparaxis bulbifera,Sparaxis bulbifera,,Sparaxis,Iridaceae,species,APC,accepted,M Spergularia diandra,Spergularia diandra,,Spergularia,Caryophyllaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised)",Spergularia diandra (Guss.) Heldr.,https://id.biodiversity.org.au/node/apni/2886696,https://id.biodiversity.org.au/taxon/apni/51295406,https://id.biodiversity.org.au/name/apni/83464,Spergularia diandra,https://id.biodiversity.org.au/name/apni/83464,https://id.biodiversity.org.au/taxon/apni/51432987,,Spergularia diandra,naturalised Sphaeromorphaea littoralis,Sphaeromorphaea littoralis,,Sphaeromorphaea,Asteraceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Sphaeromorphaea littoralis (Retz.) A.R.Bean,https://id.biodiversity.org.au/node/apni/7069871,https://id.biodiversity.org.au/node/apni/7071683,https://id.biodiversity.org.au/name/apni/246779,Sphaeromorphaea littoralis,https://id.biodiversity.org.au/name/apni/246779,https://id.biodiversity.org.au/taxon/apni/51695393,,Sphaeromorphaea littoralis,native Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia subsp. angustifolia,,Stellaria,Caryophyllaceae,subspecies,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Stellaria angustifolia Hook. subsp. angustifolia,https://id.biodiversity.org.au/node/apni/2890520,https://id.biodiversity.org.au/taxon/apni/51433015,https://id.biodiversity.org.au/name/apni/240421,Stellaria angustifolia subsp. angustifolia,https://id.biodiversity.org.au/name/apni/240421,https://id.biodiversity.org.au/taxon/apni/51432987,Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia,native -Styphelia viridis,Styphelia viridis,,Styphelia,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Styphelia viridis Andrews,https://id.biodiversity.org.au/node/apni/2912747,https://id.biodiversity.org.au/taxon/apni/51435346,https://id.biodiversity.org.au/name/apni/109318,Styphelia viridis,https://id.biodiversity.org.au/name/apni/109318,https://id.biodiversity.org.au/taxon/apni/51436079,,Styphelia viridis,native +Styphelia viridis,Styphelia viridis,,Styphelia,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Styphelia viridis Andrews,https://id.biodiversity.org.au/node/apni/2912747,https://id.biodiversity.org.au/taxon/apni/51435346,https://id.biodiversity.org.au/name/apni/109318,Styphelia viridis,https://id.biodiversity.org.au/name/apni/109318,https://id.biodiversity.org.au/taxon/apni/51738121,,Styphelia viridis,native Swainsona cadellii,Swainsona cadellii,,Swainsona,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Swainsona cadellii F.Muell. ex C.Moore,https://id.biodiversity.org.au/node/apni/2904099,https://id.biodiversity.org.au/taxon/apni/51436313,https://id.biodiversity.org.au/name/apni/76870,Swainsona cadellii,https://id.biodiversity.org.au/name/apni/76870,https://id.biodiversity.org.au/taxon/apni/51702961,,Swainsona cadellii,native Teucrium puberulum,Teucrium puberulum,,Teucrium,Lamiaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Teucrium puberulum (F.Muell.) Kattari & Bräuchler,https://id.biodiversity.org.au/taxon/apni/51288087,https://id.biodiversity.org.au/taxon/apni/51438311,https://id.biodiversity.org.au/name/apni/7660439,Teucrium puberulum,https://id.biodiversity.org.au/name/apni/7660439,https://id.biodiversity.org.au/taxon/apni/51696573,,Teucrium puberulum,native -Thelymitra kangaloonica,Thelymitra kangaloonica,,Thelymitra,Orchidaceae,species,APC,accepted,Magnoliidae,NSW,Thelymitra kangaloonica Jeanes,https://id.biodiversity.org.au/taxon/apni/51414328,https://id.biodiversity.org.au/taxon/apni/51631246,https://id.biodiversity.org.au/name/apni/233692,Thelymitra kangaloonica,https://id.biodiversity.org.au/name/apni/233692,https://id.biodiversity.org.au/taxon/apni/51697009,,Thelymitra kangaloonica,native +Thelymitra kangaloonica,Thelymitra kangaloonica,,Thelymitra,Orchidaceae,species,APC,accepted,Magnoliidae,NSW,Thelymitra kangaloonica Jeanes,https://id.biodiversity.org.au/taxon/apni/51414328,https://id.biodiversity.org.au/taxon/apni/51631246,https://id.biodiversity.org.au/name/apni/233692,Thelymitra kangaloonica,https://id.biodiversity.org.au/name/apni/233692,https://id.biodiversity.org.au/taxon/apni/51727417,,Thelymitra kangaloonica,native Thesium australe,Thesium australe,,Thesium,Santalaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic, Tas (presumed extinct)",Thesium australe R.Br.,https://id.biodiversity.org.au/node/apni/2891975,https://id.biodiversity.org.au/node/apni/2913858,https://id.biodiversity.org.au/name/apni/56224,Thesium australe,https://id.biodiversity.org.au/name/apni/56224,https://id.biodiversity.org.au/taxon/apni/51447154,,Thesium australe,native Trifolium dubium,Trifolium dubium,,Trifolium,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Trifolium dubium Sibth.,https://id.biodiversity.org.au/taxon/apni/51436351,https://id.biodiversity.org.au/taxon/apni/51436341,https://id.biodiversity.org.au/name/apni/115704,Trifolium dubium,https://id.biodiversity.org.au/name/apni/115704,https://id.biodiversity.org.au/taxon/apni/51702961,,Trifolium dubium,naturalised Veronica catenata,Veronica catenata,,Veronica,Plantaginaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), Vic (naturalised)",Veronica catenata Pennell,https://id.biodiversity.org.au/node/apni/2897164,https://id.biodiversity.org.au/taxon/apni/51632390,https://id.biodiversity.org.au/name/apni/67965,Veronica catenata,https://id.biodiversity.org.au/name/apni/67965,https://id.biodiversity.org.au/taxon/apni/51699383,,Veronica catenata,naturalised diff --git a/tests/testthat/examples/Test_2023_4/metadata.yml b/tests/testthat/examples/Test_2023_4/metadata.yml index a3d9f303..ab1c1486 100644 --- a/tests/testthat/examples/Test_2023_4/metadata.yml +++ b/tests/testthat/examples/Test_2023_4/metadata.yml @@ -144,42 +144,12 @@ contexts: description: Trait value inferred from genus-level taxon description. - value: inferred_from_family description: Trait value inferred from family-level taxon description. - - value: inferred_from_trait - description: Trait value inferred from the value of a different trait. - - value: inferred_from_taxonomy - description: Trait value inferred from a higher level taxon description. - context_property: entity measured category: entity_context var_in: entity_measured values: - value: unknown - - value: leaflet - - value: pinnae - - value: all - value: fruit - - value: infructescence - - value: valve - - value: female_cones - - value: disc_achenes - - value: ray_achenes - - value: leaf - - value: fertile_leaf - - value: sterile_leaf - - value: cauline_leaf - - value: basal_leaf - - value: upper_leaf - - value: stem_leaf - - value: basal_pinnae - - value: phyllode - - value: cladode - - value: fertile_pinnule - - value: sterile_pinnule - - value: lower_leaf - - value: lateral_leaf - - value: emergent_leaf - - value: submerged_leaf - - value: upper_pinnae - - value: scale_leaf traits: - var_in: fruit_colour trait_name: fruit_colour @@ -190,6 +160,7 @@ traits: at maturity or the dominant colours of the fruit exterior were scored. If neither were specified, all colours associated with the fruit were scored. basis_of_record: test_basis_of_record + basis_of_value: test_basis_of_value - var_in: fruit_dehiscence unit_in: .na trait_name: fruit_dehiscence @@ -198,6 +169,7 @@ traits: methods: Taxa were scored as dehiscent from a variety of terms in the text including the kind of dehiscence e.g. scepticidal, loculicidal or possessing valves. basis_of_record: test_basis_of_record + basis_of_value: test_basis_of_value life_stage: adult measurement_remarks: measurement_remarks_fruit_dehiscence - var_in: fruit_length @@ -217,6 +189,7 @@ traits: methods: The term used to describe the fruit width was stored as a measurement remark for greater clarity e.g. fruit, achene, capsule. Fruits which were spherical or round in shape were inferred as possessing the same dimensions in other planes. + basis_of_value: test_basis_of_value - var_in: fruit_width_2 trait_name: fruit_width value_type: value_type @@ -224,6 +197,7 @@ traits: methods: The term used to describe the fruit width was stored as a measurement remark for greater clarity e.g. fruit, achene, capsule. Fruits which were spherical or round in shape were inferred as possessing the same dimensions in other planes. + basis_of_value: test_basis_of_value - var_in: leaf_photosynthesis unit_in: umol/m2/s trait_name: leaf_photosynthesis @@ -251,393 +225,6 @@ traits: column. replicates: 5 substitutions: .na -taxonomic_updates: -- find: Acaena anserovina - replace: Acaena x anserovina - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Acaena ovina - replace: Acaena x ovina - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Acaena sp. Thredbo River Gorge (L.A.S.Johnson ;amp; E.F.Constable s.n., 19 - Jan 1951) - replace: Acaena sp. Thredbo River Gorge (L.A.S.Johnson & E.F.Constable s.n., 19 - Jan 1951) - reason: match_10_fuzzy. Imprecise fuzzy alignment with accepted canonical name in - APC (2022-11-21) - taxonomic_resolution: species -- find: Alstonia constricta f. Pubescent form - replace: Alstonia constricta Pubescent form - reason: match_08. Automatic alignment with synonymous name in APNI (2022-11-21) - taxonomic_resolution: species -- find: Arthropteris beckleri x tenella - replace: Arthropteris x [Arthropteris beckleri x tenella; NHNSW_2022] - reason: match_11. Rewording hybrid species name not in APC or APNI to indicate a - genus-level alignment with APC accepted genus (2022-11-22) - taxonomic_resolution: genus -- find: Atriplex sp. B sensu Jacobs (1990) - replace: Atriplex sp. B - reason: match_19. Automatic alignment with species-level canonical name in APNI - when notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Banksia spinulosa var. collina-spinulosa intergrade - replace: Banksia spinulosa var. collina - reason: match_12. Automatic alignment with infraspecific canonical name in APC accepted - when notes are ignored (2022-11-22) - taxonomic_resolution: variety -- find: Bertya tasmanica variant ;qu;Glabrous ovary;qu; - replace: Bertya tasmanica var. Glabrous ovary (T.A.James 527 & M.J.Taylor) - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: variety -- find: Blechnum fullagarii - replace: Blechnum fullagari - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Caladenia sp. A sensu Harden (1993) - replace: Caladenia sp. A - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: species -- find: Centaurea sp. A sensu Murray (1992) - replace: Centaurea sp. A - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Cephalomanes atrovirens subsp. atrovirens - replace: Cephalomanes atrovirens - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Choretrum sp. Coxs Gap (B.J.Lepschi 4218 ;amp; T.R.Lally) - replace: Choretrum sp. Coxs Gap (B.J.Lepschi 4218 & T.R.Lally) - reason: match_10_fuzzy. Imprecise fuzzy alignment with accepted canonical name in - APC (2022-11-21) - taxonomic_resolution: species -- find: Cipadessa baccifera - replace: Cipadessa baccifera - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: species -- find: Crocosmia crocosmiiflora - replace: Crocosmia x crocosmiiflora - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Cyperus bowmannii - replace: Cyperus bowmanni - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Cyperus sp. Stockton (K.L.Wilson 10541) - replace: Cyperus sp. [Cyperus sp. Stockton (K.L.Wilson 10541); NHNSW_2022] - reason: match_20. Rewording name to be recognised as genus rank, with genus accepted - by APC (2022-11-22) - taxonomic_resolution: genus -- find: Dillwynia sp. Ebor (P.C.Jobson 5318 ;amp; S.A.Mills) - replace: Dillwynia sp. Ebor (P.C.Jobson 5318 & S.A.Mills) - reason: match_17_fuzzy. Imprecise fuzzy alignment with canonical name in APNI (2022-11-21) - taxonomic_resolution: species -- find: Epidendrum radicans x secundum hybrid complex - replace: Epidendrum radicans x Epidendrum secundum - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: species -- find: Eriochilus cucullatus complex - replace: Eriochilus cucullatus - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Eucalyptus conjuncta - replace: Eucalyptus x conjuncta - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Eucalyptus dealbata subsp. dealbata - replace: Eucalyptus dealbata var. dealbata - reason: match_06. Automatic alignment with synonymous term among known canonical - names APC (2022-11-21) - taxonomic_resolution: variety -- find: Flacourtia sp. shiptons flat l w jessup gj.d3200 - replace: Flacourtia sp. Shiptons Flat (L.W.Jessup+ GJD3200) - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Genoplesium cuspidatum - replace: Genoplesium sp. Cuspidata (L.M.Copeland 3858) - reason: match_15_fuzzy. Fuzzy match alignment with species-level canonical name - in `APC known` when everything except first 2 words ignored (2022-11-22) - taxonomic_resolution: species -- find: Genoplesium sp. Charmhaven (NSW896673) - replace: Genoplesium sp. Charmhaven (NSW 896673) - reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Glycine pacifica - replace: Glycine pacifica (Grace 946) - reason: match_19. Automatic alignment with species-level canonical name in APNI - when notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Hibbertia sp. B sensu Harden (1990) - replace: Hibbertia sp. B - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Hibbertia stricta subsp. stricta - replace: Hibbertia stricta var. stricta - reason: match_06. Automatic alignment with synonymous term among known canonical - names APC (2022-11-21) - taxonomic_resolution: variety -- find: Hoffmannseggia glauca - replace: Hoffmannseggia glauca - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: species -- find: Houttuynia cordata - replace: Houttuynia cordata - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: species -- find: Impatiens balfouri - replace: Impatiens balfourii - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Kunzea capitata subsp. capitata - replace: Kunzea capitata var. capitata - reason: match_06. Automatic alignment with synonymous term among known canonical - names APC (2022-11-21) - taxonomic_resolution: variety -- find: Lenwebbia sp. Main Range (P.R.Sharpe 4877) - replace: Lenwebbia sp. Main Range (P.R.Sharpe+ 4877) - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Lepidium sp. Cooma (J.H.Maiden NSW642748) - replace: Lepidium sp. [Lepidium sp. Cooma (J.H.Maiden NSW642748); NHNSW_2022] - reason: match_20. Rewording name to be recognised as genus rank, with genus accepted - by APC (2022-11-22) - taxonomic_resolution: genus -- find: Leucopogon lanceolatus var. lanceolatus - replace: Leucopogon lanceolatus - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Luzula densiflora subsp. densiflora - replace: Luzula densiflora - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Luzula flaccida subsp. flaccida - replace: Leucas flaccida var. flaccida - reason: match_10_fuzzy. Imprecise fuzzy alignment with known canonical name in APC - (2022-11-21) - taxonomic_resolution: variety -- find: Margyricarpus pinnatus - replace: Margyricarpus pinnatus - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: species -- find: Muehlenbeckia diclina subsp. Gippsland (R.O.Makinson 1007) Makinson - replace: Muehlenbeckia diclina subsp. Gippsland (R.O.Makinson 1007) - reason: match_05. Automatic alignment with scientific name in APC accepted list - (2022-11-21) - taxonomic_resolution: subspecies -- find: Muehlenbeckia diclina subsp. Pooncarie (W.E. Mulham W811) - replace: Muehlenbeckia diclina subsp. Pooncarie (W.E.Mulham W811) - reason: match_08. Automatic alignment with synonymous name in APNI (2022-11-21) - taxonomic_resolution: subspecies -- find: Myosotis laxa subsp. caespitosa - replace: Myosotis laxa subsp. cespitosa - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: subspecies -- find: Netrostylis sp. East Coast (D.E. Albrecht 597) - replace: Netrostylis sp. [Netrostylis sp. East Coast (D.E. Albrecht 597); NHNSW_2022] - reason: match_20. Rewording name to be recognised as genus rank, with genus in APNI - (2022-11-22) - taxonomic_resolution: genus -- find: Notelaea sp. A sensu Harden (1992) - replace: Notelaea sp. A - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Opuntia sp. sensu I.Telford (1984) - replace: Opuntia sp. [Opuntia sp. sensu I.Telford (1984); NHNSW_2022] - reason: match_20. Rewording name to be recognised as genus rank, with genus accepted - by APC (2022-11-22) - taxonomic_resolution: genus -- find: Owenia reliqua - replace: Owenia x reliqua - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Pelargonium asperum - replace: Pelargonium x asperum - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Pimelea neo-anglica - replace: Pimelea neoanglica - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-22) - taxonomic_resolution: species -- find: Polyscias sambucifolia subsp. Long leaflets (P.G.Neish 208) Vic. Herbarium - replace: Polyscias sambucifolia subsp. Long leaflets (P.G.Neish 208) - reason: match_05. Automatic alignment with scientific name in APC accepted list - (2022-11-21) - taxonomic_resolution: subspecies -- find: Pomaderris andromedifolia f. ;qu;andromedifolia;qu; - replace: Pomaderris andromedifolia subsp. andromedifolia - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: subspecies -- find: Pomaderris andromedifolia f. ;qu;narrow-leaved;qu; - replace: Pomaderris andromedifolia f. 'narrow-leaved' - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: form -- find: Pomaderris andromedifolia f. ;qu;small-leaved;qu; - replace: Pomaderris andromedifolia subsp. andromedifolia - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-21) - taxonomic_resolution: subspecies -- find: Potamogeton tricarinatus auct. non F.Muell. ;amp; A.Benn. ex A.Benn. - replace: Potamogeton tricarinatus - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Prasophyllum sp. A sensu Harden (1993) - replace: Prasophyllum sp. A - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Pultenaea sp. Dingo Creek (M.A.M.Renner 9176 ;amp; J.M.Cohen) - replace: Pultenaea sp. Dingo Creek (M.A.M.Renner 9176 & J.M.Cohen) - reason: match_17_fuzzy. Imprecise fuzzy alignment with canonical name in APNI (2022-11-22) - taxonomic_resolution: species -- find: Pultenaea sp. Narrabri (R.G.Coveny 8811 ;amp; S.K.Roy) - replace: Pultenaea sp. (Narrabri R.G.Coveny+ 8811) - reason: match_12. Automatic alignment with infraspecific canonical name in APC known - names when notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Pultenaea sp. Newnes (I.R.Telford 5072 ;amp; M.D.Crisp) - replace: Pultenaea sp. Newnes (I.R.Telford 5072 & M.D.Crisp) - reason: match_17_fuzzy. Imprecise fuzzy alignment with canonical name in APNI (2022-11-22) - taxonomic_resolution: species -- find: Pultenaea sp. Shadowgraph Bluff (T. ;amp; J.Whaite 3455) - replace: Pultenaea sp. Shadowgraph Bluff (T. & J.Whaite 3455) - reason: match_17_fuzzy. Imprecise fuzzy alignment with canonical name in APNI (2022-11-22) - taxonomic_resolution: species -- find: Quassia sp. Moonee Creek (King s.n., Nov 1949) - replace: Quassia sp. 'Moonee Creek' (King s.n., Nov 1949) - reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Radermachera sinica - replace: Radermachera sinica - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: species -- find: Rotheca myricoides subsp. myricoides - replace: Rotheca myricoides - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Rubus loganobaccus - replace: Rubus loganubaccus - reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Salix matsudana x alba - replace: Salix matsudana x Salix alba - reason: Manual alignment with canonical hybrid species name in APC (Elizabeth Wenk, - 2022-11-21) - taxonomic_resolution: species -- find: Salix x fragilis var. fragilis - replace: Salix x fragilis - reason: Manual alignment with canonical hybrid species name in APC (Elizabeth Wenk, - 2022-11-21) - taxonomic_resolution: species -- find: Salix x sepulcralis var. chrysocoma - replace: Salix x sepulcralis - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: species -- find: Salix x sepulcralis var. sepulcralis - replace: Salix x sepulcralis - reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22) - taxonomic_resolution: variety -- find: Salvinia molesta - replace: Salvinia x molesta - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Sarcocornia quinqueflora subsp. quinqueflora - replace: Salicornia quinqueflora subsp. quinqueflora - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: subspecies -- find: Scleranthus sp. Fitz;qu;s Hill (J.G.West 5342) - replace: Scleranthus sp. Fitz's Hill (J.G.West 5342) - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Sebaea zeyheri subsp. cleistantha - replace: Sebaea zeyheri - reason: match_19. Automatic alignment with species-level canonical name in APNI - when notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Sida sp. B sensu Harden (1990) - replace: Sida sp. B - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Sida sp. C sensu Harden (1990) - replace: Sida sp. C - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Sorghum almum - replace: Sorghum x almum - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Sorghum bicolor subsp. almum - replace: Sorghum bicolor subsp. x almum - reason: match_08. Automatic alignment with synonymous name in APNI (2022-11-22) - taxonomic_resolution: subspecies -- find: Sorghum bicolor subsp. drummondii - replace: Sorghum bicolor subsp. x drummondii - reason: match_12. Automatic alignment with infraspecific canonical name in APC known - names when notes are ignored (2022-11-22) - taxonomic_resolution: subspecies -- find: Spiraea x billiardii - replace: Spiraea x billardii - reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Suaeda sp. A sensu Harden (1990) - replace: Suaeda sp. A - reason: match_14. Automatic alignment with species-level name known by APC when - notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Teucrium sp. D sensu Conn (1992) - replace: Teucrium sp. D Flora of New South Wales (S.A.Horton 4114) - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-22) - taxonomic_resolution: species -- find: Thelymitra irregularis - replace: Thelymitra x irregularis - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: Thelymitra merraniae - replace: Thelymitra merranae - reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-21) - taxonomic_resolution: species -- find: Thelymitra truncata - replace: Thelymitra x truncata - reason: match_14. Automatic alignment with species-level canonical name in APC accepted - when notes are ignored (2022-11-21) - taxonomic_resolution: species -- find: X Triticosecale - replace: x Triticosecale - reason: Manual matched to genus for taxon that can't be matched to species (Elizabeth - Wenk, 2022-11-22) - taxonomic_resolution: genus -- find: Acacia melvillei-homalophylla - replace: Acacia sp. [Acacia melvillei-homalophylla; NHNSW_2023] - reason: Manual matched to genus for taxon that can't be matched to species (Elizabeth - Wenk, 2023-05-24) - taxonomic_resolution: genus -exclude_observations: -- variable: taxon_name - find: Salix humboldtiana cv. ;qu;Pyramidalis;qu;, Salix matsudana cv. ;qu;Tortuosa;qu;, - Cyrtomium falcatum ;qu;Rochfordii;qu; - reason: excluding cultivars -- variable: taxon_name - find: Cipadessa baccifera, Hoffmannseggia glauca, Houttuynia cordata, Margyricarpus - pinnatus, Radermachera sinica, x Triticosecale, Euryops virgineus, Fraxinus chinensis, - Ipomoea fimbriosepala, Persicaria chinensis, Pteris nipponica, Passiflora miniata - reason: non-native, non-naturalised species +taxonomic_updates: .na +exclude_observations: .na questions: .na diff --git a/tests/testthat/examples/Test_2023_4/output/contexts.csv b/tests/testthat/examples/Test_2023_4/output/contexts.csv index 9385c35d..11a524f7 100644 --- a/tests/testthat/examples/Test_2023_4/output/contexts.csv +++ b/tests/testthat/examples/Test_2023_4/output/contexts.csv @@ -3,33 +3,5 @@ Test_2023_4,trait scoring method,method_context,scored from text,Trait value sco Test_2023_4,trait scoring method,method_context,inferred_from_species,Trait value inferred from species-level taxon description.,method_context_id,03 Test_2023_4,trait scoring method,method_context,inferred_from_genus,Trait value inferred from genus-level taxon description.,method_context_id,02 Test_2023_4,trait scoring method,method_context,inferred_from_family,Trait value inferred from family-level taxon description.,method_context_id,01 -Test_2023_4,trait scoring method,method_context,inferred_from_trait,Trait value inferred from the value of a different trait.,, -Test_2023_4,trait scoring method,method_context,inferred_from_taxonomy,Trait value inferred from a higher level taxon description.,, Test_2023_4,entity measured,entity_context,unknown,,entity_context_id,02 -Test_2023_4,entity measured,entity_context,leaflet,,, -Test_2023_4,entity measured,entity_context,pinnae,,, -Test_2023_4,entity measured,entity_context,all,,, Test_2023_4,entity measured,entity_context,fruit,,entity_context_id,01 -Test_2023_4,entity measured,entity_context,infructescence,,, -Test_2023_4,entity measured,entity_context,valve,,, -Test_2023_4,entity measured,entity_context,female_cones,,, -Test_2023_4,entity measured,entity_context,disc_achenes,,, -Test_2023_4,entity measured,entity_context,ray_achenes,,, -Test_2023_4,entity measured,entity_context,leaf,,, -Test_2023_4,entity measured,entity_context,fertile_leaf,,, -Test_2023_4,entity measured,entity_context,sterile_leaf,,, -Test_2023_4,entity measured,entity_context,cauline_leaf,,, -Test_2023_4,entity measured,entity_context,basal_leaf,,, -Test_2023_4,entity measured,entity_context,upper_leaf,,, -Test_2023_4,entity measured,entity_context,stem_leaf,,, -Test_2023_4,entity measured,entity_context,basal_pinnae,,, -Test_2023_4,entity measured,entity_context,phyllode,,, -Test_2023_4,entity measured,entity_context,cladode,,, -Test_2023_4,entity measured,entity_context,fertile_pinnule,,, -Test_2023_4,entity measured,entity_context,sterile_pinnule,,, -Test_2023_4,entity measured,entity_context,lower_leaf,,, -Test_2023_4,entity measured,entity_context,lateral_leaf,,, -Test_2023_4,entity measured,entity_context,emergent_leaf,,, -Test_2023_4,entity measured,entity_context,submerged_leaf,,, -Test_2023_4,entity measured,entity_context,upper_pinnae,,, -Test_2023_4,entity measured,entity_context,scale_leaf,,, diff --git a/tests/testthat/examples/Test_2023_4/output/taxa.csv b/tests/testthat/examples/Test_2023_4/output/taxa.csv index 7e850333..ebc83dea 100644 --- a/tests/testthat/examples/Test_2023_4/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_4/output/taxa.csv @@ -1,7 +1,7 @@ original_name,taxon_name,taxon_name_alternatives,genus,family,taxon_rank,taxonomic_dataset,taxonomic_status,subclass,taxon_distribution,scientific_name,taxon_id,taxon_ID_genus,scientific_name_id,canonical_name,cleaned_scientific_name_id,taxon_id_family,trinomial,binomial,establishment_means Abildgaardia ovata,Abildgaardia ovata,,Abildgaardia,Cyperaceae,species,APC,accepted,Magnoliidae,"NT, Qld, NSW",Abildgaardia ovata (Burm.f.) Kral,https://id.biodiversity.org.au/node/apni/2919627,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/150737,Abildgaardia ovata,https://id.biodiversity.org.au/name/apni/150737,https://id.biodiversity.org.au/taxon/apni/51460154,,Abildgaardia ovata,native Acacia alpina,Acacia alpina,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Acacia alpina F.Muell.,https://id.biodiversity.org.au/node/apni/2907301,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/58263,Acacia alpina,https://id.biodiversity.org.au/name/apni/58263,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia alpina,native -Acacia beadleana,Acacia beadleana,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Acacia beadleana R.H.Jones & J.J.Bruhl,https://id.biodiversity.org.au/node/apni/2902581,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/198624,Acacia beadleana,https://id.biodiversity.org.au/name/apni/165277,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia beadleana,native +Acacia beadleana,Acacia beadleana,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Acacia beadleana R.H.Jones & J.J.Bruhl,https://id.biodiversity.org.au/node/apni/2902581,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/198624,Acacia beadleana,https://id.biodiversity.org.au/name/apni/244690,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia beadleana,native Acacia bulgaensis,Acacia bulgaensis,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Acacia bulgaensis Tindale & S.J.Davies,https://id.biodiversity.org.au/node/apni/2889179,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/117995,Acacia bulgaensis,https://id.biodiversity.org.au/name/apni/117995,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia bulgaensis,native Acacia caroleae,Acacia caroleae,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acacia caroleae Pedley,https://id.biodiversity.org.au/node/apni/2894332,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/60225,Acacia caroleae,https://id.biodiversity.org.au/name/apni/60225,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia caroleae,native Acacia crassa,Acacia crassa,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Acacia crassa Pedley,https://id.biodiversity.org.au/node/apni/2919707,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/60887,Acacia crassa,https://id.biodiversity.org.au/name/apni/60887,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia crassa,native @@ -19,16 +19,16 @@ Alectryon coriaceus,Alectryon coriaceus,,Alectryon,Sapindaceae,species,APC,accep Alectryon oleifolius,Alectryon oleifolius,,Alectryon,Sapindaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Alectryon oleifolius (Desf.) S.T.Reynolds,https://id.biodiversity.org.au/node/apni/2900874,https://id.biodiversity.org.au/taxon/apni/51299789,https://id.biodiversity.org.au/name/apni/81066,Alectryon oleifolius,https://id.biodiversity.org.au/name/apni/81066,https://id.biodiversity.org.au/taxon/apni/51447212,,Alectryon oleifolius,native Alectryon subdentatus,Alectryon subdentatus,,Alectryon,Sapindaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Alectryon subdentatus (F.Muell. ex Benth.) Radlk.,https://id.biodiversity.org.au/node/apni/2890534,https://id.biodiversity.org.au/taxon/apni/51299789,https://id.biodiversity.org.au/name/apni/81114,Alectryon subdentatus,https://id.biodiversity.org.au/name/apni/81114,https://id.biodiversity.org.au/taxon/apni/51447212,,Alectryon subdentatus,native Amyema preissii,Amyema preissii,,Amyema,Loranthaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Amyema preissii (Miq.) Tiegh.,https://id.biodiversity.org.au/node/apni/2888430,https://id.biodiversity.org.au/taxon/apni/51438795,https://id.biodiversity.org.au/name/apni/87461,Amyema preissii,https://id.biodiversity.org.au/name/apni/87461,https://id.biodiversity.org.au/taxon/apni/51438796,,Amyema preissii,native -Angophora leiocarpa,Angophora leiocarpa,,Angophora,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Angophora leiocarpa (L.A.S.Johnson ex G.J.Leach) K.R.Thiele & Ladiges,https://id.biodiversity.org.au/node/apni/2894339,https://id.biodiversity.org.au/taxon/apni/51439560,https://id.biodiversity.org.au/name/apni/123435,Angophora leiocarpa,https://id.biodiversity.org.au/name/apni/123435,https://id.biodiversity.org.au/taxon/apni/51702983,,Angophora leiocarpa,native -Arbutus unedo,Arbutus unedo,,Arbutus,Ericaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (doubtfully naturalised), NSW (doubtfully naturalised), ACT (doubtfully naturalised), Vic (naturalised), Tas (doubtfully naturalised)",Arbutus unedo L.,https://id.biodiversity.org.au/node/apni/2904939,https://id.biodiversity.org.au/node/apni/2892910,https://id.biodiversity.org.au/name/apni/98540,Arbutus unedo,https://id.biodiversity.org.au/name/apni/98540,https://id.biodiversity.org.au/taxon/apni/51436079,,Arbutus unedo,naturalised +Angophora leiocarpa,Angophora leiocarpa,,Angophora,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Angophora leiocarpa (L.A.S.Johnson ex G.J.Leach) K.R.Thiele & Ladiges,https://id.biodiversity.org.au/node/apni/2894339,https://id.biodiversity.org.au/taxon/apni/51439560,https://id.biodiversity.org.au/name/apni/123435,Angophora leiocarpa,https://id.biodiversity.org.au/name/apni/123435,https://id.biodiversity.org.au/taxon/apni/51738744,,Angophora leiocarpa,native +Arbutus unedo,Arbutus unedo,,Arbutus,Ericaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (doubtfully naturalised), NSW (doubtfully naturalised), ACT (doubtfully naturalised), Vic (naturalised), Tas (doubtfully naturalised)",Arbutus unedo L.,https://id.biodiversity.org.au/node/apni/2904939,https://id.biodiversity.org.au/node/apni/2892910,https://id.biodiversity.org.au/name/apni/98540,Arbutus unedo,https://id.biodiversity.org.au/name/apni/98540,https://id.biodiversity.org.au/taxon/apni/51738121,,Arbutus unedo,naturalised Australina pusilla,Australina pusilla,,Australina,Urticaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic, Tas",Australina pusilla (Poir.) Gaudich.,https://id.biodiversity.org.au/node/apni/2913845,https://id.biodiversity.org.au/node/apni/2907879,https://id.biodiversity.org.au/name/apni/113875,Australina pusilla,https://id.biodiversity.org.au/name/apni/113875,https://id.biodiversity.org.au/taxon/apni/51662052,,Australina pusilla,native Burmannia disticha,Burmannia disticha,,Burmannia,Burmanniaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Burmannia disticha L.,https://id.biodiversity.org.au/node/apni/2900088,https://id.biodiversity.org.au/node/apni/2915743,https://id.biodiversity.org.au/name/apni/70173,Burmannia disticha,https://id.biodiversity.org.au/name/apni/70173,https://id.biodiversity.org.au/node/apni/2887196,,Burmannia disticha,native Bursaria spinosa subsp. spinosa,Bursaria spinosa subsp. spinosa,,Bursaria,Pittosporaceae,subspecies,APC,accepted,Magnoliidae,"SA, Qld, NSW, Vic, Tas",Bursaria spinosa Cav. subsp. spinosa,https://id.biodiversity.org.au/taxon/apni/51442337,https://id.biodiversity.org.au/taxon/apni/51442339,https://id.biodiversity.org.au/name/apni/142036,Bursaria spinosa subsp. spinosa,https://id.biodiversity.org.au/name/apni/142036,https://id.biodiversity.org.au/taxon/apni/51442315,Bursaria spinosa subsp. spinosa,Bursaria spinosa,native Calendula arvensis,Calendula arvensis,,Calendula,Asteraceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (naturalised), Tas (naturalised)",Calendula arvensis L.,https://id.biodiversity.org.au/node/apni/2891878,https://id.biodiversity.org.au/node/apni/2893748,https://id.biodiversity.org.au/name/apni/95042,Calendula arvensis,https://id.biodiversity.org.au/name/apni/95042,https://id.biodiversity.org.au/taxon/apni/51695393,,Calendula arvensis,naturalised -Callistemon purpurascens,Callistemon purpurascens,,Callistemon,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Callistemon purpurascens S.M.Douglas & S.David,https://id.biodiversity.org.au/taxon/apni/51288952,https://id.biodiversity.org.au/taxon/apni/51439657,https://id.biodiversity.org.au/name/apni/4630985,Callistemon purpurascens,https://id.biodiversity.org.au/name/apni/4630985,https://id.biodiversity.org.au/taxon/apni/51702983,,Callistemon purpurascens,native +Callistemon purpurascens,Callistemon purpurascens,,Callistemon,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Callistemon purpurascens S.M.Douglas & S.David,https://id.biodiversity.org.au/taxon/apni/51288952,https://id.biodiversity.org.au/taxon/apni/51439657,https://id.biodiversity.org.au/name/apni/4630985,Callistemon purpurascens,https://id.biodiversity.org.au/name/apni/4630985,https://id.biodiversity.org.au/taxon/apni/51738744,,Callistemon purpurascens,native Apophyllum anomalum,Capparis anomala,,Capparis,Capparaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Capparis anomala (F.Muell.) Byng & Christenh.,https://id.biodiversity.org.au/taxon/apni/51432888,https://id.biodiversity.org.au/taxon/apni/51432886,https://id.biodiversity.org.au/name/apni/50561973,Capparis anomala,https://id.biodiversity.org.au/name/apni/97697,https://id.biodiversity.org.au/taxon/apni/51433682,,Capparis anomala,native Carex leporina,Carex leporina,,Carex,Cyperaceae,species,APC,accepted,Magnoliidae,"NSW (naturalised), NI (naturalised), Vic (naturalised), Tas (naturalised)",Carex leporina L.,https://id.biodiversity.org.au/node/apni/2902492,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/135236,Carex leporina,https://id.biodiversity.org.au/name/apni/135236,https://id.biodiversity.org.au/taxon/apni/51460154,,Carex leporina,naturalised -Carex cephalotes,Carex pyrenaica var. cephalotes,,Carex,Cyperaceae,variety,APC,accepted,Magnoliidae,"NSW, Vic, Tas",Carex pyrenaica var. cephalotes (F.Muell.) Kük.,https://id.biodiversity.org.au/node/apni/2892693,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/111655,Carex pyrenaica var. cephalotes,https://id.biodiversity.org.au/name/apni/110600,https://id.biodiversity.org.au/taxon/apni/51460154,Carex pyrenaica var. cephalotes,Carex pyrenaica,native +Carex cephalotes,Carex pyrenaica var. cephalotes,,Carex,Cyperaceae,variety,APC,accepted,Magnoliidae,"NSW, Vic, Tas",Carex pyrenaica var. cephalotes (F.Muell.) Kük.,https://id.biodiversity.org.au/node/apni/2892693,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/111655,Carex pyrenaica var. cephalotes,https://id.biodiversity.org.au/name/apni/235569,https://id.biodiversity.org.au/taxon/apni/51460154,Carex pyrenaica var. cephalotes,Carex pyrenaica,native Carex raleighii,Carex raleighii,,Carex,Cyperaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic, Tas",Carex raleighii Nelmes,https://id.biodiversity.org.au/node/apni/2910405,https://id.biodiversity.org.au/taxon/apni/51460185,https://id.biodiversity.org.au/name/apni/111690,Carex raleighii,https://id.biodiversity.org.au/name/apni/111690,https://id.biodiversity.org.au/taxon/apni/51460154,,Carex raleighii,native Carmichaelia exsul,Carmichaelia exsul,,Carmichaelia,Fabaceae,species,APC,accepted,Magnoliidae,LHI,Carmichaelia exsul F.Muell.,https://id.biodiversity.org.au/node/apni/2915240,https://id.biodiversity.org.au/node/apni/8138105,https://id.biodiversity.org.au/name/apni/112335,Carmichaelia exsul,https://id.biodiversity.org.au/name/apni/112335,https://id.biodiversity.org.au/taxon/apni/51702961,,Carmichaelia exsul,native Cassinia compacta,Cassinia compacta,Cassinia accipitrum (pro parte misapplied) | Cassinia straminea (pro parte misapplied) | Cassinia telfordii (pro parte misapplied) | Cassinia accipitrum (misapplied),Cassinia,Asteraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Cassinia compacta F.Muell.,https://id.biodiversity.org.au/node/apni/2909860,https://id.biodiversity.org.au/taxon/apni/51431788,https://id.biodiversity.org.au/name/apni/54723,Cassinia compacta [alternative possible names: Cassinia accipitrum (pro parte misapplied) | Cassinia straminea (pro parte misapplied) | Cassinia telfordii (pro parte misapplied) | Cassinia accipitrum (misapplied)],,https://id.biodiversity.org.au/taxon/apni/51695393,,Cassinia compacta,native @@ -43,8 +43,8 @@ Convolvulus farinosus,Convolvulus farinosus,,Convolvulus,Convolvulaceae,species, Coprosma niphophila,Coprosma niphophila,,Coprosma,Rubiaceae,species,APC,accepted,Magnoliidae,NSW,Coprosma niphophila Orchard,https://id.biodiversity.org.au/node/apni/2910618,https://id.biodiversity.org.au/node/apni/8135850,https://id.biodiversity.org.au/name/apni/78856,Coprosma niphophila,https://id.biodiversity.org.au/name/apni/78856,https://id.biodiversity.org.au/taxon/apni/51446612,,Coprosma niphophila,native Coprosma nivalis,Coprosma nivalis,,Coprosma,Rubiaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Coprosma nivalis W.R.B.Oliv.,https://id.biodiversity.org.au/node/apni/2915002,https://id.biodiversity.org.au/node/apni/8135850,https://id.biodiversity.org.au/name/apni/78866,Coprosma nivalis,https://id.biodiversity.org.au/name/apni/78866,https://id.biodiversity.org.au/taxon/apni/51446612,,Coprosma nivalis,native Correa alba,Correa alba,,Correa,Rutaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Correa alba Andrews,https://id.biodiversity.org.au/node/apni/2906721,https://id.biodiversity.org.au/taxon/apni/51447015,https://id.biodiversity.org.au/name/apni/80283,Correa alba,https://id.biodiversity.org.au/name/apni/80283,https://id.biodiversity.org.au/taxon/apni/51461748,,Correa alba,native -Corymbia citriodora,Corymbia citriodora,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (doubtfully naturalised), Qld, NSW (native and naturalised), Vic (naturalised)",Corymbia citriodora (Hook.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2912509,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119387,Corymbia citriodora,https://id.biodiversity.org.au/name/apni/119387,https://id.biodiversity.org.au/taxon/apni/51702983,,Corymbia citriodora,native and naturalised -Corymbia eximia,Corymbia eximia,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Corymbia eximia (Schauer) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2909833,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119402,Corymbia eximia,https://id.biodiversity.org.au/name/apni/119402,https://id.biodiversity.org.au/taxon/apni/51702983,,Corymbia eximia,native +Corymbia citriodora,Corymbia citriodora,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (doubtfully naturalised), Qld, NSW (native and naturalised), Vic (naturalised)",Corymbia citriodora (Hook.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2912509,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119387,Corymbia citriodora,https://id.biodiversity.org.au/name/apni/119387,https://id.biodiversity.org.au/taxon/apni/51738744,,Corymbia citriodora,native and naturalised +Corymbia eximia,Corymbia eximia,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Corymbia eximia (Schauer) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2909833,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119402,Corymbia eximia,https://id.biodiversity.org.au/name/apni/119402,https://id.biodiversity.org.au/taxon/apni/51738744,,Corymbia eximia,native Crassula decumbens,Crassula decumbens,,Crassula,Crassulaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, ACT, Vic, Tas",Crassula decumbens Thunb.,https://id.biodiversity.org.au/node/apni/2889646,https://id.biodiversity.org.au/node/apni/2903354,https://id.biodiversity.org.au/name/apni/83855,Crassula decumbens,https://id.biodiversity.org.au/name/apni/83855,https://id.biodiversity.org.au/taxon/apni/51270792,,Crassula decumbens,native Crassula peduncularis,Crassula peduncularis,,Crassula,Crassulaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, ACT, Vic, Tas",Crassula peduncularis (Sm.) F.Meigen,https://id.biodiversity.org.au/node/apni/2895654,https://id.biodiversity.org.au/node/apni/2903354,https://id.biodiversity.org.au/name/apni/84005,Crassula peduncularis,https://id.biodiversity.org.au/name/apni/84005,https://id.biodiversity.org.au/taxon/apni/51270792,,Crassula peduncularis,native Crotalaria brevis,Crotalaria brevis,,Crotalaria,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Crotalaria brevis Domin,https://id.biodiversity.org.au/node/apni/2906180,https://id.biodiversity.org.au/taxon/apni/51300011,https://id.biodiversity.org.au/name/apni/85578,Crotalaria brevis,https://id.biodiversity.org.au/name/apni/85578,https://id.biodiversity.org.au/taxon/apni/51702961,,Crotalaria brevis,native @@ -65,31 +65,31 @@ Dillwynia floribunda,Dillwynia floribunda,,Dillwynia,Fabaceae,species,APC,accept Dinosperma erythrococcum,Dinosperma erythrococcum,,Dinosperma,Rutaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Dinosperma erythrococcum (F.Muell.) T.G.Hartley,https://id.biodiversity.org.au/node/apni/2897246,https://id.biodiversity.org.au/node/apni/2900591,https://id.biodiversity.org.au/name/apni/157718,Dinosperma erythrococcum,https://id.biodiversity.org.au/name/apni/157718,https://id.biodiversity.org.au/taxon/apni/51461748,,Dinosperma erythrococcum,native Dodonaea petiolaris,Dodonaea petiolaris,Dodonaea viscosa subsp. mucronata (pro parte misapplied),Dodonaea,Sapindaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Dodonaea petiolaris F.Muell.,https://id.biodiversity.org.au/node/apni/2921131,https://id.biodiversity.org.au/taxon/apni/51447268,https://id.biodiversity.org.au/name/apni/72184,Dodonaea petiolaris [alternative possible names: Dodonaea viscosa subsp. mucronata (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51447212,,Dodonaea petiolaris,native Dodonaea truncatiales,Dodonaea truncatiales,Dodonaea heteromorpha (pro parte misapplied) | Dodonaea heteromorpha (misapplied),Dodonaea,Sapindaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Dodonaea truncatiales F.Muell.,https://id.biodiversity.org.au/node/apni/7870563,https://id.biodiversity.org.au/taxon/apni/51447268,https://id.biodiversity.org.au/name/apni/72648,Dodonaea truncatiales [alternative possible names: Dodonaea heteromorpha (pro parte misapplied) | Dodonaea heteromorpha (misapplied)],,https://id.biodiversity.org.au/taxon/apni/51447212,,Dodonaea truncatiales,native -Dovyalis caffra,Dovyalis caffra,,Dovyalis,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised)",Dovyalis caffra (Hook.f. & Harv.) Hook.f.,https://id.biodiversity.org.au/node/apni/2888866,https://id.biodiversity.org.au/node/apni/2897632,https://id.biodiversity.org.au/name/apni/199157,Dovyalis caffra,https://id.biodiversity.org.au/name/apni/86110,https://id.biodiversity.org.au/taxon/apni/51436847,,Dovyalis caffra,naturalised +Dovyalis caffra,Dovyalis caffra,,Dovyalis,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (naturalised), NSW (naturalised)",Dovyalis caffra (Hook.f. & Harv.) Hook.f.,https://id.biodiversity.org.au/node/apni/2888866,https://id.biodiversity.org.au/node/apni/2897632,https://id.biodiversity.org.au/name/apni/199157,Dovyalis caffra,https://id.biodiversity.org.au/name/apni/199157,https://id.biodiversity.org.au/taxon/apni/51436847,,Dovyalis caffra,naturalised Elaeocarpus grandis,Elaeocarpus grandis,,Elaeocarpus,Elaeocarpaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Elaeocarpus grandis F.Muell.,https://id.biodiversity.org.au/node/apni/2895259,https://id.biodiversity.org.au/taxon/apni/51435153,https://id.biodiversity.org.au/name/apni/115772,Elaeocarpus grandis,https://id.biodiversity.org.au/name/apni/115772,https://id.biodiversity.org.au/taxon/apni/51632282,,Elaeocarpus grandis,native Eleocharis pallens,Eleocharis pallens,,Eleocharis,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Eleocharis pallens S.T.Blake,https://id.biodiversity.org.au/node/apni/2899827,https://id.biodiversity.org.au/taxon/apni/51434435,https://id.biodiversity.org.au/name/apni/67140,Eleocharis pallens,https://id.biodiversity.org.au/name/apni/67140,https://id.biodiversity.org.au/taxon/apni/51460154,,Eleocharis pallens,native Endiandra globosa,Endiandra globosa,,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Endiandra globosa Maiden & Betche,https://id.biodiversity.org.au/node/apni/2901094,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111780,Endiandra globosa,https://id.biodiversity.org.au/name/apni/111780,https://id.biodiversity.org.au/taxon/apni/51438397,,Endiandra globosa,native Endiandra muelleri,Endiandra muelleri,,Endiandra,Lauraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Endiandra muelleri Meisn.,https://id.biodiversity.org.au/node/apni/2903619,https://id.biodiversity.org.au/taxon/apni/51438414,https://id.biodiversity.org.au/name/apni/111996,Endiandra muelleri,https://id.biodiversity.org.au/name/apni/111996,https://id.biodiversity.org.au/taxon/apni/51438397,,Endiandra muelleri,native Epilobium gunnianum,Epilobium gunnianum,,Epilobium,Onagraceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic, Tas",Epilobium gunnianum Hausskn.,https://id.biodiversity.org.au/node/apni/2903068,https://id.biodiversity.org.au/taxon/apni/51440863,https://id.biodiversity.org.au/name/apni/105579,Epilobium gunnianum,https://id.biodiversity.org.au/name/apni/105579,https://id.biodiversity.org.au/taxon/apni/51440864,,Epilobium gunnianum,native -Eremophila deserti,Eremophila deserti,,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila deserti (A.Cunn. ex Benth.) Chinnock,https://id.biodiversity.org.au/node/apni/2897363,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/123426,Eremophila deserti,https://id.biodiversity.org.au/name/apni/123426,https://id.biodiversity.org.au/taxon/apni/51461527,,Eremophila deserti,native -Eremophila oppositifolia,Eremophila oppositifolia,,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila oppositifolia R.Br.,https://id.biodiversity.org.au/node/apni/7951462,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/114575,Eremophila oppositifolia,https://id.biodiversity.org.au/name/apni/114575,https://id.biodiversity.org.au/taxon/apni/51461527,,Eremophila oppositifolia,native +Eremophila deserti,Eremophila deserti,,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila deserti (A.Cunn. ex Benth.) Chinnock,https://id.biodiversity.org.au/node/apni/2897363,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/123426,Eremophila deserti,https://id.biodiversity.org.au/name/apni/123426,https://id.biodiversity.org.au/taxon/apni/51734003,,Eremophila deserti,native +Eremophila oppositifolia,Eremophila oppositifolia,,Eremophila,Scrophulariaceae,species,APC,accepted,Magnoliidae,"WA, SA, Qld, NSW, Vic",Eremophila oppositifolia R.Br.,https://id.biodiversity.org.au/node/apni/7951462,https://id.biodiversity.org.au/taxon/apni/51461526,https://id.biodiversity.org.au/name/apni/114575,Eremophila oppositifolia,https://id.biodiversity.org.au/name/apni/114575,https://id.biodiversity.org.au/taxon/apni/51734003,,Eremophila oppositifolia,native Erigeron conyzoides,Erigeron conyzoides,,Erigeron,Asteraceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Erigeron conyzoides F.Muell.,https://id.biodiversity.org.au/node/apni/2913579,https://id.biodiversity.org.au/taxon/apni/51432118,https://id.biodiversity.org.au/name/apni/73195,Erigeron conyzoides,https://id.biodiversity.org.au/name/apni/239637,https://id.biodiversity.org.au/taxon/apni/51695393,,Erigeron conyzoides,native Erythroxylum australe,Erythroxylum australe,Erythroxylum sp. Splityard Creek (L.Pedley 5360) (pro parte misapplied),Erythroxylum,Erythroxylaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Erythroxylum australe F.Muell.,https://id.biodiversity.org.au/node/apni/2912212,https://id.biodiversity.org.au/node/apni/2919669,https://id.biodiversity.org.au/name/apni/75959,Erythroxylum australe [alternative possible names: Erythroxylum sp. Splityard Creek (L.Pedley 5360) (pro parte misapplied)],,https://id.biodiversity.org.au/node/apni/2893375,,Erythroxylum australe,native Escallonia bifida,Escallonia bifida,,Escallonia,Escalloniaceae,species,APC,accepted,Magnoliidae,NSW (naturalised),Escallonia bifida Link & Otto,https://id.biodiversity.org.au/taxon/apni/51435441,https://id.biodiversity.org.au/taxon/apni/51435442,https://id.biodiversity.org.au/name/apni/116602,Escallonia bifida,https://id.biodiversity.org.au/name/apni/116602,https://id.biodiversity.org.au/taxon/apni/51435443,,Escallonia bifida,naturalised -Eucalyptus badjensis,Eucalyptus badjensis,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus badjensis Beuzev. & M.B.Welch,https://id.biodiversity.org.au/node/apni/2912724,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/57323,Eucalyptus badjensis,https://id.biodiversity.org.au/name/apni/57323,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus badjensis,native -Eucalyptus camphora,Eucalyptus camphora,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic",Eucalyptus camphora R.T.Baker,https://id.biodiversity.org.au/node/apni/2891665,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/94439,Eucalyptus camphora,https://id.biodiversity.org.au/name/apni/94439,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus camphora,native -Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus dorrigoensis (Blakely) L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2903351,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118668,Eucalyptus dorrigoensis,https://id.biodiversity.org.au/name/apni/118668,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus dorrigoensis,native -Eucalyptus yangoura,Eucalyptus globoidea,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus globoidea Blakely,https://id.biodiversity.org.au/node/apni/5270850,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/61141,Eucalyptus globoidea,https://id.biodiversity.org.au/name/apni/92470,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus globoidea,native -Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,,Eucalyptus,Myrtaceae,subspecies,APC,accepted,Magnoliidae,"SA, NSW, Vic",Eucalyptus leucoxylon subsp. pruinosa (F.Muell. ex Miq.) Boland,https://id.biodiversity.org.au/node/apni/2908258,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/77407,Eucalyptus leucoxylon subsp. pruinosa,https://id.biodiversity.org.au/name/apni/77407,https://id.biodiversity.org.au/taxon/apni/51702983,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon,native -Eucalyptus muelleriana,Eucalyptus muelleriana,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus muelleriana A.W.Howitt,https://id.biodiversity.org.au/node/apni/2888508,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/56840,Eucalyptus muelleriana,https://id.biodiversity.org.au/name/apni/56840,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus muelleriana,native -Eucalyptus nandewarica,Eucalyptus nandewarica,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus nandewarica L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2897688,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118852,Eucalyptus nandewarica,https://id.biodiversity.org.au/name/apni/118852,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus nandewarica,native -Eucalyptus olida,Eucalyptus olida,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus olida L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2914019,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118797,Eucalyptus olida,https://id.biodiversity.org.au/name/apni/118797,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus olida,native -Eucalyptus pulverulenta,Eucalyptus pulverulenta,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus pulverulenta Sims,https://id.biodiversity.org.au/taxon/apni/51440675,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/106609,Eucalyptus pulverulenta,https://id.biodiversity.org.au/name/apni/106609,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus pulverulenta,native -Eucalyptus recurva,Eucalyptus recurva,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus recurva Crisp,https://id.biodiversity.org.au/node/apni/2892273,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/101532,Eucalyptus recurva,https://id.biodiversity.org.au/name/apni/101532,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus recurva,native -Eucalyptus rossii,Eucalyptus rossii,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus rossii R.T.Baker & H.G.Sm.,https://id.biodiversity.org.au/node/apni/2900822,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/58182,Eucalyptus rossii,https://id.biodiversity.org.au/name/apni/58182,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus rossii,native -Eucalyptus scias,Eucalyptus scias,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus scias L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2893839,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/118833,Eucalyptus scias,https://id.biodiversity.org.au/name/apni/118833,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus scias,native -Eucalyptus viminalis,Eucalyptus viminalis,Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied),Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic, Tas",Eucalyptus viminalis Labill.,https://id.biodiversity.org.au/taxon/apni/51290421,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/65838,Eucalyptus viminalis [alternative possible names: Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus viminalis,native -Eucalyptus youmanii,Eucalyptus youmanii,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Eucalyptus youmanii Blakely & McKie,https://id.biodiversity.org.au/node/apni/2916227,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/92496,Eucalyptus youmanii,https://id.biodiversity.org.au/name/apni/92496,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus youmanii,native +Eucalyptus badjensis,Eucalyptus badjensis,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus badjensis Beuzev. & M.B.Welch,https://id.biodiversity.org.au/node/apni/2912724,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/57323,Eucalyptus badjensis,https://id.biodiversity.org.au/name/apni/57323,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus badjensis,native +Eucalyptus camphora,Eucalyptus camphora,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic",Eucalyptus camphora R.T.Baker,https://id.biodiversity.org.au/taxon/apni/51738742,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/94439,Eucalyptus camphora,https://id.biodiversity.org.au/name/apni/94439,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus camphora,native +Eucalyptus dorrigoensis,Eucalyptus dorrigoensis,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus dorrigoensis (Blakely) L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2903351,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/118668,Eucalyptus dorrigoensis,https://id.biodiversity.org.au/name/apni/118668,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus dorrigoensis,native +Eucalyptus yangoura,Eucalyptus globoidea,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus globoidea Blakely,https://id.biodiversity.org.au/node/apni/5270850,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/61141,Eucalyptus globoidea,https://id.biodiversity.org.au/name/apni/92470,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus globoidea,native +Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon subsp. pruinosa,,Eucalyptus,Myrtaceae,subspecies,APC,accepted,Magnoliidae,"SA, NSW, Vic",Eucalyptus leucoxylon subsp. pruinosa (F.Muell. ex Miq.) Boland,https://id.biodiversity.org.au/node/apni/2908258,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/77407,Eucalyptus leucoxylon subsp. pruinosa,https://id.biodiversity.org.au/name/apni/77407,https://id.biodiversity.org.au/taxon/apni/51738744,Eucalyptus leucoxylon subsp. pruinosa,Eucalyptus leucoxylon,native +Eucalyptus muelleriana,Eucalyptus muelleriana,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Eucalyptus muelleriana A.W.Howitt,https://id.biodiversity.org.au/node/apni/2888508,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/56840,Eucalyptus muelleriana,https://id.biodiversity.org.au/name/apni/56840,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus muelleriana,native +Eucalyptus nandewarica,Eucalyptus nandewarica,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus nandewarica L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2897688,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/118852,Eucalyptus nandewarica,https://id.biodiversity.org.au/name/apni/118852,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus nandewarica,native +Eucalyptus olida,Eucalyptus olida,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus olida L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2914019,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/118797,Eucalyptus olida,https://id.biodiversity.org.au/name/apni/118797,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus olida,native +Eucalyptus pulverulenta,Eucalyptus pulverulenta,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus pulverulenta Sims,https://id.biodiversity.org.au/taxon/apni/51440675,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/106609,Eucalyptus pulverulenta,https://id.biodiversity.org.au/name/apni/106609,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus pulverulenta,native +Eucalyptus recurva,Eucalyptus recurva,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus recurva Crisp,https://id.biodiversity.org.au/node/apni/2892273,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/101532,Eucalyptus recurva,https://id.biodiversity.org.au/name/apni/101532,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus recurva,native +Eucalyptus rossii,Eucalyptus rossii,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Eucalyptus rossii R.T.Baker & H.G.Sm.,https://id.biodiversity.org.au/node/apni/2900822,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/58182,Eucalyptus rossii,https://id.biodiversity.org.au/name/apni/58182,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus rossii,native +Eucalyptus scias,Eucalyptus scias,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NSW,Eucalyptus scias L.A.S.Johnson & K.D.Hill,https://id.biodiversity.org.au/node/apni/2893839,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/118833,Eucalyptus scias,https://id.biodiversity.org.au/name/apni/118833,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus scias,native +Eucalyptus viminalis,Eucalyptus viminalis,Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied),Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic, Tas",Eucalyptus viminalis Labill.,https://id.biodiversity.org.au/taxon/apni/51290421,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/65838,Eucalyptus viminalis [alternative possible names: Corymbia tessellaris (taxonomic synonym) | Eucalyptus dalrympleana subsp. dalrympleana (pro parte misapplied) | Eucalyptus diversifolia subsp. diversifolia (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus viminalis,native +Eucalyptus youmanii,Eucalyptus youmanii,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Eucalyptus youmanii Blakely & McKie,https://id.biodiversity.org.au/node/apni/2916227,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/92496,Eucalyptus youmanii,https://id.biodiversity.org.au/name/apni/92496,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus youmanii,native Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata var. queenslandica,,Euphorbia,Euphorbiaceae,variety,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Euphorbia inappendiculata var. queenslandica Domin,https://id.biodiversity.org.au/node/apni/7200245,https://id.biodiversity.org.au/taxon/apni/51435529,https://id.biodiversity.org.au/name/apni/92612,Euphorbia inappendiculata var. queenslandica,https://id.biodiversity.org.au/name/apni/92612,https://id.biodiversity.org.au/taxon/apni/51442249,Euphorbia inappendiculata var. queenslandica,Euphorbia inappendiculata,native Exocarpos homalocladus,Exocarpos homalocladus,,Exocarpos,Santalaceae,species,APC,accepted,Magnoliidae,LHI,Exocarpos homalocladus C.Moore & F.Muell.,https://id.biodiversity.org.au/node/apni/2898548,https://id.biodiversity.org.au/taxon/apni/51447153,https://id.biodiversity.org.au/name/apni/58158,Exocarpos homalocladus,https://id.biodiversity.org.au/name/apni/58158,https://id.biodiversity.org.au/taxon/apni/51447154,,Exocarpos homalocladus,native Exocarpos sparteus,Exocarpos sparteus,,Exocarpos,Santalaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Exocarpos sparteus R.Br.,https://id.biodiversity.org.au/node/apni/2898676,https://id.biodiversity.org.au/taxon/apni/51447153,https://id.biodiversity.org.au/name/apni/58330,Exocarpos sparteus,https://id.biodiversity.org.au/name/apni/58330,https://id.biodiversity.org.au/taxon/apni/51447154,,Exocarpos sparteus,native @@ -101,11 +101,11 @@ Gentiana wingecarribiensis,Gentiana wingecarribiensis,,Gentiana,Gentianaceae,spe Gentianella barringtonensis,Gentianella barringtonensis,,Gentianella,Gentianaceae,species,APC,accepted,Magnoliidae,NSW,Gentianella barringtonensis (L.G.Adams) Glenny,https://id.biodiversity.org.au/taxon/apni/51301045,https://id.biodiversity.org.au/taxon/apni/51301038,https://id.biodiversity.org.au/name/apni/192277,Gentianella barringtonensis,https://id.biodiversity.org.au/name/apni/192277,https://id.biodiversity.org.au/taxon/apni/51436871,,Gentianella barringtonensis,native Geranium obtusisepalum,Geranium obtusisepalum,,Geranium,Geraniaceae,species,APC,accepted,Magnoliidae,"NSW, ACT",Geranium obtusisepalum Carolin,https://id.biodiversity.org.au/node/apni/2910251,https://id.biodiversity.org.au/taxon/apni/51436946,https://id.biodiversity.org.au/name/apni/82004,Geranium obtusisepalum,https://id.biodiversity.org.au/name/apni/82004,https://id.biodiversity.org.au/taxon/apni/51436947,,Geranium obtusisepalum,native Geranium purpureum subsp. purpureum,Geranium purpureum,,Geranium,Geraniaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised)",Geranium purpureum Vill.,https://id.biodiversity.org.au/node/apni/2919721,https://id.biodiversity.org.au/taxon/apni/51436946,https://id.biodiversity.org.au/name/apni/82353,Geranium purpureum,https://id.biodiversity.org.au/name/apni/82382,https://id.biodiversity.org.au/taxon/apni/51436947,,Geranium purpureum,naturalised -Gompholobium grandiflorum,Gompholobium grandiflorum,,Gompholobium,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Gompholobium grandiflorum Sm.,https://id.biodiversity.org.au/node/apni/2909013,https://id.biodiversity.org.au/taxon/apni/51436123,https://id.biodiversity.org.au/name/apni/65291,Gompholobium grandiflorum,https://id.biodiversity.org.au/name/apni/65291,https://id.biodiversity.org.au/taxon/apni/51702961,,Gompholobium grandiflorum,native +Gompholobium grandiflorum,Gompholobium grandiflorum,,Gompholobium,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Gompholobium grandiflorum Sm.,https://id.biodiversity.org.au/node/apni/2909013,https://id.biodiversity.org.au/taxon/apni/51436123,https://id.biodiversity.org.au/name/apni/65291,Gompholobium grandiflorum,https://id.biodiversity.org.au/name/apni/65305,https://id.biodiversity.org.au/taxon/apni/51702961,,Gompholobium grandiflorum,native Goodenia varia,Goodenia varia,,Goodenia,Goodeniaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic",Goodenia varia R.Br.,https://id.biodiversity.org.au/node/apni/2910439,https://id.biodiversity.org.au/taxon/apni/51437012,https://id.biodiversity.org.au/name/apni/92079,Goodenia varia,https://id.biodiversity.org.au/name/apni/92079,https://id.biodiversity.org.au/taxon/apni/51462931,,Goodenia varia,native -Gossia bidwillii,Gossia bidwillii,,Gossia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Gossia bidwillii (Benth.) N.Snow & Guymer,https://id.biodiversity.org.au/taxon/apni/51439972,https://id.biodiversity.org.au/taxon/apni/51439958,https://id.biodiversity.org.au/name/apni/180918,Gossia bidwillii,https://id.biodiversity.org.au/name/apni/180918,https://id.biodiversity.org.au/taxon/apni/51702983,,Gossia bidwillii,native -Grevillea scortechinii,Grevillea scortechinii,,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Grevillea scortechinii (F.Muell. ex Scort.) F.Muell.,https://id.biodiversity.org.au/node/apni/2918803,https://id.biodiversity.org.au/taxon/apni/51445337,https://id.biodiversity.org.au/name/apni/63322,Grevillea scortechinii,https://id.biodiversity.org.au/name/apni/63322,https://id.biodiversity.org.au/taxon/apni/51614274,,Grevillea scortechinii,native -Hakea macraeana,Hakea macraeana,Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied),Hakea,Proteaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Hakea macraeana F.Muell.,https://id.biodiversity.org.au/node/apni/2895080,https://id.biodiversity.org.au/taxon/apni/51445456,https://id.biodiversity.org.au/name/apni/94862,Hakea macraeana [alternative possible names: Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied)],,https://id.biodiversity.org.au/taxon/apni/51614274,,Hakea macraeana,native +Gossia bidwillii,Gossia bidwillii,,Gossia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Gossia bidwillii (Benth.) N.Snow & Guymer,https://id.biodiversity.org.au/taxon/apni/51439972,https://id.biodiversity.org.au/taxon/apni/51439958,https://id.biodiversity.org.au/name/apni/180918,Gossia bidwillii,https://id.biodiversity.org.au/name/apni/180918,https://id.biodiversity.org.au/taxon/apni/51738744,,Gossia bidwillii,native +Grevillea scortechinii,Grevillea scortechinii,,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Grevillea scortechinii (F.Muell. ex Scort.) F.Muell.,https://id.biodiversity.org.au/node/apni/2918803,https://id.biodiversity.org.au/taxon/apni/51726302,https://id.biodiversity.org.au/name/apni/63322,Grevillea scortechinii,https://id.biodiversity.org.au/name/apni/63322,https://id.biodiversity.org.au/taxon/apni/51732901,,Grevillea scortechinii,native +Hakea macraeana,Hakea macraeana,Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied),Hakea,Proteaceae,species,APC,accepted,Magnoliidae,"NSW, Vic",Hakea macraeana F.Muell.,https://id.biodiversity.org.au/node/apni/2895080,https://id.biodiversity.org.au/taxon/apni/51445456,https://id.biodiversity.org.au/name/apni/94862,Hakea macraeana [alternative possible names: Hakea ochroptera (pro parte taxonomic synonym) | Hakea lissosperma (misapplied)],,https://id.biodiversity.org.au/taxon/apni/51732901,,Hakea macraeana,native Hemisteptia lyrata,Hemisteptia lyrata,,Hemisteptia,Asteraceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Hemisteptia lyrata (Bunge) Fisch. & C.A.Mey.,https://id.biodiversity.org.au/taxon/apni/51268530,https://id.biodiversity.org.au/taxon/apni/51268531,https://id.biodiversity.org.au/name/apni/230066,Hemisteptia lyrata,https://id.biodiversity.org.au/name/apni/230066,https://id.biodiversity.org.au/taxon/apni/51695393,,Hemisteptia lyrata,native Hibbertia crinita,Hibbertia crinita,,Hibbertia,Dilleniaceae,species,APC,accepted,Magnoliidae,"SA, Vic",Hibbertia crinita Toelken,https://id.biodiversity.org.au/node/apni/2899370,https://id.biodiversity.org.au/taxon/apni/51434912,https://id.biodiversity.org.au/name/apni/170069,Hibbertia crinita,https://id.biodiversity.org.au/name/apni/170069,https://id.biodiversity.org.au/taxon/apni/51434913,,Hibbertia crinita,native Hibiscus brachysiphonius,Hibiscus brachysiphonius,,Hibiscus,Malvaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Hibiscus brachysiphonius F.Muell.,https://id.biodiversity.org.au/node/apni/2891329,https://id.biodiversity.org.au/taxon/apni/51439316,https://id.biodiversity.org.au/name/apni/91736,Hibiscus brachysiphonius,https://id.biodiversity.org.au/name/apni/91736,https://id.biodiversity.org.au/taxon/apni/51439248,,Hibiscus brachysiphonius,native @@ -125,25 +125,25 @@ Lepidium foliosum,Lepidium foliosum,,Lepidium,Brassicaceae,species,APC,accepted, Lepidium oxytrichum,Lepidium oxytrichum,,Lepidium,Brassicaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Lepidium oxytrichum Sprague,https://id.biodiversity.org.au/node/apni/2915883,https://id.biodiversity.org.au/taxon/apni/51612686,https://id.biodiversity.org.au/name/apni/84027,Lepidium oxytrichum,https://id.biodiversity.org.au/name/apni/84027,https://id.biodiversity.org.au/taxon/apni/51612687,,Lepidium oxytrichum,native Lepidosperma gladiatum,Lepidosperma gladiatum,,Lepidosperma,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Lepidosperma gladiatum Labill.,https://id.biodiversity.org.au/node/apni/2896726,https://id.biodiversity.org.au/taxon/apni/51434499,https://id.biodiversity.org.au/name/apni/85937,Lepidosperma gladiatum,https://id.biodiversity.org.au/name/apni/85937,https://id.biodiversity.org.au/taxon/apni/51460154,,Lepidosperma gladiatum,native Leptomeria drupacea,Leptomeria drupacea,,Leptomeria,Santalaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic, Tas",Leptomeria drupacea (Labill.) Druce,https://id.biodiversity.org.au/node/apni/2892780,https://id.biodiversity.org.au/node/apni/2897704,https://id.biodiversity.org.au/name/apni/61625,Leptomeria drupacea,https://id.biodiversity.org.au/name/apni/61625,https://id.biodiversity.org.au/taxon/apni/51447154,,Leptomeria drupacea,native -Leptospermum continentale,Leptospermum continentale,,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic",Leptospermum continentale Joy Thomps.,https://id.biodiversity.org.au/node/apni/2917147,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/81291,Leptospermum continentale,https://id.biodiversity.org.au/name/apni/81291,https://id.biodiversity.org.au/taxon/apni/51702983,,Leptospermum continentale,native -Leptospermum obovatum,Leptospermum obovatum,,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Leptospermum obovatum Sweet,https://id.biodiversity.org.au/node/apni/2891711,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/99608,Leptospermum obovatum,https://id.biodiversity.org.au/name/apni/99608,https://id.biodiversity.org.au/taxon/apni/51702983,,Leptospermum obovatum,native -Leucopogon amplexicaulis,Leucopogon amplexicaulis,,Leucopogon,Ericaceae,species,APC,accepted,Magnoliidae,NSW,Leucopogon amplexicaulis (Rudge) R.Br.,https://id.biodiversity.org.au/node/apni/2896081,https://id.biodiversity.org.au/taxon/apni/51435325,https://id.biodiversity.org.au/name/apni/106715,Leucopogon amplexicaulis,https://id.biodiversity.org.au/name/apni/106715,https://id.biodiversity.org.au/taxon/apni/51436079,,Leucopogon amplexicaulis,native +Leptospermum continentale,Leptospermum continentale,,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic",Leptospermum continentale Joy Thomps.,https://id.biodiversity.org.au/node/apni/2917147,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/81291,Leptospermum continentale,https://id.biodiversity.org.au/name/apni/81291,https://id.biodiversity.org.au/taxon/apni/51738744,,Leptospermum continentale,native +Leptospermum obovatum,Leptospermum obovatum,,Leptospermum,Myrtaceae,species,APC,accepted,Magnoliidae,"NSW, ACT, Vic",Leptospermum obovatum Sweet,https://id.biodiversity.org.au/node/apni/2891711,https://id.biodiversity.org.au/taxon/apni/51440260,https://id.biodiversity.org.au/name/apni/99608,Leptospermum obovatum,https://id.biodiversity.org.au/name/apni/99608,https://id.biodiversity.org.au/taxon/apni/51738744,,Leptospermum obovatum,native +Leucopogon amplexicaulis,Leucopogon amplexicaulis,,Leucopogon,Ericaceae,species,APC,accepted,Magnoliidae,NSW,Leucopogon amplexicaulis (Rudge) R.Br.,https://id.biodiversity.org.au/node/apni/2896081,https://id.biodiversity.org.au/taxon/apni/51435325,https://id.biodiversity.org.au/name/apni/106715,Leucopogon amplexicaulis,https://id.biodiversity.org.au/name/apni/106715,https://id.biodiversity.org.au/taxon/apni/51738121,,Leucopogon amplexicaulis,native Lobelia pedunculata,Lobelia pedunculata,,Lobelia,Campanulaceae,species,APC,accepted,Magnoliidae,"SA, NSW, ACT, Vic, Tas",Lobelia pedunculata R.Br.,https://id.biodiversity.org.au/node/apni/2901444,https://id.biodiversity.org.au/taxon/apni/51432852,https://id.biodiversity.org.au/name/apni/106999,Lobelia pedunculata,https://id.biodiversity.org.au/name/apni/106999,https://id.biodiversity.org.au/taxon/apni/51432853,,Lobelia pedunculata,native Lobelia trigonocaulis,Lobelia trigonocaulis,,Lobelia,Campanulaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Lobelia trigonocaulis F.Muell.,https://id.biodiversity.org.au/node/apni/2901863,https://id.biodiversity.org.au/taxon/apni/51432852,https://id.biodiversity.org.au/name/apni/107808,Lobelia trigonocaulis,https://id.biodiversity.org.au/name/apni/107808,https://id.biodiversity.org.au/taxon/apni/51432853,,Lobelia trigonocaulis,native Lotononis bainesii,Lotononis bainesii,,Lotononis,Fabaceae,species,APC,accepted,Magnoliidae,"Qld (naturalised), NSW (naturalised)",Lotononis bainesii Baker,https://id.biodiversity.org.au/node/apni/2904277,https://id.biodiversity.org.au/node/apni/2898035,https://id.biodiversity.org.au/name/apni/109834,Lotononis bainesii,https://id.biodiversity.org.au/name/apni/109834,https://id.biodiversity.org.au/taxon/apni/51702961,,Lotononis bainesii,naturalised Lotus corniculatus,Lotus corniculatus,Lotus preslii (pro parte misapplied) | Lotus uliginosus (pro parte misapplied),Lotus,Fabaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), Qld (formerly naturalised), NSW (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Lotus corniculatus L.,https://id.biodiversity.org.au/node/apni/2921302,https://id.biodiversity.org.au/taxon/apni/51436215,https://id.biodiversity.org.au/name/apni/110319,Lotus corniculatus [alternative possible names: Lotus preslii (pro parte misapplied) | Lotus uliginosus (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51702961,,Lotus corniculatus,naturalised Lupinus polyphyllus,Lupinus polyphyllus,,Lupinus,Fabaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), Vic (naturalised)",Lupinus polyphyllus Lindl.,https://id.biodiversity.org.au/node/apni/2917429,https://id.biodiversity.org.au/node/apni/2918316,https://id.biodiversity.org.au/name/apni/100609,Lupinus polyphyllus,https://id.biodiversity.org.au/name/apni/100609,https://id.biodiversity.org.au/taxon/apni/51702961,,Lupinus polyphyllus,naturalised Medicago orbicularis,Medicago orbicularis,,Medicago,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (formerly naturalised)",Medicago orbicularis (L.) Bartal.,https://id.biodiversity.org.au/node/apni/2901771,https://id.biodiversity.org.au/taxon/apni/51285690,https://id.biodiversity.org.au/name/apni/59568,Medicago orbicularis,https://id.biodiversity.org.au/name/apni/59568,https://id.biodiversity.org.au/taxon/apni/51702961,,Medicago orbicularis,naturalised -Melichrus procumbens,Melichrus procumbens,,Melichrus,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Melichrus procumbens (Cav.) Druce,https://id.biodiversity.org.au/node/apni/2905836,https://id.biodiversity.org.au/node/apni/2914566,https://id.biodiversity.org.au/name/apni/114051,Melichrus procumbens,https://id.biodiversity.org.au/name/apni/114051,https://id.biodiversity.org.au/taxon/apni/51436079,,Melichrus procumbens,native +Melichrus procumbens,Melichrus procumbens,,Melichrus,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Melichrus procumbens (Cav.) Druce,https://id.biodiversity.org.au/node/apni/2905836,https://id.biodiversity.org.au/node/apni/2914566,https://id.biodiversity.org.au/name/apni/114051,Melichrus procumbens,https://id.biodiversity.org.au/name/apni/114051,https://id.biodiversity.org.au/taxon/apni/51738121,,Melichrus procumbens,native Mischocarpus australis,Mischocarpus australis,,Mischocarpus,Sapindaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Mischocarpus australis S.T.Reynolds,https://id.biodiversity.org.au/node/apni/2893744,https://id.biodiversity.org.au/taxon/apni/51389373,https://id.biodiversity.org.au/name/apni/115917,Mischocarpus australis,https://id.biodiversity.org.au/name/apni/115917,https://id.biodiversity.org.au/taxon/apni/51447212,,Mischocarpus australis,native Muehlenbeckia adpressa,Muehlenbeckia adpressa,,Muehlenbeckia,Polygonaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Muehlenbeckia adpressa (Labill.) Meisn.,https://id.biodiversity.org.au/node/apni/4750977,https://id.biodiversity.org.au/taxon/apni/51291654,https://id.biodiversity.org.au/name/apni/107852,Muehlenbeckia adpressa,https://id.biodiversity.org.au/name/apni/107852,https://id.biodiversity.org.au/taxon/apni/51444856,,Muehlenbeckia adpressa,native -Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,,Myoporum,Scrophulariaceae,subspecies,APC,accepted,Magnoliidae,"Qld, NSW",Myoporum boninense subsp. australe Chinnock,https://id.biodiversity.org.au/node/apni/7957248,https://id.biodiversity.org.au/taxon/apni/51447443,https://id.biodiversity.org.au/name/apni/117892,Myoporum boninense subsp. australe,https://id.biodiversity.org.au/name/apni/117892,https://id.biodiversity.org.au/taxon/apni/51461527,Myoporum boninense subsp. australe,Myoporum boninense,native +Myoporum boninense subsp. australe,Myoporum boninense subsp. australe,,Myoporum,Scrophulariaceae,subspecies,APC,accepted,Magnoliidae,"Qld, NSW",Myoporum boninense subsp. australe Chinnock,https://id.biodiversity.org.au/node/apni/7957248,https://id.biodiversity.org.au/taxon/apni/51447443,https://id.biodiversity.org.au/name/apni/117892,Myoporum boninense subsp. australe,https://id.biodiversity.org.au/name/apni/117892,https://id.biodiversity.org.au/taxon/apni/51734003,Myoporum boninense subsp. australe,Myoporum boninense,native Nicotiana glauca,Nicotiana glauca,,Nicotiana,Solanaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), Vic (naturalised)",Nicotiana glauca Graham,https://id.biodiversity.org.au/node/apni/2887606,https://id.biodiversity.org.au/taxon/apni/51447689,https://id.biodiversity.org.au/name/apni/77368,Nicotiana glauca,https://id.biodiversity.org.au/name/apni/77368,https://id.biodiversity.org.au/taxon/apni/51447684,,Nicotiana glauca,naturalised Nicotiana goodspeedii,Nicotiana goodspeedii,,Nicotiana,Solanaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic",Nicotiana goodspeedii H.-M.Wheeler,https://id.biodiversity.org.au/node/apni/2908652,https://id.biodiversity.org.au/taxon/apni/51447689,https://id.biodiversity.org.au/name/apni/77381,Nicotiana goodspeedii,https://id.biodiversity.org.au/name/apni/77381,https://id.biodiversity.org.au/taxon/apni/51447684,,Nicotiana goodspeedii,native Oxalis corniculata,Oxalis corniculata,,Oxalis,Oxalidaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), ChI (naturalised), NT (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Oxalis corniculata L.,https://id.biodiversity.org.au/node/apni/2909588,https://id.biodiversity.org.au/taxon/apni/51442068,https://id.biodiversity.org.au/name/apni/89460,Oxalis corniculata,https://id.biodiversity.org.au/name/apni/89460,https://id.biodiversity.org.au/taxon/apni/51442069,,Oxalis corniculata,naturalised Pandorea pandorana subsp. austrocaledonica,Pandorea pandorana,,Pandorea,Bignoniaceae,species,APC,accepted,Magnoliidae,"WA, SA (native and naturalised), Qld, NSW, LHI, NI (presumed extinct), Vic (native and naturalised), Tas",Pandorea pandorana (Andrews) Steenis,https://id.biodiversity.org.au/taxon/apni/51269199,https://id.biodiversity.org.au/taxon/apni/51269200,https://id.biodiversity.org.au/name/apni/91117,Pandorea pandorana,https://id.biodiversity.org.au/name/apni/141640,https://id.biodiversity.org.au/taxon/apni/51439229,,Pandorea pandorana,native and naturalised Paraserianthes lophantha,Paraserianthes lophantha,,Paraserianthes,Fabaceae,species,APC,accepted,Magnoliidae,"WA (native and naturalised), SA (naturalised), NSW (naturalised), NI (naturalised), Vic (naturalised), Tas (naturalised)",Paraserianthes lophantha (Willd.) I.C.Nielsen,https://id.biodiversity.org.au/taxon/apni/51286820,https://id.biodiversity.org.au/taxon/apni/51286819,https://id.biodiversity.org.au/name/apni/116755,Paraserianthes lophantha,https://id.biodiversity.org.au/name/apni/116755,https://id.biodiversity.org.au/taxon/apni/51702961,,Paraserianthes lophantha,native and naturalised -Parentucellia latifolia,Parentucellia latifolia,,Parentucellia,Orobanchaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Parentucellia latifolia (L.) Caruel,https://id.biodiversity.org.au/taxon/apni/51291069,https://id.biodiversity.org.au/taxon/apni/51291062,https://id.biodiversity.org.au/name/apni/96753,Parentucellia latifolia,https://id.biodiversity.org.au/name/apni/96753,https://id.biodiversity.org.au/taxon/apni/51291037,,Parentucellia latifolia,naturalised +Parentucellia latifolia,Parentucellia latifolia,,Parentucellia,Orobanchaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Parentucellia latifolia (L.) Caruel,https://id.biodiversity.org.au/taxon/apni/51291069,https://id.biodiversity.org.au/taxon/apni/51291062,https://id.biodiversity.org.au/name/apni/96753,Parentucellia latifolia,https://id.biodiversity.org.au/name/apni/96753,https://id.biodiversity.org.au/taxon/apni/51734010,,Parentucellia latifolia,naturalised Hypoxis glabella var. glabella,Pauridia glabella var. glabella,,Pauridia,Hypoxidaceae,variety,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic, Tas",Pauridia glabella (R.Br.) Snijman & Kocyan var. glabella,https://id.biodiversity.org.au/node/apni/7455351,https://id.biodiversity.org.au/taxon/apni/51437983,https://id.biodiversity.org.au/name/apni/244102,Pauridia glabella var. glabella,https://id.biodiversity.org.au/name/apni/81442,https://id.biodiversity.org.au/taxon/apni/51437984,Pauridia glabella var. glabella,Pauridia glabella,native Phlegmatospermum cochlearinum,Phlegmatospermum cochlearinum,,Phlegmatospermum,Brassicaceae,species,APC,accepted,Magnoliidae,"WA, SA, NSW, Vic",Phlegmatospermum cochlearinum (F.Muell.) O.E.Schulz,https://id.biodiversity.org.au/node/apni/2915554,https://id.biodiversity.org.au/node/apni/2897988,https://id.biodiversity.org.au/name/apni/81861,Phlegmatospermum cochlearinum,https://id.biodiversity.org.au/name/apni/81861,https://id.biodiversity.org.au/taxon/apni/51612687,,Phlegmatospermum cochlearinum,native Phyla nodiflora,Phyla nodiflora,,Phyla,Verbenaceae,species,APC,accepted,Magnoliidae,"WA (native and naturalised), CoI (naturalised), NT, Qld, NSW (naturalised)",Phyla nodiflora (L.) Greene,https://id.biodiversity.org.au/node/apni/2907374,https://id.biodiversity.org.au/node/apni/2892182,https://id.biodiversity.org.au/name/apni/74617,Phyla nodiflora,https://id.biodiversity.org.au/name/apni/74617,https://id.biodiversity.org.au/taxon/apni/51448662,,Phyla nodiflora,native and naturalised @@ -157,14 +157,14 @@ Polycarpon tetraphyllum,Polycarpon tetraphyllum,,Polycarpon,Caryophyllaceae,spec Potamogeton australiensis,Potamogeton australiensis,,Potamogeton,Potamogetonaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Potamogeton australiensis A.Benn.,https://id.biodiversity.org.au/node/apni/7808489,https://id.biodiversity.org.au/node/apni/8770682,https://id.biodiversity.org.au/name/apni/65827,Potamogeton australiensis,https://id.biodiversity.org.au/name/apni/65827,https://id.biodiversity.org.au/taxon/apni/51353530,,Potamogeton australiensis,native Psoralea pinnata,Psoralea pinnata,,Psoralea,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised), Tas (naturalised)",Psoralea pinnata L.,https://id.biodiversity.org.au/node/apni/2887023,https://id.biodiversity.org.au/node/apni/8771698,https://id.biodiversity.org.au/name/apni/88820,Psoralea pinnata,https://id.biodiversity.org.au/name/apni/88820,https://id.biodiversity.org.au/taxon/apni/51702961,,Psoralea pinnata,naturalised Pultenaea ferruginea,Pultenaea ferruginea,,Pultenaea,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Pultenaea ferruginea Rudge,https://id.biodiversity.org.au/node/apni/2906803,https://id.biodiversity.org.au/taxon/apni/51436286,https://id.biodiversity.org.au/name/apni/59158,Pultenaea ferruginea,https://id.biodiversity.org.au/name/apni/59158,https://id.biodiversity.org.au/taxon/apni/51702961,,Pultenaea ferruginea,native -Rhodamnia argentea,Rhodamnia argentea,,Rhodamnia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Rhodamnia argentea Benth.,https://id.biodiversity.org.au/node/apni/2919069,https://id.biodiversity.org.au/taxon/apni/51440311,https://id.biodiversity.org.au/name/apni/68532,Rhodamnia argentea,https://id.biodiversity.org.au/name/apni/68532,https://id.biodiversity.org.au/taxon/apni/51702983,,Rhodamnia argentea,native +Rhodamnia argentea,Rhodamnia argentea,,Rhodamnia,Myrtaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Rhodamnia argentea Benth.,https://id.biodiversity.org.au/node/apni/2919069,https://id.biodiversity.org.au/taxon/apni/51440311,https://id.biodiversity.org.au/name/apni/68532,Rhodamnia argentea,https://id.biodiversity.org.au/name/apni/68532,https://id.biodiversity.org.au/taxon/apni/51738744,,Rhodamnia argentea,native Rorippa gigantea,Rorippa gigantea,,Rorippa,Brassicaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Rorippa gigantea (Hook.) Garn.-Jones,https://id.biodiversity.org.au/node/apni/2920330,https://id.biodiversity.org.au/node/apni/8442201,https://id.biodiversity.org.au/name/apni/75950,Rorippa gigantea,https://id.biodiversity.org.au/name/apni/75950,https://id.biodiversity.org.au/taxon/apni/51612687,,Rorippa gigantea,native -Rubus parvifolius,Rubus parvifolius,,Rubus,Rosaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Rubus parvifolius L.,https://id.biodiversity.org.au/node/apni/2901867,https://id.biodiversity.org.au/taxon/apni/51446575,https://id.biodiversity.org.au/name/apni/85986,Rubus parvifolius,https://id.biodiversity.org.au/name/apni/85986,https://id.biodiversity.org.au/taxon/apni/51446278,,Rubus parvifolius,native -Salix alba,Salix alba,,Salix,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised)",Salix alba L.,https://id.biodiversity.org.au/node/apni/2896377,https://id.biodiversity.org.au/node/apni/8905801,https://id.biodiversity.org.au/name/apni/59687,Salix alba [alternative possible names: NA],,https://id.biodiversity.org.au/taxon/apni/51436847,,Salix alba,naturalised +Rubus parvifolius,Rubus parvifolius,,Rubus,Rosaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Rubus parvifolius L.,https://id.biodiversity.org.au/node/apni/2901867,https://id.biodiversity.org.au/taxon/apni/51446575,https://id.biodiversity.org.au/name/apni/85986,Rubus parvifolius,https://id.biodiversity.org.au/name/apni/85986,https://id.biodiversity.org.au/taxon/apni/51737985,,Rubus parvifolius,native +Salix alba,Salix alba,Salix x fragilis nothovar. fragilis (pro parte misapplied),Salix,Salicaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), ACT (naturalised), Vic (naturalised)",Salix alba L.,https://id.biodiversity.org.au/node/apni/2896377,https://id.biodiversity.org.au/node/apni/8905801,https://id.biodiversity.org.au/name/apni/59687,Salix alba [alternative possible names: Salix x fragilis nothovar. fragilis (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51436847,,Salix alba,naturalised Schenkia australis,Schenkia australis,,Schenkia,Gentianaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic, Tas",Schenkia australis (R.Br.) G.Mans.,https://id.biodiversity.org.au/taxon/apni/51436897,https://id.biodiversity.org.au/taxon/apni/51436898,https://id.biodiversity.org.au/name/apni/200895,Schenkia australis,https://id.biodiversity.org.au/name/apni/200895,https://id.biodiversity.org.au/taxon/apni/51436871,,Schenkia australis,native Schoenus apogon,Schoenus apogon,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Schoenus apogon Roem. & Schult.,https://id.biodiversity.org.au/node/apni/2908439,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/109452,Schoenus apogon,https://id.biodiversity.org.au/name/apni/109452,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus apogon,native Schoenus brevifolius,Schoenus brevifolius,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, Vic, Tas",Schoenus brevifolius R.Br.,https://id.biodiversity.org.au/node/apni/2904000,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/109778,Schoenus brevifolius,https://id.biodiversity.org.au/name/apni/109778,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus brevifolius,native -Schoenus lepidosperma,Schoenus lepidosperma,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Schoenus lepidosperma (F.Muell.) K.L.Wilson,https://id.biodiversity.org.au/node/apni/2893030,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/141376,Schoenus lepidosperma,https://id.biodiversity.org.au/name/apni/243667,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus lepidosperma,native +Schoenus lepidosperma,Schoenus lepidosperma,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"SA, NSW, Vic, Tas",Schoenus lepidosperma (F.Muell.) K.L.Wilson,https://id.biodiversity.org.au/node/apni/2893030,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/141376,Schoenus lepidosperma,https://id.biodiversity.org.au/name/apni/141376,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus lepidosperma,native Schoenus vaginatus,Schoenus vaginatus,,Schoenus,Cyperaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Schoenus vaginatus F.Muell. ex Benth.,https://id.biodiversity.org.au/node/apni/2896591,https://id.biodiversity.org.au/taxon/apni/51460153,https://id.biodiversity.org.au/name/apni/113246,Schoenus vaginatus,https://id.biodiversity.org.au/name/apni/113246,https://id.biodiversity.org.au/taxon/apni/51460154,,Schoenus vaginatus,native Scleria rugosa,Scleria rugosa,,Scleria,Cyperaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld, NSW",Scleria rugosa R.Br.,https://id.biodiversity.org.au/node/apni/2892143,https://id.biodiversity.org.au/taxon/apni/51434752,https://id.biodiversity.org.au/name/apni/64346,Scleria rugosa,https://id.biodiversity.org.au/name/apni/64346,https://id.biodiversity.org.au/taxon/apni/51460154,,Scleria rugosa,native Senecio longipilus,Senecio longipilus,,Senecio,Asteraceae,species,APC,accepted,Magnoliidae,"NSW, Tas",Senecio longipilus I.Thomps.,https://id.biodiversity.org.au/node/apni/2907653,https://id.biodiversity.org.au/taxon/apni/51614245,https://id.biodiversity.org.au/name/apni/189666,Senecio longipilus,https://id.biodiversity.org.au/name/apni/189666,https://id.biodiversity.org.au/taxon/apni/51695393,,Senecio longipilus,native @@ -176,10 +176,10 @@ Sparaxis bulbifera,Sparaxis bulbifera,,Sparaxis,Iridaceae,species,APC,accepted,M Spergularia diandra,Spergularia diandra,,Spergularia,Caryophyllaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), NSW (naturalised), Vic (naturalised)",Spergularia diandra (Guss.) Heldr.,https://id.biodiversity.org.au/node/apni/2886696,https://id.biodiversity.org.au/taxon/apni/51295406,https://id.biodiversity.org.au/name/apni/83464,Spergularia diandra,https://id.biodiversity.org.au/name/apni/83464,https://id.biodiversity.org.au/taxon/apni/51432987,,Spergularia diandra,naturalised Sphaeromorphaea littoralis,Sphaeromorphaea littoralis,,Sphaeromorphaea,Asteraceae,species,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW, Vic",Sphaeromorphaea littoralis (Retz.) A.R.Bean,https://id.biodiversity.org.au/node/apni/7069871,https://id.biodiversity.org.au/node/apni/7071683,https://id.biodiversity.org.au/name/apni/246779,Sphaeromorphaea littoralis,https://id.biodiversity.org.au/name/apni/246779,https://id.biodiversity.org.au/taxon/apni/51695393,,Sphaeromorphaea littoralis,native Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia subsp. angustifolia,,Stellaria,Caryophyllaceae,subspecies,APC,accepted,Magnoliidae,"SA, Qld, NSW, ACT, Vic, Tas",Stellaria angustifolia Hook. subsp. angustifolia,https://id.biodiversity.org.au/node/apni/2890520,https://id.biodiversity.org.au/taxon/apni/51433015,https://id.biodiversity.org.au/name/apni/240421,Stellaria angustifolia subsp. angustifolia,https://id.biodiversity.org.au/name/apni/240421,https://id.biodiversity.org.au/taxon/apni/51432987,Stellaria angustifolia subsp. angustifolia,Stellaria angustifolia,native -Styphelia viridis,Styphelia viridis,,Styphelia,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Styphelia viridis Andrews,https://id.biodiversity.org.au/node/apni/2912747,https://id.biodiversity.org.au/taxon/apni/51435346,https://id.biodiversity.org.au/name/apni/109318,Styphelia viridis,https://id.biodiversity.org.au/name/apni/109318,https://id.biodiversity.org.au/taxon/apni/51436079,,Styphelia viridis,native +Styphelia viridis,Styphelia viridis,,Styphelia,Ericaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Styphelia viridis Andrews,https://id.biodiversity.org.au/node/apni/2912747,https://id.biodiversity.org.au/taxon/apni/51435346,https://id.biodiversity.org.au/name/apni/109318,Styphelia viridis,https://id.biodiversity.org.au/name/apni/109318,https://id.biodiversity.org.au/taxon/apni/51738121,,Styphelia viridis,native Swainsona cadellii,Swainsona cadellii,,Swainsona,Fabaceae,species,APC,accepted,Magnoliidae,NSW,Swainsona cadellii F.Muell. ex C.Moore,https://id.biodiversity.org.au/node/apni/2904099,https://id.biodiversity.org.au/taxon/apni/51436313,https://id.biodiversity.org.au/name/apni/76870,Swainsona cadellii,https://id.biodiversity.org.au/name/apni/76870,https://id.biodiversity.org.au/taxon/apni/51702961,,Swainsona cadellii,native Teucrium puberulum,Teucrium puberulum,,Teucrium,Lamiaceae,species,APC,accepted,Magnoliidae,"Qld, NSW",Teucrium puberulum (F.Muell.) Kattari & Bräuchler,https://id.biodiversity.org.au/taxon/apni/51288087,https://id.biodiversity.org.au/taxon/apni/51438311,https://id.biodiversity.org.au/name/apni/7660439,Teucrium puberulum,https://id.biodiversity.org.au/name/apni/7660439,https://id.biodiversity.org.au/taxon/apni/51696573,,Teucrium puberulum,native -Thelymitra kangaloonica,Thelymitra kangaloonica,,Thelymitra,Orchidaceae,species,APC,accepted,Magnoliidae,NSW,Thelymitra kangaloonica Jeanes,https://id.biodiversity.org.au/taxon/apni/51414328,https://id.biodiversity.org.au/taxon/apni/51631246,https://id.biodiversity.org.au/name/apni/233692,Thelymitra kangaloonica,https://id.biodiversity.org.au/name/apni/233692,https://id.biodiversity.org.au/taxon/apni/51697009,,Thelymitra kangaloonica,native +Thelymitra kangaloonica,Thelymitra kangaloonica,,Thelymitra,Orchidaceae,species,APC,accepted,Magnoliidae,NSW,Thelymitra kangaloonica Jeanes,https://id.biodiversity.org.au/taxon/apni/51414328,https://id.biodiversity.org.au/taxon/apni/51631246,https://id.biodiversity.org.au/name/apni/233692,Thelymitra kangaloonica,https://id.biodiversity.org.au/name/apni/233692,https://id.biodiversity.org.au/taxon/apni/51727417,,Thelymitra kangaloonica,native Thesium australe,Thesium australe,,Thesium,Santalaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, ACT, Vic, Tas (presumed extinct)",Thesium australe R.Br.,https://id.biodiversity.org.au/node/apni/2891975,https://id.biodiversity.org.au/node/apni/2913858,https://id.biodiversity.org.au/name/apni/56224,Thesium australe,https://id.biodiversity.org.au/name/apni/56224,https://id.biodiversity.org.au/taxon/apni/51447154,,Thesium australe,native Trifolium dubium,Trifolium dubium,,Trifolium,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), SA (naturalised), Qld (naturalised), NSW (naturalised), LHI (naturalised), NI (naturalised), ACT (naturalised), Vic (naturalised), Tas (naturalised)",Trifolium dubium Sibth.,https://id.biodiversity.org.au/taxon/apni/51436351,https://id.biodiversity.org.au/taxon/apni/51436341,https://id.biodiversity.org.au/name/apni/115704,Trifolium dubium,https://id.biodiversity.org.au/name/apni/115704,https://id.biodiversity.org.au/taxon/apni/51702961,,Trifolium dubium,naturalised Veronica catenata,Veronica catenata,,Veronica,Plantaginaceae,species,APC,accepted,Magnoliidae,"SA (naturalised), NSW (naturalised), Vic (naturalised)",Veronica catenata Pennell,https://id.biodiversity.org.au/node/apni/2897164,https://id.biodiversity.org.au/taxon/apni/51632390,https://id.biodiversity.org.au/name/apni/67965,Veronica catenata,https://id.biodiversity.org.au/name/apni/67965,https://id.biodiversity.org.au/taxon/apni/51699383,,Veronica catenata,naturalised diff --git a/tests/testthat/examples/Test_2023_4/output/traits.csv b/tests/testthat/examples/Test_2023_4/output/traits.csv index be35a67d..2ed1a87f 100644 --- a/tests/testthat/examples/Test_2023_4/output/traits.csv +++ b/tests/testthat/examples/Test_2023_4/output/traits.csv @@ -22,7 +22,7 @@ Test_2023_4,Alectryon subdentatus,020,fruit_length,8,mm,species,minimum,measurem Test_2023_4,Amyema preissii,021,fruit_colour,pink white,,,mode,,1,,seedling,,,,,Test_2003,,02,,,,Part of Test Dataset 4,01,04,Amyema preissii Test_2023_4,Angophora leiocarpa,022,fruit_width,11,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Angophora leiocarpa Test_2023_4,Capparis anomala,023,fruit_colour,purple,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Apophyllum anomalum -Test_2023_4,Arbutus unedo,024,fruit_colour,red,,metapopulation,mode,,1,,seedling,03,,,,,02,02,,,,From `australia_2` site,01,04,Arbutus unedo +Test_2023_4,Arbutus unedo,024,fruit_colour,red,,metapopulation,mode,measurement,1,,seedling,03,,,,,02,02,,,,From `australia_2` site,01,04,Arbutus unedo Test_2023_4,Australina pusilla,025,fruit_length,1,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Australina pusilla Test_2023_4,Burmannia disticha,026,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Burmannia disticha Test_2023_4,Bursaria spinosa subsp. spinosa,027,fruit_width,9,mm,species,mode,,1,field_experiment,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Bursaria spinosa subsp. spinosa @@ -40,7 +40,7 @@ Test_2023_4,Centaurium tenuiflorum,038,fruit_length,6,mm,species,mode,,1,,seedli Test_2023_4,Cestrum nocturnum,039,fruit_width,8,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Cestrum nocturnum Test_2023_4,Chthonocephalus pseudevax,040,fruit_length,0.5,mm,,mode,,1,,seedling,,,,,Test_2003,,01,,,,Part of Test Dataset 4,01,04,Chthonocephalus pseudevax Test_2023_4,Claoxylon australe,041,fruit_width,5,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Claoxylon australe -Test_2023_4,Commersonia amystia,042,fruit_width,13,mm,species,maximum,,1,field_experiment,seedling,,,,,Test_2003,,01,,,,Part of Test Dataset 4,01,04,Commersonia amystia +Test_2023_4,Commersonia amystia,042,fruit_width,13,mm,species,maximum,unknown,1,field_experiment,seedling,,,,,Test_2003,,01,,,,Part of Test Dataset 4,01,04,Commersonia amystia Test_2023_4,Commersonia salviifolia,043,fruit_width,5,mm,species,mode,,1,field_experiment,seedling,,,,,Test_2000,,01,,,,Part of Test Dataset 4,01,04,Commersonia salviifolia Test_2023_4,Convolvulus farinosus,044,fruit_width,6,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Convolvulus farinosus Test_2023_4,Coprosma niphophila,045,fruit_colour,orange red,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Coprosma niphophila @@ -49,7 +49,7 @@ Test_2023_4,Correa alba,047,fruit_length,5,mm,species,mode,,1,,seedling,,,,,Test Test_2023_4,Corymbia citriodora,048,fruit_length,15,mm,,mode,measurement,1,literature,seedling,,,,,Test_2003,,01,,,,Part of Test Dataset 4,01,04,Corymbia citriodora Test_2023_4,Corymbia eximia,049,fruit_length,13,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Corymbia eximia Test_2023_4,Crassula decumbens,050,fruit_dehiscence,dehiscent,,population,mode,,1,,juvenile,01,,,,Test_2003,01,02,,,2020,Remarks for `fruit_dehiscence`,01,04,Crassula decumbens -Test_2023_4,Crassula peduncularis,051,fruit_dehiscence,dehiscent,,population,mode,,1,literature,adult,03,,,,Test_2003,02,02,,,,From `australia_2` site,01,04,Crassula peduncularis +Test_2023_4,Crassula peduncularis,051,fruit_dehiscence,dehiscent,,population,mode,expert_score,1,literature,adult,03,,,,Test_2003,02,02,,,,From `australia_2` site,01,04,Crassula peduncularis Test_2023_4,Crotalaria brevis,052,fruit_colour,brown,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Crotalaria brevis Test_2023_4,Crotalaria brevis,052,fruit_length,6,mm,species,mean,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Crotalaria brevis Test_2023_4,Crotalaria grahamiana,053,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Crotalaria grahamiana @@ -63,7 +63,7 @@ Test_2023_4,Cyperus sculptus,060,fruit_length,1,mm,species,mode,,1,,seedling,,,, Test_2023_4,Dampiera fusca,061,fruit_colour,brown,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Dampiera fusca Test_2023_4,Davidsonia johnsonii,062,fruit_length,30,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Davidsonia johnsonii Test_2023_4,Daviesia arenaria,063,fruit_length,7,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Daviesia arenaria -Test_2023_4,Solori involuta,064,fruit_dehiscence,indehiscent,,population,mode,,1,literature,adult,03,,,,Test_2003,02,02,,,,From `australia_2` site,01,02,Derris involuta +Test_2023_4,Solori involuta,064,fruit_dehiscence,indehiscent,,population,mode,measurement,1,literature,adult,03,,,,Test_2003,02,02,,,,From `australia_2` site,01,02,Derris involuta Test_2023_4,Dichromochlamys dentatifolia,065,fruit_length,1.8,mm,,mode,,1,field_experiment,seedling,,,,,Test_2003,,01,,,,Part of Test Dataset 4,01,04,Dichromochlamys dentatifolia Test_2023_4,Dillwynia cinerascens,066,fruit_length,5,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Dillwynia cinerascens Test_2023_4,Dillwynia floribunda,067,fruit_length,4,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Dillwynia floribunda @@ -103,7 +103,7 @@ Test_2023_4,Eucalyptus globoidea,097,fruit_width,6,mm,species,mode,,1,field_expe Test_2023_4,Eucalyptus youmanii,098,fruit_length,12,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus youmanii Test_2023_4,Eucalyptus youmanii,099,fruit_width,9,mm,species,mode,,1,field_experiment,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Eucalyptus youmanii Test_2023_4,Euphorbia inappendiculata var. queenslandica,100,fruit_length,1.5,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Euphorbia inappendiculata var. queenslandica -Test_2023_4,Exocarpos homalocladus,101,fruit_width,8,mm,species,maximum,,1,field_experiment,seedling,,,,,Test_2000,,02,,,,Part of Test Dataset 4,01,04,Exocarpos homalocladus +Test_2023_4,Exocarpos homalocladus,101,fruit_width,8,mm,species,maximum,measurement,1,field_experiment,seedling,,,,,Test_2000,,02,,,,Part of Test Dataset 4,01,04,Exocarpos homalocladus Test_2023_4,Exocarpos sparteus,102,fruit_length,5,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Exocarpos sparteus Test_2023_4,Ficus henneana,103,fruit_length,15,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Ficus henneana Test_2023_4,Freesia leichtlinii subsp. leichtlinii x Freesia leichtlinii subsp. alba,104,fruit_colour,green,,metapopulation,mode,,1,,seedling,03,,,,,02,02,,,,From `australia_2` site,01,04,Freesia hybrid @@ -124,7 +124,7 @@ Test_2023_4,Hibbertia crinita,118,fruit_dehiscence,dehiscent,,species,,,1,,adult Test_2023_4,Hibiscus brachysiphonius,119,fruit_length,15,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Hibiscus brachysiphonius Test_2023_4,Hibiscus sturtii,120,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Hibiscus sturtii Test_2023_4,Hypericum elodes,121,fruit_length,4,mm,species,mean,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Hypericum elodes -Test_2023_4,Pauridia glabella var. glabella,122,fruit_dehiscence,dehiscent,,population,mode,,1,literature,adult,03,,,,Test_2003,02,02,,,,From `australia_2` site,01,02,Hypoxis glabella var. glabella +Test_2023_4,Pauridia glabella var. glabella,122,fruit_dehiscence,dehiscent,,population,mode,unknown,1,literature,adult,03,,,,Test_2003,02,02,,,,From `australia_2` site,01,02,Hypoxis glabella var. glabella Test_2023_4,Imperata cylindrica,123,fruit_length,1,mm,species,minimum,measurement,1,literature,seedling,,,,,Test_2000,,02,,,2006-03,Part of Test Dataset 4,01,04,Imperata cylindrica Test_2023_4,Imperata cylindrica,124,fruit_length,1,mm,species,minimum,measurement,1,literature,seedling,,,,,Test_2000,,02,,,2007-03,Part of Test Dataset 4,01,04,Imperata cylindrica Test_2023_4,Indigofera triflora,125,fruit_length,30,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Indigofera triflora @@ -181,10 +181,10 @@ Test_2023_4,Phyla nodiflora,165,leaf_stomatal_conductance,0.1,mol{H2O}/m2/s,spec Test_2023_4,Phyla nodiflora,165,leaf_stomatal_conductance,0.37,mol{H2O}/m2/s,species,raw,measurement,5,field_experiment,seedling,,,,,,,02,,,,Part of Test Dataset 4,02,04,Phyla nodiflora Test_2023_4,Phyla nodiflora,165,leaf_stomatal_conductance,0.6,mol{H2O}/m2/s,species,raw,measurement,5,field_experiment,seedling,,,,,,,02,,,,Part of Test Dataset 4,02,04,Phyla nodiflora Test_2023_4,Picris barbarorum,166,fruit_length,7.5,mm,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Picris barbarorum -Test_2023_4,Pimelea ligustrina subsp. ligustrina,167,fruit_colour,green,,metapopulation,mode,,1,literature,seedling,03,,,,Test_2003,02,02,,,,From `australia_2` site,01,03,Pimelea ligustrina subsp. ligustrina +Test_2023_4,Pimelea ligustrina subsp. ligustrina,167,fruit_colour,green,,metapopulation,mode,measurement,1,literature,seedling,03,,,,Test_2003,02,02,,,,From `australia_2` site,01,03,Pimelea ligustrina subsp. ligustrina Test_2023_4,Pinus pinea,168,fruit_colour,brown,,species,mode,,1,,seedling,,,,,,,02,,,,Part of Test Dataset 4,01,04,Pinus pinea Test_2023_4,Pisum sativum var. arvense,169,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Pisum sativum var. arvense -Test_2023_4,Pittosporum erioloma,170,fruit_dehiscence,dehiscent,,,mode,,1,literature,adult,,,,,Test_2003,,02,,,,,01,04,Pittosporum erioloma +Test_2023_4,Pittosporum erioloma,170,fruit_dehiscence,dehiscent,,,mode,measurement,1,literature,adult,,,,,Test_2003,,02,,,,,01,04,Pittosporum erioloma Test_2023_4,Plantago turrifera,171,fruit_length,3,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Plantago turrifera Test_2023_4,Polycarpon tetraphyllum,172,fruit_dehiscence,dehiscent,,species,mode,,1,,adult,,,,,,,02,,,,,01,02,Polycarpon tetraphyllum Test_2023_4,Potamogeton australiensis,173,fruit_length,4,mm,species,mode,,1,,seedling,,,,,,,01,,,,Part of Test Dataset 4,01,04,Potamogeton australiensis diff --git a/tests/testthat/examples/Test_2023_5/README.md b/tests/testthat/examples/Test_2023_5/README.md index 81a9a017..a9702e6c 100644 --- a/tests/testthat/examples/Test_2023_5/README.md +++ b/tests/testthat/examples/Test_2023_5/README.md @@ -3,15 +3,17 @@ This dataset is for testing: - `individual_id` for wide datasets -- Different `bibtype`s and secondary and original sources (also check methods table), with `source_id` column (check joining to methods table somewhere else?) +- Different `bibtype`s and secondary and original sources (also check methods table), with `source_id` column - No locations or contexts - Units read in from a column (check unit conversions are working) - Bins and ranges have units that are converted correctly -Lizzy recommends this dataset for testing units: -*"And if you're hunting for a dataset with good info to test units & source_id, maybe take some snippets from Richards_2008. There are separate columns for SLA and LMA. You could take just the rows with data for one of those and then merge them into a single column with a second column for units. And have some dummy data that is a bin - like made up lifespan data with a required unit conversion from either a column or within the metadata."* - -Test_2023_5 is a copy of Falster_2005_1 (maybe change to Richards_2008) with the following modifications: +Test_2023_5 is a copy of Richards_2008 with the following modifications: +- Added `individual_id` column and changed `entity_type` to individual (made up some values to test `individual_id`) - Added all `bibtype` options to the dataset via secondary/original sources +- Changed the `source_id` column and metadata to include more variety of sources +- Removed locations, contexts, and substitutions +- Subsetted to SLA and added units column +- Added some bin values in leaf lifespan data and add units column See output/ for expected output files. diff --git a/tests/testthat/examples/Test_2023_5/data.csv b/tests/testthat/examples/Test_2023_5/data.csv index 6cfcbcb7..6a8c1069 100644 --- a/tests/testthat/examples/Test_2023_5/data.csv +++ b/tests/testthat/examples/Test_2023_5/data.csv @@ -1,46 +1,34 @@ -Species,species_abb,site,LMA (mg mm-2),Leaf nitrogen (mg mg-1),leaf size (mm2),wood density (mg mm-3),branch mass fraction,Seed mass (mg),LASA10,LASA250,LASA50,LASA1000 -Acacia celsa,acacel,Atherton,0.145,0.0214,2786,0.498,0.67,10.3,2977,7260,3722,6824 -Acronychia acidula,acraci,Atherton,0.085,0.0243,14302,0.525,0.48,,,7560,5541,9480 -Alphitonia petriei,alppet,Atherton,0.149,0.0163,6820,0.413,0.42,27.2,,4340,3313,4335 -Glochidion hylandii,glohyl,Atherton,0.106,0.0137,3209,0.566,0.41,10.41,1993,5075,5455,8664 -Homalanthus novoguineensis,omanov,Atherton,0.082,0.022,10682,0.319,0.47,7,,2136,2158,3307 -Melicope elleryana,melell,Atherton,0.075,0.0268,6955,0.346,0.58,1.61,,4201,2860,6119 -Neolitsea dealbata,neodea,Atherton,0.093,0.0164,5228,0.352,0.58,176.1,1686,2747,3049,7504 -Polyscias australiana,polaus,Atherton,0.079,0.0154,6806,0.397,0.42,8.35,,6008,,6700 -Psychotria sp Utchee Creek,psyspp,Atherton,0.108,0.0179,11157,0.582,0,23.09,,4977,2302,2037 -Rhodomyrtus trineura,rhotri,Atherton,0.129,0.0111,3401,0.763,0.34,,4321,3803,6088,6877 -Acmena graveolens,acmgra,Cape Tribulation,0.151,0.0155,5246,0.599,0.67,,,3057,2667,7156 -Aleurites rockinghamensis,aleroc,Cape Tribulation,0.113,0.0184,73984,0.28,0.02,7077,,4194,,6209 -Alstonia scholaris,alssch,Cape Tribulation,0.107,0.0223,6182,0.361,0.46,1.53,,1854,1682,3932 -Argyrodendron peralatum,argper,Cape Tribulation,0.244,0.0119,3201,0.726,0.71,433,,3832,1689,6718 -Atractocarpus hirtus,atrhir,Cape Tribulation,0.072,0.0157,11374,0.804,0.28,,,7143,6727,6103 -Brombya platynema,bropla,Cape Tribulation,0.106,0.0188,8218,0.603,0.33,,,4261,3531,5377 -Cardwellia sublimis,carsub,Cape Tribulation,0.127,0.0128,4352,0.603,0.56,582.3,,6315,4880,8282 -Castanospermum australe,casaus,Cape Tribulation,0.117,0.0237,2765,0.587,0.37,14851,,7329,,8869 -Cleistanthus myrianthus,clemyr,Cape Tribulation,0.078,0.0228,4828,0.588,0.56,,3720,6084,5233,8559 -Cryptocarya laevigata,crylae,Cape Tribulation,0.087,0.0156,2682,0.64,0.65,1281,1391,3297,4680,7588 -Cryptocarya mackinnoniana,crymac,Cape Tribulation,0.204,0.0152,10458,0.655,0.61,204,,3277,2325,8657 -Cryptocarya murrayi,crymur,Cape Tribulation,0.155,0.0167,9960,0.674,0.39,,2693,5543,4298,5451 -Dendrocnide moroides,denmor,Cape Tribulation,0.052,0.0312,26454,0.23,0.46,0.71,,2372,,2090 -Elaeocarpus grandis,elaang,Cape Tribulation,0.122,0.0187,2762,0.499,0.47,3699,,2598,1748,4635 -Endiandra leptodendron,endlep,Cape Tribulation,0.106,0.018,3987,0.611,0.68,,1492,2412,2783,7477 -Endiandra microneura,endmic,Cape Tribulation,0.151,0.0177,3377,0.623,0.61,,3573,6344,3354,6235 -Gillbeea adenopetala,gilade,Cape Tribulation,0.126,0.0096,3678,0.43,0.46,15,,2863,3160,6549 -Haplostichanthus sp Coop. Ck,hapspp,Cape Tribulation,0.072,0.022,4685,0.668,0.36,,2430,12304,3282,2992 -Harpullia rhyticarpa,harrhy,Cape Tribulation,0.076,0.0174,40876,0.621,0.01,,,8971,5922,4669 -Hernandia albiflora,heralb,Cape Tribulation,0.069,0.0195,3806,0.447,0.33,,3123,4145,4643,6086 -Ixora biflora,ixobif,Cape Tribulation,0.081,0.01,2760,0.843,0.55,41.5,5244,3892,1969,8094 -Lasianthus strigosus,lasstr,Cape Tribulation,0.055,0.0158,3313,0.684,0.15,7,1841,5100,2379,2731 -Litsea leefeana,litlee,Cape Tribulation,0.13,0.0144,3917,0.549,0.68,263.4,3984,4141,3816,9645 -Macaranga tanarius,mactan,Cape Tribulation,0.104,0.0205,46676,0.344,0,,,3377,,3901 -Mallotus mollissimus,malmol,Cape Tribulation,0.063,0.0352,16716,0.373,0.32,31.25,1788,5580,5163,7944 -Medicosma sessiliflora,medses,Cape Tribulation,0.106,0.0153,8164,0.69,0.65,,2844,9332,6514,10298 -Melastoma cyanoides,melaff,Cape Tribulation,0.046,0.0208,4009,0.381,0.6,0.07,2960,4057,4661,6637 -Myristica insipida,myrins,Cape Tribulation,0.106,0.0185,8379,0.433,0.51,1612,,6929,4852,9273 -Pittosporum rubiginosum,pitrub,Cape Tribulation,0.065,0.0143,9931,0.728,0.28,27.94,7428,7459,5265,6548 -Psychotria dallachiana,psydal,Cape Tribulation,0.079,0.0177,2495,0.612,0.33,,4290,5666,4916,4761 -Quassia baileyana,quabai,Cape Tribulation,0.086,0.023,9624,0.501,0.42,,,5867,3216,5719 -Rockinghamia angustifolia,rocang,Cape Tribulation,0.108,0.0158,10636,0.455,0.39,19.38,,5862,4611,6098 -Syzygium gustavioides,syzgus,Cape Tribulation,0.167,0.0129,3590,0.521,0.59,48000,2833,3121,3047,6584 -Syzygium sayeri,syzsay,Cape Tribulation,0.131,0.0137,2645,0.485,0.65,841,3929,5767,4939,9836 -Trema aspera,treasp,Cape Tribulation,0.053,0.0299,2071,0.357,0.53,5.12,3578,5291,5440,6695 +name_original,AusTraits_key,SLA (cm2/g),SLA_units,leaf longevity,lifespan_units,individual_id +Eucalyptus grandis,Leuning_1991,90,cm2/g,5--15,mo,1 +Grevillea robusta,Bell_1985,97.8,cm2/g,152--364.8,d,1 +Castanospermum australe,Bell_1985,123.1,cm2/g,,,1 +Elaeocarpus angustifolius,Bell_1985,124.8,cm2/g,,,1 +Gardenia actinocarpa,Bevege_1978,223,cm2/g,,,1 +Xanthostemon chrysanthus,Bevege_1978,130,cm2/g,,,1 +Xanthostemon formosus,Bevege_1978,159,cm2/g,,,1 +Archidendron kanisii,Bevege_1978,181,cm2/g,,,1 +Archidendron whitei,Bevege_1978,230,cm2/g,60--300,d,1 +Gardenia ovularis,Lambert_1979,168,cm2/g,,,1 +Acacia aneura var. major,Lambert_1979,32.3,cm2/g,,,1 +Acacia kempeana,Lambert_1979,39.3,cm2/g,,,1 +Corymbia terminalis,Lambert_1979,36.2,cm2/g,,,1 +Hakea suberea,Lambert_1979,20,cm2/g,,,1 +Acacia lysiphloia,Lambert_1979,82.2,cm2/g,,,1 +Acacia neurocarpa,Lambert_1979,64.3,cm2/g,,,1 +Acacia shirleyi,Lambert_1979,57.3,cm2/g,,,1 +Corymbia dichromophloia,Meakins_0000,51.6,cm2/g,,,1 +Eucalyptus chlorophylla,Meakins_0000,41.7,cm2/g,,,1 +Grevillea wickhamii ssp aprica,Meakins_0000,63.9,cm2/g,,,1 +Acacia holosericea,Meakins_0000,105.4,cm2/g,,,1 +Acacia holosericea,Meakins_0000,75.9,cm2/g,,,2 +Corymbia foelscheana,Meakins_0000,58.8,cm2/g,,,1 +Corymbia foelscheana,Meakins_0000,62,cm2/g,,,2 +Corymbia foelscheana,Meakins_0000,55.7,cm2/g,,,3 +Eucalyptus patellaris,Meakins_0000,45.9,cm2/g,,,1 +Grevillea dimidiata,Meakins_0000,51.8,cm2/g,,,1 +Hakea arborescens,Meakins_0000,28,cm2/g,,,1 +Acacia auriculiformis,Meakins_0000,134,cm2/g,,,1 +Eucalyptus miniata,Meakins_0000,73.6,cm2/g,,,1 +Eucalyptus tetrodonta,Meakins_0000,56.5,cm2/g,,,1 +Grevillea pteridifolia,Meakins_0000,51,cm2/g,,,1 +Persoonia falcata,Meakins_0000,68.5,cm2/g,,,1 diff --git a/tests/testthat/examples/Test_2023_5/metadata.yml b/tests/testthat/examples/Test_2023_5/metadata.yml index e3e536d9..4b7ed91f 100644 --- a/tests/testthat/examples/Test_2023_5/metadata.yml +++ b/tests/testthat/examples/Test_2023_5/metadata.yml @@ -1,319 +1,110 @@ source: primary: - key: Test_2023_5 + key: Richards_2008 + bibtype: Unpublished + year: '2009' + author: Anna Richards and Ian J. Wright + title: 'Unpublished data: Transcription of Australian plant functional trait data + from Ian Wright''s collection of papers, Macquarie University' + original_01: + key: Bell_1985 + bibtype: Conference + year: '1985' + author: Bell + booktitle: Conference proceedings of N Australian mine rehab workshop 9 + title: Nutrient requirements for the establishment of native flora at Weipa + volume: .na + number: .na + pages: .na + original_02: + key: Bevege_1978 + bibtype: TechReport + year: '1978' + author: D. I. Bevege + institution: Queensland Department of Forestry + title: Biomass and nutrient distribution in indigenous forest ecosystems + volume: 6 + number: .na + pages: 20 + original_03: + key: Lambert_1979 + bibtype: Thesis + year: '1979' + author: M. J. Lambert + title: Sulphur relationships of native and exotic tree species + type: Masters + institution: Macquarie University, Sydney + secondary_01: + key: Leuning_1991 bibtype: Article - author: Daniel S. Falster, Mark Westoby - year: 2005 - title: Alternative height strategies among 45 dicot rain forest species from tropical - Queensland, Australia - journal: Journal of Ecology - volume: 93 - pages: 521--535 - publisher: Wiley-Blackwell - doi: 10.1111/j.0022-0477.2005.00992.x + year: '1991' + author: R. Leuning and R. N. Cromer and S. Rance + journal: Oecologia + title: Spatial distributions of foliar nitrogen and phosphorus in crowns of Eucalyptus + grandis + volume: '88' + number: '4' + pages: 504--510 + doi: 10.1007/bf00317712 + secondary_02: + key: Meakins_0000 + bibtype: Unpublished + year: unknown + author: Meakins + title: 'Unpublished data: Study of Brindabella species' contributors: data_collectors: - - last_name: Falster - given_name: Daniel - ORCID: 0000-0002-9814-092X - affiliation: Evolution & Ecology Research Centre, School of Biological, Earth, - and Environmental Sciences, UNSW Sydney, Australia + - last_name: Richards + given_name: Anna + ORCID: 0000-0002-2934-5497 + affiliation: CSIRO Land and Water, Australia additional_role: contact - - last_name: Westoby - given_name: Mark - ORCID: 0000-0001-7690-4530 - affiliation: Department of Biological Sciences, Macquarie University, Australia - dataset_curators: Elizabeth Wenk + dataset_curators: Ian Wright dataset: data_is_long_format: no custom_R_code: .na - collection_date: 2004/2004 - taxon_name: Species - location_name: site - description: Investigation into trait values correlated with plant height along - light availability and successional gradients for far north Queensland species. + collection_date: unknown/2009 + taxon_name: name_original + location_name: .na + source_id: AusTraits_key + individual_id: individual_id + description: Collection of trait data on Australian plants compiled by Anna Richards + and Ian Wright from papers basis_of_record: field life_stage: adult - sampling_strategy: Nineteen species, ranging from early to late successional status, - were selected using published sources (Hopkins & Graham 1987; Osunkoya 1996; Hyland - et al. 1999). Species selected to represent the light gradient establish and mature - in closed forest, where successional species are assumed absent. For inclusion - in this set we required that a species was known to establish and persist at low - light levels, as indicated either by published sources (Hyland et al. 1999; Osunkoya - 1996) or by scientists familiar with the vegetation (A Graham, J Wells, CSIRO - Atherton; R Jensen). Twenty-six species, experiencing a range of light levels - at maturity, from high (canopy trees) to low light (understorey shrubs), were - included. - original_file: Falster & Westoby 2005 J Ecol appendix.doc + sampling_strategy: See the individual 'additional references' for the individual + study motivations. + original_file: The portion of 'Extra ozglop data OCT07 (iAN).xls' from pre-2000 + papers or from more recent papers with very few data points; most recent/larger + datasets within Ian and Anna's compilation are in AusTraits individually. notes: none -locations: - Atherton: - description: Tropical rain forest vegetation. - elevation (m): 800 - latitude (deg): -17.1166667 - longitude (deg): 145.65 - rainfall (mm): 2000 - Cape Tribulation: - description: Complex mesophyll vine forest in tropical rain forest. - elevation (m): 25 - latitude (deg): -16.1 - longitude (deg): 145.45 - rainfall (mm): 3500 +locations: .na contexts: .na traits: -- var_in: LMA (mg mm-2) - unit_in: mg/mm2 +- var_in: SLA (cm2/g) + unit_in: SLA_units trait_name: leaf_mass_per_area - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: LMA was calculated as the leaf dry mass (oven-dried for 48 hours at 65 - deg C) divided by leaf size. It was measured on the first five fully expanded - leaves at the tip of each individual. -- var_in: Leaf nitrogen (mg mg-1) - unit_in: mg/mg - trait_name: leaf_N_per_dry_mass - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: Leaves from all individuals per species were pooled and finely ground for - nitrogen analysis. Total nitrogen concentration (%) was measured using complete - combustion gas chromatography by Waite Analytical Services, Adelaide. The first - five fully expanded leaves at the tip of each individual were used for the analysis. -- var_in: leaf size (mm2) - unit_in: mm2 - trait_name: leaf_area - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: Leaf size was calculated as the one-sided leaf area (flat bed scanner). - It was measured on the first five fully expanded leaves at the tip of each individual. -- var_in: wood density (mg mm-3) - unit_in: mg/mm3 - trait_name: wood_density - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: Wood density was calculated using 40-60 mm stem segments taken 250 mm and - 1000 mm back along a branch from the branch tip. Fresh samples were refrigerated - before processing. After removing bark material, the volume of each wood sample - was determined using Archimedes' principle (Hacke et al. 2000). Samples were submerged - in a water-filled container on a balance. The weight change (mg) recorded during - submersion corresponds to the mass of water displaced, which can be converted - to a volume using the formula, displacement weight (mg)/0.998 (mg/mm3), where - 0.998 mg/mm3 is the density of water at 20 deg C. Samples were then dried for - 4 days at 60 deg C before weighing. -- var_in: branch mass fraction - unit_in: mg/mg - trait_name: branch_mass_fraction - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: '3' - methods: Branch mass fraction was calculated as the mass side branches/total mass, - on a carbon dry mass basis. The zero values are correct - these are plants with - no branches. -- var_in: Seed mass (mg) - unit_in: mg - trait_name: seed_dry_mass - entity_type: population + entity_type: individual value_type: mean basis_of_value: measurement replicates: unknown - methods: Mean oven-dried seed mass (including seed coat but excluding seed accessories) - was estimated for all species with available field material. In total, collections - for 17 of 47 species were made. Data for an additional 12 species were drawn from - published (Osunkoya et al. 1994; Grubb et al. 1998) and unpublished (P. Juniper, - CSIRO Atherton) sources. -- var_in: LASA10 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean + methods: unknown +- var_in: leaf longevity + unit_in: lifespan_units + trait_name: leaf_lifespan + entity_type: individual + value_type: bin basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a shoot whose sapwood had a cross sectional - area of 10 mm2. In detail from Wright_2006, which used this data, No single best - point exists to compare traits such as LM/ SM, LA/SM and LA/SA when considering - a set of species that varies widely in canopy architecture and typical maximum - height (here, approximately 20 cm to 85 m). We have used several approaches (Table - 1). In one study, we made measurements on the terminal twigs of each species, - i.e. on a relatively standard developmental unit (Westoby and Wright 2003). For - species at Ash, GLP, Myall and TRF, traits were measured at each of several different - distances back down the stem from the branch tip (Falster and Westoby 2005a, 2005b - and unpublished, Pickup et al. 2005). At GHP, RHM and RHW, traits were measured - at a standard sapwood cross-sectional area (10 mm2; Pickup et al. 2005). For the - present re-analysis, we took the raw data from the previous studies and, for every - species possible, calculated patterns of leaf and stem deployment at two standard - points: at 250 mm distance from the branch tip (Ash, GLP, Myall and TRF) and at - 10 mm2 stem (Ash, Myall, TRF) or sapwood (GHP, GLP, RHM, RHW) crosssectional area - (250 mm or 10 mm2 formulation denoted as subscript in trait abbreviations). This - was done as follows. For each individual plant, total leaf and stem dry mass at - 250 mm distance was estimated by straightline interpolation from values measured - at the nearest sampling points on either side of this distance. As the dry mass - data tended to display non-linear (power) relationships with distance from the - branch tip, the interpolated values were calculated from log10-log10- transformed - data, then back-transformed to the original scale. The same approach was used - for interpolating data to the standard stem (or sapwood) cross-sectional area. - For individuals where measurements had not been made on either side of the desired - point but the nearest measurement had been made within 25 mm of 250 mm or 1 mm2 - of 10 mm2 cross-section (i.e. within 10% of the desired point), we extrapolated - (rather than interpolated) the measured data to the standard point. This allowed - us to include a number of individuals and species for which interpolation was - not possible. Still, several large-leaved, large-stemmed species from the TRF - site could not be included in the 10-mm2 crosssection dataset. No unusual tendencies - in analyses, including the extrapolated data, were seen in comparison to analyses - including interpolated data only (details not shown). To illustrate how species'' - morphology varied at the two standard sampling points, species-mean stem cross-sectional - area varied between 1.2 and 258 mm2 at 250 mm distance from the branch tip, while - the distance from the branch tip at which stem cross-sectional area reached 10 - mm2 varied from 64 to 995 mm.' -- var_in: LASA250 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a 250 mm branch segment and sapwood cross-sectional - area was determined where the branch was cut. In detail from Wright_2006, which - used this data, No single best point exists to compare traits such as LM/ SM, - LA/SM and LA/SA when considering a set of species that varies widely in canopy - architecture and typical maximum height (here, approximately 20 cm to 85 m). We - have used several approaches (Table 1). In one study, we made measurements on - the terminal twigs of each species, i.e. on a relatively standard developmental - unit (Westoby and Wright 2003). For species at Ash, GLP, Myall and TRF, traits - were measured at each of several different distances back down the stem from the - branch tip (Falster and Westoby 2005a, 2005b and unpublished, Pickup et al. 2005). - At GHP, RHM and RHW, traits were measured at a standard sapwood cross-sectional - area (10 mm2; Pickup et al. 2005). For the present re-analysis, we took the raw - data from the previous studies and, for every species possible, calculated patterns - of leaf and stem deployment at two standard points: at 250 mm distance from the - branch tip (Ash, GLP, Myall and TRF) and at 10 mm2 stem (Ash, Myall, TRF) or sapwood - (GHP, GLP, RHM, RHW) crosssectional area (250 mm or 10 mm2 formulation denoted - as subscript in trait abbreviations). This was done as follows. For each individual - plant, total leaf and stem dry mass at 250 mm distance was estimated by straightline - interpolation from values measured at the nearest sampling points on either side - of this distance. As the dry mass data tended to display non-linear (power) relationships - with distance from the branch tip, the interpolated values were calculated from - log10-log10- transformed data, then back-transformed to the original scale. The - same approach was used for interpolating data to the standard stem (or sapwood) - cross-sectional area. For individuals where measurements had not been made on - either side of the desired point but the nearest measurement had been made within - 25 mm of 250 mm or 1 mm2 of 10 mm2 cross-section (i.e. within 10% of the desired - point), we extrapolated (rather than interpolated) the measured data to the standard - point. This allowed us to include a number of individuals and species for which - interpolation was not possible. Still, several large-leaved, large-stemmed species - from the TRF site could not be included in the 10-mm2 crosssection dataset. No - unusual tendencies in analyses, including the extrapolated data, were seen in - comparison to analyses including interpolated data only (details not shown). To - illustrate how species'' morphology varied at the two standard sampling points, - species-mean stem cross-sectional area varied between 1.2 and 258 mm2 at 250 mm - distance from the branch tip, while the distance from the branch tip at which - stem cross-sectional area reached 10 mm2 varied from 64 to 995 mm.' -- var_in: LASA50 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a 50 mm branch segment and sapwood cross-sectional - area was determined where the branch was cut. In detail from Wright_2006, which - used this data, No single best point exists to compare traits such as LM/ SM, - LA/SM and LA/SA when considering a set of species that varies widely in canopy - architecture and typical maximum height (here, approximately 20 cm to 85 m). We - have used several approaches (Table 1). In one study, we made measurements on - the terminal twigs of each species, i.e. on a relatively standard developmental - unit (Westoby and Wright 2003). For species at Ash, GLP, Myall and TRF, traits - were measured at each of several different distances back down the stem from the - branch tip (Falster and Westoby 2005a, 2005b and unpublished, Pickup et al. 2005). - At GHP, RHM and RHW, traits were measured at a standard sapwood cross-sectional - area (10 mm2; Pickup et al. 2005). For the present re-analysis, we took the raw - data from the previous studies and, for every species possible, calculated patterns - of leaf and stem deployment at two standard points: at 250 mm distance from the - branch tip (Ash, GLP, Myall and TRF) and at 10 mm2 stem (Ash, Myall, TRF) or sapwood - (GHP, GLP, RHM, RHW) crosssectional area (250 mm or 10 mm2 formulation denoted - as subscript in trait abbreviations). This was done as follows. For each individual - plant, total leaf and stem dry mass at 250 mm distance was estimated by straightline - interpolation from values measured at the nearest sampling points on either side - of this distance. As the dry mass data tended to display non-linear (power) relationships - with distance from the branch tip, the interpolated values were calculated from - log10-log10- transformed data, then back-transformed to the original scale. The - same approach was used for interpolating data to the standard stem (or sapwood) - cross-sectional area. For individuals where measurements had not been made on - either side of the desired point but the nearest measurement had been made within - 25 mm of 250 mm or 1 mm2 of 10 mm2 cross-section (i.e. within 10% of the desired - point), we extrapolated (rather than interpolated) the measured data to the standard - point. This allowed us to include a number of individuals and species for which - interpolation was not possible. Still, several large-leaved, large-stemmed species - from the TRF site could not be included in the 10-mm2 crosssection dataset. No - unusual tendencies in analyses, including the extrapolated data, were seen in - comparison to analyses including interpolated data only (details not shown). To - illustrate how species'' morphology varied at the two standard sampling points, - species-mean stem cross-sectional area varied between 1.2 and 258 mm2 at 250 mm - distance from the branch tip, while the distance from the branch tip at which - stem cross-sectional area reached 10 mm2 varied from 64 to 995 mm.' -- var_in: LASA1000 - unit_in: mm2{leaf}/mm2{sapwood} - trait_name: huber_value - entity_type: population - value_type: mean - basis_of_value: measurement - replicates: 3 - methods: 'Leaf area was determined for a 1000 mm branch segment and sapwood cross-sectional - area was determined where the branch was cut. In detail from Wright_2006, which - used this data, No single best point exists to compare traits such as LM/ SM, - LA/SM and LA/SA when considering a set of species that varies widely in canopy - architecture and typical maximum height (here, approximately 20 cm to 85 m). We - have used several approaches (Table 1). In one study, we made measurements on - the terminal twigs of each species, i.e. on a relatively standard developmental - unit (Westoby and Wright 2003). For species at Ash, GLP, Myall and TRF, traits - were measured at each of several different distances back down the stem from the - branch tip (Falster and Westoby 2005a, 2005b and unpublished, Pickup et al. 2005). - At GHP, RHM and RHW, traits were measured at a standard sapwood cross-sectional - area (10 mm2; Pickup et al. 2005). For the present re-analysis, we took the raw - data from the previous studies and, for every species possible, calculated patterns - of leaf and stem deployment at two standard points: at 250 mm distance from the - branch tip (Ash, GLP, Myall and TRF) and at 10 mm2 stem (Ash, Myall, TRF) or sapwood - (GHP, GLP, RHM, RHW) crosssectional area (250 mm or 10 mm2 formulation denoted - as subscript in trait abbreviations). This was done as follows. For each individual - plant, total leaf and stem dry mass at 250 mm distance was estimated by straightline - interpolation from values measured at the nearest sampling points on either side - of this distance. As the dry mass data tended to display non-linear (power) relationships - with distance from the branch tip, the interpolated values were calculated from - log10-log10- transformed data, then back-transformed to the original scale. The - same approach was used for interpolating data to the standard stem (or sapwood) - cross-sectional area. For individuals where measurements had not been made on - either side of the desired point but the nearest measurement had been made within - 25 mm of 250 mm or 1 mm2 of 10 mm2 cross-section (i.e. within 10% of the desired - point), we extrapolated (rather than interpolated) the measured data to the standard - point. This allowed us to include a number of individuals and species for which - interpolation was not possible. Still, several large-leaved, large-stemmed species - from the TRF site could not be included in the 10-mm2 crosssection dataset. No - unusual tendencies in analyses, including the extrapolated data, were seen in - comparison to analyses including interpolated data only (details not shown). To - illustrate how species'' morphology varied at the two standard sampling points, - species-mean stem cross-sectional area varied between 1.2 and 258 mm2 at 250 mm - distance from the branch tip, while the distance from the branch tip at which - stem cross-sectional area reached 10 mm2 varied from 64 to 995 mm.' + replicates: unknown + methods: From Richards_2008_2 (unpublished); See original references, listed alphabetically + under 'additional references' substitutions: .na -taxonomic_updates: -- find: Homalanthus novoguineensis - replace: Homalanthus novo-guineensis - reason: Change spelling to align with known name in APC (Daniel Falster, 2020.05.22) - taxonomic_resolution: species -- find: Haplostichanthus sp Coop. Ck - replace: Haplostichanthus submontanus - reason: Align previous phrase name with current APC name (E. Wenk, 2020-05-25) - taxonomic_resolution: species -- find: Psychotria sp Utchee Creek - replace: Psychotria sp. Utchee Creek (H.Flecker NQNC5313) - reason: Align to name in APC (D Falster, 2020.05.23) - taxonomic_resolution: species +taxonomic_updates: .na exclude_observations: .na -questions: .na +questions: + additional_traits: Birk_1992 - has all reported values for nutrient addition treatments + as well; Feller - has root nutrient values for 2 species; Hopmans_1993 - additional + micronutrient data for wood and bark; Leigh_2003 - gas exchange data in chart, + if we get hold of the author; Leigh_2006 - lots of additional data if we contact + author; Leuning_1991 - lots of gas exchanges, Jmax, Vcmax, detailed leaf N & P + data if we contact author diff --git a/tests/testthat/examples/Test_2023_5/output/contexts.csv b/tests/testthat/examples/Test_2023_5/output/contexts.csv new file mode 100644 index 00000000..873507fd --- /dev/null +++ b/tests/testthat/examples/Test_2023_5/output/contexts.csv @@ -0,0 +1 @@ +dataset_id,context_property,category,value,description,link_id,link_vals diff --git a/tests/testthat/examples/Test_2023_5/output/contributors.csv b/tests/testthat/examples/Test_2023_5/output/contributors.csv new file mode 100644 index 00000000..49519f1e --- /dev/null +++ b/tests/testthat/examples/Test_2023_5/output/contributors.csv @@ -0,0 +1,2 @@ +dataset_id,last_name,given_name,ORCID,affiliation,additional_role +Test_2023_5,Richards,Anna,0000-0002-2934-5497,"CSIRO Land and Water, Australia",contact diff --git a/tests/testthat/examples/Test_2023_5/output/definitions.yml b/tests/testthat/examples/Test_2023_5/output/definitions.yml new file mode 100644 index 00000000..780216c1 --- /dev/null +++ b/tests/testthat/examples/Test_2023_5/output/definitions.yml @@ -0,0 +1,34 @@ +leaf_mass_per_area: + label: Leaf mass per area + description: A leaf morphology trait [TO:0000748] which is the ratio [PATO:0001470] + of the leaf dry [PATO:0001824] mass [PATO:0000125] to the leaf [PO:0025034] area + [PATO:0001323], measured on an entire leaf, including the entire leaf lamina [PO:0020039] + and the petiole [PO:0020038].;The ratio of leaf dry mass to leaf area, measured + on an entire leaf including the petiole; LMA. (The inverse of specific leaf area, + SLA.) + comments: Leaf mass per area includes measurements submitted as `specific_leaf_area` + (SLA); they are simply inverted. Leaf mass per area is explicitly measured on + an entire leaf, including the petiole. Measurements made on a piece of the leaf + lamina, excluding petiole and midrib, are a separate trait `leaf_lamina_mass_per_area`. + If measurements are made on the entire leaf lamina, but the petiole is excluded, + this should be noted in the methods or under `measurement_remarks`. + type: numeric + units: g/m2 + allowed_values_min: 1.0 + allowed_values_max: 3000.0 + entity_URI: https://w3id.org/APD/traits/trait_0011230 +leaf_lifespan: + label: Leaf lifespan + description: The duration [PATO:0001309] that an individual leaf [PO:0025034] is + attached to the stem [PO:0009047] and is physiologically functional [PATO:0001510].;Duration + of time that an individual leaf is attached to the stem and physiologically functional; + leaf longevity. + comments: Leaf lifespan is the inverse of the rate of leaf turnover. For some species, + leaflets or other portions of a leaf may be censused rather than the entire leaf + lamina. Leaf lifespan can be censused as either the rate of shedding leaves (leaf + death) or the rate of formation of new leaves (leaf birth). + type: numeric + units: mo + allowed_values_min: 1.0 + allowed_values_max: 1000.0 + entity_URI: https://w3id.org/APD/traits/trait_0030025 diff --git a/tests/testthat/examples/Test_2023_5/output/excluded_data.csv b/tests/testthat/examples/Test_2023_5/output/excluded_data.csv new file mode 100644 index 00000000..547d5fdc --- /dev/null +++ b/tests/testthat/examples/Test_2023_5/output/excluded_data.csv @@ -0,0 +1 @@ +error,dataset_id,taxon_name,observation_id,trait_name,value,unit,entity_type,value_type,basis_of_value,replicates,basis_of_record,life_stage,population_id,individual_id,repeat_measurements_id,temporal_context_id,source_id,location_id,entity_context_id,plot_context_id,treatment_context_id,collection_date,measurement_remarks,method_id,method_context_id,original_name diff --git a/tests/testthat/examples/Test_2023_5/output/locations.csv b/tests/testthat/examples/Test_2023_5/output/locations.csv new file mode 100644 index 00000000..612c4908 --- /dev/null +++ b/tests/testthat/examples/Test_2023_5/output/locations.csv @@ -0,0 +1 @@ +dataset_id,location_id,location_name,location_property,value diff --git a/tests/testthat/examples/Test_2023_5/output/metadata.yml b/tests/testthat/examples/Test_2023_5/output/metadata.yml new file mode 100644 index 00000000..5dde7c3a --- /dev/null +++ b/tests/testthat/examples/Test_2023_5/output/metadata.yml @@ -0,0 +1,86 @@ +title: 'AusTraits: a curated plant trait database for the Australian flora' +description: AusTraits is a transformative database, containing measurements on the + traits of Australia's plant taxa, standardised from hundreds of disconnected primary + sources. While this repository contains the harmonised data, the raw data and code + used to build the resource are also available on the project's GitHub repository,http://traitecoevo.github.io/traits.build. + Further information on the project is available in the associated publication and + at the project website https://austraits.org. +version: 5.0.0 +doi: 10.5281/zenodo.5112001 +structure_URI: https://github.com/traitecoevo/traits.build +geo_location: + geo_location_place: Australia + geodetic_datum: EPSG:4326 +language: en +related_identifiers: +- related_identifier_type: url + identifier: https://github.com/traitecoevo/traits.build/tree/v3.0.2 + relation_type: isCompiledBy + resource_type: dataset +- related_identifier_type: doi + identifier: 10.1038/s41597-021-01006-6 + relation_type: isCitedBy + resource_type: publication-article +references: 'Falster, Gallagher et al (2021) *AusTraits, a curated plant trait database + for the Australian flora*. Scientific Data 8: 254, https://doi.org/10.1038/s41597-021-01006-6' +publisher: Zenodo +publication_date: 27 Nov 2022 +license: + rights: CC-BY-4.0 + rights_holder: Falster, Daniel + rights_URI: https://creativecommons.org/licenses/by/4.0/ + description: Under this license, the material can be copied and redistributed in + any medium or format. It can be remixed, transformed, and built upon for any purpose, + even commercially. Re-users must give appropriate credit, provide a link to the + license, and indicate if changes were made. Re-users may not apply legal terms + or technological measures that legally restrict others from doing anything the + license permits. +subject: + subject_scheme: ANZSRC Field of Research + scheme_URI: https://linked.data.gov.au/def/anzsrc-for/2020/ + value_URI: + - https://linked.data.gov.au/def/anzsrc-for/2020/3103 + - https://linked.data.gov.au/def/anzsrc-for/2020/3104 + - https://linked.data.gov.au/def/anzsrc-for/2020/4104 + - https://linked.data.gov.au/def/anzsrc-for/2020/300703 + - https://linked.data.gov.au/def/anzsrc-for/2020/060705 + - https://linked.data.gov.au/def/anzsrc-for/2020/050202 + - https://linked.data.gov.au/def/anzsrc-for/2020/060208 + - https://linked.data.gov.au/def/anzsrc-for/2020/069902 +funding_reference: +- funder_name: Australian Research Data Commons (ARDC) + award_IRI: doi.org/10.47486/DP720 + award_number: DP720 + award_title: AusTraits, A national database on the traits of Australia's complete + flora. +- funder_name: Australian Research Data Commons (ARDC) + award_IRI: doi.org/10.47486/TD044 + award_number: TD044 + award_title: AusTraits, A national database on the traits of Australia's complete + flora. +- funder_name: Australian Research Council + award_IRI: purl.org/au-research/grants/arc/DE170100208 + award_number: DE170100208 + award_title: Discovery Early Career Researcher Award +- funder_name: Australian Research Council + award_IRI: purl.org/au-research/grants/arc/FT160100113 + award_number: FT160100113 + award_title: Future Fellowship +- funder_name: Australian Research Council + award_IRI: purl.org/au-research/grants/arc/FT100100910 + award_number: FT100100910 + award_title: Future Fellowship +creators: +- last_name: Falster + given_name: Daniel + ORCID: 0000-0002-9814-092X + affiliation: Evolution & Ecology Research Centre, UNSW Sydney, Australia +- last_name: Gallagher + given_name: Rachael + ORCID: 0000-0002-4680-8115 + affiliation: Hawkesbury Institute for the Environment, Western Sydney University, + Australia +- last_name: Elizabeth + given_name: Wenk + ORCID: 0000-0001-5640-5910 + affiliation: Evolution & Ecology Research Centre, UNSW Sydney, Australia diff --git a/tests/testthat/examples/Test_2023_5/output/methods.csv b/tests/testthat/examples/Test_2023_5/output/methods.csv new file mode 100644 index 00000000..82a66e68 --- /dev/null +++ b/tests/testthat/examples/Test_2023_5/output/methods.csv @@ -0,0 +1,3 @@ +dataset_id,trait_name,methods,method_id,description,sampling_strategy,source_primary_key,source_primary_citation,source_secondary_key,source_secondary_citation,source_original_dataset_key,source_original_dataset_citation,data_collectors,assistants,dataset_curators +Test_2023_5,leaf_mass_per_area,unknown,01,Collection of trait data on Australian plants compiled by Anna Richards and Ian Wright from papers,See the individual 'additional references' for the individual study motivations.,Richards_2008,"A. Richards and I. J. Wright. ""Unpublished data: Transcription of Australian plant functional trait data from Ian Wright's collection of papers, Macquarie University"". 2009.",Leuning_1991; Meakins_0000,"R. Leuning, R. N. Cromer, and S. Rance. ""Spatial distributions of foliar nitrogen and phosphorus in crowns of Eucalyptus grandis"". _Oecologia_ 88.4 (1991), pp. 504-510. doi: [10.1007/bf00317712](https://doi.org/10.1007%2Fbf00317712); Meakins. ""Unpublished data: Study of Brindabella species"".",Bell_1985; Bevege_1978; Lambert_1979,"Bell. ""Nutrient requirements for the establishment of native flora at Weipa"". In: _Conference proceedings of N Australian mine rehab workshop 9_. 1985; D. I. Bevege. _Biomass and nutrient distribution in indigenous forest ecosystems_. Tech. rep. Queensland Department of Forestry, 1978, p. 20; M. J. Lambert. ""Sulphur relationships of native and exotic tree species"". Masters. Macquarie University, Sydney, 1979.",Anna Richards (contact),,Ian Wright +Test_2023_5,leaf_lifespan,"From Richards_2008_2 (unpublished); See original references, listed alphabetically under 'additional references'",01,Collection of trait data on Australian plants compiled by Anna Richards and Ian Wright from papers,See the individual 'additional references' for the individual study motivations.,Richards_2008,"A. Richards and I. J. Wright. ""Unpublished data: Transcription of Australian plant functional trait data from Ian Wright's collection of papers, Macquarie University"". 2009.",Leuning_1991; Meakins_0000,"R. Leuning, R. N. Cromer, and S. Rance. ""Spatial distributions of foliar nitrogen and phosphorus in crowns of Eucalyptus grandis"". _Oecologia_ 88.4 (1991), pp. 504-510. doi: [10.1007/bf00317712](https://doi.org/10.1007%2Fbf00317712); Meakins. ""Unpublished data: Study of Brindabella species"".",Bell_1985; Bevege_1978; Lambert_1979,"Bell. ""Nutrient requirements for the establishment of native flora at Weipa"". In: _Conference proceedings of N Australian mine rehab workshop 9_. 1985; D. I. Bevege. _Biomass and nutrient distribution in indigenous forest ecosystems_. Tech. rep. Queensland Department of Forestry, 1978, p. 20; M. J. Lambert. ""Sulphur relationships of native and exotic tree species"". Masters. Macquarie University, Sydney, 1979.",Anna Richards (contact),,Ian Wright diff --git a/tests/testthat/examples/Test_2023_5/output/sources.bib b/tests/testthat/examples/Test_2023_5/output/sources.bib new file mode 100644 index 00000000..561a2f91 --- /dev/null +++ b/tests/testthat/examples/Test_2023_5/output/sources.bib @@ -0,0 +1,46 @@ +@Unpublished{Richards_2008, + year = {2009}, + author = {Anna Richards and Ian J. Wright}, + title = {{Unpublished data: Transcription of Australian plant functional trait data from Ian Wright's collection of papers, Macquarie University}}, +} + +@Conference{Bell_1985, + year = {1985}, + author = {{Bell}}, + booktitle = {Conference proceedings of N Australian mine rehab workshop 9}, + title = {{Nutrient requirements for the establishment of native flora at Weipa}}, +} + +@TechReport{Bevege_1978, + year = {1978}, + author = {D. I. Bevege}, + institution = {Queensland Department of Forestry}, + title = {{Biomass and nutrient distribution in indigenous forest ecosystems}}, + volume = {6}, + pages = {20}, +} + +@Thesis{Lambert_1979, + year = {1979}, + author = {M. J. Lambert}, + title = {{Sulphur relationships of native and exotic tree species}}, + type = {Masters}, + institution = {Macquarie University, Sydney}, +} + +@Article{Leuning_1991, + year = {1991}, + author = {R. Leuning and R. N. Cromer and S. Rance}, + journal = {Oecologia}, + title = {{Spatial distributions of foliar nitrogen and phosphorus in crowns of Eucalyptus grandis}}, + volume = {88}, + number = {4}, + pages = {504--510}, + doi = {10.1007/bf00317712}, +} + +@Unpublished{Meakins_0000, + year = {unknown}, + author = {{Meakins}}, + title = {{Unpublished data: Study of Brindabella species}}, +} diff --git a/tests/testthat/examples/Test_2023_5/output/taxa.csv b/tests/testthat/examples/Test_2023_5/output/taxa.csv new file mode 100644 index 00000000..10c289ce --- /dev/null +++ b/tests/testthat/examples/Test_2023_5/output/taxa.csv @@ -0,0 +1,31 @@ +original_name,taxon_name,taxon_name_alternatives,genus,family,taxon_rank,taxonomic_dataset,taxonomic_status,subclass,taxon_distribution,scientific_name,taxon_id,taxon_ID_genus,scientific_name_id,canonical_name,cleaned_scientific_name_id,taxon_id_family,trinomial,binomial,establishment_means +Acacia aneura var. major,Acacia aneura var. major,,Acacia,Fabaceae,variety,APC,accepted,Magnoliidae,"NT, SA, Qld, NSW",Acacia aneura var. major Pedley,https://id.biodiversity.org.au/node/apni/2888234,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/169532,Acacia aneura var. major,https://id.biodiversity.org.au/name/apni/230757,https://id.biodiversity.org.au/taxon/apni/51702961,Acacia aneura var. major,Acacia aneura,native +Acacia auriculiformis,Acacia auriculiformis,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT, Qld",Acacia auriculiformis A.Cunn. ex Benth.,https://id.biodiversity.org.au/node/apni/2900508,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/58974,Acacia auriculiformis,https://id.biodiversity.org.au/name/apni/58974,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia auriculiformis,native and naturalised +Acacia holosericea,Acacia holosericea,Acacia colei (pro parte misapplied) | Acacia colei (misapplied),Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Acacia holosericea A.Cunn. ex G.Don,https://id.biodiversity.org.au/node/apni/2908330,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/64393,Acacia holosericea [alternative possible names: Acacia colei (pro parte misapplied) | Acacia colei (misapplied)],,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia holosericea,native +Acacia kempeana,Acacia kempeana,Acacia sibirica (pro parte misapplied),Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA",Acacia kempeana F.Muell.,https://id.biodiversity.org.au/taxon/apni/51436560,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/65035,Acacia kempeana [alternative possible names: Acacia sibirica (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia kempeana,native +Acacia lysiphloia,Acacia lysiphloia,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Acacia lysiphloia F.Muell.,https://id.biodiversity.org.au/node/apni/2898828,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/66472,Acacia lysiphloia,https://id.biodiversity.org.au/name/apni/66472,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia lysiphloia,native +Acacia neurocarpa,Acacia neurocarpa,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT",Acacia neurocarpa A.Cunn. ex Hook.,https://id.biodiversity.org.au/taxon/apni/51286994,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/67333,Acacia neurocarpa,https://id.biodiversity.org.au/name/apni/67333,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia neurocarpa,native +Acacia shirleyi,Acacia shirleyi,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"NT, Qld",Acacia shirleyi Maiden,https://id.biodiversity.org.au/node/apni/2897282,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/70301,Acacia shirleyi,https://id.biodiversity.org.au/name/apni/70301,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia shirleyi,native +Archidendron kanisii,Archidendron kanisii,,Archidendron,Fabaceae,species,APC,accepted,Magnoliidae,Qld,Archidendron kanisii R.S.Cowan,https://id.biodiversity.org.au/node/apni/2910703,https://id.biodiversity.org.au/taxon/apni/51299843,https://id.biodiversity.org.au/name/apni/154409,Archidendron kanisii,https://id.biodiversity.org.au/name/apni/154409,https://id.biodiversity.org.au/taxon/apni/51702961,,Archidendron kanisii,native +Archidendron whitei,Archidendron whitei,,Archidendron,Fabaceae,species,APC,accepted,Magnoliidae,Qld,Archidendron whitei I.C.Nielsen,https://id.biodiversity.org.au/node/apni/2895435,https://id.biodiversity.org.au/taxon/apni/51299843,https://id.biodiversity.org.au/name/apni/116851,Archidendron whitei,https://id.biodiversity.org.au/name/apni/116851,https://id.biodiversity.org.au/taxon/apni/51702961,,Archidendron whitei,native +Castanospermum australe,Castanospermum australe,,Castanospermum,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, NI (doubtfully naturalised)",Castanospermum australe A.Cunn. ex Mudie,https://id.biodiversity.org.au/node/apni/2894943,https://id.biodiversity.org.au/node/apni/7226268,https://id.biodiversity.org.au/name/apni/196675,Castanospermum australe,https://id.biodiversity.org.au/name/apni/196675,https://id.biodiversity.org.au/taxon/apni/51702961,,Castanospermum australe,native and naturalised +Corymbia dichromophloia,Corymbia dichromophloia,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Corymbia dichromophloia (F.Muell.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2902117,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119396,Corymbia dichromophloia,https://id.biodiversity.org.au/name/apni/119396,https://id.biodiversity.org.au/taxon/apni/51738744,,Corymbia dichromophloia,native +Corymbia foelscheana,Corymbia foelscheana,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT",Corymbia foelscheana (F.Muell.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2892950,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119404,Corymbia foelscheana,https://id.biodiversity.org.au/name/apni/119404,https://id.biodiversity.org.au/taxon/apni/51738744,,Corymbia foelscheana,native +Corymbia terminalis,Corymbia terminalis,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"NT, SA, Qld, NSW",Corymbia terminalis (F.Muell.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/7549846,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119435,Corymbia terminalis,https://id.biodiversity.org.au/name/apni/119435,https://id.biodiversity.org.au/taxon/apni/51738744,,Corymbia terminalis,native +Elaeocarpus angustifolius,Elaeocarpus angustifolius,Elaeocarpus grandis (pro parte misapplied),Elaeocarpus,Elaeocarpaceae,species,APC,accepted,Magnoliidae,NT,Elaeocarpus angustifolius Blume,https://id.biodiversity.org.au/node/apni/2909850,https://id.biodiversity.org.au/taxon/apni/51435153,https://id.biodiversity.org.au/name/apni/115318,Elaeocarpus angustifolius [alternative possible names: Elaeocarpus grandis (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51632282,,Elaeocarpus angustifolius,native +Eucalyptus chlorophylla,Eucalyptus chlorophylla,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus chlorophylla Brooker & Done,https://id.biodiversity.org.au/node/apni/2893400,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/112391,Eucalyptus chlorophylla,https://id.biodiversity.org.au/name/apni/112391,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus chlorophylla,native +Eucalyptus grandis,Eucalyptus grandis,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), Qld, NSW",Eucalyptus grandis W.Hill,https://id.biodiversity.org.au/taxon/apni/51439812,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/75405,Eucalyptus grandis,https://id.biodiversity.org.au/name/apni/75405,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus grandis,native and naturalised +Eucalyptus miniata,Eucalyptus miniata,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus miniata A.Cunn. ex Schauer,https://id.biodiversity.org.au/node/apni/2889426,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/56460,Eucalyptus miniata,https://id.biodiversity.org.au/name/apni/56460,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus miniata,native +Eucalyptus patellaris,Eucalyptus patellaris,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NT,Eucalyptus patellaris F.Muell.,https://id.biodiversity.org.au/node/apni/2906207,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/87496,Eucalyptus patellaris,https://id.biodiversity.org.au/name/apni/87496,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus patellaris,native +Eucalyptus tetrodonta,Eucalyptus tetrodonta,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus tetrodonta F.Muell.,https://id.biodiversity.org.au/node/apni/2905964,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/55572,Eucalyptus tetrodonta,https://id.biodiversity.org.au/name/apni/55572,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus tetrodonta,native +Gardenia actinocarpa,Gardenia actinocarpa,,Gardenia,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Gardenia actinocarpa Puttock,https://id.biodiversity.org.au/taxon/apni/51293926,https://id.biodiversity.org.au/taxon/apni/51293927,https://id.biodiversity.org.au/name/apni/74954,Gardenia actinocarpa,https://id.biodiversity.org.au/name/apni/74954,https://id.biodiversity.org.au/taxon/apni/51446612,,Gardenia actinocarpa,native +Gardenia ovularis,Gardenia ovularis,,Gardenia,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Gardenia ovularis F.M.Bailey,https://id.biodiversity.org.au/node/apni/2895410,https://id.biodiversity.org.au/taxon/apni/51293927,https://id.biodiversity.org.au/name/apni/75259,Gardenia ovularis,https://id.biodiversity.org.au/name/apni/75259,https://id.biodiversity.org.au/taxon/apni/51446612,,Gardenia ovularis,native +Grevillea dimidiata,Grevillea dimidiata,,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"WA, NT",Grevillea dimidiata F.Muell.,https://id.biodiversity.org.au/node/apni/2901789,https://id.biodiversity.org.au/taxon/apni/51726302,https://id.biodiversity.org.au/name/apni/61434,Grevillea dimidiata,https://id.biodiversity.org.au/name/apni/61434,https://id.biodiversity.org.au/taxon/apni/51732901,,Grevillea dimidiata,native +Grevillea pteridifolia,Grevillea pteridifolia,,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Grevillea pteridifolia Knight,https://id.biodiversity.org.au/node/apni/2910744,https://id.biodiversity.org.au/taxon/apni/51726302,https://id.biodiversity.org.au/name/apni/111324,Grevillea pteridifolia,https://id.biodiversity.org.au/name/apni/111324,https://id.biodiversity.org.au/taxon/apni/51732901,,Grevillea pteridifolia,native +Grevillea robusta,Grevillea robusta,,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"Qld, NSW (native and naturalised), LHI (naturalised), NI (naturalised)",Grevillea robusta A.Cunn. ex R.Br.,https://id.biodiversity.org.au/node/apni/2918082,https://id.biodiversity.org.au/taxon/apni/51726302,https://id.biodiversity.org.au/name/apni/55137,Grevillea robusta,https://id.biodiversity.org.au/name/apni/55137,https://id.biodiversity.org.au/taxon/apni/51732901,,Grevillea robusta,native and naturalised +,Grevillea wickhamii ssp aprica,,,,,,,,,,,,,,,,,, +Hakea arborescens,Hakea arborescens,,Hakea,Proteaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Hakea arborescens R.Br.,https://id.biodiversity.org.au/node/apni/2897149,https://id.biodiversity.org.au/taxon/apni/51445456,https://id.biodiversity.org.au/name/apni/76681,Hakea arborescens,https://id.biodiversity.org.au/name/apni/76681,https://id.biodiversity.org.au/taxon/apni/51732901,,Hakea arborescens,native +Hakea suberea,Hakea lorea subsp. lorea,,Hakea,Proteaceae,subspecies,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Hakea lorea (R.Br.) R.Br. subsp. lorea,https://id.biodiversity.org.au/node/apni/2918427,https://id.biodiversity.org.au/taxon/apni/51445456,https://id.biodiversity.org.au/name/apni/162920,Hakea lorea subsp. lorea,https://id.biodiversity.org.au/name/apni/99787,https://id.biodiversity.org.au/taxon/apni/51732901,Hakea lorea subsp. lorea,Hakea lorea,native +Persoonia falcata,Persoonia falcata,,Persoonia,Proteaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Persoonia falcata R.Br.,https://id.biodiversity.org.au/node/apni/2904820,https://id.biodiversity.org.au/taxon/apni/51429033,https://id.biodiversity.org.au/name/apni/112478,Persoonia falcata,https://id.biodiversity.org.au/name/apni/112478,https://id.biodiversity.org.au/taxon/apni/51732901,,Persoonia falcata,native +Xanthostemon chrysanthus,Xanthostemon chrysanthus,,Xanthostemon,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Xanthostemon chrysanthus (F.Muell.) Benth.,https://id.biodiversity.org.au/node/apni/2920567,https://id.biodiversity.org.au/taxon/apni/51440420,https://id.biodiversity.org.au/name/apni/55063,Xanthostemon chrysanthus,https://id.biodiversity.org.au/name/apni/55063,https://id.biodiversity.org.au/taxon/apni/51738744,,Xanthostemon chrysanthus,native +Xanthostemon formosus,Xanthostemon formosus,,Xanthostemon,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Xanthostemon formosus Peter G.Wilson,https://id.biodiversity.org.au/taxon/apni/51440419,https://id.biodiversity.org.au/taxon/apni/51440420,https://id.biodiversity.org.au/name/apni/117195,Xanthostemon formosus,https://id.biodiversity.org.au/name/apni/117195,https://id.biodiversity.org.au/taxon/apni/51738744,,Xanthostemon formosus,native diff --git a/tests/testthat/examples/Test_2023_5/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_5/output/taxonomic_updates.csv new file mode 100644 index 00000000..3317e35b --- /dev/null +++ b/tests/testthat/examples/Test_2023_5/output/taxonomic_updates.csv @@ -0,0 +1,31 @@ +dataset_id,original_name,aligned_name,taxonomic_resolution,taxon_name +Test_2023_5,Acacia aneura var. major,Acacia aneura var. major,,Acacia aneura var. major +Test_2023_5,Acacia auriculiformis,Acacia auriculiformis,,Acacia auriculiformis +Test_2023_5,Acacia holosericea,Acacia holosericea,,Acacia holosericea +Test_2023_5,Acacia kempeana,Acacia kempeana,,Acacia kempeana +Test_2023_5,Acacia lysiphloia,Acacia lysiphloia,,Acacia lysiphloia +Test_2023_5,Acacia neurocarpa,Acacia neurocarpa,,Acacia neurocarpa +Test_2023_5,Acacia shirleyi,Acacia shirleyi,,Acacia shirleyi +Test_2023_5,Archidendron kanisii,Archidendron kanisii,,Archidendron kanisii +Test_2023_5,Archidendron whitei,Archidendron whitei,,Archidendron whitei +Test_2023_5,Castanospermum australe,Castanospermum australe,,Castanospermum australe +Test_2023_5,Corymbia dichromophloia,Corymbia dichromophloia,,Corymbia dichromophloia +Test_2023_5,Corymbia foelscheana,Corymbia foelscheana,,Corymbia foelscheana +Test_2023_5,Corymbia terminalis,Corymbia terminalis,,Corymbia terminalis +Test_2023_5,Elaeocarpus angustifolius,Elaeocarpus angustifolius,,Elaeocarpus angustifolius +Test_2023_5,Eucalyptus chlorophylla,Eucalyptus chlorophylla,,Eucalyptus chlorophylla +Test_2023_5,Eucalyptus grandis,Eucalyptus grandis,,Eucalyptus grandis +Test_2023_5,Eucalyptus miniata,Eucalyptus miniata,,Eucalyptus miniata +Test_2023_5,Eucalyptus patellaris,Eucalyptus patellaris,,Eucalyptus patellaris +Test_2023_5,Eucalyptus tetrodonta,Eucalyptus tetrodonta,,Eucalyptus tetrodonta +Test_2023_5,Gardenia actinocarpa,Gardenia actinocarpa,,Gardenia actinocarpa +Test_2023_5,Gardenia ovularis,Gardenia ovularis,,Gardenia ovularis +Test_2023_5,Grevillea dimidiata,Grevillea dimidiata,,Grevillea dimidiata +Test_2023_5,Grevillea pteridifolia,Grevillea pteridifolia,,Grevillea pteridifolia +Test_2023_5,Grevillea robusta,Grevillea robusta,,Grevillea robusta +Test_2023_5,Grevillea wickhamii ssp aprica,Grevillea wickhamii ssp aprica,, +Test_2023_5,Hakea arborescens,Hakea arborescens,,Hakea arborescens +Test_2023_5,Hakea suberea,Hakea suberea,,Hakea lorea subsp. lorea +Test_2023_5,Persoonia falcata,Persoonia falcata,,Persoonia falcata +Test_2023_5,Xanthostemon chrysanthus,Xanthostemon chrysanthus,,Xanthostemon chrysanthus +Test_2023_5,Xanthostemon formosus,Xanthostemon formosus,,Xanthostemon formosus diff --git a/tests/testthat/examples/Test_2023_5/output/traits.csv b/tests/testthat/examples/Test_2023_5/output/traits.csv new file mode 100644 index 00000000..89481b17 --- /dev/null +++ b/tests/testthat/examples/Test_2023_5/output/traits.csv @@ -0,0 +1,37 @@ +dataset_id,taxon_name,observation_id,trait_name,value,unit,entity_type,value_type,basis_of_value,replicates,basis_of_record,life_stage,population_id,individual_id,repeat_measurements_id,temporal_context_id,source_id,location_id,entity_context_id,plot_context_id,treatment_context_id,collection_date,measurement_remarks,method_id,method_context_id,original_name +Test_2023_5,Acacia aneura var. major,01,leaf_mass_per_area,309.597523219814,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Lambert_1979,,,,,unknown/2009,,01,,Acacia aneura var. major +Test_2023_5,Acacia auriculiformis,02,leaf_mass_per_area,74.6268656716418,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Meakins_0000,,,,,unknown/2009,,01,,Acacia auriculiformis +Test_2023_5,Acacia holosericea,03,leaf_mass_per_area,94.876660341556,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Meakins_0000,,,,,unknown/2009,,01,,Acacia holosericea +Test_2023_5,Acacia holosericea,04,leaf_mass_per_area,131.752305665349,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,02,,,Meakins_0000,,,,,unknown/2009,,01,,Acacia holosericea +Test_2023_5,Acacia kempeana,05,leaf_mass_per_area,254.452926208651,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Lambert_1979,,,,,unknown/2009,,01,,Acacia kempeana +Test_2023_5,Acacia lysiphloia,06,leaf_mass_per_area,121.654501216545,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Lambert_1979,,,,,unknown/2009,,01,,Acacia lysiphloia +Test_2023_5,Acacia neurocarpa,07,leaf_mass_per_area,155.52099533437,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Lambert_1979,,,,,unknown/2009,,01,,Acacia neurocarpa +Test_2023_5,Acacia shirleyi,08,leaf_mass_per_area,174.520069808028,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Lambert_1979,,,,,unknown/2009,,01,,Acacia shirleyi +Test_2023_5,Archidendron kanisii,09,leaf_mass_per_area,55.2486187845304,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Bevege_1978,,,,,unknown/2009,,01,,Archidendron kanisii +Test_2023_5,Archidendron whitei,10,leaf_lifespan,1.97260057797197--9.86300288985985,mo,individual,bin,measurement,unknown,field,adult,pop_unk,01,,,Bevege_1978,,,,,unknown/2009,,01,,Archidendron whitei +Test_2023_5,Archidendron whitei,10,leaf_mass_per_area,43.4782608695652,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Bevege_1978,,,,,unknown/2009,,01,,Archidendron whitei +Test_2023_5,Castanospermum australe,11,leaf_mass_per_area,81.2347684809098,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Bell_1985,,,,,unknown/2009,,01,,Castanospermum australe +Test_2023_5,Corymbia dichromophloia,12,leaf_mass_per_area,193.798449612403,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Meakins_0000,,,,,unknown/2009,,01,,Corymbia dichromophloia +Test_2023_5,Corymbia foelscheana,13,leaf_mass_per_area,170.068027210884,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Meakins_0000,,,,,unknown/2009,,01,,Corymbia foelscheana +Test_2023_5,Corymbia foelscheana,14,leaf_mass_per_area,161.290322580645,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,02,,,Meakins_0000,,,,,unknown/2009,,01,,Corymbia foelscheana +Test_2023_5,Corymbia foelscheana,15,leaf_mass_per_area,179.533213644524,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,03,,,Meakins_0000,,,,,unknown/2009,,01,,Corymbia foelscheana +Test_2023_5,Corymbia terminalis,16,leaf_mass_per_area,276.243093922652,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Lambert_1979,,,,,unknown/2009,,01,,Corymbia terminalis +Test_2023_5,Elaeocarpus angustifolius,17,leaf_mass_per_area,80.1282051282051,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Bell_1985,,,,,unknown/2009,,01,,Elaeocarpus angustifolius +Test_2023_5,Eucalyptus chlorophylla,18,leaf_mass_per_area,239.808153477218,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Meakins_0000,,,,,unknown/2009,,01,,Eucalyptus chlorophylla +Test_2023_5,Eucalyptus grandis,19,leaf_lifespan,5--15,mo,individual,bin,measurement,unknown,field,adult,pop_unk,01,,,Leuning_1991,,,,,unknown/2009,,01,,Eucalyptus grandis +Test_2023_5,Eucalyptus grandis,19,leaf_mass_per_area,111.111111111111,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Leuning_1991,,,,,unknown/2009,,01,,Eucalyptus grandis +Test_2023_5,Eucalyptus miniata,20,leaf_mass_per_area,135.869565217391,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Meakins_0000,,,,,unknown/2009,,01,,Eucalyptus miniata +Test_2023_5,Eucalyptus patellaris,21,leaf_mass_per_area,217.864923747277,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Meakins_0000,,,,,unknown/2009,,01,,Eucalyptus patellaris +Test_2023_5,Eucalyptus tetrodonta,22,leaf_mass_per_area,176.991150442478,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Meakins_0000,,,,,unknown/2009,,01,,Eucalyptus tetrodonta +Test_2023_5,Gardenia actinocarpa,23,leaf_mass_per_area,44.8430493273543,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Bevege_1978,,,,,unknown/2009,,01,,Gardenia actinocarpa +Test_2023_5,Gardenia ovularis,24,leaf_mass_per_area,59.5238095238095,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Lambert_1979,,,,,unknown/2009,,01,,Gardenia ovularis +Test_2023_5,Grevillea dimidiata,25,leaf_mass_per_area,193.050193050193,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Meakins_0000,,,,,unknown/2009,,01,,Grevillea dimidiata +Test_2023_5,Grevillea pteridifolia,26,leaf_mass_per_area,196.078431372549,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Meakins_0000,,,,,unknown/2009,,01,,Grevillea pteridifolia +Test_2023_5,Grevillea robusta,27,leaf_lifespan,4.99725479752899--11.9934115140696,mo,individual,bin,measurement,unknown,field,adult,pop_unk,01,,,Bell_1985,,,,,unknown/2009,,01,,Grevillea robusta +Test_2023_5,Grevillea robusta,27,leaf_mass_per_area,102.249488752556,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Bell_1985,,,,,unknown/2009,,01,,Grevillea robusta +Test_2023_5,Grevillea wickhamii ssp aprica,28,leaf_mass_per_area,156.494522691706,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Meakins_0000,,,,,unknown/2009,,01,,Grevillea wickhamii ssp aprica +Test_2023_5,Hakea arborescens,29,leaf_mass_per_area,357.142857142857,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Meakins_0000,,,,,unknown/2009,,01,,Hakea arborescens +Test_2023_5,Hakea lorea subsp. lorea,30,leaf_mass_per_area,500,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Lambert_1979,,,,,unknown/2009,,01,,Hakea suberea +Test_2023_5,Persoonia falcata,31,leaf_mass_per_area,145.985401459854,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Meakins_0000,,,,,unknown/2009,,01,,Persoonia falcata +Test_2023_5,Xanthostemon chrysanthus,32,leaf_mass_per_area,76.9230769230769,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Bevege_1978,,,,,unknown/2009,,01,,Xanthostemon chrysanthus +Test_2023_5,Xanthostemon formosus,33,leaf_mass_per_area,62.8930817610063,g/m2,individual,mean,measurement,unknown,field,adult,pop_unk,01,,,Bevege_1978,,,,,unknown/2009,,01,,Xanthostemon formosus diff --git a/tests/testthat/examples/Test_2023_6/README.md b/tests/testthat/examples/Test_2023_6/README.md index 5d065ada..5d8a98d3 100644 --- a/tests/testthat/examples/Test_2023_6/README.md +++ b/tests/testthat/examples/Test_2023_6/README.md @@ -3,10 +3,14 @@ This dataset is for testing: - `individual_id` for long datasets -- Locations (latitude and longitude ranges instead of latitude and longitude points) - Different `bibtype`s and secondary and original sources (also check methods table) +- Locations (latitude and longitude ranges instead of latitude and longitude points) +- Check `observation_id` is different for different locations (Eucalyptus grandis) and the same for the same location (Archidendron whitei) or no location (Grevillea robusta) - Replicates in a mix of character and numeric format -Test_2023_6 is a copy of X with the following modifications: +Test_2023_6 is a copy of Richards_2008 modified for Test_2023_5 with the following modifications: +- Test_2023_5 pivoted to long format +- Added locations with latitude and longitude ranges +- Added replicates in metadata with character and numeric format See output/ for expected output files. diff --git a/tests/testthat/examples/Test_2023_6/data.csv b/tests/testthat/examples/Test_2023_6/data.csv new file mode 100644 index 00000000..2f34090e --- /dev/null +++ b/tests/testthat/examples/Test_2023_6/data.csv @@ -0,0 +1,37 @@ +name_original,AusTraits_key,SLA_units,lifespan_units,individual_id,trait_name,value,location_name +Eucalyptus grandis,Leuning_1991,cm2/g,mo,1,SLA (cm2/g),90,location_1 +Eucalyptus grandis,Leuning_1991,cm2/g,mo,1,leaf longevity,5--15,location_2 +Grevillea robusta,Bell_1985,cm2/g,d,1,SLA (cm2/g),97.8, +Grevillea robusta,Bell_1985,cm2/g,d,1,leaf longevity,152--364.8, +Castanospermum australe,Bell_1985,cm2/g,NA,1,SLA (cm2/g),123.1,location_1 +Elaeocarpus angustifolius,Bell_1985,cm2/g,NA,1,SLA (cm2/g),124.8,location_1 +Gardenia actinocarpa,Bevege_1978,cm2/g,NA,1,SLA (cm2/g),223,location_1 +Xanthostemon chrysanthus,Bevege_1978,cm2/g,NA,1,SLA (cm2/g),130,location_1 +Xanthostemon formosus,Bevege_1978,cm2/g,NA,1,SLA (cm2/g),159,location_1 +Archidendron kanisii,Bevege_1978,cm2/g,NA,1,SLA (cm2/g),181,location_1 +Archidendron whitei,Bevege_1978,cm2/g,d,1,SLA (cm2/g),230,location_1 +Archidendron whitei,Bevege_1978,cm2/g,d,1,leaf longevity,60--300,location_1 +Gardenia ovularis,Lambert_1979,cm2/g,NA,1,SLA (cm2/g),168,location_1 +Acacia aneura var. major,Lambert_1979,cm2/g,NA,1,SLA (cm2/g),32.3,location_1 +Acacia kempeana,Lambert_1979,cm2/g,NA,1,SLA (cm2/g),39.3,location_1 +Corymbia terminalis,Lambert_1979,cm2/g,NA,1,SLA (cm2/g),36.2,location_1 +Hakea suberea,Lambert_1979,cm2/g,NA,1,SLA (cm2/g),20,location_1 +Acacia lysiphloia,Lambert_1979,cm2/g,NA,1,SLA (cm2/g),82.2,location_1 +Acacia neurocarpa,Lambert_1979,cm2/g,NA,1,SLA (cm2/g),64.3,location_1 +Acacia shirleyi,Lambert_1979,cm2/g,NA,1,SLA (cm2/g),57.3,location_1 +Corymbia dichromophloia,Meakins_0000,cm2/g,NA,1,SLA (cm2/g),51.6,location_1 +Eucalyptus chlorophylla,Meakins_0000,cm2/g,NA,1,SLA (cm2/g),41.7,location_1 +Grevillea wickhamii ssp aprica,Meakins_0000,cm2/g,NA,1,SLA (cm2/g),63.9,location_1 +Acacia holosericea,Meakins_0000,cm2/g,NA,1,SLA (cm2/g),105.4,location_1 +Acacia holosericea,Meakins_0000,cm2/g,NA,2,SLA (cm2/g),75.9,location_1 +Corymbia foelscheana,Meakins_0000,cm2/g,NA,1,SLA (cm2/g),58.8,location_1 +Corymbia foelscheana,Meakins_0000,cm2/g,NA,2,SLA (cm2/g),62,location_1 +Corymbia foelscheana,Meakins_0000,cm2/g,NA,3,SLA (cm2/g),55.7,location_1 +Eucalyptus patellaris,Meakins_0000,cm2/g,NA,1,SLA (cm2/g),45.9,location_1 +Grevillea dimidiata,Meakins_0000,cm2/g,NA,1,SLA (cm2/g),51.8,location_1 +Hakea arborescens,Meakins_0000,cm2/g,NA,1,SLA (cm2/g),28,location_1 +Acacia auriculiformis,Meakins_0000,cm2/g,NA,1,SLA (cm2/g),134,location_1 +Eucalyptus miniata,Meakins_0000,cm2/g,NA,1,SLA (cm2/g),73.6,location_1 +Eucalyptus tetrodonta,Meakins_0000,cm2/g,NA,1,SLA (cm2/g),56.5,location_1 +Grevillea pteridifolia,Meakins_0000,cm2/g,NA,1,SLA (cm2/g),51,location_1 +Persoonia falcata,Meakins_0000,cm2/g,NA,1,SLA (cm2/g),68.5,location_1 diff --git a/tests/testthat/examples/Test_2023_6/metadata.yml b/tests/testthat/examples/Test_2023_6/metadata.yml new file mode 100644 index 00000000..aa9b0ccf --- /dev/null +++ b/tests/testthat/examples/Test_2023_6/metadata.yml @@ -0,0 +1,120 @@ +source: + primary: + key: Richards_2008 + bibtype: Unpublished + year: '2009' + author: Anna Richards and Ian J. Wright + title: 'Unpublished data: Transcription of Australian plant functional trait data + from Ian Wright''s collection of papers, Macquarie University' + original_01: + key: Bell_1985 + bibtype: Conference + year: '1985' + author: Bell + booktitle: Conference proceedings of N Australian mine rehab workshop 9 + title: Nutrient requirements for the establishment of native flora at Weipa + volume: .na + number: .na + pages: .na + original_02: + key: Bevege_1978 + bibtype: TechReport + year: '1978' + author: D. I. Bevege + institution: Queensland Department of Forestry + title: Biomass and nutrient distribution in indigenous forest ecosystems + volume: 6 + number: .na + pages: 20 + original_03: + key: Lambert_1979 + bibtype: Thesis + year: '1979' + author: M. J. Lambert + title: Sulphur relationships of native and exotic tree species + type: Masters + institution: Macquarie University, Sydney + secondary_01: + key: Leuning_1991 + bibtype: Article + year: '1991' + author: R. Leuning and R. N. Cromer and S. Rance + journal: Oecologia + title: Spatial distributions of foliar nitrogen and phosphorus in crowns of Eucalyptus + grandis + volume: '88' + number: '4' + pages: 504--510 + doi: 10.1007/bf00317712 + secondary_02: + key: Meakins_0000 + bibtype: Unpublished + year: unknown + author: Meakins + title: 'Unpublished data: Study of Brindabella species' +contributors: + data_collectors: + - last_name: Richards + given_name: Anna + ORCID: 0000-0002-2934-5497 + affiliation: CSIRO Land and Water, Australia + additional_role: contact + dataset_curators: Ian Wright +dataset: + data_is_long_format: yes + custom_R_code: .na + collection_date: unknown/2009 + taxon_name: name_original + trait_name: trait_name + value: value + location_name: location_name + source_id: AusTraits_key + individual_id: individual_id + description: Collection of trait data on Australian plants compiled by Anna Richards + and Ian Wright from papers + basis_of_record: field + life_stage: adult + sampling_strategy: See the individual 'additional references' for the individual + study motivations. + original_file: The portion of 'Extra ozglop data OCT07 (iAN).xls' from pre-2000 + papers or from more recent papers with very few data points; most recent/larger + datasets within Ian and Anna's compilation are in AusTraits individually. + notes: none +locations: + location_1: + latitude range (deg): -27.5 to -34.5 + longitude range (deg): 114 to 122 + description: First made-up location for testing + location_2: + latitude range (deg): -11 to -26 + longitude range (deg): 129 to 138 + description: Second made-up location for testing +contexts: .na +traits: +- var_in: SLA (cm2/g) + unit_in: SLA_units + trait_name: leaf_mass_per_area + entity_type: individual + value_type: mean + basis_of_value: measurement + replicates: 3 + methods: unknown +- var_in: leaf longevity + unit_in: lifespan_units + trait_name: leaf_lifespan + entity_type: individual + value_type: bin + basis_of_value: measurement + replicates: '5' + methods: From Richards_2008_2 (unpublished); See original references, listed alphabetically + under 'additional references' +substitutions: .na +taxonomic_updates: .na +exclude_observations: .na +questions: + additional_traits: Birk_1992 - has all reported values for nutrient addition treatments + as well; Feller - has root nutrient values for 2 species; Hopmans_1993 - additional + micronutrient data for wood and bark; Leigh_2003 - gas exchange data in chart, + if we get hold of the author; Leigh_2006 - lots of additional data if we contact + author; Leuning_1991 - lots of gas exchanges, Jmax, Vcmax, detailed leaf N & P + data if we contact author diff --git a/tests/testthat/examples/Test_2023_6/output/contexts.csv b/tests/testthat/examples/Test_2023_6/output/contexts.csv new file mode 100644 index 00000000..873507fd --- /dev/null +++ b/tests/testthat/examples/Test_2023_6/output/contexts.csv @@ -0,0 +1 @@ +dataset_id,context_property,category,value,description,link_id,link_vals diff --git a/tests/testthat/examples/Test_2023_6/output/contributors.csv b/tests/testthat/examples/Test_2023_6/output/contributors.csv new file mode 100644 index 00000000..3a2bc1a3 --- /dev/null +++ b/tests/testthat/examples/Test_2023_6/output/contributors.csv @@ -0,0 +1,2 @@ +dataset_id,last_name,given_name,ORCID,affiliation,additional_role +Test_2023_6,Richards,Anna,0000-0002-2934-5497,"CSIRO Land and Water, Australia",contact diff --git a/tests/testthat/examples/Test_2023_6/output/definitions.yml b/tests/testthat/examples/Test_2023_6/output/definitions.yml new file mode 100644 index 00000000..780216c1 --- /dev/null +++ b/tests/testthat/examples/Test_2023_6/output/definitions.yml @@ -0,0 +1,34 @@ +leaf_mass_per_area: + label: Leaf mass per area + description: A leaf morphology trait [TO:0000748] which is the ratio [PATO:0001470] + of the leaf dry [PATO:0001824] mass [PATO:0000125] to the leaf [PO:0025034] area + [PATO:0001323], measured on an entire leaf, including the entire leaf lamina [PO:0020039] + and the petiole [PO:0020038].;The ratio of leaf dry mass to leaf area, measured + on an entire leaf including the petiole; LMA. (The inverse of specific leaf area, + SLA.) + comments: Leaf mass per area includes measurements submitted as `specific_leaf_area` + (SLA); they are simply inverted. Leaf mass per area is explicitly measured on + an entire leaf, including the petiole. Measurements made on a piece of the leaf + lamina, excluding petiole and midrib, are a separate trait `leaf_lamina_mass_per_area`. + If measurements are made on the entire leaf lamina, but the petiole is excluded, + this should be noted in the methods or under `measurement_remarks`. + type: numeric + units: g/m2 + allowed_values_min: 1.0 + allowed_values_max: 3000.0 + entity_URI: https://w3id.org/APD/traits/trait_0011230 +leaf_lifespan: + label: Leaf lifespan + description: The duration [PATO:0001309] that an individual leaf [PO:0025034] is + attached to the stem [PO:0009047] and is physiologically functional [PATO:0001510].;Duration + of time that an individual leaf is attached to the stem and physiologically functional; + leaf longevity. + comments: Leaf lifespan is the inverse of the rate of leaf turnover. For some species, + leaflets or other portions of a leaf may be censused rather than the entire leaf + lamina. Leaf lifespan can be censused as either the rate of shedding leaves (leaf + death) or the rate of formation of new leaves (leaf birth). + type: numeric + units: mo + allowed_values_min: 1.0 + allowed_values_max: 1000.0 + entity_URI: https://w3id.org/APD/traits/trait_0030025 diff --git a/tests/testthat/examples/Test_2023_6/output/excluded_data.csv b/tests/testthat/examples/Test_2023_6/output/excluded_data.csv new file mode 100644 index 00000000..547d5fdc --- /dev/null +++ b/tests/testthat/examples/Test_2023_6/output/excluded_data.csv @@ -0,0 +1 @@ +error,dataset_id,taxon_name,observation_id,trait_name,value,unit,entity_type,value_type,basis_of_value,replicates,basis_of_record,life_stage,population_id,individual_id,repeat_measurements_id,temporal_context_id,source_id,location_id,entity_context_id,plot_context_id,treatment_context_id,collection_date,measurement_remarks,method_id,method_context_id,original_name diff --git a/tests/testthat/examples/Test_2023_6/output/locations.csv b/tests/testthat/examples/Test_2023_6/output/locations.csv new file mode 100644 index 00000000..80789e4e --- /dev/null +++ b/tests/testthat/examples/Test_2023_6/output/locations.csv @@ -0,0 +1,7 @@ +dataset_id,location_id,location_name,location_property,value +Test_2023_6,01,location_1,description,First made-up location for testing +Test_2023_6,01,location_1,latitude range (deg),-27.5 to -34.5 +Test_2023_6,01,location_1,longitude range (deg),114 to 122 +Test_2023_6,02,location_2,description,Second made-up location for testing +Test_2023_6,02,location_2,latitude range (deg),-11 to -26 +Test_2023_6,02,location_2,longitude range (deg),129 to 138 diff --git a/tests/testthat/examples/Test_2023_6/output/metadata.yml b/tests/testthat/examples/Test_2023_6/output/metadata.yml new file mode 100644 index 00000000..5dde7c3a --- /dev/null +++ b/tests/testthat/examples/Test_2023_6/output/metadata.yml @@ -0,0 +1,86 @@ +title: 'AusTraits: a curated plant trait database for the Australian flora' +description: AusTraits is a transformative database, containing measurements on the + traits of Australia's plant taxa, standardised from hundreds of disconnected primary + sources. While this repository contains the harmonised data, the raw data and code + used to build the resource are also available on the project's GitHub repository,http://traitecoevo.github.io/traits.build. + Further information on the project is available in the associated publication and + at the project website https://austraits.org. +version: 5.0.0 +doi: 10.5281/zenodo.5112001 +structure_URI: https://github.com/traitecoevo/traits.build +geo_location: + geo_location_place: Australia + geodetic_datum: EPSG:4326 +language: en +related_identifiers: +- related_identifier_type: url + identifier: https://github.com/traitecoevo/traits.build/tree/v3.0.2 + relation_type: isCompiledBy + resource_type: dataset +- related_identifier_type: doi + identifier: 10.1038/s41597-021-01006-6 + relation_type: isCitedBy + resource_type: publication-article +references: 'Falster, Gallagher et al (2021) *AusTraits, a curated plant trait database + for the Australian flora*. Scientific Data 8: 254, https://doi.org/10.1038/s41597-021-01006-6' +publisher: Zenodo +publication_date: 27 Nov 2022 +license: + rights: CC-BY-4.0 + rights_holder: Falster, Daniel + rights_URI: https://creativecommons.org/licenses/by/4.0/ + description: Under this license, the material can be copied and redistributed in + any medium or format. It can be remixed, transformed, and built upon for any purpose, + even commercially. Re-users must give appropriate credit, provide a link to the + license, and indicate if changes were made. Re-users may not apply legal terms + or technological measures that legally restrict others from doing anything the + license permits. +subject: + subject_scheme: ANZSRC Field of Research + scheme_URI: https://linked.data.gov.au/def/anzsrc-for/2020/ + value_URI: + - https://linked.data.gov.au/def/anzsrc-for/2020/3103 + - https://linked.data.gov.au/def/anzsrc-for/2020/3104 + - https://linked.data.gov.au/def/anzsrc-for/2020/4104 + - https://linked.data.gov.au/def/anzsrc-for/2020/300703 + - https://linked.data.gov.au/def/anzsrc-for/2020/060705 + - https://linked.data.gov.au/def/anzsrc-for/2020/050202 + - https://linked.data.gov.au/def/anzsrc-for/2020/060208 + - https://linked.data.gov.au/def/anzsrc-for/2020/069902 +funding_reference: +- funder_name: Australian Research Data Commons (ARDC) + award_IRI: doi.org/10.47486/DP720 + award_number: DP720 + award_title: AusTraits, A national database on the traits of Australia's complete + flora. +- funder_name: Australian Research Data Commons (ARDC) + award_IRI: doi.org/10.47486/TD044 + award_number: TD044 + award_title: AusTraits, A national database on the traits of Australia's complete + flora. +- funder_name: Australian Research Council + award_IRI: purl.org/au-research/grants/arc/DE170100208 + award_number: DE170100208 + award_title: Discovery Early Career Researcher Award +- funder_name: Australian Research Council + award_IRI: purl.org/au-research/grants/arc/FT160100113 + award_number: FT160100113 + award_title: Future Fellowship +- funder_name: Australian Research Council + award_IRI: purl.org/au-research/grants/arc/FT100100910 + award_number: FT100100910 + award_title: Future Fellowship +creators: +- last_name: Falster + given_name: Daniel + ORCID: 0000-0002-9814-092X + affiliation: Evolution & Ecology Research Centre, UNSW Sydney, Australia +- last_name: Gallagher + given_name: Rachael + ORCID: 0000-0002-4680-8115 + affiliation: Hawkesbury Institute for the Environment, Western Sydney University, + Australia +- last_name: Elizabeth + given_name: Wenk + ORCID: 0000-0001-5640-5910 + affiliation: Evolution & Ecology Research Centre, UNSW Sydney, Australia diff --git a/tests/testthat/examples/Test_2023_6/output/methods.csv b/tests/testthat/examples/Test_2023_6/output/methods.csv new file mode 100644 index 00000000..877866c5 --- /dev/null +++ b/tests/testthat/examples/Test_2023_6/output/methods.csv @@ -0,0 +1,3 @@ +dataset_id,trait_name,methods,method_id,description,sampling_strategy,source_primary_key,source_primary_citation,source_secondary_key,source_secondary_citation,source_original_dataset_key,source_original_dataset_citation,data_collectors,assistants,dataset_curators +Test_2023_6,leaf_mass_per_area,unknown,01,Collection of trait data on Australian plants compiled by Anna Richards and Ian Wright from papers,See the individual 'additional references' for the individual study motivations.,Richards_2008,"A. Richards and I. J. Wright. ""Unpublished data: Transcription of Australian plant functional trait data from Ian Wright's collection of papers, Macquarie University"". 2009.",Leuning_1991; Meakins_0000,"R. Leuning, R. N. Cromer, and S. Rance. ""Spatial distributions of foliar nitrogen and phosphorus in crowns of Eucalyptus grandis"". _Oecologia_ 88.4 (1991), pp. 504-510. doi: [10.1007/bf00317712](https://doi.org/10.1007%2Fbf00317712); Meakins. ""Unpublished data: Study of Brindabella species"".",Bell_1985; Bevege_1978; Lambert_1979,"Bell. ""Nutrient requirements for the establishment of native flora at Weipa"". In: _Conference proceedings of N Australian mine rehab workshop 9_. 1985; D. I. Bevege. _Biomass and nutrient distribution in indigenous forest ecosystems_. Tech. rep. Queensland Department of Forestry, 1978, p. 20; M. J. Lambert. ""Sulphur relationships of native and exotic tree species"". Masters. Macquarie University, Sydney, 1979.",Anna Richards (contact),,Ian Wright +Test_2023_6,leaf_lifespan,"From Richards_2008_2 (unpublished); See original references, listed alphabetically under 'additional references'",01,Collection of trait data on Australian plants compiled by Anna Richards and Ian Wright from papers,See the individual 'additional references' for the individual study motivations.,Richards_2008,"A. Richards and I. J. Wright. ""Unpublished data: Transcription of Australian plant functional trait data from Ian Wright's collection of papers, Macquarie University"". 2009.",Leuning_1991; Meakins_0000,"R. Leuning, R. N. Cromer, and S. Rance. ""Spatial distributions of foliar nitrogen and phosphorus in crowns of Eucalyptus grandis"". _Oecologia_ 88.4 (1991), pp. 504-510. doi: [10.1007/bf00317712](https://doi.org/10.1007%2Fbf00317712); Meakins. ""Unpublished data: Study of Brindabella species"".",Bell_1985; Bevege_1978; Lambert_1979,"Bell. ""Nutrient requirements for the establishment of native flora at Weipa"". In: _Conference proceedings of N Australian mine rehab workshop 9_. 1985; D. I. Bevege. _Biomass and nutrient distribution in indigenous forest ecosystems_. Tech. rep. Queensland Department of Forestry, 1978, p. 20; M. J. Lambert. ""Sulphur relationships of native and exotic tree species"". Masters. Macquarie University, Sydney, 1979.",Anna Richards (contact),,Ian Wright diff --git a/tests/testthat/examples/Test_2023_6/output/sources.bib b/tests/testthat/examples/Test_2023_6/output/sources.bib new file mode 100644 index 00000000..561a2f91 --- /dev/null +++ b/tests/testthat/examples/Test_2023_6/output/sources.bib @@ -0,0 +1,46 @@ +@Unpublished{Richards_2008, + year = {2009}, + author = {Anna Richards and Ian J. Wright}, + title = {{Unpublished data: Transcription of Australian plant functional trait data from Ian Wright's collection of papers, Macquarie University}}, +} + +@Conference{Bell_1985, + year = {1985}, + author = {{Bell}}, + booktitle = {Conference proceedings of N Australian mine rehab workshop 9}, + title = {{Nutrient requirements for the establishment of native flora at Weipa}}, +} + +@TechReport{Bevege_1978, + year = {1978}, + author = {D. I. Bevege}, + institution = {Queensland Department of Forestry}, + title = {{Biomass and nutrient distribution in indigenous forest ecosystems}}, + volume = {6}, + pages = {20}, +} + +@Thesis{Lambert_1979, + year = {1979}, + author = {M. J. Lambert}, + title = {{Sulphur relationships of native and exotic tree species}}, + type = {Masters}, + institution = {Macquarie University, Sydney}, +} + +@Article{Leuning_1991, + year = {1991}, + author = {R. Leuning and R. N. Cromer and S. Rance}, + journal = {Oecologia}, + title = {{Spatial distributions of foliar nitrogen and phosphorus in crowns of Eucalyptus grandis}}, + volume = {88}, + number = {4}, + pages = {504--510}, + doi = {10.1007/bf00317712}, +} + +@Unpublished{Meakins_0000, + year = {unknown}, + author = {{Meakins}}, + title = {{Unpublished data: Study of Brindabella species}}, +} diff --git a/tests/testthat/examples/Test_2023_6/output/taxa.csv b/tests/testthat/examples/Test_2023_6/output/taxa.csv new file mode 100644 index 00000000..10c289ce --- /dev/null +++ b/tests/testthat/examples/Test_2023_6/output/taxa.csv @@ -0,0 +1,31 @@ +original_name,taxon_name,taxon_name_alternatives,genus,family,taxon_rank,taxonomic_dataset,taxonomic_status,subclass,taxon_distribution,scientific_name,taxon_id,taxon_ID_genus,scientific_name_id,canonical_name,cleaned_scientific_name_id,taxon_id_family,trinomial,binomial,establishment_means +Acacia aneura var. major,Acacia aneura var. major,,Acacia,Fabaceae,variety,APC,accepted,Magnoliidae,"NT, SA, Qld, NSW",Acacia aneura var. major Pedley,https://id.biodiversity.org.au/node/apni/2888234,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/169532,Acacia aneura var. major,https://id.biodiversity.org.au/name/apni/230757,https://id.biodiversity.org.au/taxon/apni/51702961,Acacia aneura var. major,Acacia aneura,native +Acacia auriculiformis,Acacia auriculiformis,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), NT, Qld",Acacia auriculiformis A.Cunn. ex Benth.,https://id.biodiversity.org.au/node/apni/2900508,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/58974,Acacia auriculiformis,https://id.biodiversity.org.au/name/apni/58974,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia auriculiformis,native and naturalised +Acacia holosericea,Acacia holosericea,Acacia colei (pro parte misapplied) | Acacia colei (misapplied),Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Acacia holosericea A.Cunn. ex G.Don,https://id.biodiversity.org.au/node/apni/2908330,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/64393,Acacia holosericea [alternative possible names: Acacia colei (pro parte misapplied) | Acacia colei (misapplied)],,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia holosericea,native +Acacia kempeana,Acacia kempeana,Acacia sibirica (pro parte misapplied),Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT, SA",Acacia kempeana F.Muell.,https://id.biodiversity.org.au/taxon/apni/51436560,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/65035,Acacia kempeana [alternative possible names: Acacia sibirica (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia kempeana,native +Acacia lysiphloia,Acacia lysiphloia,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Acacia lysiphloia F.Muell.,https://id.biodiversity.org.au/node/apni/2898828,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/66472,Acacia lysiphloia,https://id.biodiversity.org.au/name/apni/66472,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia lysiphloia,native +Acacia neurocarpa,Acacia neurocarpa,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"WA, NT",Acacia neurocarpa A.Cunn. ex Hook.,https://id.biodiversity.org.au/taxon/apni/51286994,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/67333,Acacia neurocarpa,https://id.biodiversity.org.au/name/apni/67333,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia neurocarpa,native +Acacia shirleyi,Acacia shirleyi,,Acacia,Fabaceae,species,APC,accepted,Magnoliidae,"NT, Qld",Acacia shirleyi Maiden,https://id.biodiversity.org.au/node/apni/2897282,https://id.biodiversity.org.au/taxon/apni/51471290,https://id.biodiversity.org.au/name/apni/70301,Acacia shirleyi,https://id.biodiversity.org.au/name/apni/70301,https://id.biodiversity.org.au/taxon/apni/51702961,,Acacia shirleyi,native +Archidendron kanisii,Archidendron kanisii,,Archidendron,Fabaceae,species,APC,accepted,Magnoliidae,Qld,Archidendron kanisii R.S.Cowan,https://id.biodiversity.org.au/node/apni/2910703,https://id.biodiversity.org.au/taxon/apni/51299843,https://id.biodiversity.org.au/name/apni/154409,Archidendron kanisii,https://id.biodiversity.org.au/name/apni/154409,https://id.biodiversity.org.au/taxon/apni/51702961,,Archidendron kanisii,native +Archidendron whitei,Archidendron whitei,,Archidendron,Fabaceae,species,APC,accepted,Magnoliidae,Qld,Archidendron whitei I.C.Nielsen,https://id.biodiversity.org.au/node/apni/2895435,https://id.biodiversity.org.au/taxon/apni/51299843,https://id.biodiversity.org.au/name/apni/116851,Archidendron whitei,https://id.biodiversity.org.au/name/apni/116851,https://id.biodiversity.org.au/taxon/apni/51702961,,Archidendron whitei,native +Castanospermum australe,Castanospermum australe,,Castanospermum,Fabaceae,species,APC,accepted,Magnoliidae,"Qld, NSW, NI (doubtfully naturalised)",Castanospermum australe A.Cunn. ex Mudie,https://id.biodiversity.org.au/node/apni/2894943,https://id.biodiversity.org.au/node/apni/7226268,https://id.biodiversity.org.au/name/apni/196675,Castanospermum australe,https://id.biodiversity.org.au/name/apni/196675,https://id.biodiversity.org.au/taxon/apni/51702961,,Castanospermum australe,native and naturalised +Corymbia dichromophloia,Corymbia dichromophloia,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Corymbia dichromophloia (F.Muell.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2902117,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119396,Corymbia dichromophloia,https://id.biodiversity.org.au/name/apni/119396,https://id.biodiversity.org.au/taxon/apni/51738744,,Corymbia dichromophloia,native +Corymbia foelscheana,Corymbia foelscheana,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT",Corymbia foelscheana (F.Muell.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/2892950,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119404,Corymbia foelscheana,https://id.biodiversity.org.au/name/apni/119404,https://id.biodiversity.org.au/taxon/apni/51738744,,Corymbia foelscheana,native +Corymbia terminalis,Corymbia terminalis,,Corymbia,Myrtaceae,species,APC,accepted,Magnoliidae,"NT, SA, Qld, NSW",Corymbia terminalis (F.Muell.) K.D.Hill & L.A.S.Johnson,https://id.biodiversity.org.au/node/apni/7549846,https://id.biodiversity.org.au/taxon/apni/51439690,https://id.biodiversity.org.au/name/apni/119435,Corymbia terminalis,https://id.biodiversity.org.au/name/apni/119435,https://id.biodiversity.org.au/taxon/apni/51738744,,Corymbia terminalis,native +Elaeocarpus angustifolius,Elaeocarpus angustifolius,Elaeocarpus grandis (pro parte misapplied),Elaeocarpus,Elaeocarpaceae,species,APC,accepted,Magnoliidae,NT,Elaeocarpus angustifolius Blume,https://id.biodiversity.org.au/node/apni/2909850,https://id.biodiversity.org.au/taxon/apni/51435153,https://id.biodiversity.org.au/name/apni/115318,Elaeocarpus angustifolius [alternative possible names: Elaeocarpus grandis (pro parte misapplied)],,https://id.biodiversity.org.au/taxon/apni/51632282,,Elaeocarpus angustifolius,native +Eucalyptus chlorophylla,Eucalyptus chlorophylla,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus chlorophylla Brooker & Done,https://id.biodiversity.org.au/node/apni/2893400,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/112391,Eucalyptus chlorophylla,https://id.biodiversity.org.au/name/apni/112391,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus chlorophylla,native +Eucalyptus grandis,Eucalyptus grandis,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA (naturalised), Qld, NSW",Eucalyptus grandis W.Hill,https://id.biodiversity.org.au/taxon/apni/51439812,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/75405,Eucalyptus grandis,https://id.biodiversity.org.au/name/apni/75405,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus grandis,native and naturalised +Eucalyptus miniata,Eucalyptus miniata,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus miniata A.Cunn. ex Schauer,https://id.biodiversity.org.au/node/apni/2889426,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/56460,Eucalyptus miniata,https://id.biodiversity.org.au/name/apni/56460,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus miniata,native +Eucalyptus patellaris,Eucalyptus patellaris,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,NT,Eucalyptus patellaris F.Muell.,https://id.biodiversity.org.au/node/apni/2906207,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/87496,Eucalyptus patellaris,https://id.biodiversity.org.au/name/apni/87496,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus patellaris,native +Eucalyptus tetrodonta,Eucalyptus tetrodonta,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus tetrodonta F.Muell.,https://id.biodiversity.org.au/node/apni/2905964,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/55572,Eucalyptus tetrodonta,https://id.biodiversity.org.au/name/apni/55572,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus tetrodonta,native +Gardenia actinocarpa,Gardenia actinocarpa,,Gardenia,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Gardenia actinocarpa Puttock,https://id.biodiversity.org.au/taxon/apni/51293926,https://id.biodiversity.org.au/taxon/apni/51293927,https://id.biodiversity.org.au/name/apni/74954,Gardenia actinocarpa,https://id.biodiversity.org.au/name/apni/74954,https://id.biodiversity.org.au/taxon/apni/51446612,,Gardenia actinocarpa,native +Gardenia ovularis,Gardenia ovularis,,Gardenia,Rubiaceae,species,APC,accepted,Magnoliidae,Qld,Gardenia ovularis F.M.Bailey,https://id.biodiversity.org.au/node/apni/2895410,https://id.biodiversity.org.au/taxon/apni/51293927,https://id.biodiversity.org.au/name/apni/75259,Gardenia ovularis,https://id.biodiversity.org.au/name/apni/75259,https://id.biodiversity.org.au/taxon/apni/51446612,,Gardenia ovularis,native +Grevillea dimidiata,Grevillea dimidiata,,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"WA, NT",Grevillea dimidiata F.Muell.,https://id.biodiversity.org.au/node/apni/2901789,https://id.biodiversity.org.au/taxon/apni/51726302,https://id.biodiversity.org.au/name/apni/61434,Grevillea dimidiata,https://id.biodiversity.org.au/name/apni/61434,https://id.biodiversity.org.au/taxon/apni/51732901,,Grevillea dimidiata,native +Grevillea pteridifolia,Grevillea pteridifolia,,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Grevillea pteridifolia Knight,https://id.biodiversity.org.au/node/apni/2910744,https://id.biodiversity.org.au/taxon/apni/51726302,https://id.biodiversity.org.au/name/apni/111324,Grevillea pteridifolia,https://id.biodiversity.org.au/name/apni/111324,https://id.biodiversity.org.au/taxon/apni/51732901,,Grevillea pteridifolia,native +Grevillea robusta,Grevillea robusta,,Grevillea,Proteaceae,species,APC,accepted,Magnoliidae,"Qld, NSW (native and naturalised), LHI (naturalised), NI (naturalised)",Grevillea robusta A.Cunn. ex R.Br.,https://id.biodiversity.org.au/node/apni/2918082,https://id.biodiversity.org.au/taxon/apni/51726302,https://id.biodiversity.org.au/name/apni/55137,Grevillea robusta,https://id.biodiversity.org.au/name/apni/55137,https://id.biodiversity.org.au/taxon/apni/51732901,,Grevillea robusta,native and naturalised +,Grevillea wickhamii ssp aprica,,,,,,,,,,,,,,,,,, +Hakea arborescens,Hakea arborescens,,Hakea,Proteaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Hakea arborescens R.Br.,https://id.biodiversity.org.au/node/apni/2897149,https://id.biodiversity.org.au/taxon/apni/51445456,https://id.biodiversity.org.au/name/apni/76681,Hakea arborescens,https://id.biodiversity.org.au/name/apni/76681,https://id.biodiversity.org.au/taxon/apni/51732901,,Hakea arborescens,native +Hakea suberea,Hakea lorea subsp. lorea,,Hakea,Proteaceae,subspecies,APC,accepted,Magnoliidae,"WA, NT, SA, Qld, NSW",Hakea lorea (R.Br.) R.Br. subsp. lorea,https://id.biodiversity.org.au/node/apni/2918427,https://id.biodiversity.org.au/taxon/apni/51445456,https://id.biodiversity.org.au/name/apni/162920,Hakea lorea subsp. lorea,https://id.biodiversity.org.au/name/apni/99787,https://id.biodiversity.org.au/taxon/apni/51732901,Hakea lorea subsp. lorea,Hakea lorea,native +Persoonia falcata,Persoonia falcata,,Persoonia,Proteaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Persoonia falcata R.Br.,https://id.biodiversity.org.au/node/apni/2904820,https://id.biodiversity.org.au/taxon/apni/51429033,https://id.biodiversity.org.au/name/apni/112478,Persoonia falcata,https://id.biodiversity.org.au/name/apni/112478,https://id.biodiversity.org.au/taxon/apni/51732901,,Persoonia falcata,native +Xanthostemon chrysanthus,Xanthostemon chrysanthus,,Xanthostemon,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Xanthostemon chrysanthus (F.Muell.) Benth.,https://id.biodiversity.org.au/node/apni/2920567,https://id.biodiversity.org.au/taxon/apni/51440420,https://id.biodiversity.org.au/name/apni/55063,Xanthostemon chrysanthus,https://id.biodiversity.org.au/name/apni/55063,https://id.biodiversity.org.au/taxon/apni/51738744,,Xanthostemon chrysanthus,native +Xanthostemon formosus,Xanthostemon formosus,,Xanthostemon,Myrtaceae,species,APC,accepted,Magnoliidae,Qld,Xanthostemon formosus Peter G.Wilson,https://id.biodiversity.org.au/taxon/apni/51440419,https://id.biodiversity.org.au/taxon/apni/51440420,https://id.biodiversity.org.au/name/apni/117195,Xanthostemon formosus,https://id.biodiversity.org.au/name/apni/117195,https://id.biodiversity.org.au/taxon/apni/51738744,,Xanthostemon formosus,native diff --git a/tests/testthat/examples/Test_2023_6/output/taxonomic_updates.csv b/tests/testthat/examples/Test_2023_6/output/taxonomic_updates.csv new file mode 100644 index 00000000..fb5d493a --- /dev/null +++ b/tests/testthat/examples/Test_2023_6/output/taxonomic_updates.csv @@ -0,0 +1,31 @@ +dataset_id,original_name,aligned_name,taxonomic_resolution,taxon_name +Test_2023_6,Acacia aneura var. major,Acacia aneura var. major,,Acacia aneura var. major +Test_2023_6,Acacia auriculiformis,Acacia auriculiformis,,Acacia auriculiformis +Test_2023_6,Acacia holosericea,Acacia holosericea,,Acacia holosericea +Test_2023_6,Acacia kempeana,Acacia kempeana,,Acacia kempeana +Test_2023_6,Acacia lysiphloia,Acacia lysiphloia,,Acacia lysiphloia +Test_2023_6,Acacia neurocarpa,Acacia neurocarpa,,Acacia neurocarpa +Test_2023_6,Acacia shirleyi,Acacia shirleyi,,Acacia shirleyi +Test_2023_6,Archidendron kanisii,Archidendron kanisii,,Archidendron kanisii +Test_2023_6,Archidendron whitei,Archidendron whitei,,Archidendron whitei +Test_2023_6,Castanospermum australe,Castanospermum australe,,Castanospermum australe +Test_2023_6,Corymbia dichromophloia,Corymbia dichromophloia,,Corymbia dichromophloia +Test_2023_6,Corymbia foelscheana,Corymbia foelscheana,,Corymbia foelscheana +Test_2023_6,Corymbia terminalis,Corymbia terminalis,,Corymbia terminalis +Test_2023_6,Elaeocarpus angustifolius,Elaeocarpus angustifolius,,Elaeocarpus angustifolius +Test_2023_6,Eucalyptus chlorophylla,Eucalyptus chlorophylla,,Eucalyptus chlorophylla +Test_2023_6,Eucalyptus grandis,Eucalyptus grandis,,Eucalyptus grandis +Test_2023_6,Eucalyptus miniata,Eucalyptus miniata,,Eucalyptus miniata +Test_2023_6,Eucalyptus patellaris,Eucalyptus patellaris,,Eucalyptus patellaris +Test_2023_6,Eucalyptus tetrodonta,Eucalyptus tetrodonta,,Eucalyptus tetrodonta +Test_2023_6,Gardenia actinocarpa,Gardenia actinocarpa,,Gardenia actinocarpa +Test_2023_6,Gardenia ovularis,Gardenia ovularis,,Gardenia ovularis +Test_2023_6,Grevillea dimidiata,Grevillea dimidiata,,Grevillea dimidiata +Test_2023_6,Grevillea pteridifolia,Grevillea pteridifolia,,Grevillea pteridifolia +Test_2023_6,Grevillea robusta,Grevillea robusta,,Grevillea robusta +Test_2023_6,Grevillea wickhamii ssp aprica,Grevillea wickhamii ssp aprica,, +Test_2023_6,Hakea arborescens,Hakea arborescens,,Hakea arborescens +Test_2023_6,Hakea suberea,Hakea suberea,,Hakea lorea subsp. lorea +Test_2023_6,Persoonia falcata,Persoonia falcata,,Persoonia falcata +Test_2023_6,Xanthostemon chrysanthus,Xanthostemon chrysanthus,,Xanthostemon chrysanthus +Test_2023_6,Xanthostemon formosus,Xanthostemon formosus,,Xanthostemon formosus diff --git a/tests/testthat/examples/Test_2023_6/output/traits.csv b/tests/testthat/examples/Test_2023_6/output/traits.csv new file mode 100644 index 00000000..fbc9e401 --- /dev/null +++ b/tests/testthat/examples/Test_2023_6/output/traits.csv @@ -0,0 +1,37 @@ +dataset_id,taxon_name,observation_id,trait_name,value,unit,entity_type,value_type,basis_of_value,replicates,basis_of_record,life_stage,population_id,individual_id,repeat_measurements_id,temporal_context_id,source_id,location_id,entity_context_id,plot_context_id,treatment_context_id,collection_date,measurement_remarks,method_id,method_context_id,original_name +Test_2023_6,Acacia aneura var. major,01,leaf_mass_per_area,309.597523219814,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Lambert_1979,01,,,,unknown/2009,,01,,Acacia aneura var. major +Test_2023_6,Acacia auriculiformis,02,leaf_mass_per_area,74.6268656716418,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Meakins_0000,01,,,,unknown/2009,,01,,Acacia auriculiformis +Test_2023_6,Acacia holosericea,03,leaf_mass_per_area,94.876660341556,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Meakins_0000,01,,,,unknown/2009,,01,,Acacia holosericea +Test_2023_6,Acacia holosericea,04,leaf_mass_per_area,131.752305665349,g/m2,individual,mean,measurement,3,field,adult,01,02,,,Meakins_0000,01,,,,unknown/2009,,01,,Acacia holosericea +Test_2023_6,Acacia kempeana,05,leaf_mass_per_area,254.452926208651,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Lambert_1979,01,,,,unknown/2009,,01,,Acacia kempeana +Test_2023_6,Acacia lysiphloia,06,leaf_mass_per_area,121.654501216545,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Lambert_1979,01,,,,unknown/2009,,01,,Acacia lysiphloia +Test_2023_6,Acacia neurocarpa,07,leaf_mass_per_area,155.52099533437,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Lambert_1979,01,,,,unknown/2009,,01,,Acacia neurocarpa +Test_2023_6,Acacia shirleyi,08,leaf_mass_per_area,174.520069808028,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Lambert_1979,01,,,,unknown/2009,,01,,Acacia shirleyi +Test_2023_6,Archidendron kanisii,09,leaf_mass_per_area,55.2486187845304,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Bevege_1978,01,,,,unknown/2009,,01,,Archidendron kanisii +Test_2023_6,Archidendron whitei,10,leaf_lifespan,1.97260057797197--9.86300288985985,mo,individual,bin,measurement,5,field,adult,01,01,,,Bevege_1978,01,,,,unknown/2009,,01,,Archidendron whitei +Test_2023_6,Archidendron whitei,10,leaf_mass_per_area,43.4782608695652,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Bevege_1978,01,,,,unknown/2009,,01,,Archidendron whitei +Test_2023_6,Castanospermum australe,11,leaf_mass_per_area,81.2347684809098,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Bell_1985,01,,,,unknown/2009,,01,,Castanospermum australe +Test_2023_6,Corymbia dichromophloia,12,leaf_mass_per_area,193.798449612403,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Meakins_0000,01,,,,unknown/2009,,01,,Corymbia dichromophloia +Test_2023_6,Corymbia foelscheana,13,leaf_mass_per_area,170.068027210884,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Meakins_0000,01,,,,unknown/2009,,01,,Corymbia foelscheana +Test_2023_6,Corymbia foelscheana,14,leaf_mass_per_area,161.290322580645,g/m2,individual,mean,measurement,3,field,adult,01,02,,,Meakins_0000,01,,,,unknown/2009,,01,,Corymbia foelscheana +Test_2023_6,Corymbia foelscheana,15,leaf_mass_per_area,179.533213644524,g/m2,individual,mean,measurement,3,field,adult,01,03,,,Meakins_0000,01,,,,unknown/2009,,01,,Corymbia foelscheana +Test_2023_6,Corymbia terminalis,16,leaf_mass_per_area,276.243093922652,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Lambert_1979,01,,,,unknown/2009,,01,,Corymbia terminalis +Test_2023_6,Elaeocarpus angustifolius,17,leaf_mass_per_area,80.1282051282051,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Bell_1985,01,,,,unknown/2009,,01,,Elaeocarpus angustifolius +Test_2023_6,Eucalyptus chlorophylla,18,leaf_mass_per_area,239.808153477218,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Meakins_0000,01,,,,unknown/2009,,01,,Eucalyptus chlorophylla +Test_2023_6,Eucalyptus grandis,19,leaf_mass_per_area,111.111111111111,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Leuning_1991,01,,,,unknown/2009,,01,,Eucalyptus grandis +Test_2023_6,Eucalyptus grandis,20,leaf_lifespan,5--15,mo,individual,bin,measurement,5,field,adult,02,01,,,Leuning_1991,02,,,,unknown/2009,,01,,Eucalyptus grandis +Test_2023_6,Eucalyptus miniata,21,leaf_mass_per_area,135.869565217391,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Meakins_0000,01,,,,unknown/2009,,01,,Eucalyptus miniata +Test_2023_6,Eucalyptus patellaris,22,leaf_mass_per_area,217.864923747277,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Meakins_0000,01,,,,unknown/2009,,01,,Eucalyptus patellaris +Test_2023_6,Eucalyptus tetrodonta,23,leaf_mass_per_area,176.991150442478,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Meakins_0000,01,,,,unknown/2009,,01,,Eucalyptus tetrodonta +Test_2023_6,Gardenia actinocarpa,24,leaf_mass_per_area,44.8430493273543,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Bevege_1978,01,,,,unknown/2009,,01,,Gardenia actinocarpa +Test_2023_6,Gardenia ovularis,25,leaf_mass_per_area,59.5238095238095,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Lambert_1979,01,,,,unknown/2009,,01,,Gardenia ovularis +Test_2023_6,Grevillea dimidiata,26,leaf_mass_per_area,193.050193050193,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Meakins_0000,01,,,,unknown/2009,,01,,Grevillea dimidiata +Test_2023_6,Grevillea pteridifolia,27,leaf_mass_per_area,196.078431372549,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Meakins_0000,01,,,,unknown/2009,,01,,Grevillea pteridifolia +Test_2023_6,Grevillea robusta,28,leaf_lifespan,4.99725479752899--11.9934115140696,mo,individual,bin,measurement,5,field,adult,pop_unk,01,,,Bell_1985,,,,,unknown/2009,,01,,Grevillea robusta +Test_2023_6,Grevillea robusta,28,leaf_mass_per_area,102.249488752556,g/m2,individual,mean,measurement,3,field,adult,pop_unk,01,,,Bell_1985,,,,,unknown/2009,,01,,Grevillea robusta +Test_2023_6,Grevillea wickhamii ssp aprica,29,leaf_mass_per_area,156.494522691706,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Meakins_0000,01,,,,unknown/2009,,01,,Grevillea wickhamii ssp aprica +Test_2023_6,Hakea arborescens,30,leaf_mass_per_area,357.142857142857,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Meakins_0000,01,,,,unknown/2009,,01,,Hakea arborescens +Test_2023_6,Hakea lorea subsp. lorea,31,leaf_mass_per_area,500,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Lambert_1979,01,,,,unknown/2009,,01,,Hakea suberea +Test_2023_6,Persoonia falcata,32,leaf_mass_per_area,145.985401459854,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Meakins_0000,01,,,,unknown/2009,,01,,Persoonia falcata +Test_2023_6,Xanthostemon chrysanthus,33,leaf_mass_per_area,76.9230769230769,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Bevege_1978,01,,,,unknown/2009,,01,,Xanthostemon chrysanthus +Test_2023_6,Xanthostemon formosus,34,leaf_mass_per_area,62.8930817610063,g/m2,individual,mean,measurement,3,field,adult,01,01,,,Bevege_1978,01,,,,unknown/2009,,01,,Xanthostemon formosus diff --git a/tests/testthat/examples/Test_2023_7/output/taxa.csv b/tests/testthat/examples/Test_2023_7/output/taxa.csv index 1eeab5bc..58eb53be 100644 --- a/tests/testthat/examples/Test_2023_7/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_7/output/taxa.csv @@ -1,3 +1,3 @@ original_name,taxon_name,taxon_name_alternatives,genus,family,taxon_rank,taxonomic_dataset,taxonomic_status,subclass,taxon_distribution,scientific_name,taxon_id,taxon_ID_genus,scientific_name_id,canonical_name,cleaned_scientific_name_id,taxon_id_family,trinomial,binomial,establishment_means -Eucalyptus miniata,Eucalyptus miniata,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus miniata A.Cunn. ex Schauer,https://id.biodiversity.org.au/node/apni/2889426,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/56460,Eucalyptus miniata,https://id.biodiversity.org.au/name/apni/56460,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus miniata,native -Eucalyptus tetrodonta,Eucalyptus tetrodonta,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus tetrodonta F.Muell.,https://id.biodiversity.org.au/node/apni/2905964,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/55572,Eucalyptus tetrodonta,https://id.biodiversity.org.au/name/apni/55572,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus tetrodonta,native +Eucalyptus miniata,Eucalyptus miniata,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus miniata A.Cunn. ex Schauer,https://id.biodiversity.org.au/node/apni/2889426,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/56460,Eucalyptus miniata,https://id.biodiversity.org.au/name/apni/56460,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus miniata,native +Eucalyptus tetrodonta,Eucalyptus tetrodonta,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus tetrodonta F.Muell.,https://id.biodiversity.org.au/node/apni/2905964,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/55572,Eucalyptus tetrodonta,https://id.biodiversity.org.au/name/apni/55572,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus tetrodonta,native diff --git a/tests/testthat/examples/Test_2023_8/output/taxa.csv b/tests/testthat/examples/Test_2023_8/output/taxa.csv index 1eeab5bc..58eb53be 100644 --- a/tests/testthat/examples/Test_2023_8/output/taxa.csv +++ b/tests/testthat/examples/Test_2023_8/output/taxa.csv @@ -1,3 +1,3 @@ original_name,taxon_name,taxon_name_alternatives,genus,family,taxon_rank,taxonomic_dataset,taxonomic_status,subclass,taxon_distribution,scientific_name,taxon_id,taxon_ID_genus,scientific_name_id,canonical_name,cleaned_scientific_name_id,taxon_id_family,trinomial,binomial,establishment_means -Eucalyptus miniata,Eucalyptus miniata,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus miniata A.Cunn. ex Schauer,https://id.biodiversity.org.au/node/apni/2889426,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/56460,Eucalyptus miniata,https://id.biodiversity.org.au/name/apni/56460,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus miniata,native -Eucalyptus tetrodonta,Eucalyptus tetrodonta,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus tetrodonta F.Muell.,https://id.biodiversity.org.au/node/apni/2905964,https://id.biodiversity.org.au/taxon/apni/51702982,https://id.biodiversity.org.au/name/apni/55572,Eucalyptus tetrodonta,https://id.biodiversity.org.au/name/apni/55572,https://id.biodiversity.org.au/taxon/apni/51702983,,Eucalyptus tetrodonta,native +Eucalyptus miniata,Eucalyptus miniata,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus miniata A.Cunn. ex Schauer,https://id.biodiversity.org.au/node/apni/2889426,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/56460,Eucalyptus miniata,https://id.biodiversity.org.au/name/apni/56460,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus miniata,native +Eucalyptus tetrodonta,Eucalyptus tetrodonta,,Eucalyptus,Myrtaceae,species,APC,accepted,Magnoliidae,"WA, NT, Qld",Eucalyptus tetrodonta F.Muell.,https://id.biodiversity.org.au/node/apni/2905964,https://id.biodiversity.org.au/taxon/apni/51738743,https://id.biodiversity.org.au/name/apni/55572,Eucalyptus tetrodonta,https://id.biodiversity.org.au/name/apni/55572,https://id.biodiversity.org.au/taxon/apni/51738744,,Eucalyptus tetrodonta,native diff --git a/tests/testthat/test-setup.R b/tests/testthat/test-setup.R index 2b885c3a..8819d5b3 100644 --- a/tests/testthat/test-setup.R +++ b/tests/testthat/test-setup.R @@ -618,7 +618,7 @@ test_that("`build_setup_pipeline` is working", { expect_silent(taxa2 <- read_csv_char("config/taxon_list.csv")) expect_contains(names(taxa2), vars) expect_true(length(names(taxa2)) > 2) - expect_true(nrow(taxa2) == 232) + expect_true(nrow(taxa2) == 258) ## Now try building in a controlled env, using base method base_tmp_env <- new.env() diff --git a/tests/testthat/test-xamples.R b/tests/testthat/test-xamples.R index 5ea7332c..786fb85f 100644 --- a/tests/testthat/test-xamples.R +++ b/tests/testthat/test-xamples.R @@ -175,6 +175,75 @@ testthat::test_that("Test Dataset 4 builds correctly", { # If there are repeat measurements at the species level, the code works fine because `observation_id` # is the same across rows for a given species + +testthat::test_that("Test Dataset 5 builds correctly", { + + # Test Dataset 5: Test_2023_5 + # See README.md in examples/Test_2023_5 for details about this dataset + + # Build dataset + expect_no_error( + Test_2023_5 <- test_build_dataset( + file.path(examples_dir, "Test_2023_5/metadata.yml"), + file.path(examples_dir, "Test_2023_5/data.csv"), + "Test Dataset 5", definitions, unit_conversions, schema, resource_metadata, taxon_list + ), + info = "Building Test Dataset 5") + + # Expected output + tables <- c("traits", "locations", "contexts", "methods", "excluded_data", + "taxonomic_updates", "taxa", "contributors") + expect_no_error( + expected_output <- + purrr::map( + tables, ~read_csv(sprintf("examples/Test_2023_5/output/%s.csv", .x), col_types = cols(.default = "c"))), + info = "Reading in expected output tables" + ) + # Todo: also load and test non-csv outputs + names(expected_output) <- tables + + # Check all tables are equal to expected output tables + for (v in tables) { + expect_equal(Test_2023_5[[v]], expected_output[[v]]) + } + +}) + + +testthat::test_that("Test Dataset 6 builds correctly", { + + # Test Dataset 6: Test_2023_6 + # See README.md in examples/Test_2023_6 for details about this dataset + + # Build dataset + expect_no_error( + Test_2023_6 <- test_build_dataset( + file.path(examples_dir, "Test_2023_6/metadata.yml"), + file.path(examples_dir, "Test_2023_6/data.csv"), + "Test Dataset 6", definitions, unit_conversions, schema, resource_metadata, taxon_list + ), + info = "Building Test Dataset 6") + + # Expected output + tables <- c("traits", "locations", "contexts", "methods", "excluded_data", + "taxonomic_updates", "taxa", "contributors") + expect_no_error( + expected_output <- + purrr::map( + tables, ~read_csv(sprintf("examples/Test_2023_6/output/%s.csv", .x), col_types = cols(.default = "c"))), + info = "Reading in expected output tables" + ) + # Todo: also load and test non-csv outputs + names(expected_output) <- tables + + # Check all tables are equal to expected output tables + for (v in tables) { + expect_equal(Test_2023_6[[v]], expected_output[[v]]) + } + +}) + + testthat::test_that("Test Dataset 7 builds correctly", { # Test Dataset 7: Test_2023_7 From 49a3a8cea3cb34a1bb3cab1d3a8a44d193b0a6fa Mon Sep 17 00:00:00 2001 From: Daniel Falster Date: Thu, 16 Nov 2023 15:53:58 +1100 Subject: [PATCH 22/31] Bump version: 1.0.0 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0f748602..292d7d77 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: traits.build Title: Package used to build an AusTraits data resource -Version: 0.9.0 +Version: 1.0.0 Maintainer: Daniel Falster Authors@R: c( person(given = "Daniel", family = "Falster", role = c("cre", "aut"), email = "daniel.falster@unsw.edu.au", comment = c(ORCID = "0000-0002-9814-092X")), From 1d139e84c14509d5f6b05f8741b7bf88ee238e16 Mon Sep 17 00:00:00 2001 From: Daniel Falster Date: Thu, 16 Nov 2023 15:54:11 +1100 Subject: [PATCH 23/31] Update Description and website --- DESCRIPTION | 4 +- NEWS.md | 8 +- _pkgdown.yml | 20 ++- docs/404.html | 4 +- docs/LICENSE-text.html | 4 +- docs/authors.html | 24 ++- docs/index.html | 12 +- docs/news/index.html | 11 +- docs/pkgdown.yml | 2 +- docs/reference/bib_print.html | 4 +- docs/reference/build_add_version.html | 4 +- docs/reference/build_combine.html | 4 +- docs/reference/build_setup_pipeline.html | 9 +- docs/reference/check_pivot_duplicates.html | 120 +++++++++++++++ docs/reference/check_pivot_wider.html | 113 ++++++++++++++ docs/reference/create_tree_branch.html | 4 +- docs/reference/dataset_build.html | 8 +- docs/reference/dataset_configure.html | 4 +- docs/reference/dataset_find_taxon.html | 4 +- docs/reference/dataset_process.html | 4 +- docs/reference/dataset_report.html | 28 ++-- docs/reference/dataset_test.html | 6 +- docs/reference/dataset_test_worker.html | 4 +- docs/reference/dataset_update_taxonomy.html | 117 ++++++++++++++ docs/reference/db_traits_pivot_longer.html | 143 ++++++++++++++++++ docs/reference/db_traits_pivot_wider.html | 141 +++++++++++++++++ docs/reference/get_schema.html | 4 +- docs/reference/get_unit_conversions.html | 4 +- docs/reference/index.html | 40 ++++- docs/reference/metadata_add_contexts.html | 4 +- docs/reference/metadata_add_locations.html | 4 +- .../reference/metadata_add_source_bibtex.html | 4 +- docs/reference/metadata_add_source_doi.html | 4 +- docs/reference/metadata_add_substitution.html | 4 +- .../metadata_add_substitutions_list.html | 4 +- .../metadata_add_substitutions_table.html | 4 +- .../metadata_add_taxonomic_change.html | 11 +- .../metadata_add_taxonomic_changes_list.html | 4 +- docs/reference/metadata_add_traits.html | 4 +- .../metadata_check_custom_R_code.html | 10 +- docs/reference/metadata_create_template.html | 8 +- .../metadata_exclude_observations.html | 4 +- .../metadata_find_taxonomic_change.html | 4 +- docs/reference/metadata_path_dataset_id.html | 10 +- .../metadata_remove_taxonomic_change.html | 4 +- .../metadata_update_taxonomic_change.html | 4 +- .../metadata_user_select_column.html | 4 +- .../reference/metadata_user_select_names.html | 4 +- docs/reference/notes_random_string.html | 4 +- docs/reference/notetaker_add_note.html | 4 +- docs/reference/notetaker_as_note.html | 4 +- docs/reference/notetaker_get_note.html | 4 +- docs/reference/notetaker_print_all.html | 4 +- docs/reference/notetaker_print_note.html | 4 +- docs/reference/notetaker_print_notes.html | 4 +- docs/reference/notetaker_start.html | 4 +- docs/reference/pipe.html | 4 +- .../plot_trait_distribution_beeswarm.html | 140 +++++++++++++++++ docs/reference/process_add_all_columns.html | 4 +- docs/reference/process_convert_units.html | 4 +- .../process_create_observation_id.html | 4 +- docs/reference/process_custom_code.html | 4 +- .../process_flag_excluded_observations.html | 4 +- .../process_flag_out_of_range_values.html | 4 +- .../process_flag_unsupported_characters.html | 4 +- .../process_flag_unsupported_traits.html | 4 +- .../process_flag_unsupported_values.html | 4 +- docs/reference/process_format_contexts.html | 4 +- .../process_format_contributors.html | 4 +- docs/reference/process_format_locations.html | 4 +- docs/reference/process_generate_id.html | 12 +- .../process_generate_method_ids.html | 4 +- docs/reference/process_parse_data.html | 4 +- docs/reference/process_standardise_names.html | 4 +- docs/reference/process_taxonomic_updates.html | 4 +- .../process_unit_conversion_name.html | 4 +- docs/reference/read_csv_char.html | 4 +- docs/reference/read_metadata.html | 4 +- docs/reference/read_metadata_dataset.html | 10 +- docs/reference/read_yaml.html | 4 +- docs/reference/traits.build-package.html | 10 +- docs/reference/util_append_to_list.html | 4 +- docs/reference/util_bib_to_list.html | 4 +- docs/reference/util_check_all_values_in.html | 4 +- .../util_check_disallowed_chars.html | 4 +- docs/reference/util_df_convert_character.html | 4 +- docs/reference/util_df_to_list.html | 4 +- docs/reference/util_extract_list_element.html | 4 +- docs/reference/util_get_SHA.html | 4 +- docs/reference/util_get_version.html | 4 +- docs/reference/util_kable_styling_html.html | 6 +- docs/reference/util_list_to_bib.html | 4 +- docs/reference/util_list_to_df1.html | 4 +- docs/reference/util_list_to_df2.html | 4 +- docs/reference/util_replace_null.html | 4 +- docs/reference/util_separate_and_sort.html | 4 +- docs/reference/util_standardise_doi.html | 4 +- docs/reference/write_metadata.html | 4 +- docs/reference/write_metadata_dataset.html | 4 +- docs/reference/write_plaintext.html | 4 +- docs/reference/write_yaml.html | 4 +- docs/sitemap.xml | 18 +++ 102 files changed, 1102 insertions(+), 239 deletions(-) create mode 100644 docs/reference/check_pivot_duplicates.html create mode 100644 docs/reference/check_pivot_wider.html create mode 100644 docs/reference/dataset_update_taxonomy.html create mode 100644 docs/reference/db_traits_pivot_longer.html create mode 100644 docs/reference/db_traits_pivot_wider.html create mode 100644 docs/reference/plot_trait_distribution_beeswarm.html diff --git a/DESCRIPTION b/DESCRIPTION index 292d7d77..ff4668da 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Type: Package Package: traits.build -Title: Package used to build an AusTraits data resource +Title: A workflow for harmonising trait data from diverse sources into a documented standard structure. Version: 1.0.0 Maintainer: Daniel Falster Authors@R: c( @@ -11,7 +11,7 @@ Authors@R: c( person("ARDC", role = c("fnd")), person("ARC", role = c("fnd")) ) -Description: This package enables harmonising of data from diverse sources. The code was originally built to support AusTraits, an open-source compilation of data on the traits of Australian plant species. For more information on AusTraits go to https://austraits.org. +Description: The `traits.build` package provides a workflow to harmonise trait data from diverse sources. The code was originally built to support AusTraits (see Falster et al 2021, , ) and has been generalised here to support construction of other trait databases. For detailed instructions and examples see . BugReports: https://github.com/traitecoevo/traits.build/issues URL: http://traitecoevo.github.io/traits.build/ License: BSD_2_clause + file LICENCE diff --git a/NEWS.md b/NEWS.md index 86860b02..9bb7e039 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ -# traits.build 0.9.0 +# traits.build 1.0.0 -* Moved vignettes to -* migrate code from +This is the first major release of the {traits.build} package, providing a workflow to enable harmonise data from diverse sources. The code was originally built to support AusTraits (see Falster et al 2021, , ) and has been generalised here to support construction of other trait databases. Detailed instructions are available at + +- package website: +- package book: diff --git a/_pkgdown.yml b/_pkgdown.yml index d1c1f42b..1f6113e9 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -29,7 +29,7 @@ navbar: reference: - title: Building a dataset or compilation - desc: Functions that can be used when building individual datasets and entire compilation + desc: Functions that can be used when building individual datasets and entire compilation. contents: - '`build_setup_pipeline`' - '`build_combine`' @@ -45,7 +45,7 @@ reference: - '`util_get_version`' - title: Creating metadata files - desc: functions that help you create metadata files + desc: Functions that help you create metadata files. contents: - '`dataset_test`' - '`metadata_create_template`' @@ -67,7 +67,7 @@ reference: - '`dataset_find_taxon`' - title: Reading & writing files - desc: Enable reading and wring of various file types + desc: Enable reading and wring of various file types. contents: - '`read_csv_char`' - '`read_metadata`' @@ -76,6 +76,15 @@ reference: - '`write_yaml`' - '`write_plaintext`' + - title: Working with outputs + desc: Functions to work with compiled traits.build objects. + contents: + - '`plot_trait_distribution_beeswarm`' + - '`check_pivot_duplicates`' + - '`check_pivot_wider`' + - '`db_traits_pivot_longer`' + - '`db_traits_pivot_wider`' + - title: Building a compilation (private) desc: Private functions that are called in the background when building individual datasets and entire compilation. These are only of interest to developers. contents: @@ -104,8 +113,9 @@ reference: - '`read_metadata_dataset`' - '`write_metadata_dataset`' - - title: Diverse utility functions for converting and working with various data types - desc: ~ + + - title: Diverse utility functions + desc: Diverse utility functions for converting and working with various data types. contents: - '`util_append_to_list`' - '`bib_print`' diff --git a/docs/404.html b/docs/404.html index 37ce8897..05a5b522 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ traits.build - 0.9.0 + 1.0.0
@@ -101,7 +101,7 @@

Page not found (404)