From 41cd67b6f199391180dd40511339328fbd4d1323 Mon Sep 17 00:00:00 2001 From: Elizabeth Wenk Date: Tue, 14 Jan 2025 14:19:48 +1100 Subject: [PATCH] Add field for `bibtype` Add column to methods table that documents the bibtype. This allows database users to filter data to include only specific reference type (e.g. omitting unpublished data or data from reports). --- R/process.R | 2 + inst/support/traits.build_schema.yml | 1 + .../examples/Test_2023_1/output/methods.csv | 46 +++++++++---------- .../examples/Test_2023_2/output/methods.csv | 22 ++++----- .../examples/Test_2023_3/output/methods.csv | 14 +++--- .../examples/Test_2023_4/output/methods.csv | 16 +++---- .../examples/Test_2023_5/output/methods.csv | 6 +-- .../examples/Test_2023_6/output/methods.csv | 6 +-- .../examples/Test_2023_7/output/methods.csv | 6 +-- .../examples/Test_2023_8/output/methods.csv | 6 +-- 10 files changed, 64 insertions(+), 61 deletions(-) diff --git a/R/process.R b/R/process.R index 2b1f0334..422cf68e 100644 --- a/R/process.R +++ b/R/process.R @@ -1633,6 +1633,7 @@ process_format_methods <- function(metadata, dataset_id, sources, contributors) ) source_primary_key <- metadata$source$primary$key + source_primary_type <- metadata$source$primary$bibtype source_secondary_keys <- citation_types %>% dplyr::filter(.data$type == "secondary") %>% purrr::pluck("source_id") @@ -1676,6 +1677,7 @@ process_format_methods <- function(metadata, dataset_id, sources, contributors) tibble::tibble( dataset_id = dataset_id, source_primary_key = source_primary_key, + source_primary_type = source_primary_type, source_primary_citation = bib_print(sources[[source_primary_key]]), source_secondary_key = ifelse( length(source_secondary_keys) > 0, diff --git a/inst/support/traits.build_schema.yml b/inst/support/traits.build_schema.yml index 47abc2a2..0576ad55 100644 --- a/inst/support/traits.build_schema.yml +++ b/inst/support/traits.build_schema.yml @@ -115,6 +115,7 @@ austraits: description: &description A 1-2 sentence description of the purpose of the study. sampling_strategy: &sampling_strategy A written description of how study locations were selected and how study individuals were selected. When available, this information is lifted verbatim from a published manuscript. For preserved specimens, this field ideally indicates which records were 'sampled' to measure a specific trait. source_primary_key: Citation key for the primary source in `sources`. The key is typically formatted as `Surname_year`. + source_primary_type: Citation type for the primary source in `sources`, using standard BibTex citation types (Article, Book, Misc, Online, Report, Techreport, Thesis, Unpublished). source_primary_citation: Citation for the primary source. This detail is generated from the primary source in the metadata. source_secondary_key: Citation key for the secondary source in `sources`. The key is typically formatted as `Surname_year`. source_secondary_citation: Citations for the secondary source. This detail is generated from the secondary source in the metadata. diff --git a/tests/testthat/examples/Test_2023_1/output/methods.csv b/tests/testthat/examples/Test_2023_1/output/methods.csv index a62bbd02..30f575c4 100644 --- a/tests/testthat/examples/Test_2023_1/output/methods.csv +++ b/tests/testthat/examples/Test_2023_1/output/methods.csv @@ -1,23 +1,23 @@ -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_1,leaf_mass_per_area,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.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,leaf_N_per_dry_mass,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,leaf_area,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.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,wood_density,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,seed_dry_mass,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,seed_dry_mass,Made up bin value.,02,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,huber_value,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,huber_value,"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.",02,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,huber_value,"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.",03,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,huber_value,"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.",04,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,huber_value,Should be different `method_id` here.,05,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,flowering_time,Made up flowering time values.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,plant_growth_form,Made up growth form values.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,wrong_trait_name,Test that a wrong trait name will go to excluded data.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,wood_density,Test that NA units will go to excluded data.,02,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,seed_dry_mass,Test that a unit without a unit conversion will go to excluded data.,03,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,leaf_length,Made up leaf length values to test reading in units from a column.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,leaf_photosynthesis,Test `repeat_measurements_id` at the trait level for individuals.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,leaf_stomatal_conductance,Test `repeat_measurements_id` at the trait level for populations.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,leaf_stomatal_conductance,Test `repeat_measurements_id` at the trait level for species.,02,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,leaf_stomatal_conductance,Test that `repeat_measurements_id` is not made for traits where `repeat_measurements_id` is set to FALSE but have already been entered with `repeat_measurements_id` as TRUE from another column.,03,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_1,seed_dry_mass,Test unit conversions for bins with a fixed trait-level unit.,04,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +dataset_id,trait_name,methods,method_id,description,sampling_strategy,source_primary_key,source_primary_type,source_primary_citation,source_secondary_key,source_secondary_citation,source_original_dataset_key,source_original_dataset_citation,data_collectors,assistants,dataset_curators +Test_2023_1,leaf_mass_per_area,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.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,leaf_N_per_dry_mass,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,leaf_area,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.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,wood_density,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,seed_dry_mass,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,seed_dry_mass,Made up bin value.,02,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,huber_value,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,huber_value,"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.",02,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,huber_value,"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.",03,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,huber_value,"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.",04,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,huber_value,Should be different `method_id` here.,05,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,flowering_time,Made up flowering time values.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,plant_growth_form,Made up growth form values.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,wrong_trait_name,Test that a wrong trait name will go to excluded data.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,wood_density,Test that NA units will go to excluded data.,02,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,seed_dry_mass,Test that a unit without a unit conversion will go to excluded data.,03,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,leaf_length,Made up leaf length values to test reading in units from a column.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,leaf_photosynthesis,Test `repeat_measurements_id` at the trait level for individuals.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,leaf_stomatal_conductance,Test `repeat_measurements_id` at the trait level for populations.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,leaf_stomatal_conductance,Test `repeat_measurements_id` at the trait level for species.,02,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,leaf_stomatal_conductance,Test that `repeat_measurements_id` is not made for traits where `repeat_measurements_id` is set to FALSE but have already been entered with `repeat_measurements_id` as TRUE from another column.,03,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_1,seed_dry_mass,Test unit conversions for bins with a fixed trait-level unit.,04,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_1,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk diff --git a/tests/testthat/examples/Test_2023_2/output/methods.csv b/tests/testthat/examples/Test_2023_2/output/methods.csv index d3a332bf..c85f36bb 100644 --- a/tests/testthat/examples/Test_2023_2/output/methods.csv +++ b/tests/testthat/examples/Test_2023_2/output/methods.csv @@ -1,11 +1,11 @@ -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_2,leaf_mass_per_area,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.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_2,leaf_N_per_dry_mass,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_2,leaf_area,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.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_2,wood_density,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_2,branch_mass_fraction,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_2,seed_dry_mass,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_2,huber_value,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_2,huber_value,"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.",02,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_2,huber_value,"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.",03,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk -Test_2023_2,huber_value,"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.",04,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +dataset_id,trait_name,methods,method_id,description,sampling_strategy,source_primary_key,source_primary_type,source_primary_citation,source_secondary_key,source_secondary_citation,source_original_dataset_key,source_original_dataset_citation,data_collectors,assistants,dataset_curators +Test_2023_2,leaf_mass_per_area,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.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_2,leaf_N_per_dry_mass,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_2,leaf_area,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.,01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_2,wood_density,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_2,branch_mass_fraction,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_2,seed_dry_mass,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_2,huber_value,"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.",01,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_2,huber_value,"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.",02,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_2,huber_value,"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.",03,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk +Test_2023_2,huber_value,"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.",04,Investigation into trait values correlated with plant height along light availability and successional gradients for far north Queensland species.,"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.",Test_2023_2,Article,"D. S. Falster and M. Westoby. ""Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia"". _Journal of Ecology_ 93 (2005), pp. 521-535. doi: [10.1111/j.0022-0477.2005.00992.x](https://doi.org/10.1111%2Fj.0022-0477.2005.00992.x).",,,,,"Daniel Falster (contact), Mark Westoby",,Elizabeth Wenk diff --git a/tests/testthat/examples/Test_2023_3/output/methods.csv b/tests/testthat/examples/Test_2023_3/output/methods.csv index b7f074cc..e91931b2 100644 --- a/tests/testthat/examples/Test_2023_3/output/methods.csv +++ b/tests/testthat/examples/Test_2023_3/output/methods.csv @@ -1,7 +1,7 @@ -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_3,fruit_colour,"When specified in the taxon description, only the colours of the fruit at maturity or the dominant colours of the fruit exterior were scored. If neither were specified, all colours associated with the fruit were scored.",01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_3,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk -Test_2023_3,fruit_dehiscence,"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.",01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_3,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk -Test_2023_3,fruit_length,"The term used to describe the fruit length 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.",01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_3,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk -Test_2023_3,fruit_width,"Minimum fruit width; 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.",01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_3,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk -Test_2023_3,fruit_width,"Maximum fruit width; 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.",02,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_3,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk -Test_2023_3,flowering_time,Made up flowering time values.,01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_3,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk +dataset_id,trait_name,methods,method_id,description,sampling_strategy,source_primary_key,source_primary_type,source_primary_citation,source_secondary_key,source_secondary_citation,source_original_dataset_key,source_original_dataset_citation,data_collectors,assistants,dataset_curators +Test_2023_3,fruit_colour,"When specified in the taxon description, only the colours of the fruit at maturity or the dominant colours of the fruit exterior were scored. If neither were specified, all colours associated with the fruit were scored.",01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_3,Online,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk +Test_2023_3,fruit_dehiscence,"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.",01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_3,Online,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk +Test_2023_3,fruit_length,"The term used to describe the fruit length 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.",01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_3,Online,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk +Test_2023_3,fruit_width,"Minimum fruit width; 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.",01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_3,Online,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk +Test_2023_3,fruit_width,"Maximum fruit width; 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.",02,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_3,Online,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk +Test_2023_3,flowering_time,Made up flowering time values.,01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_3,Online,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk diff --git a/tests/testthat/examples/Test_2023_4/output/methods.csv b/tests/testthat/examples/Test_2023_4/output/methods.csv index c75536b4..6c786b28 100644 --- a/tests/testthat/examples/Test_2023_4/output/methods.csv +++ b/tests/testthat/examples/Test_2023_4/output/methods.csv @@ -1,8 +1,8 @@ -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_4,fruit_colour,"When specified in the taxon description, only the colours of the fruit at maturity or the dominant colours of the fruit exterior were scored. If neither were specified, all colours associated with the fruit were scored.",01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_4,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk -Test_2023_4,fruit_dehiscence,"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.",01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_4,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk -Test_2023_4,fruit_length,"The term used to describe the fruit length 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.",01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_4,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk -Test_2023_4,fruit_width,"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.",01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_4,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk -Test_2023_4,leaf_photosynthesis,Test `repeat_measurements_id` at the trait level for long datasets.,01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_4,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk -Test_2023_4,leaf_stomatal_conductance,Test `repeat_measurements_id` at the trait level for populations and species.,01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_4,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk -Test_2023_4,leaf_stomatal_conductance,Test that `repeat_measurements_id` is not made for traits where `repeat_measurements_id` is set to FALSE but have already been entered with `repeat_measurements_id` as TRUE from another column.,02,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_4,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk +dataset_id,trait_name,methods,method_id,description,sampling_strategy,source_primary_key,source_primary_type,source_primary_citation,source_secondary_key,source_secondary_citation,source_original_dataset_key,source_original_dataset_citation,data_collectors,assistants,dataset_curators +Test_2023_4,fruit_colour,"When specified in the taxon description, only the colours of the fruit at maturity or the dominant colours of the fruit exterior were scored. If neither were specified, all colours associated with the fruit were scored.",01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_4,Online,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk +Test_2023_4,fruit_dehiscence,"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.",01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_4,Online,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk +Test_2023_4,fruit_length,"The term used to describe the fruit length 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.",01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_4,Online,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk +Test_2023_4,fruit_width,"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.",01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_4,Online,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk +Test_2023_4,leaf_photosynthesis,Test `repeat_measurements_id` at the trait level for long datasets.,01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_4,Online,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk +Test_2023_4,leaf_stomatal_conductance,Test `repeat_measurements_id` at the trait level for populations and species.,01,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_4,Online,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk +Test_2023_4,leaf_stomatal_conductance,Test that `repeat_measurements_id` is not made for traits where `repeat_measurements_id` is set to FALSE but have already been entered with `repeat_measurements_id` as TRUE from another column.,02,Plant growth form data extracted from the NT Flora Online,"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 text using R coding script. Sentences and phrases were categorised using a large glossary of botanical terminology as referring to one of the following, the entire organism, stem, leaf, flower, fruit/seed, roots and environment/habitat. Key terms corresponding to trait values in AusTraits were then extracted from these smaller chunks of text using a reference table containing a) the AusTraits trait name, b) the AusTraits trait value and c) terms to search for in the text. The resulting traits were then checked manually using a subset of ~500 taxa to search for errors and update the reference table and coding script accordingly. The process was repeated iteratively to remove any wrongly classified trait values and to ensure as many correct trait values as possible were captured using the algorithm. Where possible, unclassified taxa were inferred as possessing a trait value from a higher-level taxonomic description e.g. the fruit type of all taxa in the Adenanthos genus were scored as `achene`, which was mentioned only in the genus description.",Test_2023_4,Online,"N. H. of New South Wales. _The Plant Information Network System of The Royal Botanic Gardens and Domain Trust Version 2.0._. accessed on 6 May, 2022.. 2023. url: [https://plantnet.rbgsyd.nsw.gov.au/](https://plantnet.rbgsyd.nsw.gov.au/).",,,,,"Marco Duretto, David Coleman",,Elizabeth Wenk diff --git a/tests/testthat/examples/Test_2023_5/output/methods.csv b/tests/testthat/examples/Test_2023_5/output/methods.csv index 82a66e68..0c0cceb5 100644 --- a/tests/testthat/examples/Test_2023_5/output/methods.csv +++ b/tests/testthat/examples/Test_2023_5/output/methods.csv @@ -1,3 +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 +dataset_id,trait_name,methods,method_id,description,sampling_strategy,source_primary_key,source_primary_type,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,Unpublished,"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,Unpublished,"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/methods.csv b/tests/testthat/examples/Test_2023_6/output/methods.csv index 877866c5..945a9d0c 100644 --- a/tests/testthat/examples/Test_2023_6/output/methods.csv +++ b/tests/testthat/examples/Test_2023_6/output/methods.csv @@ -1,3 +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 +dataset_id,trait_name,methods,method_id,description,sampling_strategy,source_primary_key,source_primary_type,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,Unpublished,"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,Unpublished,"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_7/output/methods.csv b/tests/testthat/examples/Test_2023_7/output/methods.csv index f432e6be..b1340a10 100644 --- a/tests/testthat/examples/Test_2023_7/output/methods.csv +++ b/tests/testthat/examples/Test_2023_7/output/methods.csv @@ -1,3 +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_7,leaf_photosynthesis,"The A-ci curves were analysed using the spreadsheet utility (version 2007.1) provided by Sharkey et al. (2007). The spreadsheet utility fits the photosynthesis model of Farquhar et al. (1980) to the observed CO2 response curve. Estimates are generated of the maximum Rubisco carboxylation rate, Vcmax (umol CO2 m-2 s-1); the electron transport rate, J (umol electrons m-2 s-1); triose phosphate use, TPU (umol triose phosphate m-2 s-1); day respiration, Rd (umol CO2 m-2 s-1); and mesophyll conductance to CO2, gm (umol m-2 s-1 Pa-1). The spreadsheet utility provides estimates of these parameters normalized to 25 deg C to facilitate comparisons with measurements made at other leaf temperatures. An additional column in the data.csv file, 'Vcmax atTleaf (umol m-2 s-1)', provides Vcmax values at the measured leaf temperature and the column 'Tleaf (deg C)' indicates the leaf temperatures during gas exchange measurements.",01,Leaf-level photosynthetic parameters of species in the closely related genera Eucalyptus and Corymbia were assessed along a strong rainfall gradient in northern Australia.,"Leaf gas exchange measurements were made at six sites along a sub-continental rainfall gradient in northern Australia (Fig. 1). The sites covered a latitudinal range from approximately 12 deg S to 23 deg S, with corresponding MAP ranging from approximately 1700 mm to 300 mm (Table 1). Two canopy tree species characteristic of each site were selected for measurements. All of the selected species were from the genus Eucalyptus, or the closely related genus Corymbia (Table 1). Two individuals of each of the two species at each site were selected for measurements. A total of six leaves were sampled from each species at each site. Canopy access was achieved with a 16 m elevated work platform at the four more northerly sites, and with ladders or from the ground at the two more southerly sites where trees were shorter.",Test_2023_7,"L. A. Cernusak, L. B. Hutley, J. Beringer, J. A. Holtum, and B. L. Turner. ""Photosynthetic physiology of eucalypts along a sub-continental rainfall gradient in northern Australia"". _Agricultural and Forest Meteorology_ 151.11 (2011), pp. 1462-1470. doi: [10.1016/j.agrformet.2011.01.006](https://doi.org/10.1016%2Fj.agrformet.2011.01.006).",,,,,Lucas Cernusak (contact),,Elizabeth Wenk -Test_2023_7,leaf_stomatal_conductance,"Values used are from the first step of the A-ci curve, where CO2 was approximately 400 ppm and PAR 1200 umol m-2 s-1. In detail, two portable photosynthesis systems (Li-6400, LiCor Inc., Lincoln, NE, USA) were used to measure the response of photosynthesis to intercellular CO2 concentration (A-ci curve) and to light (light response curve). The two systems were cross calibrated, and gave unbiased results with respect to each other. The measurement sequence for each sampled leaf started with the A-ci curve and then proceeded to the light response curve. The CO2 concentration (umol mol-1) entering the leaf gas exchange cuvette was altered in the following sequence: 400, 280, 230, 150, 70, 40, 230, 400, 640, 980, and 1200. A measurement of photosynthesis was logged approximately 2 min after each step change in CO2 concentration entering the cuvette. Irradiance during the A-ci curve measurements was set at 2000 umol photosynthetically active radiation (PAR) m-2 s-1, supplied by an artificial light source (6400-02B LED, LiCor Inc.). At the conclusion of the A-ci curve, the light response curve was measured on the same leaf. The CO2 concentration of air entering the cuvette was maintained at 1200 umol mol-1, and irradiance (umol PAR m-2 s-1) was altered in the following sequence: 2000, 1500, 1000, 500, 200, 120, 70, 40, 20, and 0. A measurement of photosynthesis was logged approximately 2 min after each step change in irradiance. We endeavoured to maintain the leaf-to-air vapour pressure difference (D) and the leaf temperature (T) constant across sites and within a site for each sample leaf during A-ci and light response measurements. The target D was 2.5 kPa and the target T was 33 deg C. Mean site values (mean +/- 1 SD) for T during measurements ranged from 32.3 +/- 0.6 deg C at the Howard Springs site to 33.9 +/- 2.0 deg C at the Boulia site. Mean site values during measurements for D ranged from 2.1 +/- 0.2 kPa at the Howard Springs site to 3.1 +/- 0.7 kPa at the Boulia site. Measurements at all sites except the Boulia site took place between 2 and 15 September 2008. Measurements at the Boulia site took place between 5 and 8 December 2008. Precipitation at the Boulia site does not show as highly pronounced a seasonal variation as the more northerly sites. A cumulative precipitation of 56 mm was recorded at the Boulia Airport in the nine months preceding the measurement campaign (http://www.bom.gov.au/index.shtml). Gas exchange measurements were taken between 0800 h and 1700 h local time at each site.",01,Leaf-level photosynthetic parameters of species in the closely related genera Eucalyptus and Corymbia were assessed along a strong rainfall gradient in northern Australia.,"Leaf gas exchange measurements were made at six sites along a sub-continental rainfall gradient in northern Australia (Fig. 1). The sites covered a latitudinal range from approximately 12 deg S to 23 deg S, with corresponding MAP ranging from approximately 1700 mm to 300 mm (Table 1). Two canopy tree species characteristic of each site were selected for measurements. All of the selected species were from the genus Eucalyptus, or the closely related genus Corymbia (Table 1). Two individuals of each of the two species at each site were selected for measurements. A total of six leaves were sampled from each species at each site. Canopy access was achieved with a 16 m elevated work platform at the four more northerly sites, and with ladders or from the ground at the two more southerly sites where trees were shorter.",Test_2023_7,"L. A. Cernusak, L. B. Hutley, J. Beringer, J. A. Holtum, and B. L. Turner. ""Photosynthetic physiology of eucalypts along a sub-continental rainfall gradient in northern Australia"". _Agricultural and Forest Meteorology_ 151.11 (2011), pp. 1462-1470. doi: [10.1016/j.agrformet.2011.01.006](https://doi.org/10.1016%2Fj.agrformet.2011.01.006).",,,,,Lucas Cernusak (contact),,Elizabeth Wenk +dataset_id,trait_name,methods,method_id,description,sampling_strategy,source_primary_key,source_primary_type,source_primary_citation,source_secondary_key,source_secondary_citation,source_original_dataset_key,source_original_dataset_citation,data_collectors,assistants,dataset_curators +Test_2023_7,leaf_photosynthesis,"The A-ci curves were analysed using the spreadsheet utility (version 2007.1) provided by Sharkey et al. (2007). The spreadsheet utility fits the photosynthesis model of Farquhar et al. (1980) to the observed CO2 response curve. Estimates are generated of the maximum Rubisco carboxylation rate, Vcmax (umol CO2 m-2 s-1); the electron transport rate, J (umol electrons m-2 s-1); triose phosphate use, TPU (umol triose phosphate m-2 s-1); day respiration, Rd (umol CO2 m-2 s-1); and mesophyll conductance to CO2, gm (umol m-2 s-1 Pa-1). The spreadsheet utility provides estimates of these parameters normalized to 25 deg C to facilitate comparisons with measurements made at other leaf temperatures. An additional column in the data.csv file, 'Vcmax atTleaf (umol m-2 s-1)', provides Vcmax values at the measured leaf temperature and the column 'Tleaf (deg C)' indicates the leaf temperatures during gas exchange measurements.",01,Leaf-level photosynthetic parameters of species in the closely related genera Eucalyptus and Corymbia were assessed along a strong rainfall gradient in northern Australia.,"Leaf gas exchange measurements were made at six sites along a sub-continental rainfall gradient in northern Australia (Fig. 1). The sites covered a latitudinal range from approximately 12 deg S to 23 deg S, with corresponding MAP ranging from approximately 1700 mm to 300 mm (Table 1). Two canopy tree species characteristic of each site were selected for measurements. All of the selected species were from the genus Eucalyptus, or the closely related genus Corymbia (Table 1). Two individuals of each of the two species at each site were selected for measurements. A total of six leaves were sampled from each species at each site. Canopy access was achieved with a 16 m elevated work platform at the four more northerly sites, and with ladders or from the ground at the two more southerly sites where trees were shorter.",Test_2023_7,Article,"L. A. Cernusak, L. B. Hutley, J. Beringer, J. A. Holtum, and B. L. Turner. ""Photosynthetic physiology of eucalypts along a sub-continental rainfall gradient in northern Australia"". _Agricultural and Forest Meteorology_ 151.11 (2011), pp. 1462-1470. doi: [10.1016/j.agrformet.2011.01.006](https://doi.org/10.1016%2Fj.agrformet.2011.01.006).",,,,,Lucas Cernusak (contact),,Elizabeth Wenk +Test_2023_7,leaf_stomatal_conductance,"Values used are from the first step of the A-ci curve, where CO2 was approximately 400 ppm and PAR 1200 umol m-2 s-1. In detail, two portable photosynthesis systems (Li-6400, LiCor Inc., Lincoln, NE, USA) were used to measure the response of photosynthesis to intercellular CO2 concentration (A-ci curve) and to light (light response curve). The two systems were cross calibrated, and gave unbiased results with respect to each other. The measurement sequence for each sampled leaf started with the A-ci curve and then proceeded to the light response curve. The CO2 concentration (umol mol-1) entering the leaf gas exchange cuvette was altered in the following sequence: 400, 280, 230, 150, 70, 40, 230, 400, 640, 980, and 1200. A measurement of photosynthesis was logged approximately 2 min after each step change in CO2 concentration entering the cuvette. Irradiance during the A-ci curve measurements was set at 2000 umol photosynthetically active radiation (PAR) m-2 s-1, supplied by an artificial light source (6400-02B LED, LiCor Inc.). At the conclusion of the A-ci curve, the light response curve was measured on the same leaf. The CO2 concentration of air entering the cuvette was maintained at 1200 umol mol-1, and irradiance (umol PAR m-2 s-1) was altered in the following sequence: 2000, 1500, 1000, 500, 200, 120, 70, 40, 20, and 0. A measurement of photosynthesis was logged approximately 2 min after each step change in irradiance. We endeavoured to maintain the leaf-to-air vapour pressure difference (D) and the leaf temperature (T) constant across sites and within a site for each sample leaf during A-ci and light response measurements. The target D was 2.5 kPa and the target T was 33 deg C. Mean site values (mean +/- 1 SD) for T during measurements ranged from 32.3 +/- 0.6 deg C at the Howard Springs site to 33.9 +/- 2.0 deg C at the Boulia site. Mean site values during measurements for D ranged from 2.1 +/- 0.2 kPa at the Howard Springs site to 3.1 +/- 0.7 kPa at the Boulia site. Measurements at all sites except the Boulia site took place between 2 and 15 September 2008. Measurements at the Boulia site took place between 5 and 8 December 2008. Precipitation at the Boulia site does not show as highly pronounced a seasonal variation as the more northerly sites. A cumulative precipitation of 56 mm was recorded at the Boulia Airport in the nine months preceding the measurement campaign (http://www.bom.gov.au/index.shtml). Gas exchange measurements were taken between 0800 h and 1700 h local time at each site.",01,Leaf-level photosynthetic parameters of species in the closely related genera Eucalyptus and Corymbia were assessed along a strong rainfall gradient in northern Australia.,"Leaf gas exchange measurements were made at six sites along a sub-continental rainfall gradient in northern Australia (Fig. 1). The sites covered a latitudinal range from approximately 12 deg S to 23 deg S, with corresponding MAP ranging from approximately 1700 mm to 300 mm (Table 1). Two canopy tree species characteristic of each site were selected for measurements. All of the selected species were from the genus Eucalyptus, or the closely related genus Corymbia (Table 1). Two individuals of each of the two species at each site were selected for measurements. A total of six leaves were sampled from each species at each site. Canopy access was achieved with a 16 m elevated work platform at the four more northerly sites, and with ladders or from the ground at the two more southerly sites where trees were shorter.",Test_2023_7,Article,"L. A. Cernusak, L. B. Hutley, J. Beringer, J. A. Holtum, and B. L. Turner. ""Photosynthetic physiology of eucalypts along a sub-continental rainfall gradient in northern Australia"". _Agricultural and Forest Meteorology_ 151.11 (2011), pp. 1462-1470. doi: [10.1016/j.agrformet.2011.01.006](https://doi.org/10.1016%2Fj.agrformet.2011.01.006).",,,,,Lucas Cernusak (contact),,Elizabeth Wenk diff --git a/tests/testthat/examples/Test_2023_8/output/methods.csv b/tests/testthat/examples/Test_2023_8/output/methods.csv index 0e7df995..3b1b0651 100644 --- a/tests/testthat/examples/Test_2023_8/output/methods.csv +++ b/tests/testthat/examples/Test_2023_8/output/methods.csv @@ -1,3 +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_8,leaf_photosynthesis,"The A-ci curves were analysed using the spreadsheet utility (version 2007.1) provided by Sharkey et al. (2007). The spreadsheet utility fits the photosynthesis model of Farquhar et al. (1980) to the observed CO2 response curve. Estimates are generated of the maximum Rubisco carboxylation rate, Vcmax (umol CO2 m-2 s-1); the electron transport rate, J (umol electrons m-2 s-1); triose phosphate use, TPU (umol triose phosphate m-2 s-1); day respiration, Rd (umol CO2 m-2 s-1); and mesophyll conductance to CO2, gm (umol m-2 s-1 Pa-1). The spreadsheet utility provides estimates of these parameters normalized to 25 deg C to facilitate comparisons with measurements made at other leaf temperatures. An additional column in the data.csv file, 'Vcmax atTleaf (umol m-2 s-1)', provides Vcmax values at the measured leaf temperature and the column 'Tleaf (deg C)' indicates the leaf temperatures during gas exchange measurements.",01,Leaf-level photosynthetic parameters of species in the closely related genera Eucalyptus and Corymbia were assessed along a strong rainfall gradient in northern Australia.,"Leaf gas exchange measurements were made at six sites along a sub-continental rainfall gradient in northern Australia (Fig. 1). The sites covered a latitudinal range from approximately 12 deg S to 23 deg S, with corresponding MAP ranging from approximately 1700 mm to 300 mm (Table 1). Two canopy tree species characteristic of each site were selected for measurements. All of the selected species were from the genus Eucalyptus, or the closely related genus Corymbia (Table 1). Two individuals of each of the two species at each site were selected for measurements. A total of six leaves were sampled from each species at each site. Canopy access was achieved with a 16 m elevated work platform at the four more northerly sites, and with ladders or from the ground at the two more southerly sites where trees were shorter.",Test_2023_8,"L. A. Cernusak, L. B. Hutley, J. Beringer, J. A. Holtum, and B. L. Turner. ""Photosynthetic physiology of eucalypts along a sub-continental rainfall gradient in northern Australia"". _Agricultural and Forest Meteorology_ 151.11 (2011), pp. 1462-1470. doi: [10.1016/j.agrformet.2011.01.006](https://doi.org/10.1016%2Fj.agrformet.2011.01.006).",,,,,Lucas Cernusak (contact),,Elizabeth Wenk -Test_2023_8,leaf_stomatal_conductance,"Values used are from the first step of the A-ci curve, where CO2 was approximately 400 ppm and PAR 1200 umol m-2 s-1. In detail, two portable photosynthesis systems (Li-6400, LiCor Inc., Lincoln, NE, USA) were used to measure the response of photosynthesis to intercellular CO2 concentration (A-ci curve) and to light (light response curve). The two systems were cross calibrated, and gave unbiased results with respect to each other. The measurement sequence for each sampled leaf started with the A-ci curve and then proceeded to the light response curve. The CO2 concentration (umol mol-1) entering the leaf gas exchange cuvette was altered in the following sequence: 400, 280, 230, 150, 70, 40, 230, 400, 640, 980, and 1200. A measurement of photosynthesis was logged approximately 2 min after each step change in CO2 concentration entering the cuvette. Irradiance during the A-ci curve measurements was set at 2000 umol photosynthetically active radiation (PAR) m-2 s-1, supplied by an artificial light source (6400-02B LED, LiCor Inc.). At the conclusion of the A-ci curve, the light response curve was measured on the same leaf. The CO2 concentration of air entering the cuvette was maintained at 1200 umol mol-1, and irradiance (umol PAR m-2 s-1) was altered in the following sequence: 2000, 1500, 1000, 500, 200, 120, 70, 40, 20, and 0. A measurement of photosynthesis was logged approximately 2 min after each step change in irradiance. We endeavoured to maintain the leaf-to-air vapour pressure difference (D) and the leaf temperature (T) constant across sites and within a site for each sample leaf during A-ci and light response measurements. The target D was 2.5 kPa and the target T was 33 deg C. Mean site values (mean +/- 1 SD) for T during measurements ranged from 32.3 +/- 0.6 deg C at the Howard Springs site to 33.9 +/- 2.0 deg C at the Boulia site. Mean site values during measurements for D ranged from 2.1 +/- 0.2 kPa at the Howard Springs site to 3.1 +/- 0.7 kPa at the Boulia site. Measurements at all sites except the Boulia site took place between 2 and 15 September 2008. Measurements at the Boulia site took place between 5 and 8 December 2008. Precipitation at the Boulia site does not show as highly pronounced a seasonal variation as the more northerly sites. A cumulative precipitation of 56 mm was recorded at the Boulia Airport in the nine months preceding the measurement campaign (http://www.bom.gov.au/index.shtml). Gas exchange measurements were taken between 0800 h and 1700 h local time at each site.",01,Leaf-level photosynthetic parameters of species in the closely related genera Eucalyptus and Corymbia were assessed along a strong rainfall gradient in northern Australia.,"Leaf gas exchange measurements were made at six sites along a sub-continental rainfall gradient in northern Australia (Fig. 1). The sites covered a latitudinal range from approximately 12 deg S to 23 deg S, with corresponding MAP ranging from approximately 1700 mm to 300 mm (Table 1). Two canopy tree species characteristic of each site were selected for measurements. All of the selected species were from the genus Eucalyptus, or the closely related genus Corymbia (Table 1). Two individuals of each of the two species at each site were selected for measurements. A total of six leaves were sampled from each species at each site. Canopy access was achieved with a 16 m elevated work platform at the four more northerly sites, and with ladders or from the ground at the two more southerly sites where trees were shorter.",Test_2023_8,"L. A. Cernusak, L. B. Hutley, J. Beringer, J. A. Holtum, and B. L. Turner. ""Photosynthetic physiology of eucalypts along a sub-continental rainfall gradient in northern Australia"". _Agricultural and Forest Meteorology_ 151.11 (2011), pp. 1462-1470. doi: [10.1016/j.agrformet.2011.01.006](https://doi.org/10.1016%2Fj.agrformet.2011.01.006).",,,,,Lucas Cernusak (contact),,Elizabeth Wenk +dataset_id,trait_name,methods,method_id,description,sampling_strategy,source_primary_key,source_primary_type,source_primary_citation,source_secondary_key,source_secondary_citation,source_original_dataset_key,source_original_dataset_citation,data_collectors,assistants,dataset_curators +Test_2023_8,leaf_photosynthesis,"The A-ci curves were analysed using the spreadsheet utility (version 2007.1) provided by Sharkey et al. (2007). The spreadsheet utility fits the photosynthesis model of Farquhar et al. (1980) to the observed CO2 response curve. Estimates are generated of the maximum Rubisco carboxylation rate, Vcmax (umol CO2 m-2 s-1); the electron transport rate, J (umol electrons m-2 s-1); triose phosphate use, TPU (umol triose phosphate m-2 s-1); day respiration, Rd (umol CO2 m-2 s-1); and mesophyll conductance to CO2, gm (umol m-2 s-1 Pa-1). The spreadsheet utility provides estimates of these parameters normalized to 25 deg C to facilitate comparisons with measurements made at other leaf temperatures. An additional column in the data.csv file, 'Vcmax atTleaf (umol m-2 s-1)', provides Vcmax values at the measured leaf temperature and the column 'Tleaf (deg C)' indicates the leaf temperatures during gas exchange measurements.",01,Leaf-level photosynthetic parameters of species in the closely related genera Eucalyptus and Corymbia were assessed along a strong rainfall gradient in northern Australia.,"Leaf gas exchange measurements were made at six sites along a sub-continental rainfall gradient in northern Australia (Fig. 1). The sites covered a latitudinal range from approximately 12 deg S to 23 deg S, with corresponding MAP ranging from approximately 1700 mm to 300 mm (Table 1). Two canopy tree species characteristic of each site were selected for measurements. All of the selected species were from the genus Eucalyptus, or the closely related genus Corymbia (Table 1). Two individuals of each of the two species at each site were selected for measurements. A total of six leaves were sampled from each species at each site. Canopy access was achieved with a 16 m elevated work platform at the four more northerly sites, and with ladders or from the ground at the two more southerly sites where trees were shorter.",Test_2023_8,Article,"L. A. Cernusak, L. B. Hutley, J. Beringer, J. A. Holtum, and B. L. Turner. ""Photosynthetic physiology of eucalypts along a sub-continental rainfall gradient in northern Australia"". _Agricultural and Forest Meteorology_ 151.11 (2011), pp. 1462-1470. doi: [10.1016/j.agrformet.2011.01.006](https://doi.org/10.1016%2Fj.agrformet.2011.01.006).",,,,,Lucas Cernusak (contact),,Elizabeth Wenk +Test_2023_8,leaf_stomatal_conductance,"Values used are from the first step of the A-ci curve, where CO2 was approximately 400 ppm and PAR 1200 umol m-2 s-1. In detail, two portable photosynthesis systems (Li-6400, LiCor Inc., Lincoln, NE, USA) were used to measure the response of photosynthesis to intercellular CO2 concentration (A-ci curve) and to light (light response curve). The two systems were cross calibrated, and gave unbiased results with respect to each other. The measurement sequence for each sampled leaf started with the A-ci curve and then proceeded to the light response curve. The CO2 concentration (umol mol-1) entering the leaf gas exchange cuvette was altered in the following sequence: 400, 280, 230, 150, 70, 40, 230, 400, 640, 980, and 1200. A measurement of photosynthesis was logged approximately 2 min after each step change in CO2 concentration entering the cuvette. Irradiance during the A-ci curve measurements was set at 2000 umol photosynthetically active radiation (PAR) m-2 s-1, supplied by an artificial light source (6400-02B LED, LiCor Inc.). At the conclusion of the A-ci curve, the light response curve was measured on the same leaf. The CO2 concentration of air entering the cuvette was maintained at 1200 umol mol-1, and irradiance (umol PAR m-2 s-1) was altered in the following sequence: 2000, 1500, 1000, 500, 200, 120, 70, 40, 20, and 0. A measurement of photosynthesis was logged approximately 2 min after each step change in irradiance. We endeavoured to maintain the leaf-to-air vapour pressure difference (D) and the leaf temperature (T) constant across sites and within a site for each sample leaf during A-ci and light response measurements. The target D was 2.5 kPa and the target T was 33 deg C. Mean site values (mean +/- 1 SD) for T during measurements ranged from 32.3 +/- 0.6 deg C at the Howard Springs site to 33.9 +/- 2.0 deg C at the Boulia site. Mean site values during measurements for D ranged from 2.1 +/- 0.2 kPa at the Howard Springs site to 3.1 +/- 0.7 kPa at the Boulia site. Measurements at all sites except the Boulia site took place between 2 and 15 September 2008. Measurements at the Boulia site took place between 5 and 8 December 2008. Precipitation at the Boulia site does not show as highly pronounced a seasonal variation as the more northerly sites. A cumulative precipitation of 56 mm was recorded at the Boulia Airport in the nine months preceding the measurement campaign (http://www.bom.gov.au/index.shtml). Gas exchange measurements were taken between 0800 h and 1700 h local time at each site.",01,Leaf-level photosynthetic parameters of species in the closely related genera Eucalyptus and Corymbia were assessed along a strong rainfall gradient in northern Australia.,"Leaf gas exchange measurements were made at six sites along a sub-continental rainfall gradient in northern Australia (Fig. 1). The sites covered a latitudinal range from approximately 12 deg S to 23 deg S, with corresponding MAP ranging from approximately 1700 mm to 300 mm (Table 1). Two canopy tree species characteristic of each site were selected for measurements. All of the selected species were from the genus Eucalyptus, or the closely related genus Corymbia (Table 1). Two individuals of each of the two species at each site were selected for measurements. A total of six leaves were sampled from each species at each site. Canopy access was achieved with a 16 m elevated work platform at the four more northerly sites, and with ladders or from the ground at the two more southerly sites where trees were shorter.",Test_2023_8,Article,"L. A. Cernusak, L. B. Hutley, J. Beringer, J. A. Holtum, and B. L. Turner. ""Photosynthetic physiology of eucalypts along a sub-continental rainfall gradient in northern Australia"". _Agricultural and Forest Meteorology_ 151.11 (2011), pp. 1462-1470. doi: [10.1016/j.agrformet.2011.01.006](https://doi.org/10.1016%2Fj.agrformet.2011.01.006).",,,,,Lucas Cernusak (contact),,Elizabeth Wenk