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update hex?
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@adelegem
adelegem committed Nov 19, 2024
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Expand Up @@ -8,7 +8,7 @@
coverage](https://codecov.io/gh/traitecoevo/saltbush/graph/badge.svg)](https://app.codecov.io/gh/traitecoevo/saltbush)
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# saltbush
# saltbush <img src="man/figures/saltbush_hex.png" align="right" width="120"/>

*saltbush* processes drone imagery and ausplot vegetation survey data to
calculate spectral + taxonomic diversity values for assessment of the
Expand Down Expand Up @@ -44,11 +44,14 @@ calculate spectral + taxonomic diversity values for assessment of the
``` r
my.data <- ausplotsR::get_ausplots(my.Plot_IDs=c("SATFLB0004", "QDAMGD0022", "NTASTU0002"), veg.PI=TRUE)$veg.PI
#> Calling the database. Please wait...
#> downloading (search) [---------------] ( 1%) time: 00:00:00downloading (search) [===============] (100%) time: 00:00:00
#> 200
#> User-supplied Plot_IDs located.
#> Calling the database. Please wait...
#> downloading (site) [-----------------] ( 1%) time: 00:00:00downloading (site) [=================] (100%) time: 00:00:00
#> 200
#> Calling the database. Please wait...
#> downloading (veg_pi) [---------------] ( 1%) time: 00:00:00downloading (veg_pi) [===============] (100%) time: 00:00:00
#> 200
```

Expand All @@ -59,79 +62,95 @@ my.data <- ausplotsR::get_ausplots(my.Plot_IDs=c("SATFLB0004", "QDAMGD0022", "NT
field_diversity <- calculate_field_diversity(my.data)
field_diversity
#> $field_diversity
#> species_richness shannon_diversity simpson_diversity pielou_evenness
#> 1 28 2.379688 0.8649789 0.7141483
#> 2 22 2.200076 0.8509874 0.7117585
#> 3 20 2.179534 0.8242833 0.7275464
#> 4 18 2.149992 0.8375000 0.7438460
#> exp_shannon inv_simpson site
#> 1 10.801533 7.406252 SATFLB0004-58658
#> 2 9.025696 6.710843 NTASTU0002-58429
#> 3 8.842187 5.690977 QDAMGD0022-53501
#> 4 8.584786 6.153846 SATFLB0004-53705
#> species_richness shannon_diversity simpson_diversity
#> 1 28 2.379688 0.8649789
#> 2 22 2.200076 0.8509874
#> 3 20 2.179534 0.8242833
#> 4 18 2.149992 0.8375000
#> pielou_evenness exp_shannon inv_simpson site
#> 1 0.7141483 10.801533 7.406252 SATFLB0004-58658
#> 2 0.7117585 9.025696 6.710843 NTASTU0002-58429
#> 3 0.7275464 8.842187 5.690977 QDAMGD0022-53501
#> 4 0.7438460 8.584786 6.153846 SATFLB0004-53705
#>
#> $community_matrices
#> $community_matrices$`SATFLB0004-58658`
#> Acacia pravifolia Alectryon oleifolius subsp. canescens Arthropodium
#> 1 2 1 13
#> Bursaria spinosa subsp. spinosa Callitris glaucophylla Carrichtera annua
#> 1 12 110 23
#> Cassinia laevis Daucus glochidiatus Dodonaea viscosa subsp. angustissima
#> 1 17 1 37
#> Eremophila deserti Eucalyptus intertexta Hakea leucoptera subsp. leucoptera
#> 1 1 115 42
#> Leiocarpa semicalva subsp. semicalva Lomandra multiflora subsp. dura Millotia
#> 1 1 1 3
#> Na Olearia decurrens Oxalis perennans Pauridia glabella var. glabella Poaceae
#> 1 7 18 1 8 2
#> Ptilotus obovatus Rhagodia parabolica Scleranthus pungens Sida petrophila
#> 1 22 49 3 2
#> Triodia Wahlenbergia Wurmbea Xanthorrhoea quadrangulata
#> 1 1 1 1 2
#> Acacia pravifolia Alectryon oleifolius subsp. canescens
#> 1 2 1
#> Arthropodium Bursaria spinosa subsp. spinosa Callitris glaucophylla
#> 1 13 12 110
#> Carrichtera annua Cassinia laevis Daucus glochidiatus
#> 1 23 17 1
#> Dodonaea viscosa subsp. angustissima Eremophila deserti
#> 1 37 1
#> Eucalyptus intertexta Hakea leucoptera subsp. leucoptera
#> 1 115 42
#> Leiocarpa semicalva subsp. semicalva
#> 1 1
#> Lomandra multiflora subsp. dura Millotia Na Olearia decurrens
#> 1 1 3 7 18
#> Oxalis perennans Pauridia glabella var. glabella Poaceae
#> 1 1 8 2
#> Ptilotus obovatus Rhagodia parabolica Scleranthus pungens
#> 1 22 49 3
#> Sida petrophila Triodia Wahlenbergia Wurmbea
#> 1 2 1 1 1
#> Xanthorrhoea quadrangulata
#> 1 2
#>
#> $community_matrices$`NTASTU0002-58429`
#> Atalaya hemiglauca Bauhinia cunninghamii
#> 1 1 2
#> Brachychiton diversifolius subsp. diversifolius Brachychiton paradoxus
#> 1 3 1
#> Chrysopogon fallax Corymbia confertiflora Corymbia polycarpa
#> 1 77 21 47
#> Corymbia terminalis Dichanthium fecundum Dodonaea oxyptera
#> 1 103 98 2
#> Dolichandrone filiformis Erythrophleum chlorostachys Eucalyptus chlorophylla
#> 1 2 25 29
#> Eucalyptus pruinosa Eulalia aurea Flueggea virosa subsp. melanthesoides
#> 1 26 6 1
#> Gardenia ewartii subsp. ewartii Glycine tomentella Na Schizachyrium fragile
#> 1 3 6 2 1
#> Terminalia canescens Themeda triandra
#> 1 8 168
#> Brachychiton diversifolius subsp. diversifolius
#> 1 3
#> Brachychiton paradoxus Chrysopogon fallax Corymbia confertiflora
#> 1 1 77 21
#> Corymbia polycarpa Corymbia terminalis Dichanthium fecundum
#> 1 47 103 98
#> Dodonaea oxyptera Dolichandrone filiformis
#> 1 2 2
#> Erythrophleum chlorostachys Eucalyptus chlorophylla
#> 1 25 29
#> Eucalyptus pruinosa Eulalia aurea
#> 1 26 6
#> Flueggea virosa subsp. melanthesoides
#> 1 1
#> Gardenia ewartii subsp. ewartii Glycine tomentella Na
#> 1 3 6 2
#> Schizachyrium fragile Terminalia canescens Themeda triandra
#> 1 1 8 168
#>
#> $community_matrices$`QDAMGD0022-53501`
#> Amaranthus mitchellii Aristida latifolia Astrebla elymoides
#> 1 1 7 27
#> Astrebla pectinata Boerhavia schomburgkiana Bothriochloa ewartiana
#> 1 57 1 6
#> Cenchrus ciliaris Chloris pectinata Cynodon convergens Cyperus gilesii
#> 1 32 1 1 3
#> Dactyloctenium radulans Eulalia aurea Iseilema vaginiflorum Na
#> 1 4 3 2 2
#> Neptunia dimorphantha Poaceae Sida fibulifera Sida goniocarpa
#> 1 1 11 4 4
#> Sporobolus actinocladus Vachellia farnesiana
#> 1 5 3
#> Cenchrus ciliaris Chloris pectinata Cynodon convergens
#> 1 32 1 1
#> Cyperus gilesii Dactyloctenium radulans Eulalia aurea
#> 1 3 4 3
#> Iseilema vaginiflorum Na Neptunia dimorphantha Poaceae
#> 1 2 2 1 11
#> Sida fibulifera Sida goniocarpa Sporobolus actinocladus
#> 1 4 4 5
#> Vachellia farnesiana
#> 1 3
#>
#> $community_matrices$`SATFLB0004-53705`
#> Acacia ligulata Alectryon oleifolius Bursaria spinosa subsp. spinosa
#> 1 1 7 4
#> Callitris glaucophylla Carrichtera annua Cassinia laevis
#> 1 108 5 19
#> Dodonaea viscosa subsp. angustissima Eremophila deserti Eucalyptus intertexta
#> 1 16 7 97
#> Hakea leucoptera Olearia decurrens Ptilotus obovatus Rhagodia parabolica
#> 1 32 10 31 43
#> Scleranthus pungens Senna artemisioides subsp. x artemisioides
#> 1 1 1
#> Sida petrophila Triodia Xanthorrhoea quadrangulata
#> 1 15 1 3
#> Acacia ligulata Alectryon oleifolius
#> 1 1 7
#> Bursaria spinosa subsp. spinosa Callitris glaucophylla
#> 1 4 108
#> Carrichtera annua Cassinia laevis
#> 1 5 19
#> Dodonaea viscosa subsp. angustissima Eremophila deserti
#> 1 16 7
#> Eucalyptus intertexta Hakea leucoptera Olearia decurrens
#> 1 97 32 10
#> Ptilotus obovatus Rhagodia parabolica Scleranthus pungens
#> 1 31 43 1
#> Senna artemisioides subsp. x artemisioides Sida petrophila Triodia
#> 1 1 15 1
#> Xanthorrhoea quadrangulata
#> 1 3
```

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