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adelegemadelegem
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update field div output cols
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‎R/calculate_field_diversity.R

Lines changed: 10 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -22,7 +22,7 @@ calculate_field_diversity <- function(survey_data){
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# loop thru each unique site
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for (survey in ausplot_surveys) {
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# Filter data for the current site
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# filter data for the current site
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site_survey_data <- survey_data |>
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dplyr::filter(site_unique == survey)
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@@ -48,19 +48,24 @@ calculate_field_diversity <- function(survey_data){
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inv_simpson <- vegan::diversity(community_matrix[, -1], index = 'invsimpson')
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subplot_diversity <- subplot_diversity |>
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dplyr::mutate(shannon_diversity = shannon_diversity,
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dplyr::mutate(site_location_name = substr(survey, 1, 10),
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shannon_diversity = shannon_diversity,
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simpson_diversity = simpson_diversity,
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pielou_evenness = shannon_diversity / log(species_richness),
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exp_shannon = exp(shannon_diversity),
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inv_simpson = inv_simpson,
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survey = survey)
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inv_simpson = inv_simpson)
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# order columns
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subplot_diversity <- subplot_diversity |>
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dplyr::select(site_location_name, everything())
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# store result for current site
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all_site_results[[survey]] <- subplot_diversity
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}
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# combine into one df
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field_diversity <- dplyr::bind_rows(all_site_results, .id = "site")
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field_diversity <- dplyr::bind_rows(all_site_results, .id = "site_unique")
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return(list(
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field_diversity = field_diversity,

‎README.Rmd

Lines changed: 15 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -34,25 +34,16 @@ library(saltbush)
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remotes::install_github("traitecoevo/saltbush")
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```
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## Usage
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## Spectral metrics
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### Spectral diversity metrics:
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+ co-efficient of variance (CV)
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+ spectral variance (SV)
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+ convex hull volume (CHV)
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### Taxonomic diversity metrics:
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+ species richness
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+ shannon's diversity index
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+ simpson's diversity index
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+ pielou's evenness
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+ exponential shannon's index
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+ inverse simpson's index
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## Usage
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## Spectral metrics
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1. List raster files and area of interest files
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```{r}
@@ -84,15 +75,24 @@ head(metrics)
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## Taxonomic metrics
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### Taxonomic diversity metrics:
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+ species richness
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+ shannon's diversity index
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+ simpson's diversity index
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+ pielou's evenness
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+ exponential shannon's index
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+ inverse simpson's index
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1. Download example plot data from AusPlots. The `veg.PI` part extracts the point intercept data from the AusPlots data structure.
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```{r}
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my.data <- ausplotsR::get_ausplots(my.Plot_IDs=c("SATFLB0004", "QDAMGD0022", "NTASTU0002"), veg.PI=TRUE)$veg.PI
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```
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93-
2. Calculate diversity from the point intercepts using different diversity metrics
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2. Calculate diversity from the point intercepts using different diversity metrics. The output is a list which includes taxonomic metrics, and also community matrices for checks.
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```{r}
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field_diversity <- calculate_field_diversity(my.data)
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field_diversity
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field_diversity$field_diversity
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```

‎README.md

Lines changed: 26 additions & 81 deletions
Original file line numberDiff line numberDiff line change
@@ -21,25 +21,16 @@ calculate spectral + taxonomic diversity values for assessment of the
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remotes::install_github("traitecoevo/saltbush")
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```
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## Usage
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## Spectral metrics
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### Spectral diversity metrics:
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- co-efficient of variance (CV)
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- spectral variance (SV)
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- convex hull volume (CHV)
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### Taxonomic diversity metrics:
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- species richness
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- shannon’s diversity index
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- simpson’s diversity index
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- pielou’s evenness
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- exponential shannon’s index
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- inverse simpson’s index
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## Usage
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## Spectral metrics
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1. List raster files and area of interest files
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``` r
@@ -79,6 +70,15 @@ head(metrics)
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## Taxonomic metrics
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### Taxonomic diversity metrics:
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- species richness
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- shannon’s diversity index
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- simpson’s diversity index
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- pielou’s evenness
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- exponential shannon’s index
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- inverse simpson’s index
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1. Download example plot data from AusPlots. The `veg.PI` part extracts
8383
the point intercept data from the AusPlots data structure.
8484

@@ -97,75 +97,20 @@ my.data <- ausplotsR::get_ausplots(my.Plot_IDs=c("SATFLB0004", "QDAMGD0022", "NT
9797
```
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2. Calculate diversity from the point intercepts using different
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diversity metrics
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diversity metrics. The output is a list which includes taxonomic
101+
metrics, and also community matrices for checks.
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``` r
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field_diversity <- calculate_field_diversity(my.data)
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field_diversity
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#> $field_diversity
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#> site species_richness shannon_diversity simpson_diversity pielou_evenness exp_shannon
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#> 1 SATFLB0004-58658 28 2.379688 0.8649789 0.7141483 10.801533
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#> 2 NTASTU0002-58429 22 2.200076 0.8509874 0.7117585 9.025696
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#> 3 QDAMGD0022-53501 20 2.179534 0.8242833 0.7275464 8.842187
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#> 4 SATFLB0004-53705 18 2.149992 0.8375000 0.7438460 8.584786
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#> inv_simpson survey
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#> 1 7.406252 SATFLB0004-58658
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#> 2 6.710843 NTASTU0002-58429
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#> 3 5.690977 QDAMGD0022-53501
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#> 4 6.153846 SATFLB0004-53705
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#>
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#> $community_matrices
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#> $community_matrices$`SATFLB0004-58658`
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#> Acacia pravifolia Alectryon oleifolius subsp. canescens Arthropodium
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#> 1 2 1 13
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#> Bursaria spinosa subsp. spinosa Callitris glaucophylla Carrichtera annua Cassinia laevis
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#> 1 12 110 23 17
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#> Daucus glochidiatus Dodonaea viscosa subsp. angustissima Eremophila deserti Eucalyptus intertexta
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#> 1 1 37 1 115
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#> Hakea leucoptera subsp. leucoptera Leiocarpa semicalva subsp. semicalva
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#> 1 42 1
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#> Lomandra multiflora subsp. dura Millotia Na Olearia decurrens Oxalis perennans
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#> 1 1 3 7 18 1
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#> Pauridia glabella var. glabella Poaceae Ptilotus obovatus Rhagodia parabolica Scleranthus pungens
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#> 1 8 2 22 49 3
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#> Sida petrophila Triodia Wahlenbergia Wurmbea Xanthorrhoea quadrangulata
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#> 1 2 1 1 1 2
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#>
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#> $community_matrices$`NTASTU0002-58429`
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#> Atalaya hemiglauca Bauhinia cunninghamii Brachychiton diversifolius subsp. diversifolius
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#> 1 1 2 3
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#> Brachychiton paradoxus Chrysopogon fallax Corymbia confertiflora Corymbia polycarpa
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#> 1 1 77 21 47
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#> Corymbia terminalis Dichanthium fecundum Dodonaea oxyptera Dolichandrone filiformis
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#> 1 103 98 2 2
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#> Erythrophleum chlorostachys Eucalyptus chlorophylla Eucalyptus pruinosa Eulalia aurea
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#> 1 25 29 26 6
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#> Flueggea virosa subsp. melanthesoides Gardenia ewartii subsp. ewartii Glycine tomentella Na
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#> 1 1 3 6 2
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#> Schizachyrium fragile Terminalia canescens Themeda triandra
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#> 1 1 8 168
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#>
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#> $community_matrices$`QDAMGD0022-53501`
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#> Amaranthus mitchellii Aristida latifolia Astrebla elymoides Astrebla pectinata
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#> 1 1 7 27 57
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#> Boerhavia schomburgkiana Bothriochloa ewartiana Cenchrus ciliaris Chloris pectinata
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#> 1 1 6 32 1
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#> Cynodon convergens Cyperus gilesii Dactyloctenium radulans Eulalia aurea Iseilema vaginiflorum Na
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#> 1 1 3 4 3 2 2
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#> Neptunia dimorphantha Poaceae Sida fibulifera Sida goniocarpa Sporobolus actinocladus
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#> 1 1 11 4 4 5
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#> Vachellia farnesiana
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#> 1 3
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#>
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#> $community_matrices$`SATFLB0004-53705`
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#> Acacia ligulata Alectryon oleifolius Bursaria spinosa subsp. spinosa Callitris glaucophylla
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#> 1 1 7 4 108
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#> Carrichtera annua Cassinia laevis Dodonaea viscosa subsp. angustissima Eremophila deserti
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#> 1 5 19 16 7
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#> Eucalyptus intertexta Hakea leucoptera Olearia decurrens Ptilotus obovatus Rhagodia parabolica
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#> 1 97 32 10 31 43
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#> Scleranthus pungens Senna artemisioides subsp. x artemisioides Sida petrophila Triodia
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#> 1 1 1 15 1
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#> Xanthorrhoea quadrangulata
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#> 1 3
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field_diversity$field_diversity
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#> site_unique site_location_name species_richness shannon_diversity simpson_diversity
107+
#> 1 SATFLB0004-58658 SATFLB0004 28 2.379688 0.8649789
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#> 2 NTASTU0002-58429 NTASTU0002 22 2.200076 0.8509874
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#> 3 QDAMGD0022-53501 QDAMGD0022 20 2.179534 0.8242833
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#> 4 SATFLB0004-53705 SATFLB0004 18 2.149992 0.8375000
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#> pielou_evenness exp_shannon inv_simpson
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#> 1 0.7141483 10.801533 7.406252
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#> 2 0.7117585 9.025696 6.710843
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#> 3 0.7275464 8.842187 5.690977
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#> 4 0.7438460 8.584786 6.153846
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```

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