more intuitive field div list names

traitecoevo · Nov 20, 2024 · c0a4e29 · c0a4e29
1 parent fd8696c
commit c0a4e29
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Showing 4 changed files with 19 additions and 19 deletions.
diff --git a/R/calculate_field_diversity.R b/R/calculate_field_diversity.R
@@ -26,7 +26,7 @@ calculate_field_diversity <- function(survey_data){
     site_survey_data <- survey_data |>
       dplyr::filter(site_unique == survey)
 
-    subplot_diversity <- site_survey_data |>
+    plot_diversity <- site_survey_data |>
       tidyr::drop_na(standardised_name) |>
       dplyr::filter(!standardised_name %in% c('Dead grass', 'Dead shrub')) |>
       #group_by(subplot_id) |>
@@ -47,7 +47,7 @@ calculate_field_diversity <- function(survey_data){
     simpson_diversity <- vegan::diversity(community_matrix[, -1], index = "simpson")
     inv_simpson <- vegan::diversity(community_matrix[, -1], index = 'invsimpson')
 
-    subplot_diversity <- subplot_diversity |>
+    plot_diversity <- plot_diversity |>
       dplyr::mutate(site_location_name = substr(survey, 1, 10),
              shannon_diversity = shannon_diversity,
              simpson_diversity = simpson_diversity,
@@ -56,19 +56,19 @@ calculate_field_diversity <- function(survey_data){
              inv_simpson = inv_simpson)
 
     # order columns
-    subplot_diversity <- subplot_diversity |>
+    plot_diversity <- plot_diversity |>
       dplyr::select(site_location_name, everything())
 
 
     # store  result for  current site
-    all_site_results[[survey]] <- subplot_diversity
+    all_site_results[[survey]] <- plot_diversity
   }
 
   # combine into one df
-  field_diversity <- dplyr::bind_rows(all_site_results, .id = "site_unique")
+  taxonomic_diversity <- dplyr::bind_rows(all_site_results, .id = "site_unique")
 
   return(list(
-    field_diversity = field_diversity,
+    taxonomic_diversity = taxonomic_diversity,
     community_matrices = community_matrices
   ))
 }
diff --git a/README.Rmd b/README.Rmd
@@ -94,5 +94,5 @@ my.data <- ausplotsR::get_ausplots(my.Plot_IDs=c("SATFLB0004", "QDAMGD0022", "NT
 
 ```{r}
 field_diversity <- calculate_field_diversity(my.data)
-field_diversity$field_diversity
+field_diversity$taxonomic_diversity
 ```
diff --git a/README.md b/README.md
@@ -102,15 +102,15 @@ my.data <- ausplotsR::get_ausplots(my.Plot_IDs=c("SATFLB0004", "QDAMGD0022", "NT
 
 ``` r
 field_diversity <- calculate_field_diversity(my.data)
-field_diversity$field_diversity
-#>        site_unique site_location_name species_richness shannon_diversity simpson_diversity
-#> 1 SATFLB0004-58658         SATFLB0004               28          2.379688         0.8649789
-#> 2 NTASTU0002-58429         NTASTU0002               22          2.200076         0.8509874
-#> 3 QDAMGD0022-53501         QDAMGD0022               20          2.179534         0.8242833
-#> 4 SATFLB0004-53705         SATFLB0004               18          2.149992         0.8375000
-#>   pielou_evenness exp_shannon inv_simpson
-#> 1       0.7141483   10.801533    7.406252
-#> 2       0.7117585    9.025696    6.710843
-#> 3       0.7275464    8.842187    5.690977
-#> 4       0.7438460    8.584786    6.153846
+field_diversity$taxonomic_diversity
+#>        site_unique site_location_name species_richness shannon_diversity
+#> 1 SATFLB0004-58658         SATFLB0004               28          2.379688
+#> 2 NTASTU0002-58429         NTASTU0002               22          2.200076
+#> 3 QDAMGD0022-53501         QDAMGD0022               20          2.179534
+#> 4 SATFLB0004-53705         SATFLB0004               18          2.149992
+#>   simpson_diversity pielou_evenness exp_shannon inv_simpson
+#> 1         0.8649789       0.7141483   10.801533    7.406252
+#> 2         0.8509874       0.7117585    9.025696    6.710843
+#> 3         0.8242833       0.7275464    8.842187    5.690977
+#> 4         0.8375000       0.7438460    8.584786    6.153846
 ```
diff --git a/tests/testthat/test-field_diversity.R b/tests/testthat/test-field_diversity.R
@@ -4,7 +4,7 @@ ausplot.pi.data <- ausplotsR::get_ausplots(my.Plot_IDs=
 test_that('field_diversity works', {
 field_diversity <- calculate_field_diversity(ausplot.pi.data)
 expect_true(
-field_diversity$field_diversity$species_richness==
+field_diversity$taxonomic_diversity$species_richness==
   length(na.omit(unique(ausplot.pi.data$standardised_name)))
 )
 })