Merge branch 'add_species_categories' of https://github.com/FRBCesab/…

…funbiogeo into add_species_categories

R/fb_plot_number_sites_by_species.R

@@ -19,21 +19,49 @@
 #' fb_plot_number_sites_by_species(site_species)
 #' 
 #' # Add a vertical cutoff line (40% of sites)
-#' fb_plot_number_sites_by_species(site_species, 0.4)
+#' fb_plot_number_sites_by_species(site_species, threshold = 0.4)
 fb_plot_number_sites_by_species <- function(
-  site_species, threshold_sites_proportion = NULL
+  site_species, species_categories = NULL, threshold_sites_proportion = NULL
 ) {
 
   # Check ----------------------------------------------------------------------
   check_site_species(site_species)
+  check_species_categories(species_categories)
+
 
   if (!is.null(threshold_sites_proportion)) {
     check_threshold_proportion(threshold_sites_proportion, "site")
   }
 
+
+  # Splitting species by category
+  species_split <- list(single_cat = species_traits[["species"]])
+  category_name <- "single_cat"
+
+  if (!is.null(species_categories)) {
+
+    category_name <- colnames(species_categories)[2]
+
+    species_split <- split(
+      species_categories[, 1], species_categories[, 2]
+    )
+
+  }
+
+
+  # Split sites according to species' categories
+  site_species_categories <- lapply(
+    species_split,
+    function(x) site_species[, c("site", x), drop = FALSE]
+  )
+
   # Get the numbers
-  number_sites_by_species <- fb_count_sites_by_species(site_species)
-  n_species <- nrow(site_species)
+  number_sites_by_species <- lapply(
+    site_species_categories, fb_count_sites_by_species
+  )
+  n_species <- lapply(site_species_categories, nrow)
+
+
 
   # Construct y-axis breaks
   # Under 25 observation, label everyone of them
@@ -68,6 +96,20 @@ fb_plot_number_sites_by_species <- function(
     levels = rev(number_sites_by_species$species)
   )
 
+  # Manage conditional faceting
+  if (is.null(species_categories)) {
+
+    category_facet <- NULL
+
+  } else {
+
+    category_facet <- ggplot2::facet_wrap(
+      ggplot2::vars(
+        !!rlang::sym(category_name)), scales = "free"
+    )
+
+  }
+
   # Clean environment
   rm(site_species)
 

tests/testthat/test-fb_plot_site_traits_completeness.R

@@ -33,4 +33,5 @@ test_that("fb_plot_site_traits_completeness works", {
       )
     )
   )
+
 })