From 450411f46319c55fa1989835cf8a066af41eb2c8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Matthias=20Greni=C3=A9?= <matthias.grenie@ens-lyon.fr>
Date: Tue, 23 Jul 2024 11:38:27 +0200
Subject: [PATCH] Implement it for fb_plot_site_traits_completeness()

---
 R/fb_plot_number_sites_by_species.R           | 50 +++++++++++++++++--
 .../test-fb_plot_site_traits_completeness.R   |  1 +
 2 files changed, 47 insertions(+), 4 deletions(-)

diff --git a/R/fb_plot_number_sites_by_species.R b/R/fb_plot_number_sites_by_species.R
index 7e32ff66..5b095387 100644
--- a/R/fb_plot_number_sites_by_species.R
+++ b/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)
   
diff --git a/tests/testthat/test-fb_plot_site_traits_completeness.R b/tests/testthat/test-fb_plot_site_traits_completeness.R
index 75b67700..c26f151b 100644
--- a/tests/testthat/test-fb_plot_site_traits_completeness.R
+++ b/tests/testthat/test-fb_plot_site_traits_completeness.R
@@ -33,4 +33,5 @@ test_that("fb_plot_site_traits_completeness works", {
       )
     )
   )
+  
 })