# biodivMapR2 v2.4.5

## change
- biodivMapR_full_classif: add possibility to set compute_beta = TRUE or FALSE
- remove TODO.md
- use regular expression '\\.' when searching for strings including '.':
- define 'get_samples_from_tiles' in independent file

Author: jbferet

NAMESPACE

@@ -58,6 +58,7 @@ export(get_raster_diversity)
 export(get_raster_diversity_mw)
 export(get_raster_diversity_tile)
 export(get_raster_extent)
+export(get_samples_from_plots)
 export(get_samples_from_tiles)
 export(get_si_tiles_from_raster)
 export(get_spectralSpecies)

NEWS.md

@@ -3,6 +3,7 @@
 - biodivMapR_full_classif: add possibility to set compute_beta = TRUE or FALSE 
 - remove TODO.md
 - use regular expression '\\.' when searching for strings including '.': 
+- define 'get_samples_from_tiles' in independent file
 
 # biodivMapR2 v2.4.4
 ## fix

R/biodivMapR_full_classif.R

@@ -11,6 +11,7 @@
 #'
 #' @return diversity_maps_ground
 #' @importFrom dissUtils diss
+#' @importFrom terra vect crs rast extract values aggregate writeRaster
 #' @export
 
 biodivMapR_full_classif <- function(input_raster_path, output_dir, window_size,
@@ -41,12 +42,6 @@ biodivMapR_full_classif <- function(input_raster_path, output_dir, window_size,
 
     plots_beta <- plots[sample(x = seq_along(plots), nb_samples_beta,
                                replace = FALSE)]
-    get_samples_from_plots <- function(x, y){
-      x <- terra::vect(x)
-      res <- terra::extract(x = y, y = x, raw = TRUE, ID = FALSE)
-      res <- c(unlist(res))
-      return(res)
-    }
     samples <- lapply(X = plots_beta, FUN = get_samples_from_plots,
                       y = terra::rast(input_raster_path))
 
@@ -95,6 +90,12 @@ biodivMapR_full_classif <- function(input_raster_path, output_dir, window_size,
                                         alpha_metrics = alpha_metrics,
                                         Hill_order = 1, pcelim = pcelim)
   cell_order <- unlist(lapply(extracted_val, '[[', 'cell'))
+  if (is.null(Beta_info)){
+    elim <- which(names(alphabeta)=='PCoA_BC')
+    if (length(elim) > 0)
+      alphabeta <- alphabeta[-elim]
+  }
+
 
   # save diversity maps
   diversity_maps_ground <- list()

R/define_grid.R

@@ -8,7 +8,8 @@
 
 define_grid <- function(raster_path, cellsize){
   rast_obj <- terra::rast(raster_path)[[1]]
-  mask_polygon <- terra::as.polygons(x = terra::ext(rast_obj))
+  mask_polygon <- terra::as.polygons(x = terra::ext(rast_obj),
+                                     crs=terra::crs(rast_obj))
   aoi <- sf::st_as_sf(mask_polygon, quiet = T)
   crs_init <- sf::st_crs(aoi)
   aoi <- sf::st_multipolygon(aoi$geometry)

R/get_samples_from_plots.R

@@ -0,0 +1,15 @@
+#' extracts samples defined by a vector layer from a raster
+#'
+#' @param x spatVector vector layer
+#' @param y spatRaster raster
+#'
+#' @return res
+#' @importFrom terra vect extract
+#' @export
+#' 
+get_samples_from_plots <- function(x, y){
+  x <- terra::vect(x)
+  res <- terra::extract(x = y, y = x, raw = TRUE, ID = FALSE)
+  res <- c(unlist(res))
+  return(res)
+}