fix names for features in get_plots_from_tiles and get_samples_from_tiles

Author: jbferet

R/biodivMapR_tiles.R

@@ -40,6 +40,7 @@ biodivMapR_tiles <- function(feature_dir, list_features, mask_dir = NULL,
   # load kmeans and beta info if exist
   Kmeans_path <- file.path(output_dir, 'Kmeans_info.RData')
   Beta_path <- file.path(output_dir, 'Beta_info.RData')
+  Kmeans_info <- Beta_info <- NULL
   if (file.exists(Kmeans_path) & file.exists(Beta_path)){
     load(Kmeans_path)
     load(Beta_path)

R/get_plots_from_tiles.R

@@ -26,9 +26,12 @@ get_plots_from_tiles <- function(plotID, plots2sel, listfiles, feat_list,
       # read rasters
       rastID <- terra::rast(tileSI)
       for (feat in feat_list){
+        feat2 <- feat
+        if (!feat == 'mask')
+          feat2 <- paste0('_',feat, '.')
         # whichfeat <- which(stringr::str_detect(basename(terra::sources(rastID)), feat) )
         whichfeat <- which(grepl(x = basename(terra::sources(rastID)),
-                                 pattern = feat))
+                                 pattern = feat2))
         names(rastID)[whichfeat] <- feat
       }
       validvals <- length(na.omit(terra::values(rastID[[1]])))

R/get_samples_from_tiles.R

@@ -27,8 +27,11 @@ get_samples_from_tiles <- function(plotID, pix2sel, listfiles, feat_list,
     if (all(file.exists(tileSI))){
       rastID <- terra::rast(tileSI)
       for (feat in feat_list){
+        feat2 <- feat
+        if (!feat == 'mask')
+          feat2 <- paste0('_',feat, '.')
         whichfeat <- which(grepl(x = basename(terra::sources(rastID)),
-                                 pattern = paste0('_',feat, '.')))
+                                 pattern = feat2))
         names(rastID)[whichfeat] <- feat
       }
       selpix <- terra::spatSample(x = rastID, size = as.numeric(pix2sel),