fix hill mapping

Author: jbferet

R/biodivMapR_full_tiles.R

@@ -44,6 +44,11 @@ biodivMapR_full_tiles <- function(feature_dir, list_features, mask_dir = NULL,
   mosaic_output <- options$mosaic_output
   weightIRQ <- options$weightIRQ
 
+  # # adjust hill name if required
+  # if ('hill' %in% alphametrics){
+  #
+  # }
+
   # sample data if not already sampled
   samples <- biodivMapR_sample(feature_dir = feature_dir,
                                list_features = list_features,

R/run_biodivMapR_plot.R

@@ -35,6 +35,8 @@ run_biodivMapR_plot <- function(id, feature_dir, mask_dir = NULL,
 
   betanames <- paste0('beta_',id)
   alphanames <- paste0(alphametrics,'_',id)
+  if ('hill' %in% alphametrics)
+    alphanames[alphametrics=='hill'] <- paste0('hill_', Hill_order,'_',id)
   functionalname <- NULL
   if (!is.null(FDmetric))
     functionalname <- paste0(FDmetric,'_',id)

R/save_diversity_maps_mw.R

@@ -48,11 +48,11 @@ save_diversity_maps_mw <- function(input_raster_path,
     terra::values(template_rast[[1]]) <- ab_div_metrics[[idx]]$mean
     names(template_rast[[1]]) <- paste('mean', idx)
     # define output raster name
-    if (is.null(output_raster_name[[idx2]]))
+    if (is.null(output_raster_name[[idx]]))
       output_raster <- file.path(output_dir, paste0(idx2, '_mean'))
-    if (!is.null(output_raster_name[[idx2]]))
+    if (!is.null(output_raster_name[[idx]]))
       output_raster <- file.path(output_dir,
-                                 paste0(output_raster_name[[idx2]], '_mean'))
+                                 paste0(output_raster_name[[idx]], '_mean'))
 
     if (filetype%in%c('GTiff', 'COG'))
       output_raster <- paste0(output_raster, '.tiff')
@@ -66,11 +66,11 @@ save_diversity_maps_mw <- function(input_raster_path,
     terra::values(template_rast[[1]]) <- ab_div_metrics[[idx]]$sd
     names(template_rast[[1]]) <- paste('sd', idx)
     # define output raster name
-    if (is.null(output_raster_name[[idx2]]))
+    if (is.null(output_raster_name[[idx]]))
       output_raster <- file.path(output_dir, paste0(idx2, '_sd'))
-    if (!is.null(output_raster_name[[idx2]]))
+    if (!is.null(output_raster_name[[idx]]))
       output_raster <- file.path(output_dir,
-                                 paste0(output_raster_name[[idx2]], '_sd'))
+                                 paste0(output_raster_name[[idx]], '_sd'))
     if (filetype%in%c('GTiff', 'COG'))
       output_raster <- paste0(output_raster, '.tiff')
     terra::writeRaster(x = template_rast, filename = output_raster,
@@ -111,7 +111,7 @@ save_diversity_maps_mw <- function(input_raster_path,
 
   if (is.null(output_raster_name[['beta']]))
     output_raster <- file.path(output_dir, 'beta')
-  if (!is.null(output_raster_name[[idx2]]))
+  if (!is.null(output_raster_name[['beta']]))
     output_raster <- file.path(output_dir, output_raster_name[['beta']])
   if (filetype%in%c('GTiff', 'COG'))
     output_raster <- paste0(output_raster, '.tiff')

R/save_diversity_maps_tile.R

@@ -39,7 +39,8 @@ save_diversity_maps_tile <- function(input_raster_path,
 
   for (idx in alphametrics) {
     idx2 <- idx
-    if (idx == 'hill') idx2 <- paste0(idx, '_', Hill_order)
+    if (idx == 'hill')
+      idx2 <- paste0(idx, '_', Hill_order)
     # Mean value
     # produce a template
     template_rast <- terra::rast(input_raster_path[[1]])