Iss5 (#11)

* adding ncdf4 package to the list to be compatible with GSDE dataset files

* adding GSDE script, adjustments in the main calling script, adding necessary documentation

* correcting typo in the subsetting part -  to

Author: kasra-keshavarz

assets/renv.lock

@@ -160,6 +160,14 @@
         "nlme"
       ]
     },
+    "ncdf4": {
+      "Package": "ncdf4",
+      "Version": "1.19",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "7c902f18c0be04c8767b94019ffe8063",
+      "Requirements": []
+    },
     "nlme": {
       "Package": "nlme",
       "Version": "3.1-153",

assets/stats.R

@@ -41,9 +41,14 @@ Sys.getenv("R_LIBS_USER")
 install.packages(renv_source_package, repos=NULL, type="source", quiet=TRUE);
 renv::activate(virtual_env_path);
 renv::restore(lockfile=lockfile_path, prompt=FALSE);
+print('here!')
 
 # produce necessary stats and print a csv file
-r <- raster::raster(vrt_path);
+if (tools::file_ext(vrt_path) == 'nc') {
+  r <- terra::rast(vrt_path)
+} else {
+  r <- raster::raster(vrt_path);
+}
 p <- sf::st_read(shapefile_path, quiet=TRUE);
 
 # check the CRS of the shapefile

extract-gis.sh

@@ -325,6 +325,11 @@ case "${geotiff,,}" in
     call_processing_func "$(dirname $0)/modis/modis.sh"
     ;;
 
+  # GSDE
+  "gsde")
+    call_processing_func "$(dirname $0)/gsde/gsde.sh"
+    ;;
+  
   # Depth to Bedrock
   "depth-to-bedrock" | "depth_to_bedrock" | "dtb" | "depth-to_bedrock" | "depth_to_bedrock")
     call_processing_func "$(dirname $0)/depth_to_bedrock/depth_to_bedrock.sh"