fix var names

EvolEcolGroup · Sep 12, 2023 · e3905fe · e3905fe
1 parent 2e38302
commit e3905fe
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Showing 2 changed files with 13 additions and 7 deletions.
diff --git a/R/download_worldclim_future.R b/R/download_worldclim_future.R
@@ -16,9 +16,7 @@ download_worldclim_future <- function(dataset, bio_var, filename){
   # get resolution from the dataset name and convert it to the original
   res_conversion <- data.frame(our_res = c("10m","5m","2.5m", "0.5m"),
                                       wc_res = c("10m","5m", "2.5m", "30s"))
-  wc_res <- res_conversion$wc_res[res_conversion$our_res==substr(dataset,
-                                                                  start = regexpr("_\\d+\\.?\\d+m",dataset)+1,
-                                                                  stop=nchar(dataset))]
+  wc_res <- res_conversion$wc_res[res_conversion$our_res==tail(strsplit(dataset,"_")[[1]],1)]
   gcm <- c("ACCESS-CM2", "BCC-CSM2-MR", "CMCC-ESM2", "EC-Earth3-Veg", "FIO-ESM-2-0",
            "GFDL-ESM4", "GISS-E2-1-G", "HadGEM3-GC31-LL", "INM-CM5-0", "IPSL-CM6A-LR",
            "MIROC6", "MPI-ESM1-2-HR", "MRI-ESM2-0", "UKESM1-0-LL")
@@ -73,12 +71,18 @@ download_worldclim_future <- function(dataset, bio_var, filename){
 
   var_names <- names(wc_list[[1]])
   sds_list <- list()
-  for (i_var in var_names){
-    sds_list[[i_var]]<-terra::rast(lapply(wc_list, terra::subset,subset=i_var))
-    names(sds_list[[i_var]])<-rep(i_var,nlyr((sds_list[[i_var]])))
+  for (i in 1:length(var_names)){
+    i_var <- var_names[i]
+    if (!any(postfix %in% c("bioc","elev"))){
+      new_var_name <-paste0(var_prefix,sprintf("%02d",i))
+    } else {
+      new_var_name <- i_var
+    }
+    sds_list[[new_var_name]]<-terra::rast(lapply(wc_list, terra::subset,subset=i_var))
+    names(sds_list[[new_var_name]])<-rep(new_var_name,nlyr((sds_list[[new_var_name]])))
   }
   wc_sds <- terra::sds(sds_list)
-  
+
   terra::writeCDF(wc_sds,filename=filename, compression=9, 
                   overwrite=TRUE)
   # fix time axis (this is a workaround if we open the file with sf)

diff --git a/data-raw/helper_functions/verify_files_by_dataset.R b/data-raw/helper_functions/verify_files_by_dataset.R
@@ -1,5 +1,6 @@
 # verify that all the variables in the tables are actually found in the files
 # this requires all data to have been downloaded
+library(pastclim)
 full_meta <- pastclim:::dataset_list_included
 in_dir <- get_data_path()
 problem_rows <- vector()
@@ -9,6 +10,7 @@ for (i in 1:nrow(full_meta)){
   nc_in <- ncdf4::nc_open(file.path(in_dir, full_meta$file_name[i]))
   if (!full_meta$ncvar[i] %in% names(nc_in$var)){
     message("problem with ",full_meta$ncvar[i]," in ", full_meta$file_name[i],"\n")
+    stop("we had a problem")
     problem_rows[i]<-TRUE
   } else {
     problem_rows[i]<-FALSE