exporting combine_netcdf instead of just internal function

NAMESPACE

@@ -4,6 +4,7 @@ export("%>%")
 export(build_era5_land_request)
 export(build_era5_request)
 export(clearskyrad)
+export(combine_netcdf)
 export(converthumidity)
 export(extract_clim)
 export(extract_clima)

R/combine_netcdf.R

@@ -0,0 +1,93 @@
+#' Combines a series of netCDFs that all have the same spatial extent,
+#' set of variables, and units of time
+#' @param filenames a list of filenames for netCDFs you wish to combine
+#' @param combined_name the name of the combined netCDF, must end with ".nc"
+#'
+#' @return No object is returned, the combined netCDF file is written to disk
+#' with the name specified by `combined_name`
+#' @export
+combine_netcdf <- function(filenames, combined_name) {
+  # Check that combined_name includes ".nc"
+  if (substr(combined_name, nchar(combined_name)-3+1, nchar(combined_name)) != ".nc") {
+    stop("Value provided to argument `combined_name` must end with .nc")
+  }
+
+  files <- lapply(filenames, function(x) {
+    ncdf4::nc_open(x)
+  })
+
+  # Pull out first file for reference specs
+  nc <- files[[1]]
+  # Remove file metadata from vars
+  varnames <- names(nc$var)
+  varnames <- varnames[!grepl("number|expver", varnames)]
+  # Create an empty list to populate
+  vars_list <- vector(mode = "list", length = length(varnames))
+  data_list <- vector(mode = "list", length = length(varnames))
+  # One variable at a time
+  for (i in 1:length(varnames)) {
+    varname <- varnames[i]
+    # Get the variable from each of the netCDFs
+    vars_dat <- lapply(files, function(x) {
+      ncdf4::ncvar_get(x, varname)
+    })
+
+    # Then bind all of the arrays together using abind, flexibly called via do.call
+    data_list[[i]] <- do.call(abind::abind, list(
+      ... = vars_dat,
+      along = 3
+    ))
+
+    # To populate the time dimension, need to pull out the time values from each
+    # netCDF
+    timevals <- lapply(files, function(x) {
+      extract_timedim(x)$vals
+    })
+
+    # Create a netCDF variable
+    vars_list[[i]] <- ncdf4::ncvar_def(
+      name = varname,
+      units = nc$var[varname][[varname]]$units,
+      # Pull dimension names, units, and values from file1
+      dim = list(
+        # Longitude
+        ncdf4::ncdim_def(
+          nc$dim$longitude$name, nc$dim$longitude$units,
+          nc$dim$longitude$vals
+        ),
+        # Latitude
+        ncdf4::ncdim_def(
+          nc$dim$latitude$name, nc$dim$latitude$units,
+          nc$dim$latitude$vals
+        ),
+        # Time
+        ncdf4::ncdim_def(
+          extract_timedim(nc)$name, extract_timedim(nc)$units,
+          # Combination of values of all files
+          do.call(c, timevals)
+        )
+      )
+    )
+  }
+
+  # Create a new file
+  file_combined <- ncdf4::nc_create(
+    # Filename from param combined_name
+    filename = combined_name,
+    # We need to define the variables here
+    vars = vars_list
+  )
+
+
+  # And write to it (must write one variable at a time with ncdf4)
+  for (i in 1:length(varnames)) {
+    ncdf4::ncvar_put(
+      nc = file_combined,
+      varid = varnames[i],
+      vals = data_list[[i]]
+    )
+  }
+
+  # Finally, close the file
+  ncdf4::nc_close(file_combined)
+}

R/internal.R

@@ -387,97 +387,6 @@ uni_dates <- function(start_time, end_time) {
   return(df)
 }
 
-#' Combines a series of netCDFs that all have the same spatial extent,
-#' set of variables, and units of time
-#' @param filenames a list of filenames for netCDFs you wish to combine
-#' @param combined_name the name of the combined netCDF, ending with ".nc"
-#' @noRd
-combine_netcdf <- function(filenames, combined_name) {
-  # Check that combined_name includes ".nc"
-  if (substr(combined_name, nchar(combined_name)-3+1, nchar(combined_name)) != ".nc") {
-    stop("Value provided to argument `combined_name` must end with .nc")
-  }
-
-  files <- lapply(filenames, function(x) {
-    ncdf4::nc_open(x)
-  })
-
-  # Pull out first file for reference specs
-  nc <- files[[1]]
-  # Remove file metadata from vars
-  varnames <- names(nc$var)
-  varnames <- varnames[!grepl("number|expver", varnames)]
-  # Create an empty list to populate
-  vars_list <- vector(mode = "list", length = length(varnames))
-  data_list <- vector(mode = "list", length = length(varnames))
-  # One variable at a time
-  for (i in 1:length(varnames)) {
-    varname <- varnames[i]
-    # Get the variable from each of the netCDFs
-    vars_dat <- lapply(files, function(x) {
-      ncdf4::ncvar_get(x, varname)
-    })
-
-    # Then bind all of the arrays together using abind, flexibly called via do.call
-    data_list[[i]] <- do.call(abind::abind, list(
-      ... = vars_dat,
-      along = 3
-    ))
-
-    # To populate the time dimension, need to pull out the time values from each
-    # netCDF
-    timevals <- lapply(files, function(x) {
-      extract_timedim(x)$vals
-    })
-
-    # Create a netCDF variable
-    vars_list[[i]] <- ncdf4::ncvar_def(
-      name = varname,
-      units = nc$var[varname][[varname]]$units,
-      # Pull dimension names, units, and values from file1
-      dim = list(
-        # Longitude
-        ncdf4::ncdim_def(
-          nc$dim$longitude$name, nc$dim$longitude$units,
-          nc$dim$longitude$vals
-        ),
-        # Latitude
-        ncdf4::ncdim_def(
-          nc$dim$latitude$name, nc$dim$latitude$units,
-          nc$dim$latitude$vals
-        ),
-        # Time
-        ncdf4::ncdim_def(
-          extract_timedim(nc)$name, extract_timedim(nc)$units,
-          # Combination of values of all files
-          do.call(c, timevals)
-        )
-      )
-    )
-  }
-
-  # Create a new file
-  file_combined <- ncdf4::nc_create(
-    # Filename from param combined_name
-    filename = combined_name,
-    # We need to define the variables here
-    vars = vars_list
-  )
-
-
-  # And write to it (must write one variable at a time with ncdf4)
-  for (i in 1:length(varnames)) {
-    ncdf4::ncvar_put(
-      nc = file_combined,
-      varid = varnames[i],
-      vals = data_list[[i]]
-    )
-  }
-
-  # Finally, close the file
-  ncdf4::nc_close(file_combined)
-}
-
 #' Function to find the longest shared substring among a vector of strings, used
 #'to identify file_prefix for a list of requests
 #' @param strings a list or vector of strings to search for a common substring