data-raw/helper_functions/verify_files_by_dataset.R

In EvolEcolGroup/pastclim: Manipulate Time Series of Palaeoclimate Reconstructions

# 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()
for (i in 1:nrow(full_meta)) {
  pastclim::download_dataset(
    dataset = as.character(full_meta$dataset[i]),
    bio_variables = full_meta$variable[i]
  )
  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
  }
  ncdf4::nc_close(nc_in)
}

if (any(problem_rows)) {
  which(problem_rows)
} else {
  cat("all files are fine")
}