R/get_biome_classes.R

In EvolEcolGroup/pastclim: Manipulate Time Series of Palaeoclimate Reconstructions

#' Get the biome classes for a dataset.
#'
#' Get a full list of biomes and how their id as coded in the biome variable
#' for a given dataset.
#'
#' @param dataset string defining dataset to be downloaded (a list of possible
#' values can be obtained with [list_available_datasets()]). This function
#' will not work on custom datasets.
#' @returns a data.frame with columns id and category.
#'
#' @export

get_biome_classes <- function(dataset) {
  data_path <- get_data_path()
  # test that we ahve the biome variable
  check_var_downloaded("biome", dataset)
  # get file name for biome
  this_file <- get_file_for_dataset("biome", dataset)$file_name
  this_file <- file.path(data_path, this_file)
  nc_in <- ncdf4::nc_open(this_file)
  biome_attributes <- ncdf4::ncatt_get(nc_in, "biome")
  # format the table
  if (dataset == "Beyer2020" | dataset == "Example") {
    indeces_biomes <- which(substr(names(biome_attributes), 1, 5) == "biome")
    biome_categories <- data.frame(
      id = 0:(length(indeces_biomes) - 1),
      category = unlist(biome_attributes[indeces_biomes])
    )
    row.names(biome_categories) <- NULL
  } else if (dataset == "Krapp2021") {
    biomes_string <- trimws(unlist(strsplit(biome_attributes$biomes,
      split =
        ";"
    )))
    biomes_string <- biomes_string[-length(biomes_string)]
    biomes_string <- substr(biomes_string, 4, nchar(biomes_string))
    biome_categories <- data.frame(
      id = seq_len(length(biomes_string)),
      category = biomes_string
    )
  }
  ncdf4::nc_close(nc_in)
  return(biome_categories)
}