R/download_gpdd.R

In boettiger-lab/gpdd: Download datasets from the Global Population Dynamics Database

#' Download and Save Data from GPDD.
#'
#' @author Zihao Li, \email{zihao0104@@berkeley.edu}
#' @name download_gpdd
#' @param dataset_name A string of the name of the dataset.
#' @param dir A directory to which the datasets will be downloaded.
#' @param overwrite Indicates whether to overwrite existing datasets or not.
#' @return The requested dataset in tibble format.
#' @importFrom readr read_csv
#' @export
#' @examples
#' download_gpdd()
#' download_gpdd(c("gpdd_data", "gpdd_timeperiod"))

download_gpdd <- function(dataset_name = c("gpdd_data",
                                           "gpdd_main",
                                           "gpdd_timeperiod",
                                           "gpdd_taxon",
                                           "gpdd_datasource",
                                           "gpdd_biotope",
                                           "gpdd_location"), 
                          dir = rappdirs::user_data_dir("gpdd"),
                          overwrite = "Ask") {
  dir.create(rappdirs::user_data_dir("gpdd"), recursive = TRUE, showWarnings = FALSE)
  for (i in 1:length(dataset_name)) {
    csv_name <- paste(dataset_name[i], ".csv", sep = '')
    check_character(dataset_name[i])
    check_name(dataset_name[i])
    if (file.exists(file.path(dir, csv_name)) && overwrite == "Ask" && interactive()) {
      ans <- ask_yn(
        dataset_name[i], " already exists. ",
        "Overwrite?"
      )
    }
    if ((file.exists(file.path(dir, csv_name)) && overwrite == "Yes") 
        | !file.exists(file.path(dir, csv_name)) 
        | (file.exists(file.path(dir, csv_name)) && overwrite == "Ask" && interactive() && ans)) {
      message("Downloading ", dataset_name[i], ". This may take a while")
      data <- switch(dataset_name[i],
                     gpdd_data = readr::read_csv("https://knb.ecoinformatics.org/knb/d1/mn/v2/object/df35b.233.1",
                                                 col_types = "iidddddddd"),
                     gpdd_main = readr::read_csv("https://knb.ecoinformatics.org/knb/d1/mn/v2/object/df35b.234.1",
                                                 col_types = "iiiiiccccccccdddcdcdddcdd"),
                     gpdd_timeperiod = readr::read_csv("https://knb.ecoinformatics.org/knb/d1/mn/v2/object/df35b.235.1", 
                                                       col_types = "iccidd"),
                     gpdd_taxon = readr::read_csv("https://knb.ecoinformatics.org/knb/d1/mn/v2/object/df35b.236.1", 
                                                  col_types = "iccccccccccc"),
                     gpdd_datasource = readr::read_csv("https://knb.ecoinformatics.org/knb/d1/mn/v2/object/df35b.237.1", 
                                                       col_types = "icdcccccc"),
                     gpdd_biotope = readr::read_csv("https://knb.ecoinformatics.org/knb/d1/mn/v2/object/df35b.238.1", 
                                                    col_types = "icc"),
                     gpdd_location = readr::read_csv("https://knb.ecoinformatics.org/knb/d1/mn/v2/object/df35b.239.1", 
                                                     col_types = "iccccccddcddcddddddddcdd")
      )
      readr::write_csv(data, path = file.path(dir, csv_name))
    }
    else if (file.exists(file.path(dir, csv_name)) && overwrite == "Ask" && interactive() && !ans) {
      message("Not overwriting ", dataset_name[i], ". Proceeding to the next datast.")
    }
    else if (file.exists(file.path(dir, csv_name)) && overwrite == "No") {
      message(paste(dataset_name[i], "already exists. Not overwriting. Proceeding to the next dataset.", sep = ' '))
    }
  }
  message("\nDownload finished.")
}