R/get_katsianis.R

In ropensci/c14bazAAR: Download and Prepare C14 Dates from Different Source Databases

#' @rdname db_getter_backend
#' @export

get_katsianis <- function(db_url = get_db_url("katsianis")) {

  check_connection_to_url(db_url)

  # download and unzip data
  temp <- tempfile(fileext = ".zip")

  utils::download.file(
    db_url,
    temp,
    mode="wb",
    quiet = TRUE
  )

  unzip_path <- file.path(tempdir(), "c14bazAAR_get_katsianis")
  db_path <- utils::unzip(
    temp,
    exdir = unzip_path
  )

  # read data
  katsianis <- data.table::fread(
    db_path[grepl("/C14Samples.txt", db_path)],
    sep = "\t",
    drop = c(
      "DBID",
      "OthLabID",
      "OthDateCode",
      "Problems",
      "OthMeasures"
    ),
    colClasses = "character",
    showProgress = FALSE
  ) %>%
    base::replace(., . == "", NA) %>%
    dplyr::transmute(
      labnr = .data[["LabID"]],
      c14age = .data[["CRA"]],
      c14std = .data[["Error"]],
      c13val = .data[["DC13"]],
      method = .data[["DateMethod"]],
      material = .data[["Material"]],
      species = .data[["Species"]],
      site = .data[["SiteName"]],
      sitetype = .data[["SiteType"]],
      region = .data[["AdminRegion"]],
      country = .data[["Country"]],
      feature = .data[["SiteContext"]],
      period = .data[["SitePhase"]],
      culture = .data[["CulturalPeriod"]],
      lat = .data[["Latitude"]],
      lon = .data[["Longitude"]],
      shortref = .data[["Source"]],
      comment = .data[["Comments"]]
    ) %>% dplyr::mutate(
      sourcedb = "katsianis",
      sourcedb_version = get_db_version("katsianis")
    ) %>%
    as.c14_date_list()

  # remove files in file system
  unlink(temp)
  unlink(unzip_path, recursive = T)

  return(katsianis)
}