R/odkc_tt_as_wastd_tto.R

In dbca-wa/etlTurtleNesting: Data ETL of Turtle Nesting Census Data from ODK Central to WAStD

#' Transform odkc_data$track_tally into WAStD TrackTallyObservations.
#'
#' @param data The tibble of Turtle Track Tallies,
#'   e.g. \code{odkc_data$track_tally}.
#' @return A tibble suitable to
#'   \code{\link{wastd_POST}("track-tally")}
#' @export
#' @examples
#' \dontrun{
#' data("odkc_data", package = "wastdr")
#' tto <- odkc_tt_as_wastd_tto(odkc_data$track_tally)
#'
#' tto %>%
#'   wastd_POST("track-tally",
#'     api_url = Sys.getenv("WASTDR_API_DEV_URL"),
#'     api_token = Sys.getenv("WASTDR_API_DEV_TOKEN")
#'   )
#' }
odkc_tt_as_wastd_tto <- function(data) {
  data %>%
    wastdr::sf_as_tbl() %>%
    dplyr::select(
      dplyr::starts_with(
        c("id", "fb_", "gn_", "lh_", "hb_", "or_", "unk_")
      )
    ) %>%
    tidyr::pivot_longer(-id, names_to = "tracktype", values_to = "tally") %>%
    tidyr::separate(
      "tracktype",
      c("species", "species2", "no", "nest_age", "nest_type"),
      sep = "_",
      extra = "merge"
    ) %>%
    dplyr::select(-"species2", -"no") %>%
    tidyr::drop_na("tally") %>%
    dplyr::transmute(
      source = 2,
      source_id = id,
      encounter_source = "odk",
      encounter_source_id = id,
      species = dplyr::case_when(
        species == "fb" ~ "natator-depressus",
        species == "gn" ~ "chelonia-mydas",
        species == "hb" ~ "eretmochelys-imbricata",
        species == "lh" ~ "caretta-caretta",
        species == "or" ~ "lepidochelys-olivacea",
        species == "unk" ~ "cheloniidae-fam"
      ),
      # nest_age: fresh, old, unknown, missed
      nest_age = nest_age %>% stringr::str_replace("hatched", "old"),
      # nest_type: track-not-assessed, false-crawl, successful-crawl,
      # track-unsure, nest, hatched-nest, body-pit
      nest_type = dplyr::case_when(
        nest_type == "successful_crawls" ~ "successful-crawl",
        nest_type == "tracks" ~ "track-not-assessed",
        nest_type == "false_crawls" ~ "false-crawl",
        nest_type == "tracks_unsure" ~ "track-unsure",
        nest_type == "tracks_not_assessed" ~ "track-not-assessed",
        nest_type == "nests" ~ "hatched-nest"
      ),
      tally = tally
    ) %>%
    dplyr::filter_at(
      dplyr::vars(-source, -source_id, -encounter_source, -encounter_source_id),
      dplyr::any_vars(!is.na(.))
    )
}

# usethis::use_test("odkc_tt_as_wastd_tto")