R/obis-to-h.R

In EMODnet/OBIShmpr: Link and query OBIS occurence data with a variety of marine habitat data

#' Get OBIS occurences matched to layers of evironmental data
#'
#' function to get OBIS records for a given species and match to IAP and Bio-Oracle temperatures
#' if save_all_recs == TRUE, this full matched dataset will be saved before summarising
#' function returns a summary of temperature affinity of the species
#'
#' @param sp_id validates species Aphia ID
#' @param check_match whether to check validity of `sp_id`.
#' @param layers character vector of habitat layers to match
#' @param overwrite whether to re-download and overwrite already downloaded layers
#' @inheritParams get_obis_recs
#' @return an `sf` object, one row for each species occurence returned from obis.
#' Column include requested OBIS metadata through `fields` argument plus a column
#' for each layer environmental layer requested containing data retuned for each
#' occurence location.
#' @importFrom rlang .env
#' @export
#'
#' @examples
#' \dontrun{
#' obis_match_habitat(sp_id = 325567, layers = c(
#'   "BO_bathymean",
#'   "BO2_phosphateltmax_bdmean", "BO2_salinitymin_ss",
#'   "rock50cm", "april", "march"
#' ))
#' }
obis_match_habitat <- function(sp_id, layers,
                               fields = c(
                                 "decimalLongitude", "decimalLatitude",
                                 "minimumDepthInMeters", "maximumDepthInMeters", "depth",
                                 "eventDate", "year", "month",
                                 "scientificName", "aphiaID"
                               ),
                               # save_all_recs = TRUE,
                               check_match = FALSE,
                               validate_sp_id = FALSE,
                               geometry = NULL,
                               ignore_failures = FALSE,
                               overwrite = FALSE) {
  if (check_match == TRUE) {
    # TODO
  }

  # Get OBIS records
  obis_recs <- get_obis_recs(
    sp_id = sp_id,
    validate_sp_id = validate_sp_id,
    geometry = geometry,
    ignore_failures = ignore_failures
  )
  if (is.null(obis_recs)) {
    return(NULL)
  } else {
    obis_recs <- obis_recs %>%
      checkmate_obis_recs(crs = 4326)
  }

  # split layers according to dataset_source
  layers_by_data_source <- layer_info %>%
    dplyr::filter(.data$layer_code %in% .env$layers) %>%
    split(x = .$layer_code, f = .$dataset_source)


  extr <- NULL

  if ("sedmaps" %in% names(layers_by_data_source)) {
    extr <- dplyr::bind_cols(
      extr,
      get_sedm(obis_recs, layers_by_data_source[["sedmaps"]])
    )
  }
  if ("sdmpredictors" %in% names(layers_by_data_source)) {
    extr <- dplyr::bind_cols(
      extr,
      get_spdm(obis_recs, layers_by_data_source[["sdmpredictors"]])
    )
  }

  dplyr::bind_cols(obis_recs, extr[, layers])
}