R/set_observer.R

In corella: Prepare, Manipulate and Check Data to Comply with Darwin Core Standard

#' Set, create or modify columns with information of who made an observation
#'
#' @description
#' Format fields that contain information about who made a specific observation
#' of an organism to a `tibble` using Darwin Core Standard.
#'
#' In practice this is no different from using `mutate()`, but gives some
#' informative errors, and serves as a useful lookup for fields in
#' the Darwin Core Standard.
#' @param .df A `data.frame` or `tibble` that the column should be appended to.
#' @param recordedBy Names of people, groups, or organizations responsible for
#' recording the original occurrence. The primary collector or observer should
#' be listed first.
#' @param recordedByID The globally unique identifier for the person, people,
#' groups, or organizations responsible for recording the original occurrence.
#' @param .keep Control which columns from .data are retained in the output.
#' Note that unlike [dplyr::mutate()], which defaults to `"all"` this defaults to
#' `"unused"`; i.e. only keeps Darwin Core columns, and not those columns used to
#' generate them.
#' @returns A `tibble` with the requested fields added/reformatted.
#' @details
#' Examples of `recordedBy` values:
#' * `José E. Crespo`
#'
#' Examples of `recordedByID` values:
#' * 	`c("https://orcid.org/0000-0002-1825-0097", "https://orcid.org/0000-0002-1825-0098")`
#'
#' @examples
#' df <- tibble::tibble(
#'   name = c("Crinia Signifera", "Crinia Signifera", "Litoria peronii"),
#'   latitude = c(-35.27, -35.24, -35.83),
#'   longitude = c(149.33, 149.34, 149.34),
#'   eventDate = c("2010-10-14", "2010-10-14", "2010-10-14"),
#'   observer = c("David Attenborough", "David Attenborough", "David Attenborough")
#'   )
#'
#' # Reformat columns to Darwin Core terms
#' df |>
#'   set_observer(
#'     recordedBy = observer
#'     )
#'
#' @importFrom dplyr mutate
#' @importFrom purrr map
#' @importFrom purrr pluck
#' @importFrom rlang abort
#' @importFrom rlang quo_is_null
#' @importFrom rlang enquos
#' @importFrom rlang zap
#' @importFrom purrr map
#' @importFrom purrr keep
#' @export
set_observer <- function(
    .df,
    recordedBy = NULL,
    recordedByID = NULL,
    .keep = "unused"
){

  if(missing(.df)){
    abort(".df is missing, with no default")
  }

  fn_args <- ls()

  # capture arguments as a list of quosures
  # NOTE: enquos() must be listed alphabetically
  fn_quos <- enquos(recordedBy, recordedByID)
  names(fn_quos) <- fn_args

  # find arguments that are NULL but exist already in `df`
  # then remove their names before `mutate()`
  # otherwise, these DwC columns are deleted by `mutate(.keep = "unused")`
  fn_quo_is_null <- fn_quos |>
    purrr::map(\(user_arg)
               rlang::quo_is_null(user_arg)) |>
    unlist()

  null_col_exists_in_df <- fn_quo_is_null & (names(fn_quos) %in% colnames(.df))

  if(any(null_col_exists_in_df)){
    fn_quos <- fn_quos |>
      purrr::keep(!names(fn_quos) %in% names(which(null_col_exists_in_df)))
  }

  # Update df
  result <- .df |>
    mutate(!!!fn_quos,
           .keep = .keep)

  check_missing_all_args(fn_call = match.call(),
                         fn_args = fn_args,
                         user_cols = colnames(result))

  # inform user which columns will be checked
  matched_cols <- names(result)[names(result) %in% fn_args]
  col_progress_bar(cols = matched_cols)

  # run column checks
  check_recordedBy(result, level = "abort")
  check_recordedByID(result, level = "abort")

  result
}


#' Check recordedBy
#' @param level what action should the function take for non-conformance?
#' Defaults to `"inform"`.
#' @noRd
#' @keywords Internal
check_recordedBy <- function(.df,
                             level = c("inform", "warn", "abort")
){
  level <- match.arg(level)
  if(any(colnames(.df) == "recordedBy")){
    .df |>
      select("recordedBy") |>
      check_is_string(level = level)
  }
  .df
}


#' check recordedByID
#' @param level what action should the function take for non-conformance?
#' Defaults to `"inform"`.
#' @noRd
#' @keywords Internal
check_recordedByID <- function(.df,
                             level = c("inform", "warn", "abort")
){
  level <- match.arg(level)
  if(any(colnames(.df) == "recordedByID")){
    .df |>
      select("recordedByID") |>
      check_is_string(level = level)
    # could check if contains "orchid.org"?
  }
  .df
}