R/check_identifiers.R

In delimtools: Helper Functions for Species Delimitation Analysis

#' Checks for Differences Between Identifiers in Metadata and DNA Sequence Files
#'
#' @description
#' `check_identifiers()` checks for differences between identifiers in metadata
#' and DNA sequence files.
#'
#' @param data an object of class [tbl_df][tibble::tbl_df] containing sequence metadata.
#' @param identifier column in `data` which contains sequence identifiers.
#' @param dna a [DNAbin][ape::DNAbin] object.
#'
#' @details
#' `check_identifiers()` is a helper function to check for inconsistencies
#' between identifiers in metadata and DNA sequences files, such as absence, mistyping,
#' duplicated entries, or differences in size lengths. If any of these problems are found,
#' warnings will appear in `Console` and corrections should be made to prevent
#' unintended consequences later. A list containing erroneous identifiers is returned
#' invisibly.
#'
#' @return
#' A list containing erroneus identifiers between metadata and sequence file.
#'
#' @author
#' Pedro S. Bittencourt, Rupert A. Collins.
#'
#' @examples
#' check_identifiers(geophagus_info, "gbAccession", geophagus)
#'
#' @export
check_identifiers <- function(data, identifier, dna) {
  id1 <- dplyr::pull(data, {{ identifier }})
  id2 <- names(dna)

  if (length(id1) != length(id2)) {
    get_diff <- function(x, y) {
      xdiff <- x[!x %in% y] |> unique()
      ydiff <- y[!y %in% x] |> unique()

      invisible(list(ydiff, xdiff))
    }

    gdiff <- get_diff(id1, id2)


    cli::cli_abort(c("Identifiers are not of equal length:",
      "x" = "You've supplied inputs with size lengths of {length(id1)} and {length(id2)}.",
      "i" = "Identifiers absent in {.arg {deparse(substitute(data))}}:",
      stringr::str_flatten_comma(gdiff[[1]]),
      "i" = "Identifiers absent in {.arg {deparse(substitute(dna))}}:",
      stringr::str_flatten_comma(gdiff[[2]])
    ))
  }

  if (any(duplicated(id1) | duplicated(id2))) {
    cli::cli_abort(c("Duplicate identifiers found.",
      "x" = "You've supplied inputs with duplicated identifier names.",
      "i" = "Duplicated identifiers in {.arg {deparse(substitute(data))}}:",
      stringr::str_flatten_comma(id1[vctrs::vec_duplicate_detect(id1)]),
      "i" = "Duplicated identifiers in {.arg {deparse(substitute(dna))}}:",
      stringr::str_flatten_comma(id2[vctrs::vec_duplicate_detect(id2)])
    ))
  }

  diff <- dplyr::symdiff(id1, id2)

  if (rlang::is_empty(diff)) {
    cli::cli_alert_success(c("Identifiers are the same across files."))
  } else {
    diff <- vctrs::vec_chop(diff, sizes = c(length(diff) / 2, length(diff) / 2))
    names(diff) <- c(
      "Identifiers absent or mistyped in deparse(substitute(data))}",
      "Identifiers absent or mistyped in deparse(substitute(dna))}"
    )

    cli::cli_warn(c("Identifiers must be identical across files.",
      "x" = "The identifiers bellow are either absent or mistyped.",
      "i" = "Identifiers absent or mistyped in {.arg {deparse(substitute(data))}}:",
      stringr::str_flatten_comma(diff[[1]]),
      "i" = "Identifiers absent or mistyped in {.arg {deparse(substitute(dna))}}:",
      stringr::str_flatten_comma(diff[[2]])
    ))
    invisible(diff)
  }
}