update_det.R

#' @name update_det
#'
#' @title Update by determined specimens
#'
#' @description
#' Reference specimens can be integrated in slot **layers** within a
#' [vegtable-class] object.
#' Updated entries in the specimens can be updated in slot **samples** by using
#' this function.
#' Alternatively expert opinions can be inserted and applied in case of
#' disagreement with the original records.
#'
#' @param x A [vegtable-class] object to be updated.
#' @param specimens A character vector indicating the names of tables included
#'     in slot **layers** with updates to be applied.
#'     Note that they will be applied in the same order of the vector in the
#'     case of multiple updates.
#' @param ... Further arguments (not yet in use).
#'
#' @rdname update_det
#'
#' @exportMethod update_det
#'
setGeneric(
  "update_det",
  function(x, specimens, ...) {
    standardGeneric("update_det")
  }
)

#' @rdname update_det
#'
#' @aliases update_det,vegtable-method
#'
setMethod(
  "update_det", signature(x = "vegtable", specimens = "character"),
  function(x, specimens, ...) {
    if (any(!specimens %in% names(x@layers))) {
      stop(paste(
        "Some values in 'specimens' are not included",
        "as layer in 'x'."
      ))
    }
    for (i in specimens) {
      if (!"TaxonUsageID" %in% colnames(x@layers[[i]])) {
        stop(paste0(
          "At \"", i, "\", column 'TaxonUsageID' is ",
          "mandatory in list of specimens."
        ))
      }
      specimens_tab <- x@layers[[i]][x@layers[[i]][, i] %in%
        x@samples[, i], ]
      if (any(!specimens_tab$TaxonUsageID %in%
        x@species@taxonNames$TaxonUsageID)) {
        stop(paste0(
          "At \"", i, "\", some taxon usage names ",
          "are not included in slot 'species'."
        ))
      }
      x@samples$TaxonUsageID <- replace_idx(
        x@samples$TaxonUsageID,
        x@samples[, i], specimens_tab[, i],
        specimens_tab$TaxonUsageID
      )
    }
    # In the case that taxa2samples was applied before
    if ("TaxonConceptID" %in% colnames(x@samples)) {
      warning("You may like to repeat 'taxa2samples()' on 'x'.")
    }
    return(x)
  }
)