R/quick_rename.R

In alexology/biomonitoR: biomonitoring indices and metrics

#' quick_rename
#'
#' This function allow the user to change the wrong taxa names according to the deault reference databases implemented in `biomonitoR`.
#' @param x a data.frame as specified in details
#' @param group biotic group of interest. Possible values are `mi` for macroinvertebrates, `mf` for macrophytes `fi` for fish and `di` for diatoms. Default to `mi`.
#' @param write_table if TRUE `quick_rename()` will save a txt file with changes provided by the user.
#' @keywords as_biomonitor
#' @details data.frame must have a column called "Taxa" where put species, genus or family names. See data(macro_ex) for an example dataset.\cr
#' The function `quick_rename()` will suggest correct name while allowing the user to insert a name (Enter taxon name).
#' @export
#' @importFrom utils menu
#' @seealso \code{\link{asBiomonitor}}
#' @examples
#' data(macro_ex)
#' macro_ex_mod <- quick_rename(macro_ex, group = "mi")
quick_rename <- function(x, group = "mi", write_table = FALSE) {
  if (is.null(group) == TRUE) {
    stop("Please provide a valid group")
  }

  if (!any(names(x) %in% "Taxa")) (stop(" A column called Taxa is missing"))

  dfName <- deparse(substitute(x))
  tempNames <- suggestUserNames(x, group = group)

  if (length(tempNames) == 0) {
    message("All names are correct")
    return(x)
  }
  else {
    wrong <- tempNames$wrongNames
    correct <- tempNames$correctNames
    result <- as.character(x$Taxa)
    n <- length(wrong)
    if (length(wrong) != length(correct)) {
      stop("pattern and replacement do not have the same length.")
    }
    for (i in 1:n) {
      result[which(result == wrong[i])] <- correct[i]
    }

    x$Taxa <- result
    if (any(x$Taxa == "REMOVe")) {
      x <- x[x$Taxa != "REMOVe", ]
    }

    x$Taxa <- factor(sub("_", " ", x$Taxa))

    # write.table if needed by the user, allowing to overwrite or not
    if (write_table) {
      dfNameChange <- paste0(dfName, "_mod", ".txt")
      if (dfNameChange %in% list.files(path = ".")) {
        choice.list <- c("Overwrite", "Quit")
        res <- menu(choice.list, title = paste("Overwrite the existing ", dfNameChange, " file?", sep = ""))
        if (res == 1) {
          write.table(x, file = dfNameChange, quote = TRUE, append = FALSE, row.names = FALSE)
        }
        else {
          stop("Operation stopped by the user")
        }
      } else {
        write.table(x, file = dfNameChange, quote = TRUE, append = FALSE, row.names = FALSE)
      }
    }

    x
  }
}