R/matcher.R

In sckott/splister: Match Species Lists Against Reference List

#' Match spp list to reference list
#'
#' @export
#' @param spplist Input species list, a character vector
#' @param ref Reference taxon data.frame, or file path
#' @param against (character) What column to match against in data.frame.
#' Ignored if a vector given
#'
#' @examples \dontrun{
#' x <- c('Salmo trutta', 'Oncorhynchus clarkii', 'Salmo Linnaeus',
#' 'Oncorhynchus clarkii', 'Salvelinus fontinalis', 'Salvelinus confluentus')
#' y <- system.file("examples", "worms_salmo.csv", package = "splister")
#' dat <- unique(read.csv(y, stringsAsFactors = FALSE))
#' matcher(spplist = x, ref = dat, against = "scientificName")
#' }
#'
#' @examples
#' # read from file
#' x <- system.file("examples", "iucn_dat.csv", package = "splister")
#' x <- read.csv(x, stringsAsFactors = FALSE)[,-1]
#' y <- system.file("examples", "worms_sample.csv", package = "splister")
#' spp <- x$sciname[1:200L]
#' res <- matcher(spplist = spp, ref = y, against = "scientificName")
#' unique(sapply(res, attr, "match"))
#' df <- data.frame(original = spp, taxon = unlist(res),
#'    match = sapply(res, attr, "match"))
#' df[df$match == "replace", ]
matcher <- function(spplist, ref, against = NULL) {
  UseMethod("matcher")
}

#' @export
#' @rdname matcher
matcher.character <- function(spplist, ref, against = NULL) {
  if (!is(ref, "data.frame")) ref <- readr::read_csv(ref)
  unname(lapply(spplist, function(z) {
    ex <- ref[ref[[against]] %in% z, against]
    if (length(ex) == 0) {
      df <- ref[grep(z, ref[[against]]), ]
      if (NROW(df) == 0) {
        structure(NA, match = "not_found")
      } else if (NROW(df) > 1) {
        ask(df, z, against)
      } else {
        structure(df[, against], match = "replace")
      }
    } else {
      structure(ex, match = "exact")
    }
  }))
}