R/taxonRectification.R

In occCite: Querying and Managing Large Biodiversity Occurrence Datasets

#' @title Taxon Rectification
#'
#' @description An function that takes an input taxonomic name, checks against
#' taxonomic database, returns vector for use in database queries, as well as
#' warnings if the name is invalid.
#'
#' @param taxName A string that, ideally, is a taxonomic name
#'
#' @param datasources A vector of taxonomic data sources implemented in
#' \code{taxize::gnr_resolve()}. See the
#' \href{http://gni.globalnames.org/}{Global Names List} for more information.
#'
#' @param skipTaxize If \code{skipTaxize = TRUE}, occCite will skip taxonomic
#'  rectification using taxize, which has been orphaned on CRAN. Setting this
#'  option to `TRUE` will result in a check for the \code{taxize} package before taxonomic
#'  rectification is attempted. *The code using `taxize` has been disabled to comply with CRAN.*
#'
#' @return A string with the closest match according to
#' \code{taxize::gnr_resolve()}, and a list of taxonomic data sources that
#' contain the matching name.
#'
#' @examples
#' # Inputting taxonomic name and specifying what taxonomic sources to search
#' taxonRectification(
#'   taxName = "Buteo buteo hartedi",
#'   datasources = "National Center for Biotechnology Information",
#'   skipTaxize = TRUE
#' )
#' @export
#'

taxonRectification <- function(taxName = NULL, datasources = NULL,
                               skipTaxize = FALSE) {

  if (!is.logical(skipTaxize)) {
    warning(paste0(
      "You have not used a logical operator to\n",
      "specify whether occCite should skip taxize-\n",
      "based taxonomic rectification."
    ))
    return(NULL)
  }

  if(!skipTaxize){
    # if(!requireNamespace("taxize", quietly = TRUE)){
      warning(paste0("Package taxize unavailable. Skipping taxonomic rectification."))
      skipTaxize <- TRUE
    # }
  }

  if(skipTaxize){
    resolvedNames <- data.frame(taxName, taxName, "Not rectified.")
    colnames(resolvedNames) <- c(
      "Input Name",
      "Best Match",
      "Searched Taxonomic Databases w/ Matches"
    )
    resolvedNames <- as.data.frame(resolvedNames)
    return(resolvedNames)
  }
  # else{
  #   # Checks for source connectivity
  #   if(requireNamespace("taxize")){
  #     tryCatch(
  #       expr = sources <- taxize::gnr_datasources(),
  #       error = function(e) {
  #         message(paste("GNR server unreachable; please try again later. \n"))
  #       }
  #     )}
  #
  #   if (!exists("sources")) {
  #     return(invisible(NULL))
  #   }
  #
  #   # Are user-input databases included in data sources for Global Names Resolver?
  #   if (!is.null(datasources)) {
  #     for (db in datasources) {
  #       notInDB <- character()
  #       if (!(db %in% sources$title)) {
  #         notInDB <- append(notInDB, db)
  #       }
  #     }
  #     if (length(notInDB) != 0) {
  #       warning(paste0(
  #         "Following sources not found in\n",
  #         "Global Names Index source list: ",
  #         paste(notInDB, collapse = ", ")
  #       ))
  #     }
  #     # Remove invalid sources from datasources
  #     datasources <- datasources[!datasources %in% notInDB]
  #   }
  #
  #   # Populating vector of data sources if no valid sources are supplied
  #   if (length(datasources) == 0) {
  #     warning(paste0(
  #       "No valid taxonomic data sources supplied.\n",
  #       "Populating default list from all available sources."
  #     ))
  #     datasources <- sources$title
  #   }
  #
  #   # Resolving the user-input taxonomic names
  #   sourceIDs <- sources$id[sources$title %in% datasources]
  #   # Protects from error when gnr_resolve gets complete list of data sources
  #   if (nrow(sources) == length(sourceIDs)) {
  #     sourceIDs <- NULL
  #   }
  #   taxonomicDatabaseMatches <- vector("list")
  #   if(requireNamespace("taxize")){
  #     temp <- taxize::gnr_resolve(sci = taxName, data_source_ids = sourceIDs)
  #   }
  #   if (nrow(temp) == 0) {
  #     bestMatch <- "No match"
  #     taxonomicDatabaseMatches <- "No match"
  #     warning(paste(taxName,
  #                   " is not found in any of the taxonomic data sources specified.",
  #                   sep = ""
  #     ))
  #   } else {
  #     bestMatch <- temp[order(temp$score), ]$matched_name[1]
  #     matchingSources <- temp$data_source_title[temp$matched_name == bestMatch]
  #     taxonomicDatabaseMatches <- paste(matchingSources, collapse = "; ")
  #   }
  #
  #   # Building the results table
  #   resolvedNames <- data.frame(taxName, bestMatch, taxonomicDatabaseMatches)
  #   colnames(resolvedNames) <- c(
  #     "Input Name",
  #     "Best Match",
  #     "Searched Taxonomic Databases w/ Matches"
  #   )
  #   resolvedNames <- as.data.frame(resolvedNames)
  #
  #   return(resolvedNames)
  # }
}