R/Clean_species.R

In RadicalCommEcol/CleanR: Clean all the data! (I wish)

#' @name clean_species
#'
#' @title Helper function to clean taxonomy.
#'
#' @description This correct misspellings, synonyms and flags not recognizes species.
#'
#' @param species A vector of species to check
#'
#' @return data.frame of original and corrected species.
#'
#' @examples
#' \dontrun{
#' species <- c("Osmia rufa", "Osmia bicornis", "Osmia ruffa",
#'            "Osmia wikifluqie", "watermelon pie", "Osmia sp.")
#' clean_species(species)
#' }
#' @export
clean_species <- function(species, verbose = TRUE, db = "itis"){
  species <- as.character(species)
  #misspellings
  species2 <- unique(species)
  temp <- gnr_resolve(species2, best_match_only = TRUE, canonical = TRUE)
  dat <- merge(data.frame(species2), temp[,c("user_supplied_name", "matched_name2")],
               by.x = "species2", by.y = "user_supplied_name", all.x = TRUE)
  #synonims
  #here we ca save time by re-doing a unique() and removing NA's
  species3 <- unique(dat$matched_name2)
  species3 <- species3[!is.na(species3)]
  temp <- synonyms(species3, db = db)
  synonym_ids <- grep(pattern = "acc_name", temp) #is this the optimal solution?
  accepted_names <- unlist(lapply(temp[synonym_ids], '[', "acc_name"),
                           use.names = FALSE)
  synonym_names <- species3
  synonym_names[synonym_ids] <- accepted_names[1]
  key <- data.frame(species3, synonym_names)
  dat <- merge(dat, key,
               by.x = "matched_name2", by.y = "species3", all.x = TRUE)
  #clean non accepted species
  species4 <- unique(dat$synonym_names)
  species4 <- species4[!is.na(species4)]
  out2 <- tax_name(as.character(species4), get = "species", db = "both", pref = "itis", verbose = verbose)
  out2_u <- unique(out2$species)
  final_names <- species4
  final_names[which(!species4 %in% out2_u)] <- NA
  key2 <- data.frame(species4, final_names)
  dat <- merge(dat, key2,
               by.x = "synonym_names", by.y = "species4", all.x = TRUE)
  #output
  dat <- merge(data.frame(species), dat, by.x = "species", by.y = "species2",
               all.x = TRUE)
  dat[,c(1,3,2,4)]
}