R/speciesCode2speciesType.R

In bcgov/BCForestGroundSample: BC forest ground sample compilation

#' Group species into deciduous and coniferous species group
#'
#'
#' @description This function is to group species into deciduous and
#'              coniferous species types based on BC species code and \code{sp_type} lookup table.
#'              This function uses hardcoded \code{sp_type} lookup table.
#' @param species character, Tree basic species code, which is SPECIES in VRI original data.
#'
#'
#' @return Species type: \code{D}-deciduous species and \code{C}-coniferous species.
#'         \code{NA}, with a warning message, is given if a species fails to be grouped.
#'
#' @importFrom data.table ':='
#'
#' @export
#' @docType methods
#' @rdname speciesCode2speciesType
#'
#' @author Yong Luo
#'
setGeneric("speciesCode2speciesType",
           function(species) {
             standardGeneric("speciesCode2speciesType")
           })

#' @rdname speciesCode2speciesType
setMethod(
  "speciesCode2speciesType",
  signature = c(species = "character"),
  definition = function(species){
    ## hardcoded lookup table
    tempdata <- data.table(uniObs = 1:length(species),
                           SPECIES = species)
    sp_type <- unique(lookup_species()[,.(SPECIES, SP_TYPE)], by = "SPECIES")
    tempdata <- merge(tempdata, sp_type, by = "SPECIES", all.x = TRUE)
    if(nrow(tempdata[is.na(SP_TYPE)]) > 0){
      warning("Species code can not find a species type, NA is produced.")
    }
    return(tempdata[order(uniObs)]$SP_TYPE)
  })