R/speciesNames.R

In miquelcaceres/IFNdyn: IFN forest dynamics and scenario analysis

#' Translate IFN species codes to names
#'
#' Translates the IFN species codes given in \code{x} to strings with species names. Function \code{speciesNames} returns IFN species names,
#' whereas function \code{speciesNamesModels} returns names according to the species list used in the development of IFN models. Function \code{functionalGroups} returns
#' the functional group (conifer or hardwood) corresponding to the species names of models.
#'
#' @param x numeric vector of species codes
#'
#' @return A character vector with species names (or names of species groups) corresponding to the input codes.
#' @name speciesNames
#' @aliases speciesNames speciesNamesModels functionalGroups
#'
#' @examples
#'
#' data(exampleTreeData)
#' speciesNames(exampleTreeData$Species)
#'
speciesNames<-function(x) {
  nms = rep("", length(x))
  if(length(x)>0) {
    for(i in 1:length(x)) {
      sel = (biomass_species_match$ID_TAXON == x[i])
      if(sum(sel)>0) {
        nms[i] = biomass_species_match$LATIN_TAXON[sel]
      }
    }
  }
  return(nms)
}
#' @rdname speciesNames
speciesNamesModels<-function(x) {
  species_selection = get("species_selection")
  sp_list = strsplit(as.character(species_selection$species), split=",")
  nms = rep("", length(x))
  for(i in 1:length(sp_list)) {
    sps = sp_list[[i]]
    nms[as.character(x) %in% sps] = as.character(species_selection$names[i])
  }
  return(nms)
}
#' @rdname speciesNames
functionalGroups<-function(x) {
  FG = c(rep("conifer",13), rep("hardwood",14))
  species_selection = get("species_selection")
  sp_list = strsplit(as.character(species_selection$species), split=",")
  nms = rep("", length(x))
  for(i in 1:length(sp_list)) {
    sps = sp_list[[i]]
    nms[as.character(x) %in% sps] = FG[i]
  }
  return(nms)
}