R/pullSpeciesCodes.R

In ecology-rocks/MakeMyForests: SORTIE-ND Preparation From Forest Inventory Data

#' Get Species Codes From A Reference Table
#' 
#' @param speciesList A character vector of the species shortcodes 
#'     (look them up in USDA PLANTs database)
#' @param refDataFrame A dataframe containing at least two columns:
#'     SPECIES_SYMBOL and SPCD
#' @return Returns a vector of species codes from the reference dataframe.
#' @export 
#' @examples 
#' 
#' sampleList <- c("ABCO", "ABMA")
#' ## RefSpecies is an included reference species list for CA
#' 
#' pullSpeciesCodes(sampleList, RefSpecies)


## Get species codes from the reference table
pullSpeciesCodes <- function(speciesList, refDataFrame=""){
  
  ## if a custom data.frame is not specified, load the default data.
  if(is.character(refDataFrame)){
      refDataFrame <- get("RefSpecies")
  }
  ##initialize counter and storage variables
  store <- NULL
  
  #start looping through
  for(i in 1:length(speciesList)){
    
    ##for each i, subset according to the 
    ##correct species symbol to get the 
    ##FIA tree code
    store[i] <- subset(refDataFrame, 
                       SPECIES_SYMBOL==speciesList[i], 
                       select="SPCD")
  }	
  ## return our results in a vector
  store <- unlist(store)
  if(length(store) > 0){
    return(store)
  } else{
    stop("Sorry, nothing found.")
  }
}