R/PRE_FATE.abundBraunBlanquet.R

In leca-dev/RFate: FATE with R

### HEADER #####################################################################
##' @title Transform Braun-Blanquet values into relative abundances
##' 
##' @name PRE_FATE.abundBraunBlanquet
##'
##' @author Maya Guéguen
##' 
##' @description This script is designed to transform Braun-Blanquet abundance 
##' information into relative abundances or average recovery values
##' (between 0 and 100).
##'              
##' @param abund a \code{vector} with abundance values from Braun-Blanquet
##' (\code{+, r, 1, 2, 3, 4, 5}), and with \code{NA} when no information
##' 
##' @details 
##' 
##' Braun-Blanquet values allow to estimate the abundance-dominance of a 
##' species based on an estimation of the number of individuals and the 
##' covering surface. A correspondence has been defined between this index and 
##' average recovery values :
##' 
##' \code{| Braun-Blanquet | Recovery class (\%) | Average recovery (\%) |} \cr
##' ____________________________________________________________ \cr
##' \code{| + ............ | ............... <1 | ................ 0.5 |} \cr
##' \code{| 1 ............ | .............. 1-5 | .................. 3 |} \cr
##' \code{| 2 ............ | ............. 5-25 | ................. 15 |} \cr
##' \code{| 3 ............ | ............ 25-50 | ............... 37.5 |} \cr
##' \code{| 4 ............ | ............ 50-75 | ............... 62.5 |} \cr
##' \code{| 5 ............ | ........... 75-100 | ............... 87.5 |} \cr
##' ##' ____________________________________________________________ \cr
##' \code{| 0 ............ | .................. | .................. 0 |} \cr
##' \code{| NA ........... | .................. | ................. NA |} \cr
##' 
##' 
##' \emph{\cr \cr
##' Braun-Blanquet J., Roussine N. & Nègre R., 1952. Les groupements végétaux de 
##' la France méditerranéenne. Dir. Carte Group. Vég. Afr. Nord , CNRS, 292 p.}
##' 
##' \emph{Baudière A. & Serve L., 1975. Les groupements végétaux du Plade 
##' Gorra-Blanc (massif du Puigmal, Pyrénées Orientales). Essai d'interprétation 
##' phytosociologique et phytogéographique. Nat. Monsp., sér. Bot., 25, 5-21.}
##' 
##' \emph{Foucault B. (de), 1980. Les prairies du bocage virois (Basse-Normandie, 
##' France). Typologie phytosociologique et essai de reconstitution des séries 
##' évolutives herbagères. Doc. Phytosoc., N.S., 5, 1-109.}
##' 
##' @return A \code{vector} with numerical values between \code{0} and 
##' \code{100} corresponding to the median of each recovery class.
##' 
##' @keywords abundance, Braun-Blanquet
##' 
##' @examples
##' 
##' abund_BB = sample(x = c(NA, "+", "r", 1:5), size = 100, replace = TRUE)
##' abund = PRE_FATE.abundBraunBlanquet(abund_BB)
##' summary(abund)
##' 
##' @export
##' 
##' @importFrom stats na.exclude
##'
## END OF HEADER ###############################################################


PRE_FATE.abundBraunBlanquet = function(abund){
  ## CHECK parameter abund
  if (.testParam_notDef(abund))
  {
    .stopMessage_notDef("abund")
  } else
  {
    abund = as.character(abund)
    .testParam_notInValues.m("abund", abund, c(NA, "NA", 0, "+", "r", 1:5))
  }
  
  ## Convert Braun-Blanquet abundance classes into median coverage percentage
  if (length(na.exclude(abund)) > 0) {
    abund = sapply(abund, function(x){
      x = as.character(x)
      if (is.na(x) | x == "") {
        return(NA)
      } else if (x == "0") {
        return(0)
      } else if (x == "+" | x == "r") {
        return(0.5)
      } else if (x == "1") {
        return(3)
      } else if (x == "2") {
        return(15)
      } else if (x == "3") {
        return(37.5)
      } else if (x == "4") {
        return(62.5)
      } else if (x == "5") {
        return(87.5)
      } else {
        return(NA)
      }
    })
  }
  
  abund = as.numeric(abund)
  return(abund)
}