R/DrawDeterm.R

In EcoFoG/vernabota: Association between vernacular and botanical names for Guyafor data

#' Attribute the most likely full species name
#'
#' @description This function attributes the full species name corresponding to
#'   the highest value of alpha to a given tree.
#'
#' @param AlphaV data.table with the botanical information in the first 4 columns
#'   and one column for the vernacular name of interested, created in the
#'   function DrawBota
#'
#' @param levelAsso Level of association depending on the available information
#'   ("AssoByGenus", "AssoByFam" or "AssoByVern")
#'
#' @param VernName2Sim The vernacular name of the tree for which we want to get
#'   a full botanical name (character)
#'
#' @return This function returns a list with two elements: the first one is the
#'   associated botanical name and the second one the method of association
#'   (AssoByGenus, AssoByGenusT, AssoByFam, AssoByFamT, AssoByVern or
#'   AssoByVernT).
#'
#' @details This function performs the following steps:
#'  - Get the species for which the value of alpha is the highest
#'  - if there are no tie, return the value of this species and the associated
#'  correction code
#'  - if there is a tie, draw a species randomly within these species
#'
#' @export
#'
#'
#'
DrawDeterm <- function(AlphaV, levelAsso, VernName2Sim) {

  # create an empty vector to store the result
  res <- list(as.character(NA),as.character(NA))

  Spmax <- AlphaV[alphaV==max(alphaV),GenSp]
  # if no tie
  if (length(Spmax)==1) {
    res[1] <- as.character(Spmax)
    res[2] <- paste(levelAsso, "Determ", sep="")
  } else {
    # if tie
    res[1] <- as.character(sample(x=Spmax, size=1))
    res[2] <- paste(levelAsso, "DetermT", sep="")
    warning(paste("There were several species with the same probability of association for ", VernName2Sim,
                  ", the species was chosen randomly on a tree by tree basis"))
  }
  return(res)
}