R/Thresholds_TMLA.R

In andrefaa/ENM_TheMetaLand: Create and process Ecological Niche, including several pre- and post-processing methods

Thresholds_TMLA <- function(Eval,
                            Eval_JS,
                            sensV) {
  #Calculates Model Threhsolds
  res <- NULL
  
  #Dismo Thresholds
  ThrDis <- c("kappa", "spec_sens", "no_omission", "sensitivity")
  nom <- c("MAX_KAPPA", "MAX_TSS", "LPT", "SENSITIVITY")
  if (is.null(sensV)) {
    ThrDis <- unlist(sapply(ThrDis, function(x)
      dismo::threshold(Eval)[x]))
  } else{
    ThrDis <-
      unlist(sapply(ThrDis, function(x)
        dismo::threshold(Eval, sensitivity = sensV)[x]))
  }
  names(ThrDis) <- NULL
  PosI <- lapply(as.list(ThrDis), function(x)
    which(Eval@t %in% x))
  TPR <- sapply(PosI, function(x)
    Eval@TPR[x])
  names(TPR) <- NULL
  TNR <- sapply(PosI, function(x)
    Eval@TNR[x])
  names(TNR) <- NULL
  resD <- cbind.data.frame(THR = nom, THR_VALUE = ThrDis, TPR, TNR)
  res <- rbind(res, resD)
  
  #Jaccard Thresholds
  PosII <- which(Eval@t == Eval_JS$JaccardTHR)
  TP_TN <- c(Eval_JS$TPR[PosII], Eval_JS$TNR[PosII])
  resJ <-
    cbind.data.frame(
      THR = "JACCARD",
      THR_VALUE = Eval_JS$JaccardTHR,
      TPR = TP_TN[1],
      TNR = TP_TN[2]
    )
  res <- rbind(res, resJ)
  
  #Sorensen Thresholds
  PosIII <- which(Eval@t == Eval_JS$SorensenTHR)
  TP_TN <- c(Eval_JS$TPR[PosIII], Eval_JS$TNR[PosIII])
  resS <-
    cbind.data.frame(
      THR = "SORENSEN",
      THR_VALUE = Eval_JS$SorensenTHR,
      TPR = TP_TN[1],
      TNR = TP_TN[2]
    )
  res <- rbind(res, resS)
  
  return(res)
}