R/ecospat.CommunityEval.R

In ecospat: Spatial Ecology Miscellaneous Methods

ecospat.CommunityEval <- function(eval, pred, proba, ntir, verbose = FALSE) {
  if (proba == FALSE) {
    ntir <- 1
    pred2 <- pred
  }
  
  Rdev <- over <- under <- succ <- sens <- spec <- kappa <- tss <- sim <- jac <- matrix(nrow = nrow(eval), 
    ncol = ntir, 
    dimnames = list(rownames(eval), c(1:ntir)))
  
  for (i in 1:ntir) {
    if (proba == TRUE) {
      pred2 <- matrix(nrow = nrow(pred), ncol = ncol(pred))
      for (k in 1:nrow(pred)) {
        pred2[k, ] <- rbinom(n = ncol(pred), size = 1, 
                             prob = as.numeric(pred[k, ]))
      }
    }
    errors <- 2 * pred2 + eval
          # if 0 true negative
          # if 1 false negative
          # if 2 false positive
          # if 3 true positive
    for (j in 1:nrow(errors)) {
      a <- length(which(errors[j, ] == 3))
      b <- length(which(errors[j, ] == 2))
      c <- length(which(errors[j, ] == 1))
      d <- length(which(errors[j, ] == 0))
      n <- ncol(errors)
      
      Rdev[j, i] <- sum(eval[j, ]) - sum(pred2[j, ])
      over[j, i] <- b/(b + d)
      under[j, i] <- c/(a + c)
      succ[j, i] <- (a + d)/n
      sens[j, i] <- a/(a + b)
      spec[j, i] <- d/(c + d)
      kappa[j, i] <- (((a+d)/n)-(((a+c)*(a+b)+(b+d)*(d+c))
                     /(n^2)))/(1-(((a+c)*(a+b)+(b+d)*(d+c))/(n^2)))  ## Kappa
      tss[j, i] <- sens[j, i] + spec[j, i] - 1
      sim[j, i] <- (2 * a)/(2 * a + b + c)
      jac[j, i] <- a/(a + b + c)
    }
    if(verbose) cat("trial", i, "on", ntir, "\n")
  }
  res <- list(Rdev, over, under, succ, sens, spec, kappa, tss, sim, jac)
  names(res) <- c("deviation.rich.pred", "overprediction", 
                  "underprediction", "prediction.success", 
                  "sensitivity", "specificity", "kappa", 
                  "TSS", "similarity", "Jaccard")
  return(res)
}