R/softmax.R

In pamr: Pam: Prediction Analysis for Microarrays

softmax <-function(x, gap = FALSE) {
  d <- dim(x)
  maxdist <- x[, 1]
  pclass <- rep(1, d[1])
  for(i in seq(2, d[2])) {
    l <- x[, i] > maxdist
    pclass[l] <- i
    maxdist[l] <- x[l, i]
  }
  dd <- dimnames(x)[[2]]
  if(gap) {
    x <- abs(maxdist - x)
    x[cbind(seq(d[1]), pclass)] <- drop(x %*% rep(1, d[2]))
    gaps <- do.call("pmin", data.frame(x))
  }
  pclass <- if(is.null(dd) || !length(dd))
    pclass
  else
    factor(pclass, levels = seq(d[2]), labels = dd)
  if(gap)
    list(class = pclass, gaps = gaps)
  else
    pclass
}