R/predict.train.R

predict.list <- function(object, ...)
{
  
  out <- lapply(object, predict, ... = ...)
  if(!is.null(names(object))) names(out) <- names(object)
  out
}

predict.train <- function(object, newdata = NULL, type = "raw", na.action = na.omit, ...)
{
  if(all(names(object) != "modelInfo")) {
    object <- update(object, param = NULL)
  }
  if(!is.null(object$modelInfo$library))
    for(i in object$modelInfo$library) 
      do.call("require", list(package = i))
  if(!(type %in% c("raw", "prob"))) stop("type must be either \"raw\" or \"prob\"")
  if(type == "prob")
  {
    if (is.null(object$modelInfo$prob))
      stop("only classification models that produce probabilities are allowed")
  }
  
  if(!is.null(newdata))
  {
    if (inherits(object, "train.formula"))
    {
      newdata <- as.data.frame(newdata)
      rn <- row.names(newdata)
      Terms <- delete.response(object$terms)
      m <- model.frame(Terms, newdata, na.action = na.action, xlev = object$xlevels)
      if (!is.null(cl <- attr(Terms, "dataClasses"))) 
        .checkMFClasses(cl, m)
      keep <- match(row.names(m), rn)
      newdata <- model.matrix(Terms, m, contrasts = object$contrasts)
      xint <- match("(Intercept)", colnames(newdata), nomatch = 0)
      if (xint > 0) 
        newdata <- newdata[, -xint, drop = FALSE]   
    }
  }
  else {
    if(!is.null(object$trainingData))
    {            
      newdata <- if(object$method == "pam") object$finalModel$xData else object$trainingData
      ##newdata$.outcome <-NULL
    } else stop("please specify data via newdata")
  }
  
  if(type == "prob")
  {
    out <- extractProb(list(object),
                       unkX = newdata,
                       unkOnly = TRUE,
                       ...)
    obsLevels <- levels(object)
    out <- out[, obsLevels, drop = FALSE]
  } else {
    out <- extractPrediction(list(object),
                             unkX = newdata,
                             unkOnly = TRUE,
                             ...)$pred
  }
  
  out  
}

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caret documentation built on May 2, 2019, 5:47 p.m.