extractPrediction {caret}R Documentation

Extract predictions and class probabilities from train objects

Description

This function loops through a number of train objects and calculates the training and test data predictions and class probabilities

Usage

extractPrediction(object, testX = NULL, testY = NULL, unkX = NULL, 
   unkOnly = !is.null(unkX) & is.null(testX), verbose = FALSE)

extractProb(object, testX = NULL,  testY = NULL,  unkX = NULL, 
   unkOnly = !is.null(unkX) & is.null(testX),  verbose = FALSE)

Arguments

object a list of objects of the class train. The objects must have been generated with fitBest = FALSE and returnData = TRUE.
testX an optional set of data to predict
testY an optional outcome corresponding to the data given in testX
unkX another optional set of data to predict without known outcomes
unkOnly a logical to bypass training and test set predictions. This is useful if speed is needed for unknown samples.
verbose a logical for printing messages

Details

The optimal tuning values given in the tuneValue slot of the finalModel object are used to predict.

Value

For extractPrediction, a data frame with columns:

obs the observed training and test data
pred predicted values
model the type of model used to predict
dataType "Training", "Test" or "Unknown" depending on what was specified

For extractProb, a data frame. There is a column for each class containing the probabilities. The remaining columns are the same as above (although the pred column is the predicted class)

Author(s)

Max Kuhn

Examples

   ## Not run: 
data(Satellite)
numSamples <- dim(Satellite)[1]
set.seed(716)

varIndex <- 1:numSamples

trainSamples <- sample(varIndex, 150)

varIndex <- (1:numSamples)[-trainSamples]
testSamples <- sample(varIndex, 100)

varIndex <- (1:numSamples)[-c(testSamples, trainSamples)]
unkSamples <- sample(varIndex, 50)

trainX <- Satellite[trainSamples, -37]
trainY <- Satellite[trainSamples, 37]

testX <- Satellite[testSamples, -37]
testY <- Satellite[testSamples, 37]

unkX <- Satellite[unkSamples, -37]

knnFit <- train(trainX, trainY, "knn")
rpartFit <- train(trainX, trainY, "rpart")

predTargets <- extractPrediction(list(knnFit, rpartFit), testX = testX, testY = testY, unkX = unkX)
   
  ## End(Not run)

[Package caret version 2.29 Index]