predict.train

From caret v4.27 by Max Kuhn

Extract predictions and class probabilities from train objects

These functions can be used for a single train object or to loop through a number of train objects to calculate the training and test data predictions and class probabilities.

Keywords: manip

Usage

## S3 method for class 'list':
predict(object, ...)
## S3 method for class 'train':
predict(object, newdata = NULL, type = "raw", ...)
extractPrediction(models,
                  testX = NULL, testY = NULL,
                  unkX = NULL, 
                  unkOnly = !is.null(unkX) & is.null(testX),
                  verbose = FALSE)
extractProb(models,
            testX = NULL,  testY = NULL,
            unkX = NULL, 
            unkOnly = !is.null(unkX) & is.null(testX),
            verbose = FALSE)

Arguments

object: For predict.train, an object of class train. For predict.list, a list of objects of class train.
newdata: an optional set of data to predict on. If NULL, then the original training data are used
type: either "raw" or "prob", for the number/class predictions or class probabilities, respectively. Class probabilities are not available for all classification models
models: 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
...: additional arguments to be passed to other methods

Details

These functions are wrappers for the specific prediction functions in each modeling package. In each case, the optimal tuning values given in the tuneValue slot of the finalModel object are used to predict.

To get simple predictions for a new data set, the predict function can be used.

To get predictions for a series of models at once, a list of train objects can be passes to the predict function and a list of model predictions will be returned.

The two extraction functions can be used to get the predictions and observed outcomes at once for the training, test and/or unknown samples at once in a single data frame (instead of a list of just the predictions). These objects can then be passes to plotObsVsPred or plotClassProbs.

Value

For predict.train, a vector of predictions if type = "raw" or a data frame of class probabilites for type = "probs". In the latter case, there are columns for each class.
For predict.list, a list results. Each element is produced by predict.train.
For extractPrediction, a data frame with columns:
obsthe observed training and test data
predpredicted values
modelthe 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)

References

Kuhn (2008), ``Building Predictive Models in R Using the caret'' (http://www.jstatsoft.org/v28/i05/)

Examples

library(mlbench)
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")

predict(knnFit)
predict(knnFit, newdata = testX)
predict(knnFit, type = "prob")

bothModels <- list(
                   knn = knnFit,
                   tree = rpartFit)

predict(bothModels)

predTargets <- extractPrediction(
                                 bothModels,
                                 testX = testX,
                                 testY = testY,
                                 unkX = unkX)

Documentation reproduced from package caret, version 4.27, License: GPL-2

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