caret: Classification and Regression Training

Misc functions for training and plotting classification and regression models

AuthorMax Kuhn. Contributions from Jed Wing, Steve Weston, Andre Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer and the R Core Team
Date of publication2014-06-03 16:38:57
MaintainerMax Kuhn <Max.Kuhn@pfizer.com>
LicenseGPL-2
Version6.0-30
http://caret.r-forge.r-project.org/

View on R-Forge

Man pages

as.table.confusionMatrix: Save Confusion Table Results

avNNet: Neural Networks Using Model Averaging

bag: A General Framework For Bagging

bagEarth: Bagged Earth

bagFDA: Bagged FDA

BloodBrain: Blood Brain Barrier Data

BoxCoxTrans: Box-Cox and Exponential Transformations

calibration: Probability Calibration Plot

caret-internal: Internal Functions

cars: Kelly Blue Book resale data for 2005 model year GM cars

classDist: Compute and predict the distances to class centroids

confusionMatrix: Create a confusion matrix

confusionMatrix.train: Estimate a Resampled Confusion Matrix

cox2: COX-2 Activity Data

createDataPartition: Data Splitting functions

dhfr: Dihydrofolate Reductase Inhibitors Data

diff.resamples: Inferential Assessments About Model Performance

dotplot.varImp.train: Create a dotplot of variable importance values

downSample: Down- and Up-Sampling Imbalanced Data

dummyVars: Create A Full Set of Dummy Variables

extractPrediction: Extract predictions and class probabilities from train...

featurePlot: Wrapper for Lattice Plotting of Predictor Variables

filterVarImp: Calculation of filter-based variable importance

findCorrelation: Determine highly correlated variables

findLinearCombos: Determine linear combinations in a matrix

format.bagEarth: Format 'bagEarth' objects

generateExprVal.method.trimMean: Generate Expression Values from Probes

GermanCredit: German Credit Data

icr: Independent Component Regression

knn3: k-Nearest Neighbour Classification

knnreg: k-Nearest Neighbour Regression

lattice: Lattice functions for plotting resampling results

lattice.diff.resamples: Lattice Functions for Visualizing Resampling Differences

lattice.resamples: Lattice Functions for Visualizing Resampling Results

lattice.rfe: Lattice functions for plotting resampling results of...

lift: Lift Plot

maxDissim: Maximum Dissimilarity Sampling

mdrr: Multidrug Resistance Reversal (MDRR) Agent Data

modelLookup: Tools for Models Available in 'train'

models: A List of Available Models in train

nearZeroVar: Identification of near zero variance predictors

normalize2Reference: Quantile Normalize Columns of a Matrix Based on a Reference...

normalize.AffyBatch.normalize2Reference: Quantile Normalization to a Reference Distribution

nullModel: Fit a simple, non-informative model

oil: Fatty acid composition of commercial oils

panel.lift: Lattice Panel Functions for Lift Plots

panel.needle: Needle Plot Lattice Panel

pcaNNet: Neural Networks with a Principal Component Step

plotClassProbs: Plot Predicted Probabilities in Classification Models

plotObsVsPred: Plot Observed versus Predicted Results in Regression and...

plot.rfe: Plot RFE Performance Profiles

plot.train: Plot Method for the train Class

plot.varImp.train: Plotting variable importance measures

plsda: Partial Least Squares and Sparse Partial Least Squares...

postResample: Calculates performance across resamples

pottery: Pottery from Pre-Classical Sites in Italy

prcomp.resamples: Principal Components Analysis of Resampling Results

predict.bagEarth: Predicted values based on bagged Earth and FDA models

predict.knn3: Predictions from k-Nearest Neighbors

predict.knnreg: Predictions from k-Nearest Neighbors Regression Model

predictors: List predictors used in the model

preProcess: Pre-Processing of Predictors

print.confusionMatrix: Print method for confusionMatrix

print.train: Print Method for the train Class

resampleHist: Plot the resampling distribution of the model statistics

resamples: Collation and Visualization of Resampling Results

resampleSummary: Summary of resampled performance estimates

rfe: Backwards Feature Selection

rfeControl: Controlling the Feature Selection Algorithms

rfeFunctions: Backwards Feature Selection Helper Functions

sbf: Selection By Filtering (SBF)

sbfControl: Control Object for Selection By Filtering (SBF)

sbfFunctions: Selection By Filtering (SBF) Helper Functions

segmentationData: Cell Body Segmentation

selection: Selecting tuning Parameters

sensitivity: Calculate sensitivity, specificity and predictive values

spatialSign: Compute the multivariate spatial sign

summary.bagEarth: Summarize a bagged earth or FDA fit

tecator: Fat, Water and Protein Content of Meat Samples

train: Fit Predictive Models over Different Tuning Parameters

trainControl: Control parameters for train

twoClassSim: Two-Class Simulations

update.train: Update or Re-fit a Model

varImp: Calculation of variable importance for regression and...

Functions

absorp Man page
anovaScores Man page
as.matrix.confusionMatrix Man page
as.table.confusionMatrix Man page
avNNet Man page
avNNet.default Man page
avNNet.formula Man page
bag Man page
bagControl Man page
bag.default Man page
bagEarth Man page
bagEarth.default Man page
bagEarth.formula Man page
bagEarthStats Man page
bagFDA Man page
bagFDA.default Man page
bagFDA.formula Man page
bbbDescr Man page
best Man page
BloodBrain Man page
BoxCoxTrans Man page
BoxCoxTrans.default Man page
bwplot.diff.resamples Man page
bwplot.resamples Man page
calibration Man page
calibration.default Man page
calibration.formula Man page
caretFuncs Man page
caretSBF Man page
caretTheme Man page
cars Man page
cforestStats Man page
checkConditionalX Man page
checkInstall Man page
checkResamples Man page
classDist Man page
classDist.default Man page
cluster Man page
cluster.resamples Man page
confusionMatrix Man page
confusionMatrix.default Man page
confusionMatrix.rfe Man page
confusionMatrix.sbf Man page
confusionMatrix.table Man page
confusionMatrix.train Man page
contr.dummy Man page
contr.ltfr Man page
cox2 Man page
cox2Class Man page
cox2Descr Man page
cox2IC50 Man page
createDataPartition Man page
createFolds Man page
createModel Man page
createMultiFolds Man page
createResample Man page
createTimeSlices Man page
ctreeBag Man page
defaultSummary Man page
densityplot.diff.resamples Man page
densityplot.resamples Man page
densityplot.rfe Man page
densityplot.train Man page
dhfr Man page
diff.resamples Man page
dotPlot Man page
dotplot.diff.resamples Man page
dotplot.resamples Man page
downSample Man page
dummyVars Man page
dummyVars.default Man page
endpoints Man page
expandParameters Man page
expoTrans Man page
expoTrans.default Man page
extractPrediction Man page
extractProb Man page
fattyAcids Man page
featurePlot Man page
filterVarImp Man page
findCorrelation Man page
findLinearCombos Man page
flatTable Man page
format.bagEarth Man page
gamFormula Man page
gamFuncs Man page
gamScores Man page
generateExprVal.method.trimMean Man page
GermanCredit Man page
getModelInfo Man page
getTrainPerf Man page
ggplot.rfe Man page
ggplot.train Man page
hasTerms Man page
histogram.rfe Man page
histogram.train Man page
icr Man page
icr.default Man page
icr.formula Man page
ipredStats Man page
knn3 Man page
knn3.data.frame Man page
knn3.formula Man page
knn3.matrix Man page
knn3Train Man page
knnreg Man page
knnreg Man page
knnreg.data.frame Man page
knnreg.default Man page
knnreg.formula Man page
knnreg.matrix Man page
knnregTrain Man page
ldaBag Man page
ldaFuncs Man page
ldaSBF Man page
levelplot.diff.resamples Man page
lift Man page
lift.default Man page
lift.formula Man page
lmFuncs Man page
lmSBF Man page
logBBB Man page
lrFuncs Man page
maxDissim Man page
mdrr Man page
mdrrClass Man page
mdrrDescr Man page
MeanSD Man page
minDiss Man page
modelCor Man page
modelLookup Man page
models Man page
nbBag Man page
nbFuncs Man page
nbSBF Man page
nearZeroVar Man page
negPredValue Man page
negPredValue.default Man page
negPredValue.matrix Man page
negPredValue.table Man page
nnetBag Man page
normalize2Reference Man page
normalize.AffyBatch.normalize2Reference Man page
nullModel Man page
nullModel.default Man page
oil Man page
oilType Man page
oneSE Man page
panel.calibration Man page
panel.lift Man page
panel.lift2 Man page
panel.needle Man page
parallelplot.resamples Man page
pcaNNet Man page
pcaNNet.default Man page
pcaNNet.formula Man page
pickSizeBest Man page
pickSizeTolerance Man page
pickVars Man page
plotClassProbs Man page
plotObsVsPred Man page
plot.prcomp.resamples Man page
plot.rfe Man page
plot.train Man page
plot.varImp.train Man page
plsBag Man page
plsda Man page
plsda.default Man page
posPredValue Man page
posPredValue.default Man page
posPredValue.matrix Man page
posPredValue.table Man page
postResample Man page
pottery Man page
potteryClass Man page
prcomp.resamples Man page
predict.avNNet Man page
predict.bag Man page
predict.bagEarth Man page
predict.bagFDA Man page
predict.BoxCoxTrans Man page
predict.classDist Man page
predict.dummyVars Man page
predict.expoTrans Man page
predict.icr Man page
predictionFunction Man page
predict.knn3 Man page
predict.knnreg Man page
predict.list Man page
predict.nullModel Man page
predictors Man page
predictors.default Man page
predictors.formula Man page
predictors.list Man page
predictors.rfe Man page
predictors.sbf Man page
predictors.terms Man page
predictors.train Man page
predict.pcaNNet Man page
predict.plsda Man page
predict.preProcess Man page
predict.rfe Man page
predict.sbf Man page
predict.splsda Man page
predict.train Man page
preProcess Man page
preProcess.default Man page
print.bagEarth Man page
print.bagFDA Man page
print.confusionMatrix Man page
print.train Man page
probFunction Man page
progress Man page
R2 Man page
resampleHist Man page
resamples Man page
resamples.default Man page
resampleSummary Man page
resampleWrapper Man page
rfe Man page
rfeControl Man page
rfe.default Man page
rfeIter Man page
rfFuncs Man page
rfSBF Man page
rfStats Man page
RMSE Man page
sbf Man page
sbfControl Man page
sbf.default Man page
sbf.formula Man page
sbfIter Man page
segmentationData Man page
sensitivity Man page
sensitivity.default Man page
sensitivity.matrix Man page
sensitivity.table Man page
sortImp Man page
sort.resamples Man page
spatialSign Man page
spatialSign.data.frame Man page
spatialSign.default Man page
spatialSign.matrix Man page
specificity Man page
specificity.default Man page
specificity.matrix Man page
specificity.table Man page
splom.resamples Man page
splsda Man page
splsda.default Man page
stripplot.rfe Man page
stripplot.train Man page
sumDiss Man page
summary.bagEarth Man page
summary.bagFDA Man page
summary.diff.resamples Man page
summary.resamples Man page
svmBag Man page
tecator Man page
tolerance Man page
train Man page
trainControl Man page
train.default Man page
train.formula Man page
train_model_list Man page
treebagFuncs Man page
treebagSBF Man page
twoClassSim Man page
twoClassSummary Man page
update.train Man page
upSample Man page
varImp Man page
varImp.bagEarth Man page
varImp.bagFDA Man page
varImp.C5.0 Man page
varImp.classbagg Man page
varImp.cubist Man page
varImp.dsa Man page
varImp.earth Man page
varImp.fda Man page
varImp.gam Man page
varImp.gbm Man page
varImp.glmnet Man page
varImp.JRip Man page
varImp.lm Man page
varImp.multinom Man page
varImp.mvr Man page
varImp.nnet Man page
varImp.pamrtrained Man page
varImp.PART Man page
varImp.plsda Man page
varImp.randomForest Man page
varImp.RandomForest Man page
varImp.regbagg Man page
varImp.rfe Man page
varImp.rpart Man page
varImp.train Man page
xyplot.calibration Man page
xyplot.lift Man page
xyplot.resamples Man page
xyplot.rfe Man page
xyplot.train Man page

Files

caret/.Rinstignore
caret/DESCRIPTION
caret/NAMESPACE
caret/R
caret/R/BoxCoxTrans.R caret/R/PLS.R caret/R/aaa.R caret/R/adaptive.R caret/R/additive.R caret/R/aucRoc.R caret/R/avNNet.R caret/R/bag.R caret/R/bagEarth.R caret/R/bagFDA.R caret/R/basic2x2Stats.R caret/R/calibration.R caret/R/caretTheme.R caret/R/classDist.R caret/R/classLevels.R caret/R/confusionMatrix.R caret/R/createDataPartition.R caret/R/createFolds.R caret/R/createModel.R caret/R/createResample.R caret/R/createTimeSlices.R caret/R/diag.R caret/R/dotplot.varImp.train.R caret/R/dummyVar.R caret/R/expoTrans.R caret/R/extractPrediction.R caret/R/extractProb.R caret/R/featurePlot.R caret/R/filterVarImp.R caret/R/findCorrelation.R caret/R/findLinearCombos.R caret/R/format.bagEarth.R caret/R/generateExprVal.method.trimMean.R caret/R/getTrainPerf.R caret/R/ggplot.R caret/R/icr.R caret/R/knn3.R caret/R/knn3Train.R caret/R/knnreg.R caret/R/lattice.train.R caret/R/lift.R caret/R/maxDissim.R caret/R/misc.R caret/R/modelLookup.R caret/R/nearZeroVar.R caret/R/negPredValue.R caret/R/normalize.AffyBatch.normalize2Reference.R caret/R/normalize2Reference.R caret/R/panel.needle.R caret/R/pcaNNet.R caret/R/plot.train.R caret/R/plot.varImp.train.R caret/R/plotClassProbs.R caret/R/plotObsVsPred.R caret/R/plsda.R caret/R/posPredValue.R caret/R/postResample.R caret/R/preProcess.R caret/R/predict.PLS.R caret/R/predict.train.R caret/R/predictionFunction.R caret/R/predictors.R caret/R/print.confusionMatrix.R caret/R/print.mars.R caret/R/print.train.R caret/R/print.varImp.train.R caret/R/probFunction.R caret/R/resampleHist.R caret/R/resampleSummary.R caret/R/resampleWrapper.R caret/R/resamples.R caret/R/rfe.R caret/R/roc.R caret/R/rocPoint.R caret/R/sampling.R caret/R/selectByFilter.R caret/R/selection.R caret/R/sensitivity.R caret/R/sortImp.R caret/R/spatialSign.R caret/R/specificty.R caret/R/splsda.R caret/R/suggestions.R caret/R/train.default.R caret/R/trainControl.R caret/R/twoClassSim.R caret/R/updates.R caret/R/varImp.R caret/R/varImp.train.R caret/R/workflows.R
caret/data
caret/data/BloodBrain.RData
caret/data/GermanCredit.RData
caret/data/cars.RData
caret/data/cox2.RData
caret/data/datalist
caret/data/dhfr.RData
caret/data/mdrr.RData
caret/data/oil.RData
caret/data/pottery.RData
caret/data/segmentationData.RData
caret/data/tecator.RData
caret/inst
caret/inst/NEWS.Rd
caret/inst/models
caret/inst/models/models.RData
caret/man
caret/man/BloodBrain.Rd caret/man/BoxCoxTrans.Rd caret/man/GermanCredit.Rd caret/man/as.table.confusionMatrix.Rd caret/man/avNNet.Rd caret/man/bag.Rd caret/man/bagEarth.Rd caret/man/bagFDA.Rd caret/man/calibration.Rd caret/man/caret-internal.Rd caret/man/cars.Rd caret/man/classDist.Rd caret/man/confusionMatrix.Rd caret/man/confusionMatrix.train.Rd caret/man/cox2.Rd caret/man/createDataPartition.Rd caret/man/dhfr.Rd caret/man/diff.resamples.Rd caret/man/dotplot.varImp.train.Rd caret/man/downSample.Rd caret/man/dummyVars.Rd caret/man/extractPrediction.Rd caret/man/featurePlot.Rd caret/man/filterVarImp.Rd caret/man/findCorrelation.Rd caret/man/findLinearCombos.Rd caret/man/format.bagEarth.Rd caret/man/generateExprVal.method.trimMean.Rd caret/man/icr.Rd caret/man/knn3.Rd caret/man/knnreg.Rd caret/man/lattice.Rd caret/man/lattice.diff.resamples.Rd caret/man/lattice.resamples.Rd caret/man/lattice.rfe.Rd caret/man/lift.Rd caret/man/maxDissim.Rd caret/man/mdrr.Rd caret/man/modelLookup.Rd caret/man/models.Rd caret/man/nearZeroVar.Rd caret/man/normalize.AffyBatch.normalize2Reference.Rd caret/man/normalize2Reference.Rd caret/man/nullModel.Rd caret/man/oil.Rd caret/man/panel.lift.Rd caret/man/panel.needle.Rd caret/man/pcaNNet.Rd caret/man/plot.rfe.Rd caret/man/plot.train.Rd caret/man/plot.varImp.train.Rd caret/man/plotClassProbs.Rd caret/man/plotObsVsPred.Rd caret/man/plsda.Rd caret/man/postResample.Rd caret/man/pottery.Rd caret/man/prcomp.resamples.Rd caret/man/preProcess.Rd caret/man/predict.bagEarth.Rd caret/man/predict.knn3.Rd caret/man/predict.knnreg.Rd caret/man/predictors.Rd caret/man/print.confusionMatrix.Rd caret/man/print.train.Rd caret/man/resampleHist.Rd caret/man/resampleSummary.Rd caret/man/resamples.Rd caret/man/rfe.Rd caret/man/rfeControl.Rd caret/man/rfeFunctions.Rd caret/man/sbf.Rd caret/man/sbfControl.Rd caret/man/sbfFunctions.Rd caret/man/segmentationData.Rd caret/man/selection.Rd caret/man/sensitivity.Rd caret/man/spatialSign.Rd caret/man/summary.bagEarth.Rd caret/man/tecator.Rd caret/man/train.Rd caret/man/trainControl.Rd caret/man/twoClassSim.Rd caret/man/update.train.Rd caret/man/varImp.Rd
caret/src
caret/src/caret.c
caret/vignettes
caret/vignettes/caret.Rnw
caret/vignettes/caret.pdf

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