All functions

BloodBrain

Blood Brain Barrier Data

BoxCoxTrans() print(<BoxCoxTrans>) predict(<BoxCoxTrans>)

Box-Cox and Exponential Transformations

GermanCredit

German Credit Data

Sacramento

Sacramento CA Home Prices

as.matrix(<confusionMatrix>)

Confusion matrix as a table

avNNet() print(<avNNet>) predict(<avNNet>)

Neural Networks Using Model Averaging

bag() bagControl() predict(<bag>) print(<bag>) summary(<bag>) print(<summary.bag>) ldaBag plsBag nbBag ctreeBag svmBag nnetBag

A General Framework For Bagging

bagEarth() print(<bagEarth>)

Bagged Earth

bagFDA() print(<bagFDA>)

Bagged FDA

calibration() print(<calibration>) xyplot(<calibration>) ggplot(<calibration>)

Probability Calibration Plot

pickSizeBest() pickSizeTolerance() pickVars() caretFuncs ldaFuncs treebagFuncs gamFuncs rfFuncs lmFuncs nbFuncs lrFuncs

Backwards Feature Selection Helper Functions

caretSBF anovaScores() gamScores()

Selection By Filtering (SBF) Helper Functions

cars

Kelly Blue Book resale data for 2005 model year GM cars

classDist() predict(<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() createFolds() createMultiFolds() createTimeSlices() groupKFold() createResample()

Data Splitting functions

densityplot(<rfe>)

Lattice functions for plotting resampling results of recursive feature selection

dhfr

Dihydrofolate Reductase Inhibitors Data

diff(<resamples>) summary(<diff.resamples>) compare_models()

Inferential Assessments About Model Performance

dotPlot()

Create a dotplot of variable importance values

dotplot(<diff.resamples>)

Lattice Functions for Visualizing Resampling Differences

downSample()

Down- and Up-Sampling Imbalanced Data

dummyVars() print(<dummyVars>) predict(<dummyVars>) contr.ltfr() class2ind()

Create A Full Set of Dummy Variables

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

gafs(<default>) gafs(<recipe>)

Genetic algorithm feature selection

gafs_initial() gafs_lrSelection() gafs_spCrossover() gafs_raMutation() gafs_nlrSelection() gafs_rwSelection() gafs_tourSelection() gafs_uCrossover()

Ancillary genetic algorithm functions

getSamplingInfo()

Get sampling info from a train model

histogram(<train>)

Lattice functions for plotting resampling results

icr(<formula>) icr(<default>) predict(<icr>)

Independent Component Regression

index2vec()

Convert indicies to a binary vector

knn3() print(<knn3>) knn3Train()

k-Nearest Neighbour Classification

knnreg() print(<knnreg>) knnregTrain()

k-Nearest Neighbour Regression

learning_curve_dat()

Create Data to Plot a Learning Curve

lift() print(<lift>) xyplot(<lift>) ggplot(<lift>)

Lift Plot

maxDissim() minDiss() sumDiss()

Maximum Dissimilarity Sampling

mdrr

Multidrug Resistance Reversal (MDRR) Agent Data

modelLookup() checkInstall() getModelInfo()

Tools for Models Available in train

train_model_list

A List of Available Models in train

nearZeroVar() checkConditionalX() checkResamples()

Identification of near zero variance predictors

nullModel() predict(<nullModel>)

Fit a simple, non-informative model

oil

Fatty acid composition of commercial oils

oneSE() tolerance()

Selecting tuning Parameters

panel.lift2()

Lattice Panel Functions for Lift Plots

panel.needle()

Needle Plot Lattice Panel

pcaNNet() print(<pcaNNet>) predict(<pcaNNet>)

Neural Networks with a Principal Component Step

plot(<gafs>) ggplot(<gafs>) ggplot(<safs>)

Plot Method for the gafs and safs Classes

ggplot(<rfe>) plot(<rfe>)

Plot RFE Performance Profiles

ggplot(<train>) plot(<train>)

Plot Method for the train Class

plot(<varImp.train>) ggplot(<varImp.train>)

Plotting variable importance measures

plotClassProbs()

Plot Predicted Probabilities in Classification Models

plotObsVsPred()

Plot Observed versus Predicted Results in Regression and Classification Models

plsda() predict(<plsda>)

Partial Least Squares and Sparse Partial Least Squares Discriminant Analysis

defaultSummary() postResample() twoClassSummary() mnLogLoss() multiClassSummary() prSummary()

Calculates performance across resamples

pottery

Pottery from Pre-Classical Sites in Italy

prcomp(<resamples>) plot(<prcomp.resamples>)

Principal Components Analysis of Resampling Results

preProcess() predict(<preProcess>)

Pre-Processing of Predictors

predict(<bagEarth>) predict(<bagFDA>)

Predicted values based on bagged Earth and FDA models

predict(<gafs>)

Predict new samples

predict(<knn3>)

Predictions from k-Nearest Neighbors

predict(<knnreg>)

Predictions from k-Nearest Neighbors Regression Model

extractPrediction() extractProb() predict(<train>)

Extract predictions and class probabilities from train objects

predictors()

List predictors used in the model

print(<confusionMatrix>)

Print method for confusionMatrix

print(<train>)

Print Method for the train Class

recall() precision() F_meas()

Calculate recall, precision and F values

resampleHist()

Plot the resampling distribution of the model statistics

resampleSummary()

Summary of resampled performance estimates

resamples() sort(<resamples>) summary(<resamples>) as.matrix(<resamples>) as.data.frame(<resamples>) modelCor() print(<resamples>)

Collation and Visualization of Resampling Results

rfe() rfeIter() update(<rfe>)

Backwards Feature Selection

rfeControl()

Controlling the Feature Selection Algorithms

safs()

Simulated annealing feature selection

gafsControl() safsControl()

Control parameters for GA and SA feature selection

safs_initial() safs_perturb() safs_prob() caretSA treebagSA rfSA

Ancillary simulated annealing functions

sbf() predict(<sbf>)

Selection By Filtering (SBF)

sbfControl()

Control Object for Selection By Filtering (SBF)

scat

Morphometric Data on Scat

segmentationData

Cell Body Segmentation

negPredValue() posPredValue() sensitivity()

Calculate sensitivity, specificity and predictive values

spatialSign()

Compute the multivariate spatial sign

summary(<bagEarth>) summary(<bagFDA>)

Summarize a bagged earth or FDA fit

tecator

Fat, Water and Protein Content of Meat Samples

thresholder()

Generate Data to Choose a Probability Threshold

train()

Fit Predictive Models over Different Tuning Parameters

trainControl()

Control parameters for train

SLC14_1() SLC14_2() LPH07_1() LPH07_2() twoClassSim()

Simulation Functions

update(<safs>)

Update or Re-fit a SA or GA Model

update(<train>)

Update or Re-fit a Model

varImp()

Calculation of variable importance for regression and classification models

varImp(<gafs>)

Variable importances for GAs and SAs

var_seq()

Sequences of Variables for Tuning

xyplot(<resamples>) parallelplot(<resamples>) splom(<resamples>) densityplot(<resamples>) bwplot(<resamples>) dotplot(<resamples>) ggplot(<resamples>)

Lattice Functions for Visualizing Resampling Results