caret: Classification and Regression Training

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Misc functions for training and plotting classification and regression models.

Author
Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer, Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau, Andrew Ziem, Luca Scrucca, Yuan Tang, Can Candan, and Tyler Hunt.
Date of publication
2016-11-10 08:18:44
Maintainer
Max Kuhn <mxkuhn@gmail.com>
License
GPL (>= 2)
Version
6.0-73
URLs

View on CRAN

Man pages

as.matrix.confusionMatrix
Confusion matrix as a table
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
caretFuncs
Backwards Feature Selection Helper Functions
caret-internal
Internal Functions
caretSBF
Selection By Filtering (SBF) Helper 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
densityplot.rfe
Lattice functions for plotting resampling results of...
dhfr
Dihydrofolate Reductase Inhibitors Data
diff.resamples
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
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
Genetic algorithm feature selection
gafs_initial
Ancillary genetic algorithm functions
GermanCredit
German Credit Data
getSamplingInfo
Get sampling info from a train model
histogram.train
Lattice functions for plotting resampling results
icr.formula
Independent Component Regression
index2vec
Convert indicies to a binary vector
knn3
k-Nearest Neighbour Classification
knnreg
k-Nearest Neighbour Regression
learing_curve_dat
Create Data to Plot a Learning Curve
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
nullModel
Fit a simple, non-informative model
oil
Fatty acid composition of commercial oils
oneSE
Selecting tuning Parameters
panel.lift2
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
plot.gafs
Plot Method for the gafs and safs Classes
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.gafs
Predict new samples
predict.knn3
Predictions from k-Nearest Neighbors
predict.knnreg
Predictions from k-Nearest Neighbors Regression Model
predictors
List predictors used in the model
predict.train
Extract predictions and class probabilities from train...
preProcess
Pre-Processing of Predictors
print.confusionMatrix
Print method for confusionMatrix
print.train
Print Method for the train Class
recall
Calculate recall, precision and F values
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
Sacramento
Sacramento CA Home Prices
safs
Simulated annealing feature selection
safsControl
Control parameters for GA and SA feature selection
safs_initial
Ancillary simulated annealing functions
sbf
Selection By Filtering (SBF)
sbfControl
Control Object for Selection By Filtering (SBF)
scat
Morphometric Data on Scat
segmentationData
Cell Body Segmentation
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
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...
varImp.gafs
Variable importances for GAs and SAs
var_seq
Sequences of Variables for Tuning
xyplot.resamples
Lattice Functions for Visualizing Resampling Results

Files in this package

caret
caret/inst
caret/inst/NEWS.Rd
caret/inst/models
caret/inst/models/sampling.RData
caret/inst/models/models.RData
caret/inst/doc
caret/inst/doc/caret.Rnw
caret/inst/doc/caret.pdf
caret/inst/doc/caret.R
caret/tests
caret/tests/testthat.R
caret/tests/testthat
caret/tests/testthat/preProcess_methods.R
caret/tests/testthat/test_models_bagEarth.R
caret/tests/testthat/test_nearZeroVar.R
caret/tests/testthat/trim_glm.R
caret/tests/testthat/trim_train.R
caret/tests/testthat/test_confusionMatrix.R
caret/tests/testthat/test_sampling_options.R
caret/tests/testthat/preProcess.R
caret/tests/testthat/test_glmnet_varImp.R
caret/tests/testthat/test_minimal.R
caret/tests/testthat/trim_rpart.R
caret/tests/testthat/test_mnLogLoss.R
caret/tests/testthat/trim_C5.R
caret/tests/testthat/trim_bayesglm.R
caret/tests/testthat/test_bad_class_options.R
caret/tests/testthat/test_twoClassSummary.R
caret/tests/testthat/trim.R
caret/tests/testthat/test_BoxCox.R
caret/tests/testthat/trim_glmnet.R
caret/tests/testthat/trim_treebag.R
caret/tests/testthat/test_Dummies.R
caret/src
caret/src/caret.c
caret/NAMESPACE
caret/data
caret/data/segmentationData.RData
caret/data/tecator.RData
caret/data/cars.RData
caret/data/cox2.RData
caret/data/BloodBrain.RData
caret/data/scat.RData
caret/data/dhfr.RData
caret/data/pottery.RData
caret/data/mdrr.RData
caret/data/datalist
caret/data/Sacramento.RData
caret/data/GermanCredit.RData
caret/data/oil.RData
caret/R
caret/R/lattice.train.R
caret/R/varImp.R
caret/R/dotplot.varImp.train.R
caret/R/plot.varImp.train.R
caret/R/print.varImp.train.R
caret/R/resampleWrapper.R
caret/R/predictors.R
caret/R/dummyVar.R
caret/R/findLinearCombos.R
caret/R/avNNet.R
caret/R/aaa.R
caret/R/splsda.R
caret/R/specificity.R
caret/R/bag.R
caret/R/knnreg.R
caret/R/getTrainPerf.R
caret/R/resampleHist.R
caret/R/learning_curve.R
caret/R/featurePlot.R
caret/R/bagFDA.R
caret/R/workflows.R
caret/R/spatialSign.R
caret/R/plsda.R
caret/R/confusionMatrix.R
caret/R/reg_sims.R
caret/R/updates.R
caret/R/common_code.R
caret/R/modelLookup.R
caret/R/ggplot.R
caret/R/plot.train.R
caret/R/prec_rec.R
caret/R/print.mars.R
caret/R/caret-package.R
caret/R/varImp.train.R
caret/R/createDataPartition.R
caret/R/extractPrediction.R
caret/R/preProcess.R
caret/R/extractProb.R
caret/R/pcaNNet.R
caret/R/classDist.R
caret/R/nearZeroVar.R
caret/R/basic2x2Stats.R
caret/R/predictionFunction.R
caret/R/findCorrelation.R
caret/R/selection.R
caret/R/lift.R
caret/R/sampling.R
caret/R/plotObsVsPred.R
caret/R/bagEarth.R
caret/R/classLevels.R
caret/R/negPredValue.R
caret/R/createResample.R
caret/R/panel.needle.R
caret/R/print.train.R
caret/R/resamples.R
caret/R/format.bagEarth.R
caret/R/rfe.R
caret/R/plotClassProbs.R
caret/R/trainControl.R
caret/R/diag.R
caret/R/calibration.R
caret/R/trim.R
caret/R/suggestions.R
caret/R/filterVarImp.R
caret/R/posPredValue.R
caret/R/sensitivity.R
caret/R/expoTrans.R
caret/R/createModel.R
caret/R/BoxCoxTrans.R
caret/R/gafs.R
caret/R/resampleSummary.R
caret/R/misc.R
caret/R/selectByFilter.R
caret/R/additive.R
caret/R/postResample.R
caret/R/adaptive.R
caret/R/maxDissim.R
caret/R/heldout.R
caret/R/probFunction.R
caret/R/twoClassSim.R
caret/R/safs.R
caret/R/knn3.R
caret/R/sortImp.R
caret/R/icr.R
caret/R/caretTheme.R
caret/R/train.default.R
caret/R/predict.PLS.R
caret/R/predict.train.R
caret/vignettes
caret/vignettes/caret.Rnw
caret/vignettes/train_algo.pdf
caret/vignettes/algorithm.tex
caret/MD5
caret/build
caret/build/vignette.rds
caret/DESCRIPTION
caret/man
caret/man/prcomp.resamples.Rd
caret/man/avNNet.Rd
caret/man/bagEarth.Rd
caret/man/plot.rfe.Rd
caret/man/gafs_initial.Rd
caret/man/models.Rd
caret/man/rfe.Rd
caret/man/var_seq.Rd
caret/man/update.train.Rd
caret/man/sbfControl.Rd
caret/man/caret-internal.Rd
caret/man/sensitivity.Rd
caret/man/plsda.Rd
caret/man/xyplot.resamples.Rd
caret/man/spatialSign.Rd
caret/man/sbf.Rd
caret/man/BoxCoxTrans.Rd
caret/man/preProcess.Rd
caret/man/tecator.Rd
caret/man/findLinearCombos.Rd
caret/man/diff.resamples.Rd
caret/man/modelLookup.Rd
caret/man/dotPlot.Rd
caret/man/as.matrix.confusionMatrix.Rd
caret/man/knn3.Rd
caret/man/plotObsVsPred.Rd
caret/man/predict.bagEarth.Rd
caret/man/plot.train.Rd
caret/man/predict.knn3.Rd
caret/man/calibration.Rd
caret/man/nullModel.Rd
caret/man/densityplot.rfe.Rd
caret/man/twoClassSim.Rd
caret/man/predict.gafs.Rd
caret/man/predict.knnreg.Rd
caret/man/pcaNNet.Rd
caret/man/maxDissim.Rd
caret/man/panel.lift2.Rd
caret/man/oneSE.Rd
caret/man/oil.Rd
caret/man/panel.needle.Rd
caret/man/createDataPartition.Rd
caret/man/resampleSummary.Rd
caret/man/bag.Rd
caret/man/train.Rd
caret/man/learing_curve_dat.Rd
caret/man/safs_initial.Rd
caret/man/postResample.Rd
caret/man/dotplot.diff.resamples.Rd
caret/man/knnreg.Rd
caret/man/pottery.Rd
caret/man/Sacramento.Rd
caret/man/featurePlot.Rd
caret/man/GermanCredit.Rd
caret/man/safs.Rd
caret/man/plotClassProbs.Rd
caret/man/lift.Rd
caret/man/icr.formula.Rd
caret/man/confusionMatrix.Rd
caret/man/predictors.Rd
caret/man/scat.Rd
caret/man/predict.train.Rd
caret/man/confusionMatrix.train.Rd
caret/man/bagFDA.Rd
caret/man/format.bagEarth.Rd
caret/man/trainControl.Rd
caret/man/caretFuncs.Rd
caret/man/findCorrelation.Rd
caret/man/recall.Rd
caret/man/downSample.Rd
caret/man/update.safs.Rd
caret/man/resampleHist.Rd
caret/man/BloodBrain.Rd
caret/man/print.confusionMatrix.Rd
caret/man/cars.Rd
caret/man/caretSBF.Rd
caret/man/varImp.gafs.Rd
caret/man/mdrr.Rd
caret/man/safsControl.Rd
caret/man/segmentationData.Rd
caret/man/rfeControl.Rd
caret/man/dummyVars.Rd
caret/man/summary.bagEarth.Rd
caret/man/getSamplingInfo.Rd
caret/man/varImp.Rd
caret/man/dhfr.Rd
caret/man/plot.varImp.train.Rd
caret/man/index2vec.Rd
caret/man/cox2.Rd
caret/man/plot.gafs.Rd
caret/man/resamples.Rd
caret/man/gafs.default.Rd
caret/man/print.train.Rd
caret/man/filterVarImp.Rd
caret/man/classDist.Rd
caret/man/nearZeroVar.Rd
caret/man/histogram.train.Rd
caret/.Rinstignore