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 |

https://github.com/topepo/caret/ |

**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

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

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