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 and the R Core Team |

Date of publication | 2014-06-03 16:38:57 |

Maintainer | Max Kuhn <Max.Kuhn@pfizer.com> |

License | GPL-2 |

Version | 6.0-30 |

http://caret.r-forge.r-project.org/ |

**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...

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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