├── .Rbuildignore ├── .github ├── .gitignore ├── CODEOWNERS ├── ISSUE_TEMPLATE.md └── workflows │ ├── R-CMD-check.yaml │ ├── pr-commands.yaml │ └── test-coverage.yaml ├── .gitignore ├── README.md ├── RegressionTests ├── Code │ ├── ANFIS.R │ ├── AdaBag.R │ ├── AdaBoost.M1.R │ ├── Boruta.R │ ├── C5.0.R │ ├── C5.0Cost.R │ ├── C5.0Rules.R │ ├── C5.0Tree.R │ ├── CSimca.R │ ├── DENFIS.R │ ├── FH.GBML.R │ ├── FIR.DM.R │ ├── FRBCS.CHI.R │ ├── FRBCS.W.R │ ├── FS.HGD.R │ ├── GFS.FR.MOGUL.R │ ├── GFS.GCCL.R │ ├── GFS.LT.RS.R │ ├── GFS.Thrift.R │ ├── HYFIS.R │ ├── J48.R │ ├── JRip.R │ ├── LMT.R │ ├── Linda.R │ ├── LogitBoost.R │ ├── M5.R │ ├── M5Rules.R │ ├── Mlda.R │ ├── ORFlog.R │ ├── ORFpls.R │ ├── ORFridge.R │ ├── ORFsvm.R │ ├── OneR.R │ ├── PART.R │ ├── PRIM.R │ ├── PenalizedLDA.R │ ├── QdaCov.R │ ├── RFlda.R │ ├── RRFglobal.R │ ├── RSimca.R │ ├── Rborist.R │ ├── SBC.R │ ├── SLAVE.R │ ├── WM.R │ ├── ada.R │ ├── adaboost.R │ ├── amdai.R │ ├── avMxnet.R │ ├── avNNet.R │ ├── awnb.R │ ├── awtan.R │ ├── bag.R │ ├── bagEarth.R │ ├── bagEarthGCV.R │ ├── bagFDA.R │ ├── bagFDAGCV.R │ ├── bam.R │ ├── bartMachine.R │ ├── bayesglm.R │ ├── bdk.R │ ├── binda.R │ ├── blackboost.R │ ├── blasso.R │ ├── blassoAveraged.R │ ├── bridge.R │ ├── brnn.R │ ├── bstSm.R │ ├── bstTree.R │ ├── cforest.R │ ├── ctree.R │ ├── ctree2.R │ ├── cubist.R │ ├── dda.R │ ├── deepboost.R │ ├── dnn.R │ ├── dwdLinear.R │ ├── dwdPoly.R │ ├── dwdRadial.R │ ├── earth.R │ ├── elm.R │ ├── enet.R │ ├── enpls.R │ ├── enpls.fs.R │ ├── evtree.R │ ├── extraTrees.R │ ├── fda.R │ ├── foba.R │ ├── ga.R │ ├── gam.R │ ├── gamSpline.R │ ├── gamboost.R │ ├── gbm.R │ ├── gbm_h2o.R │ ├── gcvEarth.R │ ├── glm.R │ ├── glm.nb.R │ ├── glmStepAIC.R │ ├── glmboost.R │ ├── glmnet.R │ ├── glmnet_h2o.R │ ├── gpls.R │ ├── hda.R │ ├── hdda.R │ ├── hdrda.R │ ├── icr.R │ ├── kernelpls.R │ ├── kknn.R │ ├── knn.R │ ├── knnImpute.R │ ├── krlsPoly.R │ ├── krlsRadial.R │ ├── lars.R │ ├── lars2.R │ ├── lasso.R │ ├── lda.R │ ├── lda2.R │ ├── leapBackward.R │ ├── leapForward.R │ ├── leapSeq.R │ ├── lm.R │ ├── lmStepAIC.R │ ├── loclda.R │ ├── logicBag.R │ ├── logreg.R │ ├── lssvmRadial.R │ ├── lvq.R │ ├── manb.R │ ├── mda.R │ ├── mlp.R │ ├── mlpKerasDecay.R │ ├── mlpKerasDecayCost.R │ ├── mlpKerasDropout.R │ ├── mlpKerasDropoutCost.R │ ├── mlpML.R │ ├── mlpSGD.R │ ├── mlpWeightDecay.R │ ├── mlpWeightDecayML.R │ ├── monmlp.R │ ├── msaenet.R │ ├── multinom.R │ ├── mxnet.R │ ├── mxnetAdam.R │ ├── naive_bayes.R │ ├── nb.R │ ├── nbDiscrete.R │ ├── nbSearch.R │ ├── neuralnet.R │ ├── nnet.R │ ├── nnls.R │ ├── nodeHarvest.R │ ├── null.R │ ├── oblique.tree.R │ ├── ordinalNet.R │ ├── ordinalRF.R │ ├── ownn.R │ ├── pam.R │ ├── partDSA.R │ ├── pcaNNet.R │ ├── pcr.R │ ├── pda.R │ ├── pda2.R │ ├── penalized.R │ ├── plr.R │ ├── pls.R │ ├── plsRglm.R │ ├── polr.R │ ├── ppr.R │ ├── pre.R │ ├── preprocess_back.R │ ├── protoclass.R │ ├── pythonKnnReg.R │ ├── qda.R │ ├── qrf.R │ ├── qrnn.R │ ├── rFerns.R │ ├── randomGLM.R │ ├── ranger.R │ ├── rbf.R │ ├── rbfDDA.R │ ├── rda.R │ ├── regLogistic.R │ ├── relaxo.R │ ├── rf.R │ ├── rfRules.R │ ├── rfe_gam.R │ ├── rfe_issue485.R │ ├── rfe_lda.R │ ├── rfe_lm.R │ ├── rfe_lr.R │ ├── rfe_nb.R │ ├── rfe_rf.R │ ├── rfe_train.R │ ├── rfe_treebag.R │ ├── ridge.R │ ├── rknn.R │ ├── rknnBel.R │ ├── rlda.R │ ├── rlm.R │ ├── rmda.R │ ├── rocc.R │ ├── rotationForest.R │ ├── rotationForestCp.R │ ├── rpart.R │ ├── rpart1SE.R │ ├── rpart2.R │ ├── rpartCost.R │ ├── rpartScore.R │ ├── rqlasso.R │ ├── rqnc.R │ ├── rrlda.R │ ├── rvmLinear.R │ ├── rvmPoly.R │ ├── rvmRadial.R │ ├── sa.R │ ├── sbf_lda.R │ ├── sbf_lm.R │ ├── sbf_nb.R │ ├── sbf_rf.R │ ├── sbf_train.R │ ├── sbf_treebag.R │ ├── sda.R │ ├── sddaLDA.R │ ├── sddaQDA.R │ ├── sdwd.R │ ├── simpls.R │ ├── slda.R │ ├── smda.R │ ├── snn.R │ ├── sparseLDA.R │ ├── spikeslab.R │ ├── spls.R │ ├── stepLDA.R │ ├── stepQDA.R │ ├── subsampling.R │ ├── superpc.R │ ├── svmBoundrangeString.R │ ├── svmExpoString.R │ ├── svmLinear.R │ ├── svmLinear2.R │ ├── svmLinear3.R │ ├── svmLinearWeights.R │ ├── svmLinearWeights2.R │ ├── svmPoly.R │ ├── svmRadial.R │ ├── svmRadialCost.R │ ├── svmRadialSigma.R │ ├── svmRadialWeights.R │ ├── svmSpectrumString.R │ ├── tan.R │ ├── tanSearch.R │ ├── treebag.R │ ├── trimming.R │ ├── vglmAdjCat.R │ ├── vglmContRatio.R │ ├── vglmCumulative.R │ ├── widekernelpls.R │ ├── wsrf.R │ ├── xgbDART.R │ ├── xgbLinear.R │ ├── xgbTree.R │ └── xyf.R ├── compare.R ├── expected_preprocess.R ├── make_markdown_files.R ├── markdown_functions.R ├── move_files.R ├── preProcess.R └── test_results │ ├── ANFIS.md │ ├── AdaBag.md │ ├── AdaBoost.M1.md │ ├── C5.0.md │ ├── C5.0Cost.md │ ├── C5.0Rules.md │ ├── C5.0Tree.md │ ├── CSimca.md │ ├── DENFIS.md │ ├── FH.GBML.md │ ├── FIR.DM.md │ ├── FRBCS.CHI.md │ ├── FRBCS.W.md │ ├── FS.HGD.md │ ├── GFS.FR.MOGUL.md │ ├── GFS.LT.RS.md │ ├── GFS.THRIFT.md │ ├── HYFIS.md │ ├── J48.md │ ├── JRip.md │ ├── LMT.md │ ├── Linda.md │ ├── LogitBoost.md │ ├── M5.md │ ├── M5Rules.md │ ├── ORFlog.md │ ├── ORFpls.md │ ├── ORFridge.md │ ├── ORFsvm.md │ ├── OneR.md │ ├── PART.md │ ├── PenalizedLDA.md │ ├── QdaCov.md │ ├── RRFglobal.md │ ├── RSimca.md │ ├── Rborist.md │ ├── WM.md │ ├── ada.md │ ├── adaboost.md │ ├── amdai.md │ ├── avNNet.md │ ├── awnb.md │ ├── awtan.md │ ├── bag.md │ ├── bagEarthGCV.md │ ├── bagFDA.md │ ├── bagFDAGCV.md │ ├── bam.md │ ├── bartMachine.md │ ├── bayesglm.md │ ├── binda.md │ ├── blackboost.md │ ├── blasso.md │ ├── blassoAveraged.md │ ├── bridge.md │ ├── brnn.md │ ├── bstSm.md │ ├── bstTree.md │ ├── cforest.md │ ├── ctree.md │ ├── ctree2.md │ ├── cubist.md │ ├── dda.md │ ├── deepboost.md │ ├── dnn.md │ ├── dwdLinear.md │ ├── dwdPoly.md │ ├── dwdRadial.md │ ├── earth.md │ ├── elm.md │ ├── enet.md │ ├── evtree.md │ ├── extraTrees.md │ ├── fda.md │ ├── foba.md │ ├── gam.md │ ├── gamSpline.md │ ├── gamboost.md │ ├── gbm.md │ ├── gbm_h2o.md │ ├── gcvEarth.md │ ├── glm.md │ ├── glm.nb.md │ ├── glmStepAIC.md │ ├── glmboost.md │ ├── glmnet.md │ ├── gpls.md │ ├── hda.md │ ├── hdda.md │ ├── hdrda.md │ ├── icr.md │ ├── kernelpls.md │ ├── kknn.md │ ├── knn.md │ ├── krlsPoly.md │ ├── krlsRadial.md │ ├── lars.md │ ├── lars2.md │ ├── lasso.md │ ├── lda.md │ ├── lda2.md │ ├── leapBackward.md │ ├── leapForward.md │ ├── leapSeq.md │ ├── lm.md │ ├── lmStepAIC.md │ ├── loclda.md │ ├── logicBag.md │ ├── logreg.md │ ├── lssvmRadial.md │ ├── lvq.md │ ├── manb.md │ ├── mda.md │ ├── mlp.md │ ├── mlpML.md │ ├── mlpSGD.md │ ├── mlpWeightDecay.md │ ├── mlpWeightDecayML.md │ ├── multinom.md │ ├── nb.md │ ├── nbDiscrete.md │ ├── nbSearch.md │ ├── neuralnet.md │ ├── nnet.md │ ├── nnls.md │ ├── nodeHarvest.md │ ├── oblique.tree.md │ ├── ordinalNet.md │ ├── ownn.md │ ├── pam.md │ ├── partDSA.md │ ├── pcaNNet.md │ ├── pcr.md │ ├── pda.md │ ├── pda2.md │ ├── penalized.md │ ├── plr.md │ ├── pls.md │ ├── plsRglm.md │ ├── polr.md │ ├── ppr.md │ ├── protoclass.md │ ├── pythonKnnReg.md │ ├── qda.md │ ├── qrf.md │ ├── qrnn.md │ ├── rFerns.md │ ├── randomGLM.md │ ├── ranger.md │ ├── rda.md │ ├── relaxo.md │ ├── rf.md │ ├── rfRules.md │ ├── rfe_lda.md │ ├── rfe_lm.md │ ├── rfe_lr.md │ ├── rfe_nb.md │ ├── rfe_rf.md │ ├── rfe_train.md │ ├── rfe_treebag.md │ ├── ridge.md │ ├── rlda.md │ ├── rlm.md │ ├── rmda.md │ ├── rocc.md │ ├── rotationForest.md │ ├── rotationForestCp.md │ ├── rpart.md │ ├── rpart1SE.md │ ├── rpart2.md │ ├── rpartCost.md │ ├── rpartScore.md │ ├── rqlasso.md │ ├── rqnc.md │ ├── rrlda.md │ ├── rvmLinear.md │ ├── rvmPoly.md │ ├── rvmRadial.md │ ├── sbf_lda.md │ ├── sbf_lm.md │ ├── sbf_nb.md │ ├── sbf_rf.md │ ├── sbf_treebag.md │ ├── sda.md │ ├── sdwd.md │ ├── simpls.md │ ├── slda.md │ ├── smda.md │ ├── snn.md │ ├── sparseLDA.md │ ├── spikeslab.md │ ├── spls.md │ ├── stepLDA.md │ ├── stepQDA.md │ ├── superpc.md │ ├── svmExpoString.md │ ├── svmLinear.md │ ├── svmLinear2.md │ ├── svmLinear3.md │ ├── svmLinearWeights.md │ ├── svmLinearWeights22.md │ ├── svmPoly.md │ ├── svmRadial.md │ ├── svmRadialCost.md │ ├── svmRadialSigma.md │ ├── svmRadialWeights.md │ ├── svmSpectrumString.md │ ├── tan.md │ ├── treebag.md │ ├── trimming.md │ ├── vglmAdjCat.md │ ├── vglmContRatio.md │ ├── vglmCumulative.md │ ├── widekernelpls.md │ └── wsrf.md ├── bookdown ├── 01-Visualizations.Rmd ├── 02-PreProcessing.Rmd ├── 03-Splitting.Rmd ├── 04-Basic.Rmd ├── 05-Model-List.Rmd ├── 06-Tags.Rmd ├── 07-Similarity.Rmd ├── 08-Parallel.Rmd ├── 09-Random-Search.Rmd ├── 10-Sampling.Rmd ├── 11-Recipes.Rmd ├── 12-Custom-Models.Rmd ├── 13-Adaptive-Resampling.Rmd ├── 14-Importance.Rmd ├── 15-Misc-Functions.Rmd ├── 16-Performance.Rmd ├── 17-Feature-Selection.Rmd ├── 18-Filters.Rmd ├── 19-RFE.Rmd ├── 20-GA.Rmd ├── 21-SA.Rmd ├── 22-Datasets.Rmd ├── 23-Session-Info.Rmd ├── caret_doc.Rproj ├── index.Rmd ├── make_files.R ├── premade │ ├── Algo1.png │ ├── Algo2.png │ ├── FEq.png │ ├── MaxDissim.gif │ ├── TrainAlgo.png │ ├── cm.jpg │ ├── cm.pdf │ ├── parallel.png │ └── tol.png ├── redirects │ ├── Accepts_Case_Weights.html │ ├── Bagging.html │ ├── Bayesian_Model.html │ ├── Binary_Predictors_Only.html │ ├── Boosting.html │ ├── Categorical_Predictors_Only.html │ ├── Cost_Sensitive_Learning.html │ ├── Discriminant_Analysis.html │ ├── Distance_Weighted_Discrimination.html │ ├── Ensemble_Model.html │ ├── Feature_Extraction.html │ ├── Feature_Selection_Wrapper.html │ ├── GA.html │ ├── Gaussian_Process.html │ ├── Generalized_Additive_Model.html │ ├── Generalized_Linear_Model.html │ ├── Handle_Missing_Predictor_Data.html │ ├── Implicit_Feature_Selection.html │ ├── Kernel_Method.html │ ├── L1_Regularization.html │ ├── L2_Regularization.html │ ├── Linear_Classifier.html │ ├── Linear_Regression.html │ ├── Logic_Regression.html │ ├── Logistic_Regression.html │ ├── Mixture_Model.html │ ├── Model_Tree.html │ ├── Multivariate_Adaptive_Regression_Splines.html │ ├── Neural_Network.html │ ├── Oblique_Tree.html │ ├── Ordinal_Outcomes.html │ ├── Partial_Least_Squares.html │ ├── Polynomial_Model.html │ ├── Prototype_Models.html │ ├── Quantile_Regression.html │ ├── ROC_Curves.html │ ├── Radial_Basis_Function.html │ ├── Random_Forest.html │ ├── Regularization.html │ ├── Relevance_Vector_Machines.html │ ├── Ridge_Regression.html │ ├── Robust_Methods.html │ ├── Robust_Model.html │ ├── Rule_Based_Model.html │ ├── SA.html │ ├── Self_Organising_Maps.html │ ├── String_Kernel.html │ ├── Support_Vector_Machines.html │ ├── Text_Mining.html │ ├── Tree_Based_Model.html │ ├── Two_Class_Only.html │ ├── adaptive.html │ ├── bytag.html │ ├── custom_models.html │ ├── featureselection.html │ ├── filters.html │ ├── modelList.html │ ├── other.html │ ├── parallel.html │ ├── preprocess.html │ ├── random.html │ ├── rfe.html │ ├── sampling.html │ ├── splitting.html │ ├── training.html │ └── varimp.html ├── style.css └── toc.css ├── codecov.yml ├── deprecated ├── PLS.R ├── generateExprVal.method.trimMean.R ├── generateExprVal.method.trimMean.Rd ├── normalize.AffyBatch.normalize2Reference.R ├── normalize.AffyBatch.normalize2Reference.Rd └── normalize2Reference.R ├── docs ├── survival_thoughts.Rmd └── survival_thoughts.md ├── html ├── Algo1.png ├── Algo2.png ├── FEq.png ├── GA.Rhtml ├── README.md ├── SA.Rhtml ├── TrainAlgo.png ├── adaptive.Rhtml ├── bytag.Rhtml ├── cache │ ├── __packages │ ├── custom_lb_pred_c750307340bfbdbec19a6828e04f4667.RData │ ├── custom_lb_pred_c750307340bfbdbec19a6828e04f4667.rdb │ ├── custom_lb_pred_c750307340bfbdbec19a6828e04f4667.rdx │ ├── custom_sonar_70733b2ad211d556bf0e6ecd376c0b9a.RData │ ├── custom_sonar_70733b2ad211d556bf0e6ecd376c0b9a.rdb │ └── custom_sonar_70733b2ad211d556bf0e6ecd376c0b9a.rdx ├── carrot.png ├── cm.png ├── custom_models.Rhtml ├── custom_models.html ├── d3.v3.js ├── d3.v3.min.js ├── datasets.Rhtml ├── featureSelection.Rhtml ├── filters.Rhtml ├── images │ ├── img01.jpg │ ├── img02.jpg │ └── img03.png ├── index.Rhtml ├── makeHTML.R ├── misc.Rhtml ├── other.Rhtml ├── parallel.Rhtml ├── parallel.png ├── preprocess.Rhtml ├── random.Rhtml ├── rfe.Rhtml ├── sampling.Rhtml ├── similarity.Rhtml ├── splitting.Rhtml ├── style.css ├── table.png ├── table.tiff ├── template.html ├── tol.pdf ├── tol.png ├── tol.tiff ├── training.Rhtml ├── varImp.Rhtml └── visualizations.Rhtml ├── models ├── README.md ├── deprecated │ ├── Boruta.R │ ├── GFS.GCCL.R │ ├── avMxnet.R │ ├── bdk.R │ ├── enpls.R │ ├── enpls.fs.R │ ├── oblique.tree.R │ ├── pythonKnnReg.R │ ├── rknn.R │ ├── rknnBel.R │ ├── sddaLDA.R │ └── sddaQDA.R ├── files │ ├── ANFIS.R │ ├── AdaBag.R │ ├── AdaBoost.M1.R │ ├── BstLm.R │ ├── C5.0.R │ ├── C5.0Cost.R │ ├── C5.0Rules.R │ ├── C5.0Tree.R │ ├── CSimca.R │ ├── DENFIS.R │ ├── FH.GBML.R │ ├── FIR.DM.R │ ├── FRBCS.CHI.R │ ├── FRBCS.W.R │ ├── FS.HGD.R │ ├── GFS.FR.MOGUL.R │ ├── GFS.LT.RS.R │ ├── GFS.THRIFT.R │ ├── HYFIS.R │ ├── J48.R │ ├── JRip.R │ ├── LMT.R │ ├── Linda.R │ ├── LogitBoost.R │ ├── M5.R │ ├── M5Rules.R │ ├── Mlda.R │ ├── ORFlog.R │ ├── ORFpls.R │ ├── ORFridge.R │ ├── ORFsvm.R │ ├── OneR.R │ ├── PART.R │ ├── PRIM.R │ ├── PenalizedLDA.R │ ├── QdaCov.R │ ├── RFlda.R │ ├── RRF.R │ ├── RRFglobal.R │ ├── RSimca.R │ ├── Rborist.R │ ├── SBC.R │ ├── SLAVE.R │ ├── WM.R │ ├── ada.R │ ├── adaboost.R │ ├── amdai.R │ ├── avNNet.R │ ├── awnb.R │ ├── awtan.R │ ├── bag.R │ ├── bagEarth.R │ ├── bagEarthGCV.R │ ├── bagFDA.R │ ├── bagFDAGCV.R │ ├── bam.R │ ├── bartMachine.R │ ├── bayesglm.R │ ├── binda.R │ ├── blackboost.R │ ├── blasso.R │ ├── blassoAveraged.R │ ├── bridge.R │ ├── brnn.R │ ├── bstSm.R │ ├── bstTree.R │ ├── cforest.R │ ├── chaid.R │ ├── ctree.R │ ├── ctree2.R │ ├── cubist.R │ ├── dda.R │ ├── deepboost.R │ ├── dnn.R │ ├── dwdLinear.R │ ├── dwdPoly.R │ ├── dwdRadial.R │ ├── earth.R │ ├── elm.R │ ├── enet.R │ ├── evtree.R │ ├── extraTrees.R │ ├── fda.R │ ├── foba.R │ ├── gam.R │ ├── gamLoess.R │ ├── gamSpline.R │ ├── gamboost.R │ ├── gaussprLinear.R │ ├── gaussprPoly.R │ ├── gaussprRadial.R │ ├── gbm.R │ ├── gbm_h2o.R │ ├── gcvEarth.R │ ├── glm.R │ ├── glm.nb.R │ ├── glmStepAIC.R │ ├── glmboost.R │ ├── glmnet.R │ ├── glmnet_h2o.R │ ├── gpls.R │ ├── hda.R │ ├── hdda.R │ ├── hdrda.R │ ├── icr.R │ ├── kernelpls.R │ ├── kknn.R │ ├── knn.R │ ├── krlsPoly.R │ ├── krlsRadial.R │ ├── lars.R │ ├── lars2.R │ ├── lasso.R │ ├── lda.R │ ├── lda2.R │ ├── leapBackward.R │ ├── leapForward.R │ ├── leapSeq.R │ ├── lm.R │ ├── lmStepAIC.R │ ├── loclda.R │ ├── logicBag.R │ ├── logreg.R │ ├── lssvmLinear.R │ ├── lssvmPoly.R │ ├── lssvmRadial.R │ ├── lvq.R │ ├── manb.R │ ├── mda.R │ ├── mlp.R │ ├── mlpKerasDecay.R │ ├── mlpKerasDecayCost.R │ ├── mlpKerasDropout.R │ ├── mlpKerasDropoutCost.R │ ├── mlpML.R │ ├── mlpSGD.R │ ├── mlpWeightDecay.R │ ├── mlpWeightDecayML.R │ ├── monmlp.R │ ├── msaenet.R │ ├── multinom.R │ ├── mxnet.R │ ├── mxnetAdam.R │ ├── naive_bayes.R │ ├── nb.R │ ├── nbDiscrete.R │ ├── nbSearch.R │ ├── neuralnet.R │ ├── nnet.R │ ├── nnls.R │ ├── nodeHarvest.R │ ├── null.R │ ├── ordinalNet.R │ ├── ordinalRF.R │ ├── ownn.R │ ├── pam.R │ ├── parRF.R │ ├── partDSA.R │ ├── pcaNNet.R │ ├── pcr.R │ ├── pda.R │ ├── pda2.R │ ├── penalized.R │ ├── plr.R │ ├── pls.R │ ├── plsRglm.R │ ├── polr.R │ ├── ppr.R │ ├── pre.R │ ├── protoclass.R │ ├── qda.R │ ├── qrf.R │ ├── qrnn.R │ ├── rFerns.R │ ├── randomGLM.R │ ├── ranger.R │ ├── rbf.R │ ├── rbfDDA.R │ ├── rda.R │ ├── regLogistic.R │ ├── relaxo.R │ ├── rf.R │ ├── rfRules.R │ ├── ridge.R │ ├── rlda.R │ ├── rlm.R │ ├── rmda.R │ ├── rocc.R │ ├── rotationForest.R │ ├── rotationForestCp.R │ ├── rpart.R │ ├── rpart1SE.R │ ├── rpart2.R │ ├── rpartCost.R │ ├── rpartScore.R │ ├── rqlasso.R │ ├── rqnc.R │ ├── rrlda.R │ ├── rvmLinear.R │ ├── rvmPoly.R │ ├── rvmRadial.R │ ├── sda.R │ ├── sdwd.R │ ├── simpls.R │ ├── slda.R │ ├── smda.R │ ├── snn.R │ ├── sparseLDA.R │ ├── spikeslab.R │ ├── spls.R │ ├── stepLDA.R │ ├── stepQDA.R │ ├── superpc.R │ ├── svmBoundrangeString.R │ ├── svmExpoString.R │ ├── svmLinear.R │ ├── svmLinear2.R │ ├── svmLinear3.R │ ├── svmLinearWeights.R │ ├── svmLinearWeights2.R │ ├── svmPoly.R │ ├── svmRadial.R │ ├── svmRadialCost.R │ ├── svmRadialSigma.R │ ├── svmRadialWeights.R │ ├── svmSpectrumString.R │ ├── tan.R │ ├── tanSearch.R │ ├── treebag.R │ ├── vbmpRadial.R │ ├── vglmAdjCat.R │ ├── vglmContRatio.R │ ├── vglmCumulative.R │ ├── widekernelpls.R │ ├── wsrf.R │ ├── xgbDART.R │ ├── xgbLinear.R │ ├── xgbTree.R │ └── xyf.R ├── parseModels.R └── sampling_methods.R ├── pkg └── caret │ ├── .Rbuildignore │ ├── .Rinstignore │ ├── .github │ └── .gitignore │ ├── DESCRIPTION │ ├── NAMESPACE │ ├── R │ ├── BoxCoxTrans.R │ ├── aaa.R │ ├── adaptive.R │ ├── additive.R │ ├── avNNet.R │ ├── bag.R │ ├── bagEarth.R │ ├── bagFDA.R │ ├── basic2x2Stats.R │ ├── calibration.R │ ├── caret-package.R │ ├── caretTheme.R │ ├── classDist.R │ ├── classLevels.R │ ├── common_code.R │ ├── confusionMatrix.R │ ├── createDataPartition.R │ ├── createModel.R │ ├── createResample.R │ ├── diag.R │ ├── dotplot.varImp.train.R │ ├── dummyVar.R │ ├── expoTrans.R │ ├── extractPrediction.R │ ├── extractProb.R │ ├── featurePlot.R │ ├── filterVarImp.R │ ├── findCorrelation.R │ ├── findLinearCombos.R │ ├── format.bagEarth.R │ ├── gafs.R │ ├── getTrainPerf.R │ ├── ggplot.R │ ├── heldout.R │ ├── icr.R │ ├── knn3.R │ ├── knnreg.R │ ├── lattice.train.R │ ├── learning_curve.R │ ├── lift.R │ ├── maxDissim.R │ ├── misc.R │ ├── modelLookup.R │ ├── nearZeroVar.R │ ├── negPredValue.R │ ├── panel.needle.R │ ├── pcaNNet.R │ ├── plot.train.R │ ├── plot.varImp.train.R │ ├── plotClassProbs.R │ ├── plotObsVsPred.R │ ├── plsda.R │ ├── posPredValue.R │ ├── postResample.R │ ├── preProcess.R │ ├── prec_rec.R │ ├── predict.PLS.R │ ├── predict.train.R │ ├── predictionFunction.R │ ├── predictors.R │ ├── print.mars.R │ ├── print.train.R │ ├── print.varImp.train.R │ ├── probFunction.R │ ├── reg_sims.R │ ├── resampleHist.R │ ├── resampleSummary.R │ ├── resampleWrapper.R │ ├── resamples.R │ ├── rfe.R │ ├── safs.R │ ├── sampling.R │ ├── selectByFilter.R │ ├── selection.R │ ├── sensitivity.R │ ├── sortImp.R │ ├── spatialSign.R │ ├── specificity.R │ ├── splsda.R │ ├── suggestions.R │ ├── thresholder.R │ ├── train.default.R │ ├── trainControl.R │ ├── train_recipes.R │ ├── trim.R │ ├── twoClassSim.R │ ├── updates.R │ ├── varImp.R │ ├── varImp.train.R │ └── workflows.R │ ├── caret.Rproj │ ├── data │ ├── BloodBrain.RData │ ├── GermanCredit.RData │ ├── Sacramento.RData │ ├── cars.RData │ ├── cox2.RData │ ├── datalist │ ├── dhfr.RData │ ├── mdrr.RData │ ├── oil.RData │ ├── pottery.RData │ ├── scat.RData │ ├── segmentationData.RData │ └── tecator.RData │ ├── inst │ ├── CITATION │ ├── NEWS.Rd │ └── models │ │ ├── models.RData │ │ └── sampling.RData │ ├── man │ ├── BloodBrain.Rd │ ├── BoxCoxTrans.Rd │ ├── GermanCredit.Rd │ ├── Sacramento.Rd │ ├── as.matrix.confusionMatrix.Rd │ ├── avNNet.Rd │ ├── bag.Rd │ ├── bagEarth.Rd │ ├── bagFDA.Rd │ ├── calibration.Rd │ ├── caret-internal.Rd │ ├── caretFuncs.Rd │ ├── caretSBF.Rd │ ├── cars.Rd │ ├── classDist.Rd │ ├── confusionMatrix.Rd │ ├── confusionMatrix.train.Rd │ ├── cox2.Rd │ ├── createDataPartition.Rd │ ├── densityplot.rfe.Rd │ ├── dhfr.Rd │ ├── diff.resamples.Rd │ ├── dotPlot.Rd │ ├── dotplot.diff.resamples.Rd │ ├── downSample.Rd │ ├── dummyVars.Rd │ ├── featurePlot.Rd │ ├── filterVarImp.Rd │ ├── findCorrelation.Rd │ ├── findLinearCombos.Rd │ ├── format.bagEarth.Rd │ ├── gafs.default.Rd │ ├── gafs_initial.Rd │ ├── getSamplingInfo.Rd │ ├── histogram.train.Rd │ ├── icr.formula.Rd │ ├── index2vec.Rd │ ├── knn3.Rd │ ├── knnreg.Rd │ ├── learning_curve_dat.Rd │ ├── lift.Rd │ ├── maxDissim.Rd │ ├── mdrr.Rd │ ├── modelLookup.Rd │ ├── models.Rd │ ├── nearZeroVar.Rd │ ├── nullModel.Rd │ ├── oil.Rd │ ├── oneSE.Rd │ ├── panel.lift2.Rd │ ├── panel.needle.Rd │ ├── pcaNNet.Rd │ ├── plot.gafs.Rd │ ├── plot.rfe.Rd │ ├── plot.train.Rd │ ├── plot.varImp.train.Rd │ ├── plotClassProbs.Rd │ ├── plotObsVsPred.Rd │ ├── plsda.Rd │ ├── postResample.Rd │ ├── pottery.Rd │ ├── prcomp.resamples.Rd │ ├── preProcess.Rd │ ├── predict.bagEarth.Rd │ ├── predict.gafs.Rd │ ├── predict.knn3.Rd │ ├── predict.knnreg.Rd │ ├── predict.train.Rd │ ├── predictors.Rd │ ├── print.confusionMatrix.Rd │ ├── print.train.Rd │ ├── recall.Rd │ ├── resampleHist.Rd │ ├── resampleSummary.Rd │ ├── resamples.Rd │ ├── rfe.Rd │ ├── rfeControl.Rd │ ├── safs.Rd │ ├── safsControl.Rd │ ├── safs_initial.Rd │ ├── sbf.Rd │ ├── sbfControl.Rd │ ├── scat.Rd │ ├── segmentationData.Rd │ ├── sensitivity.Rd │ ├── spatialSign.Rd │ ├── summary.bagEarth.Rd │ ├── tecator.Rd │ ├── thresholder.Rd │ ├── train.Rd │ ├── trainControl.Rd │ ├── twoClassSim.Rd │ ├── update.safs.Rd │ ├── update.train.Rd │ ├── varImp.Rd │ ├── varImp.gafs.Rd │ ├── var_seq.Rd │ └── xyplot.resamples.Rd │ ├── src │ └── caret.c │ ├── tests │ ├── testthat.R │ └── testthat │ │ ├── test_BoxCox.R │ │ ├── test_Dummies.R │ │ ├── test_bad_class_options.R │ │ ├── test_classDist.R │ │ ├── test_confusionMatrix.R │ │ ├── test_data_spliting.R │ │ ├── test_gafs.R │ │ ├── test_ggplot.R │ │ ├── test_glmnet_varImp.R │ │ ├── test_minimal.R │ │ ├── test_misc.R │ │ ├── test_mnLogLoss.R │ │ ├── test_models_bagEarth.R │ │ ├── test_multiclassSummary.R │ │ ├── test_nearZeroVar.R │ │ ├── test_preProcess.R │ │ ├── test_preProcess_internals.R │ │ ├── test_preProcess_methods.R │ │ ├── test_ptypes.R │ │ ├── test_recipe_fs.R │ │ ├── test_recipe_upsample.R │ │ ├── test_resamples.R │ │ ├── test_safs.R │ │ ├── test_sampling_options.R │ │ ├── test_sparse_Matrix.R │ │ ├── test_spatialSign.R │ │ ├── test_tibble.R │ │ ├── test_twoClassSummary.R │ │ ├── test_updates.R │ │ ├── test_varImp.R │ │ ├── trim.R │ │ ├── trim_C5.R │ │ ├── trim_bayesglm.R │ │ ├── trim_glm.R │ │ ├── trim_glmnet.R │ │ ├── trim_rpart.R │ │ ├── trim_train.R │ │ └── trim_treebag.R │ └── vignettes │ └── caret.Rmd └── release_process ├── Open_Data_Science_Conference ├── caret.Rnw ├── caret.pdf ├── caret.tex ├── coverage_12.png ├── min_graph.pdf ├── new_graph.pdf ├── old_graph.pdf ├── outline.md └── test_coverage_report.png ├── README.md ├── make_model_Rd.R ├── reverse_depends.R ├── talk ├── caret.Rnw ├── caret.pdf └── outline.md ├── update_biocmanager.R 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