useDynLib(caret)
import(foreach, methods, plyr, reshape2, ggplot2, lattice, nlme, BradleyTerry2)
importFrom(car, powerTransform, yjPower)
importFrom(stats, prcomp, hclust)


export(anovaScores,
       avNNet,
       avNNet.default,
       bag,
       bag.default,
       bagControl,
       bagEarth,
       bagEarth.default,
       bagEarth.formula,
       bagEarthStats,
       bagFDA,
       bagFDA.default,
       bagFDA.formula,
       best,
       BoxCoxTrans,
       calibration,
       caretFuncs,
       caretGA,
       caretSA,
       caretSBF,
       caretTheme,
       cforestStats,
       checkConditionalX,
       checkInstall,
       checkResamples,
       classDist,
       classDist.default,
       cluster,
       cluster.resamples,
       compare_models,
       confusionMatrix,
       confusionMatrix.train,
       contr.dummy,
       contr.ltfr,
       createDataPartition,
       createFolds,
       createModel,
       createMultiFolds,
       createResample,
       createTimeSlices,
       ctreeBag,
       defaultSummary,
       densityplot.rfe,
       densityplot.train,
       dotPlot,
       downSample,
       dummyVars,
       dummyVars.default,
       expandParameters,
       expoTrans,
       extractPrediction,
       extractProb,
       featurePlot,
       filterVarImp,
       findCorrelation,
       findLinearCombos,
       flatTable,
       gafs_initial,
       gafs_lrSelection,
       gafs_rwSelection,
       gafs_tourSelection,
       gafs_uCrossover,
       gafs_spCrossover,
       gafs_raMutation,
       gafs,
       gafs.default, 
       gafsControl,
       gamFormula,
       gamFuncs,
       gamScores,
       getModelInfo,
       getTrainPerf,
       ggplot.rfe,
       ggplot.train,
       hasTerms,
       histogram.rfe,
       icr,
       icr.default,
       icr.formula,
       index2vec,
       ipredStats,
       knn3,
       knn3.formula,
       knn3.matrix,
       knn3.data.frame,
       knn3Train,
       knnreg,
       knnreg.data.frame,
       knnreg.default,
       knnreg.matrix,
       knnregTrain,
       ldaBag,
       ldaFuncs,
       ldaSBF,
       lift,
       lmFuncs,
       lmSBF,
       lrFuncs,
       LPH07_1,
       LPH07_2,
       maxDissim,
       MeanSD,
       minDiss,
       modelCor,
       modelLookup,
       nbBag,
       nbFuncs,
       nbSBF,
       nearZeroVar,
       nzv,
       negPredValue,
       negPredValue.default,
       negPredValue.table,
       nnetBag,
       nullModel,
       nullModel.default,
       oneSE,
       panel.calibration,       
       panel.lift,
       panel.lift2,
       panel.needle,
       parallelplot.resamples,
       pcaNNet,
       pcaNNet.default,
       pickSizeBest,
       pickSizeTolerance,
       pickVars,
       plot.gafs,
       plot.rfe,
       plot.train,
       plotClassProbs,
       plotObsVsPred,
       plsBag,
       plsda,
       plsda.default,
       posPredValue,
       posPredValue.default,
       posPredValue.table,
       postResample,
       predict.avNNet,
       predict.bag,
       predict.bagEarth,
       predict.bagFDA,
       predict.classDist,
       predict.dummyVars,
       predict.gafs,
       predict.icr,
       predict.knn3,
       predict.knnreg,
       predict.list,
       predict.nullModel,
       predict.pcaNNet,
       predict.plsda,
       predict.preProcess,
       predict.splsda,
       predict.train,
       predictionFunction,
       predictors,
       preProcess,
       preProcess.default,
       print.train,
       probFunction,
       progress,
       R2,
       resampleHist,
       resamples,
       resamples.default,
       resampleSummary,
       resampleWrapper,
       rfe,
       rfe.default,
       rfeControl,
       rfeIter,
       rfFuncs,
       rfGA, 
       rfSA,
       rfSBF,
       rfStats,
       RMSE,
       safs_initial,
       safs_perturb, 
       safs_prob,
       safs,
       safs.default, 
       safsControl,
       sbf,
       sbf.default,
       sbf.formula,
       sbfControl,
       sbfIter,
       sensitivity,
       sensitivity.default,
       sensitivity.table,
       SLC14_1,
       SLC14_2,
       sortImp,
       spatialSign,
       spatialSign.data.frame,
       spatialSign.default,
       spatialSign.matrix,
       specificity,
       specificity.default,
       specificity.table,
       splsda,
       splsda.default,
       stripplot.rfe,
       sumDiss,
       summary.bagEarth,
       summary.bagFDA,
       svmBag,
       tolerance,
       train,
       train.default,
       train.formula,
       trainControl,
       treebagFuncs,
       treebagGA,
       treebagSA,
       treebagSBF,
       twoClassSim,
       twoClassSummary,
       upSample,
       varImp,
       varImp.bagEarth,
       varImp.bagFDA,
       varImp.plsda,
       well_numbered,
       xyplot.rfe
       )

S3method(confusionMatrix, default)
S3method(confusionMatrix, train)
S3method(spatialSign,     default)
S3method(enumLC,          default)
S3method(train,           default)
S3method(plsda,           default)
S3method(splsda,          default)
S3method(bagEarth,        default)
S3method(bagFDA,          default)
S3method(preProcess,      default)
S3method(pcaNNet,         default)
S3method(avNNet,          default)
S3method(sensitivity,     default)
S3method(specificity,     default)
S3method(posPredValue,    default)
S3method(negPredValue,    default)
S3method(rfe,             default)
S3method(classDist,       default)
S3method(knnreg,          default)
S3method(sbf,             default)
S3method(nullModel,       default)
S3method(resamples,       default)
S3method(icr,             default)
S3method(bag,             default)
S3method(dummyVars,       default)
S3method(BoxCoxTrans,     default)
S3method(cluster,         default)
S3method(expoTrans,       default)

S3method(calibration, formula)
S3method(lift,        formula)
S3method(train,       formula)
S3method(pcaNNet,     formula)
S3method(avNNet,      formula)
S3method(rfe,         formula)
S3method(knnreg,      formula)
S3method(sbf,         formula)
S3method(icr,         formula)

S3method(varImp, train)
S3method(varImp, rpart)
S3method(varImp, randomForest)
S3method(varImp, gbm)
S3method(varImp, classbagg)
S3method(varImp, regbagg)
S3method(varImp, pamrtrained)
S3method(varImp, lm)
S3method(varImp, glm)
S3method(varImp, mvr)
S3method(varImp, earth)
S3method(varImp, bagEarth)
S3method(varImp, bagFDA)
S3method(varImp, RandomForest)
S3method(varImp, rfe)
S3method(varImp, sbf)
S3method(varImp, dsa)
S3method(varImp, plsda)
S3method(varImp, fda)
S3method(varImp, multinom)
S3method(varImp, cubist)
S3method(varImp, RRF)
S3method(varImp, PART)
S3method(varImp, JRip)
S3method(varImp, C5.0)
S3method(varImp, nnet)
S3method(varImp, glmnet)
S3method(varImp, gam)
S3method(varImp, gafs)
S3method(varImp, safs) 

S3method(densityplot, train)
S3method(histogram,   train)
S3method(stripplot,   train)
S3method(xyplot,      train)
S3method(xyplot,      lift)
S3method(xyplot,      calibration)

S3method(densityplot, rfe)
S3method(histogram,   rfe)
S3method(stripplot,   rfe)
S3method(xyplot,      rfe)

S3method(densityplot, sbf)
S3method(histogram,   sbf)

S3method(densityplot, resamples)
S3method(bwplot,      resamples)
S3method(dotplot,     resamples)
S3method(splom,       resamples)
S3method(xyplot,      resamples)
S3method(parallelplot,resamples)
S3method(prcomp,      resamples)
S3method(cluster,     resamples)

S3method(densityplot, diff.resamples)
S3method(bwplot,      diff.resamples)
S3method(levelplot,   diff.resamples)
S3method(dotplot,     diff.resamples)

S3method(plot,  train)
S3method(plot,  varImp.train)
S3method(plot,  rfe)
S3method(plot,  prcomp.resamples)
S3method(plot,  lift)
S3method(plot,  calibration)
S3method(plot,  gafs)
S3method(plot,  safs) 

S3method(confusionMatrix,  train)
S3method(confusionMatrix,  rfe)
S3method(confusionMatrix,  sbf)

S3method(print, train)
S3method(print, varImp.train)
S3method(print, confusionMatrix)
S3method(print, confusionMatrix.train)
S3method(print, confusionMatrix.rfe)
S3method(print, confusionMatrix.sbf)
S3method(print, knn3)
S3method(print, plsda)
S3method(print, splsda)
S3method(print, bagEarth)
S3method(print, bagFDA)
S3method(print, summary.bagEarth)
S3method(print, summary.bagFDA)
S3method(print, preProcess)
S3method(print, pcaNNet)
S3method(print, avNNet)
S3method(print, rfe)
S3method(print, classDist)
S3method(print, knnreg)
S3method(print, sbf)
S3method(print, nullModel)
S3method(print, resamples)
S3method(print, summary.resamples)
S3method(print, diff.resamples)
S3method(print, summary.diff.resamples)
S3method(print, icr)
S3method(print, bag)
S3method(print, summary.bag)
S3method(print, prcomp.resamples)
S3method(print, dummyVars)
S3method(print, BoxCoxTrans)
S3method(print, lift)
S3method(print, calibration)
S3method(print, expoTrans)
S3method(print, gafs)
S3method(print, safs) 

S3method(predict, plsda)
S3method(predict, splsda)
S3method(predict, knn3)
S3method(predict, bagEarth)
S3method(predict, bagFDA)
S3method(predict, preProcess)
S3method(predict, pcaNNet)
S3method(predict, avNNet)
S3method(predict, list)
S3method(predict, train)
S3method(predict, classDist)
S3method(predict, knnreg)
S3method(predict, nullModel)
S3method(predict, sbf)
S3method(predict, icr)
S3method(predict, bag)
S3method(predict, rfe)
S3method(predict, dummyVars)
S3method(predict, BoxCoxTrans)
S3method(predict, expoTrans)
S3method(predict, gafs)
S3method(predict, safs) 

S3method(summary, bagEarth)
S3method(summary, bagFDA)
S3method(summary, train)

S3method(residuals, train)

S3method(format, bagEarth)

S3method(predictors, train)
S3method(predictors, terms)
S3method(predictors, formula)
S3method(predictors, list)
S3method(predictors, default)
S3method(predictors, rfe)
S3method(predictors, sbf)
S3method(predictors, gafs)
S3method(predictors, safs) 

S3method(confusionMatrix, table)

S3method(sensitivity, table)
S3method(specificity, table)

S3method(posPredValue,    table)
S3method(negPredValue,    table)

S3method(posPredValue,    matrix)
S3method(negPredValue,    matrix)

S3method(as.table,  confusionMatrix)
S3method(as.matrix, confusionMatrix)

S3method(summary, resamples)
S3method(summary, bag)

S3method(diff, resamples)
S3method(sort, resamples)

S3method(summary, diff.resamples)

S3method(update, train)
S3method(update, rfe)
S3method(update, gafs)
S3method(update, safs) 

S3method(fitted, train)
S3method(residuals, train)

S3method(levels, train)

S3method(ggplot, train)
S3method(ggplot, rfe)

S3method(oob_pred, train)
S3method(oob_pred, rfe)
S3method(oob_pred, sbf)
S3method(oob_pred, list)

S3method(gafs, default)
S3method(safs, default)