import(lattice)
import(BiocGenerics)
import(mclust)
import(MASS)
import(kernlab) ## previously only imported ksvm
import(knitr)

importFrom(class, knn)
importFrom(RColorBrewer, brewer.pal)
importFrom(stats4, plot)
importFrom(proxy, simil)
importFrom(MSBVAR, rmultnorm)
importFrom(scales, col2hcl, alpha)
importFrom(caret, createFolds, confusionMatrix, plsda, predict.plsda)
importFrom(sampling, strata)
importFrom(e1071, svm, naiveBayes)
importFrom(nnet, nnet)
importFrom(randomForest, randomForest)

exportClasses(GenRegRes)

exportMethods(chi2,
              show,
              ## machine learning
              MLearn,
              getWarnings,
              getSeed,
              getF1Scores,
              f1Count,
              levelPlot,
              plot)

export(getPredictions,
       getMarkers,
       minClassScore,
       minMarkers,
       addMarkers,
       empPvalues,
       getStockcol, getStockpch,
       setStockcol, setStockpch,
       getUnknowncol, getUnknownpch,
       setUnknowncol, setUnknownpch,
       ## -- plotting
       plot2D,
       addLegend,
       plotDist,
       ## -- machine learning
       plsdaRegularisation, plsdaOptimisation, plsdaOptimization, 
       plsdaPrediction, plsdaClassification,
       svmRegularisation, svmOptimisation, svmOptimization, 
       svmPrediction, svmClassification, 
       ksvmRegularisation, ksvmOptimisation, ksvmOptimization,
       ksvmPrediction, ksvmClassification, 
       knnRegularisation, knnOptimisation, knnOptimization,
       knnPrediction, knnClassification, 
       nbRegularisation, nbOptimisation, nbOptimization,
       nbPrediction, nbClassification, 
       nnetRegularisation, nnetOptimisation, nnetOptimization, 
       nnetPrediction, nnetClassification,
       perTurboOptimisation, perTurboOptimization, perTurboClassification, 
       getParams, 
       getRegularisedParams, getRegularizedParams,       
       rfRegularisation, rfOptimisation, rfOptimization, 
       rfPrediction, rfClassification, 
       phenoDisco,
       makeNaData, makeNaData2, whichNA
       )

