import("methods")
import("tools")
import("BiocGenerics")
import("Biobase")
import("annotate")
import("MASS")
import("rpart")
import("sfsmisc")
import("pls")
import("rda")
import("shiny")
import("ggvis")
import("fpc")
import(threejs)
import(mlbench)

importFrom(gbm, gbm, predict.gbm)

importFrom("genefilter", "rowttests")
importFrom("stats4", "plot")
importFrom("cluster", "silhouette")
importFrom("gdata", "drop.levels")

importFrom("RColorBrewer", "brewer.pal")

importFrom("hwriter", "hwrite")

exportClasses( 
	"varImpStruct",
#	"raboostCont", "daboostCont",
	"classifierOutput", "learnerSchema", #"nonstandardLearnerSchema",
	"xvalSpec", "clusteringOutput")
	
exportMethods("show", "RObject", "confuMat", "trainInd",
              "precision", "recall", "sensitivity", "macroF1",
              "F1", "acc", "tp", "tn", "fp", "fn", "specificity",
              "MLearn", "planarPlot", "Predict", "getVarImp", 
              "trainScores","trainPredictions",
              "testScores", "testPredictions",
              "predictions", "predScores", "predScore", 
              "fsHistory", "report", "getDist", "getConverter")

export(randomForestI, knnI, dldaI, nnetI, rpartI, 
       ldaI, svmI, ldaI.predParms, qdaI, glmI.logistic, 
       RABI, lvqI, naiveBayesI, baggingI, knn2, dlda2, 
       rab, lvq, RAB, DAB, plsda2, svm2, ksvm2, 
       xvalSpec, getVarImp, balKfold.xvspec, rdacvI, rdacvML,
       rdaI, rdaML, 
       plotXvalRDA, makeLearnerSchema, standardMLIConverter, sldaI, 
       fs.absT, fs.probT, ksvmI, knn.cvI, knn.cv2, 
       adaI, fs.topVariance, hclustI, kmeansI, pamI,
       blackboostI,
       gbm2, BgbmI, plsdaI,
       confuTab) 

S3method("print", "rdacvML")
S3method("print", "rdaML")
S3method("predict", "classifierOutput")

exportMethods("plot")
export(hclustWidget, mlearnWidget)

exportClasses("projectedLearner")
export(projectLearnerToGrid)
exportMethods("learnerIn3D", "plotOne")

export(plspinHcube)

# recommended
importFrom("grDevices", "colorRampPalette")
importFrom("graphics", "axis", "barplot", "legend", "pairs", "par",
             "points", "text")
importFrom("stats", "as.formula", "cutree", "dist", "hclust", "median",
             "model.frame", "model.matrix", "model.response", "na.fail",
             "prcomp", "predict", "quantile", "terms", "var")

