useDynLib(Rtreemix)

import(Biobase)
import(methods)
import(graph)

importFrom("Hmisc", "rcorr")

##import(Rgraphviz)
importFrom("graphics", "plot")

## Classes to be exported
exportClasses(RtreemixData, RtreemixModel,
              RtreemixSim, RtreemixStats, RtreemixGPS)

## Methods to be exported
exportMethods(initialize, print, show,
          Sample, Events, Patients, Description, sampleSize, eventsNum, ##RtreemixData
          "Events<-", "Patients<-", "Description<-",  ##RtreemixData
          Weights, "Weights<-", WeightsCI, Resp, CompleteMat, Star, Trees, numTrees, getTree, getData, plot, ## RtreemixModel
              Model, LogLikelihoods, WLikelihoods, getResp, ## RtreemixStats
              SamplingMode, SamplingParam, GPS, gpsCI, ## RtreemixGPS
          SimPatterns, SamplingTimes, WaitingTimes, getModel, noDraws, ## RtreemixSim
              fit, bootstrap, likelihoods, gps, confIntGPS, sim, generate, distribution ## other methods
              )

## Functions to be exported
export(Pval.dist, kullback.leibler, L1.dist, cosin.dist, L2.norm, euclidian.dist, rank.cor.dist, ## similarity measures for vectors
       get.tree.levels, comp.models, comp.models.levels, comp.trees, comp.trees.levels, ## similarity measures for tree topologies
       stability.sim  ## stability analysis function
       )