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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(adaptivePermulation)
export(asymmRerootingMethod)
export(boxPlotTest)
export(calculateCorPermuted)
export(calculatePermulatedPaths_apply)
export(categoricalPermulations)
export(char2Paths)
export(char2PathsCategorical)
export(char2TreeCategorical)
export(click_select_foreground_branches)
export(combinePermData)
export(compareRateModels)
export(correlateWithBinaryPhenotype)
export(correlateWithCategoricalPhenotype)
export(correlateWithContinuousPhenotype)
export(edgeVars)
export(estimatePhangornTree)
export(estimatePhangornTreeAll)
export(fastwilcoxGMTall)
export(filterByCriteria)
export(fixPseudoroot)
export(foreground2Paths)
export(foreground2Tree)
export(foreground2TreeClades)
export(generatePermulatedBinPhen)
export(generatePermulatedBinPhenSSMBatched)
export(getAllCor)
export(getAllCorExtantOnly)
export(getAllResiduals)
export(getAncLiks)
export(getBinaryPermulationInputsFromTree)
export(getEnrichPermPvals)
export(getEnrichPerms)
export(getEnrichPermsCategorical)
export(getForegroundInfoClades)
export(getLRnullDistribution)
export(getLikelihoodRatio)
export(getMatrixFromAbbr)
export(getPermPvalsCategorical)
export(getPermsBinary)
export(getPermsBinaryExtantOnly)
export(getPermsContinuous)
export(getPermsContinuousExtantOnly)
export(getRealEnrichments)
export(getStat)
export(getStatesAtNodes)
export(getStatesFromPhenTree)
export(makeBinaryPaths)
export(matchAllNodesClades)
export(namePathsWSpecies)
export(permpvalcor)
export(permpvalenrich)
export(permutevec)
export(plotPositivesFromPermulations)
export(plotRers)
export(plotTreeCategorical)
export(plotTreeHighlightBranches)
export(pruneTree)
export(read.gmt)
export(readTrees)
export(returnRersAsNewickStrings)
export(returnRersAsTree)
export(returnRersAsTreesAll)
export(searchRateModels)
export(simBinPheno)
export(simBinPhenoCC)
export(simBinPhenoCCmidpoint)
export(simBinPhenoRank)
export(simBinPhenoSSM)
export(simBinPhenoVec)
export(simpermvec)
export(simulatevec)
export(tree2Paths)
export(tree2PathsClades)
export(treePlotNew)
export(treePlotRers)
export(visCompareTwoRateModels)
import(Rcpp)
importFrom(Rcpp,evalCpp)
useDynLib(RERconverge)