# Generated by roxygen2: do not edit by hand

S3method(summary,morphyPtr)
export(AddTip)
export(AllAncestors)
export(AllDescendantEdges)
export(AllSplitPairings)
export(AllTBR)
export(AncestorEdge)
export(ApeTime)
export(AsBinary)
export(C_MorphyLength)
export(C_node_depth)
export(CalculateTreeDistance)
export(CladeSizes)
export(Cladewise)
export(CollapseEdge)
export(CollapseNode)
export(ConsensusWithout)
export(DescendantEdges)
export(DoubleFactorial)
export(DropSingleSplits)
export(EdgeAncestry)
export(EdgeListSearch)
export(EnforceOutgroup)
export(Entropy)
export(Evaluate)
export(ExtractTaxa)
export(Fitch)
export(FitchSteps)
export(ForestSplits)
export(GetMorphyLength)
export(IC1Spr)
export(ICPerStep)
export(ICS)
export(ICSteps)
export(IWBootstrap)
export(IWDestroyMorphy)
export(IWInitMorphy)
export(IWMultiRatchet)
export(IWRatchet)
export(IWRatchetConsensus)
export(IWScore)
export(IWScoreMorphy)
export(IWTreeSearch)
export(InfoAmounts)
export(Jackknife)
export(JointInformation)
export(ListToMatrix)
export(LnRooted)
export(LnUnrooted)
export(LnUnrootedMult)
export(LnUnrootedSplits)
export(LogDoubleFactorial.int)
export(LogTreesConsistentWithTwoSplits)
export(LogTreesMatchingSplit)
export(LogisticPoints)
export(MarkMissing)
export(MatchingSplitDistance)
export(MatchingSplitDistanceSplits)
export(MatrixToList)
export(MatrixToPhyDat)
export(MinimumSteps)
export(MorphyBootstrap)
export(MorphyErrorCheck)
export(MorphyLength)
export(MorphyTreeLength)
export(MorphyWeights)
export(MultiRatchet)
export(MultiSplitInformation)
export(MutualArborealInfo)
export(MutualArborealInfoSplits)
export(MutualClusterInfo)
export(MutualClusterInfoSplits)
export(N1Spr)
export(NJTree)
export(NNI)
export(NNISwap)
export(NPartitionPairs)
export(NRooted)
export(NUnrooted)
export(NUnrootedMult)
export(NUnrootedSplits)
export(NewickTree)
export(NeworderPhylo)
export(NeworderPruningwise)
export(NonDuplicateRoot)
export(NyeSplitSimilarity)
export(NyeTreeSimilarity)
export(OrderEdgesNumberNodes)
export(PhyDat)
export(PhyDat2Morphy)
export(PhyToString)
export(Postorder)
export(PostorderEdges)
export(Preorder)
export(PrepareDataIW)
export(PrepareDataProfile)
export(ProfileBootstrap)
export(ProfileDestroyMorphy)
export(ProfileInitMorphy)
export(ProfileRatchet)
export(ProfileScore)
export(ProfileScoreMorphy)
export(ProfileTreeSearch)
export(Pruningwise)
export(RandomMorphyTree)
export(RandomTree)
export(RandomTreeScore)
export(Ratchet)
export(RatchetConsensus)
export(ReadAsPhyDat)
export(ReadCharacters)
export(ReadTntAsPhyDat)
export(ReadTntCharacters)
export(ReadTntTree)
export(RearrangeEdges)
export(Renumber)
export(RenumberEdges)
export(RenumberTips)
export(RenumberTree)
export(RightmostCharacter)
export(RootTree)
export(RootedNNI)
export(RootedNNISwap)
export(RootedSPR)
export(RootedSPRSwap)
export(RootedTBR)
export(RootedTBRSwap)
export(SPR)
export(SPRSwap)
export(SPRWarning)
export(SampleOne)
export(SetMorphyWeights)
export(SingleCharMorphy)
export(SingleTaxonTree)
export(SortTree)
export(SplitEntropy)
export(SplitFrequency)
export(SplitInformation)
export(SplitMatchProbability)
export(SplitMutualInformation)
export(SplitNumber)
export(SplitPairingInformationIndex)
export(SplitVariationOfInformation)
export(SplitsCompatible)
export(SplitsRepeated)
export(StopUnlessBifurcating)
export(StringToPhyDat)
export(Suboptimality)
export(Subtree)
export(SuccessiveApproximations)
export(SuccessiveWeights)
export(SupportColor)
export(SupportColour)
export(TBR)
export(TBRMoves)
export(TBRSwap)
export(TBRWarning)
export(TNTText2Tree)
export(TipsAreColumns)
export(TipsAreNames)
export(Tree2Bipartitions)
export(Tree2Splits)
export(TreeSearch)
export(TreeSplits)
export(TreesConsistentWithTwoSplits)
export(TreesMatchingSplit)
export(UniqueExceptHits)
export(UniqueSplits)
export(UnloadMorphy)
export(UnloadTreeSearch)
export(UnrootedTreesMatchingSplit)
export(VariationOfArborealInfo)
export(VariationOfArborealInfoSplits)
export(VisualizeMatching)
export(WithOneExtraStep)
export(mpl_apply_tipdata)
export(mpl_attach_rawdata)
export(mpl_attach_symbols)
export(mpl_delete_Morphy)
export(mpl_delete_rawdata)
export(mpl_first_down_recon)
export(mpl_first_up_recon)
export(mpl_get_charac_weight)
export(mpl_get_num_charac)
export(mpl_get_num_internal_nodes)
export(mpl_get_numtaxa)
export(mpl_get_symbols)
export(mpl_init_Morphy)
export(mpl_new_Morphy)
export(mpl_second_down_recon)
export(mpl_second_up_recon)
export(mpl_set_charac_weight)
export(mpl_set_num_internal_nodes)
export(mpl_set_parsim_t)
export(mpl_translate_error)
export(mpl_update_lower_root)
export(mpl_update_tip)
importFrom(R.cache,addMemoization)
importFrom(Rdpack,reprompt)
importFrom(ape,bind.tree)
importFrom(ape,consensus)
importFrom(ape,drop.tip)
importFrom(ape,edgelabels)
importFrom(ape,nj)
importFrom(ape,nodelabels)
importFrom(ape,plot.phylo)
importFrom(ape,read.tree)
importFrom(ape,reorder.phylo)
importFrom(ape,root)
importFrom(ape,rtree)
importFrom(ape,write.tree)
importFrom(clue,solve_LSAP)
importFrom(colorspace,diverge_hcl)
importFrom(colorspace,qualitative_hcl)
importFrom(graphics,legend)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(memoise,memoise)
importFrom(phangorn,Ancestors)
importFrom(phangorn,Descendants)
importFrom(phangorn,allDescendants)
importFrom(phangorn,dist.hamming)
importFrom(phangorn,phyDat)
importFrom(stats,nls)
useDynLib(TreeSearch, .registration = TRUE)
