# Generated by roxygen2: do not edit by hand

S3method("!",Splits)
S3method("%in%",Splits)
S3method("%in%",default)
S3method("+",Splits)
S3method("-",Splits)
S3method("[[",Splits)
S3method(AllTipLabels,Splits)
S3method(AllTipLabels,TreeNumber)
S3method(AllTipLabels,list)
S3method(AllTipLabels,matrix)
S3method(AllTipLabels,multiPhylo)
S3method(AllTipLabels,phylo)
S3method(ApePostorder,list)
S3method(ApePostorder,multiPhylo)
S3method(ApePostorder,phylo)
S3method(ArtificialExtinction,matrix)
S3method(ArtificialExtinction,phyDat)
S3method(Cladewise,list)
S3method(Cladewise,matrix)
S3method(Cladewise,multiPhylo)
S3method(Cladewise,phylo)
S3method(CladisticInfo,list)
S3method(CladisticInfo,multiPhylo)
S3method(CladisticInfo,phylo)
S3method(CollapseNode,phylo)
S3method(ConsensusWithout,list)
S3method(ConsensusWithout,multiPhylo)
S3method(ConsensusWithout,phylo)
S3method(DropTip,multiPhylo)
S3method(DropTip,phylo)
S3method(EnforceOutgroup,character)
S3method(EnforceOutgroup,phylo)
S3method(MakeTreeBinary,list)
S3method(MakeTreeBinary,multiPhylo)
S3method(MakeTreeBinary,phylo)
S3method(NSplits,"NULL")
S3method(NSplits,ClusterTable)
S3method(NSplits,Splits)
S3method(NSplits,character)
S3method(NSplits,list)
S3method(NSplits,multiPhylo)
S3method(NSplits,numeric)
S3method(NSplits,phylo)
S3method(NTip,Splits)
S3method(NTip,default)
S3method(NTip,list)
S3method(NTip,matrix)
S3method(NTip,multiPhylo)
S3method(NTip,phylo)
S3method(NodeDepth,list)
S3method(NodeDepth,matrix)
S3method(NodeDepth,multiPhylo)
S3method(NodeDepth,phylo)
S3method(NodeOrder,list)
S3method(NodeOrder,matrix)
S3method(NodeOrder,multiPhylo)
S3method(NodeOrder,phylo)
S3method(Postorder,list)
S3method(Postorder,multiPhylo)
S3method(Postorder,numeric)
S3method(Postorder,phylo)
S3method(Preorder,list)
S3method(Preorder,multiPhylo)
S3method(Preorder,numeric)
S3method(Preorder,phylo)
S3method(Pruningwise,list)
S3method(Pruningwise,multiPhylo)
S3method(Pruningwise,phylo)
S3method(RenumberTips,list)
S3method(RenumberTips,multiPhylo)
S3method(RenumberTips,phylo)
S3method(RootNode,list)
S3method(RootNode,multiPhylo)
S3method(RootNode,numeric)
S3method(RootNode,phylo)
S3method(RootNodeDistance,character)
S3method(RootNodeDistance,numeric)
S3method(RootOnNode,"NULL")
S3method(RootOnNode,list)
S3method(RootOnNode,multiPhylo)
S3method(RootOnNode,phylo)
S3method(RootTree,"NULL")
S3method(RootTree,list)
S3method(RootTree,multiPhylo)
S3method(RootTree,phylo)
S3method(RootedTreeWithShape,integer64)
S3method(RootedTreeWithShape,numeric)
S3method(SisterSize,character)
S3method(SisterSize,numeric)
S3method(SplitImbalance,Splits)
S3method(SplitImbalance,phylo)
S3method(SplitsInBinaryTree,"NULL")
S3method(SplitsInBinaryTree,Splits)
S3method(SplitsInBinaryTree,default)
S3method(SplitsInBinaryTree,list)
S3method(SplitsInBinaryTree,multiPhylo)
S3method(SplitsInBinaryTree,numeric)
S3method(SplitsInBinaryTree,phylo)
S3method(TCIContext,numeric)
S3method(TCIContext,phylo)
S3method(TipLabels,Splits)
S3method(TipLabels,TreeNumber)
S3method(TipLabels,character)
S3method(TipLabels,default)
S3method(TipLabels,list)
S3method(TipLabels,matrix)
S3method(TipLabels,multiPhylo)
S3method(TipLabels,numeric)
S3method(TipLabels,phyDat)
S3method(TipLabels,phylo)
S3method(TipsInSplits,Splits)
S3method(TipsInSplits,phylo)
S3method(TotalCopheneticIndex,list)
S3method(TotalCopheneticIndex,multiPhylo)
S3method(TotalCopheneticIndex,phylo)
S3method(UnrootTree,"NULL")
S3method(UnrootTree,list)
S3method(UnrootTree,multiPhylo)
S3method(UnrootTree,phylo)
S3method(WriteTntCharacters,matrix)
S3method(WriteTntCharacters,phyDat)
S3method(as.Newick,list)
S3method(as.Newick,multiPhylo)
S3method(as.Newick,phylo)
S3method(as.Splits,Splits)
S3method(as.Splits,list)
S3method(as.Splits,logical)
S3method(as.Splits,matrix)
S3method(as.Splits,multiPhylo)
S3method(as.Splits,phylo)
S3method(as.TreeNumber,character)
S3method(as.TreeNumber,multiPhylo)
S3method(as.TreeNumber,phylo)
S3method(as.character,Splits)
S3method(as.integer64,TreeNumber)
S3method(as.logical,Splits)
S3method(as.phylo,TreeNumber)
S3method(as.phylo,integer64)
S3method(as.phylo,numeric)
S3method(c,Splits)
S3method(duplicated,Splits)
S3method(length,Splits)
S3method(match,Splits)
S3method(match,default)
S3method(match,list)
S3method(names,Splits)
S3method(print,Splits)
S3method(print,TreeNumber)
S3method(summary,Splits)
S3method(unique,Splits)
export("%in%")
export(.CompatibleRaws)
export(.CompatibleSplit)
export(.RandomParent)
export(.UnrootedKeys)
export(AddTip)
export(AddTipEverywhere)
export(AllAncestors)
export(AllDescendantEdges)
export(AllTipLabels)
export(AncestorEdge)
export(ApePostorder)
export(ApeTime)
export(ArtEx)
export(ArtificialExtinction)
export(BalancedTree)
export(CharacterInformation)
export(CladeSizes)
export(Cladewise)
export(CladisticInfo)
export(CladisticInformation)
export(CollapseEdge)
export(CollapseNode)
export(CompatibleSplits)
export(ConsensusWithout)
export(DescendantEdges)
export(DoubleFactorial)
export(DoubleFactorial64)
export(DropTip)
export(EdgeAncestry)
export(EdgeDistances)
export(EnforceOutgroup)
export(ExtractTaxa)
export(ForestSplits)
export(IC1Spr)
export(LabelSplits)
export(LeafLabelInterchange)
export(ListAncestors)
export(LnDoubleFactorial)
export(LnDoubleFactorial.int)
export(LnRooted)
export(LnRooted.int)
export(LnSplitMatchProbability)
export(LnTreesMatchingSplit)
export(LnTreesMatchingTree)
export(LnUnrooted)
export(LnUnrooted.int)
export(LnUnrootedMult)
export(LnUnrootedSplits)
export(LnUnrootedTreesMatchingSplit)
export(Log2DoubleFactorial)
export(Log2Rooted)
export(Log2Rooted.int)
export(Log2TreesMatchingSplit)
export(Log2TreesMatchingTree)
export(Log2Unrooted)
export(Log2Unrooted.int)
export(Log2UnrootedMult)
export(Log2UnrootedSplits)
export(Log2UnrootedTreesMatchingSplit)
export(LogDoubleFactorial)
export(LogDoubleFactorial.int)
export(MRCA)
export(MSTEdges)
export(MSTLength)
export(MakeTreeBinary)
export(MarkMissing)
export(MatrixToPhyDat)
export(MultiSplitInformation)
export(N1Spr)
export(NDescendants)
export(NJTree)
export(NPartitionPairs)
export(NPartitions)
export(NRooted)
export(NRooted64)
export(NRootedShapes)
export(NSplits)
export(NTip)
export(NUnrooted)
export(NUnrooted64)
export(NUnrootedMult)
export(NUnrootedShapes)
export(NUnrootedSplits)
export(NewickTree)
export(NeworderPhylo)
export(NeworderPruningwise)
export(NexusTokens)
export(NodeDepth)
export(NodeOrder)
export(NonDuplicateRoot)
export(PairwiseDistances)
export(PectinateTree)
export(PhyDat)
export(PhyDatToMatrix)
export(PhyDatToString)
export(PhyToString)
export(PhydatToString)
export(PhylogeneticInfo)
export(PhylogeneticInformation)
export(Postorder)
export(PostorderEdges)
export(Preorder)
export(Pruningwise)
export(RandomTree)
export(ReadAsPhyDat)
export(ReadCharacters)
export(ReadTntAsPhyDat)
export(ReadTntCharacters)
export(ReadTntTree)
export(Renumber)
export(RenumberEdges)
export(RenumberTips)
export(RenumberTree)
export(RightmostCharacter)
export(RootNode)
export(RootNodeDist)
export(RootNodeDistance)
export(RootOnNode)
export(RootTree)
export(RootedTreeShape)
export(RootedTreeWithShape)
export(SampleOne)
export(SingleTaxonTree)
export(SisterSize)
export(SortTree)
export(SplitFrequency)
export(SplitImbalance)
export(SplitInformation)
export(SplitMatchProbability)
export(SplitNumber)
export(SplitsInBinaryTree)
export(StarTree)
export(StringToPhyDat)
export(Subsplit)
export(Subtree)
export(SupportColor)
export(SupportColour)
export(TCIContext)
export(TNTText2Tree)
export(TipLabels)
export(TipsInSplits)
export(TntText2Tree)
export(TotalCopheneticIndex)
export(TreeIsRooted)
export(TreeSplits)
export(TreesMatchingSplit)
export(TreesMatchingTree)
export(TrivialSplits)
export(UnrootTree)
export(UnrootedKeys)
export(UnrootedTreeKey)
export(UnrootedTreeShape)
export(UnrootedTreeWithKey)
export(UnrootedTreeWithShape)
export(UnrootedTreesMatchingSplit)
export(UnshiftTree)
export(WithoutTrivialSplits)
export(WriteTntCharacters)
export(as.Newick)
export(as.Splits)
export(as.TreeNumber)
export(doubleFactorials)
export(in.Splits)
export(logDoubleFactorials)
export(match)
export(replicate64)
export(sapply64)
export(vapply64)
importFrom(R.cache,addMemoization)
importFrom(Rdpack,reprompt)
importFrom(ape,as.phylo)
importFrom(ape,bind.tree)
importFrom(ape,collapse.singles)
importFrom(ape,consensus)
importFrom(ape,drop.tip)
importFrom(ape,edgelabels)
importFrom(ape,is.rooted)
importFrom(ape,nj)
importFrom(ape,read.tree)
importFrom(ape,reorder.phylo)
importFrom(ape,root)
importFrom(ape,write.tree)
importFrom(bit64,as.integer64)
importFrom(bit64,integer64)
importFrom(colorspace,diverge_hcl)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(phangorn,Ancestors)
importFrom(phangorn,Descendants)
importFrom(phangorn,dist.hamming)
importFrom(phangorn,phyDat)
importFrom(stats,as.dist)
importFrom(stats,runif)
importFrom(utils,globalVariables)
useDynLib(TreeTools, .registration = TRUE)
