Function reference • TreeTools

Tree manipulation Functions for editing phylogenetic trees.
`AddTip()` `AddTipEverywhere()`	Add a tip to a phylogenetic tree
`CollapseNode()` `CollapseEdge()`	Collapse nodes on a phylogenetic tree
`ConsensusWithout()` `MarkMissing()`	Reduced consensus, omitting specified taxa
`DropTip` `DropTip.phylo` `DropTip.Splits` `DropTipPhylo` `DropTip.multiPhylo` `DropTip.list` `DropTip.NULL` `KeepTipPreorder` `KeepTipPostorder` `KeepTip`	Drop leaves from tree
`EnforceOutgroup()`	Generate a tree with a specified outgroup
`ImposeConstraint()` `AddUnconstrained()`	Force a tree to match a constraint
`KeptPaths()`	Paths present in reduced tree
`KeptVerts()`	Identify vertices retained when leaves are dropped
`LeafLabelInterchange()`	Leaf label interchange
`MakeTreeBinary()`	Generate binary tree by collapsing polytomies
`Renumber()`	Renumber a tree's nodes and tips
`RenumberTips` `RenumberTips.phylo` `RenumberTips.multiPhylo` `RenumberTips.list` `RenumberTips.NULL`	Renumber a tree's tips
`RootTree()` `RootOnNode()` `UnrootTree()`	Root or unroot a phylogenetic tree
`SortTree()`	Sort tree
`Subtree()`	Extract a subtree
`TipTimedTree()`	Display time-calibrated tree using tip information only
`SingleTaxonTree()` `ZeroTaxonTree()`	Generate trivial trees
Tree navigation Functions to navigate phylogenetic trees.
`CladeSizes()`	Clade sizes
`DescendantEdges()` `AllDescendantEdges()`	Identify descendant edges
`EdgeAncestry()`	Ancestors of an edge
`EdgeDistances()`	Distance between edges
`ListAncestors()` `AllAncestors()`	List ancestors
`MRCA()`	Most recent common ancestor
`NDescendants()`	Count descendants for each node in a tree
`NodeDepth()`	Distance of each node from tree exterior
`NodeOrder()`	Number of edges incident to each node in a tree
`RootNode()`	Which node is a tree's root?
Tree creation Functions to generate phylogenetic trees.
`ConstrainedNJ()`	Constrained neighbour-joining tree
`RandomTree()` `PectinateTree()` `BalancedTree()` `StarTree()`	Generate pectinate, balanced or random trees
`NJTree()`	Generate a neighbour joining tree
`as.TreeNumber()` `as.phylo(<numeric>)` `as.phylo(<TreeNumber>)` `as.MixedBase()` `as.phylo(<MixedBase>)`	Unique integer indices for bifurcating tree topologies
`SingleTaxonTree()` `ZeroTaxonTree()`	Generate trivial trees
`is.TreeNumber()`	Is an object a `TreeNumber` object?
`print(<TreeNumber>)`	Print `TreeNumber` object
Tree properties Functions describing properties of trees.
`CladisticInfo()` `PhylogeneticInfo()` `PhylogeneticInformation()` `CladisticInformation()`	Cladistic information content of a tree
`Consensus()`	Construct consensus trees
`SisterSize()` `RootNodeDistance()` `RootNodeDist()`	"Stemwardness" of a leaf
`TotalCopheneticIndex()` `TCIContext()`	Total Cophenetic Index
`ConsensusWithout()` `MarkMissing()`	Reduced consensus, omitting specified taxa
`NSplits` `NPartitions` `NSplits.phylo` `NSplits.list` `NSplits.multiPhylo` `NSplits.Splits` `NSplits.numeric` `NSplits.NULL` `NSplits.ClusterTable` `NSplits.character`	Number of distinct splits
`NTip()`	Number of leaves in a phylogenetic tree
`PathLengths()`	Calculate length of paths between each pair of vertices within tree
`SplitsInBinaryTree` `SplitsInBinaryTree.list` `SplitsInBinaryTree.multiPhylo` `SplitsInBinaryTree.numeric` `SplitsInBinaryTree.NULL` `SplitsInBinaryTree.default` `SplitsInBinaryTree.Splits` `SplitsInBinaryTree.phylo`	Maximum splits in an n-leaf tree
`TipLabels()` `AllTipLabels()`	Extract tip labels
`TreeIsRooted()`	Is tree rooted?
`RoguePlot()`	Visualize position of rogue taxa
`PairwiseDistances()`	Distances between each pair of trees
Phylogenetic data Functions for modifying and evaluating datasets.
`MatrixToPhyDat()` `PhyDatToMatrix()`	Convert between matrices and `phyDat` objects
`StringToPhyDat()` `StringToPhydat()` `PhyToString()` `PhyDatToString()` `PhydatToString()`	Convert between strings and `phyDat` objects
`ArtificialExtinction()` `ArtEx()`	Artificial Extinction
Parsers Functions to parse or write files.
`as.Newick()`	Write a phylogenetic tree in Newick format
`ApeTime()`	Read modification time from "ape" Nexus file
`ExtractTaxa()` `NexusTokens()`	Extract taxa from a matrix block
`NewickTree()`	Write Newick Tree
`ReadCharacters()` `ReadTntCharacters()` `ReadNotes()` `ReadAsPhyDat()` `ReadTntAsPhyDat()` `PhyDat()`	Read phylogenetic characters from file
`StringToPhyDat()` `StringToPhydat()` `PhyToString()` `PhyDatToString()` `PhydatToString()`	Convert between strings and `phyDat` objects
`ReadTntTree()` `TntText2Tree()` `TNTText2Tree()`	Parse TNT Tree
`WriteTntCharacters()`	Write morphological character matrix to TNT file
`EndSentence()`	Add full stop to end of a sentence
`MorphoBankDecode()`	Decode MorphoBank text
`RightmostCharacter()`	Rightmost character of string
`Unquote()`	Remove quotation marks from a string
`ReadMrBayesTrees()` `ReadMrBayes()` `MrBayesTrees()`	Read posterior tree sample produced by MrBayes
Split manipulation Functions that manipulate bipartition splits.
`DropTip` `DropTip.phylo` `DropTip.Splits` `DropTipPhylo` `DropTip.multiPhylo` `DropTip.list` `DropTip.NULL` `KeepTipPreorder` `KeepTipPostorder` `KeepTip`	Drop leaves from tree
`Subsplit()`	Subset of a split on fewer leaves
`TrivialSplits()` `WithoutTrivialSplits()`	Identify and remove trivial splits
`LabelSplits()`	Label splits
`NSplits` `NPartitions` `NSplits.phylo` `NSplits.list` `NSplits.multiPhylo` `NSplits.Splits` `NSplits.numeric` `NSplits.NULL` `NSplits.ClusterTable` `NSplits.character`	Number of distinct splits
`NTip()`	Number of leaves in a phylogenetic tree
`PolarizeSplits()`	Polarize splits on a single taxon
`SplitFrequency()` `SplitNumber()` `ForestSplits()` `TreeSplits()`	Frequency of splits
`as.Splits()` `as.logical(<Splits>)`	Convert object to `Splits`
`SplitsInBinaryTree` `SplitsInBinaryTree.list` `SplitsInBinaryTree.multiPhylo` `SplitsInBinaryTree.numeric` `SplitsInBinaryTree.NULL` `SplitsInBinaryTree.default` `SplitsInBinaryTree.Splits` `SplitsInBinaryTree.phylo`	Maximum splits in an n-leaf tree
`TipLabels()` `AllTipLabels()`	Extract tip labels
`TipsInSplits()` `SplitImbalance()`	Tips contained within splits
`in.Splits()` `match()` `%in%`(<Splits>,<Splits>)	Split matching
`xor()`	Exclusive OR operation
Information and combinatorics Functions to calculate factorial quantities.
`N1Spr()` `IC1Spr()`	Number of trees one SPR step away
`DoubleFactorial()` `DoubleFactorial64()` `LnDoubleFactorial()` `Log2DoubleFactorial()` `LogDoubleFactorial()` `LnDoubleFactorial.int()` `LogDoubleFactorial.int()`	Double factorial
`NPartitionPairs()`	Distributions of tips consistent with a partition pair
`CladisticInfo()` `PhylogeneticInfo()` `PhylogeneticInformation()` `CladisticInformation()`	Cladistic information content of a tree
`NRooted()` `NUnrooted()` `NRooted64()` `NUnrooted64()` `LnUnrooted()` `LnUnrooted.int()` `Log2Unrooted()` `Log2Unrooted.int()` `LnRooted()` `LnRooted.int()` `Log2Rooted()` `Log2Rooted.int()` `LnUnrootedSplits()` `Log2UnrootedSplits()` `NUnrootedSplits()` `LnUnrootedMult()` `Log2UnrootedMult()` `NUnrootedMult()`	Number of trees
`TreesMatchingTree()` `LnTreesMatchingTree()` `Log2TreesMatchingTree()`	Number of trees containing a tree
`CharacterInformation()`	Character information content
`SplitInformation()` `MultiSplitInformation()`	Phylogenetic information content of splitting leaves into two partitions
`SplitMatchProbability()` `LnSplitMatchProbability()`	Probability of matching this well
`TreesMatchingSplit()` `LnTreesMatchingSplit()` `Log2TreesMatchingSplit()`	Number of trees matching a bipartition split
`UnrootedTreesMatchingSplit()` `LnUnrootedTreesMatchingSplit()` `Log2UnrootedTreesMatchingSplit()`	Number of trees consistent with split
Split support Calculate and depict support for splits (‘edges’ / ‘nodes’) in trees.
`LabelSplits()`	Label splits
`SplitFrequency()` `SplitNumber()` `ForestSplits()` `TreeSplits()`	Frequency of splits
`SupportColour()` `SupportColor()`	Colour for node support value
Datasets Data that accompanies the package.
`brewer`	Brewer palettes
`doubleFactorials`	Double factorials
`Lobo.data` `Lobo.phy`	Data from Zhang et al. 2016
`logDoubleFactorials`	Natural logarithms of double factorials
`nRootedShapes` `nUnrootedShapes`	Number of rooted / unrooted tree shapes
Utility functions Miscellaneous functions to simplify or expedite basic functionality.
`as.multiPhylo()`	Convert object to `multiPhylo` class
`as.ClusterTable()`	Convert phylogenetic tree to `ClusterTable`
`as.matrix(<ClusterTable>)` `print(<ClusterTable>)` `summary(<ClusterTable>)`	S3 methods for `ClusterTable` objects
`Hamming()`	Hamming distance between taxa in a phylogenetic dataset
`MSTEdges()` `MSTLength()`	Minimum spanning tree
`RightmostCharacter()`	Rightmost character of string
`SampleOne()`	Quickly sample
`sapply64()` `vapply64()` `replicate64()`	Apply a function that returns 64-bit integers over a list or vector
`sort(<multiPhylo>)` `==`(<phylo>) `<`(<phylo>) `>`(<phylo>) `==`(<MixedBase>) `<`(<MixedBase>) `>`(<MixedBase>)	Sort a list of phylogenetic trees
`UnshiftTree()`	Add tree to start of list
Developer functions Efficient functions without input checks, for developers
`edge_to_splits()`	Efficiently convert edge matrix to splits

Reference

Tree manipulation

Tree navigation

Tree creation

Tree properties

Phylogenetic data

Parsers

Split manipulation

Information and combinatorics

Split support

Datasets

Utility functions

Developer functions