Package index

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() DropTipPhylo() 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(): 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

Functions to navigate phylogenetic trees.

CladeSizes(): Clade sizes

DescendantEdges() DescendantTips() AllDescendantEdges(): Identify descendant edges

EdgeAncestry(): Ancestors of an edge

EdgeDistances(): Distance between edges

ListAncestors() AllAncestors(): List ancestors

MRCA(): Most recent common ancestor

MatchEdges() MatchNodes(): Match nodes and edges between trees

NDescendants(): Count descendants for each node in a tree

NodeDepth(): Distance of each node from tree exterior

NodeNumbers(): Numeric index of each node in a tree NodeNumbers() returns a sequence corresponding to the nodes in a tree

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() YuleTree() 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

J1Index() JQIndex(): Robust universal tree balance index

SisterSize() RootNodeDistance() RootNodeDist(): "Stemwardness" of a leaf

TotalCopheneticIndex() TCIContext(): Total Cophenetic Index

ConsensusWithout() MarkMissing(): Reduced consensus, omitting specified taxa

MatchEdges() MatchNodes(): Match nodes and edges between trees

NSplits() NPartitions(): Number of distinct splits

NTip(): Number of leaves in a phylogenetic tree

NodeNumbers(): Numeric index of each node in a tree NodeNumbers() returns a sequence corresponding to the nodes in a tree

PathLengths(): Calculate length of paths between each pair of vertices within tree

SplitsInBinaryTree(): 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

TopologyOnly(): Remove metadata from 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() DropTipPhylo() 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(): 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(): 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