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() KeepTip() DropTipPhylo() KeepTipPreorder() KeepTipPostorder(): Drop leaves from tree
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(): 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() 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
Cherries(): Count cherries in a tree
ConsensusWithout() MarkMissing(): Reduced consensus, omitting specified taxa
LongBranch(): Identify taxa with long branches
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?
Treeness() Stemminess(): Relative length of internal branches
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.

Decompose(): Decompose additive (ordered) phylogenetic characters
MatrixToPhyDat() PhyDatToMatrix(): Convert between matrices and phyDat objects
StringToPhyDat() StringToPhydat() PhyToString() PhyDatToString() PhydatToString(): Convert between strings and phyDat objects
Reweight(): Reweight phylogenetic characters
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() ReadTNTCharacters() ReadNotes() ReadAsPhyDat() ReadTntAsPhyDat() 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
MatchStrings(): Check for mismatch between character vectors
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() KeepTip() DropTipPhylo() KeepTipPreorder() KeepTipPostorder(): Drop leaves from tree
SplitConsistent() SplitConflicts(): Identify consistent / conflicting splits
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(): 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
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() 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(): 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.matrix(<ClusterTable>) print(<ClusterTable>) summary(<ClusterTable>): S3 methods for ClusterTable objects
as.ClusterTable(): Convert phylogenetic tree to ClusterTable
Hamming(): Hamming distance between taxa in a phylogenetic dataset
MSTEdges() MSTLength(): Minimum spanning tree
SampleOne(): Select element at random
TipTimedTree(): Display time-calibrated tree using tip information only
UnshiftTree(): Add tree to start of list
as.multiPhylo(): Convert object to multiPhylo class
match(<phylo>,<phylo>) match(<multiPhylo>,<phylo>) match(<phylo>,<multiPhylo>) match(<multiPhylo>,<multiPhylo>) `%in%`(<multiPhylo>,<multiPhylo>) `%in%`(<multiPhylo>,<phylo>) `%in%`(<phylo>,<multiPhylo>) `%in%`(<phylo>,<phylo>): Tree matching
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

Developer functions

Efficient functions without input checks, for developers

edge_to_splits(): Efficiently convert edge matrix to splits