R: Create, Modify and Analyse Phylogenetic Trees

# Create, Modify and Analyse Phylogenetic Trees

## Documentation for package ‘TreeTools’ version 1.5.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G I K L M N P R S T U V W misc

## -- A --

AddTip | Add a tip to a phylogenetic tree
AddTipEverywhere | Add a tip to a phylogenetic tree
AddUnconstrained | Force a tree to match a constraint
AllAncestors | List ancestors
AllDescendantEdges | Identify descendant edges
AllTipLabels | Extract tip labels
AllTipLabels.list | Extract tip labels
AllTipLabels.matrix | Extract tip labels
AllTipLabels.multiPhylo | Extract tip labels
AllTipLabels.phylo | Extract tip labels
AllTipLabels.Splits | Extract tip labels
AllTipLabels.TreeNumber | Extract tip labels
ApeTime | Read modification time from 'ape' Nexus file
ArtEx | Artificial Extinction
ArtificialExtinction | Artificial Extinction
ArtificialExtinction.matrix | Artificial Extinction
ArtificialExtinction.phyDat | Artificial Extinction
as.logical.Splits | Convert object to 'Splits'
as.multiPhylo | Convert object to 'multiPhylo' class
as.multiPhylo.list | Convert object to 'multiPhylo' class
as.multiPhylo.phyDat | Convert object to 'multiPhylo' class
as.multiPhylo.phylo | Convert object to 'multiPhylo' class
as.multiPhylo.Splits | Convert object to 'multiPhylo' class
as.Newick | Write a phylogenetic tree in Newick format
as.Newick.list | Write a phylogenetic tree in Newick format
as.Newick.multiPhylo | Write a phylogenetic tree in Newick format
as.Newick.phylo | Write a phylogenetic tree in Newick format
as.phylo.numeric | Unique integer indices for bifurcating tree topologies
as.phylo.TreeNumber | Unique integer indices for bifurcating tree topologies
as.Splits | Convert object to 'Splits'
as.Splits.list | Convert object to 'Splits'
as.Splits.logical | Convert object to 'Splits'
as.Splits.matrix | Convert object to 'Splits'
as.Splits.multiPhylo | Convert object to 'Splits'
as.Splits.phylo | Convert object to 'Splits'
as.Splits.Splits | Convert object to 'Splits'
as.TreeNumber | Unique integer indices for bifurcating tree topologies
as.TreeNumber.character | Unique integer indices for bifurcating tree topologies
as.TreeNumber.multiPhylo | Unique integer indices for bifurcating tree topologies
as.TreeNumber.phylo | Unique integer indices for bifurcating tree topologies

## -- B --

BalancedTree | Generate pectinate, balanced or random trees
brewer | Brewer palettes

## -- C --

CharacterInformation | Character information content
CladeSizes | Clade sizes
CladisticInfo | Cladistic information content of a tree
CladisticInfo.list | Cladistic information content of a tree
CladisticInfo.multiPhylo | Cladistic information content of a tree
CladisticInfo.phylo | Cladistic information content of a tree
CladisticInfo.Splits | Cladistic information content of a tree
CladisticInformation | Cladistic information content of a tree
CollapseEdge | Collapse nodes on a phylogenetic tree
CollapseNode | Collapse nodes on a phylogenetic tree
CollapseNode.phylo | Collapse nodes on a phylogenetic tree
Consensus | Consensus trees
ConsensusWithout | Reduced consensus, omitting specified taxa
ConsensusWithout.list | Reduced consensus, omitting specified taxa
ConsensusWithout.multiPhylo | Reduced consensus, omitting specified taxa
ConsensusWithout.phylo | Reduced consensus, omitting specified taxa
ConstrainedNJ | Constrained neighbour-joining tree

## -- D --

DescendantEdges | Identify descendant edges
DoubleFactorial | Double factorial
DoubleFactorial64 | Double factorial
doubleFactorials | Double factorials
DropTip | Drop tips from tree
DropTip.multiPhylo | Drop tips from tree
DropTip.phylo | Drop tips from tree

## -- E --

EdgeAncestry | Ancestors of an edge
EdgeDistances | Distance between edges
EndSentence | Add full stop to end of a sentence
EnforceOutgroup | Generate a tree with a specific outgroup
EnforceOutgroup.character | Generate a tree with a specific outgroup
EnforceOutgroup.phylo | Generate a tree with a specific outgroup

## -- F --

ForestSplits | Frequency of splits

## -- G --

GenerateTree | Generate pectinate, balanced or random trees

## -- I --

IC1Spr | Number of trees one SPR step away
ImposeConstraint | Force a tree to match a constraint
in.Splits | Split matching

## -- K --

KeepTip | Drop tips from tree

## -- L --

LabelSplits | Label splits
LeafLabelInterchange | Leaf label interchange
ListAncestors | List ancestors
LnDoubleFactorial | Double factorial
LnDoubleFactorial.int | Double factorial
LnRooted | Number of trees
LnRooted.int | Number of trees
LnSplitMatchProbability | Probability of matching this well
LnTreesMatchingSplit | Number of trees matching a bipartition split
LnTreesMatchingTree | Number of trees containing a tree
LnUnrooted | Number of trees
LnUnrooted.int | Number of trees
LnUnrootedMult | Number of trees
LnUnrootedSplits | Number of trees
LnUnrootedTreesMatchingSplit | Number of trees consistent with split
Lobo.data | Data from Zhang et al. 2016
Lobo.phy | Data from Zhang et al. 2016
Log2DoubleFactorial | Double factorial
Log2Rooted | Number of trees
Log2Rooted.int | Number of trees
Log2TreesMatchingSplit | Number of trees matching a bipartition split
Log2TreesMatchingTree | Number of trees containing a tree
Log2Unrooted | Number of trees
Log2Unrooted.int | Number of trees
Log2UnrootedMult | Number of trees
Log2UnrootedSplits | Number of trees
Log2UnrootedTreesMatchingSplit | Number of trees consistent with split
LogDoubleFactorial | Double factorial
LogDoubleFactorial.int | Double factorial
logDoubleFactorials | Natural logarithms of double factorials

## -- M --

MakeTreeBinary | Generate binary tree by collapsing polytomies
MarkMissing | Reduced consensus, omitting specified taxa
match | Split matching
match.list | Split matching
match.Splits | Split matching
MorphoBankDecode | Decode MorphoBank text
MRCA | Most recent common ancestor
MSTEdges | Minimum spanning tree
MSTLength | Minimum spanning tree
MultiSplitInformation | Phylogenetic information content of splitting leaves into two partitions

## -- N --

N1Spr | Number of trees one SPR step away
NDescendants | Count descendants for each node in a tree
NewickTree | Write Newick Tree
NJTree | Generate a neighbour joining tree
NodeDepth | Distance of each node from tree exterior
NodeOrder | Order of each node in a tree
NPartitionPairs | Distributions of tips consistent with a partition pair
NPartitions | Number of distinct splits
NRooted | Number of trees
NRooted64 | Number of trees
nRootedShapes | Number of rooted / unrooted tree shapes
NSplits | Number of distinct splits
NSplits.character | Number of distinct splits
NSplits.ClusterTable | Number of distinct splits
NSplits.list | Number of distinct splits
NSplits.multiPhylo | Number of distinct splits
NSplits.NULL | Number of distinct splits
NSplits.numeric | Number of distinct splits
NSplits.phylo | Number of distinct splits
NSplits.Splits | Number of distinct splits
NTip | Number of leaves in a phylogenetic tree
NTip.default | Number of leaves in a phylogenetic tree
NTip.list | Number of leaves in a phylogenetic tree
NTip.matrix | Number of leaves in a phylogenetic tree
NTip.multiPhylo | Number of leaves in a phylogenetic tree
NTip.phyDat | Number of leaves in a phylogenetic tree
NTip.phylo | Number of leaves in a phylogenetic tree
NTip.Splits | Number of leaves in a phylogenetic tree
NUnrooted | Number of trees
NUnrooted64 | Number of trees
NUnrootedMult | Number of trees
nUnrootedShapes | Number of rooted / unrooted tree shapes
NUnrootedSplits | Number of trees

## -- P --

PairwiseDistances | Distances between each pair of trees
PectinateTree | Generate pectinate, balanced or random trees
PhyDat | Read phylogenetic characters from file
PhyDatToString | Convert between strings and 'phyDat' objects
PhydatToString | Convert between strings and 'phyDat' objects
PhylogeneticInfo | Cladistic information content of a tree
PhylogeneticInformation | Cladistic information content of a tree
PhyToString | Convert between strings and 'phyDat' objects
PolarizeSplits | Polarize splits on a single taxon
print.TreeNumber | Print 'TreeNumber' object

## -- R --

RandomTree | Generate pectinate, balanced or random trees
ReadAsPhyDat | Read phylogenetic characters from file
ReadCharacters | Read phylogenetic characters from file
ReadNotes | Read phylogenetic characters from file
ReadTntAsPhyDat | Read phylogenetic characters from file
ReadTntCharacters | Read phylogenetic characters from file
ReadTntTree | Parse TNT Tree
Renumber | Renumber a tree's nodes and tips
RenumberTips | Renumber a tree's tips
RenumberTips.list | Renumber a tree's tips
RenumberTips.multiPhylo | Renumber a tree's tips
RenumberTips.NULL | Renumber a tree's tips
RenumberTips.phylo | Renumber a tree's tips
replicate64 | Apply a function that returns 64-bit integers over a list or vector
RightmostCharacter | Rightmost character of string
RootNode | Which node is a tree's root?
RootNodeDist | 'Stemwardness' of a leaf
RootNodeDistance | 'Stemwardness' of a leaf
RootNodeDistance.character | 'Stemwardness' of a leaf
RootNodeDistance.numeric | 'Stemwardness' of a leaf
RootOnNode | Root or unroot a phylogenetic tree
RootTree | Root or unroot a phylogenetic tree

## -- S --

sapply64 | Apply a function that returns 64-bit integers over a list or vector
SingleTaxonTree | Generate a single taxon tree
SisterSize | 'Stemwardness' of a leaf
SisterSize.character | 'Stemwardness' of a leaf
SisterSize.numeric | 'Stemwardness' of a leaf
SortTree | Sort tree
SortTree.list | Sort tree
SortTree.multiPhylo | Sort tree
SortTree.phylo | Sort tree
SplitFrequency | Frequency of splits
SplitImbalance | Tips contained within splits
SplitImbalance.phylo | Tips contained within splits
SplitImbalance.Splits | Tips contained within splits
SplitInformation | Phylogenetic information content of splitting leaves into two partitions
SplitMatchProbability | Probability of matching this well
SplitNumber | Frequency of splits
Splits | Convert object to 'Splits'
SplitsInBinaryTree | Maximum splits in an _n_-leaf tree
SplitsInBinaryTree.default | Maximum splits in an _n_-leaf tree
SplitsInBinaryTree.list | Maximum splits in an _n_-leaf tree
SplitsInBinaryTree.multiPhylo | Maximum splits in an _n_-leaf tree
SplitsInBinaryTree.NULL | Maximum splits in an _n_-leaf tree
SplitsInBinaryTree.numeric | Maximum splits in an _n_-leaf tree
SplitsInBinaryTree.phylo | Maximum splits in an _n_-leaf tree
SplitsInBinaryTree.Splits | Maximum splits in an _n_-leaf tree
StarTree | Generate pectinate, balanced or random trees
Stemwardness | 'Stemwardness' of a leaf
StringToPhyDat | Convert between strings and 'phyDat' objects
StringToPhydat | Convert between strings and 'phyDat' objects
Subsplit | Subset of a split on fewer leaves
Subtree | Extract a subtree
SupportColor | Colour for node support value
SupportColour | Colour for node support value

## -- T --

TCIContext | Total Cophenetic Index
TCIContext.numeric | Total Cophenetic Index
TipLabels | Extract tip labels
TipLabels.character | Extract tip labels
TipLabels.default | Extract tip labels
TipLabels.list | Extract tip labels
TipLabels.matrix | Extract tip labels
TipLabels.multiPhylo | Extract tip labels
TipLabels.numeric | Extract tip labels
TipLabels.phyDat | Extract tip labels
TipLabels.phylo | Extract tip labels
TipLabels.Splits | Extract tip labels
TipLabels.TreeNumber | Extract tip labels
TipsInSplits | Tips contained within splits
TipsInSplits.phylo | Tips contained within splits
TipsInSplits.Splits | Tips contained within splits
TNTText2Tree | Parse TNT Tree
TntText2Tree | Parse TNT Tree
TotalCopheneticIndex | Total Cophenetic Index
TreeIsRooted | Is tree rooted?
TreeNumber | Unique integer indices for bifurcating tree topologies
TreesMatchingSplit | Number of trees matching a bipartition split
TreesMatchingTree | Number of trees containing a tree
TreeSplits | Frequency of splits
TrivialSplits | Identify and remove trivial splits

## -- U --

Unquote | Remove quotation marks from a string
UnrootedTreesMatchingSplit | Number of trees consistent with split
UnrootTree | Root or unroot a phylogenetic tree
UnshiftTree | Add tree to start of list

## -- V --

vapply64 | Apply a function that returns 64-bit integers over a list or vector

## -- W --

WithoutTrivialSplits | Identify and remove trivial splits
WriteTntCharacters | Write morphological character matrix to TNT file
WriteTntCharacters.matrix | Write morphological character matrix to TNT file
WriteTntCharacters.phyDat | Write morphological character matrix to TNT file

## -- misc --

%in% | Split matching
%in%.Splits | Split matching