TreeTools v1.4.1

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Create, Modify and Analyse Phylogenetic Trees

Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of node support; calculation of ancestor-descendant relationships; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.

Functions in TreeTools

Name Description
ArtificialExtinction Artificial Extinction
ApeTime Read modification time from 'ape' Nexus file
ConsensusWithout Consensus without taxa
CompatibleSplits Which splits are compatible?
AddTip Add a tip to a phylogenetic tree
AncestorEdge Ancestral edge
CladeSizes Clade sizes
CharacterInformation Character information content
ExtractTaxa Extract taxa from a matrix block
GenerateTree Generate pectinate, balanced or random trees
ListAncestors List ancestors
Lobo.data Data from Zhang et al. 2016
DescendantEdges Identify descendant edges
DoubleFactorial Double factorial
NSplits Number of distinct splits
NRooted Number of trees
NTip Number of leaves in a phylogenetic tree
NewickTree Write Newick Tree
RootTree Root or unroot a phylogenetic tree
RootNode Which node is a tree's root?
MatrixToPhyDat Convert between matrices and phyDat objects
EdgeDistances Distance between edges
MakeTreeBinary Generate binary tree by collapsing polytomies
EnforceOutgroup Generate a tree with a specific outgroup
Subsplit Subset of a split on fewer leaves
Neworder Reorder edges of a phylogenetic tree
DropTip Drop tips from tree
ReadTntTree Parse TNT Tree
ReadCharacters Read phylogenetic characters from file
unrootedKeys Integer representing shape of a tree
CladisticInfo Cladistic information content of a tree
TrivialSplits Identify and remove trivial splits
SplitInformation Phylogenetic information content of splitting leaves into two partitions
RenumberTree Reorder trees
SplitMatchProbability Probability of matching this well
UnrootedTreesMatchingSplit Number of trees consistent with split
NodeDepth Distance of each node from tree exterior
RightmostCharacter Rightmost character of string
EdgeAncestry Ancestors of an edge
LabelSplits Label splits
LeafLabelInterchange Leaf label interchange
TreeTools-package TreeTools
NJTree Generate a neighbour joining tree
.RandomParent Random parent vector
N1Spr Number of trees one SPR step away
CollapseNode Collapse nodes on a phylogenetic tree
brewer Brewer palettes
MSTEdges Minimum spanning tree
MRCA Most recent common ancestor
TreesMatchingTree Number of trees containing a tree
TreesMatchingSplit Number of trees matching a bipartition split
Subtree Extract a subtree
doubleFactorials Double factorials
NDescendants Count descendants for each node in a tree
logDoubleFactorials Natural logarithms of double factorials
SortTree Sort tree
SplitFrequency Frequency of splits
TipsInSplits Tips contained within splits
TotalCopheneticIndex Total Cophenetic Index
as.Splits Convert object to Splits
as.Newick Write a phylogenetic tree in Newick format
NPartitionPairs Distributions of tips consistent with a partition pair
StringToPhyDat Convert between strings and phyDat objects
PairwiseDistances Distances between each pair of trees
SampleOne Quickly sample
NodeOrder Order of each node in a tree
Renumber Renumber a tree's nodes and tips
NonDuplicateRoot Non-duplicate root
TipLabels Extract tip labels
RenumberTips Renumber a tree's tips
SupportColour Colour for node support value
UnshiftTree Add tree to start of list
SplitsInBinaryTree Maximum splits in an n-leaf tree
SingleTaxonTree Generate a single taxon tree
Stemwardness 'Stemwardness' of a leaf
TreeIsRooted Is tree rooted?
print.TreeNumber Print TreeNumber object
sapply64 Apply a function that returns 64-bit integers over a list or vector
WriteTntCharacters Write morphological character matrix to TNT file
match Split matching
TreeNumber Unique integer indices for bifurcating tree topologies
nRootedShapes Number of rooted / unrooted tree shapes
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Vignettes of TreeTools

Name
filesystem-navigation.Rmd
load-data.Rmd
load-trees.Rmd
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Details

License GPL (>= 3)
Copyright Incorporates C/C++ code from 'ape' by Emmanuel Paradis
URL https://ms609.github.io/TreeTools/, https://github.com/ms609/TreeTools/
BugReports https://github.com/ms609/TreeTools/issues/
SystemRequirements C++14
LinkingTo Rcpp
RdMacros Rdpack
LazyData true
ByteCompile true
Encoding UTF-8
Language en-GB
VignetteBuilder knitr
RoxygenNote 7.1.1
NeedsCompilation yes
Packaged 2020-12-08 16:13:44 UTC; ms609
Repository CRAN
Date/Publication 2020-12-09 08:30:20 UTC

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