TreeDist v1.1.1

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by Martin R. Smith View Source

Distances Between Phylogenetic Trees

Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith, 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Calculates the median of a set of trees under any distance metric.

Functions in TreeDist

Name	Description
JaccardRobinsonFoulds	Jaccard-Robinson-Foulds metric
ReportMatching	List clades as text
MatchingSplitDistance	Matching Split Distance
SplitSharedInformation	Shared information content of two splits
SplitsCompatible	Are splits compatible?
Robinson-Foulds	Robinson-Foulds distances, with adjustments for phylogenetic information content
LAPJV	Solve linear assignment problem using LAPJV
VisualizeMatching	Visualise a matching
MeilaVariationOfInformation	Use variation of clustering information to compare pairs of splits
.MASTSizeEdges	Calculate MAST size from edge matrices.
MASTSize	Maximum Agreement Subtree size
NyeSimilarity	Nye et al. (2006) tree comparison
PathDist	Path distance
Entropy	Entropy in bits
SPRDist	Approximate Subtree Prune and Regraft distance
GeneralizedRF	Generalized Robinson-Foulds distance
SplitEntropy	Entropy of two splits
SplitwiseInfo	Information content of splits within a tree
TreeDist-package	TreeDist: Distances between Phylogenetic Trees
NNIDist	Approximate Nearest Neighbour Interchange distance
ClusteringEntropy	Clustering entropy of all splits within a tree
NormalizeInfo	Normalize information against total present in both starting trees
TreeDistPlot	Plot a simple tree
CompareAll	Distances between each pair of trees
.TreeDistance	Calculate distance between trees, or lists of trees
.PairMean	Mean of two numbers
AllSplitPairings	Variation of information for all split pairings
median.multiPhylo	Median of a set of trees
TreeDistance	Information-based generalized Robinson-Foulds distances
CalculateTreeDistance	Wrapper for tree distance calculations
KendallColijn	Kendall-Colijn distance
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Vignettes of TreeDist

Name
Generalized-RF.Rmd
Robinson-Foulds.Rmd
Using-TreeDist.Rmd
information.Rmd
using-distances.Rmd
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Details

Type	Package
License	GPL (>= 3)
Copyright	Incorporates Jonker-Volgenant Linear Assignment Problem implementation by Roy Jonker, modified by Yong Yang after Yi Cao.
URL	https://ms609.github.io/TreeDist, https://github.com/ms609/TreeDist
BugReports	https://github.com/ms609/TreeDist/issues
Additional_repositories	https://ms609.github.io/packages
RdMacros	Rdpack
VignetteBuilder	knitr
LinkingTo	Rcpp
SystemRequirements	C++11
LazyData	true
ByteCompile	true
Encoding	UTF-8
Language	en-GB
X-schema.org-keywords	phylogenetics, tree-distance
RoxygenNote	7.1.1
NeedsCompilation	yes
Packaged	2020-07-09 13:16:53 UTC; ms609
Repository	CRAN
Date/Publication	2020-07-10 15:40:02 UTC

imports	ape (>= 5.0) , colorspace , memoise , phangorn (>= 2.2.1) , TreeTools (>= 1.1.0)
suggests	bookdown , cluster , kdensity , knitr , MASS , Quartet , Rcpp , Rdpack , rmarkdown , Ternary (>= 1.1.2) , testthat , TreeDistData (> 0.1.0) , TreeSearch , vdiffr
depends	R (>= 3.4.0) , stats
Contributors	Roy Jonker, Yong Yang, Yi Cao