TreeDist v1.1.1

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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

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