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TreeDist (version 1.1.1)

Distances Between Phylogenetic Trees

Description

Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith, 2020) ; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) , including the Nye et al. (2006) metric ; the Matching Split Distance (Bogdanowicz & Giaro 2012) ; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance , and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) . Calculates the median of a set of trees under any distance metric.

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Install

install.packages('TreeDist')

Monthly Downloads

695

Version

1.1.1

License

GPL (>= 3)

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Maintainer

Martin R. Smith

Last Published

July 10th, 2020

Functions in TreeDist (1.1.1)

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