Tree distance measures

Functions for calculating distances between pairs of trees.

TreeDistance() SharedPhylogeneticInfo() DifferentPhylogeneticInfo() PhylogeneticInfoDistance() ClusteringInfoDistance() ExpectedVariation() MutualClusteringInfo() SharedPhylogeneticInfoSplits() MutualClusteringInfoSplits() MatchingSplitInfo() MatchingSplitInfoDistance() MatchingSplitInfoSplits()

Information-based generalized Robinson–Foulds distances

NyeSimilarity() NyeSplitSimilarity()

Nye et al. (2006) tree comparison

KendallColijn() KCVector() PathVector() SplitVector() KCDiameter()

Kendall–Colijn distance

MatchingSplitDistance() MatchingSplitDistanceSplits()

Matching Split Distance

JaccardRobinsonFoulds() JaccardSplitSimilarity()

Jaccard–Robinson–Foulds metric

MASTSize() MASTInfo()

Maximum Agreement Subtree size

NNIDist() NNIDiameter()

Approximate Nearest Neighbour Interchange distance

PathDist()

Path distance

InfoRobinsonFoulds() InfoRobinsonFouldsSplits() RobinsonFoulds() RobinsonFouldsMatching() RobinsonFouldsSplits()

Robinson–Foulds distances, with adjustments for phylogenetic information content

SPRDist()

Approximate Subtree Prune and Regraft distance

Tree space

Functions used for the construction, evaluation and exploration of tree space.

MapTrees() Project()

Graphical user interface for mapping distances and analysing tree space

MappingQuality() ProjectionQuality()

Quality of mapped distances

SpectralEigens() SpectralClustering()

Eigenvalues for spectral clustering

median(<multiPhylo>)

Median of a set of trees

Information

Functions addressing the information content and entropy of splits.

AllSplitPairings()

Variation of information for all split pairings

Entropy()

Entropy in bits

MeilaVariationOfInformation() MeilaMutualInformation()

Use variation of clustering information to compare pairs of splits

SplitsCompatible()

Are splits compatible?

SplitEntropy()

Entropy of two splits

SplitSharedInformation() SplitDifferentInformation() TreesConsistentWithTwoSplits() LnTreesConsistentWithTwoSplits() Log2TreesConsistentWithTwoSplits() Log2TreesConsistentWithTwoSplits()

Shared information content of two splits

SplitwiseInfo() ClusteringEntropy() ClusteringInfo() ConsensusInfo()

Information content of splits within a tree

Utility functions

Functions to facilitate interaction with the package.

Plot3()

Pseudo-3D plotting

as.ClusterTable()

Convert phylogenetic tree to ClusterTable

as.matrix(<ClusterTable>) print(<ClusterTable>) summary(<ClusterTable>)

S3 methods for ClusterTable objects

CompareAll()

Distances between each pair of trees

median(<multiPhylo>)

Median of a set of trees

LAPJV()

Solve linear assignment problem using LAPJV

VisualizeMatching()

Visualise a matching