Function reference • TreeDist

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()`	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
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?
`ClusteringEntropy()` `ClusteringInfo()`	Clustering entropy of all splits within a tree
`SplitEntropy()`	Entropy of two splits
`SplitSharedInformation()` `SplitDifferentInformation()` `TreesConsistentWithTwoSplits()` `LnTreesConsistentWithTwoSplits()`	Shared information content of two splits
`SplitwiseInfo()`	Information content of splits within a tree
Utility functions Functions to facilitate interaction with the package.
`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

Reference

Tree distance measures

Information

Utility functions