Calculate and Map Distances Between Phylogenetic Trees

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Documentation for package ‘TreeDist’ version 2.7.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

AllSplitPairings	Variation of information for all split pairings
cluster-statistics	Cluster size statistics
ClusteringEntropy	Information content of splits within a tree
ClusteringEntropy.list	Information content of splits within a tree
ClusteringEntropy.multiPhylo	Information content of splits within a tree
ClusteringEntropy.phylo	Information content of splits within a tree
ClusteringEntropy.Splits	Information content of splits within a tree
ClusteringInfo	Information content of splits within a tree
ClusteringInfo.list	Information content of splits within a tree
ClusteringInfo.multiPhylo	Information content of splits within a tree
ClusteringInfo.phylo	Information content of splits within a tree
ClusteringInfo.Splits	Information content of splits within a tree
ClusteringInfoDist	Information-based generalized Robinson–Foulds distances
ClusteringInfoDistance	Information-based generalized Robinson–Foulds distances
CompareAll	Distances between each pair of trees
ConsensusInfo	Information content of splits within a tree
DifferentPhylogeneticInfo	Information-based generalized Robinson–Foulds distances
DistanceFromMedian	Cluster size statistics
DistFromMed	Cluster size statistics
Entropy	Entropy in bits
ExpectedVariation	Information-based generalized Robinson–Foulds distances
GetParallel	Calculate distances in parallel
InfoRobinsonFoulds	Robinson–Foulds distances, with adjustments for phylogenetic information content
InfoRobinsonFouldsSplits	Robinson–Foulds distances, with adjustments for phylogenetic information content
JaccardRobinsonFoulds	Jaccard–Robinson–Foulds metric
JaccardSplitSimilarity	Jaccard–Robinson–Foulds metric
KCDiameter	Kendall–Colijn distance
KCVector	Kendall–Colijn distance
KendallColijn	Kendall–Colijn distance
KMeansPP	k-means++ clustering
LAPJV	Solve linear assignment problem using LAPJV
LnTreesConsistentWithTwoSplits	Shared information content of two splits
Log2TreesConsistentWithTwoSplits	Shared information content of two splits
MappingQuality	Faithfulness of mapped distances
MapTrees	Graphical user interface for mapping distances and analysing tree space
MASTInfo	Maximum Agreement Subtree size
MASTSize	Maximum Agreement Subtree size
MatchingSplitDistance	Matching Split Distance
MatchingSplitDistanceSplits	Matching Split Distance
MatchingSplitInfo	Information-based generalized Robinson–Foulds distances
MatchingSplitInfoDistance	Information-based generalized Robinson–Foulds distances
MatchingSplitInfoSplits	Information-based generalized Robinson–Foulds distances
MeanCentDist	Cluster size statistics
MeanCentroidDist	Cluster size statistics
MeanCentroidDistance	Cluster size statistics
MeanMSTEdge	Cluster size statistics
MeanNN	Cluster size statistics
median.multiPhylo	Median of a set of trees
MeilaMutualInformation	Use variation of clustering information to compare pairs of splits
MeilaVariationOfInformation	Use variation of clustering information to compare pairs of splits
MSTSegments	Add minimum spanning tree to plot, colouring by stress
MutualClusteringInfo	Information-based generalized Robinson–Foulds distances
MutualClusteringInformation	Information-based generalized Robinson–Foulds distances
MutualClusteringInfoSplits	Information-based generalized Robinson–Foulds distances
NNIDiameter	Approximate Nearest Neighbour Interchange distance
NNIDist	Approximate Nearest Neighbour Interchange distance
NyeSimilarity	Nye _et al_. (2006) tree comparison
NyeSplitSimilarity	Nye _et al_. (2006) tree comparison
PathDist	Path distance
PathVector	Kendall–Colijn distance
PhylogeneticInfoDistance	Information-based generalized Robinson–Foulds distances
Plot3	Pseudo-3D plotting
Project	Graphical user interface for mapping distances and analysing tree space
ProjectionQuality	Faithfulness of mapped distances
Robinson-Foulds	Robinson–Foulds distances, with adjustments for phylogenetic information content
RobinsonFoulds	Robinson–Foulds distances, with adjustments for phylogenetic information content
RobinsonFouldsInfo	Robinson–Foulds distances, with adjustments for phylogenetic information content
RobinsonFouldsMatching	Robinson–Foulds distances, with adjustments for phylogenetic information content
RobinsonFouldsSplits	Robinson–Foulds distances, with adjustments for phylogenetic information content
SetParallel	Calculate distances in parallel
SharedPhylogeneticInfo	Information-based generalized Robinson–Foulds distances
SharedPhylogeneticInfoSplits	Information-based generalized Robinson–Foulds distances
SpectralClustering	Eigenvalues for spectral clustering
SpectralEigens	Eigenvalues for spectral clustering
SplitDifferentInformation	Shared information content of two splits
SplitEntropy	Entropy of two splits
SplitsCompatible	Are splits compatible?
SplitSharedInformation	Shared information content of two splits
SplitVector	Kendall–Colijn distance
SplitwiseInfo	Information content of splits within a tree
SPRDist	Approximate Subtree Prune and Regraft distance
StartParallel	Calculate distances in parallel
StopParallel	Calculate distances in parallel
StrainCol	Add minimum spanning tree to plot, colouring by stress
SumOfRanges	Cluster size statistics
SumOfVariances	Cluster size statistics
SumOfVars	Cluster size statistics
TreeDistance	Information-based generalized Robinson–Foulds distances
TreeInfo	Information content of splits within a tree
TreesConsistentWithTwoSplits	Shared information content of two splits
VisualizeMatching	Visualise a matching