# Calculate and Map Distances Between Phylogenetic Trees

## Documentation for package ‘TreeDist’ version 2.11.0

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

## Help Pages

A C D E G H I J K L M N P R S T V

## -- A --

AHMI | Hierarchical Mutual Information
AllSplitPairings | Variation of information for all split pairings
as.HPart | Hierarchical partition structure
as.HPart.default | Hierarchical partition structure
as.HPart.HPart | Hierarchical partition structure
as.HPart.list | Hierarchical partition structure
as.HPart.phylo | Hierarchical partition structure
as.phylo.HPart | Hierarchical partition structure

## -- C --

clone | Clone / duplicate an object 'clone()' physically duplicates objects
clone.HPart | Clone / duplicate an object 'clone()' physically duplicates objects
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

## -- D --

DifferentPhylogeneticInfo | Information-based generalized Robinson–Foulds distances
DisplayMatching | Visualize a matching
DistanceFromMedian | Cluster size statistics
DistFromMed | Cluster size statistics

## -- E --

EHMI | Hierarchical Mutual Information
Entropy | Entropy in bits
ExpectedVariation | Information-based generalized Robinson–Foulds distances

## -- G --

GetParallel | Calculate distances in parallel

## -- H --

HierarchicalMutualInfo | Hierarchical Mutual Information
HMI | Hierarchical Mutual Information
HPart | Hierarchical partition structure

## -- I --

InfoRobinsonFoulds | Robinson–Foulds distances, with adjustments for phylogenetic information content
InfoRobinsonFouldsSplits | Robinson–Foulds distances, with adjustments for phylogenetic information content
is.HPart | Hierarchical partition structure
Islands | Find islands from distance matrix

## -- J --

JaccardRobinsonFoulds | Jaccard–Robinson–Foulds metric
JaccardSplitSimilarity | Jaccard–Robinson–Foulds metric

## -- K --

KCDiameter | Kendall–Colijn distance
KCVector | Kendall–Colijn distance
KendallColijn | Kendall–Colijn distance
KMeansPP | k-means++ clustering

## -- L --

LAPJV | Solve linear assignment problem using LAPJV
LnTreesConsistentWithTwoSplits | Shared information content of two splits
Log2TreesConsistentWithTwoSplits | Shared information content of two splits

## -- M --

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

## -- N --

NNIDiameter | Approximate Nearest Neighbour Interchange distance
NNIDist | Approximate Nearest Neighbour Interchange distance
Ntropy | Entropy in bits
NyeSimilarity | Nye _et al_. (2006) tree comparison
NyeSplitSimilarity | Nye _et al_. (2006) tree comparison

## -- P --

PathDist | Path distance
PathVector | Kendall–Colijn distance
PhylogeneticInfoDistance | Information-based generalized Robinson–Foulds distances
plot.HPart | Hierarchical partition structure
Plot3 | Pseudo-3D plotting
PlotMatching | Visualize a matching
print.HPart | Hierarchical partition structure
Project | Graphical user interface for mapping distances and analysing tree space
ProjectionQuality | Faithfulness of mapped distances

## -- R --

ReduceTrees | Collapse areas of agreement between two trees
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

## -- S --

SelfHMI | Hierarchical Mutual Information
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 the Subtree Prune and Regraft (SPR) distance.
SPRDist.list | Approximate the Subtree Prune and Regraft (SPR) distance.
SPRDist.multiPhylo | Approximate the Subtree Prune and Regraft (SPR) distance.
SPRDist.phylo | Approximate the Subtree Prune and Regraft (SPR) 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

## -- T --

TreeDistance | Information-based generalized Robinson–Foulds distances
TreeInfo | Information content of splits within a tree
TreesConsistentWithTwoSplits | Shared information content of two splits

## -- V --

VisualiseMatching | Visualize a matching
VisualizeMatching | Visualize a matching