# Calculate and Map Distances Between Phylogenetic Trees

## Documentation for package ‘TreeDist’ version 2.9.1

- 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
Islands | Find islands from distance matrix
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
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
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
TreeDistance | Information-based generalized Robinson–Foulds distances
TreeInfo | Information content of splits within a tree
TreesConsistentWithTwoSplits | Shared information content of two splits
VisualizeMatching | Visualize a matching