MASTSize: Maximum Agreement Subtree size

In ms609/TreeDist: Calculate and Map Distances Between Phylogenetic Trees

Maximum Agreement Subtree size

Description

Calculate the size or phylogenetic information content \insertCiteSteel2006TreeDist of the maximum agreement subtree between two phylogenetic trees, i.e. the largest tree that can be obtained from both tree1 and tree2 by deleting, but not rearranging, leaves, using the algorithm of \insertCiteValiente2009;textualTreeDist.

Usage

MASTSize(tree1, tree2 = tree1, rooted = TRUE)

MASTInfo(tree1, tree2 = tree1, rooted = TRUE)

Arguments

tree1, tree2	Trees of class phylo, or lists of such trees to undergo pairwise comparison.
rooted	Logical specifying whether to treat the trees as rooted.

Details

Implemented for trees with up to 4096 tips. Contact the maintainer if you need to process larger trees.

Value

MASTSize() returns an integer specifying the number of leaves in the maximum agreement subtree.

MASTInfo() returns a vector or matrix listing the phylogenetic information content, in bits, of the maximum agreement subtree.

Author(s)

Martin R. Smith ([e-mail])

References

\insertAllCited

See Also

phangorn::mast(), a slower implementation that also lists the leaves contained within the subtree.

Other tree distances: JaccardRobinsonFoulds(), KendallColijn(), MatchingSplitDistance(), NNIDist(), NyeSimilarity(), PathDist(), Robinson-Foulds, SPRDist(), TreeDistance()

Examples

 # for as.phylo, BalancedTree, PectinateTree:
library("TreeTools", quietly = TRUE)

MASTSize(PectinateTree(8), BalancedTree(8))
MASTInfo(PectinateTree(8), BalancedTree(8))

MASTSize(BalancedTree(7), as.phylo(0:3, 7))
MASTSize(as.phylo(0:3, 7), PectinateTree(7))

MASTInfo(BalancedTree(7), as.phylo(0:3, 7))
MASTInfo(as.phylo(0:3, 7), PectinateTree(7))

MASTSize(list(Bal = BalancedTree(7), Pec = PectinateTree(7)),
         as.phylo(0:3, 7))
MASTInfo(list(Bal = BalancedTree(7), Pec = PectinateTree(7)),
         as.phylo(0:3, 7))

CompareAll(as.phylo(0:4, 8), MASTSize)
CompareAll(as.phylo(0:4, 8), MASTInfo)

ms609/TreeDist documentation built on April 5, 2024, 12:07 a.m.