bin.multiPhylo: Bin Trees

In distory: Distance Between Phylogenetic Histories

Bin Trees

Description

Bins trees according to branching topology.

Usage

bin.multiPhylo(treelist)

Arguments

treelist

A list of trees that can be passed to dist.phylo (see the help for dist.phylo for acceptable formats).

Details

Bins trees according to branching topology. Two trees are considered to have the same topology if the same set of partitions of tips are produced by the edges, which corresponds to the same branching up to rearrangement of tips.

Value

Returns a numeric vector of bin ids. Bin ids are assigned in order of the first tree in that bin, that is, the first k unique trees in the list passed will be assigned bins 1..k in order of appearance.

Author(s)

John Chakerian

References

Chakerian, J. and Holmes, S. P. Computational Tools for Evaluating Phylogenetic and Heirarchical Clustering Trees. arXiv:1006.1015v1.

See Also

dist.multiPhylo

Examples

data(woodmouse)
otree <- root(fastme.ols(dist.dna(woodmouse)), "No305", resolve.root=TRUE)
breps <- 500

trees <- boot.phylo(otree, woodmouse, B=breps, function(x)
        root(fastme.ols(dist.dna(x)), "No305", resolve.root=TRUE),trees=TRUE)

combined.trees <- c(list(otree), trees$trees)

bin.multiPhylo(combined.trees)

distory documentation built on Oct. 8, 2024, 1:07 a.m.