orthant.boundary.tree: Orthant Boundary Tree

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/orthant.boundary.tree.R

Description

Produces a degenerate tree on the boundary between trees that differ by one split.

Usage

1

Arguments

x

The tree in the first orthant.

y

The tree in the second orthant.

Details

The tree found is the tree on the boundary between the two orthants such that it is on the straight line connecting the two trees when one orthant is thought of as being the (-,+) quadrant and the second orthant as being the (+,+) quadrant, where the (0,y) line is the particular boundary in question.

Value

Returns an object of class 'phylo' representing the boundary tree.

Author(s)

John Chakerian <[email protected]>

References

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

See Also

mcmc.target.seq

Examples

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data(woodmouse)
otree <- root(fastme.ols(dist.dna(woodmouse)), "No305", resolve.root=TRUE)
breps = 200

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)

binning <- bin.multiPhylo(combined.trees)

tree.a <- combined.trees[[match(1, binning)]]
i = 2
max.bin = max(binning)
tree.b <- combined.trees[[match(2, binning)]]

while(length(distinct.edges(tree.a,tree.b)) > 1 && i < max.bin)
{
    i = i + 1
    tree.b = combined.trees[[match(i, binning)]]
}

plot(orthant.boundary.tree(tree.a, tree.b))

distory documentation built on May 29, 2017, 10:19 p.m.