orthant.boundary.tree: Orthant Boundary Tree

Description

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

Usage

orthant.boundary.tree(x,y)

Arguments

The tree in the first orthant.

The tree in the second orthant.

Value

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

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.

References

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

Examples

Run this code

# NOT RUN {
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))
# }

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