R: Orthant Boundary Tree

orthant.boundary.tree {distory} | R Documentation

## 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

`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

### 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

    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))

[Package distory version 1.4.4 Index]