Orthant Boundary Tree
Produces a degenerate tree on the boundary between trees that differ by one split.
orthant.boundary.tree(x,y)
x |
The tree in the first orthant. |
y |
The tree in the second orthant. |
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.
Returns an object of class 'phylo' representing the boundary tree.
John Chakerian
Chakerian, J. and Holmes, S. P. Computational Tools for Evaluating Phylogenetic and Heirarchical Clustering Trees. arXiv:1006.1015v1.
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))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.