ape (version 5.8)

compute.brtime: Compute and Set Branching Times

Description

This function computes the branch lengths of a tree giving its branching times (aka node ages or heights).

Usage

compute.brtime(phy, method = "coalescent", force.positive = NULL)

Value

An object of class "phylo" with branch lengths and ultrametric.

Arguments

phy

an object of class "phylo".

method

either "coalescent" (the default), or a numeric vector giving the branching times.

force.positive

a logical value (see details).

Author

Emmanuel Paradis

Details

By default, a set of random branching times is generated from a simple coalescent, and the option force.positive is set to TRUE so that no branch length is negative.

If a numeric vector is passed to method, it is taken as the branching times of the nodes with respect to their numbers (i.e., the first element of method is the branching time of the node numbered \(n + 1\) [= the root], the second element of the node numbered \(n + 2\), and so on), so force.positive is set to FALSE. This may result in negative branch lengths. To avoid this, one should use force.positive = TRUE in which case the branching times are eventually reordered.

See Also

compute.brlen, branching.times

Examples

tr <- rtree(10)
layout(matrix(1:4, 2))
plot(compute.brtime(tr)); axisPhylo()
plot(compute.brtime(tr, force.positive = FALSE)); axisPhylo()
plot(compute.brtime(tr, 1:9)); axisPhylo() # a bit nonsense
plot(compute.brtime(tr, 1:9, TRUE)); axisPhylo()
layout(1)