compute.brtime: Compute and Set Branching Times

View source: R/compute.brtime.R

compute.brtimeR Documentation

Compute and Set Branching Times


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


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



an object of class "phylo".


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


a logical value (see 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.


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


Emmanuel Paradis

See Also

compute.brlen, branching.times


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()

ape documentation built on March 31, 2023, 6:56 p.m.