compute.brtime
Compute and Set Branching Times
This function computes the branch lengths of a tree giving its branching times (aka node ages or heights).
- Keywords
- manip
Usage
compute.brtime(phy, method = "coalescent", force.positive = NULL)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).
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.
Value
An object of class "phylo" with branch lengths and ultrametric.
See Also
Examples
# NOT RUN {
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)
# }