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)
# }