compute.brtime {ape} | R Documentation |
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)
phy |
an object of class |
method |
either |
force.positive |
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
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() layout(1)