compute.brlen {ape} | R Documentation |
This function computes branch lengths of a tree using different methods.
compute.brlen(phy, method = "Grafen", power = 1, ...)
phy |
an object of class |
method |
the method to be used to compute the branch lengths;
this must be one of the followings: (i) |
power |
The power at which heights must be raised (see below). |
... |
further argument(s) to be passed to |
Grafen's (1989) computation of branch lengths: each node is given a ‘height’, namely the number of leaves of the subtree minus one, 0 for leaves. Each height is scaled so that root height is 1, and then raised at power 'rho' (> 0). Branch lengths are then computed as the difference between height of lower node and height of upper node.
If one or several numeric values are provided as method
, they
are recycled if necessary. If a function is given instead, further
arguments are given in place of ...
(they must be named, see
examples).
Zero-length branches are not treated as multichotomies, and thus may
need to be collapsed (see di2multi
).
An object of class phylo
with branch lengths.
Julien Dutheil dutheil@evolbio.mpg.de and Emmanuel Paradis
Grafen, A. (1989) The phylogenetic regression. Philosophical Transactions of the Royal society of London. Series B. Biological Sciences, 326, 119–157.
read.tree
for a description of phylo
objects,
di2multi
, multi2di
data(bird.orders) plot(compute.brlen(bird.orders, 1)) plot(compute.brlen(bird.orders, runif, min = 0, max = 5)) layout(matrix(1:4, 2, 2)) plot(compute.brlen(bird.orders, power=1), main=expression(rho==1)) plot(compute.brlen(bird.orders, power=3), main=expression(rho==3)) plot(compute.brlen(bird.orders, power=0.5), main=expression(rho==0.5)) plot(compute.brlen(bird.orders, power=0.1), main=expression(rho==0.1)) layout(1)