Hi John.
There is no problem simulating discrete characters on non-ultrametric
trees. You can use sim.char in geiger, sim.history in phytools, or a
number of other functions, in fact.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 9/26/2016 4:11 PM, John Denton wrote:
Hi all,
I'm curious to know whether there is a function for evolving discrete character
data onto a non-ultrametric tree. I know sim.char() can technically produce
output given a non-ultrametric tree, and the documentation does not specify
that it is a requirement, but all the example trees I have seen applied with
this function are ultrametric.
What are the consequences of using sim.char() or similar functions on a tree
generated by something like rtree(), rather than rcoal() or sim.bdtree()? Are
there ways to make equivalencies, as through some kind of regression or
transformation?
Thanks!
~John
John S. S. Denton, Ph.D.
Department of Vertebrate Paleontology
American Museum of Natural History
www.johnssdenton.com
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