Speaking of OUwie, the paper just came out today:
Jeremy M. Beaulieu, Dwueng-Chwuan Jhwueng, Carl Boettiger Brian C. OMeara.
MODELING STABILIZING SELECTION: EXPANDING THE ORNSTEIN-UHLENBECK MODEL OF
ADAPTIVE EVOLUTION. Evolution, Accepted Article, DOI:
10./j.1558-5646.2012.01619.x (link:
Hi Rafael.
I don't want to speak on behalf of the authors who are also on this
list, but OUwie can read in modified phylo objects created by the
phytools functions read.simmap make.simmap.
All the best, Liam
--
Liam J. Revell
University of Massachusetts Boston
web:
ah, I see. Thanks! Indeed, if I simulate trees with make.simmap or sim.history,
they work fine. But the trees I read in with read.simmap I still get the error:
OUwie(arv,randdat,model='BM1',simmap.tree=T)
Begin subplex optimization routine -- Starting value: 1
Error in which(edges[i, 5:(k + 4)]
Hi Rafael, Hi Liam~
Just wanted to quickly chime in by saying that yes, OUwie can read in SIMMAP
objects. This feature should be available in the current version posted on
CRAN. If not there you can definitely download it off R-Forge. Rafael -- let me
know if you have any issues, and don't
Thanks for the response, Liam. I just tried out OUwie and it works.
However, it appears to only fit 1 variable at a time (I only get one sigma
squared value).
When running some tests with OUCH, I found that sigma squared is different
when one variable is fit to an OU model, versus when multiple
Just wanted to note that there's a fundamental difference between the
way OUCH is handling the multivariate traits and the way geiger and
similar packages are handling it. If you're giving geiger a data
frame with multiple traits, it is fitting each independently, just
saving you the trouble from
That helps alot, Carl, thank you. So to bring this back to my original
question, it sounds like the only way to get sigma squared values from a
multivariate OU model is with OUCH. I'm currently not able to get results
because of convergence issues. Does that mean that I simply won't be able
to get
