Hello Tom,
I will answer some of your questions below, Emmanuel and others may be better
placed to reply to some of your questions:
On 12, Mar 2012, at 7:49 PM, Tom Schoenemann wrote:
Thanks Rob and Alejandro,
OK, I did as suggested and ran a PGLS with A ~ B + C. I was hoping for some
Dear Diogo,
the following function should give you the p-values (physo.obs.p) you
are looking for:
# obs : observed phylosor-values (distance matrix)
# rand : list of distance matrices from the phylosor.rnd-function
ses.physo - function(obs, rand){
rand - t(as.data.frame(lapply(rand,
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
Hi,
thanks Rafael and Emmanuel for further input into this problem. I have
followed Rafael's advice and tried to use MCMCglmm with the help of
Shinichi Nakagawa. This seems to provide again sensible results, however
I would also be interested in following the procedure suggested by
Emmanuel,
The Call for Lightning Talks is now open for the 2012 conference on Informatics
for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at
http://ievobio.org/ocs2/index.php/ievobio/2012. See below for instructions.
Lightning talks are short presentations of 5 minutes. They are ideal for
