Hi Martin.
Without more information or your input file, it's hard for me to
evaluate why read.simmap is hanging. Did you run:
tree-read.simmap(filename,format=nexus,version=1.5)
If you have your discrete character data in R, you can also use the
phytools function make.simmap to generate stochastic maps. Make sure
that you are using a recent version of phytools (=0.2-26; =0.2-33 for
uncertain/unknown tip states; =0.2-37 for non-symmetric transition
matrices) as earlier versions are buggy.
My advice would be to use make.simmap to generate stochastic maps (or
read them from file), and then use OUwie (in the package OUwie) to fit a
multiple optima OU model to each mapped tree.
For discrete character x and continuous trait y (each vectors in the
same order with names(x)=names(y)=species names); and a phylogeny, tree, do:
library(phytools)
library(OUwie)
mtrees-make.simmap(tree,x,nsim=100)
XX-data.frame(names(x),x,y)
result-lapply(mtrees,OUwie,data=XX,model=OUM,simmap.tree=TRUE)
This just gives you a giant list of the results returned by OUwie for
each tree. It would probably be a good idea to organize your results of
interest more sensibly than this so that they can be easily aggregated
across mappings.
Good luck. All the best, Liam
Liam J. Revell, Assistant 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 4/5/2013 6:13 PM, Martin Turcotte wrote:
Dear forum,
I am trying to conduct an ouch analysis and for it I must determine the
ancestral selective regime at each node in my tree. To do so I need to conduct
ancestral reconstruction on discrete unordered data. To my knowledge no package
can do this in R (I hope I am wrong) and thus I used Mesquite's function to
'Trace Character History'. The problem is exporting this information to R.
In Mesquite the only export option I see is 'Export Ancestral State
Trace' but the only option is SIMMAP 1.5 format. I tried opening this file
using phytools'read.simmap but it just hangs. I can open the file with
FigTree and I can see the Nodel labels but when I export the tree as a nexus
file it does not save the model labels.
Any advice would be appreciated.
thanks,
Mart
Martin Turcotte, Ph. D.
Dept. of Biology
University of Toronto at Mississauga
3359 Mississauga Road North, Mississauga,
Ontario, Canada, L5L 1C6
http://individual.utoronto.ca/martinturcotte
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