Hi Karla,
You may consider using the methods we developed in this paper:
Paradis E., Tedesco P. A. & Hugueny B. 2013. Quantifying variation in
speciation and extinction rates with clade data. Evolution 67: 3617–3627.
The associated R code is available on-line as SI of the paper.
Best,
Emmanuel
Le 08/01/2015 13:50, Karla Shikev a écrit :
Dear R-sig-phyloers,
I have a backbone phylogeny (~200 terminals) and diversity data (~20000
species) and a multistate character scored for each tip (including a few
polymorphisms). I'd like to estimate both possible effects of different
states of this character on lineage diversification and the transition
probabilities between states. My impression is that MuSSE wouldn't be able
to handle such high level of missing data, and other methods that I've
tried will either do one analysis or the other.
What methods would you suggest?
Thanks!
Karla
[[alternative HTML version deleted]]
_______________________________________________
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
_______________________________________________
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
