Hi Karla,
The original simple way to compare two clades, using phylogenetically
independent contrasts, is here. Newer methods may have higher power, but
this method is straightforward.
Garland, Jr., T. 1992. Rate tests for phenotypic evolution using
phylogenetically independent contrasts. The
_
De : R-sig-phylo <r-sig-phylo-boun...@r-project.org> de la part de Liam J.
Revell <liam.rev...@umb.edu>
Envoy� : dimanche 23 juillet 2017 04:07
� : Karla Shikev
Cc : R-sig-phylo@r-project.org
Objet : Re: [R-sig-phylo] comparing rates of evolution of a phenotypic trait
amon
Hi Karla.
This is not yet possible, but it would be straightforward to add. For
instance, we could let the user specify different models such as A==B!=C
vs. A!=B==C and so on, and then compare this models in a standard way. I
will try to do this soon and then get back to you & the list.
All
Thanks, Liam!
Just a quick follow-up question: in the example I saw on your webpage (with
three clades, one of which with a higher rate), how would you go about a
sort of "post-hoc" test to determine which clades differ significantly from
one another in their rates?
Karla
On Sat, Jul 22, 2017
Hi Karla.
phytools has a function called ratebytree for this. This essentially
corresponds to the 'censored' model of O'Meara et al. 2006, but we also
have a submitted manuscript describing it. I can send you that in a
second email.
For more information about using the function you can
Dear all,
I'd like to test whether the rate of evolution of a phenotypic trait (e.g.
body size) is significantly different among distantly-related clades (e.g.
mammals vs birds). I got tip data and completely resolved and callibrated
trees. One possibility would be to estimate rates and their
