I second Jon's suggestion for using phylogenetic mixed model. This seems to be
the closest to what Nicolay is after.
Yet another option is "SLOUCH" package in R, which can handle within-species
variation while performing phylogenetic corrections. Here are some example
Hope you will find a suitable solution from one of those.
> On 1 Aug 2018, at 14:37, jonnations <jonnati...@gmail.com> wrote:
> You will want to try Bayesian mixed modeling which can handle your species
> # problem by using “species” as a group level (i.e. “random”) effect. I
> would recommend r packages brms and MCMCglmm and their vignettes. Both have
> detailed “phylo” examples.
> Maybe check out the r-sig-mixed-model listserv as well. Lots of similar
> questions and good advice show up on there.
> Good luck!
> Jonathan A. Nations
> PhD Candidate
> Esselstyn Lab <http://www.museum.lsu.edu/esselstyn>
> Museum of Natural Sciences <http://sites01.lsu.edu/wp/mns>
> Louisiana State University
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