Rich FitzJohn has programmed something of what Will suggested in
diversitree: look at details in ?make.musse.multitrait. I'm not sure if
there was ever a paper published on this. We do a similar thing to Will's
idea in http://rspb.royalsocietypublishing.org/content/283/1830/20152304
(with the added complication of varying over combinations of traits, since
converting six binary traits to a 2^6 state musse model would have been a
bit ambitious given the data size [or, frankly, given any possible sampling
from the tree of life]). However, neither approach deals with hidden
sources of rate heterogeneity. Jeremy Beaulieu and Daniel Caetano are
always adding stuff to hisse that deals with hidden rates (see
preprint on a hidden
biogeography model at
https://www.biorxiv.org/content/early/2018/04/17/302729), but I don't think
anything has been peer-reviewed and published yet for this use case (I
think the core hisse model is also in RevBayes, and that may have added
options making a musse version possible). If your tree is big enough,
separating it into clades and seeing if the pattern (i.e., when converting
00 -> 1, 01 -> 2, 10 -> 3, 11 -> 4 for musse, and you find that state 3
(aka binary states 10) has highest diversification rate) is consistent
across the clades could be a good way of seeing if there are some kinds of
heterogeneity that matter.

Best,
Brian

_______________________________________________________________________
Brian O'Meara, http://www.brianomeara.info, especially Calendar
<http://brianomeara.info/calendars/omeara/>, CV
<http://brianomeara.info/cv/>, and Feedback
<http://brianomeara.info/teaching/feedback/>

Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Director for Postdoctoral Activities, National Institute for
Mathematical & Biological Synthesis <http://www.nimbios.org> (NIMBioS)



On Tue, Jun 19, 2018 at 2:03 AM Gilles Benjamin Leduc <g...@hi.is> wrote:

> Hello,
>
> Personally, I would advise you not to use a tree, for your 2 traits times
> 2 (+/-) makes 4 combinations, meaning a tree that is dichotomic cannot
> reveal anything!  Can you quantify your "diversification" without "rate"?
> How do you obtain your  "diversification rates"? If it is something you can
> count, you may try an old fashion Khi-square test… you would then know if
> there is a correlation…
>
> Have a nice day,
>
> Benjamin
>
>
> Le Lundi 18 Juin 2018 23:46 GMT, Elizabeth Christina Miller <
> ecmil...@email.arizona.edu> a écrit:
>
> > Hello,
> >
> > I am wondering what comparative method(s) is appropriate for testing if
> > diversification rates are highest when two traits are present together,
> > rather than one alone? Specifically, if I have two binary traits, let's
> say
> > freshwater/marine and temperate/tropical, what is the best way to test if
> > diversification rates are highest in tropical+freshwater groups, as
> opposed
> > to tropical+marine or temperate+freshwater? I think MuSSE can do this,
> but
> > my tree is large so I want to avoid issues associated with rate
> > heterogeneity. Are there any alternatives?
> >
> >
> >
> > --
> > Elizabeth Miller
> > PhD Candidate: Wiens Lab
> > Ecology and Evolutionary Biology
> > University of Arizona
> >
> >       [[alternative HTML version deleted]]
> >
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