Hi,
I think the biggest problem you'll have is interpreting the results, which I
suspect will get very complicated very quickly.
Nevertheless, if you have specific hypotheses you could feasibly build and
compare models representing them using the rayDISC function in corHMM, a bit
like a standard Pagel's test but with careful thought given to the alternative
models (and see Maddison and FitzJohn's recent warning about such tests).
An alternative might be to look at MCMCglmm (in the package of the same name)
to build a GLMM with a categorical response, but as before, I think the
interpretation will be the biggest issue. In any case, maybe other's will have
better/other suggestions?
Best wishes,
Kev
----------------------------------------------------------------------
Message: 1
Date: Fri, 22 Apr 2016 20:52:34 +0000
From: "Wu, Cheng-Chiang" <c...@oeb.harvard.edu>
To: "r-sig-phylo@r-project.org" <r-sig-phylo@r-project.org>
Subject: [R-sig-phylo] R package for testing correlation between two
multistate discrete traits on a phylogeny?
Message-ID: <676168f4-2036-45f4-9aa0-1ae29172b...@oeb.harvard.edu>
Content-Type: text/plain; charset="us-ascii"
I would like to test correlation between two multistate discrete traits (one of
four states and the other with five states) on a phylogeny.
To the best of my current knowledge, I could only find functions of R packages
for comparing continuous or/and binary discrete traits.
May I ask if anyone is aware of any function of R package that could compare
multistate discrete traits?
Thanks,
Cheng-Chiang Wu
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