Hi Maria.

I got part of the way to doing this with the function Map.Overlap (not to be confused with the related function, map.overlap) in phytools which should compute the quantities given in Table 2 of Huelsenbeck et al. The rest, I think should be straightforward to do - but I never got around to it. I will try but you may be able to figure it out yourself using Map.Overlap.


All the best, Liam

Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org

On 9/17/2016 2:40 PM, Maria Ghazali wrote:
Dear colleagues,

According to help, SIMMAP allows to test correlated evolution between two 
discrete traits with more than two levels 
(http://www.simmap.com/v1.0/pgs/hpgs/correlatedchars.html). Huelsenbeck et al. 
(2003: Stochastic Mapping of Morphological Characters. Syst.Biology, 
52(2):131–158) described this measure of association as D.

I do not have Mac, so I would like to know is there in R a function to evaluate 
D and its p value?

Thank you!

Best wishes,
Maria Ghazali

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