I do not know offhand whether there is an R implementation, but how about
Mark Pagel's 1994 method for testing whether two 0/1 characters changing
along a ohylogeny are changing independently?
J.F.
-----
j...@gs.washington.edu
Joe Felsenstein, Department of Genome Sciences and Department of Biology
Box 355065, University of Washington, Seattle, WA 98195-5065
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