Luke Harmon said -- > Yes Emmanuel is correct, fitDiscrete does not deal with polymorphic data. I > have a fix that I made for a specific project that I'm sending to Charles, > if anyone else is interested email me off-list. It's very clunky.
I suspect this is not just a technical programming issue or a matter of standardizing formats of files, but depends on what you want to assume about the mode of evolution of a polymporphic character. Not a trivial matter at all, and not one where you just want to accept any old arbitrary rule. For example there is a very old (1967) parsimony method called "polymorphism parsimony" but it makes specific assumptions -- namely that polymorphism is hard to retain along a lineage, easy to lose but hard to regain. So do you want assume that, or what? Joe ---- Joe Felsenstein [email protected] Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA _______________________________________________ R-sig-phylo mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
