[R-sig-phylo] Multistate Trait Polymorphism

Luke Harmon lukeh at uidaho.edu
Fri Apr 8 08:47:38 CEST 2011

Yes Joe is correct, there is more to this problem than meets the eye. My implementation assumes equal probability of each unknown state, which is quite different from modeling an actual polymorphic character. I'm sure that doing something different might matter in many cases.


On Apr 7, 2011, at 8:14 AM, Joe Felsenstein wrote:

> 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         joe at gs.washington.edu
> Department of Genome Sciences and Department of Biology,
> University of Washington, Box 355065, Seattle, WA 98195-5065 USA

Luke Harmon
Assistant Professor
Biological Sciences
University of Idaho
lukeh at uidaho.edu

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