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.
lh On Apr 6, 2011, at 4:28 PM, Emmanuel Paradis wrote: > Hi, > > Charles Willis wrote on 06/04/2011 01:24: >> Hi, >> I want to run some comparative methods in R (ace, fitDiscrete, etc) on a >> categorical trait that has 6 states. >> My problem is that certain taxa are polymorphic for this trait (they have >> multiple states). Is there a way to code polymorphisms in R? I know you can >> code polymorphisms in Mesquite (e.g., 1&2) and in Bayestraits (e.g., 12), >> but I cannot seem to find a description on how to code similar data in R. >> Importing polymorphic data from Mesquite (read.nexus) doesn't appear to be >> an option. >> I plan to run the analyzes coding the trait as 6 independent binary traits, >> but I wanted to see if it was possible to run it as a polymorphic multistate >> trait as well. > > ace() takes multistate characters into account. Apparently not firDiscrete(). > > Best, > > Emmanuel > >> Thanks! >> Charlie >> Duke University >> Department of Biology >> 125 Science Drive >> Durham NC 27708 >> CP (605) 553-1057 >> [email protected] >> http://www.duke.edu/~cgw6/ >> [[alternative HTML version deleted]] >> _______________________________________________ >> R-sig-phylo mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > -- > Emmanuel Paradis > IRD, Jakarta, Indonesia > http://ape.mpl.ird.fr/ > > _______________________________________________ > R-sig-phylo mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Luke Harmon Assistant Professor Biological Sciences University of Idaho 208-885-0346 [email protected] _______________________________________________ R-sig-phylo mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
