There's also the rayDISC function in the corHMM package. It can take in polymorphic data (so you can have some taxa red, some white, some red & white). Note that along the tree, it assumes that there's one state. If you wanted ancestral nodes to be validly polymorphic (not just equal chances of red and white, but a character red+white), you'd need to do as Liam suggests and create a polymorphic trait and an ordered state matrix. This is possible in ace() in ape, rayDISC() in corHMM, and probably others.
Best, Brian _______________________________________ Brian O'Meara Assistant Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Postdoc collaborators wanted: http://nimbios.org/postdocs/ Calendar: http://www.brianomeara.info/calendars/omeara On Wed, Mar 25, 2015 at 10:49 AM, Liam J. Revell <liam.rev...@umb.edu> wrote: > Hi Matt. > > What is the purpose of this? To visualize the states on the tree? Or to > conduct some kind of analysis (modeling evolution, reconstructing ancestral > states, etc.) on the tree? > > If the former, then you can use tiplabels in the ape package, and supply a > matrix to the argument pie in which each row is a tip taxon and each column > is a state. For non-polymorphic species you can just put a 1 in the column > for the state of that taxon, and zero otherwise; and for polymorphic taxa > you can put 1/(number of states in that species) - or the state > frequencies, if you have them - for each state found in that species, and > zero otherwise. > > If you're interested in, for example, reconstructing ancestral states, > then it may in fact make the most sense to treat polymorphism as another > state. In that case, you must decide if you will, for instance, require > that transitions from A -> B first pass through state AB, etc. This kind of > constraint is fairly straightforward to implement in ape's ace function. > > Let us know & I will see if I can give you any more concrete suggestions. > > All the best, Liam > > Liam J. Revell, Assistant 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 3/25/2015 7:38 AM, Koski, Matthew H wrote: > >> Hi, >> >> >> I'd like to assign multiple discrete character states to tips that are >> polymorphic. E.g., color in a given species is polymorphic (pink or white) >> so it is assigned two states for color. Is there a way to do this without >> creating an extra 'polymorphic' category? >> >> >> There is a similar question on stackoverflow with no responses yet: >> >> http://stackoverflow.com/questions/27413070/how-to- >> assign-multiple-states-for-taxa-in-discrete-character-data-set? >> >> ? >> >> ?Thanks in advance, >> >> Matt >> >> >> Matthew Koski >> University of Pittsburgh >> Biological Sciences >> Ashman Lab >> koskimatt.wix.com/matthewhkoski<http://koskimatt.wix.com/matthewhkoski> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-sig-phylo mailing list - R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> Searchable archive at http://www.mail-archive.com/r- >> sig-ph...@r-project.org/ >> >> > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
