Dear all Maybe someone has some insight here...
I am coming up against the problem, when it comes to phylogenetic analysis. Basically I want to conduct a parsimony (or other phylogenetic) analysis where "inapplicable" scores are treated as separate states *for each taxon* . I.e. I want to hypothesize shared ancestry for taxa scored with one state (let's say state 0), but not hypothesize shared ancestry for the other taxa. However, I still want to penalize a change in state from and to state 0. There are three approaches which I have thought about, but none seems to fit the bill: -Score all taxa not showing state 0 as separate states. This should do what I want, but the problem here is the limit on the number of states in most programmes. -Scoring binary presence/absence. The problem is here that it could end up being parsimonious to group the "absence" state together, when there is no reason to infer homology within (i.e. for taxa scored with) this state. -Score as 0 and inapplicable. The problem is this does not penalize a change from 0 to inapplicable. A real life example, is the shape of the ilium in crocodiles. I want to say that it is likely that a particular curve in the dorsal margin of the ilium in crocodile-line crocodilians is homologous, but I don't want to hypothesize homology of those taxa "lacking" this state. They are all equally far from each other. Thanks very much indeed Best Roland Sookias [[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/