search for: outgroup

Hi, I am having difficulty entering a 'programmable' argument into the multinom function from the nnet package. Interactively, I can get the function to work fine by calling it this way: z1=multinom(formula = class.ind(grp[-outgroup])~ (PC1 + PC2 + PC3), data=data.frame(scores)) However I need to be able to change the number of variables I am looking for in 'scores' and so am trying to call it this way... z1=multinom(formula = class.ind(grp[-outgroup])~ eval(parse(text=PCnames)), data=data.frame(scores)) ...where, f...

I've been comparing variables among objects (taxa) related by known trees, using phylogentically independent contrasts in the ape package, and want to move on to more complex models e.g. by using gls with appropriate correlation terms. My trees contain lots of (hard) polytomies and information about ancestors, which I've been including- creating fully dichotomous trees by using zero branch