search for: polytomies

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 lengths. For instance: library(ape) tree<-read.tree(text="((B1:3,(((D1:5,C1:0):5,B2:0):4,(B3:3,B4:4):0):0):0,A1:0):0;") plot(tree) Where all the B taxa arise in a tru...

Dear all, I was testing the wonderful package APE. However upon testing a particular Newick's format tree - which I think to be a non-binary tree - it yields different result as expected. > library(ape) > tree.hiv <- read.tree(text="(rat,mouse,(human,chimp));") > is.binary.tree(tree.hiv) [1] TRUE Was that a bug in APE package? - Gundala Viswanath Jakarta - Indonesia

...ansformed proportions (there are a few reasons why I've chosen these with gaussian error over binomal glmm, which I won't go into). Each probability represents a response for a single plant species (c.150 species), and I want to incorporate the phylogeny (almost fully resolved with only 2 polytomies, including branch lengths) in the error structure. There is only 1 explanatory variable, a 5-level factor. I'm using uninformative priors for fixed parameters (i.e. not specifying any priors). Here's my code: #prior model1 prior1<-list(R = list(V = diag(2)*x, n=2), G = l...