[R-sig-phylo] Colouring node pies according to a discrete character.

Dear list I am trying to plot the results of an ancestral state reconstruction of 4 discrete traits onto a single phylogeny. What I would like to do is have a pie on each node split into 4 equal segments, and then have the colour of each segment correspond to the probable trait value at that

[R-sig-phylo] What order are the tips of a tree plotted in?

Dear List I am trying to plot two trees facing each other with pie charts at the nodes indicating marginal likelihoods of an ancestral state. I have broken the plotting frame into 3 sections, with one in the centre for the tip labels. I am using text(rep()) to plot the tip labels into this

[R-sig-phylo] utilise more data by making polytomies

Hi All I have a large dataset and a large tree, however the intersection between them both is quite low. As a supplement to analyses solely on the species that appear in both the dataset and the tree I thought I could take the species that are present in the dataset and not the tree, and add

[R-sig-phylo] PGLS on a sample of trees

Hi I used the method of Kuhn et al (2011) to resolve polytomies in my tree leaving me with a posterior of thousands of trees. I was wondering how I would go about using PGLS on a sample of these trees so that the uncertainty in the resolution of the polytomies is incorporated into my analysis