[R-sig-phylo] generate liability/threshold plot from ancThresh

Hi folks, I'm trying to generate the thresholds and liabilities plot, including the posterior support values, from Revell (2014) Evolution 68(3), Figure 6B. Does anybody have a script for this? I see the liabilities output from ancThresh(), but no thresholds. Thanks! ~John John S. S.

Re: [R-sig-phylo] generate liability/threshold plot from ancThresh

Hi John. The posterior sample of the relative positions of the thresholds (if there is more than one) are output in the matrix par, i.e.: mcmc-ancThresh(...) mcmc$par ## contains the posterior sample of the thresholds To get a visualization of the posterior density you can, for instance,

[R-sig-phylo] problem with phylock package

Hi all: I am using the phylock package to read and plot a BEAST tree in R. I want to remove outgroups from my plot, therefore I used the extract.clade2() from the phylock package. But, when I try to plot the new phylogeny with the extracted clade, R quits unexpectedly. I have tried to plot that

Re: [R-sig-phylo] problem with phylock package

Hi Mariana, extract.clades2 hasn't been well tested. I wrote it for a specific dataset two years ago and I don't know if someone else has used it successfully. You can send me your tree off list and I'll see if I can fix it. Alternatively, you can identify the nodes concerned (?nodelabels,