Re: [R-sig-phylo] seemingly conflicting output from BAMM

Hi Chris- Just to add to what Jonathan wrote. This is a good question. You have two basic issues that are being confounded: (1) how much evidence is there for a rate shift overall, versus (2) how much evidence do you have bearing on the locations of specific shifts. In your case, you have lim

Re: [R-sig-phylo] seemingly conflicting output from BAMM

Hi Krzysztof, It certainly can be true that the most credible shift configuration is one where there are no inferred rate shifts, but also prefer a model with one rate shift. The issue is mentioned in the BAMM documentation BAMM looks like it found eviden

Re: [R-sig-phylo] convergence in compar.gee (ape)

Dear Sereina, The number of iterations is not output by default. You can modify the function with fix(compar.gee), find this line: geemod <- do.call("gee", list(formula, and insert this command after it: cat("number of iterations:", geemod$iterations, "\n") save and close. HTH