Hi Ben, I don’t think growTree() will help, I’m afraid. You might be able to get the inheritance rules to get the model right but there isn’t a way in growTree to simulate characters along an existing tree - the traits and topology are all simulated at the same time.
David On 20 Oct 2014, at 14:37, Ben Weinstein <[email protected]> wrote: > Hi all, > > There seem to be an ever growing number of functions for simulating > phylogenies along with traits and associated models of evolution. I'm > wondering different users suggestions for the simplest way to do the > following two cases. This is not for a full paper, but just a side > supporting analysis, so it doesn't have to be exhaustive. > > 1. Simulate a conserved trait (environmental tolerance) along a specified > sized phylogeny. > > 2. Simulate the same conserved trait along the same phylogeny but with the > additional of repulsion (character divergence) among closely related > species. > > Extra bonus would be if i could control the strength of phylogenetic > conservatism and character divergence in a nice array. > > If anyone has some general 'pseudo code' or package::function steps in this > direction i'd appreciate all feedback. > > I'm currently trying to use the growTree inheritance rules in caper, but i > haven't had much success. I've also tried tweaking the plgmm.sim function > in picante but i can't figure out what parameters would control the > repulsion and signal in the trait. > > Thanks, > > Ben Weinstein > > PS: Sorry if i double posted, wasn't sure which email address was signed > into the list. > > -- > Ben Weinstein > PhD Candidate > Ecology and Evolution > Stony Brook University > > http://benweinstein.weebly.com/ > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/[email protected]/ _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
