[R-sig-phylo] Simulated phylogenies with character divergence
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 'psudeo code' or package::function steps in this direction i'd appreciate all feedback. Thanks, Ben Weinstein -- Ben Weinstein PhD Candidate Ecology and Evolution Stony Brook University http://benweinstein.weebly.com/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Simulated phylogenies with character divergence
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 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 - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
[R-sig-phylo] Simulated phylogenies with character divergence
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 - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
