Hi Eric, The thing is that it becomes very cumbersome to write user-friendly software with generalized simulation routines to allow various (unlimited?) ad hoc changes in rates of trait evolution, selection regimes (e.g., OU), rates of speciation, etc. so, the expedient approach is often called for.
Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl=en&user=iSSbrhwAAAAJ Director, UCR Institute for the Development of Educational Applications Editor in Chief, Physiological and Biochemical Zoology Fail Lab: Episode One http://testtube.com/faillab/zoochosis-episode-one-evolution http://www.youtube.com/watch?v=c0msBWyTzU0 ________________________________________ From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Eric [eric...@hotmail.com] Sent: Saturday, August 01, 2015 1:12 AM To: Liam J. Revell Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] simulating rate shifts Hi Liam, Yes, this is what I meant. I’m a little surprised that no process-based simulation - rather than prune-and-graft - method exists. In any case, thank you for the example, it is very helpful. Regards, Eric > On Jul 31, 2015, at 8:07 PM, Liam J. Revell <liam.rev...@umb.edu> wrote: > > Hi Emmanuel & Eric. > > I think it's possible that Eric is interested in simulating shifts in the > lineage diversification (speciation and/or extinction) rate, rather than the > rate of phenotypic trait evolution. > > It is possible to simulate various scenarios of trait-based diversification > in the package diversitree, I believe; however if you are merely interested > in taking (or simulating some tree) and then imagining (and simulating) a > different diversification process for part of that tree, then this is exactly > the same as simulating first one tree under process 1 - then pruning a > subtree, simulating a replacement subtree under process 2, and attaching the > new subtree from whence the previous subtree was removed. > > Since this is easier said then done, I posted a more detailed worked example > on my blog here: > http://blog.phytools.org/2015/07/simulating-arbitrary-shift-in.html. > > All the best, Liam > > Liam J. Revell, Assistant Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://blog.phytools.org > > On 7/31/2015 10:57 AM, Emmanuel Paradis wrote: >> Hi Eric, >> >> See the function rTraitCont in ape: the parameters of the BM or OU model >> can be branch-specific, so it's easy to specify a change in parameter(s) >> at a given node. There's an example there: >> >> http://www.mpcm-evolution.org/practice/online-practical-material-chapter-13/chapter-13-2-traits >> >> >> Cheers, >> >> Emmanuel >> >> Le 30/07/2015 11:31, Eric Lewitus a écrit : >>> Hello, >>> >>> There are several functions available for simulating rate shifts in >>> trees (e.g., SimTree, TESS), but these implement tree-wide shifts, >>> which are somewhat unrealistic, rather than shifts descending from a >>> particular node. Is it possible to implement a more realistic rate >>> shifted tree? Has such a thing already been implemented? >>> >>> Thanks. >>> [[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/ >>> >>> >>> Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : >>> http://f.security-mail.net/301iAWLdbwV >>> >>> >> >> _______________________________________________ >> 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 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/
