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 <[email protected]> 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: [email protected] > 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 - [email protected] >>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>> Searchable archive at >>> http://www.mail-archive.com/[email protected]/ >>> >>> >>> Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : >>> http://f.security-mail.net/301iAWLdbwV >>> >>> >> >> _______________________________________________ >> 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]/
