Hi Brian and Cecile, Thank you so much for sharing your thoughts! Actually, my gut feeling was that standard errors of theta estimates probably won't represent plasticity, too; but it is nice to hear other people's arguments.
Best, Xiaojing On Thu, Sep 15, 2016 at 10:10 PM, Cecile Ane <cecile....@wisc.edu> wrote: > I would say no: standard errors of theta values do not have a biological > interpretation, in my opinion. > Going back to a sample from a single population and its mean: the standard > deviation of the sample has a biological interpretation (e.g > within-population variation), but the standard error does not. It has a > statistical interpretation: about estimate uncertainty. Similarly with the > OU model: the standard errors of theta estimates are also about uncertainty > in these estimates. Even in the best case scenario when the model that you > are using is correct, these standard errors would be affected by your > sample size (i.e. go down with the number of tips in your tree), whereas a > biological interpretation like plasticity should not be affected by the > sample size. > > On top of all this, a mismatch between the evolution process and the > assumed OU model would affect the theta estimates and their standard errors. > > The new version of phylolm (on github, not on CRAN) has bootstrap-based > standard errors, if you wanted to follow-up on Brian’s idea. It also has > the possibility to add measurement error in the model when analyzing data > Cécile > > > On Sep 15, 2016, at 9:11 PM, Brian O'Meara <omeara.br...@gmail.com> > wrote: > > > > That's a really cool question. I don't know. I'm pretty sure that > > practically, the answer is no (esp when you consider all the issues -- > any > > feasible OU is too simple a model to match reality, tree errors, data > > errors, etc. -- that also come into an analysis). However, I could > imagine > > that in a perfect world you could look at expected standard errors > created > > using parametric bootstrapping from the MLE of the parameters and see if > > the actual standard errors are different -- maybe it could reflect > > plasticity or some other factor. But I really don't know. You might look > at > > some of the methods that can deal with intraspecific and interspecific > > processes to get at this sort of biological question (the Felsenstein > 2008 > > Contrasts revisited paper might be interesting as a start, though it's > not > > OU and comes at this from a different direction), but it's fun to think > > about ways to go from what is treated as annoying noise to a meaningful > > signal. > > > > Best, > > Brian > > > > _______________________________________________________________________ > > Brian O'Meara, http://www.brianomeara.info, especially Calendar > > <http://brianomeara.info/calendars/omeara/>, CV > > <http://brianomeara.info/cv/>, and Feedback > > <http://brianomeara.info/teaching/feedback/> > > > > Associate Professor, Dept. of Ecology & Evolutionary Biology, UT > Knoxville > > Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville > > Associate Director for Postdoctoral Activities, National Institute for > > Mathematical & Biological Synthesis <http://www.nimbios.org> (NIMBioS) > > Communication Director, Society of Systematic Biologists > > > > On Thu, Sep 15, 2016 at 5:37 PM, Xiaojing Wei <weixx...@umn.edu> wrote: > > > >> Dear R-sig-phylo users, > >> > >> I wonder if the standard errors of the theta estimates in OU models have > >> any biologically meaningful interpretations. For instance, could it give > >> some indication of plasticity in traits, or the optimal level of > plasticity > >> in traits? Or does it simply reflect estimation uncertainty of the > >> phylogeny or the OU model? > >> > >> Thanks a lot! > >> > >> -- > >> Xiaojing Wei > >> PhD student > >> Dept. of Ecology, Evolution, and Behavior > >> University of Minnesota > >> Rm. 211 Ecology Bld., 1987 Upper Buford Cir. > >> St. Paul, 55108 > >> > >> [[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-ph...@r-project.org/ > >> > > > > [[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-ph...@r-project.org/ > > -- Xiaojing Wei PhD student Dept. of Ecology, Evolution, and Behavior University of Minnesota Rm. 211 Ecology Bld., 1987 Upper Buford Cir. St. Paul, 55108 [[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/
