Dan, All- If I understand correctly, that's a separate issue than what Ted is getting at; I think he's worried about the effect of data dredging by running all possible models (as Burnham and Anderson warn against) and not mis-parametrization of the simple model. Data-dredging will bias us toward finding complex models that fit overly well. The common solution in data mining is to subset your data and thus confirm a preferred model for one subset by testing the preference in another subset, but I don't think that can be applied to studies with a single tree.
-Dave On Tue, Mar 22, 2011 at 12:37 PM, Dan Rabosky <drabo...@berkeley.edu> wrote: > > Hi Ted- > > Others can weigh in here, but - at the very least - I would consider a model > with 2 rates as having at least 1 additional parameter (the location of the > rate shift). This seems to perform OK in practice. I admit that I have always > been a bit uncomfortable with this, though - the null hypothesis model does > not have a shift point. I think there are parallels here to finding > breakpoints in segmented regression models. Here's a paper I've been meaning > to read that might be relevant. > > Davies, R.B. (1987) Hypothesis testing when a nuisance parameter is present > only under the alternative. Biometrika 74, 33–43. > > ~Dan > > > > > > > > On Mar 22, 2011, at 10:19 AM, <tgarl...@ucr.edu> <tgarl...@ucr.edu> wrote: > >>> This can also be done using the package "diversitree", with the >>> function make.bd.split and variants thereof. You will probably >>> have to write a function to iteratively partition the tree >>> into all possible splits. >> >> Hi Dan, >> >> How would this approach deal with the problem of multiple comparisons, i.e., >> in effect testing many different hypotheses (or exploratory data mining) on >> the same data set and overall tree? >> >> Cheers, >> Ted >> >> >> Theodore Garland, Jr. >> Professor >> Department of Biology >> University of California, Riverside >> Riverside, CA 92521 >> Office Phone: (951) 827-3524 >> Wet Lab Phone: (951) 827-5724 >> Dry Lab Phone: (951) 827-4026 >> Home Phone: (951) 328-0820 >> Facsimile: (951) 827-4286 = Dept. office (not confidential) >> Email: tgarl...@ucr.edu >> >> Main Departmental page: >> http://www.biology.ucr.edu/people/faculty/Garland.html >> >> List of all Publications: >> http://www.biology.ucr.edu/people/faculty/Garland/GarlandPublications.html >> >> Garland and Rose, 2009 >> http://www.ucpress.edu/books/pages/10604.php >> >> >> ---- Original message ---- >> >> Date: Tue, 22 Mar 2011 09:44:26 -0700 >> From: Dan Rabosky <drabo...@berkeley.edu> >> Subject: Re: [R-sig-phylo] Q: Likelihood ratio test and rate shift >> test on complete dated phylogeny >> To: "R.J. den Tex" <rjden...@yahoo.com> >> Cc: r-sig-phylo@r-project.org >> >>> >>> Hi Robert- >>> >>>> (i) Can you use a Likelihood ratio test to test whether a birth >> death model fits your data better than a pure birth model? >> (likelihood scores are obtained from LASER). >>> >>> Yes, this would be valid, as the models are nested. >>> >>>> (ii) How can I test if a rate shift has occurred on a particular >> node/branch in a complete taxon phylogeny? >>> >>> There are lots of possible methods for this. Or perhaps it is >> better to say that there are lots of variants of a single general >> approach. There are the 1-rate versus 2-rate model in LASER >> (fitNDR_2rate, fitNDR_1rate) after Rabosky et al. (Proc. R. Soc. B, >> 2007); there is the MEDUSA approach, which would allow more than 1 >> rate shift across your tree (Alfaro et al., PNAS; this method is >> implemented in GEIGER). >>> >>> This can also be done using the package "diversitree", with the >> function make.bd.split and variants thereof. You will probably have >> to write a function to iteratively partition the tree into all >> possible splits. Actually, I think the diversitree calculations >> *may* be the most accurate if you have different extinction rates >> across the tree. >>> >>> There is also the method from Moore and Donoghue (2009, PNAS) - i >> think tRate is the name of the package - although I don't think this >> is distributed on the archive for R packages. >>> >>> ~Dan Rabosky >>> >>> >>> >>>> Thank you very much beforehand! >>>> >>>> Robert den Tex >>>> PhD student >>>> Dept. Evolutionary Biology >>>> EBC, Uppsala University >>>> Uppsala, >>>> Sweden >>>> >>>> _______________________________________________ >>>> R-sig-phylo mailing list >>>> R-sig-phylo@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>> >>> >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> R-sig-phylo mailing list >>> R-sig-phylo@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
