Hi Dr. Garland, I got the impression that an ultrametric tree is needed for comparative analysis from this book <http://www.springer.com/us/book/9783662435496>ch. 2 pg. 38: "most comparative analyses assume that the tree is ultrametric, as the majority of analyses deal with evolution of phenotypic traits of extant species with the underlying assumption is that the time available for phenotypic evolution is the same for all taxa".
I understand that the methodology of PGLS can use any tree form, I suppose there're different assumptions if I used an additive tree or an ultrametric tree. Could you guide me to some references that explicitly discuss about this? Is it necessary to use an ultrametric tree If I want to estimate lambda in the residual error of the gls and do a branch length transformation as Revell 2010 <http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2010.00044.x/pdf> suggested? Many thanks! Cheers, Solomon Chak ----------------------------------------------- *Solomon **Tin Chi **Chak* Ph.D. Candidate Tel: (804) 684-7484 Marine Biodiversity Laboratory <http://www.vims.edu/research/units/labgroups/marine_biodiversity/index.php> Virginia Institute of Marine Science <http://www.vims.edu/> College of William and Mary <http://www.wm.edu/> PO Box 1346 / Rt. 1208 Greate Rd., Gloucester Pt, VA 23062, USA On Thu, Jul 16, 2015 at 2:55 PM, Theodore Garland Jr < theodore.garl...@ucr.edu> wrote: > Dear Solomon, > > I don;t know where you are trying to go with this, but any proper > implementation of PGLS (I am not talking about methods that transform the > branch lengths with things like Grafen's rho, Pagel's lambda or OU models) > should be able to use any tree of any shape. This is the same as for > phylogenetically independent contrasts. > > 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 > Solomon Chak [tc...@vims.edu] > Sent: Thursday, July 16, 2015 3:31 AM > To: r-sig-phylo@r-project.org > Subject: [R-sig-phylo] PGLS with non-ultrametric tree > > Dear all, > > What are the pros and cons of the two methods to do pgls with a > non-ultrametric tree? Many thanks! > > 1) Convert the additive tree to ultrametric using penalized likelihood > (Sanderson 2002) with ape:: chronopl after cross-validation to find the > best lambda. > > 2) Use weighted least-squares in which gls(y ~ x, > correlation=corPagel(value=0.1, phy=phy, fixed=F), > weights=varFixed(~tip.heights), > data=dat) > > Cheers, > Solomon Chak > > ----------------------------------------------- > *Solomon **Tin Chi **Chak* > Ph.D. Candidate > Tel: (804) 684-7484 > Marine Biodiversity Laboratory > < > http://www.vims.edu/research/units/labgroups/marine_biodiversity/index.php > > > Virginia Institute of Marine Science <http://www.vims.edu/> > College of William and Mary <http://www.wm.edu/> > PO Box 1346 / Rt. 1208 Greate Rd., Gloucester Pt, VA 23062, USA > > [[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/ > [[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/
