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: [email protected] 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 [[email protected]] on behalf of Solomon Chak [[email protected]] Sent: Thursday, July 16, 2015 3:31 AM To: [email protected] 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 - [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]/
