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/
