Hi everyone, I have been running PGLS with gls from NLME and phyl.resid from PHYTOOLS. Most of my analyses are running well with no problems and give the same results in both packages. With just a few of my dependent variables, which happen to be evolutionary rates extracted from the program BAMM and the associated package BAMMtools, I get lambda values greater than 1 when using both gls and phyl.resid.
I have read an older post that says that lambda can theoretically be >1, but I am wondering whether it is safe to interpret results from such PGLS analyses? If I constrain lambda to be 1 (instead of 1.0015, which gls and phyl.resid return when letting them optimize lambda) the results and p-values change considerably. Any advice or experience with how to proceed or interpret results in light of lambda greater than 1 would be greatly appreciated! Thanks for your time! Regards, Zach [[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/