Hi Solomon, It’s because neither of the things you are estimating are Blomberg’s K and both are different from one another. In Caper, you are estimating Pagel’s Kappa (a branch length transformation that attempts to explain evolutionary change as punctuational [<1] vs gradual [=1] ), while in ape you are estimating Blomberg’s gamma (a transformation known as ACDC, similar to the early burst model, that is associated with accelerating [<1] or decelerating [>1] change).
Graham > On Jul 14, 2015, at 10:58 AM, Solomon Chak <tc...@vims.edu> wrote: > > Hi everyone, > > I'd like to get some opinions on why estimates of Bloomberg's k are > different using the packages ape and caper in R. > > Please see the code below for example, in which I used the same data but > got different estimates of k. In my own data, the estimated ks were > completely opposite: k=0.0001 in ape, and k=3 in caper. > > library(ape) > library(caper) > library(nlme) > data(shorebird) > > # CAPER > compdata <- comparative.data(shorebird.tree, shorebird.data, names.col = > "Species", vcv.dim=3, vcv = TRUE) > > caper.model <- pgls(log(Egg.Mass) ~ log(M.Mass) * log(F.Mass), compdata, > kappa="ML") > > summary(caper.model) # k=0.474 > > # APE > gls.model = gls(log(Egg.Mass) ~ log(M.Mass) * log(F.Mass), > correlation=corBlomberg(value = 0.1, phy=shorebird.tree), > data=shorebird.data, method="ML") > > summary(gls.model) # k = 0.9079989 > > Cheers, > Solomon Chak > solomonc...@gmail.com > Virginia Institute of Marine Science > College of William and Mary > > [[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/ _______________________________________________ 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/
