Hi Nic, It's not a problem with the branch lengths, at least not the non-ultrametricity of the tree. It's probably that the lower bound on the exponential change parameter is too low, resulting in a singular phylogenetic variance covariance matrix. Try changing the lower bound as follows:
eb.fit <- fitContinuous(phy, data, model ="EB", bounds = list(a=c(X, 0))) # where X is the lower bound you chose. You can compute an appropriate value for X if you're willing to choose a minimum rate for the end of the EB process. In this case, the lower bound would be log(min.rate) / T where T is the depth of your tree and min.rate is the ending rate. I've found a value of 10^-5 is reasonable in most cases. Graham ------------------------------------------------------------ Graham Slater Peter Buck Post-Doctoral Fellow Department of Paleobiology National Museum of Natural History The Smithsonian Institution [NHB, MRC 121] P.O. Box 37012 Washington DC 20013-7012 slat...@si.edu www.eeb.ucla.edu/gslater On Nov 4, 2012, at 11:59 AM, Nicolas Campione wrote: > Dear R Phylo List, > > I'm trying to test an Early Burst model of evolution against a tree using the > 'fitContinuous' function in 'geiger'. However, I get the following error > message, and am unsure as to what I can do to fix this: > >> fitContinuous(tree,trait,model="EB") > > Fitting EB model: > Error in solve.default(phyvcv) : > Lapack routine dgesv: system is exactly singular: U[4,4] = 0 > > My tree is based on fossil taxa and my branch lengths are calculated using > time (in millions of years). I seem to be able to test every other model, > only EB is giving me troubles. I'm pretty sure it has something to do with > the branch lengths, cause if I used other measures, such as all=1 or grafen, > I don't get an error. > > Has anybody had this issue before? > > Any assistance would be greatly appreciated. > > Cheers, > > -Nic- > > ---- > Nicolás E. Campione > M.Sc., Ph.D. Candidate > Dept. Ecology & Evolutionary Biology > University of Toronto > 25 Wilcocks St. > Toronto, ON > Canada M5S 3B2 > > Royal Ontario Museum > 100 Queen's Park > Toronto, ON > Canada M5S 2C6 > Office: 416-586-5591 > Email: nicolas.campi...@mail.utoronto.ca > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
