Just to confirm that Graham's fix works. Using the following libraries (and their dependencies) I conducted the simulations:
library(TreeSim) library(phytools) sim.bd.taxa(30,1,lambda=0.1,mu=0.05)[[1]][[1]]->tree fastBM(tree)->data fitContinuous(tree,data,model="EB") Fitting EB model: Error in solve.default(phyvcv) : Lapack routine dgesv: system is exactly singular ###This now works with a parameterized alpha (below)...not sure how good the estimates are (they were simulated under ###BM after all) fitContinuous(tree,data,model="EB", bounds=list(alpha=c(0,1))) Fitting EB model: $Trait1 $Trait1$lnl [1] -264.4297 $Trait1$beta [1] 0.8355526 $Trait1$a [1] 0.001813503 $Trait1$aic [1] 534.8593 $Trait1$aicc [1] 535.1042 $Trait1$k [1] 3 On Sun, Nov 4, 2012 at 2:01 PM, David Bapst <dwba...@uchicago.edu> wrote: > Nicolas, > Not certain how you are time-scaling your tree, but I often get warnings of > singularity from various comparative analysis functions due to the presence > of very short terminal branches. I have found that such warnings of > singularity when dealing with paleo-trees can often be avoided by adding a > very small amount to all the terminal branch lengths, say 0.001. This is > very simple to do with a few lines of code; alternatively, the function > addTermBranchLength() in the library paleotree does this automatically if a > tree is passed to it. > > Also, I would advice you to consider multiple methods for time-scaling your > tree of fossil taxa and compare results across those trees, if you are not > doing so already. In practice, I find one can sometimes give very different > results for some comparative analyses with different time-scaling methods > on the same paleontological dataset. > -Dave > > > On Sun, Nov 4, 2012 at 10:59 AM, Nicolas Campione < > nicolas.campi...@mail.utoronto.ca> 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 >> >> > > > -- > David Bapst > Dept of Geophysical Sciences > University of Chicago > 5734 S. Ellis > Chicago, IL 60637 > http://home.uchicago.edu/~dwbapst/ > http://cran.r-project.org/web/packages/paleotree/index.html > > <http://home.uchicago.edu/%7Edwbapst/> > > [[alternative HTML version deleted]] > > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > -- NEW EMAIL ADDRESS: frank.burbr...@csi.cuny.edu *********************************** Frank T. Burbrink, Ph.D. Professor Biology Department 6S-143 2800 Victory Blvd. College of Staten Island/CUNY Staten Island, New York 10314 E-Mail:frank.burbr...@csi.cuny.edu Phone:718-982-3961 Web Page: http://scholar.library.csi.cuny.edu/~fburbrink/ *********************************** ________________________________ Washington Monthly<http://www.washingtonmonthly.com/magazine/septemberoctober_2012/features/americas_bestbangforthebuck_co039461.php> magazine ranks the College of Staten Island as one of “America’s Best-Bang-for-the-Buck Colleges” _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
