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]]
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