Hi Alicia- I would not really recommend using that function. Methodologically, the approach from Rabosky (2006) has been superseded by a range of newer approaches. I would suggest explicitly fitting models of diversification that analytically account for incomplete taxon sampling. I think (but am not certain) that Treepar more or less allows you to implement those same models (and more) while modeling incomplete sampling in the present.
In any event, the fitdAICrc.batch function doesn't do anything special that you can't do by fitting the models individually, so if you still want to go that route, I suggest just fitting the specific diversification models individually. I will be removing support for those functions from laser in the very near future in light of a comprehensive overhaul to the package that is almost finished. ~Dan Rabosky On Feb 10, 2014, at 12:52 AM, Alicia Toon wrote: > I would like to compare models of diversification using deltaAICrc in laser > following Rabosky (2006). I used branch lengths from my tree and the fitAICrc > function to estimate AIC for constant and variable rate models and then used > the yuleSim function to simulate branching times using the number of taxa in > my tree. So far everything looks ok. But when I use the fitdAICrc.batch > function, the output table has NA in the y2r and dAIC columns and the p value > is not calculated correctly (it is always 0.9998 no matter what observed > value I use). > my useage for the function: > fitdAICrc.batch(null.bt, observed=20.9849, ints=100) > > Has anyone had this problem of returning NA from the fitdAICrc.batch function? > > Thanks in advance. > Alicia Toon > School of Biology > The University of Queensland > Saint Lucia > Australia > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/[email protected]/ _____________________ Dan Rabosky Assistant Professor & Curator of Herpetology Museum of Zoology & Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor, MI 48109-1079 USA [email protected] http://www-personal.umich.edu/~drabosky http://www.lsa.umich.edu/ummz/ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
