Hi Tanja,list Yes, everything is going extinct, but as you say, that shouldn't happen when mu = 0. > sim.bd.age(age=2,numbsim=3,lambda=2,mu=0,frac,mrca=FALSE,complete=FALSE) [[1]] [1] 0
[[2]] [1] 0 [[3]] [1] 0 > It's a rather malicious error in that, as you point out, it's a possible outcome when mu=0, so at first it appears nothing is wrong, but it happens every time that everything is extinct even for mu << lambda, or mu=0. It's curious that this same problem effects both TreeSim and Geiger, and that this problem appears isolated to certain architectures of computers. My guess is that it may be related to 32 bit architecture and the way ape is handling the tree, but really not sure how to debug this one. -Carl On Wed, May 18, 2011 at 12:26 PM, Stadler Tanja <tanja.stad...@env.ethz.ch>wrote: > > Hi Carl, > > the TreeSim return (arrays of 0s) could be because TreeSim returns 0 when > the tree goes extinct: > > treearray Array of numbsim trees with the time since origin / most > recent common ancestor being age. If tree goes extinct (only possible when > mrca = FALSE), returns 0. If only one extant and no extinct tips, returns 1. > > Maybe set seed and compare runs with complete=FALSE and complete=TRUE? > > Cheers Tanja > > > > > I get a similar problem when running the equivalent command in TreeSim: > > > age<-2 > lambda <- 2.0 > mu <- 0.5 > frac <-0.6 > numbsim<-3 > > sim.bd.age(age,numbsim,lambda,mu,frac,mrca=FALSE,complete=FALSE) > [[1]] > [1] 0 > > [[2]] > [1] 0 > > [[3]] > [1] 0 > > > > -- > Tanja Stadler (nee Gernhard) > > ETH Zürich > Institute of Integrative Biology > Universitätsstrasse 16 > 8092 Zürich > > eMail: tanja.stad...@env.ethz.ch<mailto:tanja.stad...@env.ethz.ch> > Phone: +41 44 632 45 48 > Office: CHN H76.1 > > http://www.tb.ethz.ch/people/tstadler > > -- Carl Boettiger UC Davis http://www.carlboettiger.info/ [[alternative HTML version deleted]]
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