That seems correct to me. The probability that the tree died out before the first speciation event (which is excluded, as Liam says) is d/(b+d).
Also Tanya Stader's TreeSim package can deal with this issue more directly. For example her function sim.bd.taxa.age has a flag for mrca: > If mrca = FALSE: The time since the origin of the process. If mrca = TRUE: > The time since the most recent common ancestor of the sampled species. --Luke On Apr 27, 2011, at 9:39 AM, Liam J. Revell wrote: > Hi Jonathan, > > I believe that the proper way to do this will depend on whether you are using > "time.stop" or "taxa.stop". > > If you are using taxa.stop, say with b, d, and taxa.stop=N, then I think that > you should do this: > > tree<-birthdeath.tree(b,d,taxa.stop=N) > tree$root.edge<-rexp(n=1,rate=(b+d)) > > If you are using time.stop, with stopping time T, then I think you should do > this: > > rt<-rexp(n=1,rate=(b+d)) > tree<-birthdeath.tree(b,d,time.stop=T-rt) # if T>rt > tree$root.edge<-rt > > In both cases, you get only trees that did not go extinct along the root edge > (that is, you exclude trees that went extinct before the first speciation). > > If this is not quite correct, I'm sure that Dan R. or Luke H. (or others) can > correct me. > > - Liam > > -- > Liam J. Revell > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: [email protected] > blog: http://phytools.blogspot.com > > On 4/27/2011 11:47 AM, Jonathan Hughes wrote: >> >> >> Howdy, >> >> I'm simulating trees using geiger's birthdeath.tree function. However, it >> already starts with two living lineages. I'd like to start with a single >> lineage and include that root node. Is there some other function that I'm >> missing? Or should I simply add ":bl;" to the end of the simulated >> phylogeny, where "bl" would be a branch of length 1/speciation rate? >> >> Thanks, >> >> Jonathan >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-sig-phylo mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > _______________________________________________ > R-sig-phylo mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Luke Harmon Assistant Professor Biological Sciences University of Idaho 208-885-0346 [email protected] [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
