Thanks very much Tanja and Joe, I think these suggestions for sorting will be very useful; we were trying to do something similar (but very "hacker-ish") and with this theoretical basis I'm sure we'll pull it off.
And for BD, the time transformation should be perfect. Thanks very much-- Andy On Tue, Apr 12, 2011 at 7:27 AM, Stadler Tanja <tanja.stad...@env.ethz.ch>wrote: > Hey Andy, > > Simulating the bifurcation times in a tree with n extant species and age t > (where t is either mrca or the origin of the first species), assuming > constant speciation and extinction rates (and possibly a sampling > probability rho), can be done within the R package TreeSim using the > function: > sim.bd.taxa.age > > Note: the output is a tree with branch length. Therefore, use > branching.times(tree) for obtaining the bifurcation times. These bifurcation > times can be put on your constrained tree topology in the following: > > 1) "sort" (or "rank") the interior nodes in your tree where each sorting is > equally likely (the resulting tree is called ranked tree, see eg > Semple&Steel Phylogenetics 2003. For sorting the nodes uniformly at random, > you can use the shuffle idea introduced in Ford, Matsen, Stadler 2009 Syst > Biol). > 2) Then the i-th largest branching time is put on the i-th node in your > tree. > > 1-2) works as ranked tree and branching time distribution are independent > under the birth-death process and each ranked tree has equal probability. > > Simulating 1) is fairly easy with this shuffle concept, if you have > questions or need help, let me know! > > Best > Tanja Stadler > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
