This function simulates stochastic birth-death trees.
Simulation can be performed conditioning on n, on t, or on both simultaneously. If both, then (for optional argument method="rejection") rejection sampling is performed whereby trees are simulated given b and t until a tree containing n taxa is found. The giving-up point can be set using the optional argument max.count.
Simulations can also be performed in continuous time (the default) or discrete time; the difference being that wait times in the continuous-time simulation come from the exponential distribution; whereas waiting times in discrete-time simulations come from the geometric distribution. In addition, discrete-time simulations allow for the possibility that multiple speciation events can occur at (exactly) the same time, so long as they are on separate branches. Finally, sometimes for stopping criterion n in discrete-time there will be a number of tips different from n. This indicates that the last event contained more than one speciation event, and a warning is printed.
method="direct" is presently experimental. It does not really perform direct sampling; however waiting times & birth or death events are sampled first - with only wait-times consistent with n and t being retained. This rejection sampling occurs one layer earlier than for method="rejection". This results in a significant (several-fold) speed-up of the code and enables sampling conditioned on n and t simultaneously for much higher b and d. At the present time, extant.only=TRUE does not work for this mode, nor does type="discrete".
Note that if ape=FALSE, then the function will run faster, and the tree is theoretically compatible with the ape "phylo" standard; however some downstream errors with functions such as bind.tree have been observed.
Lastly, under the taxon number stopping criterion (n) for a non-zero extinction rate (d>0) sometimes a tree containing fewer than n extant tips is returned because it has gone completely extinct before the end of the simulation.
pbtree(b=1, d=0, n=NULL, t=NULL, scale=NULL, nsim=1, type=c("continuous",
"discrete"), ...)A tree or set of trees as an object of class "phylo" or "multiPhylo", respectively.
Simulate stochastic birth-death trees.
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
## simulate a pure-birth tree with 400 tips
## scaled to a length of 1.0
tree<-pbtree(n=400,scale=1)
## simulate a pure-birth tree conditioning on n & t
tt<-log(50)-log(2)
tree<-pbtree(n=50,t=tt)
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