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
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 =
Hi all,
tree-birthdeath.tree(b,d,taxa.stop=N)
tree$root.edge-rexp(n=1,rate=(b+d))
If you are using time.stop, with stopping time T, then I think you should do
this:
rt-rexp(n=1,rate=(b+d))
tree-birthdeath.tree(b,d,time.stop=T-rt) # if Trt
tree$root.edge-rt
In both cases, you get
