bd.probability.extant: Birth-death probability (Stadler, 2012)
In rachelwarnock/fbdR: Calculate Birth and Death Rates

Description Usage Arguments Value References Examples

Probability of extant species phylogeny conditioned on the origin (Stadler, 2012, eq. 2) or the crown (crown = T) (Stadler, 2012, eq. 5)

1	bd.probability.extant(tree, b, d, rho = 1, mpfr = FALSE, crown = FALSE)

`tree`	Phylo object of extant taxa (the function will remove any extinct taxa prior to calculating the likelihood)
`b`	Rate of speciation (branching)
`d`	Rate of extinction (branch termination). Must be < b
`rho`	Extant species sampling probability
`crown`	If TRUE the process is conditioned on the crown (default = F)

Log likelihood

Stadler, T. 2012. How can we improve accuracy of macroevolutionary rate estimates? Systematic Biology 62: 321-329.

# simulate tree
t = TreeSim::sim.bd.taxa(100,1,1,0.1)[[1]]
# calculate birth-death probability
birth = 1
death = 0.1
bd.probability.extant(t, birth, death)