est.bd.extant: Maximum likelihood estimation of birth and death rates for a...
In rachelwarnock/fbdR: Calculate Birth and Death Rates

Description Usage Arguments Value Examples

This function maximises the likelihood of the function bd.probability.extant using optim (Nelder-Mead option)

1 2	est.bd.extant(b, d, tree, lower.b = 0.001, upper.b = 10, lower.d = 0.001, upper.d = 10, crown = FALSE, rho = 1)

`b`	Initial value for birth rate
`d`	Initial value for death rate. Must be < b
`tree`	Phylo object of extant taxa (the function will remove any extinct taxa prior to calculating the likelihood)
`lower.b`	Lower birth rate
`upper.b`	Upper birth rate
`lower.d`	Lower death rate
`upper.d`	Upper death rate
`crown`	If TRUE the process is conditioned on the crown (default = F)
`rho`	Extant species sampling probability (default = 1)

Named list including maximum likelihood estimates of birth and death rate

# simulate tree
t = TreeSim::sim.bd.taxa(100,1,1,0.1)[[1]]
# estimate birth & death rates
birth = runif(1)
death = runif(1, 0, birth)
out = est.bd.extant(birth, death, t)
# ML birth rate
out$par[1]
# ML death rate
out$par[2]