est.bd.ranges: 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.range using optim (Nelder-Mead option)

1 2	est.bd.ranges(b, d, frs, lower.b = 0.001, upper.b = 10, lower.d = 0.001, upper.d = 10, crown = FALSE)

`b`	Initial value for birth rate
`d`	Initial value for death rate
`frs`	Dataframe of species ranges
`lower.b`	Lower birth rate
`upper.b`	Upper birth rate
`lower.d`	Lower death rate
`upper.d`	Upper death rate
`crown`	If TRUE assume the process begins at the first speciation event and not the origin (default = FALSE)

Named list including maximum likelihood estimates of birth and death rate

# simulate tree & assume complete sampling
t = TreeSim::sim.bd.taxa(100,1,1,0.1)[[1]]
beta = 0.5
lambda.a = 0.1
frs <- FossilSim::sim.taxonomy(tree = t, beta = beta, lambda.a = 0.1)
# estimate birth & death rates
birth = runif(1)
death = runif(1)
out = est.bd.ranges(birth, death, frs)
# ML birth rate
out$par[1]
# ML death rate
out$par[2]