est.bd.combined: 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 and bd.probability.range using optim, either treating stratigraphic range and phylogenetic birth and death rates independently (constrained = FALSE) or constraining the parameters under the birth-death chronospecies model (constrained = TRUE).

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est.bd.combined(tree, frs, b = 0.3, d = 0.1, b.star = 1, d.star = 0.1,
  nd = 0.1, constrained = FALSE, constrained.p = 3, crown = FALSE,
  rho = 1)

`tree`	Phylo object of extant taxa (the function will remove any extinct taxa prior to calculating the likelihood)
`frs`	Dataframe of species ranges
`b`	Initial value for the phylogenetic birth rate
`d`	Initial value for the phylogenetic death rate. Must be < b
`b.star`	Initial value for the stratigraphic range birth rate
`d.star`	Initial value for the stratigraphic range death rate
`nd`	Net diversification (b - d). Must be > 0
`constrained`	If FALSE fossil and phylogenetic rates are treated as independent. If TRUE rates are constrained under the birth-death chronospecies model
`constrained.p`	Number of parameters to be estimated under the constrained model. If p = 2 rates are equal for fossils and phylogenies (this is the equal rates model, a special case of the BD chronospecies model). If p = 3 rates are not equal but b - d = b.star - d.star (this the compatible rates BD chronospecies model)
`crown`	If TRUE the process is conditioned on the crown instead of the origin (default = F)
`rho`	Extant species sampling probability (default = 1)

Named list including maximum likelihood estimates of diversification rate parameters. Under the independent rates model (constrained = FALSE) the function returns estimates of birth, death, birth.star and death.star. Under the compatible rates model (constrained = TRUE, constrained.p = 3) the function returns birth and birth.star estimates for the phylogeny and stratigraphic ranges, respectively, and a single diverification rate estimate. Under the equal rates model (constrained = TRUE, constrained.p = 2) the function returns a single set of birth and death rates applicable to both the phylogeny and stratigraphic ranges.

# simulate tree & assume complete sampling
t = TreeSim::sim.bd.taxa(100,1,1,0.1)[[1]]
# simulated mixed speciation
beta = 0.5
lambda.a = 0.1
frs <- FossilSim::sim.taxonomy(tree = t, beta = beta, lambda.a = 0.1)

# estimate birth & death rates

# The equal rates birth-death chronospecies model
out = est.bd.combined(t, frs, constrained = TRUE, constrained.p = 2)
# ML birth rate
out$par[1]
# ML death rate
out$par[2]

# The compatible rates birth-death chronospecies model
out = est.bd.combined(t, frs, constrained = TRUE, constrained.p = 3)
# ML birth rate
out$par[1]
# ML birth.star rate
out$par[2]
# ML death rate
out$par[1] - out$par[3]
# ML death.star rate
out$par[2] - out$par[3]

# The indpendent rates birth-death model
out = est.bd.combined(t, frs, constrained = FALSE)
# ML birth rate
out$par[1]
# ML birth.star rate
out$par[2]
# ML death rate
out$par[3]
# ML death.star rate
out$par[4]