fbd.likelihood.est: Maximum likelihood estimation of birth, death and sampling...

In rachelwarnock/fbdR: Calculate Birth and Death Rates

Description

Maximum likelihood estimation of birth, death and sampling rates for a given set of stratigraphic ranges under the FBD model

Usage

fbd.likelihood.est(b, d, s, k, frs, est.b = T, est.d = T, est.s = F,
  lower.b = 0.001, lower.d = 0.001, lower.s = 0.001, upper.b = 10,
  upper.d = 10, upper.s = 100, complete = F)

Arguments

b	Initial value for birth rate
d	Initial value for death rate
s	Initial value for sampling rate
k	Number of fossils
frs	Dataframe of species ranges including first birth and death time, first appearance, number of co-existing lineages and extant indicator
est.b	If TRUE estimate birth rate, else fix birth rate to the initial value (default = T)
est.d	If TRUE estimate death rate, else fix death rate to the initial value (default = T)
est.s	If TRUE estimate sampling rate, else fix death sampling to the initial value (default = F)
complete	If TRUE assume complete species sampling (default = F)

Value

Named list including parameter estimates and likelihood

Examples

# simulate tree & fossils
birth = 1
death = 0.1
t = TreeSim::sim.bd.taxa(100, 1, birth, death)[[1]]
psi = 1
f = FossilSim::sim.fossils.poisson(psi, t)
k = length(f$h)
# add extant occurrences
f = FossilSim::add.extant.occ(t, f)
# asymmetric taxon mapping
f = FossilSim::asymmetric.fossil.mapping(t, f)
# calculate range attachment times given incomplete sampling
frs = FossilSim::attachment.times(t,f)
# rename range data headers
names(frs)[2]<-"bi"
names(frs)[3]<-"di"
names(frs)[4]<-"oi"
frs = recount.extant(frs)
frs = recount.gamma(frs)
# estimate
fbd.likelihood.est(birth, death, psi, k, frs)

rachelwarnock/fbdR documentation built on Aug. 23, 2019, 3:39 a.m.