fbd.probability: FBD probability

In rachelwarnock/fbdR: Calculate Birth and Death Rates

Description

Calculate the probabilty of speciaton, extinction and sampling rates for a given set of stratigraphic ranges

Usage

recount.gamma(frs)

recount.extant(frs)

fbd.probability(frs, b, d, s, k, rho = 1, complete = F, mpfr = F)

Arguments

frs	Dataframe of species ranges
b	Rate of speciation
d	Rate of extinction
s	Rate of sampling
k	Number of fossils

Value

Log 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(tree = t, psi)
k = length(f$sp)
# add extant occurrences
f = FossilSim::sim.extant.samples(f, t)
# calculate range attachment times given incomplete sampling
frs = 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)
fbd.probability(frs, birth, death, psi, k)

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