gap.filler.rates: Calculate speciation and extinction rates using the...

In rachelwarnock/fbdR: Calculate Birth and Death Rates

Description

By default the function returns tree-wide estimates of speciation and extinction rates, which are calculated by summing taxon counts across all intervals. This approach relies on having equal length intervals.

Usage

gap.filler.rates(fossils, max.age, strata, return.intervals = FALSE)

Arguments

fossils	Dataframe of sampled fossils (sp = unique species ID. h = ages.)
strata	Number of stratigraphic intervals
return.intervals	If TRUE return per interval estimates
basin.age	Maximum age of the oldest stratigraphic interval

Value

named list with the overall speciation rate, overall extinction rate and a dataframe of per interval estimtes if return.intervals = TRUE. Note this approach does not return specation rates for the first or second interval and extinction rate for the first or last interval. Function accounts for interval length. (i.e. continuous = TRUE is hard coded)

References

Alroy, J 2014. Accurate and precise estimates of origination and extinction rates. Paleobiology 40: 374-397.

Examples

# simulate tree & fossils
t = TreeSim::sim.bd.taxa(100,1,1,0.1)[[1]]
# budding speciation
sp = FossilSim::sim.taxonomy(t)
# simulate fossils
max = FossilSim::tree.max(t)
f = FossilSim::sim.fossils.intervals(taxonomy = sp, max.age = max, strata = 10, probabilities = rep(0.5,10), use.exact.times = FALSE)
# add extant occurrences
f = FossilSim::sim.extant.samples(f, taxonomy = sp)
# calculate speciation and extinction rates
gap.filler.rates(f, max, 10)

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