three.timer.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

three.timer.rates(fossils, max.age, strata, continuous = TRUE,
  return.intervals = FALSE)

Arguments

fossils	Dataframe of sampled fossils (sp = unique species ID. h = ages.)
strata	Number of stratigraphic intervals
continuous	If TRUE calculate continuous rates (i.e. account for interval length)
return.intervals	If TRUE return per interval estimates
basin.age	Maximum age of the oldest stratigraphic interval

Details

The overall sampling probability Ps = 3t / (3t + Pt), where 3t and Pt are summed across the entire dataset
The per-interval speciation rate lamda = log(2ti+1/3t) + log(Ps)
The per-interval extinction rate mu = log(2ti/3t) + log(Ps)

Value

named list with the overall speciation rate, overall extinction rate, overall sampling rate and a dataframe of per interval estimtes if return.intervals = TRUE. Note this approach does not return rates for the first interval.

References

Alroy, J et al. 2008. Dynamics of origination and extinction in the marine fossil record. PNAS 105: 11536-11542.
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
three.timer.rates(f, max, 10)

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