uncorrected.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

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

Arguments

fossils	Dataframe of sampled fossils (sp = unique species ID. h = ages.)
max.age	Maximum age of the oldest stratigraphic interval
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

Value

named list with the overall speciation rate, overall extinction rate and a dataframe of per interval estimtes if return.intervals = TRUE.

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
uncorrected.rates(f, max, 10)

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