interval.types.bc: Categorise per interval taxon types using boundary crosser...

In rachelwarnock/fbdR: Calculate Birth and Death Rates

Description

Categorise per interval taxon types using boundary crosser categories for a set of equal length intervals

Usage

interval.types.bc(fossils, max.age, strata, return.useful = 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
return.useful	If TRUE return the branch labels used to define taxon types

Details

Taxa types are detailed in Foote (2000).
Nbt - bottom and top boundary crossers
Nbl - bottom boundary crossers only (e.g. species goes extinct)
NFt - top boundary crossers only (e.g. species originates)
NFl - species originates and becomes extinct during the same interval

Value

dataframe of per interval taxon types.

References

Foote, M. 2000. Origination and extinction components of taxonomic diversity: General problems. Paleobiology 26: 74-102.

Examples

# simulate tree & fossils
t = ape::rtree(20)
# 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)
# categorise interval types
interval.types.bc(f, max, 10)

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