interval.types.bc.pa: 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 based on presence/absence data

Usage

interval.types.bc.pa(presence.absence, intervals)

Arguments

presence.absence	Dataframe of presence/absence data. Each row represents a taxon and each column represents a time interval from oldest to youngest.
intervals	Dataframe of geological intervals.

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

set.seed(123)
# simulate tree
t = TreeSim::sim.bd.taxa(100,1,0.01,0.005)[[1]]

# simulate species
sp = FossilSim::sim.taxonomy(t)

# simulate fossils
f = FossilSim::sim.fossils.poisson(1, taxonomy = sp)
f = FossilSim::sim.extant.samples(f, taxonomy = sp)

# generate presence.absence matrix
pa = presence.absence.matrix(f, stages)

# categorise interval types
interval.types.bc.pa(pa, stages)

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