interval.types.3t: Categorise per interval taxon types using the three-timer...

In rachelwarnock/fbdR: Calculate Birth and Death Rates

Description

Categorise per interval taxon types using the three-timer approach (Alroy, 2008) for a set of equal length intervals

Usage

interval.types.3t(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 interval
return.useful	If TRUE return the branch labels used to define taxon types

Details

Taxa types are detailed in Alroy (2008) and Alroy (2014)
1. taxa sampled at all in a focal bin (Ns)
2. taxa sampled in a bin but not immediately before or after (one-timers, or 1t)
3a. taxa sampled immediately before and within the ith bin (two-timers, or 2ti) * referred to as two_t_a
3b. or within and immediately after the ith bin (2ti+1) * referred to as two_t_b
4. taxa sampled in three consecutive bins (three-timers, or 3t)
5. taxa sampled before and after but not within a bin (part-timers, or Pt)
n.b. all three timers are also two timers

Value

dataframe of per interval taxon types.

References

Alroy, J et al. 2008. Dynamics of origination and extinction in the marine fossil record. PNAS 105: 11536-11542.

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.3t(f, max, 10)

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