interval.types.gf: Categorise per interval taxon types using the gap-filler...
In rachelwarnock/fbdR: Calculate Birth and Death Rates

Description Usage Arguments Details Value References Examples

View source: R/range.calculations.tree.wide.R

Categorise per interval taxon types using the gap-filler approach (Alroy, 2014) for a set of equal length intervals

1	interval.types.gf(fossils, max.age, strata, return.useful = FALSE)

`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

Taxa types are detailed in Alroy (2014)
1. taxa sampled at all in the 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)
6. taxa sampled in i − 1 and i + 2 but not i + 1 (gap-fillers, a) * referred to as gf_a # may also be sampled in i
7. taxa sampled in i + 1 and i - 2 but not i - 1 (gap-fillers, b) * referred to as gf_b # may also be sampled in i

dataframe of per interval taxon types.

Alroy, J 2014. Accurate and precise estimates of origination and extinction rates. Paleobiology 40: 374-397.

# 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.gf(f, max, 10)