sim.interval.ages: Reassign fossil ages to user-specified stratigraphic...

In FossilSim: Simulation of Fossil and Taxonomy Data

Reassign fossil ages to user-specified stratigraphic intervals

Description

Reassign exact fossil ages using the minimum and maximum ages of a set of stratigraphic intervals. If use.species.ages = TRUE the function will respect species durations and will not return minimum and maximum bounds that may be younger or older than the species durations. This requires supplying a phylo or taxonomy object.

Usage

sim.interval.ages(
  fossils,
  tree = NULL,
  taxonomy = NULL,
  interval.ages = NULL,
  max.age = NULL,
  strata = NULL,
  use.species.ages = FALSE,
  root.edge = TRUE,
  sim.extant = FALSE
)

Arguments

fossils	Fossil object.
tree	Phylo object.
taxonomy	Taxonomy object.
interval.ages	Vector of stratigraphic interval ages, starting with the minimum age of the youngest interval and ending with the maximum age of the oldest interval.
max.age	Maximum age of the oldest stratigraphic interval.
strata	Number of stratigraphic intervals.
use.species.ages	If TRUE reassigned fossil ages will respect the speciation times. Default = FALSE.
root.edge	If TRUE include root edge.
sim.extant	If TRUE simulate age uncertainty for extant samples as well, default FALSE.

Value

An object of class fossils.

Examples

# simulate tree
t = ape::rtree(8)

# simulate fossils
rate = 2
f = sim.fossils.poisson(rate, t)
plot(f, t)

# assign a max age based on tree height
max.age = tree.max(t)

# define intervals
times = seq(0, max.age, length.out = 5)

# reassign ages
f = sim.interval.ages(f, t, interval.ages = times)

# plot output
plot(f, t, interval.ages = times)

FossilSim documentation built on Oct. 5, 2023, 5:08 p.m.