sim.fossils.intervals: Simulate fossils under a non-uniform model of preservation...

In fossilsim/fossilsim: Simulation of Fossil and Taxonomy Data

Simulate fossils under a non-uniform model of preservation for a given set of consecutive time intervals

Description

Intervals can be specified by specifying the interval boundaries using interval.ages or specifying both max.age and strata. In the second scenario all intervals will be of equal length. Preservation can be specified using rates, which represent the rates of a Poisson process in each interval, or probabilities, which represent the probabilities of sampling per interval. When using probabilities, at most one fossil per species will be sampled per interval.

Fossils can be simulated for a phylo (tree) or taxonomy (taxonomy) object. If both are specified, the function uses taxonomy. If no taxonomic information is provided, the function assumes all speciation is symmetric (i.e. bifurcating, beta = 1).

Usage

sim.fossils.intervals(
  tree = NULL,
  taxonomy = NULL,
  fossils = NULL,
  interval.ages = NULL,
  max.age = NULL,
  strata = NULL,
  probabilities = NULL,
  rates = NULL,
  ignore.taxonomy = FALSE,
  root.edge = TRUE,
  use.exact.times = TRUE
)

Arguments

tree	Phylo object.
taxonomy	Taxonomy object.
fossils	Append fossils to to an existing fossils 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.
probabilities	Probability of sampling/preservation in each interval. The number of probabilities should match the number of intervals and the first entry should correspond to youngest interval.
rates	Poisson sampling rate for each interval. The number of rates should match the number of intervals and the first entry should correspond to youngest interval.
ignore.taxonomy	Ignore species taxonomy (returns sp = NA). Default = FALSE.
root.edge	If TRUE include the root edge. Default = TRUE.
use.exact.times	If TRUE use exact sampling times. If FALSE hmin and hmax will equal the start and end times of the corresponding interval. Default = TRUE.

Value

An object of class fossils.

See Also

sim.fossils.poisson, sim.fossils.environment

Examples

# simulate tree
t = ape::rtree(6)

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

# simulate fossils using max.age and strata & probabilities
strata = 4
probability = rep(0.7, 4)
f = sim.fossils.intervals(t, max.age = max.age, strata = strata, probabilities = probability)
plot(f, t, strata = strata, show.strata = TRUE)

# simulate fossils using interval.ages & rates
times = c(0, sort(runif(3, min = 0, max = max.age)), max.age)
rates = c(5, 0, 5, 0)
f = sim.fossils.intervals(t, interval.ages = times, rates = rates)
plot(f, t, interval.ages = times, show.strata = TRUE)

# simulate fossils using taxonomy
s = sim.taxonomy(t, 0.1, 0.1, 1)
f = sim.fossils.intervals(taxonomy = s, interval.ages = times, rates = rates)
plot(f, t, interval.ages = times, show.strata = TRUE)

# append fossils to an existing fossils object
new.rates = rates * 2
f2 = sim.fossils.intervals(taxonomy = s, fossils = f, interval.ages = times, rates = new.rates)

fossilsim/fossilsim documentation built on April 23, 2024, 3:16 p.m.