sim.fossils.intervals {FossilSim}

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)