sim.fossils.intervals | R Documentation |

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`

).

```
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
)
```

`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 |

An object of class fossils.

`sim.fossils.poisson`

, `sim.fossils.environment`

```
# 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)
```

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