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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