FossilSim (version 2.4.1)

FossilSim: FossilSim: A package for simulating and plotting fossil and taxonomy data

Description

This package provides functions for simulating both taxonomy and fossil data from an existing phylogeny.

Simulating taxonomy

Taxonomy can be simulated in FossilSim under a mixed model of speciation that can incorporate three modes of speciation -- budding (or asymmetric), bifurcating (or symmetric) and anagenetic -- in addition to cryptic speciation. A description of the resulting taxonomy objects and simulation functions can be found in the "Simulating taxonomy" vignette.

Simulating fossil data

Fossils can be simulated from a phylogeny or a taxonomy under a model of constant fossil recovery or time-dependent, environment-dependent or species-dependent fossil recovery. A description of the resulting fossil objects and simulation functions can be found in the "Simulating fossils" vignette.

Plotting functions

Both taxonomy and fossil objects are provided with custom plotting functions that highlight important features of the simulated objects along the original phylogeny. More details about these functions can be found in the vignettes or by calling ?plot.taxonomy and ?plot.fossils.

Compatibility with other packages

FossilSim is designed to use phylogenies in the ape format. It provides functions to convert to and from the fossilRecordSimulation format used by the package paleotree (see the vignette "Converting from and to paleotree format"), as well as functions to convert to the zero-edge format used by BEAST2 and RevBayes (see the vignette "Exporting sampled ancestor trees").

Author

Maintainer: Joelle Barido-Sottani [copyright holder]

Authors:

• Rachel Warnock [copyright holder]

• Walker Pett [copyright holder]

• O'Reilly Joseph [copyright holder]

• Ugnė Stolz [copyright holder]

Examples

# simulate a tree using TreeSim conditioned on tip number
t = TreeSim::sim.bd.taxa(n = 10, numbsim = 1, lambda = 1, mu = 0.2)[[1]]

# simulate taxonomy under mixed speciation
s = sim.taxonomy(tree = t, beta = 0.5, lambda.a = 1, kappa = 0.1)
# plot the result
plot(s, tree = t, legend.position = "topleft")

# simulate fossils using the phylogeny and a constant fossil recovery rate
f = sim.fossils.poisson(rate = 3, tree = t)
# plot the result
plot(f, tree = t)

# simulate fossils using the taxonomy and a constant fossil recovery rate
f = sim.fossils.poisson(rate = 3, taxonomy = s)
# plot the result
plot(f, tree = t, taxonomy = s, show.taxonomy = TRUE)

# simulate fossils using time-dependent fossil recovery rates
f = sim.fossils.intervals(tree = t, rates = c(1, 0.1, 1, 0.1), max.age = tree.max(t), strata = 4)
# plot the result, with the time intervals
plot(f, tree = t, show.strata = TRUE, max.age = tree.max(t), strata = 4)