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FossilSim

R package for simulating fossil data on phylogenetic trees under mechanistic models of preservation and sampling

The latest version can be installed in R using the package devtools:

library(devtools)
install_github("fossilsim/fossilsim")

Quick start

Simulating data using FossilSim can be as simple as the following code snippets.

# simulate a tree using ape
tips = 8
t = ape::rtree(tips)
# simulate fossils using fossilsim
rate = 2
f = sim.fossils.poisson(rate, t)  
# plot the complete output
plot(f, t)
# plot the reconstructed output
plot(f, t, reconstructed = TRUE)

# simulate taxonomy using fossilsim
beta = 0.5 # probability of symmetric speciation
lambda.a = 0.1  # rate of anagenesis
s = sim.taxonomy(t, beta, lambda.a)  
# plot the output
plot(s, t, legend.position = "bottomright")

Package vignettes

The following vignettes are available via CRAN and provide detailed examples:

• General introduction to the package
• Simulating taxonomy
• Simulating fossils
• Simulating FBD trees
• Exporting sampled ancestor trees
• Converting to paleotree format

For further information and examples see the package documentation

Contributors

Joëlle Barido-Sottani
Walker Pett Joseph O’Reilly
Rachel Warnock

Citation

Joëlle Barido-Sottani et al. 2019. Methods Evolution & Ecology. FossilSim: an R package for simulating fossil occurrence data under mechanistic models of preservation and recovery

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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