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:

install.packages("BiocManager")
BiocManager::install("ggtree")
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
• Ugnė Stolz
• 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