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FossilSim

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

The latest version can be installed in R using the packagedevtools:

install.packages("BiocManager")BiocManager::install("ggtree")library(devtools)install_github("fossilsim/fossilsim")

Quick start

Simulating data usingFossilSim can be as simple as thefollowing code snippets.

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

# simulate taxonomy using fossilsimbeta = 0.5 # probability of symmetric speciationlambda.a = 0.1  # rate of anagenesiss = sim.taxonomy(t, beta, lambda.a)  # plot the outputplot(s, t, legend.position = "bottomright")

Package vignettes

The following vignettes are available via CRAN and provide detailedexamples:

• Generalintroduction to the package
• Simulatingtaxonomy
• Simulatingfossils
• SimulatingFBD trees
• Exportingsampled ancestor trees
• Convertingto paleotree format