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:
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 output plot(f, t)
# 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")
The following vignettes are available via CRAN and provide detailed examples:
Joëlle Barido-Sottani Walker Pett Joseph O'Reilly Rachel Warnock
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
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