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")
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")
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
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