Simulation of Fossil and Taxonomy Data

Simulating taxonomy and fossil data on phylogenetic trees under mechanistic models of speciation, preservation and sampling.


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 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")

Package vignettes

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

For further information and examples see the package documentation

Contributors

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

News

Reference manual

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install.packages("FossilSim")

2.1.1 by Joelle Barido-Sottani, 14 hours ago


Browse source code at https://github.com/cran/FossilSim


Authors: Rachel Warnock [aut, cph] , Joelle Barido-Sottani [aut, cre, cph] , Walker Pett [aut, cph] , O'Reilly Joseph [aut, cph]


Documentation:   PDF Manual  


GPL-3 license


Imports ape, TreeSim

Suggests paleotree, knitr, rmarkdown, devtools


See at CRAN