The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
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:
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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.