simulator_scrm {coala}

Simulator: scrm

Description

This function adds the simulator 'scrm' to the list of available simulators. It is provided via the CRAN package scrm and should be always installed alongside with coala. It should be activated automatically, and this function is only needed to change it priority.

Usage

activate_scrm(priority = 400)

Arguments

priority

The priority for this simulator. If multiple simulators can simulate a model, the one with the highest priority will be used.

References

Paul R. Staab, Sha Zhu, Dirk Metzler and Gerton Lunter (2015). "scrm: efficiently simulating long sequences using the approximated coalescent with recombination." Bioinformatics, 31(10), pp. 1680-1682. http://dx.doi.org/10.1093/bioinformatics/btu861

See Also

Other simulators: simulator_ms, simulator_msms, simulator_seqgen

Examples

# Change scrm's priority
model <- coal_model(10, 1) + feat_mutation(5)
model # scrm is used by default
activate_scrm(250)
model # Now ms is used instead (if installed)
activate_scrm(550)
model # Now scrm is used again