coala

coala-package

This package allows to specify and simulate coalescent models from
within R. The <code>introduction</code> vignette is a good place to start.

Coalescent simulators can rapidly simulate biological sequences
evolving according to a given model of evolution.
You can use this package to specify such models, to conduct the simulations
and to calculate additional statistics from the results (Staab, Metzler,
2016 <doi:10.1093/bioinformatics/btw098>).
It relies on existing simulators for doing the simulation, and currently
supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites
mutation models by combining the simulators with the program 'seq-gen'.
Coala provides functions for calculating certain summary statistics, which
can also be applied to actual biological data.
One possibility to import data is through the 'PopGenome' package
(<https://github.com/pievos101/PopGenome>).

Dirk Metzler

A Framework for Coalescent Simulation

Paul Staab

Jorge E. Amaya Romero

coala-package function

Maintainer: Dirk Metzler <a href="/link/metzler%40bio.lmu.de?package=coala&version=0.7.2" data-mini-rdoc="coala::metzler@bio.lmu.de">metzler@bio.lmu.de</a> [thesis advisor]
Authors:<ul>
<li>Paul Staab <a href="/link/develop%40paulstaab.de?package=coala&version=0.7.2" data-mini-rdoc="coala::develop@paulstaab.de">develop@paulstaab.de</a></li>
</ul>Other contributors:<ul>
<li>Jorge E. Amaya Romero [contributor]</li>
</ul>

Author

A Framework for Coalescent Simulation in R — coala-package

Maintainer: Dirk Metzler <a href='mailto:metzler@bio.lmu.de'>metzler@bio.lmu.de</a> [thesis advisor]
Authors:<ul>
<li>Paul Staab <a href='mailto:develop@paulstaab.de'>develop@paulstaab.de</a></li>
</ul>

Other contributors:<ul>
<li>Jorge E. Amaya Romero [contributor]</li>
</ul>

coala-package: A Framework for Coalescent Simulation in R

Description

Arguments

Author

See Also