coala: A Framework for Coalescent Simulation

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'.

Version: 0.7.0
Depends: R (≥ 3.1.0)
Imports: assertthat (≥ 0.1), digest, methods, parallel, R6 (≥ 2.0.1), Rcpp (≥ 0.11.0), rehh (≥ 3.0.0), scrm (≥ 1.6.0-2), stats, utils
LinkingTo: Rcpp, RcppArmadillo (≥ 0.3.810.0)
Suggests: abc (≥ 2.0), knitr, PopGenome (≥ 2.1.0), phyclust (≥ 0.1-16), rmarkdown, testthat (≥ 0.11.0)
Published: 2022-08-05
Author: Paul Staab [aut], Dirk Metzler [aut, ths, cre], Jorge E. Amaya Romero [ctb]
Maintainer: Dirk Metzler <metzler at bio.lmu.de>
BugReports: https://github.com/statgenlmu/coala/issues
License: MIT + file LICENSE
URL: https://github.com/statgenlmu/coala
NeedsCompilation: yes
Citation: coala citation info
Materials: README NEWS
CRAN checks: coala results

Documentation:

Reference manual: coala.pdf
Vignettes: Using coala for ABC
Calculating Summary Statistics for Genetic Data
Examples
Extending coala
Installing ms, msms and seqgen
Introduction

Downloads:

Package source: coala_0.7.0.tar.gz
Windows binaries: r-devel: coala_0.7.0.zip, r-release: coala_0.7.0.zip, r-oldrel: coala_0.6.1.zip
macOS binaries: r-release (arm64): coala_0.7.0.tgz, r-oldrel (arm64): coala_0.7.0.tgz, r-release (x86_64): coala_0.7.0.tgz, r-oldrel (x86_64): coala_0.7.0.tgz
Old sources: coala archive

Reverse dependencies:

Reverse suggests: jaatha, jackalope

Linking:

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