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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'. 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>).

Version: 0.7.2
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: 2024-03-04
DOI: 10.32614/CRAN.package.coala
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 Approximate Bayesian Computation
Importing Genetic Data into Coala
Examples
Adding Summary Statistics and Simulators
Using External Simulators
Introduction to Coala

Downloads:

Package source: coala_0.7.2.tar.gz
Windows binaries: r-devel: coala_0.7.2.zip, r-release: coala_0.7.2.zip, r-oldrel: coala_0.7.2.zip
macOS binaries: r-release (arm64): coala_0.7.2.tgz, r-oldrel (arm64): coala_0.7.2.tgz, r-release (x86_64): coala_0.7.2.tgz, r-oldrel (x86_64): coala_0.7.2.tgz
Old sources: coala archive

Reverse dependencies:

Reverse suggests: jaatha, jackalope

Linking:

Please use the canonical form https://CRAN.R-project.org/package=coala to link to this page.

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.