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coalescentMCMC: MCMC Algorithms for the Coalescent

Flexible framework for coalescent analyses in R. It includes a main function running the MCMC algorithm, auxiliary functions for tree rearrangement, and some functions to compute population genetic parameters. Extended description can be found in Paradis (2020) <doi:10.1201/9780429466700>. For details on the MCMC algorithm, see Kuhner et al. (1995) <doi:10.1093/genetics/140.4.1421> and Drummond et al. (2002) <doi:10.1093/genetics/161.3.1307>.

Version: 0.4-4
Depends: ape, coda, lattice
Imports: Matrix, phangorn, splines, stats, utils
Published: 2022-04-22
DOI: 10.32614/CRAN.package.coalescentMCMC
Author: Emmanuel Paradis [aut, cre, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis at ird.fr>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
Citation: coalescentMCMC citation info
Materials: NEWS
In views: Bayesian
CRAN checks: coalescentMCMC results

Documentation:

Reference manual: coalescentMCMC.pdf
Vignettes: Coalescent Models
Running coalescentMCMC

Downloads:

Package source: coalescentMCMC_0.4-4.tar.gz
Windows binaries: r-devel: coalescentMCMC_0.4-4.zip, r-release: coalescentMCMC_0.4-4.zip, r-oldrel: coalescentMCMC_0.4-4.zip
macOS binaries: r-release (arm64): coalescentMCMC_0.4-4.tgz, r-oldrel (arm64): coalescentMCMC_0.4-4.tgz, r-release (x86_64): coalescentMCMC_0.4-4.tgz, r-oldrel (x86_64): coalescentMCMC_0.4-4.tgz
Old sources: coalescentMCMC archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=coalescentMCMC 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.