Package: coalescentMCMC 0.4-4

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>.

Authors:Emmanuel Paradis [aut, cre, cph]

coalescentMCMC_0.4-4.tar.gz
coalescentMCMC_0.4-4.zip(r-4.7)coalescentMCMC_0.4-4.zip(r-4.6)coalescentMCMC_0.4-4.zip(r-4.5)
coalescentMCMC_0.4-4.tgz(r-4.6-x86_64)coalescentMCMC_0.4-4.tgz(r-4.6-arm64)coalescentMCMC_0.4-4.tgz(r-4.5-x86_64)coalescentMCMC_0.4-4.tgz(r-4.5-arm64)
coalescentMCMC_0.4-4.tar.gz(r-4.7-arm64)coalescentMCMC_0.4-4.tar.gz(r-4.7-x86_64)coalescentMCMC_0.4-4.tar.gz(r-4.6-arm64)coalescentMCMC_0.4-4.tar.gz(r-4.6-x86_64)
coalescentMCMC_0.4-4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
coalescentMCMC/json (API)
NEWS

# Install 'coalescentMCMC' in R:
install.packages('coalescentMCMC', repos = c('https://emmanuelparadis.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.56 score 18 scripts 293 downloads 16 exports 20 dependencies

Last updated from:2c49aab762. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK130
linux-devel-x86_64OK143
source / vignettesOK186
linux-release-arm64OK127
linux-release-x86_64OK131
macos-release-arm64OK106
macos-release-x86_64OK282
macos-oldrel-arm64OK121
macos-oldrel-x86_64OK225
windows-develOK95
windows-releaseOK96
windows-oldrelOK113
wasm-releaseOK103

Exports:.coalescentMCMCenvcleanMCMCtreescoalescentMCMCdcoaldcoal.lineardcoal.stepdcoal.timedcoal.time2getLastTreegetMCMCstatsgetMCMCtreesNeighborhoodRearrangementplotTHETAproba.coalescentsaveMCMCtreessim.coalescent

Dependencies:apeclicodacpp11digestfastmatchgenericsglueigraphlatticelifecyclemagrittrMatrixnlmephangornpkgconfigquadprogRcpprlangvctrs

Coalescent Models

Rendered fromCoalescentModels.Rnwusingutils::Sweaveon May 17 2026.

Last update: 2022-04-22
Started: 2012-10-02

Running coalescentMCMC

Rendered fromRunning_coalescentMCMC.Rnwusingutils::Sweaveon May 17 2026.

Last update: 2022-04-22
Started: 2012-10-02

Readme and manuals

Help Manual

Help pageTopics
Run MCMC for Coalescent TreesAIC.coalescentMCMC anova.coalescentMCMC BIC.coalescentMCMC coalescentMCMC logLik.coalescentMCMC
Density Functions of Some Time-Dependent Coalescent Modelsdcoal dcoal.linear dcoal.step dcoal.time dcoal.time2
Managing List of Trees From MCMCcleanMCMCtrees getLastTree getMCMCstats getMCMCtrees saveMCMCtrees
Plot THETA From coalescentMCMC OutputplotTHETA
Probability of Coalescenceproba.coalescent
Coalescent Simulation and Visualisationsim.coalescent
Subset MCMC Outputsubset.coalescentMCMC
Trees Operators for Running MCMCNeighborhoodRearrangement TipInterchange treeOperators