Package: coalescentMCMC 0.5

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_0.5.tar.gz
coalescentMCMC_0.5.zip(r-4.7-x86_64)coalescentMCMC_0.5.zip(r-4.7-arm64)coalescentMCMC_0.5.zip(r-4.6-x86_64)coalescentMCMC_0.5.zip(r-4.6-arm64)coalescentMCMC_0.5.zip(r-4.5-x86_64)
coalescentMCMC_0.5.tgz(r-4.6-x86_64)coalescentMCMC_0.5.tgz(r-4.6-arm64)coalescentMCMC_0.5.tgz(r-4.5-x86_64)coalescentMCMC_0.5.tgz(r-4.5-arm64)
coalescentMCMC_0.5.tar.gz(r-4.7-arm64)coalescentMCMC_0.5.tar.gz(r-4.7-x86_64)coalescentMCMC_0.5.tar.gz(r-4.6-arm64)coalescentMCMC_0.5.tar.gz(r-4.6-x86_64)
coalescentMCMC_0.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
coalescentMCMC/json (API)

# 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.

2.64 score 22 scripts 393 downloads 15 exports 20 dependencies

Last updated from:821fb04eed. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK125
linux-devel-x86_64OK141
source / vignettesOK236
linux-release-arm64OK116
linux-release-x86_64OK190
macos-release-arm64OK143
macos-release-x86_64OK229
macos-oldrel-arm64OK87
macos-oldrel-x86_64OK304
windows-devel-arm64OK207
windows-devel-x86_64OK133
windows-release-arm64OK192
windows-release-x86_64OK103
windows-oldrel-x86_64OK85
wasm-releaseOK105

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

Dependencies:apeclicodacpp11digestfastmatchgenericsglueigraphlatticelifecyclemagrittrMatrixnlmephangornpkgconfigquadprogRcpprlangvctrs

Coalescent Models
Rendered fromCoalescentModels.Rnwusingutils::Sweave

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

Running coalescentMCMC
Rendered fromRunning_coalescentMCMC.Rnwusingutils::Sweave

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