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✨
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 342 downloads 16 exports 20 dependencies

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

TargetResultTimeFilesSyslog
linux-devel-arm64OK122
linux-devel-x86_64OK179
source / vignettesOK213
linux-release-arm64OK127
linux-release-x86_64OK129
macos-release-arm64OK98
macos-release-x86_64OK267
macos-oldrel-arm64OK108
macos-oldrel-x86_64OK234
windows-develOK94
windows-releaseOK91
windows-oldrelOK87
wasm-releaseOK104

Exports:.coalescentMCMCenvcleanMCMCtreescoalescentMCMCdcoaldcoal.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