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:
coalescentMCMC_0.4-4.tar.gz
coalescentMCMC_0.4-4.zip(r-4.5)coalescentMCMC_0.4-4.zip(r-4.4)coalescentMCMC_0.4-4.zip(r-4.3)
coalescentMCMC_0.4-4.tgz(r-4.4-x86_64)coalescentMCMC_0.4-4.tgz(r-4.4-arm64)coalescentMCMC_0.4-4.tgz(r-4.3-x86_64)coalescentMCMC_0.4-4.tgz(r-4.3-arm64)
coalescentMCMC_0.4-4.tar.gz(r-4.5-noble)coalescentMCMC_0.4-4.tar.gz(r-4.4-noble)
coalescentMCMC_0.4-4.tgz(r-4.4-emscripten)coalescentMCMC_0.4-4.tgz(r-4.3-emscripten)
coalescentMCMC.pdf |coalescentMCMC.html✨
coalescentMCMC/json (API)
NEWS
| # Install 'coalescentMCMC' in R: |
| install.packages('coalescentMCMC', repos = c('https://emmanuelparadis.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 years agofrom:2c49aab762. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 07 2024 |
| R-4.5-win-x86_64 | OK | Nov 07 2024 |
| R-4.5-linux-x86_64 | OK | Nov 07 2024 |
| R-4.4-win-x86_64 | OK | Nov 07 2024 |
| R-4.4-mac-x86_64 | OK | Nov 07 2024 |
| R-4.4-mac-aarch64 | OK | Nov 07 2024 |
| R-4.3-win-x86_64 | OK | Nov 07 2024 |
| R-4.3-mac-x86_64 | OK | Nov 07 2024 |
| R-4.3-mac-aarch64 | OK | Nov 07 2024 |
Exports:.coalescentMCMCenvcleanMCMCtreescoalescentMCMCdcoaldcoal.lineardcoal.stepdcoal.timedcoal.time2getLastTreegetMCMCstatsgetMCMCtreesNeighborhoodRearrangementplotTHETAproba.coalescentsaveMCMCtreessim.coalescent
Dependencies:apeclicodacpp11digestfastmatchgenericsglueigraphlatticelifecyclemagrittrMatrixnlmephangornpkgconfigquadprogRcpprlangvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Run MCMC for Coalescent Trees | AIC.coalescentMCMC anova.coalescentMCMC BIC.coalescentMCMC coalescentMCMC logLik.coalescentMCMC |
| Density Functions of Some Time-Dependent Coalescent Models | dcoal dcoal.linear dcoal.step dcoal.time dcoal.time2 |
| Managing List of Trees From MCMC | cleanMCMCtrees getLastTree getMCMCstats getMCMCtrees saveMCMCtrees |
| Plot THETA From coalescentMCMC Output | plotTHETA |
| Probability of Coalescence | proba.coalescent |
| Coalescent Simulation and Visualisation | sim.coalescent |
| Subset MCMC Output | subset.coalescentMCMC |
| Trees Operators for Running MCMC | NeighborhoodRearrangement TipInterchange treeOperators |
