{ "_id": "6a62391635834fefe99ecaa8", "Package": "coalescentMCMC", "Version": "0.5", "Date": "2026-07-23", "Title": "MCMC Algorithms for the Coalescent", "Authors@R": "person(\"Emmanuel\", \"Paradis\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Emmanuel.Paradis@ird.fr\", comment = c(ORCID = \"0000-0003-3092-2199\"))", "ZipData": "no", "Description": "Flexible framework for coalescent analyses in R. It\nincludes a main function running the MCMC algorithm, auxiliary\nfunctions for tree rearrangement, and some functions to compute\npopulation genetic parameters. Extended description can be\nfound in Paradis (2020) . For\ndetails on the MCMC algorithm, see Kuhner et al. (1995)\n and Drummond et al. (2002)\n.", "License": "GPL (>= 2)", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-23 15:49:16 UTC", "User": "root" }, "Author": "Emmanuel Paradis [aut, cre, cph] (ORCID:\n)", "Maintainer": "Emmanuel Paradis ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-07-23 10:10:02 UTC", "RemoteUrl": "https://github.com/cran/coalescentMCMC", "RemoteRef": "HEAD", "RemoteSha": "821fb04eed4df4207441591989ac87bb351d476a", "_user": "cran", "_type": "src", "_file": "coalescentMCMC_0.5.tar.gz", "_fileid": "https://r2.ropensci.org/61857a0371f1d73ba3c994e46e20f358fd1dee447ba6f8a531ebd28264ae3b9e", "_filesize": 471027, "_sha256": "61857a0371f1d73ba3c994e46e20f358fd1dee447ba6f8a531ebd28264ae3b9e", "_expires": "2026-10-31T15:53:56.000Z", "_created": "2026-07-23T15:49:16.000Z", "_published": "2026-07-23T15:53:58.296Z", "_jobs": [ { "job": 89257993908, "time": 112, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8569841931" }, { "job": 89257993985, "time": 172, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8569857981" }, { "job": 89257993903, "time": 120, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8569846161" }, { "job": 89257993995, "time": 145, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8569859120" }, { "job": 89256900578, "time": 246, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8569780778" }, { "job": 89257993782, "time": 112, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8569841390" }, { "job": 89257993822, "time": 236, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8569894500" }, { "job": 89257993832, "time": 173, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8569873664" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/cran/actions/runs/30021981276", "_status": "success", "_upstream": "https://github.com/cran/coalescentMCMC", "_commit": { "id": "821fb04eed4df4207441591989ac87bb351d476a", "author": "Emmanuel Paradis ", "committer": "cran-robot ", "message": "version 0.5\n", "time": 1784801402 }, "_maintainer": { "name": "Emmanuel Paradis", "email": "emmanuel.paradis@ird.fr", "login": "emmanuelparadis", "description": "", "uuid": 10957055, "orcid": "0000-0003-3092-2199" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "ape", "role": "Depends" }, { "package": "coda", "role": "Depends" }, { "package": "lattice", "role": "Depends" }, { "package": "Matrix", "role": "Imports" }, { "package": "phangorn", "role": "Imports" }, { "package": "splines", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-30", "n": 1 } ], "_tags": [ { "name": "0.5", "date": "2026-07-23" } ], "_stars": 0, "_contributors": [ { "user": "emmanuelparadis", "count": 7, "uuid": 10957055 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 623, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 341, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/coalescentMCMC" }, "_searchresults": 22, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/coalescentMCMC.html", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "emmanuelparadis", "_cranurl": false, "_releases": [ { "version": "0.1", "date": "2012-10-08" }, { "version": "0.2", "date": "2013-07-19" }, { "version": "0.3", "date": "2013-10-27" }, { "version": "0.4", "date": "2013-12-04" }, { "version": "0.4-1", "date": "2015-03-03" }, { "version": "0.4-4", "date": "2022-04-22" }, { "version": "0.5", "date": "2026-07-23" } ], "_exports": [ "cleanMCMCtrees", "coalescentMCMC", "dcoal", "dcoal.linear", "dcoal.step", "dcoal.time", "dcoal.time2", "getLastTree", "getMCMCstats", "getMCMCtrees", "NeighborhoodRearrangement", "plotTHETA", "proba.coalescent", "saveMCMCtrees", "sim.coalescent" ], "_help": [ { "page": "coalesceMCMC", "title": "Run MCMC for Coalescent Trees", "topics": [ "AIC.coalescentMCMC", "anova.coalescentMCMC", "BIC.coalescentMCMC", "coalescentMCMC", "logLik.coalescentMCMC" ] }, { "page": "dcoal", "title": "Density Functions of Some Time-Dependent Coalescent Models", "topics": [ "dcoal", "dcoal.linear", "dcoal.step", "dcoal.time", "dcoal.time2" ] }, { "page": "getMCMCtrees", "title": "Managing List of Trees From MCMC", "topics": [ "cleanMCMCtrees", "getLastTree", "getMCMCstats", "getMCMCtrees", "saveMCMCtrees" ] }, { "page": "plotTHETA", "title": "Plot THETA From coalescentMCMC Output", "topics": [ "plotTHETA" ] }, { "page": "proba.coalescent", "title": "Probability of Coalescence", "topics": [ "proba.coalescent" ] }, { "page": "sim.coalescent", "title": "Coalescent Simulation and Visualisation", "topics": [ "sim.coalescent" ] }, { "page": "subset.coalescentMCMC", "title": "Subset MCMC Output", "topics": [ "subset.coalescentMCMC" ] }, { "page": "treeOperators", "title": "Trees Operators for Running MCMC", "topics": [ "NeighborhoodRearrangement", "TipInterchange", "treeOperators" ] } ], "_rundeps": [ "ape", "cli", "coda", "cpp11", "digest", "fastmatch", "generics", "glue", "igraph", "lattice", "lifecycle", "magrittr", "Matrix", "nlme", "phangorn", "pkgconfig", "quadprog", "Rcpp", "rlang", "vctrs" ], "_vignettes": [ { "source": "CoalescentModels.Rnw", "filename": "CoalescentModels.pdf", "title": "Coalescent Models", "engine": "utils::Sweave", "headings": [], "created": "2012-10-02", "modified": "2022-04-22 08:30:05", "commits": 3 }, { "source": "Running_coalescentMCMC.Rnw", "filename": "Running_coalescentMCMC.pdf", "title": "Running coalescentMCMC", "engine": "utils::Sweave", "headings": [], "created": "2012-10-02", "modified": "2022-04-22 08:30:05", "commits": 5 } ], "_score": 2.6434526764861874, "_indexed": false, "_nocasepkg": "coalescentmcmc", "_universes": [ "cran" ], "_indexurl": "https://emmanuelparadis.r-universe.dev/coalescentMCMC", "_previous": "0.4-4", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.5", "date": "2026-07-23T15:51:07.000Z", "distro": "resolute", "arch": "aarch64", "commit": "821fb04eed4df4207441591989ac87bb351d476a", "fileid": "https://r2.ropensci.org/67363257e497ca7711c3c9f99b7edbb1931aac32946096811a0b69e1f6b1a628", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/30021981276" }, { "r": "4.7.0", "os": "linux", "version": "0.5", "date": "2026-07-23T15:51:25.000Z", "distro": "resolute", "arch": "x86_64", "commit": "821fb04eed4df4207441591989ac87bb351d476a", "fileid": "https://r2.ropensci.org/2ab6312ba4bd036c721a968366241ca388697a76919e344e10a59d6d82621953", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/30021981276" }, { "r": "4.6.1", "os": "linux", "version": "0.5", "date": "2026-07-23T15:51:11.000Z", "distro": "resolute", "arch": "aarch64", "commit": "821fb04eed4df4207441591989ac87bb351d476a", "fileid": "https://r2.ropensci.org/0bc6176630ce2bd62d16658a5daa58904961070669ae771cb47076b2b181ac5a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/30021981276" }, { "r": "4.6.1", "os": "linux", "version": "0.5", "date": "2026-07-23T15:51:27.000Z", "distro": "resolute", "arch": "x86_64", "commit": "821fb04eed4df4207441591989ac87bb351d476a", "fileid": "https://r2.ropensci.org/d0766ce8cbbebd986b4c96635e0ed95d0bf8a336589f83b6a902cec2381ed185", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/30021981276" }, { "r": "4.6.0", "os": "wasm", "version": "0.5", "date": "2026-07-23T15:51:30.000Z", "arch": "emscripten", "commit": "821fb04eed4df4207441591989ac87bb351d476a", "fileid": "https://r2.ropensci.org/ee57162a982e48aab9cfc3f83d80ee5e34055bd6ebce390dbc992f9266970fc6", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/30021981276" }, { "r": "4.7.0", "os": "win", "version": "0.5", "date": "2026-07-23T15:52:38.000Z", "arch": "aarch64", "commit": "821fb04eed4df4207441591989ac87bb351d476a", "fileid": "https://r2.ropensci.org/3d08b21f4d85898a439adb33d487282541b8d53642d1da9269464185c174b83c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/30021981276" }, { "r": "4.7.0", "os": "win", "version": "0.5", "date": "2026-07-23T15:51:43.000Z", "arch": "x86_64", "commit": "821fb04eed4df4207441591989ac87bb351d476a", "fileid": "https://r2.ropensci.org/2e136be4d7f575d1a68e73ff27bff062e4444e8989a9a82e76a3b176b2069680", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/30021981276" } ] }