{
  "_id": "6a1f0c88b401979e7341ccb4",
  "Package": "coalescentMCMC",
  "Version": "0.4-4",
  "Date": "2022-04-22",
  "Title": "MCMC Algorithms for the Coalescent",
  "Authors@R": "c(person(\"Emmanuel\", \"Paradis\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Emmanuel.Paradis@ird.fr\"))",
  "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) <doi:10.1201/9780429466700>. For\ndetails on the MCMC algorithm, see Kuhner et al. (1995)\n<doi:10.1093/genetics/140.4.1421> and Drummond et al. (2002)\n<doi:10.1093/genetics/161.3.1307>.",
  "License": "GPL (>= 2)",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-17 09:28:47 UTC",
    "User": "root"
  },
  "Author": "Emmanuel Paradis [aut, cre, cph]",
  "Maintainer": "Emmanuel Paradis <Emmanuel.Paradis@ird.fr>",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://emmanuelparadis.r-universe.dev",
  "Date/Publication": "2022-04-22 08:30:05 UTC",
  "RemoteUrl": "https://github.com/cran/coalescentMCMC",
  "RemoteRef": "HEAD",
  "RemoteSha": "2c49aab762f2aa4d36974419945b881c4273ddd2",
  "MD5sum": "4b279ce24bd5d4d189a5e9ce36c8de29",
  "_user": "emmanuelparadis",
  "_type": "src",
  "_file": "coalescentMCMC_0.4-4.tar.gz",
  "_fileid": "b4c4802942aa4d50794bc4f66803874c377cee2a45962c4657005873e39a2d3e",
  "_filesize": 468378,
  "_sha256": "b4c4802942aa4d50794bc4f66803874c377cee2a45962c4657005873e39a2d3e",
  "_created": "2026-05-17T09:28:47.000Z",
  "_published": "2026-06-02T17:02:00.464Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79126891369,
      "time": 130,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7041236967"
    },
    {
      "job": 79126891291,
      "time": 143,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7041238364"
    },
    {
      "job": 79126891470,
      "time": 127,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7041236763"
    },
    {
      "job": 79126891245,
      "time": 131,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7041237150"
    },
    {
      "job": 79126891433,
      "time": 121,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7041235959"
    },
    {
      "job": 79126891476,
      "time": 225,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7041248112"
    },
    {
      "job": 79126891227,
      "time": 106,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7041234427"
    },
    {
      "job": 79126891224,
      "time": 282,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7041254913"
    },
    {
      "job": 79126890133,
      "time": 186,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7041222572"
    },
    {
      "job": 79126890427,
      "time": 103,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7364497804"
    },
    {
      "job": 79126891246,
      "time": 95,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7041233151"
    },
    {
      "job": 79126891427,
      "time": 113,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7041235165"
    },
    {
      "job": 79126891177,
      "time": 96,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7041233299"
    }
  ],
  "_buildurl": "https://github.com/r-universe/emmanuelparadis/actions/runs/25987052699",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/coalescentMCMC",
  "_commit": {
    "id": "2c49aab762f2aa4d36974419945b881c4273ddd2",
    "author": "Emmanuel Paradis <Emmanuel.Paradis@ird.fr>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.4-4\n",
    "time": 1650616205
  },
  "_maintainer": {
    "name": "Emmanuel Paradis",
    "email": "emmanuel.paradis@ird.fr",
    "login": "emmanuelparadis",
    "description": "",
    "uuid": 10957055
  },
  "_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": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "emmanuelparadis",
      "count": 6,
      "uuid": 10957055
    }
  ],
  "_userbio": {
    "uuid": 10957055,
    "type": "user",
    "name": "Emmanuel Paradis"
  },
  "_downloads": {
    "count": 293,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/coalescentMCMC"
  },
  "_searchresults": 18,
  "_rbuild": "4.6.0",
  "_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"
    }
  ],
  "_exports": [
    ".coalescentMCMCenv",
    "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": 2.5563025007672873,
  "_indexed": true,
  "_nocasepkg": "coalescentmcmc",
  "_universes": [
    "emmanuelparadis"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.4-4",
      "date": "2026-05-17T09:30:45.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "2c49aab762f2aa4d36974419945b881c4273ddd2",
      "fileid": "9713049c867ffbf5d6b51dee6f175b8e536a63e368c8d1c95d7013ef531f43dd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emmanuelparadis/actions/runs/25987052699"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.4-4",
      "date": "2026-05-17T09:30:53.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "2c49aab762f2aa4d36974419945b881c4273ddd2",
      "fileid": "62d1b4e8dd35ae9a3ef25b12b4200ef7c1e7a2502f25379e36a6682935d2b0dc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emmanuelparadis/actions/runs/25987052699"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.4-4",
      "date": "2026-05-17T09:30:44.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "2c49aab762f2aa4d36974419945b881c4273ddd2",
      "fileid": "0fade98210d69a54e616e6f8d6b432fcccf8e5fa6e8ae019ca35b11ba212d1b6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emmanuelparadis/actions/runs/25987052699"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.4-4",
      "date": "2026-05-17T09:30:44.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "2c49aab762f2aa4d36974419945b881c4273ddd2",
      "fileid": "755da2c854bdd7a16dbcc63070e4f4b908a794336d6226bcc0469445b2409303",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emmanuelparadis/actions/runs/25987052699"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.4-4",
      "date": "2026-05-17T09:30:35.000Z",
      "arch": "aarch64",
      "commit": "2c49aab762f2aa4d36974419945b881c4273ddd2",
      "fileid": "7f57e6997a2bf62e04c19c530986017d2ff6bab76b5cc3aa95786292b793b301",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emmanuelparadis/actions/runs/25987052699"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.4-4",
      "date": "2026-05-17T09:31:36.000Z",
      "arch": "x86_64",
      "commit": "2c49aab762f2aa4d36974419945b881c4273ddd2",
      "fileid": "823474f70ba7054155f119ec9c60ab3906e3a20098802fd1a9480f231a895513",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emmanuelparadis/actions/runs/25987052699"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.4-4",
      "date": "2026-05-17T09:30:25.000Z",
      "arch": "aarch64",
      "commit": "2c49aab762f2aa4d36974419945b881c4273ddd2",
      "fileid": "bb6e0d5b603faf87eec07f80b8b097e1281e4166b490dbe877ada35b9d8a35fc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emmanuelparadis/actions/runs/25987052699"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.4-4",
      "date": "2026-05-17T09:32:36.000Z",
      "arch": "x86_64",
      "commit": "2c49aab762f2aa4d36974419945b881c4273ddd2",
      "fileid": "6c38dd738b510f5a25b22a92aaffcef1ca2faf9a6c9771b0e7ed8c4e7cf5a40b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emmanuelparadis/actions/runs/25987052699"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.4-4",
      "date": "2026-05-17T09:29:58.000Z",
      "arch": "x86_64",
      "commit": "2c49aab762f2aa4d36974419945b881c4273ddd2",
      "fileid": "3c16ce9ef0d9277c4b48f4510d830d77d894438a7d79e6782fbf64b2ae19b9cb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emmanuelparadis/actions/runs/25987052699"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.4-4",
      "date": "2026-05-17T09:30:11.000Z",
      "arch": "x86_64",
      "commit": "2c49aab762f2aa4d36974419945b881c4273ddd2",
      "fileid": "3c3d7d2fb1e016c81fc952e354eafdaf3c4faca1c09f57d3a91b9534cdbd683e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emmanuelparadis/actions/runs/25987052699"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.4-4",
      "date": "2026-05-17T09:29:57.000Z",
      "arch": "x86_64",
      "commit": "2c49aab762f2aa4d36974419945b881c4273ddd2",
      "fileid": "3ca6ce929e989ec398f58f9c97fda73802438a3bdae9f6a56426f1190d304dcc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emmanuelparadis/actions/runs/25987052699"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.4-4",
      "date": "2026-06-02T17:01:01.000Z",
      "arch": "emscripten",
      "commit": "2c49aab762f2aa4d36974419945b881c4273ddd2",
      "fileid": "1dc6db0c7db12868b0dc17b06747cd4f129f7fe7f075a68aa6d17aa7b4887fc4",
      "status": "success",
      "buildurl": "https://github.com/r-universe/emmanuelparadis/actions/runs/25987052699"
    }
  ]
}