{
  "_id": "6a1f3840b401979e73428dcd",
  "Package": "rPBK",
  "Title": "Inference and Prediction of Generic Physiologically-Based\nKinetic Models",
  "Version": "0.2.5",
  "Authors@R": "c(\nperson(\"Virgile\", \"Baudrot\", role = c(\"aut\",\"cre\"), email = \"virgile.baudrot@qonfluens.com\"),\nperson(\"Sandrine\", \"Charles\", role = \"aut\"),\nperson(\"Christelle\", \"Lopes\", role = \"aut\"),\nperson(\"Ophélia\", \"Gestin\", role = \"ctb\"),\nperson(\"Dominique\", \"Lamonica\", role = \"ctb\"),\nperson(\"Aurélie\", \"Siberchicot\", role = \"ctb\")\n)",
  "BugReports": "https://gitlab.in2p3.fr/mosaic-software/rPBK/-/issues",
  "URL": "https://gitlab.in2p3.fr/mosaic-software/rPBK/",
  "Description": "Fit and simulate any kind of physiologically-based kinetic\n('PBK') models whatever the number of compartments. Moreover,\nit allows to account for any link between pairs of\ncompartments, as well as any link of each of the compartments\nwith the external medium. Such generic PBK models have today\napplications in pharmacology (PBPK models) to describe drug\neffects, in toxicology and ecotoxicology (PBTK models) to\ndescribe chemical substance effects. In case of exposure to a\nparent compound (drug or chemical) the 'rPBK' package allows to\nconsider metabolites, whatever their number and their phase (I,\nII, ...). Last but not least, package 'rPBK' can also be used\nfor dynamic flux balance analysis (dFBA) to deal with metabolic\nnetworks. See also Charles et al. (2022)\n<doi:10.1101/2022.04.29.490045>.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "Biarch": "true",
  "SystemRequirements": "GNU make",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "LazyData": "true",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-13 07:19:16 UTC",
    "User": "root"
  },
  "Author": "Virgile Baudrot [aut, cre], Sandrine Charles [aut], Christelle\nLopes [aut], Ophélia Gestin [ctb], Dominique Lamonica [ctb],\nAurélie Siberchicot [ctb]",
  "Maintainer": "Virgile Baudrot <virgile.baudrot@qonfluens.com>",
  "Config/pak/sysreqs": "make",
  "Repository": "https://virgile-baudrot.r-universe.dev",
  "Date/Publication": "2025-06-12 11:31:13 UTC",
  "RemoteUrl": "https://github.com/cran/rPBK",
  "RemoteRef": "HEAD",
  "RemoteSha": "7abd3d41e157946be646be041f86ca9b28c2496a",
  "MD5sum": "207f33ad830beacb3af4f1f42e99a973",
  "_user": "virgile-baudrot",
  "_type": "src",
  "_file": "rPBK_0.2.5.tar.gz",
  "_fileid": "d50ab427030703a20d176ceea629e3702511075d96d0aa034018a15c1d3f4e85",
  "_filesize": 669165,
  "_sha256": "d50ab427030703a20d176ceea629e3702511075d96d0aa034018a15c1d3f4e85",
  "_created": "2026-05-13T07:19:16.000Z",
  "_published": "2026-06-02T20:08:32.489Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79161820927,
      "time": 332,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6964023546"
    },
    {
      "job": 79161821015,
      "time": 345,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6964027421"
    },
    {
      "job": 79161821530,
      "time": 324,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6964021503"
    },
    {
      "job": 79161821172,
      "time": 344,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6964043180"
    },
    {
      "job": 79161821581,
      "time": 267,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "6964005319"
    },
    {
      "job": 79161821379,
      "time": 405,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "6964044197"
    },
    {
      "job": 79161820968,
      "time": 285,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6964020907"
    },
    {
      "job": 79161820808,
      "time": 648,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6964114175"
    },
    {
      "job": 79161820479,
      "time": 468,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6963926689"
    },
    {
      "job": 79161820406,
      "time": 146,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 79161821303,
      "time": 414,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6964046798"
    },
    {
      "job": 79161821335,
      "time": 380,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6964037432"
    },
    {
      "job": 79161820957,
      "time": 345,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6964026929"
    }
  ],
  "_buildurl": "https://github.com/r-universe/virgile-baudrot/actions/runs/25784207831",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/rPBK",
  "_commit": {
    "id": "7abd3d41e157946be646be041f86ca9b28c2496a",
    "author": "Virgile Baudrot <virgile.baudrot@qonfluens.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.2.5\n",
    "time": 1749727873
  },
  "_maintainer": {
    "name": "Virgile Baudrot",
    "email": "virgile.baudrot@qonfluens.com",
    "login": "virgile-baudrot",
    "uuid": 6065464
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4.0",
      "role": "Depends"
    },
    {
      "package": "BH",
      "version": ">= 1.66.0",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.0",
      "role": "LinkingTo"
    },
    {
      "package": "RcppEigen",
      "version": ">= 0.3.3.3.0",
      "role": "LinkingTo"
    },
    {
      "package": "RcppParallel",
      "version": ">= 5.0.1",
      "role": "LinkingTo"
    },
    {
      "package": "rstan",
      "version": ">= 2.26.0",
      "role": "LinkingTo"
    },
    {
      "package": "StanHeaders",
      "version": ">= 2.26.0",
      "role": "LinkingTo"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.0",
      "role": "Imports"
    },
    {
      "package": "rstan",
      "version": ">= 2.26.0",
      "role": "Imports"
    },
    {
      "package": "rstantools",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "loo",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-24",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "0.2.5",
      "date": "2025-06-12"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "virgile-baudrot",
      "count": 6,
      "uuid": 6065464
    }
  ],
  "_userbio": {
    "uuid": 6065464,
    "type": "user",
    "name": "vbaudrot"
  },
  "_downloads": {
    "count": 220,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rPBK"
  },
  "_searchresults": 3,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/rPBK.html",
    "manual.pdf"
  ],
  "_realowner": "virgile-baudrot",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.2.0",
      "date": "2022-09-01"
    },
    {
      "version": "0.2.1",
      "date": "2023-03-15"
    },
    {
      "version": "0.2.2",
      "date": "2023-09-11"
    },
    {
      "version": "0.2.3",
      "date": "2024-02-01"
    },
    {
      "version": "0.2.4",
      "date": "2024-02-26"
    },
    {
      "version": "0.2.5",
      "date": "2025-06-12"
    }
  ],
  "_exports": [
    "dataPBK",
    "export_interpolate",
    "fitPBK",
    "nested_model",
    "ppc"
  ],
  "_datasets": [
    {
      "name": "dataCompartment4",
      "title": "An example data set with 4 compartment",
      "object": "dataCompartment4",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "temps",
        "condition",
        "replicat",
        "intestin",
        "caecum",
        "cephalon",
        "reste"
      ],
      "rows": 21,
      "table": true,
      "tojson": true
    },
    {
      "name": "dataMaleGammarusSingle",
      "title": "An example data set with 1 compartment",
      "object": "dataMaleGammarusSingle",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "time",
        "expw",
        "replicate",
        "conc"
      ],
      "rows": 22,
      "table": true,
      "tojson": true
    },
    {
      "name": "fitPBK_C4",
      "title": "An example of fitPBK object",
      "object": "fitPBK_C4",
      "class": [
        "fitPBK",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "dataCompartment4",
      "title": "An example data set with 4 compartment",
      "topics": [
        "dataCompartment4"
      ]
    },
    {
      "page": "dataMaleGammarusSingle",
      "title": "An example data set with 1 compartment",
      "topics": [
        "dataMaleGammarusSingle"
      ]
    },
    {
      "page": "dataPBK",
      "title": "Create a list giving data and parameters to use in the model inference.",
      "topics": [
        "dataPBK",
        "dataPBK.data.frame",
        "nested_model",
        "nested_model.stanPBKdata"
      ]
    },
    {
      "page": "df_quant95_",
      "title": "Compute 95 credible intervals",
      "topics": [
        "df_quant95_"
      ]
    },
    {
      "page": "export_interpolate",
      "title": "Interpolate function implemented in Stan only export for checking",
      "topics": [
        "export_interpolate"
      ]
    },
    {
      "page": "fitPBK",
      "title": "Bayesian inference of TK model with Stan",
      "topics": [
        "fitPBK",
        "fitPBK.stanPBKdata"
      ]
    },
    {
      "page": "fitPBK_C4",
      "title": "An example of fitPBK object",
      "topics": [
        "fitPBK_C4"
      ]
    },
    {
      "page": "plot.fitPBK",
      "title": "Plotting method for 'fitPBK' objects",
      "topics": [
        "plot.fitPBK"
      ]
    },
    {
      "page": "PPC",
      "title": "Posterior predictive check plot",
      "topics": [
        "ppc",
        "ppc.fitPBK"
      ]
    }
  ],
  "_readme": "https://github.com/cran/rPBK/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "BH",
    "callr",
    "checkmate",
    "cli",
    "cpp11",
    "desc",
    "distributional",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "inline",
    "isoband",
    "labeling",
    "lifecycle",
    "loo",
    "magrittr",
    "matrixStats",
    "numDeriv",
    "pillar",
    "pkgbuild",
    "pkgconfig",
    "posterior",
    "processx",
    "ps",
    "QuickJSR",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RcppParallel",
    "rlang",
    "rstan",
    "rstantools",
    "S7",
    "scales",
    "StanHeaders",
    "tensorA",
    "tibble",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "Examples.Rmd",
      "filename": "Examples.html",
      "title": "Examples",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Single Compartment and Single Exposure : Male Gammarus Single",
        "Multiple Compartiment, Single Exposure - Default interaction",
        "Multiple Compartiment, Single Exposure : Change nesting"
      ],
      "created": "2022-09-01 14:10:02",
      "modified": "2022-09-01 14:10:02",
      "commits": 1
    }
  ],
  "_score": 2.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "rpbk",
  "_universes": [
    "virgile-baudrot"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.2.5",
      "date": "2026-05-13T07:23:29.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "7abd3d41e157946be646be041f86ca9b28c2496a",
      "fileid": "7a1cc8848e23927546d8289953225c88e25266d3407ac7ed0854c7215f6adbe8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/virgile-baudrot/actions/runs/25784207831"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.2.5",
      "date": "2026-05-13T07:23:37.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "7abd3d41e157946be646be041f86ca9b28c2496a",
      "fileid": "2af2ea71c09bcdede3b1979b9b80955b812263f7ad5051285f018b4864f47892",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/virgile-baudrot/actions/runs/25784207831"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.2.5",
      "date": "2026-05-13T07:23:23.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "7abd3d41e157946be646be041f86ca9b28c2496a",
      "fileid": "3c78226816f29f9fc8c9f639a8952d79f012b5630304803a35767a010c8b4c56",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/virgile-baudrot/actions/runs/25784207831"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.2.5",
      "date": "2026-05-13T07:24:31.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "7abd3d41e157946be646be041f86ca9b28c2496a",
      "fileid": "80b66eb0b5f08090efe884d291b554a45020b2792f3190cd5643d8b4aeb3378c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/virgile-baudrot/actions/runs/25784207831"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.2.5",
      "date": "2026-05-13T07:22:50.000Z",
      "arch": "aarch64",
      "commit": "7abd3d41e157946be646be041f86ca9b28c2496a",
      "fileid": "d36637bb0e10066a6a29dda1712c7f9763b0a7d35b7930a9f5daf9b8e86bce0f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/virgile-baudrot/actions/runs/25784207831"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.2.5",
      "date": "2026-05-13T07:23:34.000Z",
      "arch": "x86_64",
      "commit": "7abd3d41e157946be646be041f86ca9b28c2496a",
      "fileid": "c7d7c764055fd9ad8080ac1333af2755a06ff41b2413e94d9b1945cd112a4e88",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/virgile-baudrot/actions/runs/25784207831"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.2.5",
      "date": "2026-05-13T07:23:31.000Z",
      "arch": "aarch64",
      "commit": "7abd3d41e157946be646be041f86ca9b28c2496a",
      "fileid": "b436252c5705792d322679f2b617b8018e65e004fc451c5d1fa1cb9ac08571d0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/virgile-baudrot/actions/runs/25784207831"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.2.5",
      "date": "2026-05-13T07:25:36.000Z",
      "arch": "x86_64",
      "commit": "7abd3d41e157946be646be041f86ca9b28c2496a",
      "fileid": "04c4569aeb9135e2c2123019782222c11569b19e38f8eb2038beb066b96e2061",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/virgile-baudrot/actions/runs/25784207831"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.2.5",
      "date": "2026-05-13T07:22:55.000Z",
      "arch": "x86_64",
      "commit": "7abd3d41e157946be646be041f86ca9b28c2496a",
      "fileid": "f836bee860f170914901398ac69d577fa00bb3715069456c11187f97d90788cf",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/virgile-baudrot/actions/runs/25784207831"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.2.5",
      "date": "2026-05-13T07:22:42.000Z",
      "arch": "x86_64",
      "commit": "7abd3d41e157946be646be041f86ca9b28c2496a",
      "fileid": "7adabd8b6b1165bbb2c43e99ba2afd51430a4420c597fdb1c582290522fde440",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/virgile-baudrot/actions/runs/25784207831"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.2.5",
      "date": "2026-05-13T07:23:03.000Z",
      "arch": "x86_64",
      "commit": "7abd3d41e157946be646be041f86ca9b28c2496a",
      "fileid": "d25759b5c01f1667cfc8dc5b963491d6965d02614cb2008ba3be780f846924ca",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/virgile-baudrot/actions/runs/25784207831"
    }
  ]
}