{
  "_id": "6a1edfb3b401979e73410657",
  "Package": "denim",
  "Type": "Package",
  "Title": "Generate and Simulate Deterministic Compartmental Models",
  "Version": "1.2.3",
  "Date": "2026-01-14",
  "Authors@R": "c(\nperson(\"Thinh\", \"Ong\", , \"thinhop@oucru.org\", role = c(\"aut\", \"cph\"),\ncomment = c(ORCID = \"0000-0001-6772-9291\")),\nperson(\"Anh\", \"Phan\", , \"anhptq@oucru.org\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0000-2129-435X\")),\nperson(\"Marc\", \"Choisy\", , \"mchoisy@oucru.org\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-5187-6390\")),\nperson(\"Niels\", \"Lohman\", ,role = c(\"ctb\", \"cph\"),\ncomment=\"Author of the bundled JSON C++ library\"),\nperson(\"Bjoern\", \"Hoehrmann\", ,email = \"bjoern@hoehrmann.de\", role = c(\"ctb\", \"cph\"),\ncomment=\"Author of UTF-8 validation code in the bundled JSON C++ library\"),\nperson(\"Florian\", \"Loitsch\", ,role = c(\"ctb\", \"cph\"),\ncomment=\"Author of the binary to decimal floating-point conversion code in the bundled JSON C++ library\"),\nperson(\"Ingo\", \"Berg\", ,role = c(\"ctb\", \"cph\"),\ncomment=\"Author of the bundled MuParser C++ library\")\n)",
  "Description": "R package to build and simulate deterministic\ncompartmental models that can be semi-Markovian. Length of stay\nin each compartment can be defined to follow a parametric\ndistribution (d_exponential(), d_gamma(), d_weibull(),\nd_lognormal()) or a non-parametric distribution\n(nonparametric()).",
  "License": "MIT + file LICENSE",
  "URL": "https://drthinhong.com/denim/, https://github.com/thinhong/denim",
  "BugReports": "https://github.com/thinhong/denim/issues",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "cmake make libuv1-dev",
  "Repository": "https://thinhong.r-universe.dev",
  "Date/Publication": "2026-01-20 05:36:17 UTC",
  "RemoteUrl": "https://github.com/thinhong/denim",
  "RemoteRef": "HEAD",
  "RemoteSha": "439059c4a9823e293e16e333cc0621e169836262",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-20 07:34:26 UTC",
    "User": "root"
  },
  "Author": "Thinh Ong [aut, cph] (ORCID: <https://orcid.org/0000-0001-6772-9291>),\nAnh Phan [aut, cre] (ORCID: <https://orcid.org/0009-0000-2129-435X>),\nMarc Choisy [aut] (ORCID: <https://orcid.org/0000-0002-5187-6390>),\nNiels Lohman [ctb, cph] (Author of the bundled JSON C++ library),\nBjoern Hoehrmann [ctb, cph] (Author of UTF-8 validation code in the\nbundled JSON C++ library),\nFlorian Loitsch [ctb, cph] (Author of the binary to decimal\nfloating-point conversion code in the bundled JSON C++ library),\nIngo Berg [ctb, cph] (Author of the bundled MuParser C++ library)",
  "Maintainer": "Anh Phan <anhptq@oucru.org>",
  "MD5sum": "9a078caea6ca3c348cbc13fe16d1b23f",
  "_user": "thinhong",
  "_type": "src",
  "_file": "denim_1.2.3.tar.gz",
  "_fileid": "ea1258bc237dfdefe00d28f80e7b9a5976f41c5c68307cd402ed8016bf1006f5",
  "_filesize": 3912243,
  "_sha256": "ea1258bc237dfdefe00d28f80e7b9a5976f41c5c68307cd402ed8016bf1006f5",
  "_created": "2026-05-20T07:34:26.000Z",
  "_published": "2026-06-02T13:50:43.604Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79086099635,
      "time": 222,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7103987649"
    },
    {
      "job": 79086099498,
      "time": 210,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7103984171"
    },
    {
      "job": 79086100056,
      "time": 216,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7103986518"
    },
    {
      "job": 79086099762,
      "time": 199,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7103980691"
    },
    {
      "job": 79086099805,
      "time": 250,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7103981461"
    },
    {
      "job": 79086099637,
      "time": 329,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7104015091"
    },
    {
      "job": 79086099953,
      "time": 257,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7103983656"
    },
    {
      "job": 79086100356,
      "time": 316,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7104011700"
    },
    {
      "job": 79086098312,
      "time": 287,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7103917151"
    },
    {
      "job": 79086098338,
      "time": 181,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7359597487"
    },
    {
      "job": 79086099244,
      "time": 181,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7103976077"
    },
    {
      "job": 79086099796,
      "time": 196,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7103979749"
    },
    {
      "job": 79086100033,
      "time": 184,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7103976455"
    }
  ],
  "_buildurl": "https://github.com/r-universe/thinhong/actions/runs/26148121655",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/thinhong/denim",
  "_commit": {
    "id": "439059c4a9823e293e16e333cc0621e169836262",
    "author": "Quynh Anh <90673616+quingzz@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #49 from thinhong/reviewer-comments\n\nupdate CRAN submission details",
    "time": 1768887377
  },
  "_maintainer": {
    "name": "Anh Phan",
    "email": "anhptq@oucru.org",
    "login": "quingzz",
    "description": "Research Assistant @OUCRU-Modelling ",
    "uuid": 90673616
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "testthat",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.6",
      "role": "Imports"
    },
    {
      "package": "colorspace",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "glue",
      "role": "Imports"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "waldo",
      "role": "Suggests"
    },
    {
      "package": "xml2",
      "role": "Suggests"
    },
    {
      "package": "deSolve",
      "role": "Suggests"
    },
    {
      "package": "tidyverse",
      "role": "Suggests"
    },
    {
      "package": "DiagrammeR",
      "role": "Suggests"
    }
  ],
  "_owner": "thinhong",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-21",
      "n": 1
    },
    {
      "week": "2025-23",
      "n": 1
    },
    {
      "week": "2025-24",
      "n": 3
    },
    {
      "week": "2025-30",
      "n": 1
    },
    {
      "week": "2025-31",
      "n": 6
    },
    {
      "week": "2025-32",
      "n": 6
    },
    {
      "week": "2025-34",
      "n": 2
    },
    {
      "week": "2025-52",
      "n": 2
    },
    {
      "week": "2026-01",
      "n": 1
    },
    {
      "week": "2026-04",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "v1.2.3",
      "date": "2025-12-31"
    },
    {
      "name": "v1.2.3-z",
      "date": "2026-01-20"
    }
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "quingzz",
      "count": 125,
      "uuid": 90673616
    },
    {
      "user": "thinhong",
      "count": 82,
      "uuid": 34956551
    },
    {
      "user": "choisy",
      "count": 10,
      "uuid": 12168614
    },
    {
      "user": "tuyenhn",
      "count": 4,
      "uuid": 47712557
    }
  ],
  "_userbio": {
    "uuid": 34956551,
    "type": "user",
    "name": "Thinh Ong"
  },
  "_downloads": {
    "count": 513,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/denim"
  },
  "_devurl": "https://github.com/thinhong/denim",
  "_pkgdown": "https://drthinhong.com/denim/",
  "_searchresults": 17,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/denim.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/thinhong/denim",
  "_realowner": "thinhong",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2024-06-05"
    },
    {
      "version": "1.0.1",
      "date": "2025-03-17"
    },
    {
      "version": "1.1.0",
      "date": "2025-05-16"
    },
    {
      "version": "1.2.0",
      "date": "2025-05-30"
    },
    {
      "version": "1.2.1",
      "date": "2025-06-02"
    },
    {
      "version": "1.2.2",
      "date": "2025-08-21"
    },
    {
      "version": "1.2.3",
      "date": "2026-01-14"
    }
  ],
  "_exports": [
    "d_exponential",
    "d_gamma",
    "d_lognormal",
    "d_weibull",
    "denim_dsl",
    "mathexpr",
    "nonparametric",
    "sim"
  ],
  "_help": [
    {
      "page": "denim-package",
      "title": "denim",
      "topics": [
        "denim-package",
        "denim"
      ]
    },
    {
      "page": "d_exponential",
      "title": "Discrete exponential distribution",
      "topics": [
        "d_exponential"
      ]
    },
    {
      "page": "d_gamma",
      "title": "Discrete gamma distribution",
      "topics": [
        "d_gamma"
      ]
    },
    {
      "page": "d_lognormal",
      "title": "Discrete log-normal distribution",
      "topics": [
        "d_lognormal"
      ]
    },
    {
      "page": "d_weibull",
      "title": "Discrete Weibull distribution",
      "topics": [
        "d_weibull"
      ]
    },
    {
      "page": "denim_dsl",
      "title": "Define transitions using denim's domain-specific language (DSL)",
      "topics": [
        "denim_dsl"
      ]
    },
    {
      "page": "nonparametric",
      "title": "Nonparametric distribution transition",
      "topics": [
        "nonparametric"
      ]
    },
    {
      "page": "plot.denim",
      "title": "Overloaded plot function for denim object",
      "topics": [
        "plot.denim"
      ]
    },
    {
      "page": "sim",
      "title": "Simulator for deterministic discrete time model with memory",
      "topics": [
        "sim"
      ]
    }
  ],
  "_pkglogo": "https://github.com/thinhong/denim/raw/HEAD/man/figures/logo.svg",
  "_readme": "https://github.com/thinhong/denim/raw/HEAD/README.md",
  "_rundeps": [
    "brio",
    "callr",
    "cli",
    "colorspace",
    "crayon",
    "desc",
    "diffobj",
    "evaluate",
    "fs",
    "glue",
    "jsonlite",
    "lifecycle",
    "magrittr",
    "pkgbuild",
    "pkgload",
    "praise",
    "processx",
    "ps",
    "R6",
    "Rcpp",
    "rlang",
    "rprojroot",
    "testthat",
    "waldo",
    "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": "denim_dsl.Rmd",
      "filename": "denim_dsl.html",
      "title": "denim DSL",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Model definition in denim",
        "Denim DSL",
        "Define a classic SIR model",
        "Time varying transition",
        "R list"
      ],
      "created": "2025-06-03 06:45:48",
      "modified": "2025-07-30 09:12:26",
      "commits": 5
    },
    {
      "source": "denim.Rmd",
      "filename": "denim.html",
      "title": "denim: deterministic model with memory",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Simple SIR model with gamma distributed lengths of stay",
        "2. How the algorithm work?",
        "3. Waiting time distribution",
        "4. Multiple transitions from a compartment",
        "5. Additional examples",
        "Example 1",
        "Example 2"
      ],
      "created": "2022-03-24 04:19:37",
      "modified": "2026-01-20 05:36:17",
      "commits": 25
    },
    {
      "source": "deSolve_to_denim.Rmd",
      "filename": "deSolve_to_denim.html",
      "title": "deSolve to denim",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Migrate deSolve code to denim",
        "Original code in deSolve",
        "Model definition",
        "Model configurations",
        "Simulation",
        "Compare output"
      ],
      "created": "2024-12-10 11:04:51",
      "modified": "2025-08-01 05:11:39",
      "commits": 12
    },
    {
      "source": "nonparametric.Rmd",
      "filename": "nonparametric.html",
      "title": "nonparametric distribution",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Non-parametric vs parametric",
        "Example 1",
        "Example 2"
      ],
      "created": "2025-06-03 06:45:48",
      "modified": "2025-07-29 07:46:18",
      "commits": 3
    },
    {
      "source": "multinomial.Rmd",
      "filename": "multinomial.html",
      "title": "transition to multiple states",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Transition to multiple states in denim",
        "2. Multinomial in denim",
        "2.1. Model definition",
        "Proportion normalization",
        "2.2. Example model",
        "Model definition in denim",
        "Equivalent model definition in deSolve",
        "Run simulation and compare",
        "3. Competing risks in denim",
        "3.1. Model definition",
        "3.2. Example model"
      ],
      "created": "2025-05-23 06:58:40",
      "modified": "2025-07-30 09:12:26",
      "commits": 5
    }
  ],
  "_score": 6.582631439489637,
  "_indexed": true,
  "_nocasepkg": "denim",
  "_universes": [
    "thinhong",
    "quingzz"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.3",
      "date": "2026-05-20T07:38:08.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "439059c4a9823e293e16e333cc0621e169836262",
      "fileid": "b5d02ef81d7f2d952c27876bbab752cf019d821e3f61ce0dc72dfe04105838a0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/thinhong/actions/runs/26148121655"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.3",
      "date": "2026-05-20T07:37:56.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "439059c4a9823e293e16e333cc0621e169836262",
      "fileid": "bf8dc1deef07a60a5cc39536aa3a6de0cb6f8261243dd88067498a9985a7e0ce",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/thinhong/actions/runs/26148121655"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.2.3",
      "date": "2026-05-20T07:38:05.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "439059c4a9823e293e16e333cc0621e169836262",
      "fileid": "3a019c1f1a399e97ea3c708899292ed37a6c91ac1a0cdb07371a369ad2fe8935",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/thinhong/actions/runs/26148121655"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.2.3",
      "date": "2026-05-20T07:37:46.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "439059c4a9823e293e16e333cc0621e169836262",
      "fileid": "1ecad2e95d2436c1756d690ced1bdc12a41942d295a5e54fe1abf46f28e1e94e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/thinhong/actions/runs/26148121655"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2.3",
      "date": "2026-05-20T07:37:35.000Z",
      "arch": "aarch64",
      "commit": "439059c4a9823e293e16e333cc0621e169836262",
      "fileid": "75be271b349018e7a5966081edfb505cfd2b72d44522719c5d798949f29d41e6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/thinhong/actions/runs/26148121655"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2.3",
      "date": "2026-05-20T07:38:52.000Z",
      "arch": "x86_64",
      "commit": "439059c4a9823e293e16e333cc0621e169836262",
      "fileid": "dde2277ceb7ecf72e42e53a02c202cbdc65b7e4a865f99307e4c65fe6a752ad2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/thinhong/actions/runs/26148121655"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.2.3",
      "date": "2026-05-20T07:37:46.000Z",
      "arch": "aarch64",
      "commit": "439059c4a9823e293e16e333cc0621e169836262",
      "fileid": "cbe1df6823740650abccb5b2a5451cfca4dfd4f7992a56fb00375064fbd1f713",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/thinhong/actions/runs/26148121655"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.2.3",
      "date": "2026-05-20T07:38:38.000Z",
      "arch": "x86_64",
      "commit": "439059c4a9823e293e16e333cc0621e169836262",
      "fileid": "d3fa0393abcd54a5ac4cb84d25a84ce23462b67d72efefa7d1614ae64cc8c4c5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/thinhong/actions/runs/26148121655"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.2.3",
      "date": "2026-05-20T07:36:40.000Z",
      "arch": "x86_64",
      "commit": "439059c4a9823e293e16e333cc0621e169836262",
      "fileid": "5ec3bd95801040c53a0ec63a28b0b0dad6d8679f344009da42b2e7a5b5c9a892",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/thinhong/actions/runs/26148121655"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.2.3",
      "date": "2026-05-20T07:36:37.000Z",
      "arch": "x86_64",
      "commit": "439059c4a9823e293e16e333cc0621e169836262",
      "fileid": "d81b243fe53a750e8261dda9b50b19e6b245ed90eba3a79cfd88c1ddf52638bd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/thinhong/actions/runs/26148121655"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.2.3",
      "date": "2026-05-20T07:36:27.000Z",
      "arch": "x86_64",
      "commit": "439059c4a9823e293e16e333cc0621e169836262",
      "fileid": "825a75305cbefe4d3926761281329d9911394a4e4d3b0593e10adb60390d9d0f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/thinhong/actions/runs/26148121655"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.2.3",
      "date": "2026-06-02T13:49:18.000Z",
      "arch": "emscripten",
      "commit": "439059c4a9823e293e16e333cc0621e169836262",
      "fileid": "1f8590bf7032ffd83294b7f33b02744aa3327438d516149a40def1ef745f576a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/thinhong/actions/runs/26148121655"
    }
  ]
}