{
  "_id": "6a105073acfb0bcc41ca113e",
  "Package": "facilityepimath",
  "Title": "Analyze Mathematical Models of Healthcare Facility Transmission",
  "Version": "0.2.1",
  "Authors@R": "c(person(\"Damon\", \"Toth\", , \"damon.toth@hsc.utah.edu\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0001-7393-4814\")),\nperson(\"Centers for Disease Control and Prevention\", role=\"fnd\",\ncomment = \"Modeling Infectious Diseases in Healthcare Network award number\nU01CK000585 and Insight Net award number CDC-RFA-FT-23-0069\"))",
  "Description": "Calculate useful quantities for a user-defined\ndifferential equation model of infectious disease transmission\namong individuals in a healthcare facility. Input rates of\ntransition between states of individuals with and without the\ndisease-causing organism, distributions of states at facility\nadmission, relative infectivity of transmissible states, and\nthe facility length of stay distribution. Calculate the model\nequilibrium and the basic facility reproduction number, as\ndescribed in Toth et al. (2025)\n<doi:10.1371/journal.pcbi.1013577>.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "URL": "https://github.com/EpiForeSITE/facilityepimath",
  "BugReports": "https://github.com/EpiForeSITE/facilityepimath/issues",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "Repository": "https://epiforesite.r-universe.dev",
  "Date/Publication": "2025-11-11 00:17:31 UTC",
  "RemoteUrl": "https://github.com/EpiForeSITE/facilityepimath",
  "RemoteRef": "HEAD",
  "RemoteSha": "15afa755a01695ef613f29765acd001ff8788e5b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-10 05:36:01 UTC",
    "User": "root"
  },
  "Author": "Damon Toth [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0001-7393-4814>),\nCenters for Disease Control and Prevention [fnd] (Modeling Infectious\nDiseases in Healthcare Network award number U01CK000585 and Insight\nNet award number CDC-RFA-FT-23-0069)",
  "Maintainer": "Damon Toth <damon.toth@hsc.utah.edu>",
  "MD5sum": "d12dd325699066bbd355c04a1afbd82f",
  "_user": "epiforesite",
  "_type": "src",
  "_file": "facilityepimath_0.2.1.tar.gz",
  "_fileid": "304fb1d0120cf157dacef87c594a1a61a2ec029cc3c072a4fcba9e5b217db25b",
  "_filesize": 144767,
  "_sha256": "304fb1d0120cf157dacef87c594a1a61a2ec029cc3c072a4fcba9e5b217db25b",
  "_created": "2026-05-10T05:36:01.000Z",
  "_published": "2026-05-22T12:47:47.377Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77382351387,
      "time": 118,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6901282043"
    },
    {
      "job": 77382351419,
      "time": 115,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6901281755"
    },
    {
      "job": 77382351626,
      "time": 78,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6901277956"
    },
    {
      "job": 77382351486,
      "time": 77,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6901277882"
    },
    {
      "job": 77382350697,
      "time": 158,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6901269582"
    },
    {
      "job": 77382350810,
      "time": 98,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7160826850"
    },
    {
      "job": 77382351382,
      "time": 79,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6901278222"
    },
    {
      "job": 77382351386,
      "time": 62,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6901276507"
    },
    {
      "job": 77382351395,
      "time": 62,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6901276442"
    }
  ],
  "_buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25620873013",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/EpiForeSITE/facilityepimath",
  "_commit": {
    "id": "15afa755a01695ef613f29765acd001ff8788e5b",
    "author": "damontoth <Damon.Toth@hsc.utah.edu>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #12 from EpiForeSITE/copilot/fix-deployment-workflow-rules\n\nSkip GitHub Pages deployment on release events",
    "time": 1762820251
  },
  "_maintainer": {
    "name": "Damon Toth",
    "email": "damon.toth@hsc.utah.edu",
    "login": "damontoth",
    "uuid": 16004052,
    "orcid": "0000-0001-7393-4814"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "epiforesite",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-36",
      "n": 1
    },
    {
      "week": "2025-39",
      "n": 5
    },
    {
      "week": "2025-43",
      "n": 1
    },
    {
      "week": "2025-45",
      "n": 12
    },
    {
      "week": "2025-46",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "v0.2.0",
      "date": "2025-09-23"
    },
    {
      "name": "v0.2.1",
      "date": "2025-11-06"
    }
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "damontoth",
      "count": 126,
      "uuid": 16004052
    },
    {
      "user": "apulsipher",
      "count": 10,
      "uuid": 45372570
    },
    {
      "user": "copilot",
      "count": 3,
      "uuid": 198982749
    },
    {
      "user": "gvegayon",
      "count": 2,
      "uuid": 893619
    }
  ],
  "_userbio": {
    "uuid": 158560900,
    "type": "organization",
    "name": "ForeSITE",
    "description": "A collection of epidemic modeling and forecasting tools for ForeSITE, part of the CDC-funded InsightNet"
  },
  "_downloads": {
    "count": 203,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/facilityepimath"
  },
  "_devurl": "https://github.com/epiforesite/facilityepimath",
  "_searchresults": 9,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/facilityepimath.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/epiforesite/facilityepimath",
  "_realowner": "epiforesite",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2025-03-07"
    },
    {
      "version": "0.2.1",
      "date": "2025-11-07"
    }
  ],
  "_exports": [
    "equilib",
    "facilityeq",
    "facilityR0",
    "meanlengthofstay",
    "MGFexponential",
    "MGFgamma",
    "MGFmixedgamma"
  ],
  "_help": [
    {
      "page": "equilib",
      "title": "Calculate the equilibrium of a linear facility model",
      "topics": [
        "equilib"
      ]
    },
    {
      "page": "facilityeq",
      "title": "Calculate the equilibrium of a facility transmission model",
      "topics": [
        "facilityeq"
      ]
    },
    {
      "page": "facilityR0",
      "title": "Calculate basic reproduction number R0",
      "topics": [
        "facilityR0"
      ]
    },
    {
      "page": "meanlengthofstay",
      "title": "Calculate the mean length of stay for a linear facility model",
      "topics": [
        "meanlengthofstay"
      ]
    },
    {
      "page": "MGFexponential",
      "title": "Evaluate the moment generating function (MGF) of the exponential distribution or a derivative of the MGF",
      "topics": [
        "MGFexponential"
      ]
    },
    {
      "page": "MGFgamma",
      "title": "Evaluate the moment generating function (MGF) of the gamma distribution or a derivative of the MGF",
      "topics": [
        "MGFgamma"
      ]
    },
    {
      "page": "MGFmixedgamma",
      "title": "Evaluate the moment generating function (MGF) of the mixed gamma distribution or a derivative of the MGF",
      "topics": [
        "MGFmixedgamma"
      ]
    }
  ],
  "_readme": "https://github.com/EpiForeSITE/facilityepimath/raw/HEAD/README.md",
  "_rundeps": [
    "MASS"
  ],
  "_vignettes": [
    {
      "source": "equilibrium-and-R0.Rmd",
      "filename": "equilibrium-and-R0.html",
      "title": "Facility basic reproduction number and equilibrium calculations",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Facility Basic Reproduction Number $R_0$",
        "The S matrix; pre-invasion susceptible state transitions",
        "The C matrix; colonized state transitions",
        "The A matrix; susceptible-to-colonized state transitions and relative susceptibility",
        "The transm vector: transmission rates",
        "The initS vector: susceptible state admission distribution",
        "facilityR0 function call with $h(t)=0$",
        "The mgf function: moment generating function associated with $h(t)\\neq0$",
        "facilityR0 function call with $h(t)\\neq0$",
        "Facility model equilibrium",
        "The R matrix: recovery rates",
        "The init vector: admission state distribution",
        "facilityeq function call with $h(t)\\neq0$",
        "facilityeq function call with $h(t)=0$"
      ],
      "created": "2025-01-09 22:20:32",
      "modified": "2025-11-06 21:43:26",
      "commits": 11
    }
  ],
  "_score": 4.8750612633917,
  "_indexed": true,
  "_nocasepkg": "facilityepimath",
  "_universes": [
    "epiforesite",
    "damontoth"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.2.1",
      "date": "2026-05-10T05:37:58.000Z",
      "distro": "noble",
      "commit": "15afa755a01695ef613f29765acd001ff8788e5b",
      "fileid": "5e8d79e8b42417349555b11ae6cad02d33dfb1453c62c0a3499f010bdef234e0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25620873013"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.2.1",
      "date": "2026-05-10T05:37:56.000Z",
      "distro": "noble",
      "commit": "15afa755a01695ef613f29765acd001ff8788e5b",
      "fileid": "0a2c9b46055cc8b699d1198aaec7975951c8ade0e46577bd6fb0ad67f3566762",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25620873013"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.2.1",
      "date": "2026-05-10T05:37:21.000Z",
      "commit": "15afa755a01695ef613f29765acd001ff8788e5b",
      "fileid": "69ee599afb002c69551b21a3c2d90b824d67293b7fcf312dff55cb7bc9917d9c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25620873013"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.2.1",
      "date": "2026-05-10T05:37:23.000Z",
      "commit": "15afa755a01695ef613f29765acd001ff8788e5b",
      "fileid": "10c034c2c921f0cbd27cac0060ceb3ba57e25436e4cea872b9a1fd2b4f0159ad",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25620873013"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.2.1",
      "date": "2026-05-10T05:37:13.000Z",
      "commit": "15afa755a01695ef613f29765acd001ff8788e5b",
      "fileid": "b47ac2e83aab446a0737e5fe4849fd9ab5fa858d78b711901b2a7b25f5a16013",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25620873013"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.2.1",
      "date": "2026-05-10T05:37:02.000Z",
      "commit": "15afa755a01695ef613f29765acd001ff8788e5b",
      "fileid": "885633bd840a0ddd749b293e2ed4915fdd45e7c0fb4f5e4c185c94651dfc70de",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25620873013"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.2.1",
      "date": "2026-05-10T05:37:00.000Z",
      "commit": "15afa755a01695ef613f29765acd001ff8788e5b",
      "fileid": "34d5d1aa8c0be4b0854d8f31ab8846bf60c384c633c53e4ed5a431d39f906694",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25620873013"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.2.1",
      "date": "2026-05-22T12:47:14.000Z",
      "commit": "15afa755a01695ef613f29765acd001ff8788e5b",
      "fileid": "bb250992b4635da1211a4ed4f6a8a85409fca8a1ac971ce2b6b74f472ad77fa7",
      "status": "success",
      "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25620873013"
    }
  ]
}