{
  "_id": "6a13ea5bacfb0bcc41d2df86",
  "Package": "jointlyr",
  "Title": "Joint estimation of initial incidence and reproduction number",
  "Version": "0.0.1",
  "Authors@R": "c(person(given = \"Sangeeta\", family = \"Bhatia\",\nrole = c(\"aut\", \"cre\"),\nemail = \"s.bhatia@imperial.ac.uk\"),\nperson(given = \"Pierre\", family = \"Nouvellet\",\nrole = c(\"aut\"),\nemail = \"p.nouvellet@imperial.ac.uk\"),\nperson(given = \"Anne\", family = \"Cori\",\nrole = c(\"aut\"),\nemail = \"a.cori@imperial.ac.uk\"),\nperson(given = \"Jack\", family = \"Wardle\",\nrole = c(\"aut\"),\nemail = \"j.wardle19@imperial.ac.uk\"))",
  "Description": "Provides a Stan implementation of a method to jointly\nestimate incidence and reproduction number.",
  "License": "MIT",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.1.1",
  "Biarch": "true",
  "SystemRequirements": "GNU make",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "make libicu-dev libsodium-dev",
  "Repository": "https://mrc-ide.r-universe.dev",
  "Date/Publication": "2022-08-03 16:20:29 UTC",
  "RemoteUrl": "https://github.com/mrc-ide/jointlyr",
  "RemoteRef": "master",
  "RemoteSha": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-25 06:12:39 UTC",
    "User": "root"
  },
  "Author": "Sangeeta Bhatia [aut, cre],\nPierre Nouvellet [aut],\nAnne Cori [aut],\nJack Wardle [aut]",
  "Maintainer": "Sangeeta Bhatia <s.bhatia@imperial.ac.uk>",
  "MD5sum": "620120a1d39ce5dbb503e049232f3108",
  "_user": "mrc-ide",
  "_type": "src",
  "_file": "jointlyr_0.0.1.tar.gz",
  "_fileid": "4c8c544832aabed8fbe0282314148adf3f375ed75edece6228e4e5fd5bfbe3ef",
  "_filesize": 92481,
  "_sha256": "4c8c544832aabed8fbe0282314148adf3f375ed75edece6228e4e5fd5bfbe3ef",
  "_created": "2026-05-25T06:12:39.000Z",
  "_published": "2026-05-25T06:21:15.465Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77665434373,
      "time": 249,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7192723900"
    },
    {
      "job": 77665434372,
      "time": 267,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7192727133"
    },
    {
      "job": 77665434370,
      "time": 240,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7192722058"
    },
    {
      "job": 77665434366,
      "time": 225,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7192718811"
    },
    {
      "job": 77665434374,
      "time": 125,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7192700459"
    },
    {
      "job": 77665434414,
      "time": 424,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7192757025"
    },
    {
      "job": 77665434403,
      "time": 146,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7192704033"
    },
    {
      "job": 77665434385,
      "time": 430,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7192758209"
    },
    {
      "job": 77664931132,
      "time": 317,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7192675715"
    },
    {
      "job": 77665434394,
      "time": 178,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 77665434368,
      "time": 280,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7192729997"
    },
    {
      "job": 77665434369,
      "time": 274,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7192728522"
    },
    {
      "job": 77665434371,
      "time": 265,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7192726734"
    }
  ],
  "_buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/26386127569",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/mrc-ide/jointlyr",
  "_commit": {
    "id": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
    "author": "Robert Ashton <r.ashton@imperial.ac.uk>",
    "committer": "Robert Ashton <r.ashton@imperial.ac.uk>",
    "message": "Include EpiEstim in package imports\n",
    "time": 1659543629
  },
  "_maintainer": {
    "name": "Sangeeta Bhatia",
    "email": "s.bhatia@imperial.ac.uk"
  },
  "_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": ">= 2.18.1",
      "role": "LinkingTo"
    },
    {
      "package": "StanHeaders",
      "version": ">= 2.18.0",
      "role": "LinkingTo"
    },
    {
      "package": "EpiEstim",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.0",
      "role": "Imports"
    },
    {
      "package": "RcppParallel",
      "version": ">= 5.0.1",
      "role": "Imports"
    },
    {
      "package": "rstan",
      "version": ">= 2.18.1",
      "role": "Imports"
    },
    {
      "package": "rstantools",
      "version": ">= 2.1.1",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "mrc-ide",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "sangeetabhatia03",
      "count": 8,
      "uuid": 15316049
    },
    {
      "user": "r-ash",
      "count": 1,
      "uuid": 39248272
    }
  ],
  "_userbio": {
    "uuid": 25453642,
    "type": "organization",
    "name": "MRC Centre for Global Infectious Disease Analysis",
    "description": "MRC Centre hosted within the Department of Infectious Disease Epidemiology at Imperial College London"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/jointlyr"
  },
  "_devurl": "https://github.com/mrc-ide/jointlyr",
  "_searchresults": 1,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/jointlyr.html",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "jointly_estimate"
  ],
  "_help": [
    {
      "page": "jointlyr-package",
      "title": "The 'jointlyr' package.",
      "topics": [
        "jointlyr-package",
        "jointlyr"
      ]
    },
    {
      "page": "jointly_estimate",
      "title": "Jointly estimate I0 and Rt",
      "topics": [
        "jointly_estimate"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "aweek",
    "backports",
    "BH",
    "callr",
    "checkmate",
    "cli",
    "coarseDataTools",
    "coda",
    "cpp11",
    "data.table",
    "desc",
    "distcrete",
    "distributional",
    "dplyr",
    "EpiEstim",
    "epitrix",
    "farver",
    "fastymd",
    "fitdistrplus",
    "generics",
    "ggplot2",
    "glue",
    "grates",
    "gridExtra",
    "gtable",
    "incidence",
    "incidence2",
    "inline",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "loo",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "matrixStats",
    "mcmc",
    "MCMCpack",
    "numDeriv",
    "patchwork",
    "pillar",
    "pkgbuild",
    "pkgconfig",
    "plyr",
    "posterior",
    "processx",
    "ps",
    "purrr",
    "quantreg",
    "QuickJSR",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RcppParallel",
    "reshape2",
    "rlang",
    "rstan",
    "rstantools",
    "S7",
    "scales",
    "sodium",
    "SparseM",
    "StanHeaders",
    "stringi",
    "stringr",
    "survival",
    "tensorA",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "ympes"
  ],
  "_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": "using-jointlyr.Rmd",
      "filename": "using-jointlyr.html",
      "title": "Using jointlyr",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Set up data",
        "Incidence",
        "Serial Interval Distribution"
      ],
      "created": "2021-03-04 13:49:45",
      "modified": "2021-03-04 14:16:52",
      "commits": 3
    }
  ],
  "_score": 2,
  "_indexed": true,
  "_nocasepkg": "jointlyr",
  "_universes": [
    "mrc-ide"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.0.1",
      "date": "2026-05-25T06:16:06.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "7a487dbb98808920801ba688a815647db4ef0f6110fa392c22582bc47cc48466",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/26386127569"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.0.1",
      "date": "2026-05-25T06:16:17.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "6d981660ecda5c6e346f71eb7378a5293aec87c05692ab193494a500e544bd24",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/26386127569"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.0.1",
      "date": "2026-05-25T06:16:03.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "78b21bca4a6d038d6b8abf046eb656b67c11f5042f3294df1b61e8ab7a4c5a76",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/26386127569"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.0.1",
      "date": "2026-05-25T06:15:53.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "7f14d197c11f10da312d3c2a74043d188034b59a1d97bb2c7646eea181b51ed8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/26386127569"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.0.1",
      "date": "2026-05-25T06:14:51.000Z",
      "arch": "aarch64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "840852515017a97855c34ebdb7f759610a1bd31f940accee783392144e11420f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/26386127569"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.0.1",
      "date": "2026-05-25T06:17:30.000Z",
      "arch": "x86_64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "34255e98cb45c7071e5a9f4981f5c67b4b823d04da4cac3de461e3fc45d2244e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/26386127569"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.0.1",
      "date": "2026-05-25T06:15:03.000Z",
      "arch": "aarch64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "3a45ac1e278a0273d80448421fbdb46d0ec627f472f5b67f69eac371d4fa804a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/26386127569"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.0.1",
      "date": "2026-05-25T06:17:36.000Z",
      "arch": "x86_64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "060e523f0e3f833905e6525538ffeaaf59ef04841c9667b97108ae0b68548c4b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/26386127569"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.0.1",
      "date": "2026-05-25T06:15:27.000Z",
      "arch": "x86_64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "b441f396e83b008e0a338209ed783cd30bda2f90be9e3c7b086c47c4e974e8c3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/26386127569"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.0.1",
      "date": "2026-05-25T06:15:25.000Z",
      "arch": "x86_64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "b742bfdd21ec949445792e6eb709fb0100b5523f6692fc6cecc16db35d75d35b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/26386127569"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.0.1",
      "date": "2026-05-25T06:15:12.000Z",
      "arch": "x86_64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "292ac4cf11b24a2dd0f4609d563bf56991d919fa010b98f876121cf9bb5c6514",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/26386127569"
    }
  ]
}