{
  "_id": "6a83c927517c2dabfe2c4cce",
  "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",
  "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": "2026-08-18 02:45:40 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>",
  "_user": "mrc-ide",
  "_type": "src",
  "_file": "jointlyr_0.0.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/c8c5b6ea28fc04e8df9182635a0cf6d65eaf545c568e51a6c8493bd1e08c0b1b",
  "_filesize": 160280,
  "_sha256": "c8c5b6ea28fc04e8df9182635a0cf6d65eaf545c568e51a6c8493bd1e08c0b1b",
  "_expires": "2026-11-26T02:53:25.000Z",
  "_created": "2026-08-18T02:45:40.000Z",
  "_published": "2026-10-14T06:32:14.828Z",
  "_jobs": [
    {
      "job": 95578972307,
      "time": 223,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "9309058083"
    },
    {
      "job": 95578972450,
      "time": 265,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "9309071774"
    },
    {
      "job": 95578972318,
      "time": 200,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "9309050269"
    },
    {
      "job": 95578972372,
      "time": 241,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "9309063272"
    },
    {
      "job": 95578972305,
      "time": 171,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "9309040011"
    },
    {
      "job": 95578972301,
      "time": 377,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "9309110338"
    },
    {
      "job": 95578972360,
      "time": 148,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "9309032212"
    },
    {
      "job": 95578972304,
      "time": 291,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "9309081127"
    },
    {
      "job": 95578097470,
      "time": 298,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "9308982361"
    },
    {
      "job": 95578972298,
      "time": 196,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "9309048059"
    },
    {
      "job": 95578972335,
      "time": 294,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "9309081912"
    },
    {
      "job": 95578972405,
      "time": 354,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "9309102028"
    },
    {
      "job": 95578972379,
      "time": 326,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "9309093107"
    },
    {
      "job": 95578972457,
      "time": 342,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "9309097717"
    },
    {
      "job": 95578972317,
      "time": 305,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "9309086175"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/32092735701",
  "_status": "success",
  "_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"
  },
  "_distro": "resolute",
  "_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",
    "followers": 160,
    "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": [
    "onetbb",
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/jointlyr.html",
    "extra/manual.pdf",
    "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",
    "otel",
    "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": "libtbb",
      "package": "libtbb12",
      "headers": "libtbb-dev",
      "source": "onetbb",
      "version": "2022.3.0-2",
      "name": "onetbb",
      "homepage": "https://uxlfoundation.github.io/oneTBB/",
      "description": "parallelism library for C++ - runtime files"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "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"
  ],
  "_failure": {
    "version": "0.0.1",
    "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
    },
    "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/38150606199",
    "date": "2026-10-14T06:32:14.824Z",
    "job": {
      "job": 115715078748,
      "time": 179,
      "config": "source",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11874791177"
    }
  },
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.0.1",
      "date": "2026-08-18T02:48:48.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "https://r2.ropensci.org/c2cf8457a14f0710f9c930e975cab95f510239b8364497f4d0b493f1af4c924e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/32092735701"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.0.1",
      "date": "2026-08-18T02:49:07.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "https://r2.ropensci.org/e64d68716256119138d2fca9aa4fa5ee1afd25b1fef0ce593fa065b6db613556",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/32092735701"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.0.1",
      "date": "2026-08-18T02:48:35.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "https://r2.ropensci.org/583301003f022feebe7e0bae0c0caa838dd0a9dd636d07bb26dce3686a6c594e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/32092735701"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.0.1",
      "date": "2026-08-18T02:49:05.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "https://r2.ropensci.org/fa1855c714a008a5a4c05dd1903e16429cc55b3bd75ef16bee9c6c7f2fbbbe77",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/32092735701"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.0.1",
      "date": "2026-08-18T02:47:58.000Z",
      "arch": "aarch64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "https://r2.ropensci.org/3197a605d2b108ec81785cde2847647665aab4dfda6621e2ad95614d3f0eb04e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/32092735701"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.0.1",
      "date": "2026-08-18T02:49:44.000Z",
      "arch": "x86_64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "https://r2.ropensci.org/b3c06e4a8bc2bcb8cabea1e34569ede92a713fceebafbc38103a1d0d25e71499",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/32092735701"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.0.1",
      "date": "2026-08-18T02:47:58.000Z",
      "arch": "aarch64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "https://r2.ropensci.org/624b09ea0a7b4a543879af283fbf614c5b72264a651e22e5d502e3382cb6aebb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/32092735701"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.0.1",
      "date": "2026-08-18T02:49:01.000Z",
      "arch": "x86_64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "https://r2.ropensci.org/9d52a0aae0ee8be53b8f162aa07d5016ca371e9c390d99d0f5d6b7991bf31725",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/32092735701"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.0.1",
      "date": "2026-08-18T02:49:22.000Z",
      "arch": "emscripten",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "https://r2.ropensci.org/e0edf50190eda82df0562d4dad4e3c71c685acb29dbf6ebec3463597667fade4",
      "status": "success",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/32092735701"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.0.1",
      "date": "2026-08-18T02:49:36.000Z",
      "arch": "aarch64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "https://r2.ropensci.org/74c1429d6b4f3afef2b5a6a6ae900ca03c7e9b6f5c19df085890c7646086c534",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/32092735701"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.0.1",
      "date": "2026-08-18T02:49:11.000Z",
      "arch": "x86_64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "https://r2.ropensci.org/0e1f6f1293af3285521cb6bc383756ebeb6ac6bcfe59a63bd0ae54a4f15af69a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/32092735701"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.0.1",
      "date": "2026-08-18T02:49:09.000Z",
      "arch": "x86_64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "https://r2.ropensci.org/1369faf7e11104cd1e805f85d647fbd97bd7316a06b67dc41959f799e795b9d8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/32092735701"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.0.1",
      "date": "2026-08-18T02:50:27.000Z",
      "arch": "aarch64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "https://r2.ropensci.org/900fbedc40e2cc544752af9b5993c1b589dfea5bb7d1ccd70788d050ea0c3493",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/32092735701"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.0.1",
      "date": "2026-08-18T02:48:47.000Z",
      "arch": "x86_64",
      "commit": "614603f6c50f83d9c3305b51535eaeaebf276f6a",
      "fileid": "https://r2.ropensci.org/10c44e5cc78260de5f91cc4130ce9e4fa88582534deb88616d40d650d385eca9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/32092735701"
    }
  ]
}