{
  "_id": "6a1f38dbb401979e73428e3f",
  "Package": "surveil",
  "Title": "Time Series Models for Disease Surveillance",
  "Version": "0.3.0",
  "Date": "2024-07-07",
  "Authors@R": "person(given = \"Connor\",\nfamily = \"Donegan\",\nrole = c(\"aut\", \"cre\"),\nemail = \"connor.donegan@gmail.com\",\ncomment = c(ORCID = \"0000-0002-9698-5443\"))",
  "URL": "https://connordonegan.github.io/surveil/,\nhttps://github.com/ConnorDonegan/surveil/",
  "Description": "Fits time trend models for routine disease surveillance\ntasks and returns probability distributions for a variety of\nquantities of interest, including age-standardized rates,\nperiod and cumulative percent change, and measures of health\ninequality. The models are appropriate for count data such as\ndisease incidence and mortality data, employing a Poisson or\nbinomial likelihood and the first-difference (random-walk)\nprior for unknown risk. Optionally add a covariance matrix for\nmultiple, correlated time series models. Inference is completed\nusing Markov chain Monte Carlo via the Stan modeling language.\nReferences: Donegan, Hughes, and Lee (2022)\n<doi:10.2196/34589>; Stan Development Team (2021)\n<https://mc-stan.org>; Theil (1972, ISBN:0-444-10378-3).",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.1",
  "Biarch": "true",
  "SystemRequirements": "GNU make",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "make libicu-dev",
  "Repository": "https://connordonegan.r-universe.dev",
  "Date/Publication": "2024-07-08 16:10:42 UTC",
  "RemoteUrl": "https://github.com/connordonegan/surveil",
  "RemoteRef": "HEAD",
  "RemoteSha": "847d19fc67e7b10c67fa28cd717282b65bd4bfbe",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-11 08:48:24 UTC",
    "User": "root"
  },
  "Author": "Connor Donegan [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-9698-5443>)",
  "Maintainer": "Connor Donegan <connor.donegan@gmail.com>",
  "MD5sum": "4df7c017120535c0a6a13a2abd357c09",
  "_user": "connordonegan",
  "_type": "src",
  "_file": "surveil_0.3.0.tar.gz",
  "_fileid": "4728db1237b08360c74428ee12accd957e386ebc31ff732770dd806406025035",
  "_filesize": 1701115,
  "_sha256": "4728db1237b08360c74428ee12accd957e386ebc31ff732770dd806406025035",
  "_created": "2026-05-11T08:48:24.000Z",
  "_published": "2026-06-02T20:11:07.827Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79162252340,
      "time": 357,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6914238179"
    },
    {
      "job": 79162251816,
      "time": 366,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6914243031"
    },
    {
      "job": 79162252092,
      "time": 351,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6914236811"
    },
    {
      "job": 79162252004,
      "time": 356,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6914239949"
    },
    {
      "job": 79162252224,
      "time": 344,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6914225460"
    },
    {
      "job": 79162251977,
      "time": 1048,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6914435825"
    },
    {
      "job": 79162252274,
      "time": 382,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6914235250"
    },
    {
      "job": 79162251787,
      "time": 588,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6914307372"
    },
    {
      "job": 79162251617,
      "time": 385,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6914122856"
    },
    {
      "job": 79162251227,
      "time": 156,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 79162251854,
      "time": 440,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6914265503"
    },
    {
      "job": 79162252233,
      "time": 399,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6914251952"
    },
    {
      "job": 79162252373,
      "time": 453,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6914269473"
    }
  ],
  "_buildurl": "https://github.com/r-universe/connordonegan/actions/runs/25659752088",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/connordonegan/surveil",
  "_commit": {
    "id": "847d19fc67e7b10c67fa28cd717282b65bd4bfbe",
    "author": "ConnorDonegan <connor.donegan@gmail.com>",
    "committer": "ConnorDonegan <connor.donegan@gmail.com>",
    "message": "update vignette names\n",
    "time": 1720455042
  },
  "_maintainer": {
    "name": "Connor Donegan",
    "email": "connor.donegan@gmail.com",
    "login": "connordonegan",
    "uuid": 24845033,
    "orcid": "0000-0002-9698-5443"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "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": "rstantools",
      "version": ">= 2.1.1",
      "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": ">= 2.26.0",
      "role": "Imports"
    },
    {
      "package": "tidybayes",
      "version": ">= 3.0.0",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "version": ">= 1.0.7",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "version": ">= 0.4.0",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "version": ">= 1.1.0",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.0.0",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "version": ">= 2.0",
      "role": "Imports"
    },
    {
      "package": "scales",
      "version": ">= 0.4.0",
      "role": "Imports"
    },
    {
      "package": "ggdist",
      "version": ">= 3.0.0",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "connordonegan",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "bayesian-statistics",
    "cancer",
    "health-equity",
    "public-health",
    "rstan",
    "cpp"
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "connordonegan",
      "count": 73,
      "uuid": 24845033
    },
    {
      "user": "andrjohns",
      "count": 1,
      "uuid": 27717896
    },
    {
      "user": "pitmonticone",
      "count": 1,
      "uuid": 38562595
    }
  ],
  "_userbio": {
    "uuid": 24845033,
    "type": "user",
    "name": "Connor Donegan"
  },
  "_downloads": {
    "count": 253,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/surveil"
  },
  "_devurl": "https://github.com/connordonegan/surveil",
  "_pkgdown": "https://connordonegan.github.io/surveil/",
  "_searchresults": 18,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/surveil.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/connordonegan/surveil",
  "_realowner": "connordonegan",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2021-11-11"
    },
    {
      "version": "0.1.1",
      "date": "2022-01-03"
    },
    {
      "version": "0.2.0",
      "date": "2022-04-03"
    },
    {
      "version": "0.2.1",
      "date": "2022-08-22"
    },
    {
      "version": "0.2.2",
      "date": "2023-10-03"
    },
    {
      "version": "0.3.0",
      "date": "2024-07-08"
    }
  ],
  "_exports": [
    "apc",
    "group_diff",
    "lkj",
    "normal",
    "stan_rw",
    "standardize",
    "theil",
    "theil2",
    "waic"
  ],
  "_datasets": [
    {
      "name": "cancer",
      "title": "US cancer incidence by age, 1999-2017",
      "object": "cancer",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Year",
        "Age",
        "Count",
        "Population"
      ],
      "rows": 361,
      "table": true,
      "tojson": true
    },
    {
      "name": "msa",
      "title": "Colorectal cancer incidence by Texas MSA, 1999-2017, ages 50-79",
      "object": "msa",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Year",
        "Race",
        "MSA",
        "Count",
        "Population"
      ],
      "rows": 228,
      "table": true,
      "tojson": true
    },
    {
      "name": "standard",
      "title": "2000 U.S. standard million population",
      "object": "standard",
      "class": [
        "data.frame"
      ],
      "fields": [
        "age.id",
        "age",
        "standard_pop"
      ],
      "rows": 19,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "surveil-package",
      "title": "The 'surveil' package",
      "topics": [
        "surveil-package",
        "surveil"
      ]
    },
    {
      "page": "apc",
      "title": "Annual and cumulative percent change",
      "topics": [
        "apc",
        "apc.stand_surveil",
        "apc.surveil"
      ]
    },
    {
      "page": "cancer",
      "title": "US cancer incidence by age, 1999-2017",
      "topics": [
        "cancer"
      ]
    },
    {
      "page": "group_diff",
      "title": "Measures of pairwise inequality",
      "topics": [
        "group_diff",
        "group_diff.list",
        "group_diff.surveil"
      ]
    },
    {
      "page": "msa",
      "title": "Colorectal cancer incidence by Texas MSA, 1999-2017, ages 50-79",
      "topics": [
        "msa"
      ]
    },
    {
      "page": "plot.surveil",
      "title": "Methods for fitted 'surveil' models",
      "topics": [
        "plot.list",
        "plot.surveil",
        "print.surveil"
      ]
    },
    {
      "page": "theil_methods",
      "title": "Methods for Theil's index",
      "topics": [
        "plot.theil",
        "plot.theil_list",
        "print.theil",
        "print.theil_list"
      ]
    },
    {
      "page": "print.apc",
      "title": "Methods for APC objects",
      "topics": [
        "plot.apc",
        "print.apc"
      ]
    },
    {
      "page": "stand_surveil",
      "title": "Methods for age-standardized rates",
      "topics": [
        "plot.stand_surveil",
        "print.stand_surveil"
      ]
    },
    {
      "page": "priors",
      "title": "Prior distributions",
      "topics": [
        "lkj",
        "normal",
        "priors"
      ]
    },
    {
      "page": "stan_rw",
      "title": "Time series models for mortality and disease incidence",
      "topics": [
        "stan_rw"
      ]
    },
    {
      "page": "standard",
      "title": "2000 U.S. standard million population",
      "topics": [
        "standard"
      ]
    },
    {
      "page": "standardize",
      "title": "Age-standardized rates",
      "topics": [
        "standardize"
      ]
    },
    {
      "page": "surveil_diff",
      "title": "Methods for 'surveil_diff' objects",
      "topics": [
        "plot.surveil_diff",
        "print.surveil_diff",
        "surveil_diff"
      ]
    },
    {
      "page": "theil",
      "title": "Theil's inequality index",
      "topics": [
        "theil",
        "theil.list",
        "theil.surveil",
        "theil2"
      ]
    },
    {
      "page": "waic",
      "title": "Widely Applicable Information Criteria",
      "topics": [
        "waic"
      ]
    }
  ],
  "_pkglogo": "https://github.com/connordonegan/surveil/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/connordonegan/surveil/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "arrayhelpers",
    "backports",
    "BH",
    "callr",
    "checkmate",
    "cli",
    "coda",
    "cpp11",
    "desc",
    "distributional",
    "dplyr",
    "farver",
    "generics",
    "ggdist",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "inline",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "loo",
    "magrittr",
    "matrixStats",
    "numDeriv",
    "pillar",
    "pkgbuild",
    "pkgconfig",
    "posterior",
    "processx",
    "ps",
    "purrr",
    "quadprog",
    "QuickJSR",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RcppParallel",
    "rlang",
    "rstan",
    "rstantools",
    "S7",
    "scales",
    "StanHeaders",
    "stringi",
    "stringr",
    "svUnit",
    "tensorA",
    "tibble",
    "tidybayes",
    "tidyr",
    "tidyselect",
    "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": "age-standardization.Rmd",
      "filename": "age-standardization.html",
      "title": "Age-standardized rates",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Data",
        "Direct age-standardization",
        "Modeling age-specific risk",
        "Age-standardizing model results",
        "References"
      ],
      "created": "2022-03-29 14:26:48",
      "modified": "2024-07-08 11:47:22",
      "commits": 6
    },
    {
      "source": "surveil-mcmc.Rmd",
      "filename": "surveil-mcmc.html",
      "title": "MCMC with surveil",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Example model",
        "MCMC analysis",
        "Monte Carlo standard errors",
        "Rhat",
        "Divergent transitions",
        "References"
      ],
      "created": "2022-07-29 23:32:35",
      "modified": "2024-07-08 11:47:22",
      "commits": 5
    },
    {
      "source": "measuring-inequality.Rmd",
      "filename": "measuring-inequality.html",
      "title": "Measuring health inequality",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Concepts",
        "Demonstration",
        "Comparing age-stratified groups",
        "Measuring inequality with multiple groups",
        "References"
      ],
      "created": "2024-07-08 11:47:22",
      "modified": "2024-07-08 11:47:22",
      "commits": 1
    },
    {
      "source": "surveil-demo.Rmd",
      "filename": "surveil-demo.html",
      "title": "Using surveil for public health research",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Getting started",
        "Preparing the data",
        "Model specification",
        "The basics",
        "Binomial model",
        "Fitting the model",
        "Printing results",
        "Visualizing results",
        "Percent change",
        "MCMC diagnostics",
        "Multiple time series",
        "References"
      ],
      "created": "2022-07-29 23:32:35",
      "modified": "2024-07-08 11:47:22",
      "commits": 3
    }
  ],
  "_score": 5.15836249209525,
  "_indexed": true,
  "_nocasepkg": "surveil",
  "_universes": [
    "connordonegan"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.3.0",
      "date": "2026-05-11T08:52:26.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "847d19fc67e7b10c67fa28cd717282b65bd4bfbe",
      "fileid": "c59205a5e06fd1abbc97c63be90689bdf6f12fdac9b7e9b3b11562d97473d461",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/connordonegan/actions/runs/25659752088"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.3.0",
      "date": "2026-05-11T08:52:36.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "847d19fc67e7b10c67fa28cd717282b65bd4bfbe",
      "fileid": "8c354a422c18043f3dba5ece253ab31486820a9f609ef62da50276b25bb30fa4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/connordonegan/actions/runs/25659752088"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.3.0",
      "date": "2026-05-11T08:52:33.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "847d19fc67e7b10c67fa28cd717282b65bd4bfbe",
      "fileid": "fcc2b272b23779ee5984981797569f4b84df41901330781010c1528970e409d6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/connordonegan/actions/runs/25659752088"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.3.0",
      "date": "2026-05-11T08:52:36.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "847d19fc67e7b10c67fa28cd717282b65bd4bfbe",
      "fileid": "ad235609dec76f2497a2f8fc0e30e940ba2f5b0ac268519cb05c44ed7c9b7957",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/connordonegan/actions/runs/25659752088"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.3.0",
      "date": "2026-05-11T08:52:25.000Z",
      "arch": "aarch64",
      "commit": "847d19fc67e7b10c67fa28cd717282b65bd4bfbe",
      "fileid": "04e8b9f6e8374532753a96ce3619f7ab6b130c2d71935a3579f4d6b727d3d3d6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/connordonegan/actions/runs/25659752088"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.3.0",
      "date": "2026-05-11T08:55:54.000Z",
      "arch": "x86_64",
      "commit": "847d19fc67e7b10c67fa28cd717282b65bd4bfbe",
      "fileid": "5781b9807630a9466beadcae33d4254fb2f699fc92b86d1ae45b07bd82d6c285",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/connordonegan/actions/runs/25659752088"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.3.0",
      "date": "2026-05-11T08:52:17.000Z",
      "arch": "aarch64",
      "commit": "847d19fc67e7b10c67fa28cd717282b65bd4bfbe",
      "fileid": "33f48e3db040a74bd8265cafbd8768ae14c42f41abc8665f1387edfa2667c3b0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/connordonegan/actions/runs/25659752088"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.3.0",
      "date": "2026-05-11T08:54:14.000Z",
      "arch": "x86_64",
      "commit": "847d19fc67e7b10c67fa28cd717282b65bd4bfbe",
      "fileid": "66fbe6fd961a2378aaec0398102903b7d0ef7f02681849f125ca7c933e834091",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/connordonegan/actions/runs/25659752088"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.3.0",
      "date": "2026-05-11T08:51:38.000Z",
      "arch": "x86_64",
      "commit": "847d19fc67e7b10c67fa28cd717282b65bd4bfbe",
      "fileid": "fff68dc641b6853a590ef9500d3ed13e63c02c4a9c0e463f18326124f238b23d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/connordonegan/actions/runs/25659752088"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.3.0",
      "date": "2026-05-11T08:51:28.000Z",
      "arch": "x86_64",
      "commit": "847d19fc67e7b10c67fa28cd717282b65bd4bfbe",
      "fileid": "ea2f9b038403b93dcdd8bfc88905acc891ac21021d08c8c17be6c2dda44877fd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/connordonegan/actions/runs/25659752088"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.3.0",
      "date": "2026-05-11T08:51:40.000Z",
      "arch": "x86_64",
      "commit": "847d19fc67e7b10c67fa28cd717282b65bd4bfbe",
      "fileid": "15f81adb07dbe219b1d56e9c6d51de8c70107f8b59c1de754160f306530f6c42",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/connordonegan/actions/runs/25659752088"
    }
  ]
}