{
  "_id": "6ae5afed8d250e7ad09f359c",
  "Package": "vaxineR",
  "Type": "Package",
  "Title": "Vaccine Coverage and Outbreak Risk Analysis",
  "Version": "0.1.0",
  "Authors@R": "c(\nperson(given = \"Peiyu\", family = \"Liu\", role = c(\"aut\", \"cre\"), email = \"pyliu0620@outlook.com\"),\nperson(given = \"Matt\", family = \"Hitchings\", role = \"ctb\"),\nperson(given = \"Ira\", family = \"Longini\", role = \"ctb\")\n)",
  "Description": "Provides tools to analyze vaccine coverage data and\nsimulate potential disease outbreak scenarios. It allows users\nto calculate key epidemiological metrics such as the effective\nreproduction number (Re), outbreak probabilities, and expected\ninfection counts based on county-level vaccination rates,\ndisease characteristics, and vaccine effectiveness. The package\nincludes historical kindergarten vaccination data for Florida\ncounties and offers functions for generating summary tables,\nvisualizations, and exporting the underlying plot data.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://peiyuliu-biostats.r-universe.dev",
  "Date/Publication": "2025-09-27 15:04:21 UTC",
  "RemoteUrl": "https://github.com/peiyuliu-biostats/vaxiner",
  "RemoteRef": "HEAD",
  "RemoteSha": "3e386406d2c06f9296d767c8d88a0c0824c626a7",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-31 08:34:28 UTC",
    "User": "root"
  },
  "Author": "Peiyu Liu [aut, cre],\nMatt Hitchings [ctb],\nIra Longini [ctb]",
  "Maintainer": "Peiyu Liu <pyliu0620@outlook.com>",
  "_user": "peiyuliu-biostats",
  "_type": "src",
  "_file": "vaxineR_0.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/76e62fa4434c979ec8ce938b4b311d09a1cdefa4b30305fc4323afbb2bfb5b72",
  "_filesize": 776106,
  "_sha256": "76e62fa4434c979ec8ce938b4b311d09a1cdefa4b30305fc4323afbb2bfb5b72",
  "_expires": "2027-02-08T09:07:55.000Z",
  "_created": "2026-10-31T08:34:28.000Z",
  "_published": "2026-10-31T09:07:56.980Z",
  "_upstream": "https://github.com/peiyuliu-biostats/vaxiner",
  "_status": "success",
  "_maintainer": {
    "name": "Peiyu Liu",
    "email": "pyliu0620@outlook.com",
    "login": "peiyuliu-biostats",
    "description": "peiyuliu",
    "uuid": 199144398
  },
  "_jobs": [
    {
      "job": 124490553758,
      "time": 112,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13036498362"
    },
    {
      "job": 124490553636,
      "time": 127,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "13036202487"
    },
    {
      "job": 124490553644,
      "time": 140,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13037890160"
    },
    {
      "job": 124490553641,
      "time": 147,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13036189956"
    },
    {
      "job": 124489918283,
      "time": 186,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "13036827145"
    },
    {
      "job": 124490553631,
      "time": 102,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13037030588"
    },
    {
      "job": 124490553703,
      "time": 87,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13036223714"
    },
    {
      "job": 124490553694,
      "time": 85,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13036412205"
    },
    {
      "job": 124490553642,
      "time": 83,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13036482133"
    }
  ],
  "_buildurl": "https://github.com/r-universe/peiyuliu-biostats/actions/runs/41184941970",
  "_commit": {
    "id": "3e386406d2c06f9296d767c8d88a0c0824c626a7",
    "author": "Peiyu Liu <199144398+peiyuliu-biostats@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Update README.md",
    "time": 1758985461
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "openxlsx",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "peiyuliu-biostats",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "peiyuliu-biostats",
      "count": 5,
      "uuid": 199144398
    }
  ],
  "_userbio": {
    "uuid": 199144398,
    "type": "user",
    "name": "Peiyu Liu",
    "followers": 2,
    "description": "peiyuliu"
  },
  "_downloads": {
    "count": 265,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/vaxineR"
  },
  "_devurl": "https://github.com/peiyuliu-biostats/vaxiner",
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md",
    "extra/vaxineR.html"
  ],
  "_homeurl": "https://github.com/peiyuliu-biostats/vaxiner",
  "_realowner": "peiyuliu-biostats",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2025-09-15"
    }
  ],
  "_exports": [
    "calc_expected_infections",
    "calc_re",
    "plot_coverage_history",
    "plot_outbreak_prob",
    "plot_risk_curve",
    "prob_major_outbreak",
    "prob_sec_case",
    "summary_coverage",
    "summary_infection_risk"
  ],
  "_datasets": [
    {
      "name": "florida_vaccine_coverage",
      "title": "Kindergarten Vaccination Coverage for Florida Counties",
      "object": "florida_vaccine_coverage",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "County",
        "Year",
        "Coverage_Rate"
      ],
      "rows": 680,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "calc_expected_infections",
      "title": "Calculate the expected number of infections in a cohort",
      "topics": [
        "calc_expected_infections"
      ]
    },
    {
      "page": "calc_re",
      "title": "Calculate the effective reproduction number (Re)",
      "topics": [
        "calc_re"
      ]
    },
    {
      "page": "florida_vaccine_coverage",
      "title": "Kindergarten Vaccination Coverage for Florida Counties",
      "topics": [
        "florida_vaccine_coverage"
      ]
    },
    {
      "page": "plot_coverage_history",
      "title": "Plot Historical Vaccination Coverage Rate",
      "topics": [
        "plot_coverage_history"
      ]
    },
    {
      "page": "plot_outbreak_prob",
      "title": "Plot Outbreak Probability vs. Coverage",
      "topics": [
        "plot_outbreak_prob"
      ]
    },
    {
      "page": "plot_risk_curve",
      "title": "Plot the Risk Curve of Expected Infections",
      "topics": [
        "plot_risk_curve"
      ]
    },
    {
      "page": "prob_major_outbreak",
      "title": "Calculate the probability of a major outbreak",
      "topics": [
        "prob_major_outbreak"
      ]
    },
    {
      "page": "prob_sec_case",
      "title": "Calculate the probability of at least one secondary infection",
      "topics": [
        "prob_sec_case"
      ]
    },
    {
      "page": "summary_coverage",
      "title": "Summarize Vaccination Coverage for a Given Year",
      "topics": [
        "summary_coverage"
      ]
    },
    {
      "page": "summary_infection_risk",
      "title": "Generate an Outbreak Risk Simulation Table",
      "topics": [
        "summary_infection_risk"
      ]
    }
  ],
  "_readme": "https://github.com/peiyuliu-biostats/vaxiner/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "dplyr",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "magrittr",
    "openxlsx",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "zip"
  ],
  "_vignettes": [
    {
      "source": "using_vaxineR.Rmd",
      "filename": "using_vaxineR.html",
      "title": "Using vaxineR for Outbreak Risk Analysis",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Included Data: florida_vaccine_coverage",
        "Core Concepts: Smart Defaults",
        "Modeling a Custom Disease",
        "Visualization Functions",
        "plot_coverage_history()",
        "plot_risk_curve()",
        "Saving Plot Data"
      ],
      "created": "2025-09-09 20:36:35",
      "modified": "2025-09-09 20:36:35",
      "commits": 1
    }
  ],
  "_score": 3.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "vaxiner",
  "_universes": [
    "peiyuliu-biostats"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-10-31T08:36:18.000Z",
      "distro": "resolute",
      "commit": "3e386406d2c06f9296d767c8d88a0c0824c626a7",
      "fileid": "https://r2.ropensci.org/76e587927d9956d516cc869488ce2a927cc82f0a685c32336507ad67f8239f14",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/peiyuliu-biostats/actions/runs/41184941970"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-10-31T08:36:23.000Z",
      "distro": "resolute",
      "commit": "3e386406d2c06f9296d767c8d88a0c0824c626a7",
      "fileid": "https://r2.ropensci.org/63cd18acafabedf59831176fb8f6c2299e73101a0375a10b9808fcddee5b0462",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/peiyuliu-biostats/actions/runs/41184941970"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-10-31T09:06:04.000Z",
      "commit": "3e386406d2c06f9296d767c8d88a0c0824c626a7",
      "fileid": "https://r2.ropensci.org/cdf493a33e6bed256fff89b835476f7ffb20fead3badd2b4d2876e439ed97d1a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/peiyuliu-biostats/actions/runs/41184941970"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-10-31T09:06:42.000Z",
      "commit": "3e386406d2c06f9296d767c8d88a0c0824c626a7",
      "fileid": "https://r2.ropensci.org/48669b507eb250357fe37698383d94db552835462f7e2f50f5939e570693cd3a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/peiyuliu-biostats/actions/runs/41184941970"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.0",
      "date": "2026-10-31T08:36:25.000Z",
      "commit": "3e386406d2c06f9296d767c8d88a0c0824c626a7",
      "fileid": "https://r2.ropensci.org/b47a39ba492c8af817504de098f6f6524f6ace9f9d9d5ad7ef17a79a2d6e4713",
      "status": "success",
      "buildurl": "https://github.com/r-universe/peiyuliu-biostats/actions/runs/41184941970"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-31T08:35:35.000Z",
      "commit": "3e386406d2c06f9296d767c8d88a0c0824c626a7",
      "fileid": "https://r2.ropensci.org/77130c663c94b126d0be418c025399393b702218672ee9426218289d2d19b430",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/peiyuliu-biostats/actions/runs/41184941970"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-31T08:35:40.000Z",
      "commit": "3e386406d2c06f9296d767c8d88a0c0824c626a7",
      "fileid": "https://r2.ropensci.org/6f2224c166d149dc1bb39f189f078bcaebf5f732a574e20f080a55bbc67efe3e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/peiyuliu-biostats/actions/runs/41184941970"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-31T08:35:35.000Z",
      "commit": "3e386406d2c06f9296d767c8d88a0c0824c626a7",
      "fileid": "https://r2.ropensci.org/83e3eec8d5128c6dfcc18c3146e2bd90ef5b4206729420fe387392486f22a33d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/peiyuliu-biostats/actions/runs/41184941970"
    }
  ]
}