{
  "_id": "6a1eeb54b401979e7341228d",
  "Package": "graphPAF",
  "Title": "Estimating and Displaying Population Attributable Fractions",
  "Version": "2.0.1",
  "Authors@R": "person(given = \"John\",\nfamily = \"Ferguson\",\nemail = \"john.ferguson@universityofgalway.ie\",\nrole = c(\"aut\", \"cre\"))",
  "Description": "Estimation and display of various types of population\nattributable fraction and impact fractions. As well as the\nusual calculations of attributable fractions and impact\nfractions, functions are provided for attributable fraction\nnomograms and fan plots, continuous exposures, for pathway\nspecific population attributable fractions, and for joint,\naverage and sequential population attributable fractions.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "URL": "https://github.com/johnfergusonNUIG/graphPAF",
  "BugReports": "https://github.com/johnfergusonNUIG/graphPAF/issues",
  "VignetteBuilder": "R.rsp",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://johnfergusonnuig.r-universe.dev",
  "Date/Publication": "2026-02-13 18:20:12 UTC",
  "RemoteUrl": "https://github.com/johnfergusonnuig/graphpaf",
  "RemoteRef": "HEAD",
  "RemoteSha": "b4453d8df1c7a2e146784b69230dc35bb6935fbe",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-19 09:48:58 UTC",
    "User": "root"
  },
  "Author": "John Ferguson [aut, cre]",
  "Maintainer": "John Ferguson <john.ferguson@universityofgalway.ie>",
  "MD5sum": "fa9e93fe530d0b02cd043ee154a2335a",
  "_user": "johnfergusonnuig",
  "_type": "src",
  "_file": "graphPAF_2.0.1.tar.gz",
  "_fileid": "cdc68d40edb7f0afb7501908effdb5b6d161e61642d117484078f81f43581a87",
  "_filesize": 1477334,
  "_sha256": "cdc68d40edb7f0afb7501908effdb5b6d161e61642d117484078f81f43581a87",
  "_created": "2026-05-19T09:48:58.000Z",
  "_published": "2026-06-02T14:40:20.184Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79097365266,
      "time": 170,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7080238369"
    },
    {
      "job": 79097366083,
      "time": 172,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7080238560"
    },
    {
      "job": 79097365297,
      "time": 175,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7080239777"
    },
    {
      "job": 79097365175,
      "time": 201,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7080248436"
    },
    {
      "job": 79097364553,
      "time": 220,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7080176593"
    },
    {
      "job": 79097364888,
      "time": 113,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7360930553"
    },
    {
      "job": 79097365483,
      "time": 130,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7080224747"
    },
    {
      "job": 79097366377,
      "time": 142,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7080228324"
    },
    {
      "job": 79097366079,
      "time": 123,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7080221259"
    }
  ],
  "_buildurl": "https://github.com/r-universe/johnfergusonnuig/actions/runs/26089375765",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/johnfergusonnuig/graphpaf",
  "_commit": {
    "id": "b4453d8df1c7a2e146784b69230dc35bb6935fbe",
    "author": "John Ferguson <john.ferguson@nuigalway.ie>",
    "committer": "John Ferguson <john.ferguson@nuigalway.ie>",
    "message": "reduced size of vignette for CRAN\n",
    "time": 1771006812
  },
  "_maintainer": {
    "name": "John Ferguson",
    "email": "john.ferguson@universityofgalway.ie"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "boot",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "gtools",
      "role": "Imports"
    },
    {
      "package": "madness",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "splines",
      "role": "Imports"
    },
    {
      "package": "survival",
      "role": "Imports"
    },
    {
      "package": "R.rsp",
      "role": "Suggests"
    }
  ],
  "_owner": "johnfergusonnuig",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-07",
      "n": 4
    }
  ],
  "_tags": [],
  "_stars": 6,
  "_contributors": [
    {
      "user": "johnfergusonnuig",
      "count": 185,
      "uuid": 26142157
    },
    {
      "user": "mauriceoconnell",
      "count": 3,
      "uuid": 4921691
    }
  ],
  "_userbio": {
    "uuid": 26142157,
    "type": "user",
    "name": "John Ferguson"
  },
  "_downloads": {
    "count": 288,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/graphPAF"
  },
  "_devurl": "https://github.com/johnfergusonnuig/graphpaf",
  "_searchresults": 9,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/graphPAF.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/johnfergusonnuig/graphpaf",
  "_realowner": "johnfergusonnuig",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2022-09-22"
    },
    {
      "version": "1.0.1",
      "date": "2022-10-20"
    },
    {
      "version": "1.0.2",
      "date": "2023-02-09"
    },
    {
      "version": "2.0.0",
      "date": "2023-12-21"
    },
    {
      "version": "2.0.1",
      "date": "2026-02-16"
    }
  ],
  "_exports": [
    "automatic_fit",
    "average_paf",
    "data_clean",
    "do_sim",
    "if_bruzzi",
    "if_direct",
    "impact_fraction",
    "joint_paf",
    "PAF_calc_continuous",
    "PAF_calc_discrete",
    "paf_levin",
    "paf_miettinen",
    "plot_continuous",
    "predict_df_continuous",
    "predict_df_discrete",
    "ps_paf",
    "pspaf_discrete",
    "rf_summary",
    "risk_quantiles",
    "seq_paf",
    "sim_outnode"
  ],
  "_datasets": [
    {
      "name": "Hordaland_data",
      "title": "Simulated case control dataset for 5000 cases (individuals with chronic cough) and 5000 controls",
      "object": "Hordaland_data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "y",
        "urban.rural",
        "smoking.category",
        "occupational.exposure"
      ],
      "rows": 10000,
      "table": true,
      "tojson": true
    },
    {
      "name": "stroke_reduced",
      "title": "Simulated case control dataset for 6856 stroke cases and 6856 stroke controls",
      "object": "stroke_reduced",
      "class": [
        "data.frame"
      ],
      "fields": [
        "region",
        "case",
        "sex",
        "age",
        "smoking",
        "stress",
        "waist_hip_ratio",
        "exercise",
        "alcohol",
        "diabetes",
        "early_stage_heart_disease",
        "diet",
        "lipids",
        "education",
        "high_blood_pressure",
        "weights",
        "time",
        "event",
        "strata"
      ],
      "rows": 13712,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "automatic_fit",
      "title": "Automatic fitting of probability models in a pre-specified Bayesian network.",
      "topics": [
        "automatic_fit"
      ]
    },
    {
      "page": "average_paf",
      "title": "Calculation of average and sequential paf taking into account risk factor sequencing",
      "topics": [
        "average_paf"
      ]
    },
    {
      "page": "data_clean",
      "title": "Clean a dataset to make model fitting more efficient",
      "topics": [
        "data_clean"
      ]
    },
    {
      "page": "do_sim",
      "title": "Internal: Simulate a column from the post intervention distribution corresponding to eliminating a risk factor",
      "topics": [
        "do_sim"
      ]
    },
    {
      "page": "Hordaland_data",
      "title": "Simulated case control dataset for 5000 cases (individuals with chronic cough) and 5000 controls",
      "topics": [
        "Hordaland_data"
      ]
    },
    {
      "page": "if_bruzzi",
      "title": "Internal: Calculation of an impact fraction using the Bruzzi approach",
      "topics": [
        "if_bruzzi"
      ]
    },
    {
      "page": "if_direct",
      "title": "Internal: Calculation of an impact fraction using the direct approach",
      "topics": [
        "if_direct"
      ]
    },
    {
      "page": "impact_fraction",
      "title": "General calculations of impact fractions",
      "topics": [
        "impact_fraction"
      ]
    },
    {
      "page": "joint_paf",
      "title": "Calculation of joint attributable fractions over several risk factors taking into account risk factor sequencing",
      "topics": [
        "joint_paf"
      ]
    },
    {
      "page": "PAF_calc_continuous",
      "title": "Calculation of attributable fractions with a continuous exposure",
      "topics": [
        "PAF_calc_continuous"
      ]
    },
    {
      "page": "PAF_calc_discrete",
      "title": "Calculation of attributable fractions using a categorized risk factor",
      "topics": [
        "PAF_calc_discrete"
      ]
    },
    {
      "page": "paf_levin",
      "title": "Implementation of Levin's formula for summary data",
      "topics": [
        "paf_levin"
      ]
    },
    {
      "page": "paf_miettinen",
      "title": "Implementation of Miettinen's formula for summary data",
      "topics": [
        "paf_miettinen"
      ]
    },
    {
      "page": "plot_continuous",
      "title": "Plot hazard ratios, odds ratios or risk ratios comparing differing values of a continuous exposure to a reference level",
      "topics": [
        "plot_continuous"
      ]
    },
    {
      "page": "plot.PAF_q",
      "title": "Plot impact fractions corresponding to risk-quantiles over several risk factors",
      "topics": [
        "plot.PAF_q"
      ]
    },
    {
      "page": "plot.rf.data.frame",
      "title": "Create a fan_plot of a rf.data.frame object",
      "topics": [
        "plot.rf.data.frame"
      ]
    },
    {
      "page": "plot.SAF_summary",
      "title": "Produce plots of sequential and average PAF",
      "topics": [
        "plot.SAF_summary"
      ]
    },
    {
      "page": "predict_df_continuous",
      "title": "Internal: Create a data frame for predictions (when risk factor is continuous).",
      "topics": [
        "predict_df_continuous"
      ]
    },
    {
      "page": "predict_df_discrete",
      "title": "Internal: Create a data frame for predictions (when risk factor is discrete).",
      "topics": [
        "predict_df_discrete"
      ]
    },
    {
      "page": "print.PAF_q",
      "title": "Print out PAF_q for differing risk factors",
      "topics": [
        "print.PAF_q"
      ]
    },
    {
      "page": "print.SAF_summary",
      "title": "Print out a SAF_summary object",
      "topics": [
        "print.SAF_summary"
      ]
    },
    {
      "page": "ps_paf",
      "title": "Estimate pathway specific population attributable fractions",
      "topics": [
        "ps_paf"
      ]
    },
    {
      "page": "pspaf_discrete",
      "title": "Internal, pathway specific PAF when the mediator is discrete",
      "topics": [
        "pspaf_discrete"
      ]
    },
    {
      "page": "rf_summary",
      "title": "Create a rf.data.frame object",
      "topics": [
        "rf_summary"
      ]
    },
    {
      "page": "risk_quantiles",
      "title": "Return the vector of risk quantiles for a continuous risk factor.",
      "topics": [
        "risk_quantiles"
      ]
    },
    {
      "page": "seq_paf",
      "title": "Calculation of sequential PAF taking into account risk factor sequencing",
      "topics": [
        "seq_paf"
      ]
    },
    {
      "page": "sim_outnode",
      "title": "Internal: Simulate from the post intervention distribution corresponding to eliminating a risk factor",
      "topics": [
        "sim_outnode"
      ]
    },
    {
      "page": "stroke_reduced",
      "title": "Simulated case control dataset for 6856 stroke cases and 6856 stroke controls",
      "topics": [
        "stroke_reduced"
      ]
    }
  ],
  "_rundeps": [
    "boot",
    "cli",
    "cpp11",
    "dplyr",
    "expm",
    "farver",
    "generics",
    "ggplot2",
    "ggrepel",
    "glue",
    "gridExtra",
    "gtable",
    "gtools",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "madness",
    "magrittr",
    "MASS",
    "Matrix",
    "matrixcalc",
    "pillar",
    "pkgconfig",
    "plyr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "reshape2",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "graphPAF_vignette.pdf.asis",
      "filename": "graphPAF_vignette.pdf",
      "title": "graphPAF: An R package to estimate and display population attributable fractions",
      "engine": "R.rsp::asis",
      "headings": [],
      "created": "2023-02-07 16:28:44",
      "modified": "2025-05-09 09:26:17",
      "commits": 8
    }
  ],
  "_score": 3.778151250383644,
  "_indexed": true,
  "_nocasepkg": "graphpaf",
  "_universes": [
    "johnfergusonnuig"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.0.1",
      "date": "2026-05-19T09:51:14.000Z",
      "distro": "noble",
      "commit": "b4453d8df1c7a2e146784b69230dc35bb6935fbe",
      "fileid": "55b12519baef71341975c0bc528e73a138850833689f9f2fd0e54305fb0ed2ce",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/johnfergusonnuig/actions/runs/26089375765"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.0.1",
      "date": "2026-05-19T09:51:15.000Z",
      "distro": "noble",
      "commit": "b4453d8df1c7a2e146784b69230dc35bb6935fbe",
      "fileid": "1bd902ff83f8d525960ad39bb61381b50a9f1575f487d0295e52949fd8ae8aa9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/johnfergusonnuig/actions/runs/26089375765"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.0.1",
      "date": "2026-05-19T09:51:15.000Z",
      "commit": "b4453d8df1c7a2e146784b69230dc35bb6935fbe",
      "fileid": "cf5f84a3142dacd57644c42cd4dbb548c04bce7cfe1cf43077d8e74179980350",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/johnfergusonnuig/actions/runs/26089375765"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.0.1",
      "date": "2026-05-19T09:51:23.000Z",
      "commit": "b4453d8df1c7a2e146784b69230dc35bb6935fbe",
      "fileid": "07ac56ada0415ea68cb59875eaad8b0158c69d57e682e6255fdef220cbe730ad",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/johnfergusonnuig/actions/runs/26089375765"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.0.1",
      "date": "2026-05-19T09:50:30.000Z",
      "commit": "b4453d8df1c7a2e146784b69230dc35bb6935fbe",
      "fileid": "c5774fcce8b286b434c091d6e99dd3e383fc054339a177b34f056922c85f6bb6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/johnfergusonnuig/actions/runs/26089375765"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.0.1",
      "date": "2026-05-19T09:50:33.000Z",
      "commit": "b4453d8df1c7a2e146784b69230dc35bb6935fbe",
      "fileid": "65a8517f64ab6a2ab203b5366b70d2e855176c5f1d355843317b7a4b184c9bb7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/johnfergusonnuig/actions/runs/26089375765"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.0.1",
      "date": "2026-05-19T09:50:17.000Z",
      "commit": "b4453d8df1c7a2e146784b69230dc35bb6935fbe",
      "fileid": "985d473d06604ec1125c521d55eca843bfe59462b33614262d28889b89702b54",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/johnfergusonnuig/actions/runs/26089375765"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.0.1",
      "date": "2026-06-02T14:40:01.000Z",
      "commit": "b4453d8df1c7a2e146784b69230dc35bb6935fbe",
      "fileid": "60789b96d7be2a08f534c48c3d4dc1a1ac9958047f67d24bf0ea433a4d43b2d5",
      "status": "success",
      "buildurl": "https://github.com/r-universe/johnfergusonnuig/actions/runs/26089375765"
    }
  ]
}