{
  "_id": "6a1f2987b401979e7342403a",
  "Package": "penetrance",
  "Type": "Package",
  "Title": "Methods for Penetrance Estimation in Family-Based Studies",
  "Version": "0.1.3",
  "Authors@R": "c(\nperson(\"Sol\", \"Rosito\", email = \"bmendel@jimmy.harvard.edu\", role = \"cre\"),\nperson(\"Nicolas\", \"Kubista\", role = \"aut\"),\nperson(\"BayesMendel\", \"Lab\", role = \"aut\"),\nperson(\"Giovanni\", \"Parmigiani\", role = \"aut\"),\nperson(\"Danielle\", \"Braun\", role = \"aut\"),\nperson(\"Alice\", \"Zhang\", role = \"aut\"))",
  "Description": "Implements statistical methods for estimating disease\npenetrance in family-based studies. Penetrance refers to the\nprobability of disease manifestation in individuals carrying\nspecific genetic variants. The package provides tools for\nage-specific penetrance estimation, handling missing data, and\naccounting for ascertainment bias in family studies. Cite as:\nKubista, N., Braun, D. & Parmigiani, G. (2024) <d\n10.1093/bioadv/vbaf154>.",
  "License": "GPL-3",
  "URL": "https://github.com/bayesmendel/penetrance",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "LazyDataCompression": "xz",
  "RoxygenNote": "7.3.3",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Repository": "https://bayesmendel.r-universe.dev",
  "Date/Publication": "2026-05-15 22:30:28 UTC",
  "RemoteUrl": "https://github.com/bayesmendel/penetrance",
  "RemoteRef": "HEAD",
  "RemoteSha": "97c4e40ed7f5f2927f892c597238e0df37b2bc08",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-15 22:52:59 UTC",
    "User": "root"
  },
  "Author": "Sol Rosito [cre],\nNicolas Kubista [aut],\nBayesMendel Lab [aut],\nGiovanni Parmigiani [aut],\nDanielle Braun [aut],\nAlice Zhang [aut]",
  "Maintainer": "Sol Rosito <bmendel@jimmy.harvard.edu>",
  "MD5sum": "b864398de25868489dbad91bff8c7ea4",
  "_user": "bayesmendel",
  "_type": "src",
  "_file": "penetrance_0.1.3.tar.gz",
  "_fileid": "3cefe5249a04e13762b71f217d19879b0e3bc77c4b673b859cb4ec9941e7c07a",
  "_filesize": 1644396,
  "_sha256": "3cefe5249a04e13762b71f217d19879b0e3bc77c4b673b859cb4ec9941e7c07a",
  "_created": "2026-05-15T22:52:59.000Z",
  "_published": "2026-06-02T19:05:43.546Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79150364291,
      "time": 143,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7027975875"
    },
    {
      "job": 79150364511,
      "time": 136,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7027974716"
    },
    {
      "job": 79150364248,
      "time": 104,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7027968379"
    },
    {
      "job": 79150364052,
      "time": 101,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7027967982"
    },
    {
      "job": 79150363808,
      "time": 196,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7027949386"
    },
    {
      "job": 79150363291,
      "time": 105,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7367265260"
    },
    {
      "job": 79150364055,
      "time": 106,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7027969079"
    },
    {
      "job": 79150364234,
      "time": 91,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7027966153"
    },
    {
      "job": 79150364071,
      "time": 87,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7027965596"
    }
  ],
  "_buildurl": "https://github.com/r-universe/bayesmendel/actions/runs/25945111000",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bayesmendel/penetrance",
  "_commit": {
    "id": "97c4e40ed7f5f2927f892c597238e0df37b2bc08",
    "author": "M. S. Rosito <82741585+msrosito@users.noreply.github.com>",
    "committer": "M. S. Rosito <82741585+msrosito@users.noreply.github.com>",
    "message": "minor\n",
    "time": 1778884228
  },
  "_maintainer": {
    "name": "Sol Rosito",
    "email": "bmendel@jimmy.harvard.edu"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "clipp",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "kinship2",
      "version": ">= 1.8.5",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "scales",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "roxygen2",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bayesmendel",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-06",
      "n": 5
    },
    {
      "week": "2026-16",
      "n": 4
    },
    {
      "week": "2026-18",
      "n": 1
    },
    {
      "week": "2026-20",
      "n": 5
    }
  ],
  "_tags": [],
  "_stars": 1,
  "_contributors": [
    {
      "user": "nicokubi",
      "count": 85,
      "uuid": 39570499
    },
    {
      "user": "msrosito",
      "count": 15,
      "uuid": 82741585
    },
    {
      "user": "aalice-z",
      "count": 11,
      "uuid": 123009835
    }
  ],
  "_userbio": {
    "uuid": 51488820,
    "type": "organization",
    "name": "bayesmendel"
  },
  "_downloads": {
    "count": 175,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/penetrance"
  },
  "_devurl": "https://github.com/bayesmendel/penetrance",
  "_searchresults": 10,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/penetrance.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/bayesmendel/penetrance",
  "_realowner": "bayesmendel",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2025-03-03"
    },
    {
      "version": "0.1.1",
      "date": "2025-04-02"
    },
    {
      "version": "0.1.2",
      "date": "2026-02-05"
    }
  ],
  "_exports": [
    "absValue",
    "baseline_data_default",
    "calculate_weibull_parameters",
    "calculateBaseline",
    "calculateEmpiricalDensity",
    "calculateNCPen",
    "combine_chains_noSex",
    "distribution_data_default",
    "generate_density_plots",
    "generate_summary",
    "generate_summary_noSex",
    "imputeAges",
    "imputeAgesInit",
    "makePriors",
    "mhChain",
    "mhLogLikelihood_clipp",
    "penetrance",
    "plot_acf",
    "plot_loglikelihood",
    "plot_pdf",
    "plot_penetrance",
    "plot_trace",
    "printRejectionRates",
    "prior_params_default",
    "risk_proportion_default",
    "transformDF",
    "validate_allele_freq",
    "validate_baseline_data",
    "validate_weibull_parameters"
  ],
  "_datasets": [
    {
      "name": "out_sim",
      "title": "Simulated Output Data",
      "object": "out_sim",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "simulated_families",
      "title": "Processed Family Data",
      "object": "simulated_families",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "test_fam2",
      "title": "Processed Family Data",
      "object": "test_fam2",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "absValue",
      "title": "Function to return absolute values",
      "topics": [
        "absValue"
      ]
    },
    {
      "page": "apply_burn_in",
      "title": "Apply Burn-In",
      "topics": [
        "apply_burn_in"
      ]
    },
    {
      "page": "apply_thinning",
      "title": "Apply Thinning",
      "topics": [
        "apply_thinning"
      ]
    },
    {
      "page": "baseline_data_default",
      "title": "Default Baseline Data",
      "topics": [
        "baseline_data_default"
      ]
    },
    {
      "page": "calculate_weibull_parameters",
      "title": "Calculate Weibull Parameters",
      "topics": [
        "calculate_weibull_parameters"
      ]
    },
    {
      "page": "calculateBaseline",
      "title": "Calculate Baseline Risk",
      "topics": [
        "calculateBaseline"
      ]
    },
    {
      "page": "calculateEmpiricalDensity",
      "title": "Calculate Empirical Age Density",
      "topics": [
        "calculateEmpiricalDensity"
      ]
    },
    {
      "page": "calculateNCPen",
      "title": "Calculate Age-Specific Non-Carrier Penetrance",
      "topics": [
        "calculateNCPen"
      ]
    },
    {
      "page": "combine_chains",
      "title": "Combine Chains Function to combine the posterior samples from the multiple chains.",
      "topics": [
        "combine_chains"
      ]
    },
    {
      "page": "combine_chains_noSex",
      "title": "Combine Chains for Non-Sex-Specific Estimation",
      "topics": [
        "combine_chains_noSex"
      ]
    },
    {
      "page": "distribution_data_default",
      "title": "Default Distribution Data",
      "topics": [
        "distribution_data_default"
      ]
    },
    {
      "page": "drawBaseline",
      "title": "Draw Ages Using the Inverse CDF Method from the baseline data",
      "topics": [
        "drawBaseline"
      ]
    },
    {
      "page": "drawEmpirical",
      "title": "Draw Ages Using the Inverse CDF Method from Empirical Density",
      "topics": [
        "drawEmpirical"
      ]
    },
    {
      "page": "generate_density_plots",
      "title": "Generate Posterior Density Plots",
      "topics": [
        "generate_density_plots"
      ]
    },
    {
      "page": "generate_summary",
      "title": "Generate Summary",
      "topics": [
        "generate_summary"
      ]
    },
    {
      "page": "generate_summary_noSex",
      "title": "Generate Summary for Non-Sex-Specific Estimation",
      "topics": [
        "generate_summary_noSex"
      ]
    },
    {
      "page": "imputeAges",
      "title": "Impute Missing Ages in Family-Based Data",
      "topics": [
        "imputeAges"
      ]
    },
    {
      "page": "imputeAgesInit",
      "title": "Initialize Age Imputation",
      "topics": [
        "imputeAgesInit"
      ]
    },
    {
      "page": "imputeUnaffectedAges",
      "title": "Impute Ages for Unaffected Individuals",
      "topics": [
        "imputeUnaffectedAges"
      ]
    },
    {
      "page": "lik_noSex",
      "title": "Likelihood Calculation without Sex Differentiation",
      "topics": [
        "lik_noSex"
      ]
    },
    {
      "page": "lik.fn",
      "title": "Penetrance Function",
      "topics": [
        "lik.fn"
      ]
    },
    {
      "page": "makePriors",
      "title": "Make Priors",
      "topics": [
        "makePriors"
      ]
    },
    {
      "page": "mhChain",
      "title": "Execution of a Single Chain in Metropolis-Hastings for Cancer Risk Estimation",
      "topics": [
        "mhChain"
      ]
    },
    {
      "page": "mhLogLikelihood_clipp",
      "title": "Calculate Log Likelihood using clipp Package",
      "topics": [
        "mhLogLikelihood_clipp"
      ]
    },
    {
      "page": "mhLogLikelihood_clipp_noSex",
      "title": "Calculate Log Likelihood without Sex Differentiation",
      "topics": [
        "mhLogLikelihood_clipp_noSex"
      ]
    },
    {
      "page": "out_sim",
      "title": "Simulated Output Data",
      "topics": [
        "out_sim"
      ]
    },
    {
      "page": "penetrance",
      "title": "penetrance: A Package for Penetrance Estimation",
      "topics": [
        "penetrance-package",
        "penetrance"
      ]
    },
    {
      "page": "plot_acf",
      "title": "Plot Autocorrelation for Multiple MCMC Chains (Posterior Samples)",
      "topics": [
        "plot_acf"
      ]
    },
    {
      "page": "plot_loglikelihood",
      "title": "Plot Log-Likelihood for Multiple MCMC Chains",
      "topics": [
        "plot_loglikelihood"
      ]
    },
    {
      "page": "plot_pdf",
      "title": "Plot Weibull Probability Density Function with Credible Intervals",
      "topics": [
        "plot_pdf"
      ]
    },
    {
      "page": "plot_penetrance",
      "title": "Plot Weibull Distribution with Credible Intervals",
      "topics": [
        "plot_penetrance"
      ]
    },
    {
      "page": "plot_trace",
      "title": "Plot MCMC Trace Plots",
      "topics": [
        "plot_trace"
      ]
    },
    {
      "page": "printRejectionRates",
      "title": "Print MCMC Rejection Rates",
      "topics": [
        "printRejectionRates"
      ]
    },
    {
      "page": "prior_params_default",
      "title": "Default Prior Parameters",
      "topics": [
        "prior_params_default"
      ]
    },
    {
      "page": "risk_proportion_default",
      "title": "Default Risk Proportions",
      "topics": [
        "risk_proportion_default"
      ]
    },
    {
      "page": "simulated_families",
      "title": "Processed Family Data",
      "topics": [
        "simulated_families"
      ]
    },
    {
      "page": "test_fam2",
      "title": "Processed Family Data",
      "topics": [
        "test_fam2"
      ]
    },
    {
      "page": "transformDF",
      "title": "Transform Data Frame",
      "topics": [
        "transformDF"
      ]
    },
    {
      "page": "validate_allele_freq",
      "title": "Validate Allele Frequency Input",
      "topics": [
        "validate_allele_freq"
      ]
    },
    {
      "page": "validate_baseline_data",
      "title": "Validate Baseline Penetrance Data",
      "topics": [
        "validate_baseline_data"
      ]
    },
    {
      "page": "validate_weibull_parameters",
      "title": "Validate Weibull Parameters",
      "topics": [
        "validate_weibull_parameters"
      ]
    }
  ],
  "_readme": "https://github.com/bayesmendel/penetrance/raw/HEAD/README.md",
  "_rundeps": [
    "clipp",
    "evaluate",
    "highr",
    "kinship2",
    "knitr",
    "lattice",
    "MASS",
    "Matrix",
    "quadprog",
    "xfun",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "using_penetrance.Rmd",
      "filename": "using_penetrance.html",
      "title": "Using penetrance",
      "author": "BayesMendel Lab",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Data",
        "Age Imputation",
        "Estimation Approach",
        "Prior Specification",
        "Estimation using penetrance",
        "Example",
        "References"
      ],
      "created": "2024-08-07 13:55:02",
      "modified": "2026-04-17 22:12:27",
      "commits": 18
    },
    {
      "source": "simulation_study_real.Rmd",
      "filename": "simulation_study_real.html",
      "title": "Simulation study from empirical data with penetrance",
      "author": "BayesMendel Lab",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Goal",
        "Simulated Data",
        "Simple simulation",
        "References"
      ],
      "created": "2024-08-12 19:38:37",
      "modified": "2026-05-15 20:56:00",
      "commits": 8
    },
    {
      "source": "simulation_study.Rmd",
      "filename": "simulation_study.html",
      "title": "Simulation Study with penetrance",
      "author": "BayesMendel Lab",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Goal",
        "Simulated Data",
        "Simple simulation",
        "Comparison of estimated curves vs. data-generating curves"
      ],
      "created": "2024-08-07 13:55:02",
      "modified": "2026-05-15 21:19:54",
      "commits": 12
    }
  ],
  "_score": 5.079181246047625,
  "_indexed": true,
  "_nocasepkg": "penetrance",
  "_universes": [
    "bayesmendel"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.3",
      "date": "2026-05-15T22:55:06.000Z",
      "distro": "noble",
      "commit": "97c4e40ed7f5f2927f892c597238e0df37b2bc08",
      "fileid": "44e5992f259c60f3372fd8ece582ad4d5a6524f3c8a38450282c6382321da068",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bayesmendel/actions/runs/25945111000"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.3",
      "date": "2026-05-15T22:55:03.000Z",
      "distro": "noble",
      "commit": "97c4e40ed7f5f2927f892c597238e0df37b2bc08",
      "fileid": "a61bbc0914d16011498e7693a262112f234d8e76c6ce4a2bbbf7add2eb36e0b7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bayesmendel/actions/runs/25945111000"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.3",
      "date": "2026-05-15T22:54:36.000Z",
      "commit": "97c4e40ed7f5f2927f892c597238e0df37b2bc08",
      "fileid": "a3b60db0e7f2e254660b6cf2135dec0db3d2ef5ebf70b71f7326c32fa164951d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bayesmendel/actions/runs/25945111000"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.3",
      "date": "2026-05-15T22:54:36.000Z",
      "commit": "97c4e40ed7f5f2927f892c597238e0df37b2bc08",
      "fileid": "edcf80917a9cd3558376b997f2a4258ba60e0c6a04a8746e213425b2a49400f8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bayesmendel/actions/runs/25945111000"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.3",
      "date": "2026-05-15T22:54:21.000Z",
      "commit": "97c4e40ed7f5f2927f892c597238e0df37b2bc08",
      "fileid": "ca213ecb84953bae561a4d3eb64ee51d36423832b48f2cd314ba10485eb45a46",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bayesmendel/actions/runs/25945111000"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.3",
      "date": "2026-05-15T22:54:13.000Z",
      "commit": "97c4e40ed7f5f2927f892c597238e0df37b2bc08",
      "fileid": "a5be940ad2af3dcc6cfaae130f07cb75ffe628eb9b10bf3a231528778a9f7c67",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bayesmendel/actions/runs/25945111000"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.3",
      "date": "2026-05-15T22:54:11.000Z",
      "commit": "97c4e40ed7f5f2927f892c597238e0df37b2bc08",
      "fileid": "ead5a63ff5cd07f5a90331abd3a9053d7a326e02a4124bbd5eb419b2b77faca0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bayesmendel/actions/runs/25945111000"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.3",
      "date": "2026-06-02T19:05:18.000Z",
      "commit": "97c4e40ed7f5f2927f892c597238e0df37b2bc08",
      "fileid": "bf629e6cbdbf5528b0d008188a2696854c6b5d2d6ea8d25ad41d2669a2a4193a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bayesmendel/actions/runs/25945111000"
    }
  ]
}