{
  "_id": "6a49bf03fcd1f935c701ccdc",
  "Package": "BeviMed",
  "Type": "Package",
  "Title": "Bayesian Evaluation of Variant Involvement in Mendelian Disease",
  "Version": "7.0",
  "Encoding": "UTF-8",
  "Date": "2025-08-20",
  "Authors@R": "person(\"Daniel\", \"Greene\", email = \"dg333@cam.ac.uk\",role = c(\"aut\", \"cre\"))",
  "Description": "A fast integrative genetic association test for rare\ndiseases based on a model for disease status given allele\ncounts at rare variant sites. Probability of association, mode\nof inheritance and probability of pathogenicity for individual\nvariants are all inferred in a Bayesian framework - 'A Fast\nAssociation Test for Identifying Pathogenic Variants Involved\nin Rare Diseases', Greene et al 2017\n<doi:10.1016/j.ajhg.2017.05.015>.",
  "License": "GPL (>= 2)",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-18 10:54:27 UTC",
    "User": "root"
  },
  "Author": "Daniel Greene [aut, cre]",
  "Maintainer": "Daniel Greene <dg333@cam.ac.uk>",
  "Repository": "https://daniel-jg.r-universe.dev",
  "Date/Publication": "2025-08-22 07:30:01 UTC",
  "RemoteUrl": "https://github.com/cran/BeviMed",
  "RemoteRef": "HEAD",
  "RemoteSha": "f2caaa0b6696ffa6ac16f0731326adbb7015d10f",
  "_user": "daniel-jg",
  "_type": "src",
  "_file": "BeviMed_7.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/5112e7d57a006232952f001411b28bc87c49b401c0cbd9a9ac387fd41b1cdf2c",
  "_filesize": 382390,
  "_sha256": "5112e7d57a006232952f001411b28bc87c49b401c0cbd9a9ac387fd41b1cdf2c",
  "_expires": "2026-10-13T02:18:41.000Z",
  "_created": "2026-06-18T10:54:27.000Z",
  "_published": "2026-07-05T02:18:43.163Z",
  "_jobs": [
    {
      "job": 85185373979,
      "time": 154,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7721354008"
    },
    {
      "job": 85185373978,
      "time": 132,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7743380392"
    },
    {
      "job": 85185374116,
      "time": 139,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7721347997"
    },
    {
      "job": 85185373937,
      "time": 108,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7721337323"
    },
    {
      "job": 85185374085,
      "time": 99,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7721333947"
    },
    {
      "job": 85185373971,
      "time": 200,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7721367982"
    },
    {
      "job": 85185373975,
      "time": 99,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7721334359"
    },
    {
      "job": 85185374090,
      "time": 181,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7721360991"
    },
    {
      "job": 85185373982,
      "time": 159,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7721300023"
    },
    {
      "job": 85185373994,
      "time": 99,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7721334273"
    },
    {
      "job": 85185373983,
      "time": 113,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7721338874"
    },
    {
      "job": 85185373981,
      "time": 114,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7721339043"
    },
    {
      "job": 85185374073,
      "time": 100,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7721334267"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/27754450107",
  "_status": "success",
  "_upstream": "https://github.com/cran/BeviMed",
  "_commit": {
    "id": "f2caaa0b6696ffa6ac16f0731326adbb7015d10f",
    "author": "Daniel Greene <dg333@cam.ac.uk>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 7.0\n",
    "time": 1755847801
  },
  "_maintainer": {
    "name": "Daniel Greene",
    "email": "dg333@cam.ac.uk",
    "login": "daniel-jg",
    "description": "",
    "uuid": 25660818
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.3",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-34",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "7.0",
      "date": "2025-08-22"
    }
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "daniel-jg",
      "count": 12,
      "uuid": 25660818
    }
  ],
  "_userbio": {
    "uuid": 25660818,
    "type": "user",
    "name": "Daniel",
    "followers": 4
  },
  "_downloads": {
    "count": 703,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BeviMed"
  },
  "_mentions": 5,
  "_searchresults": 24,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/BeviMed.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "daniel-jg",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.2",
      "date": "2016-05-03"
    },
    {
      "version": "2.2",
      "date": "2016-07-05"
    },
    {
      "version": "3.0",
      "date": "2017-02-16"
    },
    {
      "version": "4.0",
      "date": "2017-03-01"
    },
    {
      "version": "5.0",
      "date": "2017-04-22"
    },
    {
      "version": "5.1",
      "date": "2017-07-03"
    },
    {
      "version": "5.3",
      "date": "2017-08-21"
    },
    {
      "version": "5.7",
      "date": "2020-03-28"
    },
    {
      "version": "5.8",
      "date": "2021-02-01"
    },
    {
      "version": "5.10",
      "date": "2024-05-29"
    },
    {
      "version": "6.0",
      "date": "2025-04-29"
    },
    {
      "version": "7.0",
      "date": "2025-08-22"
    }
  ],
  "_exports": [
    "bevimed",
    "bevimed_m",
    "bevimed_polytomous",
    "conditional_prob_pathogenic",
    "expected_explained",
    "explaining_variants",
    "extract_conditional_prob_pathogenic",
    "extract_expected_explained",
    "extract_explaining_variants",
    "extract_gamma1_evidence",
    "extract_prob_association",
    "extract_prob_pathogenic",
    "gamma0_evidence",
    "gamma1_evidence",
    "log_BF",
    "prob_association",
    "prob_association_m",
    "prob_pathogenic",
    "subset_variants"
  ],
  "_help": [
    {
      "page": "BeviMed-package",
      "title": "Bayesian Evaluation of Variant Involvement in Mendelian Disease",
      "topics": [
        "BeviMed-package",
        "BeviMed"
      ]
    },
    {
      "page": "bevimed",
      "title": "Bayesian Evaluation of Variant Involvement in Mendelian Disease",
      "topics": [
        "bevimed"
      ]
    },
    {
      "page": "bevimed_m",
      "title": "Perform inference under model gamma = 1 conditional on mode of inheritance",
      "topics": [
        "bevimed_m"
      ]
    },
    {
      "page": "bevimed_polytomous",
      "title": "Model selection for multiple association models",
      "topics": [
        "bevimed_polytomous"
      ]
    },
    {
      "page": "call_cpp",
      "title": "R interface to BeviMed c++ MCMC procedure",
      "topics": [
        "call_cpp"
      ]
    },
    {
      "page": "CI_gamma1_evidence",
      "title": "Estimate confidence interval for estimated marginal likelihood",
      "topics": [
        "CI_gamma1_evidence"
      ]
    },
    {
      "page": "conditional_prob_pathogenic",
      "title": "Calculate probability of pathogencity for variants conditional on mode of inheritance.",
      "topics": [
        "conditional_prob_pathogenic"
      ]
    },
    {
      "page": "expected_explained",
      "title": "Calculate expected number of explained cases",
      "topics": [
        "expected_explained"
      ]
    },
    {
      "page": "explaining_variants",
      "title": "Calculate expected number of pathogenic variants in cases",
      "topics": [
        "explaining_variants"
      ]
    },
    {
      "page": "extract_conditional_prob_pathogenic",
      "title": "Extract probability of pathogenicity for variant conditional on a given association model",
      "topics": [
        "extract_conditional_prob_pathogenic"
      ]
    },
    {
      "page": "extract_expected_explained",
      "title": "Extract expected number of explained cases",
      "topics": [
        "extract_expected_explained"
      ]
    },
    {
      "page": "extract_explaining_variants",
      "title": "Extract expected number of pathogenic variants in cases",
      "topics": [
        "extract_explaining_variants"
      ]
    },
    {
      "page": "extract_gamma1_evidence",
      "title": "Extract evidence for model gamma = 1",
      "topics": [
        "extract_gamma1_evidence"
      ]
    },
    {
      "page": "extract_prob_association",
      "title": "Extract the posterior probability of association",
      "topics": [
        "extract_prob_association"
      ]
    },
    {
      "page": "extract_prob_pathogenic",
      "title": "Extract variant marginal probabilities of pathogenicity",
      "topics": [
        "extract_prob_pathogenic"
      ]
    },
    {
      "page": "gamma0_evidence",
      "title": "Calculate marginal probability of observed case-control status y under model gamma = 0",
      "topics": [
        "gamma0_evidence"
      ]
    },
    {
      "page": "gamma1_evidence",
      "title": "Calculate evidence under model gamma = 1",
      "topics": [
        "gamma1_evidence"
      ]
    },
    {
      "page": "log_BF",
      "title": "Calculate log Bayes factor between an association model with a given mode of inheritance and model gamma = 0",
      "topics": [
        "log_BF"
      ]
    },
    {
      "page": "print.BeviMed",
      "title": "Print readable summary of 'BeviMed' object",
      "topics": [
        "print.BeviMed"
      ]
    },
    {
      "page": "print.BeviMed_m",
      "title": "Print 'BeviMed_m' object",
      "topics": [
        "print.BeviMed_m"
      ]
    },
    {
      "page": "print.BeviMed_summary",
      "title": "Print readable summary of 'BeviMed_summary' object.",
      "topics": [
        "print.BeviMed_summary"
      ]
    },
    {
      "page": "prob_association",
      "title": "Calculate probability of association",
      "topics": [
        "prob_association"
      ]
    },
    {
      "page": "prob_association_m",
      "title": "Calculate probability of association for one mode of inheritance",
      "topics": [
        "prob_association_m"
      ]
    },
    {
      "page": "prob_pathogenic",
      "title": "Calculate variant marginal probabilities of pathogencity",
      "topics": [
        "prob_pathogenic"
      ]
    },
    {
      "page": "stack_BeviMeds",
      "title": "Concatenate objects of class 'BeviMed_raw'",
      "topics": [
        "stack_BeviMeds"
      ]
    },
    {
      "page": "stop_chain",
      "title": "Apply the MCMC algorithm in blocks until conditions are met",
      "topics": [
        "stop_chain"
      ]
    },
    {
      "page": "subset_variants",
      "title": "Remove variants with no data for pathogenicity",
      "topics": [
        "subset_variants"
      ]
    },
    {
      "page": "sum_ML_over_PP",
      "title": "Calculate marginal likelihood from power posteriors output",
      "topics": [
        "sum_ML_over_PP"
      ]
    },
    {
      "page": "summary.BeviMed",
      "title": "Summarise a 'BeviMed' object",
      "topics": [
        "summary.BeviMed"
      ]
    },
    {
      "page": "summary.BeviMed_m",
      "title": "Summarise a 'BeviMed_m' object",
      "topics": [
        "summary.BeviMed_m"
      ]
    },
    {
      "page": "tune_proposal_sds",
      "title": "Tune proposal standard deviation for MH sampled parameters",
      "topics": [
        "tune_proposal_sds"
      ]
    },
    {
      "page": "tune_temperatures",
      "title": "Tune temperatures",
      "topics": [
        "tune_temperatures"
      ]
    }
  ],
  "_rundeps": [
    "lattice",
    "Matrix",
    "Rcpp"
  ],
  "_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": "Guide.Rnw",
      "filename": "Guide.pdf",
      "title": "BeviMed Guide",
      "engine": "knitr::knitr",
      "headings": [],
      "created": "2017-03-01 07:36:15",
      "modified": "2025-08-22 07:30:01",
      "commits": 7
    },
    {
      "source": "Intro.Rmd",
      "filename": "Intro.html",
      "title": "BeviMed Introduction",
      "author": "Daniel Greene",
      "engine": "knitr::rmarkdown",
      "headings": [
        "References"
      ],
      "created": "2016-05-03 08:20:38",
      "modified": "2024-05-30 02:41:10",
      "commits": 7
    },
    {
      "source": "vcf.Rmd",
      "filename": "vcf.html",
      "title": "BeviMed with VCFs",
      "author": "Daniel Greene",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2017-02-16 16:27:38",
      "modified": "2024-05-30 02:41:10",
      "commits": 4
    }
  ],
  "_score": 3.556302500767287,
  "_indexed": true,
  "_nocasepkg": "bevimed",
  "_universes": [
    "daniel-jg"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "7.0",
      "date": "2026-06-18T10:57:04.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "f2caaa0b6696ffa6ac16f0731326adbb7015d10f",
      "fileid": "https://r2.ropensci.org/e694aedcf3102586608e327d7a2d835c4134e890bb5544b27c5903031a0844a0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/27754450107"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "7.0",
      "date": "2026-06-19T06:44:31.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "f2caaa0b6696ffa6ac16f0731326adbb7015d10f",
      "fileid": "https://r2.ropensci.org/29bf947a2761e10ca96d5c5523c1cf840355bbbe27ed19e74dd3ddb0cb743bfb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/27754450107"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "7.0",
      "date": "2026-06-18T10:56:45.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "f2caaa0b6696ffa6ac16f0731326adbb7015d10f",
      "fileid": "https://r2.ropensci.org/64677f94c852fe1ffdc0baeafdc72a9ec7aa2100f3e89d0fac81a153cc715ee4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/27754450107"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "7.0",
      "date": "2026-06-18T10:56:09.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "f2caaa0b6696ffa6ac16f0731326adbb7015d10f",
      "fileid": "https://r2.ropensci.org/af299f187e806036598c030f96dbc90007c6f1448f8e62dbe4795ca36690ae6b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/27754450107"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "7.0",
      "date": "2026-06-18T10:56:04.000Z",
      "arch": "aarch64",
      "commit": "f2caaa0b6696ffa6ac16f0731326adbb7015d10f",
      "fileid": "https://r2.ropensci.org/8f29c5f84b308c4219a7048b1d36fda077b579cf29f6e5925303ef9ca124e27e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/27754450107"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "7.0",
      "date": "2026-06-18T10:57:22.000Z",
      "arch": "x86_64",
      "commit": "f2caaa0b6696ffa6ac16f0731326adbb7015d10f",
      "fileid": "https://r2.ropensci.org/2a8da97d769b2eba699582da92dcc91d1b76e718cd75166c451f55af096b58a3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/27754450107"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "7.0",
      "date": "2026-06-18T10:56:01.000Z",
      "arch": "aarch64",
      "commit": "f2caaa0b6696ffa6ac16f0731326adbb7015d10f",
      "fileid": "https://r2.ropensci.org/ac49429f022997dfc90c5a993130683d3c1bfa2da579c3575cfb136b3a2e6207",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/27754450107"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "7.0",
      "date": "2026-06-18T10:57:02.000Z",
      "arch": "x86_64",
      "commit": "f2caaa0b6696ffa6ac16f0731326adbb7015d10f",
      "fileid": "https://r2.ropensci.org/42b0bc824b372b2f600bd253bf0b8e589d2109347ff9d5aa86a7d6bdad1eb120",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/27754450107"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "7.0",
      "date": "2026-06-18T10:56:26.000Z",
      "arch": "emscripten",
      "commit": "f2caaa0b6696ffa6ac16f0731326adbb7015d10f",
      "fileid": "https://r2.ropensci.org/407df23905754239951746827cf98a7f0bb40560b72db4f2815eb30bc78eb08f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/27754450107"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "7.0",
      "date": "2026-06-18T10:55:52.000Z",
      "arch": "x86_64",
      "commit": "f2caaa0b6696ffa6ac16f0731326adbb7015d10f",
      "fileid": "https://r2.ropensci.org/2e333c8f704dde0359064fe73df249fde221e6dfe29d4b349ae5ae4fb3109beb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/27754450107"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "7.0",
      "date": "2026-06-18T10:55:49.000Z",
      "arch": "x86_64",
      "commit": "f2caaa0b6696ffa6ac16f0731326adbb7015d10f",
      "fileid": "https://r2.ropensci.org/74c596ba38f9e9d7c515cbb5d32ad6fd04c9437def0bdd214136deac93b1fed8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/27754450107"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "7.0",
      "date": "2026-06-18T10:55:39.000Z",
      "arch": "x86_64",
      "commit": "f2caaa0b6696ffa6ac16f0731326adbb7015d10f",
      "fileid": "https://r2.ropensci.org/9e3652470b2696e0c470f93386a5f17f263a49ea15adda08fc1abcbcce438dba",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/27754450107"
    }
  ]
}