{
  "_id": "6a116fbfacfb0bcc41cf6698",
  "Package": "ccLRforR",
  "Type": "Package",
  "Title": "Case-Control Likelihood Ratio (ccLR)",
  "Version": "1.2",
  "Authors@R": "c(\nperson(\"Damianos\", \"Michaelides\", email = \"damianosm@cing.ac.cy\", role = c(\"aut\", \"cre\")),\nperson(\"Maria\", \"Zanti\", role = \"aut\"),\nperson(\"Denise\", \"O' Mahony\", role = \"aut\"),\nperson(\"Christian\", \"Carrizosa\", role = \"aut\"),\nperson(\"Theodora\", \"Nearchou\", role = \"aut\"),\nperson(\"Kyriaki\", \"Michailidou\", role = \"aut\"))",
  "Description": "Implementation of case-control data analysis using\nlikelihood ratio approaches and logistic regression for the\nclassification of variants of uncertain significance (VUS) in\nbreast, ovarian, or custom cancer susceptibility genes.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "NeedsCompilation": "yes",
  "RoxygenNote": "7.3.3",
  "Packaged": {
    "Date": "2026-05-23 09:10:54 UTC",
    "User": "root"
  },
  "Author": "Damianos Michaelides [aut, cre], Maria Zanti [aut], Denise O'\nMahony [aut], Christian Carrizosa [aut], Theodora Nearchou\n[aut], Kyriaki Michailidou [aut]",
  "Maintainer": "Damianos Michaelides <damianosm@cing.ac.cy>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-04-23 14:16:28 UTC",
  "RemoteUrl": "https://github.com/cran/ccLRforR",
  "RemoteRef": "HEAD",
  "RemoteSha": "c9254191bc633ca25f82dee40ffc38d3a5c84ab6",
  "MD5sum": "8791a6760543dd1117b3df57a4342ee0",
  "_user": "cran",
  "_type": "src",
  "_file": "ccLRforR_1.2.tar.gz",
  "_fileid": "0e8c9e82d426dad503fa60ace374802daf289409e69c00251781431e571c6cdb",
  "_filesize": 184649,
  "_sha256": "0e8c9e82d426dad503fa60ace374802daf289409e69c00251781431e571c6cdb",
  "_created": "2026-05-23T09:10:54.000Z",
  "_published": "2026-05-23T09:13:35.500Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77511547192,
      "time": 126,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7175874153"
    },
    {
      "job": 77511547201,
      "time": 117,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7175873334"
    },
    {
      "job": 77511547204,
      "time": 122,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7175873645"
    },
    {
      "job": 77511547216,
      "time": 116,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7175873265"
    },
    {
      "job": 77511392136,
      "time": 182,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7175862458"
    },
    {
      "job": 77511547179,
      "time": 103,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7175872227"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/26328877404",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/ccLRforR",
  "_commit": {
    "id": "c9254191bc633ca25f82dee40ffc38d3a5c84ab6",
    "author": "Damianos Michaelides <damianosm@cing.ac.cy>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.2\n",
    "time": 1776953788
  },
  "_maintainer": {
    "name": "Damianos Michaelides",
    "email": "damianosm@cing.ac.cy"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.13",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-10",
      "n": 2
    },
    {
      "week": "2026-17",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "1.0",
      "date": "2026-03-03"
    },
    {
      "name": "1.1",
      "date": "2026-03-05"
    },
    {
      "name": "1.2",
      "date": "2026-04-23"
    }
  ],
  "_stars": 0,
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 568,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ccLRforR"
  },
  "_searchresults": 0,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/ccLRforR.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "manual.pdf"
  ],
  "_realowner": "cran",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0",
      "date": "2026-03-03"
    },
    {
      "version": "1.1",
      "date": "2026-03-05"
    },
    {
      "version": "1.2",
      "date": "2026-04-23"
    }
  ],
  "_exports": [
    "ccLR.grid",
    "ccLR.imp",
    "ps4.ccLR",
    "ps4.logistic"
  ],
  "_datasets": [
    {
      "name": "Antoniou",
      "title": "Breast and Ovarian Cancer Risk Rates: Dorling et al. (2021), Kuchenbaecker et al. (2017), Antoniou et al. (2003), Fortuno et al. (2024), Li et al. (2022), Hall et al. (2021), Yang et al. (2020), and Momozawa et al. (2022)",
      "object": "Antoniou",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Age",
        "BC_Penetrance_Carriers_BRCA1",
        "BC_Penetrance_Carriers_BRCA2",
        "BC_Penetrance_Carriers_PALB2"
      ],
      "rows": 81,
      "table": true,
      "tojson": true
    },
    {
      "name": "Dorling",
      "title": "Breast and Ovarian Cancer Risk Rates: Dorling et al. (2021), Kuchenbaecker et al. (2017), Antoniou et al. (2003), Fortuno et al. (2024), Li et al. (2022), Hall et al. (2021), Yang et al. (2020), and Momozawa et al. (2022)",
      "object": "Dorling",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Age",
        "BC_Penetrance_Carriers_BRCA1",
        "BC_Penetrance_Carriers_BRCA2",
        "BC_Penetrance_Carriers_ATM",
        "BC_Penetrance_Carriers_PALB2",
        "BC_Penetrance_Carriers_CHEK2"
      ],
      "rows": 81,
      "table": true,
      "tojson": true
    },
    {
      "name": "Fortuno",
      "title": "Breast and Ovarian Cancer Risk Rates: Dorling et al. (2021), Kuchenbaecker et al. (2017), Antoniou et al. (2003), Fortuno et al. (2024), Li et al. (2022), Hall et al. (2021), Yang et al. (2020), and Momozawa et al. (2022)",
      "object": "Fortuno",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Age",
        "BC_Penetrance_Carriers_TP53"
      ],
      "rows": 81,
      "table": true,
      "tojson": true
    },
    {
      "name": "Hall",
      "title": "Breast and Ovarian Cancer Risk Rates: Dorling et al. (2021), Kuchenbaecker et al. (2017), Antoniou et al. (2003), Fortuno et al. (2024), Li et al. (2022), Hall et al. (2021), Yang et al. (2020), and Momozawa et al. (2022)",
      "object": "Hall",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Age",
        "OC_Relative_Risk_Carriers_ATM"
      ],
      "rows": 81,
      "table": true,
      "tojson": true
    },
    {
      "name": "incidence_data",
      "title": "Age-specific population incidence rates for breast and ovarian cancer",
      "object": "incidence_data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Age",
        "BC_England",
        "OC_England",
        "BC_Finland",
        "OC_Finland",
        "BC_USA",
        "OC_USA",
        "BC_Japan",
        "OC_Japan"
      ],
      "rows": 81,
      "table": true,
      "tojson": true
    },
    {
      "name": "Kuchenbaecker",
      "title": "Breast and Ovarian Cancer Risk Rates: Dorling et al. (2021), Kuchenbaecker et al. (2017), Antoniou et al. (2003), Fortuno et al. (2024), Li et al. (2022), Hall et al. (2021), Yang et al. (2020), and Momozawa et al. (2022)",
      "object": "Kuchenbaecker",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Age",
        "BC_Penetrance_Carriers_BRCA1",
        "BC_Penetrance_Carriers_BRCA2",
        "OC_Penetrance_Carriers_BRCA1",
        "OC_Penetrance_Carriers_BRCA2"
      ],
      "rows": 81,
      "table": true,
      "tojson": true
    },
    {
      "name": "Li",
      "title": "Breast and Ovarian Cancer Risk Rates: Dorling et al. (2021), Kuchenbaecker et al. (2017), Antoniou et al. (2003), Fortuno et al. (2024), Li et al. (2022), Hall et al. (2021), Yang et al. (2020), and Momozawa et al. (2022)",
      "object": "Li",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Age",
        "BC_Penetrance_Carriers_TP53"
      ],
      "rows": 81,
      "table": true,
      "tojson": true
    },
    {
      "name": "Momozawa",
      "title": "Breast and Ovarian Cancer Risk Rates: Dorling et al. (2021), Kuchenbaecker et al. (2017), Antoniou et al. (2003), Fortuno et al. (2024), Li et al. (2022), Hall et al. (2021), Yang et al. (2020), and Momozawa et al. (2022)",
      "object": "Momozawa",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Age",
        "BC_Penetrance_Carriers_BRCA1",
        "BC_Penetrance_Carriers_BRCA2",
        "OC_Penetrance_Carriers_BRCA1",
        "OC_Penetrance_Carriers_BRCA2"
      ],
      "rows": 81,
      "table": true,
      "tojson": true
    },
    {
      "name": "Yang",
      "title": "Breast and Ovarian Cancer Risk Rates: Dorling et al. (2021), Kuchenbaecker et al. (2017), Antoniou et al. (2003), Fortuno et al. (2024), Li et al. (2022), Hall et al. (2021), Yang et al. (2020), and Momozawa et al. (2022)",
      "object": "Yang",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Age",
        "OC_Penetrance_Carriers_PALB2"
      ],
      "rows": 81,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ccLR_grid",
      "title": "Refined Case-Control Likelihood Ratio (ccLR) Analysis for performing Grid Search by Scaling the Relative Risk",
      "topics": [
        "ccLR.grid"
      ]
    },
    {
      "page": "ccLR_imp",
      "title": "Case-Control Likelihood Ratio (ccLR) Analysis for Imputed Genotype Data",
      "topics": [
        "ccLR.imp"
      ]
    },
    {
      "page": "ccLRforR-package",
      "title": "Case-Control Likelihood Ratio (ccLR)",
      "topics": [
        "ccLRforR-package",
        "ccLRforR"
      ]
    },
    {
      "page": "incidence_data",
      "title": "Age-specific population incidence rates for breast and ovarian cancer",
      "topics": [
        "incidence_data"
      ]
    },
    {
      "page": "PS4_ccLR",
      "title": "Case-Control Likelihood Ratio (ccLR) Analysis",
      "topics": [
        "ps4.ccLR"
      ]
    },
    {
      "page": "PS4_logistic",
      "title": "Logistic Regression PS4 Criterion",
      "topics": [
        "ps4.logistic"
      ]
    },
    {
      "page": "cancer_risk_rates",
      "title": "Breast and Ovarian Cancer Risk Rates: Dorling et al. (2021), Kuchenbaecker et al. (2017), Antoniou et al. (2003), Fortuno et al. (2024), Li et al. (2022), Hall et al. (2021), Yang et al. (2020), and Momozawa et al. (2022)",
      "topics": [
        "Antoniou",
        "Dorling",
        "Fortuno",
        "Hall",
        "Kuchenbaecker",
        "Li",
        "Momozawa",
        "risk_rates",
        "Yang"
      ]
    }
  ],
  "_rundeps": [
    "cli",
    "cpp11",
    "dplyr",
    "generics",
    "glue",
    "lifecycle",
    "magrittr",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "Rcpp",
    "rlang",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "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"
    }
  ],
  "_score": 1.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "cclrforr",
  "_universes": [
    "cran"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2",
      "date": "2026-05-23T09:13:00.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "c9254191bc633ca25f82dee40ffc38d3a5c84ab6",
      "fileid": "a6453f27c486aa13fc15e939d4cdfd8aa0acdf17a715ae926cbb7088a21820db",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26328877404"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2",
      "date": "2026-05-23T09:12:53.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "c9254191bc633ca25f82dee40ffc38d3a5c84ab6",
      "fileid": "3c65d2b2c765d8038b658a60fc2953a2c312c9878a7eea0d0383c8152bb86b1a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26328877404"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.2",
      "date": "2026-05-23T09:12:54.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "c9254191bc633ca25f82dee40ffc38d3a5c84ab6",
      "fileid": "c69d7d546ce82f47531d5c78eb30f9e1afa5e16cbcca15f15eec88ced13a98d5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26328877404"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.2",
      "date": "2026-05-23T09:12:48.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "c9254191bc633ca25f82dee40ffc38d3a5c84ab6",
      "fileid": "1cb0b36f460fefb148fb2ab41bb8966b3c761b2bce6df679d5561c0cc25f0fe8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26328877404"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.2",
      "date": "2026-05-23T09:12:57.000Z",
      "arch": "emscripten",
      "commit": "c9254191bc633ca25f82dee40ffc38d3a5c84ab6",
      "fileid": "8a33f46ab64dc985ddb7486b9f71eb090404d6c64ca7912dd4d071b564e2a746",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26328877404"
    }
  ]
}