{
  "_id": "6a498f7b6d67900babdfb7b7",
  "Package": "clipp",
  "Type": "Package",
  "Title": "Calculating Likelihoods by Pedigree Paring",
  "Version": "1.1.1",
  "Authors@R": "c(person(given = \"James\",\nfamily = \"Dowty\",\nrole = c(\"aut\", \"cre\"),\nemail = \"jgdowty@gmail.com\"),\nperson(given = \"Kevin\",\nfamily = \"Wong\",\nrole = c(\"aut\"),\nemail = \"wongck.kevin@gmail.com\"))",
  "Description": "A fast and general implementation of the Elston-Stewart\nalgorithm that can calculate the likelihoods of large and\ncomplex pedigrees. References for the Elston-Stewart algorithm\nare Elston & Stewart (1971) <doi:10.1159/000152448>, Lange &\nElston (1975) <doi:10.1159/000152714> and Cannings et al.\n(1978) <doi:10.2307/1426718>.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.1.0",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-22 10:48:08 UTC",
    "User": "root"
  },
  "Author": "James Dowty [aut, cre], Kevin Wong [aut]",
  "Maintainer": "James Dowty <jgdowty@gmail.com>",
  "Repository": "https://jgdowty.r-universe.dev",
  "Date/Publication": "2022-07-12 04:30:02 UTC",
  "RemoteUrl": "https://github.com/cran/clipp",
  "RemoteRef": "HEAD",
  "RemoteSha": "43c693b066d37882f65a1b314248ed3c1ee5bb37",
  "_user": "jgdowty",
  "_type": "src",
  "_file": "clipp_1.1.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/2b5058e0709ae95f1ae3a17e153701a88f61eb3d445a01d386772aa08a8a3f3e",
  "_filesize": 301292,
  "_sha256": "2b5058e0709ae95f1ae3a17e153701a88f61eb3d445a01d386772aa08a8a3f3e",
  "_expires": "2026-10-12T22:55:54.000Z",
  "_created": "2026-06-22T10:48:08.000Z",
  "_published": "2026-07-04T22:55:55.669Z",
  "_jobs": [
    {
      "job": 85173794383,
      "time": 109,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7790118152"
    },
    {
      "job": 85173794396,
      "time": 111,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7790119227"
    },
    {
      "job": 85173794375,
      "time": 152,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7790122508"
    },
    {
      "job": 85173794426,
      "time": 123,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7790114316"
    },
    {
      "job": 85173794194,
      "time": 172,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7790078645"
    },
    {
      "job": 85173794425,
      "time": 89,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7790110739"
    },
    {
      "job": 85173794264,
      "time": 75,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7790105943"
    },
    {
      "job": 85173794406,
      "time": 72,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7790104999"
    },
    {
      "job": 85173794429,
      "time": 67,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7790102525"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/jgdowty/actions/runs/27947125527",
  "_status": "success",
  "_upstream": "https://github.com/cran/clipp",
  "_commit": {
    "id": "43c693b066d37882f65a1b314248ed3c1ee5bb37",
    "author": "James Dowty <jgdowty@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.1.1\n",
    "time": 1657600202
  },
  "_maintainer": {
    "name": "James Dowty",
    "email": "jgdowty@gmail.com",
    "login": "jgdowty",
    "description": "",
    "uuid": 132878057
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "jgdowty",
      "count": 5,
      "uuid": 132878057
    }
  ],
  "_userbio": {
    "uuid": 132878057,
    "type": "user",
    "name": "jgdowty",
    "followers": 0
  },
  "_downloads": {
    "count": 302,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/clipp"
  },
  "_searchresults": 5,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/clipp.html",
    "extra/contents.json",
    "manual.pdf"
  ],
  "_realowner": "jgdowty",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2020-07-06"
    },
    {
      "version": "1.0.0",
      "date": "2021-05-05"
    },
    {
      "version": "1.0.1",
      "date": "2021-07-15"
    },
    {
      "version": "1.1.0",
      "date": "2021-09-07"
    },
    {
      "version": "1.1.1",
      "date": "2022-07-12"
    }
  ],
  "_exports": [
    "combine_loci",
    "geno_freq_monogenic",
    "geno_freq_phased",
    "geno_freq_polygenic",
    "genotype_probabilities",
    "pedigree_loglikelihood",
    "trans_monogenic",
    "trans_phased",
    "trans_polygenic"
  ],
  "_datasets": [
    {
      "name": "dat_large",
      "title": "Simulated data on one family with approximately 10,000 members",
      "object": "dat_large",
      "class": [
        "data.frame"
      ],
      "fields": [
        "indiv",
        "mother",
        "father",
        "sex",
        "aff",
        "age"
      ],
      "rows": 10002,
      "table": true,
      "tojson": true
    },
    {
      "name": "dat_small",
      "title": "Simulated data on 10 families with approximately 100 members each",
      "object": "dat_small",
      "class": [
        "data.frame"
      ],
      "fields": [
        "family",
        "indiv",
        "mother",
        "father",
        "sex",
        "aff",
        "age",
        "geno"
      ],
      "rows": 1018,
      "table": true,
      "tojson": true
    },
    {
      "name": "penet_large",
      "title": "A penetrance matrix relating the phenotypes in 'dat_large' to three genotypes",
      "object": "penet_large",
      "class": [
        "matrix",
        "array"
      ],
      "fields": {},
      "rows": 10002,
      "table": true,
      "tojson": true
    },
    {
      "name": "penet_small",
      "title": "A penetrance matrix relating the phenotypes of 'dat_small' to three genotypes",
      "object": "penet_small",
      "class": [
        "matrix",
        "array"
      ],
      "fields": {},
      "rows": 1018,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "clipp-package",
      "title": "clipp: Calculate Likelihoods by Pedigree Paring",
      "topics": [
        "clipp-package",
        "clipp"
      ]
    },
    {
      "page": "combine_loci",
      "title": "Combine the genotype frequencies and transition matrices of two genetic loci",
      "topics": [
        "combine_loci"
      ]
    },
    {
      "page": "dat_large",
      "title": "Simulated data on one family with approximately 10,000 members",
      "topics": [
        "dat_large"
      ]
    },
    {
      "page": "dat_small",
      "title": "Simulated data on 10 families with approximately 100 members each",
      "topics": [
        "dat_small"
      ]
    },
    {
      "page": "geno_freq_monogenic",
      "title": "Calculate genotype frequencies from allele frequencies using Hardy-Weinberg equilibrium",
      "topics": [
        "geno_freq_monogenic"
      ]
    },
    {
      "page": "geno_freq_phased",
      "title": "Calculate phased genotype frequencies from allele frequencies, assuming Hardy-Weinberg equilibrium",
      "topics": [
        "geno_freq_phased"
      ]
    },
    {
      "page": "geno_freq_polygenic",
      "title": "Genotype frequencies for the hypergeometric polygenic model",
      "topics": [
        "geno_freq_polygenic"
      ]
    },
    {
      "page": "genotype_probabilities",
      "title": "Calculate genotype probabilities for a target person",
      "topics": [
        "genotype_probabilities"
      ]
    },
    {
      "page": "pedigree_loglikelihood",
      "title": "Calculate the log-likelihoods of pedigrees",
      "topics": [
        "pedigree_loglikelihood"
      ]
    },
    {
      "page": "penet_large",
      "title": "A penetrance matrix relating the phenotypes in 'dat_large' to three genotypes",
      "topics": [
        "penet_large"
      ]
    },
    {
      "page": "penet_small",
      "title": "A penetrance matrix relating the phenotypes of 'dat_small' to three genotypes",
      "topics": [
        "penet_small"
      ]
    },
    {
      "page": "trans_monogenic",
      "title": "The transmission matrix for a single genetic locus",
      "topics": [
        "trans_monogenic"
      ]
    },
    {
      "page": "trans_phased",
      "title": "The transmission matrix for phased genotypes",
      "topics": [
        "trans_phased"
      ]
    },
    {
      "page": "trans_polygenic",
      "title": "The transmission matrix for the hypergeometric polygenic model",
      "topics": [
        "trans_polygenic"
      ]
    }
  ],
  "_rundeps": [],
  "_vignettes": [
    {
      "source": "using_clipp.Rmd",
      "filename": "using_clipp.html",
      "title": "Vignette for clipp",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Pedigree likelihoods",
        "Specifying the genetic model",
        "Calculating the pedigree likelihood",
        "Maximum likelihood estimation",
        "Incorporating known genotypes",
        "Calculating carrier probabilities",
        "Advanced notes",
        "The Elston-Stewart algorithm",
        "References"
      ],
      "created": "2022-07-12 04:30:02",
      "modified": "2022-07-12 04:30:02",
      "commits": 1
    }
  ],
  "_score": 2.4771212547196626,
  "_indexed": true,
  "_nocasepkg": "clipp",
  "_universes": [
    "jgdowty"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.1",
      "date": "2026-06-22T10:50:09.000Z",
      "distro": "noble",
      "commit": "43c693b066d37882f65a1b314248ed3c1ee5bb37",
      "fileid": "https://r2.ropensci.org/0384c3eaaeae60d725c167b4a9856d0f9b991421266018300773f05904a10216",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jgdowty/actions/runs/27947125527"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.1",
      "date": "2026-06-22T10:50:10.000Z",
      "distro": "noble",
      "commit": "43c693b066d37882f65a1b314248ed3c1ee5bb37",
      "fileid": "https://r2.ropensci.org/34a3af9dbaf10c7fe56d57e5ac93ca2095d6f783df405e3e6832052266d355df",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jgdowty/actions/runs/27947125527"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.1",
      "date": "2026-06-22T10:50:24.000Z",
      "commit": "43c693b066d37882f65a1b314248ed3c1ee5bb37",
      "fileid": "https://r2.ropensci.org/d38d6d5616516902905ddb75e5abd1e93087116f2cc3474294c0b6ec34746d47",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jgdowty/actions/runs/27947125527"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.1",
      "date": "2026-06-22T10:50:01.000Z",
      "commit": "43c693b066d37882f65a1b314248ed3c1ee5bb37",
      "fileid": "https://r2.ropensci.org/f9dc6d37a2cdd856b991c76c66158cf7e162c0aea6f3ae4e9ee9288094d822f1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jgdowty/actions/runs/27947125527"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.1",
      "date": "2026-06-22T10:50:01.000Z",
      "commit": "43c693b066d37882f65a1b314248ed3c1ee5bb37",
      "fileid": "https://r2.ropensci.org/a4a58fa703fc83fcd412a652712dd3137336c483ba0735c6e7e16178d4713ed5",
      "status": "success",
      "buildurl": "https://github.com/r-universe/jgdowty/actions/runs/27947125527"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.1",
      "date": "2026-06-22T10:49:30.000Z",
      "commit": "43c693b066d37882f65a1b314248ed3c1ee5bb37",
      "fileid": "https://r2.ropensci.org/05f1a5e8b081f41679330aee30dda51ba56f53e23ac1300be34b37fa43030ebc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jgdowty/actions/runs/27947125527"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.1",
      "date": "2026-06-22T10:49:27.000Z",
      "commit": "43c693b066d37882f65a1b314248ed3c1ee5bb37",
      "fileid": "https://r2.ropensci.org/ffbc2cbfda59eb869064d6a076155a3737fb8fe9e6cf6ab3f30018d94e52caad",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jgdowty/actions/runs/27947125527"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.1.1",
      "date": "2026-06-22T10:49:20.000Z",
      "commit": "43c693b066d37882f65a1b314248ed3c1ee5bb37",
      "fileid": "https://r2.ropensci.org/ef2d198399a71125d74b5092e231ec762c16099bb24e9c19debbff90d3cb186d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jgdowty/actions/runs/27947125527"
    }
  ]
}