{
  "_id": "6a1bd3921d7bb097a0a14eee",
  "Package": "hapassoc",
  "Version": "1.2-9",
  "Title": "Inference of Trait Associations with SNP Haplotypes and Other\nAttributes using the EM Algorithm",
  "Author": "K. Burkett <kburkett@uottawa.ca>, B. McNeney <mcneney@sfu.ca>,\nJ. Graham <jgraham@stat.sfu.ca>, with code for case-control\ndata contributed by Zhijian Chen <z11chen@math.uwaterloo.ca>",
  "Maintainer": "K. Burkett <kburkett@uottawa.ca>",
  "Description": "The following R functions are used for inference of trait\nassociations with haplotypes and other covariates in\ngeneralized linear models.  The functions are developed\nprimarily for data collected in cohort or cross-sectional\nstudies. They can accommodate uncertain haplotype phase and\nhandle missing genotypes at some SNPs.",
  "License": "GPL-2",
  "URL": "https://sfustatgen.github.io/research/hapassoc.html",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-31 06:09:52 UTC",
    "User": "root"
  },
  "Repository": "https://kmburkett.r-universe.dev",
  "Date/Publication": "2022-05-25 19:10:02 UTC",
  "RemoteUrl": "https://github.com/cran/hapassoc",
  "RemoteRef": "HEAD",
  "RemoteSha": "e844507d05200f8d818ef8b6d6f3ceb6f0d9a2d9",
  "MD5sum": "6f8b9c9d61694951c35e7c71936ca62d",
  "_user": "kmburkett",
  "_type": "src",
  "_file": "hapassoc_1.2-9.tar.gz",
  "_fileid": "6ce6b08807dcb191748bee62ff1c84b097c091f5c1ae36ca3f8597b70ac8f814",
  "_filesize": 662705,
  "_sha256": "6ce6b08807dcb191748bee62ff1c84b097c091f5c1ae36ca3f8597b70ac8f814",
  "_created": "2026-05-31T06:09:52.000Z",
  "_published": "2026-05-31T06:22:10.510Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78704542063,
      "time": 104,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7314318904"
    },
    {
      "job": 78704542071,
      "time": 134,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7314322134"
    },
    {
      "job": 78704542085,
      "time": 101,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7314318669"
    },
    {
      "job": 78704542079,
      "time": 90,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7314317420"
    },
    {
      "job": 78704542110,
      "time": 167,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7314372548"
    },
    {
      "job": 78704542100,
      "time": 295,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7314365661"
    },
    {
      "job": 78704542108,
      "time": 142,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7314379268"
    },
    {
      "job": 78704542117,
      "time": 283,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7314374317"
    },
    {
      "job": 78704419354,
      "time": 133,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7314307221"
    },
    {
      "job": 78704542032,
      "time": 96,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7314317982"
    },
    {
      "job": 78704542048,
      "time": 77,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7314316024"
    },
    {
      "job": 78704542097,
      "time": 66,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7314314847"
    },
    {
      "job": 78704542049,
      "time": 79,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7314316254"
    }
  ],
  "_buildurl": "https://github.com/r-universe/kmburkett/actions/runs/26704993357",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/hapassoc",
  "_commit": {
    "id": "e844507d05200f8d818ef8b6d6f3ceb6f0d9a2d9",
    "author": "K. Burkett <kburkett@uottawa.ca>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.2-9\n",
    "time": 1653505802
  },
  "_maintainer": {
    "name": "K. Burkett",
    "email": "kburkett@uottawa.ca",
    "login": "kmburkett",
    "description": "",
    "uuid": 39386265
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.6.0",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Depends"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "kelly-stats",
      "count": 10,
      "uuid": 716686
    },
    {
      "user": "kmburkett",
      "count": 2,
      "uuid": 39386265
    }
  ],
  "_userbio": {
    "uuid": 39386265,
    "type": "user",
    "name": "kmburkett"
  },
  "_downloads": {
    "count": 189,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/hapassoc"
  },
  "_mentions": 6,
  "_devurl": "https://github.com/sfustatgen/research",
  "_searchresults": 16,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/hapassoc.html",
    "manual.pdf"
  ],
  "_realowner": "kmburkett",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1",
      "date": "2004-01-28"
    },
    {
      "version": "0.2",
      "date": "2004-03-26"
    },
    {
      "version": "0.3",
      "date": "2004-04-14"
    },
    {
      "version": "0.4",
      "date": "2004-08-04"
    },
    {
      "version": "0.4-1",
      "date": "2004-08-27"
    },
    {
      "version": "0.5",
      "date": "2004-09-30"
    },
    {
      "version": "0.5-1",
      "date": "2004-11-04"
    },
    {
      "version": "0.6",
      "date": "2005-04-14"
    },
    {
      "version": "0.6-2",
      "date": "2005-06-10"
    },
    {
      "version": "0.7",
      "date": "2005-07-01"
    },
    {
      "version": "1.0",
      "date": "2006-04-13"
    },
    {
      "version": "1.0-1",
      "date": "2006-04-29"
    },
    {
      "version": "1.1",
      "date": "2006-09-29"
    },
    {
      "version": "1.1-1",
      "date": "2007-09-23"
    },
    {
      "version": "1.2",
      "date": "2008-07-20"
    },
    {
      "version": "1.2-1",
      "date": "2008-07-29"
    },
    {
      "version": "1.2-2",
      "date": "2008-10-14"
    },
    {
      "version": "1.2-3",
      "date": "2009-11-25"
    },
    {
      "version": "1.2-4",
      "date": "2010-07-08"
    },
    {
      "version": "1.2-5",
      "date": "2012-04-05"
    },
    {
      "version": "1.2-6",
      "date": "2012-09-22"
    },
    {
      "version": "1.2-7",
      "date": "2014-08-25"
    },
    {
      "version": "1.2-8",
      "date": "2015-05-11"
    },
    {
      "version": "1.2-9",
      "date": "2022-05-25"
    }
  ],
  "_exports": [
    "hapassoc",
    "pre.hapassoc"
  ],
  "_datasets": [
    {
      "name": "hypoDat",
      "title": "Simulated data for a hypothetical binary trait",
      "object": "hypoDat",
      "file": "hypoDat.txt.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "affected",
        "attr",
        "M1.1",
        "M1.2",
        "M2.1",
        "M2.2",
        "M3.1",
        "M3.2"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "hypoDatGeno",
      "title": "Simulated data for a hypothetical genetic SNPs",
      "object": "hypoDatGeno",
      "file": "hypoDatGeno.txt.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "affected",
        "attr",
        "M1",
        "M2",
        "M3"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "anova_hapassoc",
      "title": "Return likelihood ratio test of haplotype effect",
      "topics": [
        "anova.hapassoc"
      ]
    },
    {
      "page": "hapassoc",
      "title": "EM algorithm to fit maximum likelihood estimates of trait associations with SNP haplotypes",
      "topics": [
        "hapassoc"
      ]
    },
    {
      "page": "hypoDat",
      "title": "Simulated data for a hypothetical binary trait",
      "topics": [
        "hypoDat"
      ]
    },
    {
      "page": "hypoDatGeno",
      "title": "Simulated data for a hypothetical genetic SNPs",
      "topics": [
        "hypoDatGeno"
      ]
    },
    {
      "page": "logLik_hapassoc",
      "title": "Return log-likelihood",
      "topics": [
        "logLik.hapassoc"
      ]
    },
    {
      "page": "PreHap",
      "title": "Pre-process the data before fitting it with hapassoc",
      "topics": [
        "pre.hapassoc"
      ]
    },
    {
      "page": "summaryHap",
      "title": "Summarize results of the hapassoc function",
      "topics": [
        "summary.hapassoc"
      ]
    }
  ],
  "_rundeps": [],
  "_vignettes": [
    {
      "source": "hapassoc.Rnw",
      "filename": "hapassoc.pdf",
      "title": "hapassoc",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2014-08-25",
      "modified": "2014-08-25",
      "commits": 1
    }
  ],
  "_score": 2.982271233039569,
  "_indexed": true,
  "_nocasepkg": "hapassoc",
  "_universes": [
    "kmburkett",
    "sfustatgen"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2-9",
      "date": "2026-05-31T06:11:41.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "e844507d05200f8d818ef8b6d6f3ceb6f0d9a2d9",
      "fileid": "4ea503280b83f2630adeb92b0906de4f26740b50f006f7dafc12e5dfee3b4748",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kmburkett/actions/runs/26704993357"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2-9",
      "date": "2026-05-31T06:12:07.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "e844507d05200f8d818ef8b6d6f3ceb6f0d9a2d9",
      "fileid": "3ed64e3c2f5cab9aa9909cf035126da9300a8fee79b71e90817d7d473db5e63b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kmburkett/actions/runs/26704993357"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.2-9",
      "date": "2026-05-31T06:11:40.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "e844507d05200f8d818ef8b6d6f3ceb6f0d9a2d9",
      "fileid": "5371935ede980fa5638a010842621717857d9d610c9d6456a26ee87bd410a89d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kmburkett/actions/runs/26704993357"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.2-9",
      "date": "2026-05-31T06:11:26.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "e844507d05200f8d818ef8b6d6f3ceb6f0d9a2d9",
      "fileid": "9657c060f4a4c5d5ded954034f22466b675c4b47b37290164c4100af05b63ea4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kmburkett/actions/runs/26704993357"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2-9",
      "date": "2026-05-31T06:20:20.000Z",
      "arch": "aarch64",
      "commit": "e844507d05200f8d818ef8b6d6f3ceb6f0d9a2d9",
      "fileid": "a32bb71e7698b0a8b26de83b6f4dd4c78d2cb6556a96fb540201709c448d25bf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kmburkett/actions/runs/26704993357"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2-9",
      "date": "2026-05-31T06:18:59.000Z",
      "arch": "x86_64",
      "commit": "e844507d05200f8d818ef8b6d6f3ceb6f0d9a2d9",
      "fileid": "c5d9392c45776ab6c8180dd2c09f2f67f7e496a9d728dc939097ea6049f0ba6b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kmburkett/actions/runs/26704993357"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.2-9",
      "date": "2026-05-31T06:21:23.000Z",
      "arch": "aarch64",
      "commit": "e844507d05200f8d818ef8b6d6f3ceb6f0d9a2d9",
      "fileid": "5dec3a047e414d24527403d1f083d19427d68c8a563cda87cd766a60b0777f1a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kmburkett/actions/runs/26704993357"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.2-9",
      "date": "2026-05-31T06:20:13.000Z",
      "arch": "x86_64",
      "commit": "e844507d05200f8d818ef8b6d6f3ceb6f0d9a2d9",
      "fileid": "e5e9ce258e1375b1a44c35d28fed8b0efa007f9324db37e32b1d2a9b90b2334d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kmburkett/actions/runs/26704993357"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.2-9",
      "date": "2026-05-31T06:11:42.000Z",
      "arch": "emscripten",
      "commit": "e844507d05200f8d818ef8b6d6f3ceb6f0d9a2d9",
      "fileid": "0a8432a7b8768f5ac98177e3b70fc00774e281388747ad53b0679783d7137536",
      "status": "success",
      "buildurl": "https://github.com/r-universe/kmburkett/actions/runs/26704993357"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.2-9",
      "date": "2026-05-31T06:10:59.000Z",
      "arch": "x86_64",
      "commit": "e844507d05200f8d818ef8b6d6f3ceb6f0d9a2d9",
      "fileid": "18200f99ac5cfef4d99dacaf3531b56073585120cea23e8b16ed82af3283ba17",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kmburkett/actions/runs/26704993357"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.2-9",
      "date": "2026-05-31T06:10:52.000Z",
      "arch": "x86_64",
      "commit": "e844507d05200f8d818ef8b6d6f3ceb6f0d9a2d9",
      "fileid": "47512916b796fda0308fafcefd58950f9ad622e16d9bd037eaff90b330212639",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kmburkett/actions/runs/26704993357"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.2-9",
      "date": "2026-05-31T06:11:04.000Z",
      "arch": "x86_64",
      "commit": "e844507d05200f8d818ef8b6d6f3ceb6f0d9a2d9",
      "fileid": "e9b7ef11c1b59c53426b51d1b65b24c3c1b8b72ad986dfa4564f5e1b35bd20d9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kmburkett/actions/runs/26704993357"
    }
  ]
}