{
  "_id": "6a2122e3cd65a98ecbd1fb8f",
  "Package": "statgenIBD",
  "Type": "Package",
  "Title": "Calculation of IBD Probabilities",
  "Description": "For biparental, three and four-way crosses Identity by\nDescent (IBD) probabilities can be calculated using Hidden\nMarkov Models and inheritance vectors following Lander and\nGreen (<https://www.jstor.org/stable/29713>) and Huang\n(<doi:10.1073/pnas.1100465108>). One of a series of statistical\ngenetic packages for streamlining the analysis of typical plant\nbreeding experiments developed by Biometris.",
  "Version": "1.0.11",
  "Date": "2026-05-05",
  "Authors@R": "c(person(given = \"Martin\", \nfamily = \"Boer\",\nemail = \"martin.boer@wur.nl\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-1879-4588\")),\nperson(given = \"Bart-Jan\",\nfamily = \"van Rossum\",\nemail = \"bart-jan.vanrossum@wur.nl\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-8673-2514\")),\nperson(given = \"Wenhao\",\nfamily = \"Li\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0001-5719-5775\")),\nperson(given = \"Johannes\",\nfamily = \"Kruisselbrink\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0003-1673-5725\")))",
  "License": "GPL",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "URL": "https://biometris.github.io/statgenIBD/index.html,\nhttps://github.com/Biometris/statgenIBD/",
  "BugReports": "https://github.com/Biometris/statgenIBD/issues",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://biometris.r-universe.dev",
  "Date/Publication": "2026-05-05 09:47:26 UTC",
  "RemoteUrl": "https://github.com/biometris/statgenibd",
  "RemoteRef": "HEAD",
  "RemoteSha": "4703dcf8c372d2f98b27ee1b755445042b662568",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-04 06:55:05 UTC",
    "User": "root"
  },
  "Author": "Martin Boer [aut] (ORCID: <https://orcid.org/0000-0002-1879-4588>),\nBart-Jan van Rossum [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-8673-2514>),\nWenhao Li [ctb] (ORCID: <https://orcid.org/0000-0001-5719-5775>),\nJohannes Kruisselbrink [ctb] (ORCID:\n<https://orcid.org/0000-0003-1673-5725>)",
  "Maintainer": "Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>",
  "MD5sum": "cc01600140226d39fd79215fb8363f98",
  "_user": "biometris",
  "_type": "src",
  "_file": "statgenIBD_1.0.11.tar.gz",
  "_fileid": "5cee108a17ab16625251eb9569ea44bbaedb20cc737f1f6c75c4ce612f5f3ee8",
  "_filesize": 3190077,
  "_sha256": "5cee108a17ab16625251eb9569ea44bbaedb20cc737f1f6c75c4ce612f5f3ee8",
  "_created": "2026-06-04T06:55:05.000Z",
  "_published": "2026-06-04T07:01:55.939Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79465976459,
      "time": 192,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7405008785"
    },
    {
      "job": 79465976418,
      "time": 184,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7405005880"
    },
    {
      "job": 79465976477,
      "time": 214,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7405014480"
    },
    {
      "job": 79465976428,
      "time": 205,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7405011234"
    },
    {
      "job": 79465976441,
      "time": 148,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7404996852"
    },
    {
      "job": 79465976433,
      "time": 296,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7405034178"
    },
    {
      "job": 79465976451,
      "time": 213,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7405013189"
    },
    {
      "job": 79465976472,
      "time": 304,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7405036298"
    },
    {
      "job": 79465379180,
      "time": 269,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7404958238"
    },
    {
      "job": 79465976398,
      "time": 144,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7404996015"
    },
    {
      "job": 79465976419,
      "time": 234,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7405018945"
    },
    {
      "job": 79465976423,
      "time": 195,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7405008359"
    },
    {
      "job": 79465976408,
      "time": 221,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7405015591"
    }
  ],
  "_buildurl": "https://github.com/r-universe/biometris/actions/runs/26935862045",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/biometris/statgenibd",
  "_commit": {
    "id": "4703dcf8c372d2f98b27ee1b755445042b662568",
    "author": "Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>",
    "committer": "Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>",
    "message": "Increased version number\n",
    "time": 1777974446
  },
  "_maintainer": {
    "name": "Bart-Jan van Rossum",
    "email": "bart-jan.vanrossum@wur.nl",
    "login": "bartjanvanrossum",
    "description": "",
    "uuid": 28725410,
    "orcid": "0000-0002-8673-2514"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "R.utils",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "statgenGWAS",
      "version": ">= 1.0.9",
      "role": "Imports"
    },
    {
      "package": "stringi",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "tinytest",
      "role": "Suggests"
    }
  ],
  "_owner": "biometris",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-27",
      "n": 4
    },
    {
      "week": "2026-10",
      "n": 3
    },
    {
      "week": "2026-16",
      "n": 4
    },
    {
      "week": "2026-18",
      "n": 1
    },
    {
      "week": "2026-19",
      "n": 2
    }
  ],
  "_tags": [
    {
      "name": "v.1.0.9",
      "date": "2025-07-01"
    },
    {
      "name": "v.1.0.10",
      "date": "2026-03-02"
    },
    {
      "name": "v.1.0.11",
      "date": "2026-05-05"
    }
  ],
  "_topics": [
    "genetics",
    "hmm",
    "ibd",
    "cpp"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "bartjanvanrossum",
      "count": 262,
      "uuid": 28725410
    },
    {
      "user": "martinboer",
      "count": 18,
      "uuid": 10836537
    },
    {
      "user": "jwkruisselbrink",
      "count": 2,
      "uuid": 17898794
    }
  ],
  "_userbio": {
    "uuid": 60092315,
    "type": "organization",
    "name": "Wageningen Universtiy & Research, Biometris",
    "description": "Biometris develops statistical and mathematical methods for the quantification of biological processes and processes in our living environment."
  },
  "_downloads": {
    "count": 407,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/statgenIBD"
  },
  "_devurl": "https://github.com/biometris/statgenibd",
  "_searchresults": 8,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/statgenIBD.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/biometris/statgenibd",
  "_realowner": "biometris",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2021-08-16"
    },
    {
      "version": "1.0.1",
      "date": "2021-09-14"
    },
    {
      "version": "1.0.2",
      "date": "2021-12-10"
    },
    {
      "version": "1.0.3",
      "date": "2022-02-17"
    },
    {
      "version": "1.0.4",
      "date": "2022-03-07"
    },
    {
      "version": "1.0.5",
      "date": "2022-09-04"
    },
    {
      "version": "1.0.6",
      "date": "2023-08-30"
    },
    {
      "version": "1.0.7",
      "date": "2024-02-02"
    },
    {
      "version": "1.0.8",
      "date": "2025-02-05"
    },
    {
      "version": "1.0.9",
      "date": "2025-07-01"
    },
    {
      "version": "1.0.10",
      "date": "2026-03-02"
    },
    {
      "version": "1.0.11",
      "date": "2026-05-05"
    }
  ],
  "_exports": [
    "calcIBD",
    "getProbs",
    "readIBDs",
    "readRABBIT",
    "writeFlapjack",
    "writeIBDs"
  ],
  "_help": [
    {
      "page": "c.IBDprob",
      "title": "Concatenate function for objects of class IBDprob",
      "topics": [
        "c.IBDprob"
      ]
    },
    {
      "page": "calcIBD",
      "title": "Calculate IBD probabilities",
      "topics": [
        "calcIBD"
      ]
    },
    {
      "page": "getProbs",
      "title": "Extract Probabilities for markers",
      "topics": [
        "getProbs"
      ]
    },
    {
      "page": "plot.IBDprob",
      "title": "Plot function for objects of class IBDprob",
      "topics": [
        "plot.IBDprob"
      ]
    },
    {
      "page": "readIBDs",
      "title": "Read IBD probabilities from file",
      "topics": [
        "readIBDs"
      ]
    },
    {
      "page": "readRABBIT",
      "title": "Read IBD probabilities",
      "topics": [
        "readRABBIT"
      ]
    },
    {
      "page": "summary.IBDprob",
      "title": "Summary function for objects of class IBDprob",
      "topics": [
        "summary.IBDprob"
      ]
    },
    {
      "page": "writeFlapjack",
      "title": "Write to Flapjack format",
      "topics": [
        "writeFlapjack"
      ]
    },
    {
      "page": "writeIBDs",
      "title": "Write IBD probabilities to file.",
      "topics": [
        "writeIBDs"
      ]
    }
  ],
  "_pkglogo": "https://github.com/biometris/statgenibd/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/biometris/statgenibd/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "crayon",
    "data.table",
    "dotCall64",
    "enhancer",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "LMMsolver",
    "MASS",
    "Matrix",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppProgress",
    "rlang",
    "S7",
    "scales",
    "sommer",
    "spam",
    "statgenGWAS",
    "stringi",
    "vctrs",
    "viridisLite",
    "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"
    }
  ],
  "_vignettes": [
    {
      "source": "IBDCalculations.Rmd",
      "filename": "IBDCalculations.html",
      "title": "IBD calculations using statgenIBD",
      "author": "Bart-Jan van Rossum and Martin Boer",
      "engine": "knitr::rmarkdown",
      "headings": [
        "The statgenIBD package",
        "Population types",
        "Examples",
        "Steptoe Morex",
        "Visualizing results",
        "Pedigree plot",
        "Genetic map plot",
        "Single genotype plot",
        "Plot of IBD probabilities for all genotypes.",
        "Plot the coverage of each parent across the genome.",
        "Plot the total coverage of each parent",
        "Evaluation positions",
        "Extracting value for markers of interest",
        "Write and read tab-delimited *.txt files",
        "Write results to Flapjack format",
        "Simulated data",
        "F4",
        "C4S3",
        "Multi-cross",
        "Importing IBD probabilities computed using RABBIT",
        "References"
      ],
      "created": "2021-06-25 10:40:23",
      "modified": "2025-07-01 06:20:27",
      "commits": 45
    },
    {
      "source": "IBDFileFormat.Rmd",
      "filename": "IBDFileFormat.html",
      "title": "IBD probabilities file format",
      "author": "Johannes Kruisselbrink",
      "engine": "knitr::rmarkdown",
      "headings": [
        "File format",
        "Examples",
        "Writing IBD probabilities to a file",
        "Reading IBD probabilities from file"
      ],
      "created": "2022-08-08 08:17:26",
      "modified": "2022-08-24 10:01:13",
      "commits": 7
    }
  ],
  "_score": 5.477121254719663,
  "_indexed": true,
  "_nocasepkg": "statgenibd",
  "_universes": [
    "biometris",
    "bartjanvanrossum"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.11",
      "date": "2026-06-04T06:58:13.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "4703dcf8c372d2f98b27ee1b755445042b662568",
      "fileid": "ae9fbac1c4c5828418b4c8d45f1865f1916a30dd670115c429d21cc3c38cca23",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/26935862045"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.11",
      "date": "2026-06-04T06:58:05.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "4703dcf8c372d2f98b27ee1b755445042b662568",
      "fileid": "4d34919770d8b77b9a999d7b83d18d448805282841bc4370a23fb753f2a81abb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/26935862045"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.11",
      "date": "2026-06-04T06:58:33.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "4703dcf8c372d2f98b27ee1b755445042b662568",
      "fileid": "ea3d171b8f61e07d0c8ac19b5e0d164f4c6bb635733bd20183a0241f1d1a0881",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/26935862045"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.11",
      "date": "2026-06-04T06:58:18.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "4703dcf8c372d2f98b27ee1b755445042b662568",
      "fileid": "34c202c1a537aca42aff4f60d23fb27c813dcd8a0a4ef661af4f809f4a079efb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/26935862045"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.11",
      "date": "2026-06-04T06:57:31.000Z",
      "arch": "aarch64",
      "commit": "4703dcf8c372d2f98b27ee1b755445042b662568",
      "fileid": "8b35bb53871600d087460260b8b32f94b98b7728ac4c47ac04e7762269f36202",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/26935862045"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.11",
      "date": "2026-06-04T06:58:57.000Z",
      "arch": "x86_64",
      "commit": "4703dcf8c372d2f98b27ee1b755445042b662568",
      "fileid": "072892ca1132a67e83df0fa96a168a4b2555f0dbd3ffdad728add72569d9ba02",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/26935862045"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.11",
      "date": "2026-06-04T06:58:03.000Z",
      "arch": "aarch64",
      "commit": "4703dcf8c372d2f98b27ee1b755445042b662568",
      "fileid": "0818674ecd3097102c94b13aaf68b6979652150f6727c897e14369834e93145d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/26935862045"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.11",
      "date": "2026-06-04T06:58:58.000Z",
      "arch": "x86_64",
      "commit": "4703dcf8c372d2f98b27ee1b755445042b662568",
      "fileid": "74b6328f18caab31f2189007dc687728ed04c46b728e366a62159727213c76e0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/26935862045"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.11",
      "date": "2026-06-04T06:57:49.000Z",
      "arch": "emscripten",
      "commit": "4703dcf8c372d2f98b27ee1b755445042b662568",
      "fileid": "bb46241d6cd3cee995adc45b23c81cc64c4dc78893917d762249d64dc363e06a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/26935862045"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.11",
      "date": "2026-06-04T06:57:43.000Z",
      "arch": "x86_64",
      "commit": "4703dcf8c372d2f98b27ee1b755445042b662568",
      "fileid": "9170bfeb2de8bdf91850258bf99b14ef1fcb5c1c10c224c099fbf590cd5bc9f3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/26935862045"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.11",
      "date": "2026-06-04T06:56:53.000Z",
      "arch": "x86_64",
      "commit": "4703dcf8c372d2f98b27ee1b755445042b662568",
      "fileid": "445fe89d18699e3286aff6c8c888d12dfd446947756e7f7406b728e9fc889860",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/26935862045"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.11",
      "date": "2026-06-04T06:57:05.000Z",
      "arch": "x86_64",
      "commit": "4703dcf8c372d2f98b27ee1b755445042b662568",
      "fileid": "23b9b38e32d5cd3efc0d7a5e768953ce6b2a9a96126e3ed1af85e8972d8b7dfa",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/26935862045"
    }
  ]
}