{
  "_id": "6a59bccf09eb0996dd68d350",
  "Package": "statgenMPP",
  "Title": "QTL Mapping for Multi Parent Populations",
  "Version": "1.0.5",
  "Date": "2026-05-18",
  "Authors@R": "c(person(given = \"Martin\", \nfamily = \"Boer\",\nemail = \"martin.boer@wur.nl\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-1879-4588\")),\nperson(given = \"Wenhao\",\nfamily = \"Li\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0001-5719-5775\")),\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 = \"Fred\",\nfamily = \"van Eeuwijk\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0003-3672-2921\")))",
  "Description": "For Multi Parent Populations (MPP) Identity By Descend\n(IBD) probabilities are computed using Hidden Markov Models.\nThese probabilities are then used in a mixed model approach for\nQTL Mapping as described in Li et al.\n(<doi:10.1007/s00122-021-03919-7>).",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "URL": "https://biometris.github.io/statgenMPP/index.html,\nhttps://github.com/Biometris/statgenMPP/",
  "BugReports": "https://github.com/Biometris/statgenMPP/issues",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://biometris.r-universe.dev",
  "Date/Publication": "2026-05-18 12:55:33 UTC",
  "RemoteUrl": "https://github.com/biometris/statgenmpp",
  "RemoteRef": "HEAD",
  "RemoteSha": "b1178c8a93e4d6eb67adf32216a892f32605793e",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-17 05:20:35 UTC",
    "User": "root"
  },
  "Author": "Martin Boer [aut] (ORCID: <https://orcid.org/0000-0002-1879-4588>),\nWenhao Li [aut] (ORCID: <https://orcid.org/0000-0001-5719-5775>),\nBart-Jan van Rossum [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-8673-2514>),\nFred van Eeuwijk [ctb] (ORCID: <https://orcid.org/0000-0003-3672-2921>)",
  "Maintainer": "Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>",
  "_user": "biometris",
  "_type": "src",
  "_file": "statgenMPP_1.0.5.tar.gz",
  "_fileid": "https://r2.ropensci.org/a790b5ac1295bcca2f51900f48c75355ef7af584a4f4d5d22c8175a0fe5481eb",
  "_filesize": 3875272,
  "_sha256": "a790b5ac1295bcca2f51900f48c75355ef7af584a4f4d5d22c8175a0fe5481eb",
  "_expires": "2026-10-25T05:25:33.000Z",
  "_created": "2026-07-17T05:20:35.000Z",
  "_published": "2026-07-17T05:25:35.870Z",
  "_jobs": [
    {
      "job": 87811412164,
      "time": 141,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8397861351"
    },
    {
      "job": 87811412153,
      "time": 184,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8397872589"
    },
    {
      "job": 87811412155,
      "time": 94,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8397863760"
    },
    {
      "job": 87811412193,
      "time": 129,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8397891057"
    },
    {
      "job": 87810839146,
      "time": 264,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8397822943"
    },
    {
      "job": 87811412161,
      "time": 118,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8397855442"
    },
    {
      "job": 87811412203,
      "time": 116,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8397854992"
    },
    {
      "job": 87811412190,
      "time": 110,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8397853641"
    },
    {
      "job": 87811412181,
      "time": 123,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8397857309"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/biometris/actions/runs/29556887895",
  "_status": "success",
  "_upstream": "https://github.com/biometris/statgenmpp",
  "_commit": {
    "id": "b1178c8a93e4d6eb67adf32216a892f32605793e",
    "author": "Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>",
    "committer": "Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>",
    "message": "Updated NEWS\n",
    "time": 1779108933
  },
  "_maintainer": {
    "name": "Bart-Jan van Rossum",
    "email": "bart-jan.vanrossum@wur.nl",
    "login": "bartjanvanrossum",
    "description": "",
    "uuid": 28725410,
    "orcid": "0000-0002-8673-2514"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6",
      "role": "Depends"
    },
    {
      "package": "statgenGWAS",
      "version": ">= 1.0.9",
      "role": "Depends"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "LMMsolver",
      "version": ">= 1.0.5",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "spam",
      "role": "Imports"
    },
    {
      "package": "statgenIBD",
      "version": ">= 1.0.8",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "tinytest",
      "role": "Suggests"
    }
  ],
  "_owner": "biometris",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-21",
      "n": 6
    }
  ],
  "_tags": [
    {
      "name": "v.1.0.5",
      "date": "2026-05-18"
    }
  ],
  "_topics": [
    "genetics",
    "mpp",
    "qtl-mapping"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "bartjanvanrossum",
      "count": 259,
      "uuid": 28725410
    },
    {
      "user": "martinboer",
      "count": 31,
      "uuid": 10836537
    },
    {
      "user": "wenhaowur",
      "count": 2,
      "uuid": 17601266
    }
  ],
  "_userbio": {
    "uuid": 60092315,
    "type": "organization",
    "name": "Wageningen Universtiy & Research, Biometris",
    "followers": 40,
    "description": "Biometris develops statistical and mathematical methods for the quantification of biological processes and processes in our living environment."
  },
  "_downloads": {
    "count": 402,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/statgenMPP"
  },
  "_devurl": "https://github.com/biometris/statgenmpp",
  "_searchresults": 12,
  "_rbuild": "4.6.1",
  "_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/statgenMPP.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/biometris/statgenmpp",
  "_realowner": "biometris",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2022-03-21"
    },
    {
      "version": "1.0.1",
      "date": "2022-08-22"
    },
    {
      "version": "1.0.1.1",
      "date": "2022-08-24"
    },
    {
      "version": "1.0.2",
      "date": "2022-12-02"
    },
    {
      "version": "1.0.3",
      "date": "2024-10-29"
    },
    {
      "version": "1.0.4",
      "date": "2025-02-11"
    },
    {
      "version": "1.0.5",
      "date": "2026-05-18"
    }
  ],
  "_exports": [
    "calcIBDMPP",
    "createGDataMPP",
    "kinshipIBD",
    "readRABBITMPP",
    "selQTLMPP"
  ],
  "_datasets": [
    {
      "name": "barleyMQM",
      "title": "Pre-computed MQM output barley",
      "object": "barleyMQM",
      "class": [
        "QTLMPP",
        "GWAS"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "barleyPheno",
      "title": "Phenotypic data for awn length in barley",
      "object": "barleyPheno",
      "class": [
        "data.frame"
      ],
      "fields": [
        "genotype",
        "Awn_length",
        "cross"
      ],
      "rows": 916,
      "table": true,
      "tojson": true
    },
    {
      "name": "maizeMQM",
      "title": "Pre-computed MQM output maize",
      "object": "maizeMQM",
      "class": [
        "QTLMPP",
        "GWAS"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "maizeSQM",
      "title": "Pre-computed SQM output maize",
      "object": "maizeSQM",
      "class": [
        "QTLMPP",
        "GWAS"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "barleyMQM",
      "title": "Pre-computed MQM output barley",
      "topics": [
        "barleyMQM"
      ]
    },
    {
      "page": "barleyPheno",
      "title": "Phenotypic data for awn length in barley",
      "topics": [
        "barleyPheno"
      ]
    },
    {
      "page": "calcIBDmpp",
      "title": "IBD calculation for multi parental populations",
      "topics": [
        "calcIBDMPP"
      ]
    },
    {
      "page": "createGDataMPP",
      "title": "Create an object of class gDataMPP",
      "topics": [
        "createGDataMPP"
      ]
    },
    {
      "page": "kinshipIBD",
      "title": "Compute kinship matrix for IBD probabilities",
      "topics": [
        "kinshipIBD"
      ]
    },
    {
      "page": "maizeMQM",
      "title": "Pre-computed MQM output maize",
      "topics": [
        "maizeMQM"
      ]
    },
    {
      "page": "maizeSQM",
      "title": "Pre-computed SQM output maize",
      "topics": [
        "maizeSQM"
      ]
    },
    {
      "page": "plot.gDataMpp",
      "title": "Plot function for the class 'gDataMPP'",
      "topics": [
        "plot.gDataMPP"
      ]
    },
    {
      "page": "plot.QTLMPP",
      "title": "Plot function for the class 'QTLMPP'",
      "topics": [
        "plot.QTLMPP"
      ]
    },
    {
      "page": "print.summary.QTLMPP",
      "title": "Print summary of object of class 'summary.QTLMPP'",
      "topics": [
        "print.summary.QTLMPP"
      ]
    },
    {
      "page": "readRABBITMPP",
      "title": "Read IBD probabilities",
      "topics": [
        "readRABBITMPP"
      ]
    },
    {
      "page": "selQTLMPP",
      "title": "Multi round genome scans for QTL detection",
      "topics": [
        "selQTLMPP"
      ]
    },
    {
      "page": "summary.gDataMpp",
      "title": "Summary function for the class 'gDataMPP'",
      "topics": [
        "summary.gDataMPP"
      ]
    },
    {
      "page": "summary.QTLMPP",
      "title": "Summary function for the class 'QTLMPP'",
      "topics": [
        "summary.QTLMPP"
      ]
    }
  ],
  "_pkglogo": "https://github.com/biometris/statgenmpp/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/biometris/statgenmpp/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "data.table",
    "dotCall64",
    "enhancer",
    "farver",
    "foreach",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "isoband",
    "iterators",
    "labeling",
    "lattice",
    "lifecycle",
    "LMMsolver",
    "MASS",
    "Matrix",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppProgress",
    "rlang",
    "S7",
    "scales",
    "sommer",
    "spam",
    "statgenGWAS",
    "statgenIBD",
    "stringi",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "QTLMapping_in_MultiParentPopulations.Rmd",
      "filename": "QTLMapping_in_MultiParentPopulations.html",
      "title": "QTL Mapping in Multi-Parent Populations",
      "author": "Wenhao Li, Martin Boer, and Bart-Jan van Rossum",
      "engine": "knitr::rmarkdown",
      "headings": [
        "The statgenMPP package",
        "Example simulated data",
        "Example maize",
        "Example barley",
        "Parallel computing",
        "Summary",
        "References"
      ],
      "created": "2022-03-15 08:18:23",
      "modified": "2025-02-11 08:06:33",
      "commits": 15
    }
  ],
  "_score": 4.079181246047625,
  "_indexed": true,
  "_nocasepkg": "statgenmpp",
  "_universes": [
    "biometris",
    "bartjanvanrossum"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.5",
      "date": "2026-07-17T05:22:43.000Z",
      "distro": "resolute",
      "commit": "b1178c8a93e4d6eb67adf32216a892f32605793e",
      "fileid": "https://r2.ropensci.org/7350b5c02724c56d697cee445a8a5ab1fd55d0f4823c7e261547b8d7a8c127fa",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/29556887895"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.5",
      "date": "2026-07-17T05:23:12.000Z",
      "distro": "resolute",
      "commit": "b1178c8a93e4d6eb67adf32216a892f32605793e",
      "fileid": "https://r2.ropensci.org/b44a91c4ce0f5b01d863c6ebebd24eb56f698beb83513e1865220154d4bdb023",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/29556887895"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.5",
      "date": "2026-07-17T05:22:53.000Z",
      "commit": "b1178c8a93e4d6eb67adf32216a892f32605793e",
      "fileid": "https://r2.ropensci.org/06e66b47f9a65e84feac3ab8319aa657c3d64dcb97ac46077be289a597f37b4f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/29556887895"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0.5",
      "date": "2026-07-17T05:24:21.000Z",
      "commit": "b1178c8a93e4d6eb67adf32216a892f32605793e",
      "fileid": "https://r2.ropensci.org/f1b7570b50fa8b04192c38f27482efe94a516ba38733e4f23d0429dd85686d4c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/29556887895"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.5",
      "date": "2026-07-17T05:22:48.000Z",
      "commit": "b1178c8a93e4d6eb67adf32216a892f32605793e",
      "fileid": "https://r2.ropensci.org/63805c36f73d3eabbf85e98984dc0e486befbe12eb3762289316897c09f0ca4b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/29556887895"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.5",
      "date": "2026-07-17T05:22:02.000Z",
      "commit": "b1178c8a93e4d6eb67adf32216a892f32605793e",
      "fileid": "https://r2.ropensci.org/b0db1fe5ea12eb6f4a8574083857afdb1afed32f2514709dd8374bc5946b4df3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/29556887895"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.5",
      "date": "2026-07-17T05:21:51.000Z",
      "commit": "b1178c8a93e4d6eb67adf32216a892f32605793e",
      "fileid": "https://r2.ropensci.org/f3c982c97301806eb401be4af380351f76a450c8a51379981337b329211545f3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/29556887895"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0.5",
      "date": "2026-07-17T05:22:03.000Z",
      "commit": "b1178c8a93e4d6eb67adf32216a892f32605793e",
      "fileid": "https://r2.ropensci.org/73dca51b6a77baa1db2ea587377c0e6fa7ebf6cf5080b2e27f90c9c6c604f474",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biometris/actions/runs/29556887895"
    }
  ]
}