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  "Package": "ASMap",
  "Type": "Package",
  "Title": "Linkage Map Construction using the MSTmap Algorithm",
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  "Authors@R": "c(person(given = \"Julian\",\nfamily = \"Taylor\",\nrole = c(\"aut\", \"cre\"),\nemail = \"julian.taylor@adelaide.edu.au\"),\nperson(given = \"David\",\nfamily = \"Butler.\",\nrole = \"aut\",\nemail = \"dbutler@uow.edu.au\"))",
  "Config/testthat/edition": "3",
  "URL": "https://github.com/DrJ001/ASMap, https://drj001.github.io/ASMap/",
  "BugReports": "https://github.com/DrJ001/ASMap/issues",
  "VignetteBuilder": "knitr",
  "Description": "Functions for Accurate and Speedy linkage map\nconstruction, manipulation and diagnosis of Doubled Haploid,\nBackcross and Recombinant Inbred 'R/qtl' objects. This includes\nextremely fast linkage map clustering and optimal marker\nordering using 'MSTmap' (see Wu et al.,2008).",
  "License": "GPL (>= 2)",
  "Repository": "https://drj001.r-universe.dev",
  "Date/Publication": "2026-09-24 13:03:09 UTC",
  "RemoteUrl": "https://github.com/drj001/asmap",
  "RemoteRef": "HEAD",
  "RemoteSha": "73ff1f342ef61436c0923897cb25aff58a2b99dc",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-09-24 15:25:24 UTC",
    "User": "root"
  },
  "Author": "Julian Taylor [aut, cre],\nDavid Butler. [aut]",
  "Maintainer": "Julian Taylor <julian.taylor@adelaide.edu.au>",
  "_user": "drj001",
  "_type": "src",
  "_file": "ASMap_1.1-1.tar.gz",
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  "_created": "2026-09-24T15:25:24.000Z",
  "_published": "2026-09-24T15:45:30.984Z",
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    "author": "DrJ001 <7767208+DrJ001@users.noreply.github.com>",
    "committer": "DrJ001 <7767208+DrJ001@users.noreply.github.com>",
    "message": "Replace the PDF vignette with a short HTML introduction\n\nThe comprehensive PDF vignette has been superseded by the articles\npublished on the package website, and had become inaccurate: it showed\nfunctions R/qtl no longer exports, misstated the size of the marker set\nused in its worked example, and carried cross references broken when the\narticles were derived from it. Shipping it unchanged would send a\ndefective document to CRAN while the website carried the corrected text.\n\nThe articles are not a substitute for it as a package vignette. Vignettes\nare rendered at build time and installed, and a self contained HTML\ndocument embeds its figures, so the full set would place some ten\nmegabytes inside a tarball whose present contents amount to less than\none. The articles also link to the function reference by relative path,\nwhich resolves on the website and not in an installed document.\n\nA short introduction is therefore written for the package itself, in\nprose independent of the articles rather than excerpted from them. It\ndemonstrates each of the three stages of the workflow once, on the\nsmallest of the supplied data sets, and leaves the interpretation of each\ndiagnostic to the article devoted to it. It requires no LaTeX, which\nremoves from the package build the class of failure that led to the\narchiving of version 1.0-8.\n\nBecause the file takes the name of the package, it is also the\nintroduction to the website, and the article that formerly served that\npurpose is withdrawn in its favour. That article was the only one making\nno reference to the function documentation, and nothing else referred to\nit, so no link is broken by its removal. Retaining both would have\noffered a reader two overlapping points of entry under nearly the same\nname.\n\nThe dependency on formatR, used only by the setup of the former vignette,\nis replaced by one on rmarkdown.\n",
    "time": 1790254989
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    "name": "Julian Taylor",
    "email": "julian.taylor@adelaide.edu.au",
    "login": "drj001",
    "description": "Senior Biometrician in the Biometry Hub (@biometryhub) of the University of Adelaide. ",
    "uuid": 7767208
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  "_registered": true,
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      "package": "R",
      "version": ">= 3.0.0",
      "role": "Depends"
    },
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      "package": "qtl",
      "role": "Depends"
    },
    {
      "package": "lattice",
      "role": "Depends"
    },
    {
      "package": "fields",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "gtools",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
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      "package": "digest",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
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  ],
  "_owner": "drj001",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-38",
      "n": 4
    },
    {
      "week": "2026-39",
      "n": 34
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  "_stars": 3,
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      "uuid": 7007561
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    "name": "Julian Taylor",
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    "description": "Senior Biometrician in the Biometry Hub (@biometryhub) of the University of Adelaide. "
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  "_downloads": {
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ASMap"
  },
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  "_devurl": "https://github.com/drj001/asmap",
  "_pkgdown": "https://drj001.github.io/ASMap/",
  "_topics": [
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    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/drj001/asmap",
  "_realowner": "drj001",
  "_cranurl": true,
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      "date": "2014-09-24"
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    {
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      "date": "2014-09-30"
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      "date": "2015-02-02"
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      "version": "0.4",
      "date": "2015-04-13"
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      "version": "0.4-1",
      "date": "2015-05-04"
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    {
      "version": "0.4-4",
      "date": "2015-06-26"
    },
    {
      "version": "0.4-5",
      "date": "2015-08-17"
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    {
      "version": "0.4-7",
      "date": "2016-06-24"
    },
    {
      "version": "1.0-0",
      "date": "2017-07-11"
    },
    {
      "version": "1.0-1",
      "date": "2017-07-26"
    },
    {
      "version": "1.0-2",
      "date": "2017-09-14"
    },
    {
      "version": "1.0-4",
      "date": "2018-10-27"
    },
    {
      "version": "1.0-5",
      "date": "2023-02-11"
    },
    {
      "version": "1.0-6",
      "date": "2023-07-16"
    },
    {
      "version": "1.0-7",
      "date": "2024-01-09"
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      "date": "2024-11-01"
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      "date": "2026-09-21"
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    "alignCross",
    "breakCross",
    "combineMap",
    "fixClones",
    "genClones",
    "heatMap",
    "mergeCross",
    "mstmap",
    "mstmap.cross",
    "mstmap.data.frame",
    "pp.init",
    "profileGen",
    "profileMark",
    "pullCross",
    "pushCross",
    "pValue",
    "quickEst",
    "statGen",
    "statMark",
    "subsetCross"
  ],
  "_datasets": [
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      "name": "mapBC",
      "title": "A constructed linkage map for a backcross barley population",
      "object": "mapBC",
      "file": "mapBC.RData",
      "class": [
        "bc",
        "cross"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mapBCu",
      "title": "An unconstructed marker set for a backcross barley population",
      "object": "mapBCu",
      "file": "mapBCu.RData",
      "class": [
        "bc",
        "cross"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mapDH",
      "title": "A constructed linkage map for a doubled haploid wheat population",
      "object": "mapDH",
      "file": "mapDH.RData",
      "class": [
        "bc",
        "cross"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
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      "name": "mapDHf",
      "title": "An unconstructed marker set for a doubled haploid wheat population",
      "object": "mapDHf",
      "file": "mapDHf.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
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      "rows": 599,
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    },
    {
      "name": "mapF2",
      "title": "Simulated constructed linkage map for a self pollinated F2 barley population",
      "object": "mapF2",
      "file": "mapF2.RData",
      "class": [
        "bcsft",
        "cross"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "ASMap-package",
      "title": "Additional functions for linkage map construction and manipulation of R/qtl objects.",
      "topics": [
        "ASMap-package"
      ]
    },
    {
      "page": "alignCross",
      "title": "Graphical linkage group identity and alignment.",
      "topics": [
        "alignCross"
      ]
    },
    {
      "page": "breakCross",
      "title": "Break linkage groups of an 'qtl' cross object",
      "topics": [
        "breakCross"
      ]
    },
    {
      "page": "combineMap",
      "title": "Combine linkage maps from multiple 'qtl' cross objects",
      "topics": [
        "combineMap"
      ]
    },
    {
      "page": "fixClones",
      "title": "Consensus genotypes for clonal genotype groups",
      "topics": [
        "fixClones"
      ]
    },
    {
      "page": "genClones",
      "title": "Find and report genotype clones",
      "topics": [
        "genClones"
      ]
    },
    {
      "page": "heatMap",
      "title": "Heat map of the estimated pairwise recombination fractions and LOD linkage between markers.",
      "topics": [
        "heatMap"
      ]
    },
    {
      "page": "mapBC",
      "title": "A constructed linkage map for a backcross barley population",
      "topics": [
        "mapBC"
      ]
    },
    {
      "page": "mapBCu",
      "title": "An unconstructed marker set for a backcross barley population",
      "topics": [
        "mapBCu"
      ]
    },
    {
      "page": "mapDH",
      "title": "A constructed linkage map for a doubled haploid wheat population",
      "topics": [
        "mapDH"
      ]
    },
    {
      "page": "mapDHf",
      "title": "An unconstructed marker set for a doubled haploid wheat population",
      "topics": [
        "mapDHf"
      ]
    },
    {
      "page": "mapF2",
      "title": "Simulated constructed linkage map for a self pollinated F2 barley population",
      "topics": [
        "mapF2"
      ]
    },
    {
      "page": "mergeCross",
      "title": "Merge linkage groups of an 'qtl' cross object",
      "topics": [
        "mergeCross"
      ]
    },
    {
      "page": "mstmap.cross",
      "title": "Extremely fast linkage map construction for 'qtl' objects using MSTmap.",
      "topics": [
        "mstmap",
        "mstmap.cross"
      ]
    },
    {
      "page": "mstmap.data.frame",
      "title": "Extremely fast linkage map construction for data frame objects using MSTmap.",
      "topics": [
        "mstmap.data.frame"
      ]
    },
    {
      "page": "pp.init",
      "title": "Parameter initialization function",
      "topics": [
        "pp.init"
      ]
    },
    {
      "page": "profileGen",
      "title": "Profile individual genotype statistics for an R/qtl cross object",
      "topics": [
        "profileGen"
      ]
    },
    {
      "page": "profileMark",
      "title": "Profile individual marker and interval statistics for an R/qtl cross object",
      "topics": [
        "profileMark"
      ]
    },
    {
      "page": "pullCross",
      "title": "Pull markers from a linkage map.",
      "topics": [
        "pullCross"
      ]
    },
    {
      "page": "pushCross",
      "title": "Push markers into an established R/qtl linkage map.",
      "topics": [
        "pushCross"
      ]
    },
    {
      "page": "pValue",
      "title": "P-value graph",
      "topics": [
        "pValue"
      ]
    },
    {
      "page": "quickEst",
      "title": "Very quick estimation of genetic map distances.",
      "topics": [
        "quickEst"
      ]
    },
    {
      "page": "statGen",
      "title": "Individual genotype statistics for an R/qtl cross object",
      "topics": [
        "statGen"
      ]
    },
    {
      "page": "statMark",
      "title": "Individual marker and interval statistics for an R/qtl cross object",
      "topics": [
        "statMark"
      ]
    },
    {
      "page": "subsetCross",
      "title": "Subset an R/qtl object",
      "topics": [
        "subsetCross"
      ]
    }
  ],
  "_readme": "https://github.com/drj001/asmap/raw/HEAD/README.md",
  "_rundeps": [
    "dotCall64",
    "fields",
    "gtools",
    "lattice",
    "maps",
    "qtl",
    "RColorBrewer",
    "Rcpp",
    "spam",
    "viridisLite"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
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