{
  "_id": "6a4952c8f6c47c441949b839",
  "Type": "Package",
  "Package": "pedtools",
  "Title": "Creating and Working with Pedigrees and Marker Data",
  "Version": "2.11.0",
  "Authors@R": "person(\"Magnus Dehli\", \"Vigeland\", , \"m.d.vigeland@medisin.uio.no\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-9134-4962\"))",
  "Description": "A comprehensive collection of tools for creating,\nmanipulating and visualising pedigrees and genetic marker data.\nPedigrees can be read from text files or created on the fly\nwith built-in functions. A range of utilities enable\nmodifications like adding or removing individuals, breaking\nloops, and merging pedigrees. An online tool for creating\npedigrees interactively, based on 'pedtools', is available at\n<https://magnusdv.shinyapps.io/quickped>. 'pedtools' is the hub\nof the 'pedsuite', a collection of packages for pedigree\nanalysis. A detailed presentation of the 'pedsuite' is given in\nthe book 'Pedigree Analysis in R' (Vigeland, 2021,\nISBN:9780128244302).",
  "License": "GPL-3",
  "URL": "https://github.com/magnusdv/pedtools,\nhttps://magnusdv.github.io/pedsuite/",
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  "Repository": "https://magnusdv.r-universe.dev",
  "Date/Publication": "2026-06-29 08:09:10 UTC",
  "RemoteUrl": "https://github.com/magnusdv/pedtools",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-29 10:39:18 UTC",
    "User": "root"
  },
  "Author": "Magnus Dehli Vigeland [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-9134-4962>)",
  "Maintainer": "Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>",
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  "_created": "2026-06-29T10:39:18.000Z",
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  "_upstream": "https://github.com/magnusdv/pedtools",
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  "_topics": [
    "pedigrees",
    "pedsuite"
  ],
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  "_contributors": [
    {
      "user": "magnusdv",
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    "description": "Statistical geneticist"
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    {
      "version": "0.9.1",
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    {
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    },
    {
      "version": "2.7.0",
      "date": "2024-06-28"
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    {
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      "version": "2.9.0",
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    },
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      "version": "2.10.0",
      "date": "2026-02-01"
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  ],
  "_exports": [
    ".annotatePed",
    ".drawPed",
    ".pedAlignment",
    ".pedAnnotation",
    ".pedScaling",
    "addAllele",
    "addChild",
    "addChildren",
    "addDaughter",
    "addMarker",
    "addMarkers",
    "addParents",
    "addSibling",
    "addSon",
    "afreq",
    "afreq<-",
    "alleles",
    "allowsMutations",
    "ancestors",
    "ancestralPed",
    "as_kinship2_pedigree",
    "as.ped",
    "avuncularPed",
    "branch",
    "breakLoops",
    "children",
    "children2",
    "chrom",
    "chrom<-",
    "commonAncestors",
    "commonDescendants",
    "connectedComponents",
    "cousinPed",
    "descendants",
    "descentPaths",
    "distributeMarkers",
    "doubleCousins",
    "doubleFirstCousins",
    "drawPed",
    "emptyMarker",
    "expectedHeterozygosity",
    "expectedHomozygosity",
    "extractSingletons",
    "famid",
    "famid<-",
    "father",
    "females",
    "findLoopBreakers",
    "founderInbreeding",
    "founderInbreeding<-",
    "founders",
    "foundersFirst",
    "fullSibMating",
    "generations",
    "genotype",
    "genotype<-",
    "getAlleles",
    "getComponent",
    "getFreqDatabase",
    "getGenotypes",
    "getLocusAttributes",
    "getMap",
    "getMarkers",
    "getSex",
    "grandparents",
    "halfCousinPed",
    "halfSibPed",
    "halfSibStack",
    "halfSibTriangle",
    "harmoniseMarkers",
    "hasCommonAncestor",
    "hasInbredFounders",
    "hasLinkedMarkers",
    "hasMarkers",
    "hasParentsBeforeChildren",
    "hasSelfing",
    "hasUnbrokenLoops",
    "inbreedingLoops",
    "internalID",
    "is.marker",
    "is.markerList",
    "is.ped",
    "is.pedList",
    "is.singleton",
    "isHomozygous",
    "isXmarker",
    "leaves",
    "linearPed",
    "males",
    "marker",
    "maskPed",
    "mendelianCheck",
    "mergePed",
    "mother",
    "mutmod",
    "mutmod<-",
    "nAlleles",
    "name",
    "name<-",
    "nChildren",
    "nephews_nieces",
    "newMarker",
    "newPed",
    "niblings",
    "nMarkers",
    "nonfounders",
    "nTyped",
    "nuclearPed",
    "parents",
    "parentsBeforeChildren",
    "ped",
    "pedsize",
    "peelingOrder",
    "piblings",
    "plotPedList",
    "posMb",
    "posMb<-",
    "quadHalfFirstCousins",
    "randomPed",
    "readFreqDatabase",
    "readPed",
    "relabel",
    "removeGenotypes",
    "removeIndividuals",
    "removeMarkers",
    "reorderPed",
    "restorePed",
    "sameGenotype",
    "selectMarkers",
    "selfingPed",
    "setAfreq",
    "setAlleleLabels",
    "setAlleles",
    "setChrom",
    "setFounderInbreeding",
    "setFreqDatabase",
    "setGenotype",
    "setLocusAttributes",
    "setMap",
    "setMarkername",
    "setMarkers",
    "setMutmod",
    "setPosition",
    "setSex",
    "setSNPs",
    "siblings",
    "singleton",
    "singletons",
    "sortGenotypes",
    "spouses",
    "subnucs",
    "swapGenotypes",
    "swapSex",
    "tieLoops",
    "transferMarkers",
    "trim",
    "typedMembers",
    "unmaskPed",
    "unrelated",
    "untypedMembers",
    "validatePed",
    "whichMarkers",
    "writeFreqDatabase",
    "writePed"
  ],
  "_help": [
    {
      "page": "addAllele",
      "title": "Add allele",
      "topics": [
        "addAllele"
      ]
    },
    {
      "page": "as_kinship2_pedigree",
      "title": "Convert pedigree to kinship2 format",
      "topics": [
        "as_kinship2_pedigree"
      ]
    },
    {
      "page": "as.data.frame.ped",
      "title": "Convert ped to data.frame",
      "topics": [
        "as.data.frame.ped"
      ]
    },
    {
      "page": "as.matrix.ped",
      "title": "Convert 'ped' to matrix",
      "topics": [
        "as.matrix.ped",
        "restorePed"
      ]
    },
    {
      "page": "as.ped",
      "title": "Conversions to ped objects",
      "topics": [
        "as.ped",
        "as.ped.data.frame"
      ]
    },
    {
      "page": "breakLoops",
      "title": "Pedigree loops",
      "topics": [
        "breakLoops",
        "findLoopBreakers",
        "tieLoops"
      ]
    },
    {
      "page": "connectedComponents",
      "title": "Connected pedigree components",
      "topics": [
        "connectedComponents"
      ]
    },
    {
      "page": "distributeMarkers",
      "title": "Distribute markers evenly along a set of chromosomes",
      "topics": [
        "distributeMarkers"
      ]
    },
    {
      "page": "expectedHomozygosity",
      "title": "Expected homozygosity and heterozygosity",
      "topics": [
        "expectedHeterozygosity",
        "expectedHomozygosity"
      ]
    },
    {
      "page": "extractSingletons",
      "title": "Extract singletons from pedigree",
      "topics": [
        "extractSingletons"
      ]
    },
    {
      "page": "famid",
      "title": "Family identifier",
      "topics": [
        "famid",
        "famid.ped",
        "famid<-",
        "famid<-.ped"
      ]
    },
    {
      "page": "founderInbreeding",
      "title": "Inbreeding coefficients of founders",
      "topics": [
        "founderInbreeding",
        "founderInbreeding<-",
        "setFounderInbreeding"
      ]
    },
    {
      "page": "freqDatabase",
      "title": "Allele frequency database",
      "topics": [
        "freqDatabase",
        "getFreqDatabase",
        "readFreqDatabase",
        "setFreqDatabase",
        "writeFreqDatabase"
      ]
    },
    {
      "page": "getAlleles",
      "title": "Allele matrix manipulation",
      "topics": [
        "getAlleles",
        "removeGenotypes",
        "setAlleles"
      ]
    },
    {
      "page": "getComponent",
      "title": "Pedigree component",
      "topics": [
        "getComponent"
      ]
    },
    {
      "page": "getGenotypes",
      "title": "Genotype matrix",
      "topics": [
        "getGenotypes"
      ]
    },
    {
      "page": "getMap",
      "title": "Tabulate marker positions",
      "topics": [
        "getMap",
        "hasLinkedMarkers",
        "setMap"
      ]
    },
    {
      "page": "getSex",
      "title": "Get or set the sex of pedigree members",
      "topics": [
        "getSex",
        "setSex",
        "swapSex"
      ]
    },
    {
      "page": "harmoniseMarkers",
      "title": "Harmonise markers across components in a ped list",
      "topics": [
        "harmoniseMarkers"
      ]
    },
    {
      "page": "inbreedingLoops",
      "title": "Inbreeding loops",
      "topics": [
        "inbreedingLoops"
      ]
    },
    {
      "page": "is.marker",
      "title": "Test if something is a marker",
      "topics": [
        "is.marker",
        "is.markerList"
      ]
    },
    {
      "page": "is.ped",
      "title": "Is an object a 'ped' object?",
      "topics": [
        "is.ped",
        "is.pedList",
        "is.singleton"
      ]
    },
    {
      "page": "isHomozygous",
      "title": "Find homozygous genotypes",
      "topics": [
        "isHomozygous"
      ]
    },
    {
      "page": "locusAttributes",
      "title": "Get or set locus attributes",
      "topics": [
        "getLocusAttributes",
        "locusAttributes",
        "setLocusAttributes"
      ]
    },
    {
      "page": "marker",
      "title": "Marker objects",
      "topics": [
        "addMarker",
        "marker"
      ]
    },
    {
      "page": "marker_attach",
      "title": "Attach markers to pedigrees",
      "topics": [
        "addMarkers",
        "marker_attach",
        "setMarkers"
      ]
    },
    {
      "page": "marker_getattr",
      "title": "Get marker attributes",
      "topics": [
        "afreq",
        "afreq.list",
        "afreq.marker",
        "afreq.ped",
        "alleles",
        "alleles.list",
        "alleles.marker",
        "alleles.ped",
        "chrom",
        "chrom.list",
        "chrom.marker",
        "chrom.ped",
        "genotype",
        "genotype.marker",
        "genotype.ped",
        "marker_getattr",
        "mutmod",
        "mutmod.list",
        "mutmod.marker",
        "mutmod.ped",
        "name",
        "name.list",
        "name.marker",
        "name.ped",
        "posMb",
        "posMb.marker",
        "posMb.ped"
      ]
    },
    {
      "page": "marker_inplace",
      "title": "Set marker attributes",
      "topics": [
        "afreq<-",
        "afreq<-.list",
        "afreq<-.marker",
        "afreq<-.ped",
        "chrom<-",
        "chrom<-.list",
        "chrom<-.marker",
        "chrom<-.ped",
        "genotype<-",
        "genotype<-.marker",
        "genotype<-.ped",
        "marker_inplace",
        "mutmod<-",
        "mutmod<-.list",
        "mutmod<-.marker",
        "mutmod<-.ped",
        "name<-",
        "name<-.list",
        "name<-.marker",
        "name<-.ped",
        "posMb<-",
        "posMb<-.marker",
        "posMb<-.ped"
      ]
    },
    {
      "page": "marker_prop",
      "title": "Marker properties",
      "topics": [
        "allowsMutations",
        "allowsMutations.default",
        "allowsMutations.list",
        "allowsMutations.marker",
        "allowsMutations.ped",
        "emptyMarker",
        "emptyMarker.default",
        "emptyMarker.list",
        "emptyMarker.marker",
        "emptyMarker.ped",
        "isXmarker",
        "isXmarker.default",
        "isXmarker.list",
        "isXmarker.marker",
        "isXmarker.ped",
        "marker_prop",
        "nAlleles",
        "nAlleles.default",
        "nAlleles.list",
        "nAlleles.marker",
        "nAlleles.ped",
        "nTyped",
        "nTyped.default",
        "nTyped.list",
        "nTyped.marker",
        "nTyped.ped"
      ]
    },
    {
      "page": "marker_select",
      "title": "Select or remove attached markers",
      "topics": [
        "getMarkers",
        "marker_select",
        "removeMarkers",
        "selectMarkers",
        "whichMarkers"
      ]
    },
    {
      "page": "marker_setattr",
      "title": "Set marker attributes",
      "topics": [
        "marker_setattr",
        "setAfreq",
        "setAlleleLabels",
        "setChrom",
        "setGenotype",
        "setMarkername",
        "setPosition"
      ]
    },
    {
      "page": "maskPed",
      "title": "Mask and unmask pedigree datasets",
      "topics": [
        "maskPed",
        "unmaskPed"
      ]
    },
    {
      "page": "mendelianCheck",
      "title": "Check for Mendelian errors",
      "topics": [
        "mendelianCheck"
      ]
    },
    {
      "page": "mergePed",
      "title": "Merge two pedigrees",
      "topics": [
        "mergePed"
      ]
    },
    {
      "page": "newMarker",
      "title": "Internal marker constructor",
      "topics": [
        "newMarker"
      ]
    },
    {
      "page": "newPed",
      "title": "Internal ped constructor",
      "topics": [
        "newPed"
      ]
    },
    {
      "page": "nMarkers",
      "title": "The number of markers attached to a pedigree",
      "topics": [
        "hasMarkers",
        "nMarkers"
      ]
    },
    {
      "page": "ped",
      "title": "Pedigree construction",
      "topics": [
        "ped",
        "singleton",
        "singletons"
      ]
    },
    {
      "page": "ped_basic",
      "title": "Create basic pedigrees",
      "topics": [
        "ancestralPed",
        "avuncularPed",
        "cousinPed",
        "halfCousinPed",
        "halfSibPed",
        "linearPed",
        "nuclearPed",
        "ped_basic",
        "selfingPed"
      ]
    },
    {
      "page": "ped_complex",
      "title": "Complex pedigree structures",
      "topics": [
        "doubleCousins",
        "doubleFirstCousins",
        "fullSibMating",
        "halfSibStack",
        "halfSibTriangle",
        "ped_complex",
        "quadHalfFirstCousins"
      ]
    },
    {
      "page": "ped_internal",
      "title": "Internal ordering of pedigree members",
      "topics": [
        "foundersFirst",
        "hasParentsBeforeChildren",
        "internalID",
        "parentsBeforeChildren",
        "ped_internal",
        "reorderPed"
      ]
    },
    {
      "page": "ped_modify",
      "title": "Add/remove pedigree members",
      "topics": [
        "addChild",
        "addChildren",
        "addDaughter",
        "addParents",
        "addSibling",
        "addSon",
        "branch",
        "ped_modify",
        "removeIndividuals",
        "subset.ped",
        "trim"
      ]
    },
    {
      "page": "ped_subgroups",
      "title": "Pedigree subgroups",
      "topics": [
        "ancestors",
        "children",
        "children2",
        "commonAncestors",
        "commonDescendants",
        "descendants",
        "descentPaths",
        "father",
        "females",
        "founders",
        "grandparents",
        "leaves",
        "males",
        "mother",
        "nephews_nieces",
        "niblings",
        "nonfounders",
        "parents",
        "ped_subgroups",
        "piblings",
        "siblings",
        "spouses",
        "typedMembers",
        "unrelated",
        "untypedMembers"
      ]
    },
    {
      "page": "ped_utils",
      "title": "Pedigree utilities",
      "topics": [
        "generations",
        "hasCommonAncestor",
        "hasInbredFounders",
        "hasSelfing",
        "hasUnbrokenLoops",
        "nChildren",
        "pedsize",
        "ped_utils",
        "peelingOrder",
        "subnucs"
      ]
    },
    {
      "page": "plot.ped",
      "title": "Plot pedigree",
      "topics": [
        "drawPed",
        "plot.list",
        "plot.ped",
        "plot.pedList"
      ]
    },
    {
      "page": "plotmethods",
      "title": "Internal plot methods",
      "topics": [
        ".annotatePed",
        ".drawPed",
        ".pedAlignment",
        ".pedAnnotation",
        ".pedScaling",
        "plotmethods"
      ]
    },
    {
      "page": "plotPedList",
      "title": "Plot a collection of pedigrees.",
      "topics": [
        "plotPedList"
      ]
    },
    {
      "page": "print.nucleus",
      "title": "S3 methods",
      "topics": [
        "print.nucleus"
      ]
    },
    {
      "page": "print.ped",
      "title": "Printing pedigrees",
      "topics": [
        "print.ped"
      ]
    },
    {
      "page": "randomPed",
      "title": "Random pedigree",
      "topics": [
        "randomPed"
      ]
    },
    {
      "page": "readPed",
      "title": "Read a pedigree from file",
      "topics": [
        "readPed"
      ]
    },
    {
      "page": "relabel",
      "title": "Get or modify pedigree labels",
      "topics": [
        "labels.list",
        "labels.ped",
        "relabel"
      ]
    },
    {
      "page": "sameGenotype",
      "title": "Find markers for which two individuals have the same genotype",
      "topics": [
        "sameGenotype"
      ]
    },
    {
      "page": "setMutmod",
      "title": "Set a mutation model",
      "topics": [
        "setMutmod"
      ]
    },
    {
      "page": "setSNPs",
      "title": "Attach SNP loci to a pedigree",
      "topics": [
        "setSNPs"
      ]
    },
    {
      "page": "sortGenotypes",
      "title": "Sort the alleles in each genotype",
      "topics": [
        "sortGenotypes"
      ]
    },
    {
      "page": "swapGenotypes",
      "title": "Swap genotypes between individuals",
      "topics": [
        "swapGenotypes"
      ]
    },
    {
      "page": "transferMarkers",
      "title": "Transfer marker data",
      "topics": [
        "transferMarkers"
      ]
    },
    {
      "page": "validatePed",
      "title": "Pedigree errors",
      "topics": [
        "validatePed"
      ]
    },
    {
      "page": "writePed",
      "title": "Write a pedigree to file",
      "topics": [
        "writePed"
      ]
    }
  ],
  "_pkglogo": "https://github.com/magnusdv/pedtools/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/magnusdv/pedtools/raw/HEAD/README.md",
  "_rundeps": [
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    "knitr",
    "lattice",
    "lpSolve",
    "Matrix",
    "pedmut",
    "quadprog",
    "xfun",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "pedtools.Rmd",
      "filename": "pedtools.html",
      "title": "Introduction to the pedtools package",
      "author": "Magnus Dehli Vigeland",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Pedigrees",
        "The ped class",
        "Basic pedigree plots",
        "Built-in pedigree structures",
        "Examples of pedigree construction",
        "Example 1: Trio",
        "Example 2: An inbred child",
        "Example 3: A complex family tree",
        "Pedigree subsets",
        "Markers",
        "Creating marker objects",
        "Plotting pedigrees with marker data",
        "Markers attached to pedigrees",
        "Accessing and modifying individual markers",
        "Getting/setting/modifying many markers simultaneously"
      ],
      "created": "2018-07-26 06:36:11",
      "modified": "2025-01-25 13:59:35",
      "commits": 23
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  "_nocasepkg": "pedtools",
  "_universes": [
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