{
  "_id": "6a1ad1811d7bb097a09e221d",
  "Package": "FamAgg",
  "Type": "Package",
  "Title": "Pedigree Analysis and Familial Aggregation",
  "Version": "1.41.0",
  "Authors@R": "c(person(given = \"Johannes\", family = \"Rainer\",\nemail = \"johannes.rainer@eurac.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-6977-7147\")),\nperson(given = \"Daniel\", family = \"Taliun\",\nrole = \"ctb\"),\nperson(given = \"Christian\", family = \"Weichenberger\",\nemail = \"christian.weichenberger@eurac.edu\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-2176-0274\"))\n)",
  "Author": "J. Rainer, D. Taliun, C.X. Weichenberger",
  "Maintainer": "Johannes Rainer <johannes.rainer@eurac.edu>",
  "URL": "https://github.com/EuracBiomedicalResearch/FamAgg",
  "BugReports": "https://github.com/EuracBiomedicalResearch/FamAgg/issues",
  "VignetteBuilder": "knitr",
  "Description": "Framework providing basic pedigree analysis and plotting\nutilities as well as a variety of methods to evaluate familial\naggregation of traits in large pedigrees.",
  "Collate": "Classes.R Generics.R Deprecated.R Constructors.R\nMethods-FAData.R Methods-FAKinGroupResults.R\nMethods-FAKinSumResults.R Methods-FAGenIndexResults.R\nMethods-FAIncidenceRateResults.R\nMethods-FAStdIncidenceRateResults.R Methods-FABinTestResults.R\nutils.R matched-controls.R Methods.R plotting-functions.R\nimport-export.R zzz.R",
  "biocViews": "Genetics",
  "License": "MIT + file LICENSE",
  "Copyright": "Haplopainter1.043.pl (http://haplopainter.sourceforge.net)\nCopyright (c) 2004-2008 Holger Thiele",
  "NeedsCompilation": "no",
  "RoxygenNote": "7.1.1",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libssl-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:15 UTC",
  "RemoteUrl": "https://github.com/bioc/FamAgg",
  "RemoteRef": "HEAD",
  "RemoteSha": "e02d0e77e332d26a25ce4e547bed93d28964540a",
  "Packaged": {
    "Date": "2026-05-30 08:29:15 UTC",
    "User": "root"
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  "_created": "2026-05-30T08:29:15.000Z",
  "_published": "2026-05-30T12:01:05.912Z",
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679189337",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/FamAgg",
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  "_maintainer": {
    "name": "Johannes Rainer",
    "email": "johannes.rainer@eurac.edu",
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    "mastodon": "@jorainer@fediscience.org",
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    "orcid": "0000-0002-6977-7147",
    "description": "Computational Mass Spectrometry and Metabolomics, mostly; love R coding and Emacs; member of the Bioconductor Community Advisory Board.",
    "uuid": 5506112
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      "package": "methods",
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      "package": "Matrix",
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      "package": "BiocGenerics",
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    {
      "package": "utils",
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      "package": "survey",
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    {
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      "package": "RUnit",
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  "_owner": "bioc",
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  "_updates": [
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      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.40.0",
      "bioc": "3.23"
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  "_topics": [
    "genetics",
    "pedigree"
  ],
  "_stars": 1,
  "_contributors": [
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      "uuid": 5506112
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    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "source": "https://www.bioconductor.org/packages/stats/bioc/FamAgg"
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  "_devurl": "https://github.com/euracbiomedicalresearch/famagg",
  "_searchresults": 5,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/FamAgg.html",
    "extra/NEWS.html",
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    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
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  "_homeurl": "https://github.com/euracbiomedicalresearch/famagg",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "affectedIndividuals",
    "affectedKinshipGroups",
    "age",
    "age<-",
    "binomialTest",
    "buildPed",
    "cliqueAndTrait",
    "cliques",
    "cliques<-",
    "connectedSubgraph",
    "countGenerations",
    "doPlotPed",
    "estimateGenerations",
    "estimateTimeAtRisk",
    "export",
    "factor2matrix",
    "FAData",
    "familialIncidenceRate",
    "familialIncidenceRateTest",
    "family",
    "findFounders",
    "fsir",
    "fsirTest",
    "genealogicalIndexTest",
    "generationsFrom",
    "getAll",
    "getAncestors",
    "getChildren",
    "getCommonAncestor",
    "getExternalMatched",
    "getFounders",
    "getGenerationMatched",
    "getGenerationSexMatched",
    "getMissingMate",
    "getSexMatched",
    "getSiblings",
    "getSingletons",
    "kinship",
    "kinshipGroupTest",
    "kinshipPairs",
    "kinshipSumTest",
    "lambda",
    "ped2graph",
    "pedigree",
    "pedigree<-",
    "pedigreeSize",
    "phenotypedIndividuals",
    "plotPed",
    "plotRes",
    "probabilityTest",
    "removeSingletons",
    "result",
    "resultForId",
    "runSimulation",
    "shareKinship",
    "sliceAge",
    "subPedigree",
    "switchPlotfun",
    "timeAtRisk",
    "timeAtRisk<-",
    "timeInStrata",
    "trait",
    "trait<-",
    "traitByClique"
  ],
  "_help": [
    {
      "page": "FABinTestResults",
      "title": "Binomial test for familial aggregation",
      "topics": [
        "FABinTestResults",
        "FABinTestResults-class",
        "result,FABinTestResults-method",
        "trait<-,FABinTestResults-method",
        "[,FABinTestResults,ANY,ANY,ANY-method",
        "[,FABinTestResults,ANY-method"
      ]
    },
    {
      "page": "FAData",
      "title": "Pedigree data information",
      "topics": [
        "$",
        "$,FAData-method",
        "affectedIndividuals",
        "affectedIndividuals,FAData-method",
        "age",
        "age,FAData-method",
        "age<-",
        "age<-,FAData-method",
        "buildPed",
        "buildPed,FAData-method",
        "export",
        "export,FAData-method",
        "FAData",
        "FAData-class",
        "family",
        "family,FAData-method",
        "kinship",
        "kinship,FAData-method",
        "pedigree",
        "pedigree,FAData-method",
        "pedigree,missing-method",
        "pedigree<-",
        "pedigree<-,FAData-method",
        "pedigreeSize",
        "pedigreeSize,FAData-method",
        "phenotypedIndividuals",
        "phenotypedIndividuals,FAData-method",
        "plotPed",
        "plotPed,FAData-method",
        "show",
        "show,FAData-method",
        "trait",
        "trait,FAData-method",
        "trait<-",
        "trait<-,FAData-method",
        "[,FAData,ANY,ANY,ANY-method",
        "[,FAData,ANY-method"
      ]
    },
    {
      "page": "FAGenIndexResults",
      "title": "Genealogical Index",
      "topics": [
        "FAGenIndexResults",
        "FAGenIndexResults-class",
        "plotPed,FAGenIndexResults-method",
        "plotRes",
        "plotRes,FAGenIndexResults-method",
        "result,FAGenIndexResults-method",
        "runSimulation,FAGenIndexResults-method",
        "trait<-,FAGenIndexResults-method",
        "[,FAGenIndexResults,ANY,ANY,ANY-method",
        "[,FAGenIndexResults,ANY-method"
      ]
    },
    {
      "page": "FAIncidenceRateResults",
      "title": "Familial Incidence Rate",
      "topics": [
        "$,FAIncidenceRateResults-method",
        "FAIncidenceRateResults",
        "FAIncidenceRateResults-class",
        "familialIncidenceRate,FAIncidenceRateResults-method",
        "plotPed,FAIncidenceRateResults-method",
        "plotRes,FAIncidenceRateResults-method",
        "result,FAIncidenceRateResults-method",
        "runSimulation,FAIncidenceRateResults-method",
        "timeAtRisk",
        "timeAtRisk,FAIncidenceRateResults-method",
        "timeAtRisk<-",
        "timeAtRisk<-,FAIncidenceRateResults-method",
        "trait<-,FAIncidenceRateResults-method",
        "[,FAIncidenceRateResults,ANY,ANY,ANY-method",
        "[,FAIncidenceRateResults,ANY-method"
      ]
    },
    {
      "page": "FAKinGroupResults",
      "title": "Kinship group test",
      "topics": [
        "affectedKinshipGroups",
        "affectedKinshipGroups,FAKinGroupResults-method",
        "buildPed,FAKinGroupResults-method",
        "FAKinGroupResults",
        "FAKinGroupResults-class",
        "plotPed,FAKinGroupResults-method",
        "plotRes,FAKinGroupResults-method",
        "result,FAKinGroupResults-method",
        "runSimulation,FAKinGroupResults-method",
        "shareKinship,FAKinGroupResults-method",
        "trait<-,FAKinGroupResults-method",
        "[,FAKinGroupResults,ANY,ANY,ANY-method",
        "[,FAKinGroupResults,ANY-method"
      ]
    },
    {
      "page": "FAKinSumResults",
      "title": "Kinship sum test",
      "topics": [
        "FAKinSumResults",
        "FAKinSumResults-class",
        "plotPed,FAKinSumResults-method",
        "plotRes,FAKinSumResults-method",
        "result,FAKinSumResults-method",
        "runSimulation,FAKinSumResults-method",
        "trait<-,FAKinSumResults-method",
        "[,FAKinSumResults,ANY,ANY,ANY-method",
        "[,FAKinSumResults,ANY-method"
      ]
    },
    {
      "page": "FAProbResults",
      "title": "DEPRECATED: Probability test",
      "topics": [
        "buildPed,FAProbResults-method",
        "cliqueAndTrait",
        "cliqueAndTrait,FAProbResults-method",
        "cliques",
        "cliques,FAProbResults-method",
        "cliques<-",
        "cliques<-,FAProbResults-method",
        "FAProbResults",
        "FAProbResults-class",
        "plotPed,FAProbResults-method",
        "result",
        "result,FAProbResults-method",
        "runSimulation",
        "runSimulation,FAProbResults-method",
        "shareKinship,FAProbResults-method",
        "trait<-,FAProbResults-method",
        "traitByClique",
        "traitByClique,FAProbResults-method",
        "[,FAProbResults,ANY,ANY,ANY-method",
        "[,FAProbResults,ANY-method"
      ]
    },
    {
      "page": "FAStdIncidenceRateResults",
      "title": "Familial Standardized Incidence Rate",
      "topics": [
        "$,FAStdIncidenceRateResults-method",
        "FAStdIncidenceRateResults",
        "FAStdIncidenceRateResults-class",
        "fsir,FAStdIncidenceRateResults-method",
        "lambda",
        "lambda,FAStdIncidenceRateResults-method",
        "plotPed,FAStdIncidenceRateResults-method",
        "plotRes,FAStdIncidenceRateResults-method",
        "result,FAStdIncidenceRateResults-method",
        "resultForId",
        "resultForId,FAStdIncidenceRateResults-method",
        "runSimulation,FAStdIncidenceRateResults-method",
        "timeInStrata",
        "timeInStrata,FAStdIncidenceRateResults-method",
        "trait<-,FAStdIncidenceRateResults-method",
        "[,FAStdIncidenceRateResults,ANY,ANY,ANY-method",
        "[,FAStdIncidenceRateResults,ANY-method"
      ]
    },
    {
      "page": "defineControls",
      "title": "Define sets of control individuals for one or more given individuals",
      "topics": [
        "getAll",
        "getAll,data.frame-method",
        "getAll,FAData-method",
        "getAll,pedigree-method",
        "getAll,pedigreeList-method",
        "getExternalMatched",
        "getExternalMatched,data.frame-method",
        "getExternalMatched,FAData-method",
        "getExternalMatched,pedigree-method",
        "getExternalMatched,pedigreeList-method",
        "getGenerationMatched",
        "getGenerationMatched,data.frame-method",
        "getGenerationMatched,FAData-method",
        "getGenerationMatched,pedigree-method",
        "getGenerationMatched,pedigreeList-method",
        "getGenerationSexMatched",
        "getGenerationSexMatched,data.frame-method",
        "getGenerationSexMatched,FAData-method",
        "getGenerationSexMatched,pedigree-method",
        "getGenerationSexMatched,pedigreeList-method",
        "getSexMatched",
        "getSexMatched,data.frame-method",
        "getSexMatched,FAData-method",
        "getSexMatched,pedigree-method",
        "getSexMatched,pedigreeList-method"
      ]
    },
    {
      "page": "kinshipPairs",
      "title": "Extract pairs of individuals matching certain kinship criteria",
      "topics": [
        "kinshipPairs"
      ]
    },
    {
      "page": "FAData-analysis",
      "title": "Pedigree analysis and familial aggregation methods",
      "topics": [
        "binomialTest",
        "estimateTimeAtRisk",
        "factor2matrix",
        "familialIncidenceRate",
        "familialIncidenceRate,FAData-method",
        "familialIncidenceRateTest",
        "familialIncidenceRateTest,FAData-method",
        "fsir",
        "fsir,FAData-method",
        "fsirTest",
        "fsirTest,FAData-method",
        "genealogicalIndexTest",
        "genealogicalIndexTest,FAData-method",
        "kinshipGroupTest",
        "kinshipGroupTest,FAData-method",
        "kinshipSumTest",
        "kinshipSumTest,FAData-method",
        "PedigreeAnalysis",
        "probabilityTest",
        "probabilityTest,FAData-method",
        "sliceAge"
      ]
    },
    {
      "page": "Pedigree-utils",
      "title": "Basic pedigree utilities",
      "topics": [
        "cliques,missing-method",
        "connectedSubgraph",
        "countGenerations",
        "countGenerations,data.frame-method",
        "countGenerations,FAData-method",
        "countGenerations,pedigree-method",
        "countGenerations,pedigreeList-method",
        "estimateGenerations",
        "estimateGenerations,data.frame-method",
        "estimateGenerations,FAData-method",
        "estimateGenerations,pedigree-method",
        "estimateGenerations,pedigreeList-method",
        "findFounders",
        "findFounders,data.frame-method",
        "findFounders,FAData-method",
        "findFounders,pedigree-method",
        "findFounders,pedigreeList-method",
        "generationsFrom",
        "generationsFrom,data.frame-method",
        "generationsFrom,FAData-method",
        "generationsFrom,pedigree-method",
        "generationsFrom,pedigreeList-method",
        "getAncestors",
        "getAncestors,data.frame-method",
        "getAncestors,FAData-method",
        "getAncestors,pedigree-method",
        "getAncestors,pedigreeList-method",
        "getChildren",
        "getChildren,data.frame-method",
        "getChildren,FAData-method",
        "getChildren,pedigree-method",
        "getChildren,pedigreeList-method",
        "getCommonAncestor",
        "getCommonAncestor,data.frame-method",
        "getCommonAncestor,FAData-method",
        "getCommonAncestor,pedigree-method",
        "getCommonAncestor,pedigreeList-method",
        "getFounders",
        "getFounders,data.frame-method",
        "getFounders,FAData-method",
        "getMissingMate",
        "getMissingMate,data.frame-method",
        "getMissingMate,FAData-method",
        "getMissingMate,pedigree-method",
        "getMissingMate,pedigreeList-method",
        "getSiblings",
        "getSiblings,data.frame-method",
        "getSiblings,FAData-method",
        "getSiblings,pedigree-method",
        "getSiblings,pedigreeList-method",
        "getSingletons",
        "getSingletons,data.frame-method",
        "getSingletons,FAData-method",
        "ped2graph",
        "PedigreeUtils",
        "removeSingletons",
        "removeSingletons,data.frame-method",
        "removeSingletons,FAData-method",
        "shareKinship",
        "shareKinship,FAData-method",
        "subPedigree"
      ]
    },
    {
      "page": "plotting-functions",
      "title": "Pedigree plotting functions",
      "topics": [
        "doPlotPed",
        "switchPlotfun"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/FamAgg/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "base64enc",
    "BiocGenerics",
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    "htmlwidgets",
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    "isoband",
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    "lattice",
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      "title": "Pedigree Analysis and Familial Aggregation",
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        "Basic pedigree operations",
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