{ "_id": "6acf359cd9de2f3f33fc929d", "Package": "paramlink", "Title": "Parametric Linkage and Other Pedigree Analysis in R", "Version": "1.1-6", "Authors@R": "c(\nperson(\"Magnus Dehli\", \"Vigeland\", , \"m.d.vigeland@medisin.uio.no\", role = c(\"aut\", \"cre\")),\nperson(\"Thore\", \"Egeland\", role = \"ctb\"),\nperson(\"Guro\", \"Doerum\", role = \"ctb\")\n)", "Maintainer": "Magnus Dehli Vigeland ", "Description": "NOTE: 'PARAMLINK' HAS BEEN SUPERSEDED BY THE 'PEDSUITE'\nPACKAGES (). 'PARAMLINK'\nIS MAINTAINED ONLY FOR LEGACY PURPOSES AND SHOULD NOT BE USED\nIN NEW PROJECTS. A suite of tools for analysing pedigrees with\nmarker data, including parametric linkage analysis, forensic\ncomputations, relatedness analysis and marker simulations. The\ncore of the package is an implementation of the Elston-Stewart\nalgorithm for pedigree likelihoods, extended to allow mutations\nas well as complex inbreeding. Features for linkage analysis\ninclude singlepoint LOD scores, power analysis, and multipoint\nanalysis (the latter through a wrapper to the 'MERLIN'\nsoftware). Forensic applications include exclusion\nprobabilities, genotype distributions and conditional\nsimulations. Data from the 'Familias' software can be imported\nand analysed in 'paramlink'. Finally, 'paramlink' offers many\nutility functions for creating, manipulating and plotting\npedigrees with or without marker data (the actual plotting is\ndone by the 'kinship2' package).", "License": "GPL (>= 2)", "URL": "https://github.com/magnusdv/paramlink", "BugReports": "https://github.com/magnusdv/paramlink/issues", "Encoding": "UTF-8", "Language": "en-GB", "LazyData": "Yes", "RoxygenNote": "7.3.2", "SystemRequirements": "For multipoint linkage analysis, 'MERLIN'\n(http://csg.sph.umich.edu/abecasis/merlin/index.html).", "Repository": "https://magnusdv.r-universe.dev", "Date/Publication": "2025-07-21 20:00:48 UTC", "RemoteUrl": "https://github.com/magnusdv/paramlink", "RemoteRef": "HEAD", "RemoteSha": "fcf13f2b5c399300beb7f7bd18964cc550f7e950", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-14 07:38:14 UTC", "User": "root" }, "Author": "Magnus Dehli Vigeland [aut, cre],\nThore Egeland [ctb],\nGuro Doerum [ctb]", "_user": "magnusdv", "_type": "src", "_file": 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"title": "A consanguineous pedigree", "object": "twoloops", "class": [ "data.frame" ], "fields": [ "FAMID", "ID", "FID", "MID", "SEX", "AFF" ], "rows": 17, "table": true, "tojson": true }, { "name": "Xped", "title": "Example pedigree with X-linked disease pattern.", "object": "Xped", "class": [ "data.frame" ], "fields": [ "FAMID", "ID", "FID", "MID", "SEX", "AFF" ], "rows": 15, "table": true, "tojson": true } ], "_help": [ { "page": "allGenotypes", "title": "Genotype combinations", "topics": [ "allGenotypes", "fast.grid", "geno.grid.subset" ] }, { "page": "as.data.frame.linkdat", "title": "linkdat to data.frame conversion", "topics": [ "as.data.frame.linkdat" ] }, { "page": "as.matrix.linkdat", "title": "linkdat to matrix conversion", "topics": [ "as.matrix.linkdat", "restore_linkdat" ] }, { "page": "dominant", "title": "Example pedigree for linkage analysis", "topics": [ "dominant" ] }, { "page": "examineKinships", "title": "Check pedigree for relationship errors", "topics": [ 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Mendelian errors", "topics": [ "mendelianCheck" ] }, { "page": "mergePed", "title": "Merge two pedigrees", "topics": [ "mergePed" ] }, { "page": "merlin", "title": "MERLIN wrappers", "topics": [ "merlin", "merlinUnlikely" ] }, { "page": "oneMarkerDistribution", "title": "Genotype probability distribution", "topics": [ "oneMarkerDistribution" ] }, { "page": "pedCreate", "title": "Create simple pedigrees", "topics": [ "cousinPed", "cousinsPed", "doubleCousins", "doubleFirstCousins", "fullSibMating", "halfCousinPed", "halfCousinsPed", "halfSibStack", "nuclearPed", "pedCreate", "quadHalfFirstCousins" ] }, { "page": "pedigreeLoops", "title": "Pedigree loops", "topics": [ "breakLoops", "findLoopBreakers", "findLoopBreakers2", "pedigreeLoops", "tieLoops" ] }, { "page": "pedModify", "title": "Modify the pedigree of 'linkdat' objects", "topics": [ "addDaughter", "addOffspring", "addParents", "addSon", "branch", "pedModify", "relabel", "removeIndividuals", "swapAff", "swapSex", "trim" ] }, { 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