{ "_id": "6a3b46965cdecea1d6815b5a", "Type": "Package", "Package": "ibdsim2", "Title": "Simulation of Chromosomal Regions Shared by Family Members", "Version": "2.3.2.9000", "Authors@R": "person(\"Magnus Dehli\", \"Vigeland\", , \"m.d.vigeland@medisin.uio.no\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-9134-4962\"))", "Description": "Simulation of segments shared identical-by-descent (IBD)\nby pedigree members. Using sex specific recombination rates\nalong the human genome (Halldorsson et al. (2019)\n), phased chromosomes are\nsimulated for all pedigree members. Applications include\ncalculation of realised relatedness coefficients and IBD\nsegment distributions. 'ibdsim2' is part of the 'pedsuite'\ncollection of packages for pedigree analysis. A detailed\npresentation of the 'pedsuite', including a separate chapter on\n'ibdsim2', is available in the book 'Pedigree analysis in R'\n(Vigeland, 2021, ISBN:9780128244302). A 'Shiny' app for\nvisualising and comparing IBD distributions is available at\n.", "License": "GPL-3", "URL": "https://github.com/magnusdv/ibdsim2,\nhttps://magnusdv.github.io/pedsuite/,\nhttps://magnusdv.shinyapps.io/ibdsim2-shiny/", "Encoding": "UTF-8", "Language": "en-GB", "Roxygen": "list(markdown = TRUE)", "LazyData": "true", "Config/roxygen2/version": "8.0.0", "Repository": "https://magnusdv.r-universe.dev", "Date/Publication": "2026-06-12 08:23:23 UTC", "RemoteUrl": "https://github.com/magnusdv/ibdsim2", "RemoteRef": "HEAD", "RemoteSha": "86725ea2325dbb19ac195c341d93352a9db86b8b", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-24 02:44:18 UTC", "User": "root" }, "Author": "Magnus Dehli Vigeland [aut, cre] (ORCID:\n)", "Maintainer": "Magnus Dehli Vigeland ", "MD5sum": "40120c3494047e6582f9a3f36348c97c", "_user": "magnusdv", "_type": "src", "_file": "ibdsim2_2.3.2.9000.tar.gz", "_fileid": "07353752ea2daef7bc72dc06ff5fed103b7abe29e7ab2d6758f07067971f6ca3", "_filesize": 1631532, "_sha256": "07353752ea2daef7bc72dc06ff5fed103b7abe29e7ab2d6758f07067971f6ca3", "_created": "2026-06-24T02:44:18.000Z", "_published": "2026-06-24T02:53:10.968Z", "_distro": "resolute", "_jobs": [ { "job": 83106922730, "time": 178, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7838881282" }, { "job": 83106922734, "time": 169, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7838878944" }, { "job": 83106922729, "time": 159, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7838877370" }, { "job": 83106922782, "time": 174, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7838880168" }, { "job": 83106922743, "time": 131, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7838892327" }, { "job": 83106922750, "time": 321, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7838943369" }, { "job": 83106922736, "time": 124, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7838879481" }, { "job": 83106922747, "time": 225, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7838924725" }, { "job": 83106619106, "time": 172, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7838844908" }, { "job": 83106922652, "time": 150, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7838874907" }, { "job": 83106922685, "time": 164, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7838878311" }, { "job": 83106922699, "time": 132, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7838871220" }, { "job": 83106922688, "time": 143, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7838873166" } ], "_buildurl": "https://github.com/r-universe/magnusdv/actions/runs/28071425686", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/magnusdv/ibdsim2", "_commit": { "id": "86725ea2325dbb19ac195c341d93352a9db86b8b", "author": "Magnus Dehli Vigeland ", "committer": "Magnus Dehli Vigeland ", "message": "Add `%notin%`\n", "time": 1781252603 }, "_maintainer": { "name": "Magnus Dehli Vigeland", "email": "m.d.vigeland@medisin.uio.no", "orcid": "0000-0002-9134-4962" }, "_registered": true, "_dependencies": [ { "package": "pedtools", "version": ">= 2.8.0", "role": "Depends" }, { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "ggplot2", "role": "Imports" }, { "package": "glue", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "ribd", "version": ">= 1.7.1", "role": "Imports" }, { "package": "lubridate", "role": "Suggests" }, { "package": "MASS", "role": "Suggests" }, { "package": "patchwork", "role": "Suggests" }, { "package": "shiny", "role": "Suggests" }, { "package": "shinyjs", "role": "Suggests" }, { "package": "shinyWidgets", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "zip", "role": "Suggests" } ], "_owner": "magnusdv", "_selfowned": true, "_usedby": 2, "_updates": [ { "week": "2025-27", "n": 5 }, { "week": "2025-30", "n": 11 }, { "week": "2025-34", "n": 2 }, { "week": "2025-46", "n": 5 }, { "week": "2025-47", "n": 2 }, { "week": "2025-48", "n": 5 }, { "week": "2026-24", "n": 5 } ], "_tags": [ { "name": "v2.3.0", "date": "2025-07-22" }, { "name": "v2.3.2", "date": "2025-11-23" } ], "_topics": [ "identity-by-descent", "relatedness", "simulation", "cpp" ], "_stars": 6, "_contributors": [ { "user": "magnusdv", "count": 368, "uuid": 5310284 } ], "_userbio": { "uuid": 5310284, "type": "user", "name": "Magnus Dehli Vigeland", "followers": 48, "description": "Statistical geneticist" }, "_downloads": { "count": 437, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ibdsim2" }, "_devurl": "https://github.com/magnusdv/ibdsim2", "_pkgdown": "https://magnusdv.github.io/pedsuite/", "_searchresults": 28, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ibdsim2.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/magnusdv/ibdsim2", "_realowner": "magnusdv", "_cranurl": true, "_releases": [ { "version": "1.1", "date": "2020-06-28" }, { "version": "1.2", "date": "2020-07-11" }, { "version": "1.3.0", "date": "2020-11-13" }, { "version": "1.4.0", "date": "2021-07-24" }, { "version": "1.5.0", "date": "2022-06-07" }, { "version": "2.0.0", "date": "2023-08-17" }, { "version": "2.1.0", "date": "2024-08-17" }, { "version": "2.1.1", "date": "2024-09-08" }, { "version": "2.2.0", "date": "2025-03-03" }, { "version": "2.3.0", "date": "2025-07-22" }, { "version": "2.3.1", "date": "2025-08-22" }, { "version": "2.3.2", "date": "2025-11-23" } ], "_exports": [ "convertPos", "customMap", "estimateIdentity", "estimateInbreeding", "estimateKappa", "estimateKinship", "estimateTwoLocusIdentity", "estimateTwoLocusInbreeding", "estimateTwoLocusKappa", "estimateTwoLocusKinship", "extractIds", "findPattern", "haploDraw", "ibdsim", "karyoHaploid", "launchApp", "loadMap", "mapLen", "physRange", "plotSegmentDistribution", "profileSimIBD", "realisedIdentity", "realisedInbreeding", "realisedKappa", "realisedKinship", "segmentStats", "uniformMap", "zeroIBD" ], "_datasets": [ { "name": "legacy_decode19", "title": "Legacy version of the 'decode19' map", "object": "legacy_decode19", "class": [ "genomeMap" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "convertPos", "title": "Conversion of genetic map positions", "topics": [ "convertPos" ] }, { "page": "customMap", "title": "Custom recombination map", "topics": [ "customMap" ] }, { "page": "estimateCoeffs", "title": "Estimation of one- and two-locus relatedness coefficients", "topics": [ "estimateCoeffs", "estimateIdentity", "estimateInbreeding", "estimateKappa", "estimateKinship", "estimateTwoLocusIdentity", "estimateTwoLocusInbreeding", "estimateTwoLocusKappa", "estimateTwoLocusKinship" ] }, { "page": "extractIds", "title": "Extract ID labels from simulation output", "topics": [ "extractIds" ] }, { "page": "findPattern", "title": "Find specific IBD patterns", "topics": [ "findPattern" ] }, { "page": "haploDraw", "title": "Draw haplotypes onto a pedigree plot", "topics": [ "haploDraw" ] }, { "page": "ibdsim", "title": "IBD simulation", "topics": [ "ibdsim" ] }, { "page": "karyoDiploid", "title": "Diploid karyogram", "topics": [ "karyoDiploid" ] }, { "page": "karyogram2", "title": "Karyogram plots", "topics": [ "karyogram2" ] }, { "page": "karyoHaploid", "title": "Haploid karyogram", "topics": [ "karyoHaploid" ] }, { "page": "launchApp", "title": "Launch the ibdsim2 app", "topics": [ "launchApp" ] }, { "page": "legacy_decode19", "title": "Legacy version of the 'decode19' map", "topics": [ "legacy_decode19" ] }, { "page": "loadMap", "title": "Load a built-in genetic map", "topics": [ "loadMap" ] }, { "page": "maplengths", "title": "Physical and genetic map lengths", "topics": [ "mapLen", "mapLen.chromMap", "mapLen.genomeMap", "maplengths", "physRange", "physRange.chromMap", "physRange.genomeMap" ] }, { "page": "plotSegmentDistribution", "title": "Scatter plots of IBD segment distributions", "topics": [ "plotSegmentDistribution" ] }, { "page": "profileSimIBD", "title": "Simulate markers conditional on a given IBD pattern", "topics": [ "profileSimIBD" ] }, { "page": "realised", "title": "Realised relatedness", "topics": [ "realised", "realisedIdentity", "realisedInbreeding", "realisedKappa", "realisedKinship" ] }, { "page": "segmentStats", "title": "Summary statistics for identified segments", "topics": [ "segmentStats" ] }, { "page": "uniformMap", "title": "Uniform recombination maps", "topics": [ "uniformMap" ] }, { "page": "zeroIBD", "title": "Probability of zero IBD", "topics": [ "zeroIBD" ] } ], "_pkglogo": "https://github.com/magnusdv/ibdsim2/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/magnusdv/ibdsim2/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "evaluate", "farver", "ggplot2", "glue", "gtable", "highr", "isoband", "kinship2", "knitr", "labeling", "lattice", "lifecycle", "lpSolve", "Matrix", "pedmut", "pedtools", "quadprog", "R6", "RColorBrewer", "Rcpp", "ribd", "rlang", "S7", "scales", "slam", "vctrs", "viridisLite", "withr", "xfun", "yaml" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 5.547528576459782, "_indexed": true, "_nocasepkg": "ibdsim2", "_universes": [ "magnusdv" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.3.2.9000", "date": "2026-06-24T02:47:07.000Z", "distro": "resolute", "arch": "aarch64", "commit": "86725ea2325dbb19ac195c341d93352a9db86b8b", "fileid": "ad0473e5987a3cdfebe0fbcc83b48f7d1fdac19a3c58d8984e843afa2807fe3a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/28071425686" }, { "r": "4.7.0", "os": "linux", "version": "2.3.2.9000", "date": "2026-06-24T02:46:46.000Z", "distro": "resolute", "arch": "x86_64", "commit": "86725ea2325dbb19ac195c341d93352a9db86b8b", "fileid": "d0cd09a718fa1508594a0eab5e999885a57615fbff969bc636ba617d161fa761", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/28071425686" }, { "r": "4.6.0", "os": "linux", "version": "2.3.2.9000", "date": "2026-06-24T02:46:48.000Z", "distro": "resolute", "arch": "aarch64", "commit": "86725ea2325dbb19ac195c341d93352a9db86b8b", "fileid": "ebf51b1ebc633c51c1337802150301e2130cf82db4f7dc4bbb4cb000b865a670", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/28071425686" }, { "r": "4.6.0", "os": "linux", "version": "2.3.2.9000", "date": "2026-06-24T02:46:51.000Z", "distro": "resolute", "arch": "x86_64", "commit": "86725ea2325dbb19ac195c341d93352a9db86b8b", "fileid": "355407c4cea687698660eac778b79ff0e7f4013f949cebbbc258ffd5420e1a0d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/28071425686" }, { "r": "4.5.3", "os": "mac", "version": "2.3.2.9000", "date": "2026-06-24T02:47:56.000Z", "arch": "aarch64", "commit": "86725ea2325dbb19ac195c341d93352a9db86b8b", "fileid": "c7afd803e185d89126526b265f54912011bb00c22519b55be71e7d014b3d1013", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/28071425686" }, { "r": "4.5.3", "os": "mac", "version": "2.3.2.9000", "date": "2026-06-24T02:50:30.000Z", "arch": "x86_64", "commit": "86725ea2325dbb19ac195c341d93352a9db86b8b", "fileid": "07f6c460d6c43d3a4380168b6b111dd30af0da8c510b0709347c7366b00fed40", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/28071425686" }, { "r": "4.6.0", "os": "mac", "version": "2.3.2.9000", "date": "2026-06-24T02:46:51.000Z", "arch": "aarch64", "commit": "86725ea2325dbb19ac195c341d93352a9db86b8b", "fileid": "e138aa6803b4467e3eae05d158d5bedda348c073bfe4785042e701a258714d32", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/28071425686" }, { "r": "4.6.0", "os": "mac", "version": "2.3.2.9000", "date": "2026-06-24T02:50:08.000Z", "arch": "x86_64", "commit": "86725ea2325dbb19ac195c341d93352a9db86b8b", "fileid": "88aeb99643cea989436a28e1c39307b133eee267056c18ae6678dc92e6feeed3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/28071425686" }, { "r": "4.6.0", "os": "wasm", "version": "2.3.2.9000", "date": "2026-06-24T02:47:08.000Z", "arch": "emscripten", "commit": "86725ea2325dbb19ac195c341d93352a9db86b8b", "fileid": "1c73f6a715a0165807662c1ce6415c923b28c832652f387467cf694ac0aa4a37", "status": "success", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/28071425686" }, { "r": "4.7.0", "os": "win", "version": "2.3.2.9000", "date": "2026-06-24T02:46:09.000Z", "arch": "x86_64", "commit": "86725ea2325dbb19ac195c341d93352a9db86b8b", "fileid": "5ffabe5dbeb72ca188a0b0e28e1eae9f0cb07fda97d5acd31c8e4949988565a4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/28071425686" }, { "r": "4.5.3", "os": "win", "version": "2.3.2.9000", "date": "2026-06-24T02:45:39.000Z", "arch": "x86_64", "commit": "86725ea2325dbb19ac195c341d93352a9db86b8b", "fileid": "1443c73864006fa1eee7c39cd91d46df494ac005fcc9f938eb8d9cae58301cfe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/28071425686" }, { "r": "4.6.0", "os": "win", "version": "2.3.2.9000", "date": "2026-06-24T02:45:45.000Z", "arch": "x86_64", "commit": "86725ea2325dbb19ac195c341d93352a9db86b8b", "fileid": "e091693494cd3119ea34a642647dd830855cc3e2807214a673ed0c50b5a7d562", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/28071425686" } ] }