{ "_id": "6a1d593e1d7bb097a0a47d97", "Package": "ibdfindr", "Title": "HMM Toolkit for Inferring IBD Segments from SNP Genotypes", "Version": "0.3.1", "Authors@R": "person(\"Magnus Dehli\", \"Vigeland\", , \"m.d.vigeland@medisin.uio.no\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-9134-4962\"))", "Description": "Implements continuous-time hidden Markov models (HMMs) to\ninfer identity-by-descent (IBD) segments shared by two\nindividuals from their single-nucleotide polymorphism (SNP)\ngenotypes. Provides posterior probabilities at each marker\n(forward-backward algorithm), prediction of IBD segments\n(Viterbi algorithm), and functions for visualising results.\nSupports both autosomal data and X-chromosomal data.", "License": "GPL (>= 3)", "URL": "https://github.com/magnusdv/ibdfindr", "BugReports": "https://github.com/magnusdv/ibdfindr/issues", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Language": "en-GB", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Repository": "https://magnusdv.r-universe.dev", "Date/Publication": "2025-08-18 15:06:38 UTC", "RemoteUrl": "https://github.com/magnusdv/ibdfindr", "RemoteRef": "HEAD", "RemoteSha": "d4d52f8c01aabd4a96f4fe1f9fb5e9144ecd936b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-01 10:01:21 UTC", "User": "root" }, "Author": "Magnus Dehli Vigeland [aut, cre] (ORCID:\n)", "Maintainer": "Magnus Dehli Vigeland ", "MD5sum": "a941ba9ce3ffc202daafba2fc841375e", "_user": "magnusdv", "_type": "src", "_file": "ibdfindr_0.3.1.tar.gz", "_fileid": "82328bccd08fdfb4a9a75c43d0089e3468aaf0a460d77740ec79b920f60b3bd2", "_filesize": 406196, "_sha256": "82328bccd08fdfb4a9a75c43d0089e3468aaf0a460d77740ec79b920f60b3bd2", "_created": "2026-06-01T10:01:21.000Z", "_published": "2026-06-01T10:04:46.109Z", "_distro": "noble", "_jobs": [ { "job": 78829111821, "time": 161, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7328660990" }, { "job": 78829111855, "time": 158, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7328660085" }, { "job": 78829111765, "time": 114, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7328645486" }, { "job": 78829111791, "time": 129, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7328650583" }, { "job": 78828585296, "time": 184, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7328604929" }, { "job": 78829111761, "time": 111, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7328644485" }, { "job": 78829111782, "time": 125, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7328650233" }, { "job": 78829111750, "time": 109, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7328643483" }, { "job": 78829111764, "time": 120, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7328647616" } ], "_buildurl": "https://github.com/r-universe/magnusdv/actions/runs/26748041866", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/magnusdv/ibdfindr", "_commit": { "id": "d4d52f8c01aabd4a96f4fe1f9fb5e9144ecd936b", "author": "Magnus Dehli Vigeland ", "committer": "Magnus Dehli Vigeland ", "message": "Update README with CRAN details\n", "time": 1755529598 }, "_maintainer": { "name": "Magnus Dehli Vigeland", "email": "m.d.vigeland@medisin.uio.no", "orcid": "0000-0002-9134-4962" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2", "role": "Depends" }, { "package": "forrel", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ibdsim2", "role": "Imports" }, { "package": "pedtools", "role": "Imports" }, { "package": "ribd", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "magnusdv", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-25", "n": 12 }, { "week": "2025-26", "n": 6 }, { "week": "2025-27", "n": 7 }, { "week": "2025-28", "n": 3 }, { "week": "2025-30", "n": 13 }, { "week": "2025-31", "n": 3 }, { "week": "2025-33", "n": 1 }, { "week": "2025-34", "n": 1 } ], "_tags": [ { "name": "v0.3.1", "date": "2025-07-30" } ], "_stars": 4, "_contributors": [ { "user": "magnusdv", "count": 47, "uuid": 5310284 } ], "_userbio": { "uuid": 5310284, "type": "user", "name": "Magnus Dehli Vigeland", "description": "Statistical geneticist" }, "_downloads": { "count": 498, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ibdfindr" }, "_devurl": "https://github.com/magnusdv/ibdfindr", "_searchresults": 4, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ibdfindr.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/magnusdv/ibdfindr", "_realowner": "magnusdv", "_cranurl": true, "_releases": [ { "version": "0.3.1", "date": "2025-08-18" } ], "_exports": [ "computePR", "findIBD", "findSegments", "fitHMM", "ibdPosteriors", "plotIBD", "totalLoglik" ], "_datasets": [ { "name": "brothersX", "title": "Dataset with X-chromosomal SNP genotypes for two brothers", "object": "brothersX", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "CHROM", "MARKER", "MB", "CM", "A1", "A2", "FREQ1", "ID1", "ID2" ], "rows": 246, "table": true, "tojson": true }, { "name": "cousinsDemo", "title": "Dataset with autosomal SNP genotypes for two cousins", "object": "cousinsDemo", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "CHROM", "MARKER", "MB", "CM", "A1", "A2", "FREQ1", "ID1", "ID2" ], "rows": 3915, "table": true, "tojson": true } ], "_help": [ { "page": "brothersX", "title": "Dataset with X-chromosomal SNP genotypes for two brothers", "topics": [ "brothersX" ] }, { "page": "computePR", "title": "Precision and Recall for IBD segment calls", "topics": [ "computePR" ] }, { "page": "cousinsDemo", "title": "Dataset with autosomal SNP genotypes for two cousins", "topics": [ "cousinsDemo" ] }, { "page": "findIBD", "title": "All-in-one workflow for finding IBD segments", "topics": [ "findIBD" ] }, { "page": "findSegments", "title": "Identify IBD segments", "topics": [ "findSegments" ] }, { "page": "fitHMM", "title": "Fit a Hidden Markov Model to genotype data", "topics": [ "fitHMM" ] }, { "page": "ibdPosteriors", "title": "IBD posteriors", "topics": [ "ibdPosteriors" ] }, { "page": "plotIBD", "title": "Plot IBD segments and posteriors", "topics": [ "plotIBD" ] }, { "page": "totalLoglik", "title": "Total log-likelihood for observed data", "topics": [ "totalLoglik" ] } ], "_readme": "https://github.com/magnusdv/ibdfindr/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "evaluate", "farver", "forrel", "ggplot2", "glue", "gtable", "highr", "ibdsim2", "isoband", "kinship2", "knitr", "labeling", "lattice", "lifecycle", "lpSolve", "Matrix", "pbapply", "pedmut", "pedprobr", "pedtools", "quadprog", "R6", "RColorBrewer", "Rcpp", "ribd", "rlang", "S7", "scales", "slam", "vctrs", "verbalisr", "viridisLite", "withr", "xfun", "yaml" ], "_score": 4.681241237375588, "_indexed": true, "_nocasepkg": "ibdfindr", "_universes": [ "magnusdv" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.3.1", "date": "2026-06-01T10:03:41.000Z", "distro": "noble", "commit": "d4d52f8c01aabd4a96f4fe1f9fb5e9144ecd936b", "fileid": "cc1f38031409abe62ba15d71e9ec1c3c2920ad67316cce2ff4437783797c6b17", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/26748041866" }, { "r": "4.6.0", "os": "linux", "version": "0.3.1", "date": "2026-06-01T10:03:38.000Z", "distro": "noble", "commit": "d4d52f8c01aabd4a96f4fe1f9fb5e9144ecd936b", "fileid": "e54336609c81624475a2ef0fbf1ee2f420cbe1e23dd6e6d3fd16c168cfba1716", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/26748041866" }, { "r": "4.5.3", "os": "mac", "version": "0.3.1", "date": "2026-06-01T10:03:09.000Z", "commit": "d4d52f8c01aabd4a96f4fe1f9fb5e9144ecd936b", "fileid": "166855c2c8fed438c5d4b352247d58f211c908c0e6c0c9ac3c81f6ab7603b1e8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/26748041866" }, { "r": "4.6.0", "os": "mac", "version": "0.3.1", "date": "2026-06-01T10:03:16.000Z", "commit": "d4d52f8c01aabd4a96f4fe1f9fb5e9144ecd936b", "fileid": "a3bd335c7a2d37d689a60d45fac10c256c8caa35a676dff6e3fcdf9039a98b89", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/26748041866" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.1", "date": "2026-06-01T10:03:34.000Z", "commit": "d4d52f8c01aabd4a96f4fe1f9fb5e9144ecd936b", "fileid": "fc37b5da344e05d8e26a74ab8b64d75629a839bcb29c7f65924bebb04e9082e5", "status": "success", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/26748041866" }, { "r": "4.7.0", "os": "win", "version": "0.3.1", "date": "2026-06-01T10:03:02.000Z", "commit": "d4d52f8c01aabd4a96f4fe1f9fb5e9144ecd936b", "fileid": "41bfb9ae51fc437242101ec85f00bdc188b989c57c3ab4c0bee1f6bbdcca00b3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/26748041866" }, { "r": "4.5.3", "os": "win", "version": "0.3.1", "date": "2026-06-01T10:02:43.000Z", "commit": "d4d52f8c01aabd4a96f4fe1f9fb5e9144ecd936b", "fileid": "c6ddaa1dc5465e6176a75e9e0add8423d87a90c9639f15631049f175f7ce9a82", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/26748041866" }, { "r": "4.6.0", "os": "win", "version": "0.3.1", "date": "2026-06-01T10:02:46.000Z", "commit": "d4d52f8c01aabd4a96f4fe1f9fb5e9144ecd936b", "fileid": "a38cc12e24801b0363e425ed4c00c131aa0fbab2a07a32e3311c4dfa96211549", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/magnusdv/actions/runs/26748041866" } ] }