{ "_id": "6acbaf53fe5cc25786e924f5", "Package": "hsrecombi", "Type": "Package", "Title": "Estimation of Recombination Rate and Maternal LD in Half-Sibs", "Version": "1.1.1", "Date": "2026-04-12", "Authors@R": "c(person(\"Dörte\",\"Wittenburg\", role = c(\"aut\", \"cre\"), \nemail = \"wittenburg@fbn-dummerstorf.de\"))", "Description": "Paternal recombination rate and maternal linkage\ndisequilibrium (LD) are estimated for pairs of biallelic\nmarkers such as single nucleotide polymorphisms (SNPs) from\nprogeny genotypes and sire haplotypes. The implementation\nrelies on paternal half-sib families. If maternal half-sib\nfamilies are used, the roles of sire/dam are swapped. Multiple\nfamilies can be considered. For parameter estimation, at least\none sire has to be double heterozygous at the investigated\npairs of SNPs. Based on recombination rates, genetic distances\nbetween markers can be estimated. Markers with unusually large\nrecombination rate to markers in close proximity (i.e.\nputatively misplaced markers) shall be discarded in this\nderivation. *A pipeline is available at GitHub*\n Hampel, Teuscher,\nGomez-Raya, Doschoris, Wittenburg (2018) \"Estimation of\nrecombination rate and maternal linkage disequilibrium in\nhalf-sibs\" . Gomez-Raya (2012)\n\"Maximum likelihood estimation of linkage disequilibrium in\nhalf-sib families\" .", "License": "GPL (>= 2)", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "Language": "en-GB", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-11 15:31:35 UTC", "User": "root" }, "Author": "Dörte Wittenburg [aut, cre]", "Maintainer": "Dörte Wittenburg ", "Config/pak/sysreqs": "libxml2-dev libssl-dev", "Repository": "https://wittenburg.r-universe.dev", "Date/Publication": "2026-04-12 17:55:08 UTC", "RemoteUrl": "https://github.com/cran/hsrecombi", "RemoteRef": "HEAD", "RemoteSha": "b929bb4e8670df62aa281ab10ae87263b0db3045", "_user": "wittenburg", "_type": "src", "_file": "hsrecombi_1.1.1.tar.gz", "_fileid": "https://r2.ropensci.org/1be13d14cb0dc46130df5dc9929b456defa6adfc1feabdc33817e8f4a2528bfe", "_filesize": 196145, "_sha256": "1be13d14cb0dc46130df5dc9929b456defa6adfc1feabdc33817e8f4a2528bfe", "_expires": "2027-01-19T15:46:26.000Z", "_created": "2026-10-11T15:31:35.000Z", "_published": "2026-10-11T15:46:27.826Z", "_buildurl": "https://github.com/r-universe/wittenburg/actions/runs/38151446447", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 114506213657, "time": 112, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11707485206" }, { "job": 114506213708, "time": 130, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11707210951" }, { "job": 114506213665, "time": 93, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11706229040" }, { "job": 114506213746, "time": 134, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11706699517" }, { "job": 114506213702, "time": 182, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11706836941" }, { "job": 114506213790, "time": 315, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11707041673" }, { "job": 114506213706, "time": 180, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11706906833" }, { "job": 114506213735, "time": 713, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "" }, { "job": 114505647539, "time": 157, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11707305418" }, { "job": 114506213651, "time": 94, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11706174132" }, { "job": 114506213721, "time": 359, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11707520441" }, { "job": 114506213749, "time": 116, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11706896413" }, { "job": 114506213741, "time": 107, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11707290586" }, { "job": 114506213699, "time": 356, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11706762367" }, { "job": 114506213827, "time": 114, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11705979395" } ], "_upstream": "https://github.com/cran/hsrecombi", "_commit": { "id": "b929bb4e8670df62aa281ab10ae87263b0db3045", "author": "Dörte Wittenburg ", "committer": "cran-robot ", "message": "version 1.1.1\n", "time": 1776016508 }, "_maintainer": { "name": "Dörte Wittenburg", "email": "wittenburg@fbn-dummerstorf.de", "login": "wittenburg", "description": "", "uuid": 34709155 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 1.0.3", "role": "Imports" }, { "package": "hsphase", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "rlist", "role": "Imports" }, { "package": "quadprog", "role": "Imports" }, { "package": "curl", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "magrittr", "role": "Imports" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-13", "n": 1 }, { "week": "2026-15", "n": 1 } ], "_tags": [ { "name": "1.1.0", "date": "2026-03-27" }, { "name": "1.1.1", "date": "2026-04-12" } ], "_stars": 0, "_contributors": [ { "user": "wittenburg", "count": 12, "uuid": 34709155 } ], "_userbio": { "uuid": 34709155, "type": "user", "name": "wittenburg", "followers": 4 }, "_downloads": { "count": 463, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/hsrecombi" }, "_searchresults": 10, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/hsrecombi.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt" ], "_realowner": "wittenburg", "_cranurl": false, "_releases": [ { "version": "0.1.3", "date": "2020-03-04" }, { "version": "0.3.0", "date": "2020-05-28" }, { "version": "0.3.1", "date": "2020-08-27" }, { "version": "0.3.2", "date": "2020-10-14" }, { "version": "0.3.4", "date": "2021-03-23" }, { "version": "0.4.1", "date": "2022-03-24" }, { "version": "0.4.2", "date": "2022-03-27" }, { "version": "0.5.0", "date": "2022-11-29" }, { "version": "0.5.1", "date": "2022-12-01" }, { "version": "1.0.1", "date": "2023-06-07" }, { "version": "1.1.0", "date": "2026-03-27" }, { "version": "1.1.1", "date": "2026-04-12" } ], "_exports": [ "bestmapfun", "checkCandidates", "editraw", "felsenstein", "geneticPosition", "haldane", "hsrecombi", "karlin", "kosambi", "LDHScpp", "makehap", "makehaplist", "makehappm", "rao", "rao.inv", "startvalue" ], "_datasets": [ { "name": "daughterSire", "title": "targetregion: allocation of paternal half-sib families", "object": "targetregion", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "genotype.chr", "title": "targetregion: progeny genotypes", "object": "targetregion", "class": [ "matrix", "array" ], "fields": [], "rows": 265, "table": true, "tojson": true }, { "name": "hapSire", "title": "targetregion: sire haplotypes", "object": "targetregion", "class": [ "matrix", "array" ], "fields": [], "rows": 10, "table": true, "tojson": true }, { "name": "map.chr", "title": "targetregion: physical map", "object": "targetregion", "class": [ "data.frame" ], "fields": [ "SNP", "Chr", "locus_bp", "locus_Mb", "markername", "SNP_btau42" ], "rows": 200, "table": true, "tojson": true } ], "_help": [ { "page": "bestmapfun", "title": "Best fitting genetic-map function", "topics": [ "bestmapfun" ] }, { "page": "checkCandidates", "title": "Candidates for misplacement", "topics": [ "checkCandidates" ] }, { "page": "countNumbers", "title": "Count genotype combinations at 2 SNPs", "topics": [ "countNumbers" ] }, { "page": "daughterSire", "title": "targetregion: allocation of paternal half-sib families", "topics": [ "daughterSire" ] }, { "page": "editraw", "title": "Editing results of hsrecombi", "topics": [ "editraw" ] }, { "page": "felsenstein", "title": "Felsenstein's genetic map function", "topics": [ "felsenstein" ] }, { "page": "geneticPosition", "title": "Estimation of genetic position", "topics": [ "geneticPosition" ] }, { "page": "genotype.chr", "title": "targetregion: progeny genotypes", "topics": [ "genotype.chr" ] }, { "page": "haldane", "title": "Haldane's genetic map function", "topics": [ "haldane" ] }, { "page": "hapSire", "title": "targetregion: sire haplotypes", "topics": [ "hapSire" ] }, { "page": "hsrecombi", "title": "Estimation of recombination rate and maternal LD", "topics": [ "hsrecombi" ] }, { "page": "karlin", "title": "Liberman and Karlin's genetic map function", "topics": [ "karlin" ] }, { "page": "kosambi", "title": "Kosambi's genetic map function", "topics": [ "kosambi" ] }, { "page": "LDHScpp", "title": "Expectation Maximisation (EM) algorithm", "topics": [ "LDHScpp" ] }, { "page": "loglikfun", "title": "Calculate log-likelihood function", "topics": [ "loglikfun" ] }, { "page": "makehap", "title": "Make list of imputed sire haplotypes", "topics": [ "makehap" ] }, { "page": "makehaplist", "title": "Make list of sire haplotypes", "topics": [ "makehaplist" ] }, { "page": "makehappm", "title": "Make list of imputed haplotypes and estimate recombination rate", "topics": [ "makehappm" ] }, { "page": "map.chr", "title": "targetregion: physical map", "topics": [ "map.chr" ] }, { "page": "rao", "title": "System of genetic-map functions", "topics": [ "rao" ] }, { "page": "rao-inverse", "title": "Approximation to inverse of Rao's system of map functions", "topics": [ "rao inverse", "rao.inv" ] }, { "page": "startvalue", "title": "Start value for maternal allele and haplotype frequencies", "topics": [ "startvalue" ] }, { "page": "targetregion", "title": "Description of the targetregion data set", "topics": [ "targetregion" ] } ], "_rundeps": [ "cli", "curl", "data.table", "dplyr", "gdata", "generics", "glue", "gtools", "hsphase", "jsonlite", "lattice", "lifecycle", "magrittr", "Matrix", "pillar", "pkgconfig", "quadprog", "R6", "Rcpp", "RcppArmadillo", "rlang", "rlist", "snow", "snowfall", "tibble", "tidyselect", "utf8", "vctrs", "withr", "XML", "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": 1.3010299956639813, "_indexed": true, "_nocasepkg": "hsrecombi", "_universes": [ "wittenburg" ], "_binaries": [ { "r": "4.6.1", "os": "mac", "version": "1.1.1", "date": "2026-09-10T08:41:07.000Z", "arch": "x86_64", "commit": "b929bb4e8670df62aa281ab10ae87263b0db3045", "fileid": "https://r2.ropensci.org/e5aa2373475045fcb5dd12e3c2ac73ad58a65d2d9a20bc15e658722a6b90a255", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wittenburg/actions/runs/34455813882" }, { "r": "4.7.0", "os": "linux", "version": "1.1.1", "date": "2026-10-11T15:33:18.000Z", "distro": "resolute", "arch": "aarch64", "commit": "b929bb4e8670df62aa281ab10ae87263b0db3045", "fileid": "https://r2.ropensci.org/cc56dda533ea8148d07ea956d8ec195fbd56790f21d1ba7e8b17e3d1d8de36df", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wittenburg/actions/runs/38151446447" }, { "r": "4.7.0", "os": "linux", "version": "1.1.1", "date": "2026-10-11T15:33:31.000Z", "distro": "resolute", "arch": "x86_64", "commit": "b929bb4e8670df62aa281ab10ae87263b0db3045", "fileid": "https://r2.ropensci.org/1c66f28b544f321ac404336db50540d1e40441da55dd3de82172b5fc7c1236a4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wittenburg/actions/runs/38151446447" }, { "r": "4.6.1", "os": "linux", "version": "1.1.1", "date": "2026-10-11T15:33:09.000Z", "distro": "resolute", "arch": "aarch64", "commit": "b929bb4e8670df62aa281ab10ae87263b0db3045", "fileid": "https://r2.ropensci.org/798680e78b397f91dad16a9679fa9eb96b1ac1f322e63cff039f836987f983fc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wittenburg/actions/runs/38151446447" }, { "r": "4.6.1", "os": "linux", "version": "1.1.1", "date": "2026-10-11T15:33:29.000Z", "distro": "resolute", "arch": "x86_64", "commit": "b929bb4e8670df62aa281ab10ae87263b0db3045", "fileid": "https://r2.ropensci.org/5985545593dcb820100333cd0e73a774609c8661430b5b23c4a488c9ad7af90b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wittenburg/actions/runs/38151446447" }, { "r": "4.5.3", "os": "mac", "version": "1.1.1", "date": "2026-10-11T15:37:09.000Z", "arch": "aarch64", "commit": "b929bb4e8670df62aa281ab10ae87263b0db3045", "fileid": "https://r2.ropensci.org/671bde5d787a4284af595fbfa3517948319c6afa080d12a748bbb0eb6d3ef17a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wittenburg/actions/runs/38151446447" }, { "r": "4.5.3", "os": "mac", "version": "1.1.1", "date": "2026-10-11T15:37:06.000Z", "arch": "x86_64", "commit": "b929bb4e8670df62aa281ab10ae87263b0db3045", "fileid": "https://r2.ropensci.org/1f5fb2f262f56db1c4f4e0301daf1d9482d5f1e653f55827f85b06befde65797", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wittenburg/actions/runs/38151446447" }, { "r": "4.6.1", "os": "mac", "version": "1.1.1", "date": "2026-10-11T15:36:41.000Z", "arch": "aarch64", "commit": "b929bb4e8670df62aa281ab10ae87263b0db3045", "fileid": "https://r2.ropensci.org/100c9eb59d02452ae9fed51cba028f0f9d74465f68f3374c79aca4796401fb51", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wittenburg/actions/runs/38151446447" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.1", "date": "2026-10-11T15:33:25.000Z", "arch": "emscripten", "commit": "b929bb4e8670df62aa281ab10ae87263b0db3045", "fileid": "https://r2.ropensci.org/888a037337455fd101e00d9c194fa0ea42c6fb66fceb18a684bbe06804d6e63b", "status": "success", "buildurl": "https://github.com/r-universe/wittenburg/actions/runs/38151446447" }, { "r": "4.7.0", "os": "win", "version": "1.1.1", "date": "2026-10-11T15:36:29.000Z", "arch": "aarch64", "commit": "b929bb4e8670df62aa281ab10ae87263b0db3045", "fileid": "https://r2.ropensci.org/2e993de12ba2aeac5b617b8071a0fed6905b141c964cc96c2f9cd3738a2af932", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wittenburg/actions/runs/38151446447" }, { "r": "4.7.0", "os": "win", "version": "1.1.1", "date": "2026-10-11T15:32:45.000Z", "arch": "x86_64", "commit": "b929bb4e8670df62aa281ab10ae87263b0db3045", "fileid": "https://r2.ropensci.org/a44398d20458067c0f891111d8426101c9b805880baa905455a0fdb26ddda1a8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wittenburg/actions/runs/38151446447" }, { "r": "4.5.3", "os": "win", "version": "1.1.1", "date": "2026-10-11T15:32:42.000Z", "arch": "x86_64", "commit": "b929bb4e8670df62aa281ab10ae87263b0db3045", "fileid": "https://r2.ropensci.org/083d247a612807a567b5eceea79e7e42cc8815a93b9abeaca3fe74d98cf5f400", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wittenburg/actions/runs/38151446447" }, { "r": "4.6.1", "os": "win", "version": "1.1.1", "date": "2026-10-11T15:36:43.000Z", "arch": "aarch64", "commit": "b929bb4e8670df62aa281ab10ae87263b0db3045", "fileid": "https://r2.ropensci.org/4551a0826fd58a64adf2207674f1db87f1a478921e5e299b679d0ec3f5551171", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wittenburg/actions/runs/38151446447" }, { "r": "4.6.1", "os": "win", "version": "1.1.1", "date": "2026-10-11T15:32:45.000Z", "arch": "x86_64", "commit": "b929bb4e8670df62aa281ab10ae87263b0db3045", "fileid": "https://r2.ropensci.org/0f56edfb78b413de4aa48ef9ac5cda3742fd2d9ba0a62ffeb290437676f1b32c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wittenburg/actions/runs/38151446447" } ] }