{ "_id": "6abe28a699f7aa8c6aa53010", "Package": "simcross", "Version": "0.10", "Date": "2026-06-08", "Title": "Simulate Experimental Crosses", "Description": "Simulate and plot general experimental crosses. The focus\nis on simulating genotypes with an aim towards flexibility\nrather than speed. Meiosis is simulated following the Stahl\nmodel, in which chiasma locations are the superposition of two\nprocesses: a proportion p coming from a process exhibiting no\ninterference, and the remainder coming from a process following\nthe chi-square model.", "Author": "Karl W Broman [aut, cre]\n()", "Maintainer": "Karl W Broman ", "Authors@R": "c(person(\"Karl W\", \"Broman\", role=c(\"aut\", \"cre\"),\nemail=\"broman@wisc.edu\", comment=c(ORCID = \"0000-0002-4914-6671\")))", "License": "GPL-3", "URL": "https://kbroman.org/simcross/, https://github.com/kbroman/simcross", "BugReports": "https://github.com/kbroman/simcross/issues", "VignetteBuilder": "knitr", "LazyData": "true", "Encoding": "UTF-8", "ByteCompile": "true", "Roxygen": "list(markdown=TRUE)", "Config/roxygen2/version": "8.0.0", "Repository": "https://kbroman.r-universe.dev", "Date/Publication": "2026-07-03 12:37:27 UTC", "RemoteUrl": "https://github.com/kbroman/simcross", "RemoteRef": "HEAD", "RemoteSha": "0e52522b5252cf3c0bf65e8f11a3dc2529cdec0a", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-01 09:24:44 UTC", "User": "root" }, "_user": "kbroman", "_type": "src", "_file": "simcross_0.10.tar.gz", "_fileid": "https://r2.ropensci.org/4bf698dcad7391d9b7df9cbcf1a503feb7262fab87fcb131079274348c8f182d", "_filesize": 495994, "_sha256": "4bf698dcad7391d9b7df9cbcf1a503feb7262fab87fcb131079274348c8f182d", "_expires": "2027-01-09T09:32:20.000Z", "_created": "2026-10-01T09:24:44.000Z", "_published": "2026-10-01T09:32:22.567Z", "_jobs": [ { "job": 110305041725, "time": 184, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11151882006" }, { "job": 110305041729, "time": 216, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11152596240" }, { "job": 110305041904, "time": 155, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11151753221" }, { "job": 110305041914, "time": 195, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11152146486" }, { "job": 110305041768, "time": 126, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11151688526" }, { "job": 110305041793, "time": 315, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11152201765" }, { "job": 110305041792, "time": 122, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11151892257" }, { "job": 110305041870, "time": 227, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11151693819" }, { "job": 110303262611, "time": 300, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11151614320" }, { "job": 110305041626, "time": 124, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11151946572" }, { "job": 110305041874, "time": 397, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11151594799" }, { "job": 110305041835, "time": 162, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11152450619" }, { "job": 110305041988, "time": 130, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11152695300" }, { "job": 110305042030, "time": 386, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11152361706" }, { "job": 110305041858, "time": 114, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11151644747" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/kbroman/actions/runs/36842025422", "_status": "success", "_upstream": "https://github.com/kbroman/simcross", "_commit": { "id": "0e52522b5252cf3c0bf65e8f11a3dc2529cdec0a", "author": "Karl Broman ", "committer": "Karl Broman ", "message": "avoid pasting of badges into vignette\n", "time": 1783082247 }, "_maintainer": { "name": "Karl W Broman", "email": "broman@wisc.edu", "login": "kbroman", "mastodon": "@kbroman@rstats.me", "orcid": "0000-0002-4914-6671", "description": "Professor in Dept of Biostatistics & Medical Informatics at UW–Madison. Applied statistician working on statistical genomics.\n", "uuid": 53972 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.1.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.12.17", "role": "Imports" }, { "package": "qtl", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" }, { "package": "roxygen2", "role": "Suggests" } ], "_owner": "kbroman", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-18", "n": 3 }, { "week": "2026-19", "n": 3 }, { "week": "2026-22", "n": 2 }, { "week": "2026-23", "n": 7 }, { "week": "2026-24", "n": 2 }, { "week": "2026-25", "n": 1 }, { "week": "2026-27", "n": 1 } ], "_tags": [ { "name": "0.8", "date": "2026-05-01" }, { "name": "0.10", "date": "2026-06-09" } ], "_stars": 6, "_contributors": [ { "user": "kbroman", "count": 283, "uuid": 53972 }, { "user": "jianan", "count": 14, "uuid": 1790598 }, { "user": "dominikmueller64", "count": 1, "uuid": 22307095 } ], "_userbio": { "uuid": 53972, "type": "user", "name": "Karl Broman", "followers": 1483, "description": "Professor in Dept of Biostatistics & Medical Informatics at UW–Madison. Applied statistician working on statistical genomics.\r\n" }, "_downloads": { "count": 373, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/simcross" }, "_mentions": 1, "_devurl": "https://github.com/kbroman/simcross", "_searchresults": 28, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/simcross.html" ], "_homeurl": "https://github.com/kbroman/simcross", "_realowner": "kbroman", "_cranurl": true, "_releases": [ { "version": "0.3-6", "date": "2020-09-24" }, { "version": "0.6", "date": "2023-11-29" }, { "version": "0.8", "date": "2026-05-01" }, { "version": "0.10", "date": "2026-06-09" } ], "_exports": [ "calc_Lstar", "CCcolors", "check_pedigree", "collapse_do_alleles", "convert2geno", "convert2geno_allchr", "create_parent", "cross", "get_geno", "plot_crosslines", "plot_ind", "sim_4way_pedigree", "sim_ail_pedigree", "sim_ail_pedigree_fix_n", "sim_crossovers", "sim_do_pedigree", "sim_do_pedigree_fix_n", "sim_dof1_pedigree", "sim_from_pedigree", "sim_from_pedigree_allchr", "sim_meiosis", "sim_ril_pedigree", "where_het" ], "_datasets": [ { "name": "AILped", "title": "Example AIL pedigree", "object": "AILped", "class": [ "data.frame" ], "fields": [ "id", "mom", "dad", "sex", "generation" ], "rows": 1254, "table": true, "tojson": true }, { "name": "mouseL_cox", "title": "Mouse chromosome lengths", "object": "mouseL_cox", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "mouseL_mgi", "title": "Mouse chromosome lengths", "object": "mouseL_mgi", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "AILped", "title": "Example AIL pedigree", "topics": [ "AILped" ] }, { "page": "calc_Lstar", "title": "Calculate adjusted chromosome length for obligate chiasma", "topics": [ "calc_Lstar" ] }, { "page": "CCcolors", "title": "Collaborative Cross colors", "topics": [ "CCcolors" ] }, { "page": "check_pedigree", "title": "Check a pedigree for errors", "topics": [ "check_pedigree" ] }, { "page": "collapse_do_alleles", "title": "Collapse alleles for simulated DO genotypes", "topics": [ "collapse_do_alleles" ] }, { "page": "convert2geno", "title": "Convert continuous allele information into marker genotypes", "topics": [ "convert2geno" ] }, { "page": "convert2geno_allchr", "title": "Convert continuous allele information into marker genotypes for multiple chromosomes", "topics": [ "convert2geno_allchr" ] }, { "page": "create_parent", "title": "Create a parent object", "topics": [ "create_parent" ] }, { "page": "cross", "title": "Cross two individuals", "topics": [ "cross" ] }, { "page": "get_geno", "title": "Get genotype at a single position", "topics": [ "get_geno" ] }, { "page": "mouseL_cox", "title": "Mouse chromosome lengths", "topics": [ "mouseL_cox" ] }, { "page": "mouseL_mgi", "title": "Mouse chromosome lengths", "topics": [ "mouseL_mgi" ] }, { "page": "plot_crosslines", "title": "Plot cross lines", "topics": [ "plot_crosslines" ] }, { "page": "plot_ind", "title": "Plot an individual", "topics": [ "plot_ind" ] }, { "page": "sim_4way_pedigree", "title": "Simulate pedigree for 4-way intercross", "topics": [ "sim_4way_pedigree" ] }, { "page": "sim_ail_pedigree", "title": "Simulate AIL pedigree", "topics": [ "sim_ail_pedigree" ] }, { "page": "sim_ail_pedigree_fix_n", "title": "Simulate AIL pedigree with fixed n", "topics": [ "sim_ail_pedigree_fix_n" ] }, { "page": "sim_crossovers", "title": "Simulate crossover locations using the Stahl model", "topics": [ "sim_crossovers" ] }, { "page": "sim_do_pedigree", "title": "Simulate a pedigree for Diversity Outbred mice", "topics": [ "sim_do_pedigree" ] }, { "page": "sim_do_pedigree_fix_n", "title": "Simulate a pedigree for Diversity Outbreds for a target sample size", "topics": [ "sim_do_pedigree_fix_n" ] }, { "page": "sim_dof1_pedigree", "title": "Simulate pedigree for F1 between diversity outbreds and another inbred line", "topics": [ "sim_dof1_pedigree" ] }, { "page": "sim_from_pedigree", "title": "Simulate genotypes for pedigree", "topics": [ "sim_from_pedigree" ] }, { "page": "sim_from_pedigree_allchr", "title": "Simulate genotypes for pedigree for multiple chromosomes", "topics": [ "sim_from_pedigree_allchr" ] }, { "page": "sim_meiosis", "title": "Simulate meiosis", "topics": [ "sim_meiosis" ] }, { "page": "sim_ril_pedigree", "title": "Generate a ril pedigree", "topics": [ "sim_ril_pedigree" ] }, { "page": "where_het", "title": "Find heterozygous regions", "topics": [ "where_het" ] } ], "_pkglogo": "https://github.com/kbroman/simcross/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/kbroman/simcross/raw/HEAD/README.md", "_rundeps": [ "Rcpp" ], "_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" } ], "_vignettes": [ { "source": "simcross.Rmd", "filename": "simcross.html", "title": "R/simcross User Guide", "engine": "knitr::rmarkdown", "headings": [ "Basic functions", "Generating pedigrees", "Example AIL pedigree matrix", "Checking a pedigree matrix", "RIL pedigree", "4-way cross pedigree", "AIL pedigree", "Diversity Outbred pedigree", "Simulating from a pedigree", "Generating marker data", "Simulating multiple chromosomes", "References" ], "created": "2014-09-04 20:03:05", "modified": "2026-07-03 12:37:27", "commits": 48 } ], "_score": 6.070407321740119, "_indexed": true, "_nocasepkg": "simcross", "_universes": [ "kbroman" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.10", "date": "2026-10-01T09:27:51.000Z", "distro": "resolute", "arch": "aarch64", "commit": "0e52522b5252cf3c0bf65e8f11a3dc2529cdec0a", "fileid": "https://r2.ropensci.org/760648c0bcc14d7e1cf2a0d27e4ee2483f0f24fbdfe9448d8af381efdfd1e094", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kbroman/actions/runs/36842025422" }, { "r": "4.7.0", "os": "linux", "version": "0.10", "date": "2026-10-01T09:28:11.000Z", "distro": "resolute", "arch": "x86_64", "commit": "0e52522b5252cf3c0bf65e8f11a3dc2529cdec0a", "fileid": "https://r2.ropensci.org/f4a9243d15f78cfec54bf19c7a0d931717ba274052065bfbb28045181435dc9a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kbroman/actions/runs/36842025422" }, { "r": "4.6.1", "os": "linux", "version": "0.10", "date": "2026-10-01T09:27:24.000Z", "distro": "resolute", "arch": "aarch64", "commit": "0e52522b5252cf3c0bf65e8f11a3dc2529cdec0a", "fileid": "https://r2.ropensci.org/6ecc2d18b619cc76b09913619c59cebc1dba7ad5d71a6d4b268be6ae48453d63", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kbroman/actions/runs/36842025422" }, { "r": "4.6.1", "os": "linux", "version": "0.10", "date": "2026-10-01T09:27:54.000Z", "distro": "resolute", "arch": "x86_64", "commit": "0e52522b5252cf3c0bf65e8f11a3dc2529cdec0a", "fileid": "https://r2.ropensci.org/1e9213a632b7e44e592ea504dec4f626dbebecbbfeba5087b501b9b695b2f831", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kbroman/actions/runs/36842025422" }, { "r": "4.5.3", "os": "mac", "version": "0.10", "date": "2026-10-01T09:26:56.000Z", "arch": "aarch64", "commit": "0e52522b5252cf3c0bf65e8f11a3dc2529cdec0a", "fileid": "https://r2.ropensci.org/f595745d09e39ced3c035f411b187c03f173f5ac2a7dd7c48d19fc3575f7c15e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kbroman/actions/runs/36842025422" }, { "r": "4.5.3", "os": "mac", "version": "0.10", "date": "2026-10-01T09:29:09.000Z", "arch": "x86_64", "commit": "0e52522b5252cf3c0bf65e8f11a3dc2529cdec0a", "fileid": "https://r2.ropensci.org/65808b68fad0c9db309c25ab1b93a90609167bb9cf20c75d5c0ffc301324d0ed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kbroman/actions/runs/36842025422" }, { "r": "4.6.1", "os": "mac", "version": "0.10", "date": "2026-10-01T09:26:53.000Z", "arch": "aarch64", "commit": "0e52522b5252cf3c0bf65e8f11a3dc2529cdec0a", "fileid": "https://r2.ropensci.org/982384baa94a7980ee597204086075c0010a09d2460dcface52f2decb139e4d7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kbroman/actions/runs/36842025422" }, { "r": "4.6.1", "os": "mac", "version": "0.10", "date": "2026-10-01T09:27:40.000Z", "arch": "x86_64", "commit": "0e52522b5252cf3c0bf65e8f11a3dc2529cdec0a", "fileid": "https://r2.ropensci.org/fd0637e1de09859e818ab741462df87759cc40d9bf48f8aba2124e0e781f8bdd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kbroman/actions/runs/36842025422" }, { "r": "4.6.0", "os": "wasm", "version": "0.10", "date": "2026-10-01T09:27:17.000Z", "arch": "emscripten", "commit": "0e52522b5252cf3c0bf65e8f11a3dc2529cdec0a", "fileid": "https://r2.ropensci.org/ed8964a61fbe531bcd11c0f379c3731b7f10d4949f3b692962730bad3356ad44", "status": "success", "buildurl": "https://github.com/r-universe/kbroman/actions/runs/36842025422" }, { "r": "4.7.0", "os": "win", "version": "0.10", "date": "2026-10-01T09:30:34.000Z", "arch": "aarch64", "commit": "0e52522b5252cf3c0bf65e8f11a3dc2529cdec0a", "fileid": "https://r2.ropensci.org/b1d7ea7f348efd25fe0eba80d0d631deef6ea549c2329bc1b937a920d28aaeb4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kbroman/actions/runs/36842025422" }, { "r": "4.7.0", "os": "win", "version": "0.10", "date": "2026-10-01T09:26:12.000Z", "arch": "x86_64", "commit": "0e52522b5252cf3c0bf65e8f11a3dc2529cdec0a", "fileid": "https://r2.ropensci.org/8c89d8c427c57264527551d1d779d9c371be959c87bac751c9901e50f6e5a889", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kbroman/actions/runs/36842025422" }, { "r": "4.5.3", "os": "win", "version": "0.10", "date": "2026-10-01T09:26:28.000Z", "arch": "x86_64", "commit": "0e52522b5252cf3c0bf65e8f11a3dc2529cdec0a", "fileid": "https://r2.ropensci.org/bf06e1e748ee2897cc66214cb3b6c6bdf4c8aeb2ad2262eaf48858740f7b1317", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kbroman/actions/runs/36842025422" }, { "r": "4.6.1", "os": "win", "version": "0.10", "date": "2026-10-01T09:30:20.000Z", "arch": "aarch64", "commit": "0e52522b5252cf3c0bf65e8f11a3dc2529cdec0a", "fileid": "https://r2.ropensci.org/57300f8bd2c5e898fc0145cd508c5e5cd491fd0a54aa8dec68d8931f77835565", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kbroman/actions/runs/36842025422" }, { "r": "4.6.1", "os": "win", "version": "0.10", "date": "2026-10-01T09:26:09.000Z", "arch": "x86_64", "commit": "0e52522b5252cf3c0bf65e8f11a3dc2529cdec0a", "fileid": "https://r2.ropensci.org/b9eac02b29308ccd60055e70be9d2a69703b08c801ddd31dec7f1c705f3df74b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kbroman/actions/runs/36842025422" } ] }