{ "_id": "6a20133eb401979e7344992b", "Package": "hibayes", "Title": "Individual-Level, Summary-Level and Single-Step Bayesian\nRegression Model", "Version": "3.1.0", "Date": "2025-09-05", "Authors@R": "c(\nperson(\"Lilin\", \"Yin\", email = \"ylilin@163.com\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-4413-7976\")),\nperson(\"Haohao\", \"Zhang\", email = \"haohaozhang@whut.edu.cn\",\nrole = c(\"aut\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-7913-5228\")),\nperson(\"Xiaolei\", \"Liu\", email = \"xiaoleiliu@mail.hzau.edu.cn\",\nrole = c(\"aut\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-9954-1426\"))\n)", "Description": "A user-friendly tool to fit Bayesian regression models. It\ncan fit 3 types of Bayesian models using individual-level,\nsummary-level, and individual plus pedigree-level (single-step)\ndata for both Genomic prediction/selection (GS) and Genome-Wide\nAssociation Study (GWAS), it was designed to estimate joint\neffects and genetic parameters for a complex trait, including:\n(1) fixed effects and coefficients of covariates, (2)\nenvironmental random effects, and its corresponding variance,\n(3) genetic variance, (4) residual variance, (5) heritability,\n(6) genomic estimated breeding values (GEBV) for both genotyped\nand non-genotyped individuals, (7) SNP effect size, (8)\nphenotype/genetic variance explained (PVE) for single or\nmultiple SNPs, (9) posterior probability of association of the\ngenomic window (WPPA), (10) posterior inclusive probability\n(PIP). The functions are not limited, we will keep on going in\nenriching it with more features. References: Lilin Yin et al.\n(2025) ; Meuwissen et al. (2001)\n; Gustavo et al. (2013)\n; Habier et al. (2011)\n; Yi et al. (2008)\n; Zhou et al. (2013)\n; Moser et al. (2015)\n; Lloyd-Jones et al. (2019)\n; Henderson (1976)\n; Fernando et al. (2014)\n.", "License": "GPL-3", "Maintainer": "Lilin Yin ", "URL": "https://github.com/YinLiLin/hibayes", "BugReports": "https://github.com/YinLiLin/hibayes/issues", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "Roxygen": "list(markdown = TRUE)", "NeedsCompilation": "yes", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://yinlilin.r-universe.dev", "Date/Publication": "2025-09-06 14:20:21 UTC", "RemoteUrl": "https://github.com/yinlilin/hibayes", "RemoteRef": "HEAD", "RemoteSha": "d72cbe3dcdc9813ff0c19e46a40572ccb9cc9589", "Packaged": { "Date": "2026-06-03 11:35:13 UTC", "User": "root" }, "Author": "Lilin Yin [aut, cre, cph] (ORCID:\n),\nHaohao Zhang [aut, cph] (ORCID:\n),\nXiaolei Liu [aut, cph] (ORCID: )", "MD5sum": "e9ca1f5cc46d12896f011f1a45c962bf", "_user": "yinlilin", "_type": "src", "_file": "hibayes_3.1.0.tar.gz", "_fileid": "6d59e4e9522e18929770e5939254323d716ed7090016e181e22b1ffb62614d08", "_filesize": 337569, "_sha256": "6d59e4e9522e18929770e5939254323d716ed7090016e181e22b1ffb62614d08", "_created": "2026-06-03T11:35:13.000Z", "_published": "2026-06-03T11:42:54.655Z", "_distro": "noble", "_jobs": [ { "job": 79284745103, "time": 245, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "7383534328" }, { "job": 79284745040, "time": 213, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7383522854" }, { "job": 79284745026, "time": 217, "config": "linux-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7383524739" }, { "job": 79284745058, "time": 215, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7383523322" }, { "job": 79284745081, "time": 182, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7383504881" }, { "job": 79284745102, "time": 324, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7383556367" }, { "job": 79284745135, "time": 316, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7383540247" }, { "job": 79284745193, "time": 353, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7383563927" }, { "job": 79284028052, "time": 253, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7383447171" }, { "job": 79284745014, "time": 103, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 79284745133, "time": 177, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7383510192" }, { "job": 79284745131, "time": 256, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7383541539" }, { "job": 79284745030, "time": 258, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7383538862" } ], "_buildurl": "https://github.com/r-universe/yinlilin/actions/runs/26881937113", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/yinlilin/hibayes", "_commit": { "id": "d72cbe3dcdc9813ff0c19e46a40572ccb9cc9589", "author": "Lilin Yin ", "committer": "Lilin Yin ", "message": "v3.1.0\n", "time": 1757168421 }, "_maintainer": { "name": "Lilin Yin", "email": "ylilin@163.com", "login": "yinlilin", "description": "Quantitative Genetics and Statistical Genomics -- Keep smile to life & stay hungry for knowledge", "uuid": 12557293, "orcid": "0000-0003-4413-7976" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3.0", "role": "Depends" }, { "package": "bigmemory", "role": "Depends" }, { "package": "Matrix", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "version": ">= 0.9.600.0.0", "role": "LinkingTo" }, { "package": "RcppProgress", "role": "LinkingTo" }, { "package": "BH", "role": "LinkingTo" }, { "package": "bigmemory", "role": "LinkingTo" }, { "package": "Matrix", "role": "LinkingTo" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "CMplot", "role": "Imports" } ], "_owner": "yinlilin", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-36", "n": 1 } ], "_tags": [], "_stars": 58, "_contributors": [ { "user": "yinlilin", "count": 136, "uuid": 12557293 }, { "user": "hyacz", "count": 12, "uuid": 9551197 } ], "_userbio": { "uuid": 12557293, "type": "user", "name": "Lilin Yin", "description": "Quantitative Genetics and Statistical Genomics -- Keep smile to life & stay hungry for knowledge" }, "_downloads": { "count": 552, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/hibayes" }, "_mentions": 1, "_devurl": "https://github.com/yinlilin/hibayes", "_searchresults": 16, "_topics": [ "openblas", "cpp", "openmp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/hibayes.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/yinlilin/hibayes", "_realowner": "yinlilin", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2021-12-10" }, { "version": "1.0.1", "date": "2022-01-13" }, { "version": "1.1.0", "date": "2022-05-25" }, { "version": "2.0.0", "date": "2022-11-20" }, { "version": "3.0.0", "date": "2023-09-01" }, { "version": "3.0.1", "date": "2023-11-28" }, { "version": "3.0.2", "date": "2024-01-19" }, { "version": "3.0.3", "date": "2024-02-20" }, { "version": "3.1.0", "date": "2025-09-05" } ], "_exports": [ "CMplot", "ibrm", "ldmat", "new", "packageVersion", "read_plink", "read.delim", "read.table", "sbrm", "ssbrm", "write.table" ], "_help": [ { "page": "ibrm", "title": "Bayes model", "topics": [ "ibrm" ] }, { "page": "ldmat", "title": "LD variance-covariance matrix calculation", "topics": [ "ldmat" ] }, { "page": "read_plink", "title": "data load", "topics": [ "read_plink" ] }, { "page": "sbrm", "title": "SBayes model", "topics": [ "sbrm" ] }, { "page": "ssbrm", "title": "Single-step Bayes model", "topics": [ "ssbrm" ] } ], "_readme": "https://github.com/yinlilin/hibayes/raw/HEAD/README.md", "_rundeps": [ "BH", "bigmemory", "bigmemory.sri", "cli", "CMplot", "glue", "lattice", "lifecycle", "magrittr", "Matrix", "Rcpp", "RcppArmadillo", "RcppProgress", "rlang", "stringi", "stringr", "uuid", "vctrs" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_score": 4.666517980554881, "_indexed": true, "_nocasepkg": "hibayes", "_universes": [ "yinlilin" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.1.0", "date": "2026-06-03T11:39:07.000Z", "distro": "noble", "arch": "aarch64", "commit": "d72cbe3dcdc9813ff0c19e46a40572ccb9cc9589", "fileid": "90d53bf298f573a4c31364499a2e0c8dc1e79a0d7e51545fe94d3b452f2e5c25", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/yinlilin/actions/runs/26881937113" }, { "r": "4.7.0", "os": "linux", "version": "3.1.0", "date": "2026-06-03T11:38:36.000Z", "distro": "noble", "arch": "x86_64", "commit": "d72cbe3dcdc9813ff0c19e46a40572ccb9cc9589", "fileid": "22636806973710398cc8a0c3fe4bc0ccbddd96e40ae113cf61513f42786d4faf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yinlilin/actions/runs/26881937113" }, { "r": "4.6.0", "os": "linux", "version": "3.1.0", "date": "2026-06-03T11:38:39.000Z", "distro": "noble", "arch": "aarch64", "commit": "d72cbe3dcdc9813ff0c19e46a40572ccb9cc9589", "fileid": "1bd9cf4e23676f89725d5b20be968321d0f8d42d03efe1e1528798ca87d8e623", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/yinlilin/actions/runs/26881937113" }, { "r": "4.6.0", "os": "linux", "version": "3.1.0", "date": "2026-06-03T11:38:39.000Z", "distro": "noble", "arch": "x86_64", "commit": "d72cbe3dcdc9813ff0c19e46a40572ccb9cc9589", "fileid": "c2c48c3c3de0add6fc70b477133f9ccccb5eb01f00abcca77eb2c90a3c2a9773", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yinlilin/actions/runs/26881937113" }, { "r": "4.5.3", "os": "mac", "version": "3.1.0", "date": "2026-06-03T11:38:27.000Z", "arch": "aarch64", "commit": "d72cbe3dcdc9813ff0c19e46a40572ccb9cc9589", "fileid": "714b22e22ab2c6f46855ab13f546c13a9d3c2dc1304a6b86cdb9d415af70c501", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yinlilin/actions/runs/26881937113" }, { "r": "4.5.3", "os": "mac", "version": "3.1.0", "date": "2026-06-03T11:39:42.000Z", "arch": "x86_64", "commit": "d72cbe3dcdc9813ff0c19e46a40572ccb9cc9589", "fileid": "3899d284706d55b42896b176449618cc2de25038c79532e7fa37bd0aec68ba9b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yinlilin/actions/runs/26881937113" }, { "r": "4.6.0", "os": "mac", "version": "3.1.0", "date": "2026-06-03T11:39:01.000Z", "arch": "aarch64", "commit": "d72cbe3dcdc9813ff0c19e46a40572ccb9cc9589", "fileid": "ed3c8635392239d303ce726835531888c6effef1f3e8823358a79a6f7a9fbb4f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yinlilin/actions/runs/26881937113" }, { "r": "4.6.0", "os": "mac", "version": "3.1.0", "date": "2026-06-03T11:39:46.000Z", "arch": "x86_64", "commit": "d72cbe3dcdc9813ff0c19e46a40572ccb9cc9589", "fileid": "cf18414e11a2b0bcf6572f9f4386502321a5229acda100bf28fc42b598aa3deb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yinlilin/actions/runs/26881937113" }, { "r": "4.7.0", "os": "win", "version": "3.1.0", "date": "2026-06-03T11:37:51.000Z", "arch": "x86_64", "commit": "d72cbe3dcdc9813ff0c19e46a40572ccb9cc9589", "fileid": "b7e82e2d4a539fb5f5ed39118dd86ee18ee832b5a93e32dc113e18f506e53159", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yinlilin/actions/runs/26881937113" }, { "r": "4.5.3", "os": "win", "version": "3.1.0", "date": "2026-06-03T11:38:36.000Z", "arch": "x86_64", "commit": "d72cbe3dcdc9813ff0c19e46a40572ccb9cc9589", "fileid": "2ae25041bc4f90cb591aebf4118b7c6a37e49127c64664fcf1cb8d9f73414eca", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yinlilin/actions/runs/26881937113" }, { "r": "4.6.0", "os": "win", "version": "3.1.0", "date": "2026-06-03T11:38:09.000Z", "arch": "x86_64", "commit": "d72cbe3dcdc9813ff0c19e46a40572ccb9cc9589", "fileid": "caebad567b6440fdb9d49910a3ca15fe73c097730141dfa69f72a78bae1f86af", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yinlilin/actions/runs/26881937113" } ] }