{ "_id": "6a17edd5acfb0bcc41da5017", "Package": "beam", "Type": "Package", "Title": "Fast Bayesian Inference in Large Gaussian Graphical Models", "Version": "2.0.4", "Date": "2025-03-14", "Author": "Gwenael G.R. Leday [cre, aut], Ilaria Speranza [aut], Harry\nGray [ctb]", "Authors@R": "c(person(\"Gwenael G.R.\",\"Leday\", role=c(\"cre\", \"aut\"), email=\"gwenael.leday@proton.me\"), person(\"Ilaria\", \"Speranza\", role = \"aut\"), person(\"Harry\", \"Gray\", role = \"ctb\"))", "Maintainer": "Gwenael G.R. Leday ", "Description": "Fast Bayesian inference of marginal and conditional\nindependence structures from high-dimensional data. Leday and\nRichardson (2019), Biometrics, .", "LazyLoad": "yes", "License": "GPL (>=2.0)", "LazyData": "TRUE", "NeedsCompilation": "yes", "RoxygenNote": "7.3.2", "URL": "https://github.com/gleday/beam", "Encoding": "UTF-8", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://gleday.r-universe.dev", "Date/Publication": "2026-02-27 12:42:45 UTC", "RemoteUrl": "https://github.com/gleday/beam", "RemoteRef": "HEAD", "RemoteSha": "31e6e2faa75c90936b6fc4c8a160d0b3925437d4", "Packaged": { "Date": "2026-05-28 07:03:33 UTC", "User": "root" }, "MD5sum": "8bc65f5e5131ca6323016cd6c0f299a2", "_user": "gleday", "_type": "src", "_file": "beam_2.0.4.tar.gz", "_fileid": "78e219fb668b5592375c1cd5a4d381458cf501af000ee617516174a2fccfad71", "_filesize": 677237, "_sha256": "78e219fb668b5592375c1cd5a4d381458cf501af000ee617516174a2fccfad71", "_created": "2026-05-28T07:03:33.000Z", "_published": "2026-05-28T07:25:09.007Z", "_distro": "noble", "_jobs": [ { "job": 78240554427, "time": 161, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7259709023" }, { "job": 78240554482, "time": 171, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7259711895" }, { "job": 78240554380, "time": 166, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7259710867" }, { "job": 78240554345, "time": 168, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7259710786" }, { "job": 78240554358, "time": 233, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7259775765" }, { "job": 78240554473, "time": 280, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7260009593" }, { "job": 78240554344, "time": 394, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7259841898" }, { "job": 78240554353, "time": 272, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7259941631" }, { "job": 78240073899, "time": 217, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7259666964" }, { "job": 78240554310, "time": 621, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "" }, { "job": 78240554343, "time": 146, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7259704756" }, { "job": 78240554398, "time": 348, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7259760563" }, { "job": 78240554367, "time": 146, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7259704677" } ], "_buildurl": "https://github.com/r-universe/gleday/actions/runs/26559876158", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/gleday/beam", "_commit": { "id": "31e6e2faa75c90936b6fc4c8a160d0b3925437d4", "author": "gleday ", "committer": "gleday ", "message": "update R CMD check yaml\n", "time": 1772196165 }, "_maintainer": { "name": "Gwenael G.R. Leday", "email": "gwenael.leday@proton.me", "login": "gleday", "description": "Statistician | Data Science, Machine Learning & High-Dimensional Data Analysis", "uuid": 11835850 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "BH", "role": "LinkingTo" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "fdrtool", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "knitr", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "assertthat", "role": "Imports" }, { "package": "covr", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "gleday", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-36", "n": 4 }, { "week": "2025-38", "n": 2 }, { "week": "2026-09", "n": 4 } ], "_tags": [], "_topics": [ "bayesian-inference", "covariance-matrix-estimation", "empirical-bayes", "graphical-models", "high-dimensional-inference", "machine-learning", "network-analysis", "precision-matrix-estimation", "statistics", "openblas", "cpp" ], "_stars": 0, "_contributors": [ { "user": "gleday", "count": 38, "uuid": 11835850 }, { "user": "gehoffman", "count": 1, "uuid": 8697260 } ], "_userbio": { "uuid": 11835850, "type": "user", "name": "Gwenael Leday", "description": "Statistician | Data Science, Machine Learning & High-Dimensional Data Analysis" }, "_downloads": { "count": 211, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/beam" }, "_devurl": "https://github.com/gleday/beam", "_searchresults": 18, "_rbuild": "4.6.0", "_assets": [ "extra/beam.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/gleday/beam", "_realowner": "gleday", "_cranurl": true, "_releases": [ { "version": "1.0", "date": "2018-03-28" }, { "version": "1.0.1", "date": "2018-04-18" }, { "version": "1.0.2", "date": "2018-05-03" }, { "version": "2.0.0", "date": "2020-01-26" }, { "version": "2.0.1", "date": "2020-01-28" }, { "version": "2.0.2", "date": "2020-05-29" }, { "version": "2.0.4", "date": "2025-04-11" } ], "_exports": [ "beam", "beam.select", "bgraph", "cond", "lightbeam", "marg", "mcor", "pcor", "plotAdj", "plotCor", "plotML", "postExpOmega", "postExpSigma", "print", "show", "summary", "ugraph" ], "_datasets": [ { "name": "TCPAprad", "title": "Protein expression data.", "object": "TCPAprad", "class": [ "matrix", "array" ], "fields": [ "X14.3.3_beta", "X14.3.3_epsilon", "X14.3.3_zeta", "X4E.BP1", "X4E.BP1_pS65", "X4E.BP1_pT37T46", "X4E.BP1_pT70", "X53BP1", "A.Raf_pS299", "ACC_pS79", "ACC1", "Acetyl.a.Tubulin.Lys40", "ACVRL1", "Akt", "Akt_pS473", "Akt_pT308", "AMPK_alpha", "AMPK_pT172", "Annexin.1", "Annexin_VII", "AR", "ARHI", "ASNS", "ATM", "B.Raf", "Bad_pS112", "Bak", "Bap1.c.4", "Bax", "Bcl.2", "Bcl.xL", "Beclin", "beta.Catenin", "Bid", "Bim", "BRCA2", "c.Jun_pS73", "c.Kit", "c.Met_pY1235", "c.Myc", "C.Raf", "C.Raf_pS338", "Caspase.7_cleavedD198", "Caveolin.1", "CD20", "CD31", "CD49b", "CDK1", "Chk1", "Chk1_pS345", "Chk2", "Chk2_pT68", "cIAP", "Claudin.7", "Collagen_VI", "Cyclin_B1", "Cyclin_D1", "Cyclin_E1", "Cyclin_E2", "DJ.1", "Dvl3", "E.Cadherin", "eEF2", "eEF2K", "EGFR", "EGFR_pY1068", "EGFR_pY1173", "eIF4E", "eIF4G", "ER.alpha", "ER.alpha_pS118", "ERK2", "ETS.1", "FASN", "Fibronectin", "FOXO3a", "FoxM1", "FOXO3a_pS318_S321", "G6PD", "GAB2", "GAPDH", "GATA3", "GSK3.alpha.beta", "GSK3.alpha.beta_pS21_S9", "GSK3_pS9", "HER2", "HER2_pY1248", "HER3", "HER3_pY1289", "Heregulin", "HSP70", "IGFBP2", "INPP4B", "IRS1", "JNK_pT183_Y185", "JNK2", "Ku80", "Lck", "LKB1", "MAPK_pT202_Y204", "MEK1", "MEK1_pS217_S221", "MIG.6", "Mre11", "MSH2", "MSH6", "mTOR", "mTOR_pS2448", "MYH11", "Myosin.IIa_pS1943", "N.Cadherin", "N.Ras", "NDRG1_pT346", "NF.kB.p65_pS536", "NF2", "Notch1", "P.Cadherin", "p21", "p27", "p27_pT157", "p27_pT198", "p38_MAPK", "p38_pT180_Y182", "p53", "p62.LCK.ligand", "p70S6K", "p70S6K_pT389", "p90RSK", "p90RSK_pT359_S363", "PAI.1", "Paxillin", "PCNA", "PDCD4", "PDK1", "PDK1_pS241", "PEA.15", "PEA15_pS116", "PI3K.p110.alpha", "PI3K.p85", "PKC.alpha", "PKC.alpha_pS657", "PKC.delta_pS664", "PKC.pan_BetaII_pS660", "PR", "PRAS40_pT246", "PRDX1", "PREX1", "PTEN", "Rab11", "Rab.25", "Rad50", "Rad51", "Raptor", "Rb_pS807_S811", "RBM15", "Rictor", "Rictor_pT1135", "S6", "S6_pS235_S236", "S6_pS240_S244", "SCD1", "SF2", "Shc_pY317", "Smad1", "Smad3", "Smad4", "Src", "Src_pY416", "Src_pY527", "STAT3_pY705", "STAT5.alpha", "Stathmin", "Syk", "TAZ", "TFRC", "TIGAR", "Transglutaminase", "TSC1", "Tuberin", "Tuberin_pT1462", "VEGFR2", "VHL", "XBP1", "XRCC1", "YAP", "YAP_pS127", "YB.1", "YB.1_pS102", "JAB1" ], "rows": 164, "table": true, "tojson": true } ], "_help": [ { "page": "beam-package", "title": "Fast Bayesian Inference in Large Gaussian Graphical Models", "topics": [ "beam-package" ] }, { "page": "beam", "title": "Bayesian inference in large Gaussian graphical models", "topics": [ "beam" ] }, { "page": "beam-class", "title": "Class beam", "topics": [ "beam-class", "bgraph", "bgraph,beam-method", "cond", "cond,beam-method", "marg", "marg,beam-method", "mcor", "mcor,beam-method", "pcor", "pcor,beam-method", "plotCor", "plotCor,beam-method", "plotML", "plotML,beam-method", "postExpOmega", "postExpOmega,beam-method", "postExpSigma", "postExpSigma,beam-method", "print,beam-method", "show,beam-method", "summary,beam-method", "ugraph", "ugraph,beam-method" ] }, { "page": "beam.select", "title": "Edge selection with multiple testing and error control", "topics": [ "beam.select" ] }, { "page": "beam.select-class", "title": "Class beam.select", "topics": [ "beam.select-class", "bgraph,beam.select-method", "cond,beam.select-method", "marg,beam.select-method", "mcor,beam.select-method", "pcor,beam.select-method", "plotAdj", "plotAdj,beam.select-method", "plotML,beam.select-method", "print,beam.select-method", "show,beam.select-method", "summary,beam.select-method", "ugraph,beam.select-method" ] }, { "page": "lightbeam", "title": "Fast inference of a conditional independence graph", "topics": [ "lightbeam" ] }, { "page": "TCPAprad", "title": "Protein expression data.", "topics": [ "TCPAprad" ] } ], "_pkglogo": "https://github.com/gleday/beam/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/gleday/beam/raw/HEAD/README.md", "_rundeps": [ "assertthat", "BH", "cli", "cpp11", "evaluate", "fdrtool", "glue", "highr", "igraph", "knitr", "lattice", "lifecycle", "magrittr", "Matrix", "pkgconfig", "Rcpp", "RcppArmadillo", "rlang", "vctrs", "xfun", "yaml" ], "_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" } ], "_score": 3.431363764158987, "_indexed": true, "_nocasepkg": "beam", "_universes": [ "gleday" ], "_binaries": [ { "r": "4.6.0", "os": "wasm", "version": "2.0.4", "date": "2026-05-22T23:00:35.000Z", "arch": "emscripten", "commit": "31e6e2faa75c90936b6fc4c8a160d0b3925437d4", "fileid": "f8f3bf0631cefdb9590e83c3d4502cdf96b9074d20ce95f1fac3d71c7a8a7d21", "status": "success", "buildurl": "https://github.com/r-universe/gleday/actions/runs/25043965211" }, { "r": "4.7.0", "os": "linux", "version": "2.0.4", "date": "2026-05-28T07:06:06.000Z", "distro": "noble", "arch": "aarch64", "commit": "31e6e2faa75c90936b6fc4c8a160d0b3925437d4", "fileid": "8ac9fe7417a9e8c5aef637ca3883ba875954555bd683c420946281f3c14e91b7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/gleday/actions/runs/26559876158" }, { "r": "4.7.0", "os": "linux", "version": "2.0.4", "date": "2026-05-28T07:06:14.000Z", "distro": "noble", "arch": "x86_64", "commit": "31e6e2faa75c90936b6fc4c8a160d0b3925437d4", "fileid": "a5a9d5b4ac5a971fa6365126891210b6ca5f11be3a30b842c2d505b8808c42a8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/gleday/actions/runs/26559876158" }, { "r": "4.6.0", "os": "linux", "version": "2.0.4", "date": "2026-05-28T07:06:13.000Z", "distro": "noble", "arch": "aarch64", "commit": "31e6e2faa75c90936b6fc4c8a160d0b3925437d4", "fileid": "33a171628d8d7481d17ea763161aa7ecc8bbbfeaf63e23ea870570f6b0b40d69", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/gleday/actions/runs/26559876158" }, { "r": "4.6.0", "os": "linux", "version": "2.0.4", "date": "2026-05-28T07:06:18.000Z", "distro": "noble", "arch": "x86_64", "commit": "31e6e2faa75c90936b6fc4c8a160d0b3925437d4", "fileid": "9659ca8210639ea3df8284315863d6edef7c052f2a283ae73fbe636fb2e6c80f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/gleday/actions/runs/26559876158" }, { "r": "4.5.3", "os": "mac", "version": "2.0.4", "date": "2026-05-28T07:10:25.000Z", "arch": "aarch64", "commit": "31e6e2faa75c90936b6fc4c8a160d0b3925437d4", "fileid": "e25979a00fdd8bb8ff1891920c45af1d4b53aa58d0c1597c3a16d4efba8a4ea5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/gleday/actions/runs/26559876158" }, { "r": "4.5.3", "os": "mac", "version": "2.0.4", "date": "2026-05-28T07:23:19.000Z", "arch": "x86_64", "commit": "31e6e2faa75c90936b6fc4c8a160d0b3925437d4", "fileid": "9dcac74442be5016e4fff5fedce416232fa32126630d820cced281fc49429618", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/gleday/actions/runs/26559876158" }, { "r": "4.6.0", "os": "mac", "version": "2.0.4", "date": "2026-05-28T07:11:01.000Z", "arch": "aarch64", "commit": "31e6e2faa75c90936b6fc4c8a160d0b3925437d4", "fileid": "9f524ff78391bbe82f8d8e1146766185b468c555e1789e5ac319cb13af65b2d5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/gleday/actions/runs/26559876158" }, { "r": "4.6.0", "os": "mac", "version": "2.0.4", "date": "2026-05-28T07:19:33.000Z", "arch": "x86_64", "commit": "31e6e2faa75c90936b6fc4c8a160d0b3925437d4", "fileid": "dce95265f0f4253bafbe2b64c63600d3309ed66d5cb430a77a49319d69b68521", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/gleday/actions/runs/26559876158" }, { "r": "4.7.0", "os": "win", "version": "2.0.4", "date": "2026-05-28T07:05:18.000Z", "arch": "x86_64", "commit": "31e6e2faa75c90936b6fc4c8a160d0b3925437d4", "fileid": "1a405136b7ba44ea3ae656ebfbd3c1d654e3b5c463d0862e820803f4fe56111e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/gleday/actions/runs/26559876158" }, { "r": "4.5.3", "os": "win", "version": "2.0.4", "date": "2026-05-28T07:08:07.000Z", "arch": "x86_64", "commit": "31e6e2faa75c90936b6fc4c8a160d0b3925437d4", "fileid": "e23486d6d0645bdf8027cf4acfa2d69ad80f737dea5a20dcb66382898c6f3ce7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/gleday/actions/runs/26559876158" }, { "r": "4.6.0", "os": "win", "version": "2.0.4", "date": "2026-05-28T07:05:13.000Z", "arch": "x86_64", "commit": "31e6e2faa75c90936b6fc4c8a160d0b3925437d4", "fileid": "d1355c30a84fec0bfb989805c0336ae7a630771bc33fee045bee2e5df41a24ae", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/gleday/actions/runs/26559876158" } ] }