{
  "_id": "6a2e5d3a3efcd9bda430d796",
  "Package": "psbcSpeedUp",
  "Title": "Penalized Semiparametric Bayesian Cox Models",
  "Version": "2.1.1",
  "Authors@R": "c(person(\"Zhi\", \"Zhao\", role=c(\"aut\",\"cre\"), email = \"zhi.zhao@medisin.uio.no\"), \nperson(\"Manuela\", \"Zucknick\", role=c(\"aut\")),\nperson(\"Maral\", \"Saadati\", role=c(\"aut\")),\nperson(\"Axel\", \"Benner\", role=c(\"aut\")))",
  "Maintainer": "Zhi Zhao <zhi.zhao@medisin.uio.no>",
  "Description": "Algorithms to speed up the Bayesian Lasso Cox model (Lee\net al., Int J Biostat, 2011 <doi:10.2202/1557-4679.1301>) and\nthe Bayesian Lasso Cox with mandatory variables (Zucknick et\nal. Biometrical J, 2015 <doi:10.1002/bimj.201400160>).",
  "URL": "https://github.com/ocbe-uio/psbcSpeedUp",
  "BugReports": "https://github.com/ocbe-uio/psbcSpeedUp/issues",
  "License": "GPL-3",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "LazyData": "true",
  "NeedsCompilation": "yes",
  "SystemRequirements": "C++17",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev",
  "Repository": "https://ocbe-uio.r-universe.dev",
  "Date/Publication": "2025-09-30 15:24:10 UTC",
  "RemoteUrl": "https://github.com/ocbe-uio/psbcSpeedUp",
  "RemoteRef": "HEAD",
  "RemoteSha": "502743f25daa5c2b2a38247117b6b8ab65584e45",
  "Packaged": {
    "Date": "2026-06-14 07:41:14 UTC",
    "User": "root"
  },
  "Author": "Zhi Zhao [aut, cre],\nManuela Zucknick [aut],\nMaral Saadati [aut],\nAxel Benner [aut]",
  "MD5sum": "4b49dd6ae1947339642350482ea98bc6",
  "_user": "ocbe-uio",
  "_type": "src",
  "_file": "psbcSpeedUp_2.1.1.tar.gz",
  "_fileid": "6c77384ff43a00ae8371f0023ca41da8e5fabfcff40ee566ecb44dbbeeb08075",
  "_filesize": 541060,
  "_sha256": "6c77384ff43a00ae8371f0023ca41da8e5fabfcff40ee566ecb44dbbeeb08075",
  "_created": "2026-06-14T07:41:14.000Z",
  "_published": "2026-06-14T07:50:18.273Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 81259444380,
      "time": 473,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7618826988"
    },
    {
      "job": 81259444366,
      "time": 225,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7618790369"
    },
    {
      "job": 81259444370,
      "time": 177,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7618781639"
    },
    {
      "job": 81259444357,
      "time": 199,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7618786033"
    },
    {
      "job": 81259444379,
      "time": 111,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7618771328"
    },
    {
      "job": 81259444382,
      "time": 332,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7618806102"
    },
    {
      "job": 81259444322,
      "time": 121,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7618772536"
    },
    {
      "job": 81259444318,
      "time": 279,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7618797833"
    },
    {
      "job": 81259145088,
      "time": 284,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7618754495"
    },
    {
      "job": 81259444289,
      "time": 155,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7618778224"
    },
    {
      "job": 81259444312,
      "time": 168,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7618780112"
    },
    {
      "job": 81259444320,
      "time": 163,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7618779352"
    },
    {
      "job": 81259444314,
      "time": 174,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7618781227"
    }
  ],
  "_buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/27492105934",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/ocbe-uio/psbcSpeedUp",
  "_commit": {
    "id": "502743f25daa5c2b2a38247117b6b8ab65584e45",
    "author": "zhizuio <zhi.zhao@medisin.uio.no>",
    "committer": "zhizuio <zhi.zhao@medisin.uio.no>",
    "message": "remove output folders\n",
    "time": 1759245850
  },
  "_maintainer": {
    "name": "Zhi Zhao",
    "email": "zhi.zhao@medisin.uio.no",
    "login": "zhizuio",
    "description": "",
    "uuid": 39630023
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "version": ">= 0.9.000",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "GGally",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "survival",
      "role": "Imports"
    },
    {
      "package": "riskRegression",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "ocbe-uio",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-39",
      "n": 2
    },
    {
      "week": "2025-40",
      "n": 19
    }
  ],
  "_tags": [
    {
      "name": "v2.1.0",
      "date": "2025-09-30"
    }
  ],
  "_topics": [
    "bayesian-cox-models",
    "bayesian-lasso",
    "omics-data",
    "survival-analysis",
    "openblas",
    "cpp",
    "openmp"
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "zhizuio",
      "count": 56,
      "uuid": 39630023
    },
    {
      "user": "fatihki",
      "count": 1,
      "uuid": 95696168
    }
  ],
  "_userbio": {
    "uuid": 58079878,
    "type": "organization",
    "name": "Oslo Centre for Biostatistics and Epidemiology",
    "followers": 58,
    "description": "This is where we host most of the scientific software we produce at OCBE, a joint center between the University of Oslo and the Oslo University Hospital."
  },
  "_downloads": {
    "count": 232,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/psbcSpeedUp"
  },
  "_devurl": "https://github.com/ocbe-uio/psbcspeedup",
  "_searchresults": 0,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/psbcSpeedUp.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ocbe-uio/psbcspeedup",
  "_realowner": "ocbe-uio",
  "_cranurl": true,
  "_releases": [
    {
      "version": "2.0.3",
      "date": "2023-10-02"
    },
    {
      "version": "2.0.4",
      "date": "2023-10-12"
    },
    {
      "version": "2.0.5",
      "date": "2023-12-08"
    },
    {
      "version": "2.0.6",
      "date": "2024-03-21"
    },
    {
      "version": "2.0.7",
      "date": "2024-07-01"
    },
    {
      "version": "2.1.0",
      "date": "2025-10-03"
    }
  ],
  "_exports": [
    "plotBrier",
    "psbcSpeedUp"
  ],
  "_datasets": [
    {
      "name": "exampleData",
      "title": "Simulated data set",
      "object": "exampleData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "coef.psbcSpeedUp",
      "title": "coef method for class 'psbcSpeedUp'",
      "topics": [
        "coef.psbcSpeedUp"
      ]
    },
    {
      "page": "exampleData",
      "title": "Simulated data set",
      "topics": [
        "exampleData"
      ]
    },
    {
      "page": "plot.psbcSpeedUp",
      "title": "create a plot of estimated coefficients",
      "topics": [
        "plot.psbcSpeedUp"
      ]
    },
    {
      "page": "plotBrier",
      "title": "Time-dependent Brier scores",
      "topics": [
        "plotBrier"
      ]
    },
    {
      "page": "predict.psbcSpeedUp",
      "title": "Predict survival risk",
      "topics": [
        "predict.psbcSpeedUp"
      ]
    },
    {
      "page": "psbcSpeedUp",
      "title": "Function to Fit the Bayesian Cox Lasso Model",
      "topics": [
        "psbcSpeedUp"
      ]
    }
  ],
  "_readme": "https://github.com/ocbe-uio/psbcSpeedUp/raw/HEAD/README.md",
  "_rundeps": [
    "backports",
    "base64enc",
    "bslib",
    "cachem",
    "checkmate",
    "cli",
    "cluster",
    "cmprsk",
    "codetools",
    "colorspace",
    "cpp11",
    "crayon",
    "data.table",
    "diagram",
    "digest",
    "doParallel",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "forcats",
    "foreach",
    "foreign",
    "Formula",
    "fs",
    "future",
    "future.apply",
    "generics",
    "GGally",
    "ggplot2",
    "ggstats",
    "glmnet",
    "globals",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "Hmisc",
    "hms",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "lattice",
    "lava",
    "lifecycle",
    "listenv",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "memoise",
    "mets",
    "mime",
    "multcomp",
    "mvtnorm",
    "nlme",
    "nnet",
    "numDeriv",
    "parallelly",
    "patchwork",
    "pillar",
    "pkgconfig",
    "plotrix",
    "polspline",
    "prettyunits",
    "prodlim",
    "progress",
    "progressr",
    "Publish",
    "purrr",
    "quantreg",
    "R6",
    "ranger",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "riskRegression",
    "rlang",
    "rmarkdown",
    "rms",
    "rpart",
    "rstudioapi",
    "S7",
    "sandwich",
    "sass",
    "scales",
    "shape",
    "SparseM",
    "SQUAREM",
    "stringi",
    "stringr",
    "survival",
    "TH.data",
    "tibble",
    "tidyr",
    "tidyselect",
    "timereg",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "yaml",
    "zoo"
  ],
  "_sysdeps": [
    {
      "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"
    }
  ],
  "_vignettes": [
    {
      "source": "BayesCox.Rmd",
      "filename": "BayesCox.html",
      "title": "Penalized Semiparametric Bayesian Cox Models",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Examples",
        "Run a Bayesian Lasso Cox with mandatory variables",
        "Plot posterior estimates of regression coefficients",
        "Plot time-dependent Brier scores",
        "Predict survival probabilities and cumulative hazards",
        "References"
      ],
      "created": "2023-12-08 00:02:55",
      "modified": "2025-09-30 15:24:10",
      "commits": 5
    }
  ],
  "_score": 4.477121254719663,
  "_indexed": true,
  "_nocasepkg": "psbcspeedup",
  "_universes": [
    "ocbe-uio",
    "zhizuio"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.1.1",
      "date": "2026-06-14T07:48:54.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "502743f25daa5c2b2a38247117b6b8ab65584e45",
      "fileid": "32729d2badb59e9b37bfd97be738235e2a9ed1006cadcf020c15b96c7884c34e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/27492105934"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.1.1",
      "date": "2026-06-14T07:44:42.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "502743f25daa5c2b2a38247117b6b8ab65584e45",
      "fileid": "06a773a4b5f9a1d4aae55bc3d99d8a15a57e619d0be7a63d228206ab1295f51a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/27492105934"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.1.1",
      "date": "2026-06-14T07:43:59.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "502743f25daa5c2b2a38247117b6b8ab65584e45",
      "fileid": "81212c4f98d44233d7823d47d4dc51e92323066aac0c29e7f53eee427604c151",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/27492105934"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.1.1",
      "date": "2026-06-14T07:44:18.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "502743f25daa5c2b2a38247117b6b8ab65584e45",
      "fileid": "68843511b93f7ce7c7b922e30b36273c865afa887ccc89988a9a241d00c9de06",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/27492105934"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.1.1",
      "date": "2026-06-14T07:43:15.000Z",
      "arch": "aarch64",
      "commit": "502743f25daa5c2b2a38247117b6b8ab65584e45",
      "fileid": "ea630e8e9d00c5b49873342b5ff00b71571ddc472047325872ecacb169222d20",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/27492105934"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.1.1",
      "date": "2026-06-14T07:45:45.000Z",
      "arch": "x86_64",
      "commit": "502743f25daa5c2b2a38247117b6b8ab65584e45",
      "fileid": "5e445c1672a1cbb625da4e2a22a82ba9f0761bd98fe60c4ae2299b3477ec60a5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/27492105934"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.1.1",
      "date": "2026-06-14T07:43:17.000Z",
      "arch": "aarch64",
      "commit": "502743f25daa5c2b2a38247117b6b8ab65584e45",
      "fileid": "04da52178d9f6e5f67567cf085a56c2486f0cd83707cc9dc7c7ce2d256169125",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/27492105934"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.1.1",
      "date": "2026-06-14T07:43:29.000Z",
      "arch": "x86_64",
      "commit": "502743f25daa5c2b2a38247117b6b8ab65584e45",
      "fileid": "f8b93b8f5385968d6eb6af5da83c4544e185a064b69311cda2f08d5d90194777",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/27492105934"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.1.1",
      "date": "2026-06-14T07:44:18.000Z",
      "arch": "emscripten",
      "commit": "502743f25daa5c2b2a38247117b6b8ab65584e45",
      "fileid": "5fcf5bd012d6cb4dc51f917d3bf0f7becf445564ea64be23eadf3f27dfd0e8da",
      "status": "success",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/27492105934"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.1.1",
      "date": "2026-06-14T07:43:07.000Z",
      "arch": "x86_64",
      "commit": "502743f25daa5c2b2a38247117b6b8ab65584e45",
      "fileid": "fc4b417f0ed5a58987f665179cbe111a4c10d78db427d71ebc0cb0028b865fde",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/27492105934"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.1.1",
      "date": "2026-06-14T07:43:00.000Z",
      "arch": "x86_64",
      "commit": "502743f25daa5c2b2a38247117b6b8ab65584e45",
      "fileid": "04d103cb39eb4594d8ebb66834e44f79441d65b4069d8fe115235ace4bfd216a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/27492105934"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.1.1",
      "date": "2026-06-14T07:43:23.000Z",
      "arch": "x86_64",
      "commit": "502743f25daa5c2b2a38247117b6b8ab65584e45",
      "fileid": "895347df72d1b3276c8a0c0e2ac423b25f1d96a43fc73434d66c8b5576f233e7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/27492105934"
    }
  ]
}