{
  "_id": "6a1acd8e1d7bb097a09df3e5",
  "Package": "graper",
  "Type": "Package",
  "Title": "Adaptive penalization in high-dimensional regression and\nclassification with external covariates using variational Bayes",
  "Version": "1.29.0",
  "Authors@R": "c(person(\"Britta\", \"Velten\", email = \"britta.velten@gmail.com\", \nrole = c(\"aut\", \"cre\")),\nperson(\"Wolfgang\", \"Huber\", role=c(\"aut\"), email=\"wolfgang.huber@embl.de\"))",
  "Date": "2018-10-26",
  "License": "GPL (>= 2)",
  "Description": "This package enables regression and classification on\nhigh-dimensional data with different relative strengths of\npenalization for different feature groups, such as different\nassays or omic types. The optimal relative strengths are chosen\nadaptively. Optimisation is performed using a variational Bayes\napproach.",
  "Encoding": "UTF-8",
  "biocViews": "Regression, Bayesian, Classification",
  "RoxygenNote": "6.1.1",
  "VignetteBuilder": "knitr",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:49:19 UTC",
  "RemoteUrl": "https://github.com/bioc/graper",
  "RemoteRef": "HEAD",
  "RemoteSha": "ba611e23de4b1648faa7e7e7b283aaa7d4291eaf",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-30 08:10:14 UTC",
    "User": "root"
  },
  "Author": "Britta Velten [aut, cre],\nWolfgang Huber [aut]",
  "Maintainer": "Britta Velten <britta.velten@gmail.com>",
  "MD5sum": "98ba846704da999bf1c4893d3a3cbdf7",
  "_user": "bioc",
  "_type": "src",
  "_file": "graper_1.29.0.tar.gz",
  "_fileid": "c78a707bbdebcd0d75a609c5448c1889a0b3d45acb93357cd499a4dd1507de7f",
  "_filesize": 674503,
  "_sha256": "c78a707bbdebcd0d75a609c5448c1889a0b3d45acb93357cd499a4dd1507de7f",
  "_created": "2026-05-30T08:10:14.000Z",
  "_published": "2026-05-30T11:44:14.844Z",
  "_jobs": [
    {
      "job": 78635693441,
      "time": 169,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306742732"
    },
    {
      "job": 78635693461,
      "time": 311,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306755805"
    },
    {
      "job": 78635693459,
      "time": 197,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306745273"
    },
    {
      "job": 78635693485,
      "time": 178,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306743543"
    },
    {
      "job": 78635693458,
      "time": 185,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306744119"
    },
    {
      "job": 78635693471,
      "time": 131,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307928330"
    },
    {
      "job": 78635693452,
      "time": 461,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306770251"
    },
    {
      "job": 78635693457,
      "time": 146,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307929958"
    },
    {
      "job": 78635693529,
      "time": 376,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306762603"
    },
    {
      "job": 78635492155,
      "time": 240,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306725685"
    },
    {
      "job": 78635693449,
      "time": 116,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306737720"
    },
    {
      "job": 78635693434,
      "time": 206,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306746086"
    },
    {
      "job": 78635693426,
      "time": 157,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306741350"
    },
    {
      "job": 78635693437,
      "time": 170,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306742731"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 8
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678822418",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/graper",
  "_commit": {
    "id": "ba611e23de4b1648faa7e7e7b283aaa7d4291eaf",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380559
  },
  "_maintainer": {
    "name": "Britta Velten",
    "email": "britta.velten@gmail.com",
    "login": "bv2",
    "description": "Tenure-Track professor for Multifactorial Data Analysis and Machine Learning at University Heidelberg",
    "uuid": 24564697
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "BH",
      "role": "LinkingTo"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-26",
      "n": 2
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.29.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.28.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "regression",
    "bayesian",
    "classification",
    "openblas",
    "cpp"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 370,
    "source": "https://www.bioconductor.org/packages/stats/bioc/graper"
  },
  "_mentions": 1,
  "_searchresults": 21,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/graper.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "getPIPs",
    "graper",
    "makeExampleData",
    "makeExampleDataWithUnequalGroups",
    "plotELBO",
    "plotGroupPenalties",
    "plotPosterior"
  ],
  "_help": [
    {
      "page": "coef.graper",
      "title": "Get estimated coefficients from a graper object",
      "topics": [
        "coef.graper"
      ]
    },
    {
      "page": "getPIPs",
      "title": "Get posterior inclusion probabilities per feature",
      "topics": [
        "getPIPs"
      ]
    },
    {
      "page": "graper",
      "title": "Fit a regression model with graper",
      "topics": [
        "graper"
      ]
    },
    {
      "page": "makeExampleData",
      "title": "Simulate example data from the graper model",
      "topics": [
        "makeExampleData"
      ]
    },
    {
      "page": "makeExampleDataWithUnequalGroups",
      "title": "Simulate example data from the graper model with groups of unequal size",
      "topics": [
        "makeExampleDataWithUnequalGroups"
      ]
    },
    {
      "page": "plotELBO",
      "title": "Plot evidence lower bound",
      "topics": [
        "plotELBO"
      ]
    },
    {
      "page": "plotGroupPenalties",
      "title": "Plot group-wise penalties",
      "topics": [
        "plotGroupPenalties"
      ]
    },
    {
      "page": "plotPosterior",
      "title": "Plot posterior distributions",
      "topics": [
        "plotPosterior"
      ]
    },
    {
      "page": "predict.graper",
      "title": "Predict response on new data",
      "topics": [
        "predict.graper"
      ]
    },
    {
      "page": "print.graper",
      "title": "Print a graper object",
      "topics": [
        "print.graper"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/graper/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "cli",
    "cowplot",
    "cpp11",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "Matrix",
    "matrixStats",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "S7",
    "scales",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_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"
    }
  ],
  "_vignettes": [
    {
      "source": "example_linear.Rmd",
      "filename": "example_linear.html",
      "title": "Vignette illustrating the use of graper in linear regression",
      "author": "Britta Velten",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Make example data with four groups",
        "Fit the model",
        "Training diagnostics",
        "Posterior distribtions",
        "Model coefficients and intercept",
        "Posterior inclusion probabilities per feature",
        "Group-wise penalites",
        "Make predictions"
      ],
      "created": "2018-07-13 10:17:14",
      "modified": "2019-01-29 16:43:47",
      "commits": 16
    },
    {
      "source": "example_logistic.Rmd",
      "filename": "example_logistic.html",
      "title": "Vignette illustrating the use of graper in logistic regression",
      "author": "Britta Velten",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Make example data with four groups",
        "Fit the model",
        "Posterior distribtions",
        "Model coefficients and intercept",
        "Make predictions"
      ],
      "created": "2018-10-01 13:19:33",
      "modified": "2019-06-20 12:13:59",
      "commits": 15
    }
  ],
  "_score": 4.799340549453582,
  "_indexed": true,
  "_nocasepkg": "graper",
  "_universes": [
    "bioc",
    "bv2"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-05-30T08:15:12.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "ba611e23de4b1648faa7e7e7b283aaa7d4291eaf",
      "fileid": "165dab15727de3b6cb077336ffc853a5a0f7e1d3c24c6b761695ee37f86fe2d1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678822418"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-05-30T08:13:14.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "ba611e23de4b1648faa7e7e7b283aaa7d4291eaf",
      "fileid": "21126e92e3fd3256dd1462cc21b9bb37badbc0e5e51a94ee3b8c331d5e703343",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678822418"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-05-30T08:13:02.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "ba611e23de4b1648faa7e7e7b283aaa7d4291eaf",
      "fileid": "006c2021922768d7280db33cef43d50a072e93644ea31333e236ddcf1867093f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678822418"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-05-30T08:13:00.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "ba611e23de4b1648faa7e7e7b283aaa7d4291eaf",
      "fileid": "be03a2184fe94a656ee1ef729876e835935760d10060674e4c0a43a4a5b4094b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678822418"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-05-30T11:42:51.000Z",
      "arch": "aarch64",
      "commit": "ba611e23de4b1648faa7e7e7b283aaa7d4291eaf",
      "fileid": "625b3fed104961ba1f29fbc1d115922ed86c004bcaf76fa579dccac7951db2dc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678822418"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-05-30T08:15:55.000Z",
      "arch": "x86_64",
      "commit": "ba611e23de4b1648faa7e7e7b283aaa7d4291eaf",
      "fileid": "3790ad8c8c0a2283dc43f0eda1235b5c3425f40277d4da110d2407ab34abd2da",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678822418"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-05-30T11:43:04.000Z",
      "arch": "aarch64",
      "commit": "ba611e23de4b1648faa7e7e7b283aaa7d4291eaf",
      "fileid": "fce49d41a5e1dec2bd53ec39ac6e900e2d933cb1b1b82ab388ef86bdc375915e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678822418"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-05-30T08:14:40.000Z",
      "arch": "x86_64",
      "commit": "ba611e23de4b1648faa7e7e7b283aaa7d4291eaf",
      "fileid": "8e4da34cd22d6298bcf65ab6650e7492d1beb9683b3405f64e0f08ff045bde71",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678822418"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.29.0",
      "date": "2026-05-30T08:12:40.000Z",
      "arch": "emscripten",
      "commit": "ba611e23de4b1648faa7e7e7b283aaa7d4291eaf",
      "fileid": "3d4dae2928e7a0efd38e99e981cf45331fb5a00206d3c3bc78970067ecc1cc80",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678822418"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-05-30T08:13:01.000Z",
      "arch": "x86_64",
      "commit": "ba611e23de4b1648faa7e7e7b283aaa7d4291eaf",
      "fileid": "c7676b2c5d3751dadd0a454efecdc4d3ad8cba5b4fe5abe5036fdec6677a070f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678822418"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-05-30T08:12:04.000Z",
      "arch": "x86_64",
      "commit": "ba611e23de4b1648faa7e7e7b283aaa7d4291eaf",
      "fileid": "4d9a3675b6883099c672139768b0147b804d3c522b463d8a0d20b16ee407072a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678822418"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-05-30T08:12:14.000Z",
      "arch": "x86_64",
      "commit": "ba611e23de4b1648faa7e7e7b283aaa7d4291eaf",
      "fileid": "321caa40359e7823cd79522f6c85c2e5c870ca7f04c32e8253e09cfda249d7ee",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678822418"
    }
  ]
}