{
  "_id": "6a3637003efcd9bda43f8ae2",
  "Package": "xrnet",
  "Type": "Package",
  "Title": "Hierarchical Regularized Regression",
  "Version": "1.0.1",
  "Authors@R": "c(\nperson(\"Garrett\", \"Weaver\", email = \"gweaverdev@icloud.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-9918-8386\")),\nperson(\"Dixin\", \"Shen\", email = \"dixinshe@usc.edu\", role = c(\"aut\")),\nperson(\"Juan Pablo\", \"Lewinger\", email = \"lewinger@usc.edu\", role = c(\"ctb\", \"ths\")))",
  "URL": "https://github.com/USCbiostats/xrnet,\nhttps://uscbiostats.github.io/xrnet/",
  "Description": "Fits hierarchical regularized regression models to\nincorporate potentially informative external data, Weaver and\nLewinger (2019) <doi:10.21105/joss.01761>. Utilizes coordinate\ndescent to efficiently fit regularized regression models both\nwith and without external information with the most common\npenalties used in practice (i.e. ridge, lasso, elastic net).\nSupport for standard R matrices, sparse matrices and big.matrix\nobjects.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.1",
  "BugReports": "https://github.com/USCbiostats/xrnet/issues",
  "Repository": "https://uscbiostats.r-universe.dev",
  "Date/Publication": "2025-12-17 17:43:44 UTC",
  "RemoteUrl": "https://github.com/uscbiostats/xrnet",
  "RemoteRef": "HEAD",
  "RemoteSha": "e171fe742488a548e8e461b7a5398ffd308fa053",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-20 06:36:34 UTC",
    "User": "root"
  },
  "Author": "Garrett Weaver [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-9918-8386>),\nDixin Shen [aut],\nJuan Pablo Lewinger [ctb, ths]",
  "Maintainer": "Garrett Weaver <gweaverdev@icloud.com>",
  "MD5sum": "72f0023483aeec8d69b65df86c750c0d",
  "_user": "uscbiostats",
  "_type": "src",
  "_file": "xrnet_1.0.1.tar.gz",
  "_fileid": "c10a5ad7df47b9d0e144f3922875d93eac8e210a0a23c29720a1492730972d88",
  "_filesize": 522485,
  "_sha256": "c10a5ad7df47b9d0e144f3922875d93eac8e210a0a23c29720a1492730972d88",
  "_created": "2026-06-20T06:36:34.000Z",
  "_published": "2026-06-20T06:45:20.676Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 82462399830,
      "time": 167,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7762894167"
    },
    {
      "job": 82462399852,
      "time": 178,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7762895112"
    },
    {
      "job": 82462399853,
      "time": 166,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7762894024"
    },
    {
      "job": 82462399850,
      "time": 180,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7762895252"
    },
    {
      "job": 82462399825,
      "time": 124,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7762888233"
    },
    {
      "job": 82462399832,
      "time": 203,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7762898125"
    },
    {
      "job": 82462399836,
      "time": 103,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7762885769"
    },
    {
      "job": 82462399837,
      "time": 459,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7762928205"
    },
    {
      "job": 82462185397,
      "time": 203,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7762871911"
    },
    {
      "job": 82462399817,
      "time": 134,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7762889453"
    },
    {
      "job": 82462399843,
      "time": 174,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7762894395"
    },
    {
      "job": 82462399846,
      "time": 185,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7762896059"
    },
    {
      "job": 82462399822,
      "time": 166,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7762893487"
    }
  ],
  "_buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/27863019157",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/uscbiostats/xrnet",
  "_commit": {
    "id": "e171fe742488a548e8e461b7a5398ffd308fa053",
    "author": "gweaverbiodev <10748110+gweaverbiodev@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #53 from USCbiostats/gw/cran-submit-2025-12\n\nadd cran-submission",
    "time": 1765993424
  },
  "_maintainer": {
    "name": "Garrett Weaver",
    "email": "gweaverdev@icloud.com",
    "login": "gweaverbiodev",
    "description": "",
    "uuid": 10748110,
    "orcid": "0000-0002-9918-8386"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppEigen",
      "role": "LinkingTo"
    },
    {
      "package": "BH",
      "role": "LinkingTo"
    },
    {
      "package": "bigmemory",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.19",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "bigmemory",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "Matrix",
      "role": "Suggests"
    },
    {
      "package": "doParallel",
      "role": "Suggests"
    }
  ],
  "_owner": "uscbiostats",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-51",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 10,
  "_contributors": [
    {
      "user": "gweaverbiodev",
      "count": 59,
      "uuid": 10748110
    },
    {
      "user": "dixinshen",
      "count": 4,
      "uuid": 19754255
    },
    {
      "user": "danielskatz",
      "count": 2,
      "uuid": 2913845
    },
    {
      "user": "gvegayon",
      "count": 1,
      "uuid": 893619
    }
  ],
  "_userbio": {
    "uuid": 10712919,
    "type": "organization",
    "name": "USC Division of Biostatistics",
    "followers": 41,
    "description": "Organization for USC Division of Biostatistics"
  },
  "_downloads": {
    "count": 281,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/xrnet"
  },
  "_devurl": "https://github.com/uscbiostats/xrnet",
  "_pkgdown": "https://uscbiostats.github.io/xrnet/",
  "_searchresults": 10,
  "_topics": [
    "cpp"
  ],
  "_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/readme.html",
    "extra/readme.md",
    "extra/xrnet.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/uscbiostats/xrnet",
  "_realowner": "uscbiostats",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.6",
      "date": "2020-02-28"
    },
    {
      "version": "0.1.7",
      "date": "2020-03-01"
    },
    {
      "version": "1.0.0",
      "date": "2024-07-16"
    },
    {
      "version": "1.0.1",
      "date": "2025-12-18"
    }
  ],
  "_exports": [
    "define_enet",
    "define_lasso",
    "define_penalty",
    "define_ridge",
    "tune_xrnet",
    "xrnet",
    "xrnet_control"
  ],
  "_datasets": [
    {
      "name": "ext_linear",
      "title": "Simulated external data",
      "object": "GaussianExample",
      "class": [
        "matrix",
        "array"
      ],
      "fields": {},
      "rows": 50,
      "table": true,
      "tojson": true
    },
    {
      "name": "x_linear",
      "title": "Simulated example data for hierarchical regularized linear regression",
      "object": "GaussianExample",
      "class": [
        "matrix",
        "array"
      ],
      "fields": {},
      "rows": 200,
      "table": true,
      "tojson": true
    },
    {
      "name": "y_linear",
      "title": "Simulated outcome data",
      "object": "GaussianExample",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "coef.tune_xrnet",
      "title": "Get coefficient estimates from \"tune_xrnet\" model object.",
      "topics": [
        "coef.tune_xrnet"
      ]
    },
    {
      "page": "coef.xrnet",
      "title": "Get coefficient estimates from \"xrnet\" model object.",
      "topics": [
        "coef.xrnet"
      ]
    },
    {
      "page": "define_enet",
      "title": "Define elastic net regularization object for predictor and external data",
      "topics": [
        "define_enet"
      ]
    },
    {
      "page": "define_lasso",
      "title": "Define lasso regularization object for predictor and external data",
      "topics": [
        "define_lasso"
      ]
    },
    {
      "page": "define_penalty",
      "title": "Define regularization object for predictor and external data.",
      "topics": [
        "define_penalty"
      ]
    },
    {
      "page": "define_ridge",
      "title": "Define ridge regularization object for predictor and external data",
      "topics": [
        "define_ridge"
      ]
    },
    {
      "page": "ext_linear",
      "title": "Simulated external data",
      "topics": [
        "ext_linear"
      ]
    },
    {
      "page": "plot.tune_xrnet",
      "title": "Plot k-fold cross-validation error grid",
      "topics": [
        "plot.tune_xrnet"
      ]
    },
    {
      "page": "predict.tune_xrnet",
      "title": "Predict function for \"tune_xrnet\" object",
      "topics": [
        "predict.tune_xrnet"
      ]
    },
    {
      "page": "predict.xrnet",
      "title": "Predict function for \"xrnet\" object",
      "topics": [
        "predict.xrnet"
      ]
    },
    {
      "page": "tune_xrnet",
      "title": "k-fold cross-validation for hierarchical regularized regression",
      "topics": [
        "tune_xrnet"
      ]
    },
    {
      "page": "x_linear",
      "title": "Simulated example data for hierarchical regularized linear regression",
      "topics": [
        "x_linear"
      ]
    },
    {
      "page": "xrnet",
      "title": "Fit hierarchical regularized regression model",
      "topics": [
        "xrnet"
      ]
    },
    {
      "page": "xrnet_control",
      "title": "Control function for xrnet fitting",
      "topics": [
        "xrnet_control"
      ]
    },
    {
      "page": "y_linear",
      "title": "Simulated outcome data",
      "topics": [
        "y_linear"
      ]
    }
  ],
  "_pkglogo": "https://github.com/uscbiostats/xrnet/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/uscbiostats/xrnet/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "bigmemory",
    "bigmemory.sri",
    "codetools",
    "foreach",
    "iterators",
    "Rcpp",
    "RcppEigen",
    "uuid"
  ],
  "_sysdeps": [
    {
      "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": 4.653212513775344,
  "_indexed": true,
  "_nocasepkg": "xrnet",
  "_universes": [
    "uscbiostats",
    "gweaverbiodev"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-06-20T06:39:24.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "e171fe742488a548e8e461b7a5398ffd308fa053",
      "fileid": "2001dd35440663e28b2ec3561775161c2b8241929dd85d9a6b4003563c8ab374",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/27863019157"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-06-20T06:39:25.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "e171fe742488a548e8e461b7a5398ffd308fa053",
      "fileid": "3b30ef3cd526e185398c49c4fc2901d1b095ac3fca16644f52bb6f68e1e3d2f1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/27863019157"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-06-20T06:39:25.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "e171fe742488a548e8e461b7a5398ffd308fa053",
      "fileid": "9dba393e8f7145e753a04b891568cc3b9bf0fd80065ca5b314990f2da650edd8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/27863019157"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-06-20T06:39:25.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "e171fe742488a548e8e461b7a5398ffd308fa053",
      "fileid": "14d0438a858334e6ed9b2bab31b3c4b5d4d10689c71b16afc8f9f5315d6b64d1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/27863019157"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-06-20T06:38:37.000Z",
      "arch": "aarch64",
      "commit": "e171fe742488a548e8e461b7a5398ffd308fa053",
      "fileid": "c36778f3d13dd4169ce93c9b1c34d6220de1714a1af68c3628cb1eedf7dbeea2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/27863019157"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-06-20T06:39:30.000Z",
      "arch": "x86_64",
      "commit": "e171fe742488a548e8e461b7a5398ffd308fa053",
      "fileid": "2fdce5800878f7312728ba6fd007e534a1309ecd3c5145e5d1961403d3adf7e0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/27863019157"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-06-20T06:38:27.000Z",
      "arch": "aarch64",
      "commit": "e171fe742488a548e8e461b7a5398ffd308fa053",
      "fileid": "e9527b659f87cfb2b09e1c66717e5acaf1fc1d3514af183f9ab8d833cc4bda53",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/27863019157"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-06-20T06:42:07.000Z",
      "arch": "x86_64",
      "commit": "e171fe742488a548e8e461b7a5398ffd308fa053",
      "fileid": "b1cc384196ced6b00d2ae84041d506d9a29bdf2d5d795d15595d8aa2c4bce4be",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/27863019157"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.1",
      "date": "2026-06-20T06:39:18.000Z",
      "arch": "emscripten",
      "commit": "e171fe742488a548e8e461b7a5398ffd308fa053",
      "fileid": "bb64c3305ee089126dcdb9efefe7030e05bd26c712388bde2861621d15545497",
      "status": "success",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/27863019157"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-20T06:38:50.000Z",
      "arch": "x86_64",
      "commit": "e171fe742488a548e8e461b7a5398ffd308fa053",
      "fileid": "4b6192df71bfeaa77a2c7f9067c5a1f9d9d1da0088cd4393898b9ef62216488e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/27863019157"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-20T06:38:42.000Z",
      "arch": "x86_64",
      "commit": "e171fe742488a548e8e461b7a5398ffd308fa053",
      "fileid": "4370d7a1b9b11e5cffe8f311ac9a11740d1fc80626e4ef99a4c8b991137f6164",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/27863019157"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-20T06:38:33.000Z",
      "arch": "x86_64",
      "commit": "e171fe742488a548e8e461b7a5398ffd308fa053",
      "fileid": "ba3e1bfbf55677df9ee99944420854542f53724fb8cb133ffbd37463a13bd23b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/27863019157"
    }
  ]
}