{
  "_id": "6a101b07acfb0bcc41c86d79",
  "Type": "Package",
  "Package": "hierNest",
  "Title": "Penalized Regression with Hierarchical Nested Parameterization\nStructure",
  "Version": "1.0.2",
  "Date": "2026-03-02",
  "Authors@R": "c(\nperson(\"Ziren\", \"Jiang\",,\"jian0746@umn.edu\", role = c(\"aut\",\"cre\")),\nperson(\"Jared\", \"Huling\",,\"huling@umn.edu\", role = \"aut\"),\nperson(\"Jue\", \"Hou\",,\"hou00123@umn.edu\", role = \"aut\"),\nperson(\"Lingfeng\", \"Huo\", role = \"aut\"),\nperson(\"Daniel J.\", \"McDonald\", role = \"ctb\"),\nperson(\"Xiaoxuan\", \"Liang\", role = \"ctb\"),\nperson(\"Anibal\", \"Solon Heinsfeld\", role = \"ctb\"),\nperson(\"Aaron\", \"Cohen\", role = \"ctb\"),\nperson(\"Yi\", \"Yang\", role = \"ctb\"),\nperson(\"Hui\", \"Zou\", role = \"ctb\"),\nperson(\"Jerome\", \"Friedman\", role = \"ctb\"),\nperson(\"Trevor\", \"Hastie\", role = \"ctb\"),\nperson(\"Rob\", \"Tibshirani\", role = \"ctb\"),\nperson(\"Balasubramanian\", \"Narasimhan\", role = \"ctb\"),\nperson(\"Kenneth\", \"Tay\", role = \"ctb\"),\nperson(\"Noah\", \"Simon\", role = \"ctb\"),\nperson(\"Junyang\", \"Qian\", role = \"ctb\"),\nperson(\"James\", \"Yang\", role = \"ctb\")\n)",
  "Description": "Efficient implementation of penalized regression with\nhierarchical nested parametrization for grouped data. The\npackage provides penalized regression methods that decompose\nsubgroup specific effects into shared global effects, Major\nsubgroup specific effects, and Minor subgroup specific effects,\nenabling structured borrowing of information across related\nclinical subgroups. Both lasso and hierarchical overlapping\ngroup lasso penalties are supported to encourage sparsity while\nrespecting the nested subgroup structure. Efficient computation\nis achieved through a modified design matrix representation and\na custom majorization minimization algorithm for overlapping\ngroup penalties.",
  "License": "GPL (>= 2)",
  "Config/testthat/edition": "3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "NeedsCompilation": "yes",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.3",
  "Maintainer": "Ziren Jiang <jian0746@umn.edu>",
  "URL": "https://github.com/ZirenJiang/hierNest",
  "BugReports": "https://github.com/ZirenJiang/hierNest/issues",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev",
  "Repository": "https://zirenjiang.r-universe.dev",
  "Date/Publication": "2026-04-11 02:24:19 UTC",
  "RemoteUrl": "https://github.com/zirenjiang/hiernest",
  "RemoteRef": "HEAD",
  "RemoteSha": "633fb2c53e4b9ece51405adeee4cd997aba1d8ee",
  "Packaged": {
    "Date": "2026-05-14 09:17:19 UTC",
    "User": "root"
  },
  "Author": "Ziren Jiang [aut, cre],\nJared Huling [aut],\nJue Hou [aut],\nLingfeng Huo [aut],\nDaniel J. McDonald [ctb],\nXiaoxuan Liang [ctb],\nAnibal Solon Heinsfeld [ctb],\nAaron Cohen [ctb],\nYi Yang [ctb],\nHui Zou [ctb],\nJerome Friedman [ctb],\nTrevor Hastie [ctb],\nRob Tibshirani [ctb],\nBalasubramanian Narasimhan [ctb],\nKenneth Tay [ctb],\nNoah Simon [ctb],\nJunyang Qian [ctb],\nJames Yang [ctb]",
  "MD5sum": "951499d0e2606799884c10d8495f3140",
  "_user": "zirenjiang",
  "_type": "src",
  "_file": "hierNest_1.0.2.tar.gz",
  "_fileid": "11ff5f0c92bd19b3288584b49a2de88c8e2e52f898980f59d241445b0001d64b",
  "_filesize": 400683,
  "_sha256": "11ff5f0c92bd19b3288584b49a2de88c8e2e52f898980f59d241445b0001d64b",
  "_created": "2026-05-14T09:17:19.000Z",
  "_published": "2026-05-22T08:59:51.547Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77348339553,
      "time": 160,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6991185734"
    },
    {
      "job": 77348339593,
      "time": 172,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6991189391"
    },
    {
      "job": 77348340256,
      "time": 162,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6991186914"
    },
    {
      "job": 77348339949,
      "time": 173,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6991189842"
    },
    {
      "job": 77348340163,
      "time": 143,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6991181644"
    },
    {
      "job": 77348340054,
      "time": 449,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6991267733"
    },
    {
      "job": 77348339576,
      "time": 150,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6991183081"
    },
    {
      "job": 77348339824,
      "time": 230,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6991205476"
    },
    {
      "job": 77348338979,
      "time": 275,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6991141346"
    },
    {
      "job": 77348339063,
      "time": 132,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7156720973"
    },
    {
      "job": 77348339744,
      "time": 155,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6991184294"
    },
    {
      "job": 77348340191,
      "time": 131,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6991178219"
    },
    {
      "job": 77348340210,
      "time": 166,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6991187717"
    }
  ],
  "_buildurl": "https://github.com/r-universe/zirenjiang/actions/runs/25851944067",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/zirenjiang/hiernest",
  "_commit": {
    "id": "633fb2c53e4b9ece51405adeee4cd997aba1d8ee",
    "author": "ZirenJiang <jian0746@umn.edu>",
    "committer": "ZirenJiang <jian0746@umn.edu>",
    "message": "bug fix\n",
    "time": 1775874259
  },
  "_maintainer": {
    "name": "Ziren Jiang",
    "email": "jian0746@umn.edu",
    "login": "zirenjiang",
    "uuid": 126919204
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "cli",
      "role": "Imports"
    },
    {
      "package": "dotCall64",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "version": ">= 1.1.4",
      "role": "Imports"
    },
    {
      "package": "RSpectra",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "version": ">= 1.3.0",
      "role": "Imports"
    },
    {
      "package": "rTensor",
      "role": "Imports"
    },
    {
      "package": "pROC",
      "role": "Imports"
    },
    {
      "package": "plotly",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "gglasso",
      "role": "Suggests"
    },
    {
      "package": "glmnet",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "splines",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "zirenjiang",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-28",
      "n": 1
    },
    {
      "week": "2025-31",
      "n": 1
    },
    {
      "week": "2025-45",
      "n": 2
    },
    {
      "week": "2025-46",
      "n": 1
    },
    {
      "week": "2026-07",
      "n": 1
    },
    {
      "week": "2026-12",
      "n": 4
    },
    {
      "week": "2026-13",
      "n": 10
    },
    {
      "week": "2026-15",
      "n": 5
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "zirenjiang",
      "count": 40,
      "uuid": 126919204
    },
    {
      "user": "jaredhuling",
      "count": 10,
      "uuid": 3196112
    }
  ],
  "_userbio": {
    "uuid": 126919204,
    "type": "user",
    "name": "ZirenJiang"
  },
  "_downloads": {
    "count": 393,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/hierNest"
  },
  "_devurl": "https://github.com/zirenjiang/hiernest",
  "_searchresults": 9,
  "_topics": [
    "fortran"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/hierNest.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/zirenjiang/hiernest",
  "_realowner": "zirenjiang",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2026-03-24"
    },
    {
      "version": "1.0.2",
      "date": "2026-04-18"
    }
  ],
  "_exports": [
    "%>%",
    "cv.hierNest",
    "gr_one_norm",
    "gr_two_norm",
    "grouped_one_norm",
    "grouped_two_norm",
    "grouped_zero_norm",
    "hierNest",
    "make_irls_warmup",
    "one_norm",
    "plot_contribution",
    "predict_hierNest",
    "sp_group_norm",
    "two_norm",
    "zero_norm"
  ],
  "_datasets": [
    {
      "name": "example_data",
      "title": "Example dataset",
      "object": "example_data",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "coef.cv.hierNest",
      "title": "Extract subgroup-specific coefficients from a cv.hierNest object",
      "topics": [
        "coef.cv.hierNest"
      ]
    },
    {
      "page": "coef.cv.sparsegl",
      "title": "Extract coefficients from a `cv.sparsegl` object.",
      "topics": [
        "coef.cv.sparsegl"
      ]
    },
    {
      "page": "coef.sparsegl",
      "title": "Extract model coefficients from a `sparsegl` object.",
      "topics": [
        "coef.sparsegl"
      ]
    },
    {
      "page": "cv.hierNest",
      "title": "Cross-validated hierarchical nested regularization for subgroup models",
      "topics": [
        "cv.hierNest"
      ]
    },
    {
      "page": "estimate_risk",
      "title": "Calculate information criteria.",
      "topics": [
        "estimate_risk"
      ]
    },
    {
      "page": "example_data",
      "title": "Example dataset",
      "topics": [
        "example_data"
      ]
    },
    {
      "page": "hierNest",
      "title": "Fit Hierarchical Nested Regularization Model (hierNest)",
      "topics": [
        "hierNest"
      ]
    },
    {
      "page": "make_irls_warmup",
      "title": "Create starting values for iterative reweighted least squares",
      "topics": [
        "make_irls_warmup"
      ]
    },
    {
      "page": "overlapping_gl",
      "title": "Fit an Overlapping Group Lasso Model",
      "topics": [
        "overlapping_gl"
      ]
    },
    {
      "page": "plot_contribution",
      "title": "Boxplot or bar chart of per-covariate contributions to the linear predictor",
      "topics": [
        "plot_contribution"
      ]
    },
    {
      "page": "plot.cv.hierNest",
      "title": "Plot method for cv.hierNest objects",
      "topics": [
        "plot.cv.hierNest"
      ]
    },
    {
      "page": "predict_hierNest",
      "title": "Predict Method for hierNest Objects",
      "topics": [
        "predict_hierNest"
      ]
    },
    {
      "page": "predict.cv.sparsegl",
      "title": "Make predictions from a `cv.sparsegl` object.",
      "topics": [
        "predict.cv.sparsegl"
      ]
    },
    {
      "page": "predict.sparsegl",
      "title": "Make predictions from a `sparsegl` object.",
      "topics": [
        "predict.sparsegl"
      ]
    },
    {
      "page": "grouped_sp_norm",
      "title": "Calculate common norms",
      "topics": [
        "grouped_one_norm",
        "grouped_sp_norm",
        "grouped_two_norm",
        "grouped_zero_norm",
        "gr_one_norm",
        "gr_two_norm",
        "one_norm",
        "sp_group_norm",
        "two_norm",
        "zero_norm"
      ]
    }
  ],
  "_readme": "https://github.com/zirenjiang/hiernest/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "base64enc",
    "bslib",
    "cachem",
    "cli",
    "cpp11",
    "crosstalk",
    "curl",
    "data.table",
    "digest",
    "dotCall64",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "Matrix",
    "memoise",
    "mime",
    "openssl",
    "otel",
    "pillar",
    "pkgconfig",
    "plotly",
    "pROC",
    "promises",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "rlang",
    "rmarkdown",
    "RSpectra",
    "rTensor",
    "S7",
    "sass",
    "scales",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "yaml"
  ],
  "_sysdeps": [
    {
      "shlib": "libgfortran",
      "package": "libgfortran5",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "fortran",
      "homepage": "http://gcc.gnu.org/",
      "description": "Runtime library for GNU Fortran applications"
    }
  ],
  "_vignettes": [
    {
      "source": "hierNest_vignette.Rmd",
      "filename": "hierNest_vignette.html",
      "title": "Getting Started with hierNest",
      "author": "Ziren Jiang, Lingfeng Huo, Jue Hou, and Jared D. Huling",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Motivation",
        "Two penalization strategies",
        "Package scope",
        "Installation",
        "The hier_info matrix",
        "Example data",
        "Fitting the model",
        "hierNest() — fit at a single penalty level",
        "cv.hierNest() — cross-validated tuning parameter selection",
        "Cross-validation methods",
        "Recommended: grid search",
        "Single hyperparameter pair (fast)",
        "User-supplied grid",
        "Inspecting the cross-validated fit",
        "Visualizing the estimated effects",
        "Coefficient heatmap",
        "Subgroup effect heatmap",
        "Methodological background",
        "Hierarchical reparameterization",
        "Overlapping group lasso penalty",
        "Computation",
        "Session information"
      ],
      "created": "2026-03-20 00:39:53",
      "modified": "2026-03-20 00:39:53",
      "commits": 1
    }
  ],
  "_score": 4.6020599913279625,
  "_indexed": true,
  "_nocasepkg": "hiernest",
  "_universes": [
    "zirenjiang"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.2",
      "date": "2026-05-14T09:19:47.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "633fb2c53e4b9ece51405adeee4cd997aba1d8ee",
      "fileid": "5af6fa47564638c8a071fd2123f7529a55833f1aca1ddafd65380f3bdb2d0521",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zirenjiang/actions/runs/25851944067"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.2",
      "date": "2026-05-14T09:19:51.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "633fb2c53e4b9ece51405adeee4cd997aba1d8ee",
      "fileid": "eed3f2aa42c8b79b134bd11487edcfadcd1217ef5dd144c6bc23ccde39fe2b77",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zirenjiang/actions/runs/25851944067"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.2",
      "date": "2026-05-14T09:19:51.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "633fb2c53e4b9ece51405adeee4cd997aba1d8ee",
      "fileid": "8903ce6f381a4fc163e8bbc4589cf0f40fcddfd317d4567542fe95561c7482ae",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zirenjiang/actions/runs/25851944067"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.2",
      "date": "2026-05-14T09:19:52.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "633fb2c53e4b9ece51405adeee4cd997aba1d8ee",
      "fileid": "425b82313da234b5053cc9c657eebd37d39b0e4cb83b162472e91bf140006723",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zirenjiang/actions/runs/25851944067"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.2",
      "date": "2026-05-14T09:19:25.000Z",
      "arch": "aarch64",
      "commit": "633fb2c53e4b9ece51405adeee4cd997aba1d8ee",
      "fileid": "fde3b9df52cffd37edc7437c74558585f832559bb1ca32aebeba19ae2c25d789",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zirenjiang/actions/runs/25851944067"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.2",
      "date": "2026-05-14T09:22:48.000Z",
      "arch": "x86_64",
      "commit": "633fb2c53e4b9ece51405adeee4cd997aba1d8ee",
      "fileid": "0cf9acde15a7ebd17287768de780dc8d746010cb4cc9ff3cd637deb1f2625cef",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zirenjiang/actions/runs/25851944067"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.2",
      "date": "2026-05-14T09:19:28.000Z",
      "arch": "aarch64",
      "commit": "633fb2c53e4b9ece51405adeee4cd997aba1d8ee",
      "fileid": "ad5ea11f99081274db76527c407d2e4a86ff3c3413e73a6e7ab760c1d5d53d50",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zirenjiang/actions/runs/25851944067"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.2",
      "date": "2026-05-14T09:20:18.000Z",
      "arch": "x86_64",
      "commit": "633fb2c53e4b9ece51405adeee4cd997aba1d8ee",
      "fileid": "c106334d9e9d2100ce981bb18cb1ec82143365e026dc9030a8b3af4bd3b58351",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zirenjiang/actions/runs/25851944067"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.2",
      "date": "2026-05-14T09:19:08.000Z",
      "arch": "x86_64",
      "commit": "633fb2c53e4b9ece51405adeee4cd997aba1d8ee",
      "fileid": "0f08d88b842ee34e45eeb6469be18064762c4673ca25b73feb53da3e3adfd759",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zirenjiang/actions/runs/25851944067"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.2",
      "date": "2026-05-14T09:18:49.000Z",
      "arch": "x86_64",
      "commit": "633fb2c53e4b9ece51405adeee4cd997aba1d8ee",
      "fileid": "1e2239b057fe0718ae18497faa53740e40b5a32cb9ad17dc73cf093c1ba74474",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zirenjiang/actions/runs/25851944067"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.2",
      "date": "2026-05-14T09:18:54.000Z",
      "arch": "x86_64",
      "commit": "633fb2c53e4b9ece51405adeee4cd997aba1d8ee",
      "fileid": "1745a339b3e64ac8c3ec04d20bc40a69cb519017a0a3dcd1bcb25837dbdbb71e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zirenjiang/actions/runs/25851944067"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.2",
      "date": "2026-05-22T08:59:31.000Z",
      "arch": "emscripten",
      "commit": "633fb2c53e4b9ece51405adeee4cd997aba1d8ee",
      "fileid": "2ea6151642bc8c2d611da77245155718b4a1abcb43edbe4c76e877b04fae3b81",
      "status": "success",
      "buildurl": "https://github.com/r-universe/zirenjiang/actions/runs/25851944067"
    }
  ]
}