{
  "_id": "6a1eb14eb25058d4daadbbd3",
  "Package": "groupedSurv",
  "Type": "Package",
  "Title": "Efficient Estimation of Grouped Survival Models Using the Exact\nLikelihood Function",
  "Version": "1.0.5.1",
  "Date": "2023-09-28",
  "Author": "Jiaxing Lin [aut], Alexander Sibley [aut], Tracy Truong [aut],\nKouros Owzar [aut], Zhiguo Li [aut], Layne Rogers [ctb], Yu\nJiang [ctb], Janice McCarthy [ctb], Andrew Allen [ctb]",
  "Maintainer": "Alexander Sibley <dcibioinformatics@duke.edu>",
  "Description": "These 'Rcpp'-based functions compute the efficient score\nstatistics for grouped time-to-event data (Prentice and\nGloeckler, 1978), with the optional inclusion of baseline\ncovariates. Functions for estimating the parameter of interest\nand nuisance parameters, including baseline hazards, using\nmaximum likelihood are also provided. A parallel set of\nfunctions allow for the incorporation of family structure of\nrelated individuals (e.g., trios). Note that the current\nimplementation of the frailty model (Ripatti and Palmgren,\n2000) is sensitive to departures from model assumptions, and\nshould be considered experimental. For these data, the exact\nproportional-hazards-model-based likelihood is computed by\nevaluating multiple variable integration. The integration is\naccomplished using the 'Cuba' library (Hahn, 2005), and the\nsource files are included in this package. The maximization\nprocess is carried out using Brent's algorithm, with the C++\ncode file from John Burkardt and John Denker (Brent, 2002).",
  "License": "GPL (>= 2)",
  "VignetteBuilder": "knitr",
  "BuildVignettes": "yes",
  "NeedsCompilation": "yes",
  "RoxygenNote": "6.0.1",
  "Packaged": {
    "Date": "2026-06-02 10:23:17 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://dcibioinformatics.r-universe.dev",
  "Date/Publication": "2023-09-28 22:30:39 UTC",
  "RemoteUrl": "https://github.com/cran/groupedSurv",
  "RemoteRef": "HEAD",
  "RemoteSha": "dea1f25933e6250160c0943bc66422848c13db5b",
  "MD5sum": "f36b7a6a7d5558c0d7fc9f92e120cbeb",
  "_user": "dcibioinformatics",
  "_type": "src",
  "_file": "groupedSurv_1.0.5.1.tar.gz",
  "_fileid": "e9c0fa75d14ff111a72ab5e694afbe132149b7015b6205fe029ae9df13bfbf95",
  "_filesize": 456297,
  "_sha256": "e9c0fa75d14ff111a72ab5e694afbe132149b7015b6205fe029ae9df13bfbf95",
  "_created": "2026-06-02T10:23:17.000Z",
  "_published": "2026-06-02T10:32:46.339Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79049989889,
      "time": 180,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7355190579"
    },
    {
      "job": 79049989884,
      "time": 185,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7355191172"
    },
    {
      "job": 79049989913,
      "time": 198,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7355196626"
    },
    {
      "job": 79049989897,
      "time": 185,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7355191265"
    },
    {
      "job": 79049989905,
      "time": 115,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7355224490"
    },
    {
      "job": 79049989951,
      "time": 278,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7355231632"
    },
    {
      "job": 79049989995,
      "time": 144,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7355241583"
    },
    {
      "job": 79049989949,
      "time": 447,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7355294209"
    },
    {
      "job": 79049247189,
      "time": 276,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7355129477"
    },
    {
      "job": 79049989895,
      "time": 156,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7355182293"
    },
    {
      "job": 79049989978,
      "time": 235,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7355207022"
    },
    {
      "job": 79049989920,
      "time": 158,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7355182921"
    },
    {
      "job": 79049989945,
      "time": 206,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7355198167"
    }
  ],
  "_buildurl": "https://github.com/r-universe/dcibioinformatics/actions/runs/26813469932",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/groupedSurv",
  "_commit": {
    "id": "dea1f25933e6250160c0943bc66422848c13db5b",
    "author": "Alexander Sibley <dcibioinformatics@duke.edu>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.0.5.1\n",
    "time": 1695940239
  },
  "_maintainer": {
    "name": "Alexander Sibley",
    "email": "dcibioinformatics@duke.edu"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppEigen",
      "role": "LinkingTo"
    },
    {
      "package": "BH",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.4",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "qvalue",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "snplist",
      "role": "Suggests"
    },
    {
      "package": "BEDMatrix",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_userbio": {
    "uuid": 74666632,
    "type": "organization",
    "name": "DCI Bioinformatics Shared Resource"
  },
  "_downloads": {
    "count": 225,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/groupedSurv"
  },
  "_mentions": 1,
  "_searchresults": 3,
  "_topics": [
    "cpp",
    "openmp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/groupedSurv.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "dcibioinformatics",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2018-05-11"
    },
    {
      "version": "1.0.1",
      "date": "2018-05-15"
    },
    {
      "version": "1.0.2",
      "date": "2018-06-22"
    },
    {
      "version": "1.0.3",
      "date": "2018-06-29"
    },
    {
      "version": "1.0.4",
      "date": "2019-12-02"
    },
    {
      "version": "1.0.4.1",
      "date": "2020-02-02"
    },
    {
      "version": "1.0.4.2",
      "date": "2020-11-12"
    },
    {
      "version": "1.0.4.3",
      "date": "2022-08-05"
    },
    {
      "version": "1.0.5",
      "date": "2023-01-25"
    },
    {
      "version": "1.0.5.1",
      "date": "2023-09-28"
    }
  ],
  "_exports": [
    "alphaEstFam",
    "betaEst",
    "betaEstFam",
    "geneStat",
    "groupedSurv",
    "groupedSurvFam",
    "PvalueFam",
    "thetaEst",
    "varEstFam",
    "varLLFam"
  ],
  "_help": [
    {
      "page": "groupedSurv-package",
      "title": "Efficient Estimation of Grouped Survival Models Using the Exact Likelihood Function",
      "topics": [
        "groupedSurv-package"
      ]
    },
    {
      "page": "alphaEstFam",
      "title": "Estimate the Interval Baseline Survival Rates for the Grouped Failure Time Model",
      "topics": [
        "alphaEstFam"
      ]
    },
    {
      "page": "betaEst",
      "title": "Estimate the Parameter of Interest for the Grouped Survival Model",
      "topics": [
        "betaEst"
      ]
    },
    {
      "page": "betaEstFam",
      "title": "Estimate the Fixed Effect Parameter for the Frailty Model",
      "topics": [
        "betaEstFam"
      ]
    },
    {
      "page": "geneStat",
      "title": "Compute Gene-Level Statistics Based on Efficient Score Statistics for the Grouped Survival Model",
      "topics": [
        "geneStat"
      ]
    },
    {
      "page": "groupedSurv",
      "title": "Compute the Efficient Score Statistic for the Grouped Survival Model",
      "topics": [
        "groupedSurv"
      ]
    },
    {
      "page": "groupedSurvFam",
      "title": "Compute the Efficient Score Statistic for the Frailty Model",
      "topics": [
        "groupedSurvFam"
      ]
    },
    {
      "page": "PvalueFam",
      "title": "Estimate P-values of the Efficient Score Statistics for the Frailty Model",
      "topics": [
        "PvalueFam"
      ]
    },
    {
      "page": "thetaEst",
      "title": "Estimate the Baseline Survival Rates and Covariate Parameters for the Grouped Survival Model",
      "topics": [
        "thetaEst"
      ]
    },
    {
      "page": "varEstFam",
      "title": "Estimate the Frailty Variance for the Frailty Model",
      "topics": [
        "varEstFam"
      ]
    },
    {
      "page": "varLLFam",
      "title": "Log-Likelihood of the Frailty Variance for the Discrete-Time Frailty Model",
      "topics": [
        "varLLFam"
      ]
    }
  ],
  "_rundeps": [
    "BH",
    "cli",
    "codetools",
    "cpp11",
    "doParallel",
    "farver",
    "foreach",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "iterators",
    "labeling",
    "lifecycle",
    "magrittr",
    "plyr",
    "qvalue",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "reshape2",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_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"
    },
    {
      "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": "groupedSurv.Rnw",
      "filename": "groupedSurv.pdf",
      "title": "groupedSurv",
      "engine": "knitr::knitr",
      "headings": [],
      "created": "2018-05-11 10:16:47",
      "modified": "2022-08-05 18:10:02",
      "commits": 8
    }
  ],
  "_score": 2,
  "_indexed": true,
  "_nocasepkg": "groupedsurv",
  "_universes": [
    "dcibioinformatics"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.5.1",
      "date": "2026-06-02T10:26:20.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "dea1f25933e6250160c0943bc66422848c13db5b",
      "fileid": "5457321e7bb55f769528a66f337c4ae9ee4562e51855331cb7c4472ef052c091",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dcibioinformatics/actions/runs/26813469932"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.5.1",
      "date": "2026-06-02T10:26:19.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "dea1f25933e6250160c0943bc66422848c13db5b",
      "fileid": "65e116dc3eecafafb78a0a83b40ad39b7ef7c1764683d37975c009a942678e0f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dcibioinformatics/actions/runs/26813469932"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.5.1",
      "date": "2026-06-02T10:26:34.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "dea1f25933e6250160c0943bc66422848c13db5b",
      "fileid": "86f228e604531ee387caed467b89cd0c82f2b81647828da13640763fdd7cb53b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dcibioinformatics/actions/runs/26813469932"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.5.1",
      "date": "2026-06-02T10:26:20.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "dea1f25933e6250160c0943bc66422848c13db5b",
      "fileid": "7bcef8f7233e78032c8c11210f05484da69854d58706d8fdf3267892a6265be1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dcibioinformatics/actions/runs/26813469932"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.5.1",
      "date": "2026-06-02T10:28:11.000Z",
      "arch": "aarch64",
      "commit": "dea1f25933e6250160c0943bc66422848c13db5b",
      "fileid": "57cdb67e895b340bb9ba7ecb766b117bd5d363777ac4d97a92db85a6ec584afd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dcibioinformatics/actions/runs/26813469932"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.5.1",
      "date": "2026-06-02T10:27:41.000Z",
      "arch": "x86_64",
      "commit": "dea1f25933e6250160c0943bc66422848c13db5b",
      "fileid": "51e83e5b762e6c9dc799afb462c12e9ef962d64eefee4fef13afe09cb14891ec",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dcibioinformatics/actions/runs/26813469932"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.5.1",
      "date": "2026-06-02T10:28:53.000Z",
      "arch": "aarch64",
      "commit": "dea1f25933e6250160c0943bc66422848c13db5b",
      "fileid": "a92089eeb0e9eb64a261d7bde24fc7564b4a3a293a976396661f40d46fc53d11",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dcibioinformatics/actions/runs/26813469932"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.5.1",
      "date": "2026-06-02T10:29:51.000Z",
      "arch": "x86_64",
      "commit": "dea1f25933e6250160c0943bc66422848c13db5b",
      "fileid": "f3b5bf39d2518d7ebdf91012b9ece95eba94663ecba0476c6dfe5a9f4e78b56f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dcibioinformatics/actions/runs/26813469932"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.5.1",
      "date": "2026-06-02T10:26:18.000Z",
      "arch": "emscripten",
      "commit": "dea1f25933e6250160c0943bc66422848c13db5b",
      "fileid": "c683049ce478a2ca525923db62af3236ebb5871fd7f47a364dd263a26bef5aaa",
      "status": "success",
      "buildurl": "https://github.com/r-universe/dcibioinformatics/actions/runs/26813469932"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.5.1",
      "date": "2026-06-02T10:25:50.000Z",
      "arch": "x86_64",
      "commit": "dea1f25933e6250160c0943bc66422848c13db5b",
      "fileid": "1f1ae830d6d140d2714fd8916f022d83517d0a76dd12bb0555cd12be08654963",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dcibioinformatics/actions/runs/26813469932"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.5.1",
      "date": "2026-06-02T10:25:17.000Z",
      "arch": "x86_64",
      "commit": "dea1f25933e6250160c0943bc66422848c13db5b",
      "fileid": "4b72aba050293dc5eccdcb38f5a734f811929a16b00496521a049fed405e29e1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dcibioinformatics/actions/runs/26813469932"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.5.1",
      "date": "2026-06-02T10:25:28.000Z",
      "arch": "x86_64",
      "commit": "dea1f25933e6250160c0943bc66422848c13db5b",
      "fileid": "70b1a23b47ade5f560057091af4d8bf499f9324596569dc6a25b6b75df9ee5d6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dcibioinformatics/actions/runs/26813469932"
    }
  ]
}