{
  "_id": "6a1171d5acfb0bcc41cf78fb",
  "Package": "swjm",
  "Title": "Stagewise Variable Selection for Joint Models of Semi-Competing\nRisks",
  "Version": "0.1.1",
  "Authors@R": "c(\nperson(family=\"Huling\", given=\"Jared D.\", role = c(\"aut\", \"cre\"),\nemail = \"jaredhuling@gmail.com\"),\nperson(family=\"Huo\", given=\"Lingfeng\", role = c(\"aut\")),\nperson(family=\"Jiang\", given=\"Ziren\", role = \"aut\"),\nperson(family=\"Hou\", given=\"Jue\", role = \"aut\"),\nperson(given = \"Sy Han (Steven)\", family = \"Chiou\", role = \"ctb\"),\nperson(given = \"Chiung-Yu\", family = \"Huang\", role = \"ctb\"))",
  "Description": "Implements stagewise regression for variable selection in\njoint models of recurrent events and terminal events\n(semi-competing risks). Supports two model frameworks: the\njoint frailty model (Cox-type) and the joint scale-change model\n(AFT-type). Provides cooperative lasso, lasso, and group lasso\npenalties with cross-validation for tuning parameter selection\nvia cross-fitted estimating equations.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake",
  "Repository": "https://jaredhuling.r-universe.dev",
  "Date/Publication": "2026-04-23 12:51:20 UTC",
  "RemoteUrl": "https://github.com/jaredhuling/swjm",
  "RemoteRef": "HEAD",
  "RemoteSha": "cee664142ae8322955797885fe7e0ba02bc722af",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-23 09:16:23 UTC",
    "User": "root"
  },
  "Author": "Jared D. Huling [aut, cre],\nLingfeng Huo [aut],\nZiren Jiang [aut],\nJue Hou [aut],\nSy Han (Steven) Chiou [ctb],\nChiung-Yu Huang [ctb]",
  "Maintainer": "Jared D. Huling <jaredhuling@gmail.com>",
  "MD5sum": "ec5aed198b0dee09d4c47531c95d530e",
  "_user": "jaredhuling",
  "_type": "src",
  "_file": "swjm_0.1.1.tar.gz",
  "_fileid": "b93e467a0972b2feaa59b3bb2fd5aeeea5d3007e8a06da3babbe262ffeb54ba7",
  "_filesize": 3018985,
  "_sha256": "b93e467a0972b2feaa59b3bb2fd5aeeea5d3007e8a06da3babbe262ffeb54ba7",
  "_created": "2026-05-23T09:16:23.000Z",
  "_published": "2026-05-23T09:22:29.728Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77511825553,
      "time": 181,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7175909172"
    },
    {
      "job": 77511825554,
      "time": 194,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7175910338"
    },
    {
      "job": 77511825550,
      "time": 199,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7175910836"
    },
    {
      "job": 77511825559,
      "time": 198,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7175910600"
    },
    {
      "job": 77511825571,
      "time": 107,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7175905139"
    },
    {
      "job": 77511825555,
      "time": 226,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7175919793"
    },
    {
      "job": 77511825565,
      "time": 99,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7175904923"
    },
    {
      "job": 77511825558,
      "time": 309,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7175920942"
    },
    {
      "job": 77511334884,
      "time": 600,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7175893108"
    },
    {
      "job": 77511825532,
      "time": 137,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7175905337"
    },
    {
      "job": 77511825538,
      "time": 177,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7175908771"
    },
    {
      "job": 77511825537,
      "time": 154,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7175906845"
    },
    {
      "job": 77511825534,
      "time": 231,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7175913640"
    }
  ],
  "_buildurl": "https://github.com/r-universe/jaredhuling/actions/runs/26328855832",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/jaredhuling/swjm",
  "_commit": {
    "id": "cee664142ae8322955797885fe7e0ba02bc722af",
    "author": "Jared Huling <jaredhuling@gmail.com>",
    "committer": "Jared Huling <jaredhuling@gmail.com>",
    "message": "cran R_NamespaceRegistry fix\n",
    "time": 1776948680
  },
  "_maintainer": {
    "name": "Jared D. Huling",
    "email": "jaredhuling@gmail.com",
    "login": "jaredhuling",
    "description": "Associate Professor in the Division of Biostatistics & Health Data Science at the University of Minnesota",
    "uuid": 3196112
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.14",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.14",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "reReg",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "survival",
      "role": "Suggests"
    },
    {
      "package": "timeROC",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "jaredhuling",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-11",
      "n": 9
    },
    {
      "week": "2026-12",
      "n": 15
    },
    {
      "week": "2026-13",
      "n": 13
    },
    {
      "week": "2026-14",
      "n": 7
    },
    {
      "week": "2026-15",
      "n": 3
    },
    {
      "week": "2026-16",
      "n": 6
    },
    {
      "week": "2026-17",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_userbio": {
    "uuid": 3196112,
    "type": "user",
    "name": "Jared Huling",
    "description": "Associate Professor in the Division of Biostatistics & Health Data Science at the University of Minnesota"
  },
  "_downloads": {
    "count": 530,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/swjm"
  },
  "_devurl": "https://github.com/jaredhuling/swjm",
  "_searchresults": 8,
  "_topics": [
    "openblas",
    "cpp",
    "openmp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/swjm.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/jaredhuling/swjm",
  "_realowner": "jaredhuling",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2026-04-21"
    }
  ],
  "_exports": [
    "baseline_hazard",
    "cv_stagewise",
    "generate_data",
    "generate_data_jfm",
    "generate_data_jscm",
    "stagewise_fit"
  ],
  "_help": [
    {
      "page": "swjm-package",
      "title": "swjm: Stagewise Variable Selection for Joint Models of Semi-Competing Risks",
      "topics": [
        "swjm-package",
        "swjm"
      ]
    },
    {
      "page": "baseline_hazard",
      "title": "Cumulative Baseline Hazard Step Functions",
      "topics": [
        "baseline_hazard"
      ]
    },
    {
      "page": "cv_stagewise",
      "title": "Cross-Validation for Stagewise Variable Selection",
      "topics": [
        "cv_stagewise"
      ]
    },
    {
      "page": "generate_data",
      "title": "Generate Simulated Data for Joint Models",
      "topics": [
        "generate_data"
      ]
    },
    {
      "page": "generate_data_jfm",
      "title": "Generate Simulated Data for the Joint Frailty Model (JFM)",
      "topics": [
        "generate_data_jfm"
      ]
    },
    {
      "page": "generate_data_jscm",
      "title": "Generate Simulated Data for the Joint Scale-Change Model (JSCM)",
      "topics": [
        "generate_data_jscm"
      ]
    },
    {
      "page": "plot.swjm_cv",
      "title": "Plot Cross-Validation Results",
      "topics": [
        "plot.swjm_cv"
      ]
    },
    {
      "page": "plot.swjm_path",
      "title": "Plot a Stagewise Coefficient Path",
      "topics": [
        "plot.swjm_path"
      ]
    },
    {
      "page": "plot.swjm_pred",
      "title": "Plot Predicted Survival Curves and Predictor Contributions",
      "topics": [
        "plot.swjm_pred"
      ]
    },
    {
      "page": "predict.swjm_cv",
      "title": "Predict from a Cross-Validated Joint Model Fit",
      "topics": [
        "predict.swjm_cv"
      ]
    },
    {
      "page": "stagewise_fit",
      "title": "Fit a Stagewise Regularization Path",
      "topics": [
        "stagewise_fit"
      ]
    }
  ],
  "_readme": "https://github.com/jaredhuling/swjm/raw/HEAD/README.md",
  "_rundeps": [
    "BB",
    "cli",
    "cpp11",
    "dfoptim",
    "directlabels",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "MASS",
    "Matrix",
    "mgcv",
    "nleqslv",
    "nlme",
    "nloptr",
    "numDeriv",
    "optimx",
    "pracma",
    "quadprog",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "reda",
    "reReg",
    "rlang",
    "rootSolve",
    "S7",
    "scales",
    "scam",
    "splines2",
    "SQUAREM",
    "survival",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_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": "swjm.Rmd",
      "filename": "swjm.html",
      "title": "Stagewise Variable Selection for Joint Semi-Competing Risk Models",
      "author": "Lingfeng Huo, Ziren Jiang, Jue Hou, Jared D. Huling",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "1. Statistical Background",
        "1.1 Semi-Competing Risks",
        "1.2 Joint Frailty Model (JFM)",
        "1.3 Joint Scale-Change Model (JSCM)",
        "1.4 Stagewise Variable Selection",
        "1.5 Cross-Validation",
        "2. Installation",
        "3. Data Format",
        "4. Simulating Data",
        "4.1 Joint Frailty Model data",
        "4.2 Joint Scale-Change Model data",
        "5. Joint Frailty Model (JFM) Workflow",
        "5.1 Fit the Stagewise Regularization Path",
        "5.2 Explore the Regularization Path",
        "5.3 Plot the Coefficient Path",
        "5.4 Cross-Validation",
        "5.5 Plot the CV Results",
        "5.6 Extract Coefficients and Summarize",
        "5.7 Baseline Hazard",
        "5.8 Survival Prediction",
        "6. Other Penalty Types (JFM)",
        "6.1 Lasso",
        "6.2 Group Lasso",
        "6.3 Comparing Penalties",
        "7. Joint Scale-Change Model (JSCM) Workflow",
        "7.1 Fit the Stagewise Path",
        "7.2 Cross-Validation",
        "7.3 Results",
        "7.4 Baseline Hazard (JSCM)",
        "7.5 Survival Prediction and AFT Interpretation",
        "8. Interpreting Output",
        "8.1 Alpha and Beta Conventions",
        "8.2 Cooperative Lasso and Variable Grouping",
        "8.3 Survival Curve Interpretation",
        "9. Default Parameters",
        "10. Model Evaluation",
        "10.1 Coefficient Recovery",
        "10.2 Time-Varying AUC",
        "11. References"
      ],
      "created": "2026-03-15 22:06:54",
      "modified": "2026-04-05 16:52:55",
      "commits": 6
    }
  ],
  "_score": 4.544068044350276,
  "_indexed": true,
  "_nocasepkg": "swjm",
  "_universes": [
    "jaredhuling"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-05-23T09:19:04.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "cee664142ae8322955797885fe7e0ba02bc722af",
      "fileid": "232078c607c7032ea4d438d8c4d562f0b6940748f274910eef87233493786678",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jaredhuling/actions/runs/26328855832"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-05-23T09:19:11.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "cee664142ae8322955797885fe7e0ba02bc722af",
      "fileid": "b6d7e08546a3d8f26d254517397d57102cab9e3ae761551f9fdaf1c8f36994fa",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jaredhuling/actions/runs/26328855832"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-05-23T09:19:22.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "cee664142ae8322955797885fe7e0ba02bc722af",
      "fileid": "ed739287391f195205e215cdaf0cf75a0439d54997a267164603297f51300e56",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jaredhuling/actions/runs/26328855832"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-05-23T09:19:14.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "cee664142ae8322955797885fe7e0ba02bc722af",
      "fileid": "9abf8fbcd502976940ac3d5ced186e761de4f6402a126aa2475ab5898e273a8f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jaredhuling/actions/runs/26328855832"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-05-23T09:18:37.000Z",
      "arch": "aarch64",
      "commit": "cee664142ae8322955797885fe7e0ba02bc722af",
      "fileid": "b3e9ec83c627cdb81608f491edeb3933e657ea4d15413fbcc28c02e0138cd255",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jaredhuling/actions/runs/26328855832"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-05-23T09:20:39.000Z",
      "arch": "x86_64",
      "commit": "cee664142ae8322955797885fe7e0ba02bc722af",
      "fileid": "e01745b83dc3b1ab8f7d223bf667aec07c05d8ad34f746b6b5ade929b2704d28",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jaredhuling/actions/runs/26328855832"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-05-23T09:18:34.000Z",
      "arch": "aarch64",
      "commit": "cee664142ae8322955797885fe7e0ba02bc722af",
      "fileid": "28b85c3f60f784a906600a0e2143086edfdf316948248def15c066805503df75",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jaredhuling/actions/runs/26328855832"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-05-23T09:20:30.000Z",
      "arch": "x86_64",
      "commit": "cee664142ae8322955797885fe7e0ba02bc722af",
      "fileid": "56771b77c53ad8da8fb21f3372f4b82c772fb15bb132733985577c83d577b26f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jaredhuling/actions/runs/26328855832"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.1",
      "date": "2026-05-23T09:19:05.000Z",
      "arch": "emscripten",
      "commit": "cee664142ae8322955797885fe7e0ba02bc722af",
      "fileid": "f1902de8b4558f3c7118a60019c4f0742192f022353fb93bc669130d80e71c4f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/jaredhuling/actions/runs/26328855832"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-05-23T09:18:06.000Z",
      "arch": "x86_64",
      "commit": "cee664142ae8322955797885fe7e0ba02bc722af",
      "fileid": "3f7210546d18c91f146aed5729cb60035b604779b5bb8be794a1a48b89da4de5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jaredhuling/actions/runs/26328855832"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-05-23T09:18:03.000Z",
      "arch": "x86_64",
      "commit": "cee664142ae8322955797885fe7e0ba02bc722af",
      "fileid": "ea693700b21dde4aad9aa17a9524f98859683ea01592e50cfff7d4445adf3a03",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jaredhuling/actions/runs/26328855832"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-05-23T09:18:55.000Z",
      "arch": "x86_64",
      "commit": "cee664142ae8322955797885fe7e0ba02bc722af",
      "fileid": "146949396c2c9502f6aaf90109a17447b34f2de5951c97dc142679e2431b1599",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jaredhuling/actions/runs/26328855832"
    }
  ]
}