{
  "_id": "6ad1c1410edca5be25021df0",
  "Package": "clinstats",
  "Title": "Clinical Research Statistics Toolkit",
  "Version": "0.1.2",
  "Authors@R": "c(\nperson(\"Feng\", \"Gao\", email = \"gaofeng21cn@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Lina\", \"Zhu\", role = \"ctb\"),\nperson(\"Wei\", \"Wang\", role = \"ctb\")\n)",
  "Description": "Statistical utilities that recur in clinical and\ntranslational research workflows: receiver operating\ncharacteristic (ROC) summaries, odds ratios, univariable and\nmultivariable Cox and logistic regression tables,\ntime-dependent survival cut points, resampling-based Cox\nscreening, TCGA clinical extraction, and expression-matrix\ncleaning. Includes curated colorectal cancer clinical datasets\nassembled from public repositories, a Quarto report template,\nand tidy data-frame output that is convenient for both\ninteractive and programmatic use.",
  "License": "Apache License (>= 2)",
  "URL": "https://github.com/gflab/clinstats",
  "BugReports": "https://github.com/gflab/clinstats/issues",
  "Config/testthat/edition": "3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "Roxygen": "list(markdown = TRUE)",
  "Config/roxygen2/version": "8.1.0",
  "Repository": "https://gflab.r-universe.dev",
  "Date/Publication": "2026-09-16 05:07:48 UTC",
  "RemoteUrl": "https://github.com/gflab/clinstats",
  "RemoteRef": "main",
  "RemoteSha": "ac4cc66ddb925bb3eeb67db404d9c3239765e814",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-16 06:12:20 UTC",
    "User": "root"
  },
  "Author": "Feng Gao [aut, cre],\nLina Zhu [ctb],\nWei Wang [ctb]",
  "Maintainer": "Feng Gao <gaofeng21cn@gmail.com>",
  "_user": "gflab",
  "_type": "src",
  "_file": "clinstats_0.1.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/d1ec7519f3a7475252996d6a68ddde9f78ca9afdc7ea5d7e5d03f4478e2cbaa5",
  "_filesize": 250217,
  "_sha256": "d1ec7519f3a7475252996d6a68ddde9f78ca9afdc7ea5d7e5d03f4478e2cbaa5",
  "_expires": "2027-01-24T06:16:31.000Z",
  "_created": "2026-10-16T06:12:20.000Z",
  "_published": "2026-10-16T06:16:33.737Z",
  "_buildurl": "https://github.com/r-universe/gflab/actions/runs/38859566570",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 116839651462,
      "time": 127,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12028123501"
    },
    {
      "job": 116839651585,
      "time": 148,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12028583759"
    },
    {
      "job": 116839651439,
      "time": 200,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12028782874"
    },
    {
      "job": 116839651430,
      "time": 176,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12028976738"
    },
    {
      "job": 116838660508,
      "time": 201,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12028418773"
    },
    {
      "job": 116839651451,
      "time": 119,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12028698249"
    },
    {
      "job": 116839651521,
      "time": 83,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12028742951"
    },
    {
      "job": 116839651527,
      "time": 109,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12028716979"
    },
    {
      "job": 116839651421,
      "time": 76,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12027834317"
    }
  ],
  "_upstream": "https://github.com/gflab/clinstats",
  "_commit": {
    "id": "ac4cc66ddb925bb3eeb67db404d9c3239765e814",
    "author": "Feng GAO <gaofeng21cn@hotmail.com>",
    "committer": "Feng GAO <gaofeng21cn@hotmail.com>",
    "message": "Document the r-universe binaries\n\nPrebuilt binaries for Linux, macOS, and Windows are published from\ngflab.r-universe.dev, so installing no longer needs a compiler. The GitHub\nroute is unchanged.\n",
    "time": 1789535268
  },
  "_maintainer": {
    "name": "Feng Gao",
    "email": "gaofeng21cn@gmail.com"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1",
      "role": "Depends"
    },
    {
      "package": "cli",
      "role": "Imports"
    },
    {
      "package": "future.apply",
      "role": "Imports"
    },
    {
      "package": "pROC",
      "role": "Imports"
    },
    {
      "package": "survival",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "withr",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "gflab",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-38",
      "n": 7
    }
  ],
  "_tags": [
    {
      "name": "v0.1.0",
      "date": "2026-09-15"
    },
    {
      "name": "v0.1.1",
      "date": "2026-09-16"
    },
    {
      "name": "v0.1.2",
      "date": "2026-09-16"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "gaofeng21cn",
      "count": 7,
      "uuid": 5626387
    }
  ],
  "_userbio": {
    "uuid": 70964803,
    "type": "organization",
    "name": "FengGao Lab @ SYSU",
    "followers": 1,
    "description": "Medical AI and translational cancer research at Sun Yat-sen University."
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/clinstats"
  },
  "_devurl": "https://github.com/gflab/clinstats",
  "_searchresults": 1,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/clinstats.html",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_cranurl": false,
  "_exports": [
    "clean_expression",
    "copy_report_template",
    "cox_table",
    "evaluate_model",
    "logistic_table",
    "odds_ratio",
    "oncotype_crc",
    "resample_cox",
    "roc_summary",
    "survival_cutoff",
    "survival_response",
    "tcga_clinical"
  ],
  "_datasets": [
    {
      "name": "clin_crc",
      "title": "Curated colorectal cancer clinical data",
      "object": "clin_crc",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample",
        "sex",
        "age",
        "tnm.stage",
        "tnm.t",
        "tnm.n",
        "tnm.m",
        "lymphnodes",
        "tumor.location",
        "grade",
        "chemotherapy.adjuvant",
        "rfs.event",
        "rfs.delay",
        "os.event",
        "os.delay",
        "dfs.event",
        "dfs.delay",
        "mmr.status",
        "cimp.status",
        "cin.status",
        "tp53.mutation",
        "kras.mutation",
        "braf.mutation",
        "dataset",
        "cms"
      ],
      "rows": 2816,
      "table": true,
      "tojson": true
    },
    {
      "name": "clin_crc_cell",
      "title": "Curated colorectal cancer clinical data",
      "object": "clin_crc_cell",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample",
        "sex",
        "age",
        "tnm.stage",
        "tnm.t",
        "tnm.n",
        "tnm.m",
        "lymphnodes",
        "tumor.location",
        "grade",
        "chemotherapy.adjuvant",
        "rfs.event",
        "rfs.delay",
        "os.event",
        "os.delay",
        "dfs.event",
        "dfs.delay",
        "mmr.status",
        "cimp.status",
        "cin.status",
        "tp53.mutation",
        "kras.mutation",
        "braf.mutation",
        "dataset",
        "cms"
      ],
      "rows": 2865,
      "table": true,
      "tojson": true
    },
    {
      "name": "clin_crc_gf",
      "title": "Curated colorectal cancer clinical data",
      "object": "clin_crc_gf",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample",
        "sex",
        "age",
        "tnm.stage",
        "tnm.t",
        "tnm.n",
        "tnm.m",
        "lymphnodes",
        "tumor.location",
        "grade",
        "chemotherapy.adjuvant",
        "rfs.event",
        "rfs.delay",
        "os.event",
        "os.delay",
        "dfs.event",
        "dfs.delay",
        "mmr.status",
        "cimp.status",
        "cin.status",
        "tp53.mutation",
        "kras.mutation",
        "braf.mutation",
        "dataset",
        "cms"
      ],
      "rows": 2868,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "clean_expression",
      "title": "Clean an expression matrix and collapse duplicated gene columns",
      "topics": [
        "clean_expression"
      ]
    },
    {
      "page": "clin_crc",
      "title": "Curated colorectal cancer clinical data",
      "topics": [
        "clin_crc",
        "clin_crc_cell",
        "clin_crc_gf"
      ]
    },
    {
      "page": "copy_report_template",
      "title": "Copy the bundled Quarto analysis report template",
      "topics": [
        "copy_report_template"
      ]
    },
    {
      "page": "cox_table",
      "title": "Regression tables for clinical variables",
      "topics": [
        "cox_table",
        "logistic_table"
      ]
    },
    {
      "page": "evaluate_model",
      "title": "Evaluate a prediction model on training and test data",
      "topics": [
        "evaluate_model"
      ]
    },
    {
      "page": "odds_ratio",
      "title": "Odds ratio for a marker with a binary outcome",
      "topics": [
        "odds_ratio"
      ]
    },
    {
      "page": "oncotype_crc",
      "title": "Oncotype DX colon cancer recurrence score",
      "topics": [
        "oncotype_crc"
      ]
    },
    {
      "page": "resample_cox",
      "title": "Resampling-based Cox screening of candidate markers",
      "topics": [
        "resample_cox"
      ]
    },
    {
      "page": "roc_summary",
      "title": "Summarise the diagnostic performance of a numeric marker",
      "topics": [
        "roc_summary"
      ]
    },
    {
      "page": "survival_cutoff",
      "title": "Survival cut point optimising the Youden index",
      "topics": [
        "survival_cutoff"
      ]
    },
    {
      "page": "survival_response",
      "title": "Build a survival response from a clinical data frame",
      "topics": [
        "survival_response"
      ]
    },
    {
      "page": "tcga_clinical",
      "title": "Extract clinical variables from a legacy TCGA clinical table",
      "topics": [
        "tcga_clinical"
      ]
    }
  ],
  "_readme": "https://github.com/gflab/clinstats/raw/main/README.md",
  "_rundeps": [
    "cli",
    "codetools",
    "digest",
    "future",
    "future.apply",
    "globals",
    "glue",
    "lattice",
    "lifecycle",
    "listenv",
    "magrittr",
    "Matrix",
    "parallelly",
    "pillar",
    "pkgconfig",
    "pROC",
    "Rcpp",
    "rlang",
    "survival",
    "tibble",
    "utf8",
    "vctrs",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "clinstats.Rmd",
      "filename": "clinstats.html",
      "title": "Getting started with clinstats",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Bundled data",
        "Regression tables",
        "Marker evaluation",
        "Expression data",
        "Reproducibility"
      ],
      "created": "2026-09-15 18:01:58",
      "modified": "2026-09-16 01:08:44",
      "commits": 2
    }
  ],
  "_score": 2.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "clinstats",
  "_universes": [
    "gflab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-10-16T06:14:31.000Z",
      "distro": "resolute",
      "commit": "ac4cc66ddb925bb3eeb67db404d9c3239765e814",
      "fileid": "https://r2.ropensci.org/32b8f3008a55ef7c0cdaf18d1ab7d0f9d08ee0039cf45acd00be15ed262f6c86",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gflab/actions/runs/38859566570"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-10-16T06:14:46.000Z",
      "distro": "resolute",
      "commit": "ac4cc66ddb925bb3eeb67db404d9c3239765e814",
      "fileid": "https://r2.ropensci.org/6dc51e5470291d064ba7a06c1e7a03f5ab3219d96c5e0e4c40c639f0a3faf0cd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gflab/actions/runs/38859566570"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-10-16T06:15:17.000Z",
      "commit": "ac4cc66ddb925bb3eeb67db404d9c3239765e814",
      "fileid": "https://r2.ropensci.org/4789a4a100bbf36fb560df9895f92fcb7c40017e0a66f9f2308028a344312860",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gflab/actions/runs/38859566570"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-10-16T06:14:49.000Z",
      "commit": "ac4cc66ddb925bb3eeb67db404d9c3239765e814",
      "fileid": "https://r2.ropensci.org/1553cf2c6c30fa232581f5c4b4675dab90bf0f9fe8854a0c341c7d3ab52da157",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gflab/actions/runs/38859566570"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.2",
      "date": "2026-10-16T06:14:38.000Z",
      "commit": "ac4cc66ddb925bb3eeb67db404d9c3239765e814",
      "fileid": "https://r2.ropensci.org/e4eab9a0bf6f1935cfc232bc2de3ab5beaa3a41753b678881f7e7e0ae6ccec73",
      "status": "success",
      "buildurl": "https://github.com/r-universe/gflab/actions/runs/38859566570"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-10-16T06:13:44.000Z",
      "commit": "ac4cc66ddb925bb3eeb67db404d9c3239765e814",
      "fileid": "https://r2.ropensci.org/6f28004933a216af4aa6329d90d2504aa5072d8cba1e9b4d03f9c01f94898bf2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gflab/actions/runs/38859566570"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-10-16T06:14:01.000Z",
      "commit": "ac4cc66ddb925bb3eeb67db404d9c3239765e814",
      "fileid": "https://r2.ropensci.org/85b171a030df5a3fb2171fd22019f1a8515edcdd828b159bd9ebec92a4e89bb4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gflab/actions/runs/38859566570"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-10-16T06:13:37.000Z",
      "commit": "ac4cc66ddb925bb3eeb67db404d9c3239765e814",
      "fileid": "https://r2.ropensci.org/12c71e0cce48393dc73b7abecbd257b3e0809e63f897f405b063eb94ae22a2b4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gflab/actions/runs/38859566570"
    }
  ]
}