{
  "_id": "6a129b68acfb0bcc41d0e715",
  "Package": "bhm",
  "Type": "Package",
  "Title": "Biomarker Threshold Models",
  "Version": "1.20",
  "Date": "2025-04-29",
  "Author": "Bingshu E. Chen [aut, cre]",
  "Maintainer": "Bingshu E. Chen <bingshu.chen@queensu.ca>",
  "Authors@R": "c(person(given = c(\"Bingshu\", \"E.\"), family = \"Chen\", role = c(\"aut\", \"cre\"), email = \"bingshu.chen@queensu.ca\"))",
  "Description": "Contains tools to fit both predictive and prognostic\nbiomarker effects using biomarker threshold models and\ncontinuous threshold models. Evaluate the treatment effect,\nbiomarker effect and treatment-biomarker interaction using\nprobability index measurement. Test for treatment-biomarker\ninteraction using residual bootstrap method.",
  "License": "GPL (>=2)",
  "LazyLoad": "yes",
  "Repository": "https://statapps.r-universe.dev",
  "Date/Publication": "2025-04-27 00:09:40 UTC",
  "RemoteUrl": "https://github.com/statapps/bhm",
  "RemoteRef": "HEAD",
  "RemoteSha": "8762ac7a0c9cfb4b27f07e7b21f465e276f7c516",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-24 06:28:38 UTC",
    "User": "root"
  },
  "MD5sum": "9704b00eb906deffd046a0172b4ad588",
  "_user": "statapps",
  "_type": "src",
  "_file": "bhm_1.20.tar.gz",
  "_fileid": "b6505a36ca6222af2a3a99d53935d6eb31bcc8bb9facba27d6bd6cc482e7bfdc",
  "_filesize": 239190,
  "_sha256": "b6505a36ca6222af2a3a99d53935d6eb31bcc8bb9facba27d6bd6cc482e7bfdc",
  "_created": "2026-05-24T06:28:38.000Z",
  "_published": "2026-05-24T06:32:08.900Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77577351371,
      "time": 143,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7182894230"
    },
    {
      "job": 77577351369,
      "time": 139,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7182893990"
    },
    {
      "job": 77577351370,
      "time": 141,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7182891588"
    },
    {
      "job": 77577351366,
      "time": 180,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7182893789"
    },
    {
      "job": 77577224969,
      "time": 155,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7182879033"
    },
    {
      "job": 77577351365,
      "time": 97,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7182889492"
    },
    {
      "job": 77577351372,
      "time": 103,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7182890172"
    },
    {
      "job": 77577351373,
      "time": 103,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7182890006"
    },
    {
      "job": 77577351375,
      "time": 97,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7182889373"
    }
  ],
  "_buildurl": "https://github.com/r-universe/statapps/actions/runs/26353971605",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/statapps/bhm",
  "_commit": {
    "id": "8762ac7a0c9cfb4b27f07e7b21f465e276f7c516",
    "author": "b3chen <b3chen@local.host>",
    "committer": "b3chen <b3chen@local.host>",
    "message": "ggkm\n",
    "time": 1745712580
  },
  "_maintainer": {
    "name": "Bingshu E. Chen",
    "email": "bingshu.chen@queensu.ca",
    "login": "statapps",
    "description": "",
    "uuid": 19355054
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "coda",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "role": "Depends"
    },
    {
      "package": "gridExtra",
      "role": "Depends"
    },
    {
      "package": "lpl",
      "role": "Depends"
    },
    {
      "package": "survival",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    }
  ],
  "_owner": "statapps",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 2,
  "_contributors": [
    {
      "user": "statapps",
      "count": 77,
      "uuid": 19355054
    }
  ],
  "_userbio": {
    "uuid": 19355054,
    "type": "user",
    "name": "statapps"
  },
  "_downloads": {
    "count": 317,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bhm"
  },
  "_devurl": "https://github.com/statapps/bhm",
  "_searchresults": 9,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/bhm.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/statapps/bhm",
  "_realowner": "statapps",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.1",
      "date": "2016-10-11"
    },
    {
      "version": "1.11",
      "date": "2017-05-11"
    },
    {
      "version": "1.13",
      "date": "2017-12-20"
    },
    {
      "version": "1.15",
      "date": "2019-07-30"
    },
    {
      "version": "1.16",
      "date": "2020-04-13"
    },
    {
      "version": "1.17",
      "date": "2021-12-04"
    },
    {
      "version": "1.18",
      "date": "2022-08-31"
    },
    {
      "version": "1.19",
      "date": "2025-04-26"
    }
  ],
  "_exports": [
    "arns",
    "ars",
    "bhm",
    "bhm.default",
    "bhm.formula",
    "bhmControl",
    "bhmFit",
    "bhmGibbs",
    "brm",
    "brm.default",
    "brm.formula",
    "dpicexp",
    "gendat.glm",
    "gendat.surv",
    "ggkm",
    "glmpLRT",
    "glmpLRT.default",
    "glmpLRT.formula",
    "hpicexp",
    "Hpicexp",
    "llm",
    "llm.default",
    "llm.formula",
    "mpl",
    "mpl.formula",
    "mplFit",
    "picfit",
    "picreg",
    "pIndex",
    "pIndex.default",
    "pIndex.formula",
    "pIndexControl",
    "pIndexFit",
    "pIndexLocal",
    "pIndexThreshold",
    "plot.bhm",
    "plot.brm",
    "plot.glmpLRT",
    "plot.llm",
    "plot.pIndex",
    "plot.resboot",
    "plot.residuals.brm",
    "plot.rmscb",
    "ppicexp",
    "print.bhm",
    "print.brm",
    "print.glmpLRT",
    "print.llm",
    "print.mpl",
    "print.picreg",
    "print.pIndex",
    "print.resboot",
    "print.rmscb",
    "print.summary.bhm",
    "print.summary.brm",
    "prolikFit",
    "qpicexp",
    "resboot",
    "resboot.default",
    "resboot.formula",
    "residuals.brm",
    "rmscb",
    "rmscb.default",
    "rmscb.formula",
    "rmsControl",
    "rpicexp",
    "rpwexp",
    "summary.bhm",
    "summary.brm",
    "summary.glmpLRT",
    "summary.picreg",
    "summary.rmscb",
    "thm.fit",
    "thm.lik",
    "x.cdf"
  ],
  "_datasets": [
    {
      "name": "data",
      "title": "dataset",
      "object": "data",
      "file": "data.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "stime",
        "cstatus",
        "z",
        "x"
      ],
      "rows": 300,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "bhm-package",
      "title": "An R package for the biomarker threshold models",
      "topics": [
        "bhm-package",
        "bhm-doc"
      ]
    },
    {
      "page": "ars",
      "title": "Function to perform Adaptive Rejection Sampling",
      "topics": [
        "arns",
        "ars",
        "rpwexp"
      ]
    },
    {
      "page": "bhm",
      "title": "Fitting Biomarker Threshold Models",
      "topics": [
        "bhm",
        "bhm.default",
        "bhm.formula",
        "bhmFit",
        "bhmGibbs",
        "prolikFit",
        "summary.bhm",
        "thm.fit",
        "thm.lik",
        "x.cdf"
      ]
    },
    {
      "page": "control",
      "title": "Auxiliary function for bhm fitting",
      "topics": [
        "bhmControl",
        "prolikControl"
      ]
    },
    {
      "page": "brm",
      "title": "Fitting Biomarker Continuous Threshold Models",
      "topics": [
        "brm",
        "brm.default",
        "brm.formula",
        "residuals.brm",
        "summary.brm"
      ]
    },
    {
      "page": "data",
      "title": "dataset",
      "topics": [
        "data",
        "gendat.glm",
        "gendat.surv"
      ]
    },
    {
      "page": "ggkm",
      "title": "Creates a Kaplan-Meier plot with at risk tables below",
      "topics": [
        "ggkm"
      ]
    },
    {
      "page": "glmpLRT",
      "title": "Penalized likelihood ratio test for the generalized linear models.",
      "topics": [
        "glmpLRT",
        "glmpLRT.default",
        "glmpLRT.formula",
        "plot.glmpLRT",
        "print.glmpLRT",
        "summary.glmpLRT"
      ]
    },
    {
      "page": "llm",
      "title": "Fit an L-shape linear model",
      "topics": [
        "llm",
        "llm.default",
        "llm.formula",
        "plot.llm",
        "print.llm"
      ]
    },
    {
      "page": "mpl",
      "title": "Joint models for clustered data with binary and survival outcomes.",
      "topics": [
        "mpl",
        "mpl.formula",
        "mplFit"
      ]
    },
    {
      "page": "pIndex",
      "title": "Probability Index for Survival Time Difference",
      "topics": [
        "pIndex",
        "pIndex.default",
        "pIndex.formula",
        "pIndexFit",
        "pIndexLocal",
        "pIndexThreshold"
      ]
    },
    {
      "page": "pIndexControl",
      "title": "Auxiliary function for pIndex fitting",
      "topics": [
        "pIndexControl"
      ]
    },
    {
      "page": "plot",
      "title": "Plot a fitted biomarker threhold model",
      "topics": [
        "plot.bhm",
        "plot.brm",
        "plot.pIndex",
        "plot.resboot",
        "plot.residuals.brm"
      ]
    },
    {
      "page": "print",
      "title": "print a fitted object or a summary of fitted object",
      "topics": [
        "print.bhm",
        "print.brm",
        "print.mpl",
        "print.picreg",
        "print.pIndex",
        "print.resboot",
        "print.summary.bhm",
        "print.summary.brm"
      ]
    },
    {
      "page": "resboot",
      "title": "Rresidual Bootstrap Test (RBT) for treatment-biomarker interaction",
      "topics": [
        "resboot",
        "resboot.default",
        "resboot.formula"
      ]
    },
    {
      "page": "rmscb",
      "title": "Fitting Restricted Mean Survival Time Models with a Continuous Biomarker",
      "topics": [
        "plot.rmscb",
        "print.rmscb",
        "rmscb",
        "rmscb.default",
        "rmscb.formula",
        "rmsControl",
        "summary.rmscb"
      ]
    },
    {
      "page": "picexp",
      "title": "The Piecewise Exponential Distribution",
      "topics": [
        "dpicexp",
        "Hpicexp",
        "hpicexp",
        "picfit",
        "picreg",
        "ppicexp",
        "qpicexp",
        "rpicexp",
        "summary.picreg"
      ]
    }
  ],
  "_readme": "https://github.com/statapps/bhm/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "coda",
    "cpp11",
    "farver",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "lpl",
    "MASS",
    "Matrix",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "survival",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_score": 3,
  "_indexed": true,
  "_nocasepkg": "bhm",
  "_universes": [
    "statapps"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.20",
      "date": "2026-05-24T06:30:35.000Z",
      "distro": "noble",
      "commit": "8762ac7a0c9cfb4b27f07e7b21f465e276f7c516",
      "fileid": "71cd4d7d444a57f1b2a841f7e37ebb18ba2d694f34dfad15028fbf1f546a879b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/statapps/actions/runs/26353971605"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.20",
      "date": "2026-05-24T06:30:34.000Z",
      "distro": "noble",
      "commit": "8762ac7a0c9cfb4b27f07e7b21f465e276f7c516",
      "fileid": "48c562f56fbb4f2bc435815af1c13ce0066084e22acd6e4bd2a855da7e5b3162",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/statapps/actions/runs/26353971605"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.20",
      "date": "2026-05-24T06:30:31.000Z",
      "commit": "8762ac7a0c9cfb4b27f07e7b21f465e276f7c516",
      "fileid": "77cb9a2d79bb61f8966e42bcbce0b529e61bcfe4a2c3fcb59bca1fe729293508",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/statapps/actions/runs/26353971605"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.20",
      "date": "2026-05-24T06:30:42.000Z",
      "commit": "8762ac7a0c9cfb4b27f07e7b21f465e276f7c516",
      "fileid": "bb9040797c31bdd0bda5370f1f38fe7537ccecc28e2e9fe64b0a7837cdc34d73",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/statapps/actions/runs/26353971605"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.20",
      "date": "2026-05-24T06:30:32.000Z",
      "commit": "8762ac7a0c9cfb4b27f07e7b21f465e276f7c516",
      "fileid": "ad839c297ff5046165112185b13a8ec7d20350de2051e04cc6f622ab3cb56027",
      "status": "success",
      "buildurl": "https://github.com/r-universe/statapps/actions/runs/26353971605"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.20",
      "date": "2026-05-24T06:29:52.000Z",
      "commit": "8762ac7a0c9cfb4b27f07e7b21f465e276f7c516",
      "fileid": "d98ab898dd21ec6d9b349a9581bf39d521106002873023050804b56b90ed8293",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/statapps/actions/runs/26353971605"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.20",
      "date": "2026-05-24T06:29:53.000Z",
      "commit": "8762ac7a0c9cfb4b27f07e7b21f465e276f7c516",
      "fileid": "75d4c2ff14883022763643ab052278f367d0c0afe78b05eec97a907137ef9815",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/statapps/actions/runs/26353971605"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.20",
      "date": "2026-05-24T06:29:47.000Z",
      "commit": "8762ac7a0c9cfb4b27f07e7b21f465e276f7c516",
      "fileid": "740f26f095689bfd9fe37dc245f1b8c2aed9bca48f1a8d120f3ac9116c676bad",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/statapps/actions/runs/26353971605"
    }
  ]
}