{
  "_id": "6ad4aa5a7774b2311ffeadb1",
  "Package": "bhm",
  "Type": "Package",
  "Title": "Biomarker Threshold Models",
  "Version": "1.20",
  "Date": "2026-08-29",
  "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": "2026-09-18 13:24:38 UTC",
  "RemoteUrl": "https://github.com/statapps/bhm",
  "RemoteRef": "HEAD",
  "RemoteSha": "a46cf8752606155d0f2c49570575141a59a3bde2",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-18 11:12:36 UTC",
    "User": "root"
  },
  "_user": "statapps",
  "_type": "src",
  "_file": "bhm_1.20.tar.gz",
  "_fileid": "https://r2.ropensci.org/468e3ea6293305069562814aa14271ef98a22a6fad25459a396e17605c9c8fd1",
  "_filesize": 266443,
  "_sha256": "468e3ea6293305069562814aa14271ef98a22a6fad25459a396e17605c9c8fd1",
  "_expires": "2027-01-26T11:15:36.000Z",
  "_created": "2026-10-18T11:12:36.000Z",
  "_published": "2026-10-18T11:15:38.393Z",
  "_buildurl": "https://github.com/r-universe/statapps/actions/runs/39122152456",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 117660280944,
      "time": 116,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12135275060"
    },
    {
      "job": 117660280965,
      "time": 131,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12133969224"
    },
    {
      "job": 117660280955,
      "time": 99,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12135180878"
    },
    {
      "job": 117660280966,
      "time": 140,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12134671786"
    },
    {
      "job": 117659815553,
      "time": 140,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12134408481"
    },
    {
      "job": 117660280967,
      "time": 79,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12135096280"
    },
    {
      "job": 117660281009,
      "time": 73,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12134926064"
    },
    {
      "job": 117660281063,
      "time": 101,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12134322841"
    },
    {
      "job": 117660281144,
      "time": 86,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12134612874"
    }
  ],
  "_upstream": "https://github.com/statapps/bhm",
  "_commit": {
    "id": "a46cf8752606155d0f2c49570575141a59a3bde2",
    "author": "statapps <19355054+statapps@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Update README.md",
    "time": 1789737878
  },
  "_maintainer": {
    "name": "Bingshu E. Chen",
    "email": "bingshu.chen@queensu.ca",
    "login": "statapps",
    "description": "",
    "uuid": 19355054
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "coda",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "role": "Depends"
    },
    {
      "package": "lpl",
      "role": "Depends"
    },
    {
      "package": "survival",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    }
  ],
  "_owner": "statapps",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-38",
      "n": 8
    }
  ],
  "_tags": [],
  "_stars": 2,
  "_contributors": [
    {
      "user": "statapps",
      "count": 80,
      "uuid": 19355054
    }
  ],
  "_userbio": {
    "uuid": 19355054,
    "type": "user",
    "name": "statapps",
    "followers": 2
  },
  "_downloads": {
    "count": 407,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bhm"
  },
  "_devurl": "https://github.com/statapps/bhm",
  "_searchresults": 9,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/bhm.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_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",
    "coxpLRT",
    "coxpLRT.default",
    "coxpLRT.formula",
    "coxpLRTcvPredErr",
    "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.coxpLRT",
    "plot.glmpLRT",
    "plot.llm",
    "plot.pIndex",
    "plot.resboot",
    "plot.residuals.brm",
    "plot.rmscb",
    "ppicexp",
    "predict.coxpLRT",
    "print.bhm",
    "print.brm",
    "print.coxpLRT",
    "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",
    "resbootCox",
    "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": "coxpLRT",
      "title": "Penalized Likelihood Ratio Test for a Biomarker Threshold Effect in the Cox Proportional Hazards Model",
      "topics": [
        "coxpLRT",
        "coxpLRT.default",
        "coxpLRT.formula",
        "coxpLRTcvPredErr",
        "resbootCox"
      ]
    },
    {
      "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.coxpLRT",
        "plot.pIndex",
        "plot.resboot",
        "plot.residuals.brm"
      ]
    },
    {
      "page": "predict",
      "title": "Predict Method for Model Fits in the 'bhm' package",
      "topics": [
        "predict.coxpLRT"
      ]
    },
    {
      "page": "print",
      "title": "print a fitted object or a summary of fitted object",
      "topics": [
        "print.bhm",
        "print.brm",
        "print.coxpLRT",
        "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",
    "matrixStats",
    "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": "2026-10-18T11:14:21.000Z",
      "distro": "resolute",
      "commit": "a46cf8752606155d0f2c49570575141a59a3bde2",
      "fileid": "https://r2.ropensci.org/8671a33e2c08179276b3dcb87d4fe0cdafddd06d6a1da03492672fa46f2f1043",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/statapps/actions/runs/39122152456"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.20",
      "date": "2026-10-18T11:14:24.000Z",
      "distro": "resolute",
      "commit": "a46cf8752606155d0f2c49570575141a59a3bde2",
      "fileid": "https://r2.ropensci.org/5c12e0bd375ed828987fc23544e05bddc99349b6e0638ec9a1be7866a4c9d490",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/statapps/actions/runs/39122152456"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.20",
      "date": "2026-10-18T11:14:04.000Z",
      "commit": "a46cf8752606155d0f2c49570575141a59a3bde2",
      "fileid": "https://r2.ropensci.org/220fc03406f382664ce8736529de7e48688d7d3062e53721e8c482c416aa607e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/statapps/actions/runs/39122152456"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.20",
      "date": "2026-10-18T11:14:40.000Z",
      "commit": "a46cf8752606155d0f2c49570575141a59a3bde2",
      "fileid": "https://r2.ropensci.org/153a4d5d7497563081ec538473e8cad00d7b991aea0a3b168fd96c35571407e2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/statapps/actions/runs/39122152456"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.20",
      "date": "2026-10-18T11:14:14.000Z",
      "commit": "a46cf8752606155d0f2c49570575141a59a3bde2",
      "fileid": "https://r2.ropensci.org/5e6940edd9a16a55ffb58cefbe5adf351b95497e7bbe71cd9a23da02f7d84b18",
      "status": "success",
      "buildurl": "https://github.com/r-universe/statapps/actions/runs/39122152456"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.20",
      "date": "2026-10-18T11:13:36.000Z",
      "commit": "a46cf8752606155d0f2c49570575141a59a3bde2",
      "fileid": "https://r2.ropensci.org/7d151138d4d8dcd472ab1ea146f4b820454772b499460ed473a7bb1add74309a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/statapps/actions/runs/39122152456"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.20",
      "date": "2026-10-18T11:13:45.000Z",
      "commit": "a46cf8752606155d0f2c49570575141a59a3bde2",
      "fileid": "https://r2.ropensci.org/0e92008cb58379ca8c7ed07abe2abd97fbe1ce2481cee0687a4e5740f7067c0f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/statapps/actions/runs/39122152456"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.20",
      "date": "2026-10-18T11:13:40.000Z",
      "commit": "a46cf8752606155d0f2c49570575141a59a3bde2",
      "fileid": "https://r2.ropensci.org/66e8b5fb269fd7bf5edff3ee0aaef09827971bc82090ae336f7bb8844e9a811f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/statapps/actions/runs/39122152456"
    }
  ]
}