{
  "_id": "6a1be3341d7bb097a0a18fe7",
  "Package": "Umpire",
  "Version": "2.0.11",
  "Date": "2025-02-04",
  "Title": "Simulating Realistic Gene Expression and Clinical Data",
  "Authors@R": "c(person(\"Kevin R.\", \"Coombes\", role = c(\"aut\", \"cre\"),\nemail = \"krc@silicovore.com\"),\nperson(\"Jiexin\", \"Zhang\", role = c(\"aut\")),\nperson(\"Caitlin E.\", \"Coombes\", role = c(\"aut\")))",
  "Description": "The Ultimate Microrray Prediction, Reality and Inference\nEngine (UMPIRE) is a package to facilitate the simulation of\nrealistic microarray data sets with links to associated\noutcomes. See Zhang and Coombes (2012)\n<doi:10.1186/1471-2105-13-S13-S1>. Version 2.0 adds the ability\nto simulate realistic mixed-typed clinical data.",
  "License": "Apache License (== 2.0)",
  "URL": "http://oompa.r-forge.r-project.org/",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-31 07:24:53 UTC",
    "User": "root"
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  "Author": "Kevin R. Coombes [aut, cre], Jiexin Zhang [aut], Caitlin E.\nCoombes [aut]",
  "Maintainer": "Kevin R. Coombes <krc@silicovore.com>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2025-02-05 01:54:51 UTC",
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  "_published": "2026-05-31T07:28:52.768Z",
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    "message": "version 2.0.11\n",
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    "description": "Unofficial read-only mirror of all CRAN R packages"
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    "extra/citation.json",
    "extra/citation.txt",
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      "date": "2020-11-10"
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    "alterMean",
    "alterSD",
    "BlockHyperParameters",
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    "CancerEngine",
    "CancerModel",
    "ClinicalEngine",
    "ClinicalNoiseModel",
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    "covar",
    "Engine",
    "EngineWithActivity",
    "getDaisyTypes",
    "getDataTypes",
    "IndependentLogNormal",
    "IndependentNormal",
    "invGammaMultiple",
    "makeBlockStructure",
    "makeDataTypes",
    "MixedTypeEngine",
    "MVN",
    "ncol",
    "nComponents",
    "nHitsPerPattern",
    "NoiseModel",
    "normalOffset",
    "NormalVsCancerEngine",
    "NormalVsCancerModel",
    "nPatterns",
    "nPossibleHits",
    "nrow",
    "outcomeCoefficients",
    "rand",
    "summary",
    "survivalCoefficients",
    "SurvivalModel"
  ],
  "_help": [
    {
      "page": "e33-addControl",
      "title": "Method \"addControl\"",
      "topics": [
        "addControl",
        "addControl,ANY-method",
        "addControl,CancerEngine-method",
        "addControl,CancerModel-method",
        "addControl-method"
      ]
    },
    {
      "page": "e20-alterMean-method",
      "title": "Methods \"alterMean\" and \"alterSD\"",
      "topics": [
        "alterMean",
        "alterMean,ANY-method",
        "alterMean-method",
        "alterSD",
        "alterSD,ANY-method",
        "alterSD-method"
      ]
    },
    {
      "page": "e15-BlockHyperParameters-class",
      "title": "The \"BlockHyperParameters\" Class",
      "topics": [
        "BlockHyperParameters",
        "BlockHyperParameters-class",
        "makeBlockStructure"
      ]
    },
    {
      "page": "e21-blur-method",
      "title": "Method \"blur\"",
      "topics": [
        "blur",
        "blur,ANY-method",
        "blur-method"
      ]
    },
    {
      "page": "e14-CancerEngine-class",
      "title": "The \"CancerEngine\" Class",
      "topics": [
        "CancerEngine",
        "CancerEngine-class",
        "ClinicalEngine",
        "nComponents,CancerEngine-method",
        "nrow,CancerEngine-method",
        "rand,CancerEngine-method",
        "summary,CancerEngine-method"
      ]
    },
    {
      "page": "e13-CancerModel-class",
      "title": "The \"CancerModel\" Class",
      "topics": [
        "CancerModel",
        "CancerModel-class",
        "ncol,CancerModel-method",
        "nHitsPerPattern",
        "nPatterns",
        "nPossibleHits",
        "nrow,CancerModel-method",
        "outcomeCoefficients",
        "rand,CancerModel-method",
        "summary,CancerModel-method",
        "survivalCoefficients"
      ]
    },
    {
      "page": "e30-clinicalNoiseModel",
      "title": "A Noise Model for Clinical Data",
      "topics": [
        "ClinicalNoiseModel"
      ]
    },
    {
      "page": "e01-Engine-class",
      "title": "The \"Engine\" Class",
      "topics": [
        "alterMean,Engine-method",
        "alterSD,Engine-method",
        "Engine",
        "Engine-class",
        "nComponents,Engine-method",
        "nrow,Engine-method",
        "rand,Engine-method",
        "summary,Engine-method"
      ]
    },
    {
      "page": "e02-EngineWithActivity-class",
      "title": "The \"EngineWithActivity\" Class",
      "topics": [
        "EngineWithActivity",
        "EngineWithActivity-class",
        "rand,EngineWithActivity-method",
        "summary,EngineWithActivity-method"
      ]
    },
    {
      "page": "e04-IndependentLogNormal-class",
      "title": "The \"IndependentLogNormal\" Class",
      "topics": [
        "alterMean,IndependentLogNormal-method",
        "alterSD,IndependentLogNormal-method",
        "IndependentLogNormal",
        "IndependentLogNormal-class",
        "nrow,IndependentLogNormal-method",
        "rand,IndependentLogNormal-method",
        "summary,IndependentLogNormal-method"
      ]
    },
    {
      "page": "e03-IndependentNormal-class",
      "title": "The \"IndependentNormal\" Class",
      "topics": [
        "alterMean,IndependentNormal-method",
        "alterSD,IndependentNormal-method",
        "IndependentNormal",
        "IndependentNormal-class",
        "nrow,IndependentNormal-method",
        "rand,IndependentNormal-method",
        "summary,IndependentNormal-method"
      ]
    },
    {
      "page": "e31-setDataTypes",
      "title": "Discretize a Continuous Data Set to Mixed Types",
      "topics": [
        "getDaisyTypes",
        "getDataTypes",
        "makeDataTypes"
      ]
    },
    {
      "page": "e32-mixedTypeEngine",
      "title": "The \"MixedTypeEngine\" Class",
      "topics": [
        "MixedTypeEngine",
        "MixedTypeEngine-class",
        "rand,MixedTypeEngine-method",
        "summary,MixedTypeEngine-method"
      ]
    },
    {
      "page": "e05-MVN-class",
      "title": "The \"MVN\" Class",
      "topics": [
        "alterMean,MVN-method",
        "alterSD,MVN-method",
        "correl",
        "covar",
        "MVN",
        "MVN-class",
        "nrow,MVN-method",
        "rand,MVN-method",
        "summary,MVN-method"
      ]
    },
    {
      "page": "e23-nComponents-method",
      "title": "Method \"nComponents\"",
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        "nComponents",
        "nComponents,ANY-method",
        "nComponents-method"
      ]
    },
    {
      "page": "e09-NoiseModel-class",
      "title": "The \"NoiseModel\" Class",
      "topics": [
        "blur,NoiseModel-method",
        "NoiseModel",
        "NoiseModel-class",
        "summary,NoiseModel-method"
      ]
    },
    {
      "page": "e16-normalVcancer",
      "title": "Simulating Cancer Versus Normal Datasets",
      "topics": [
        "NormalVsCancerEngine",
        "NormalVsCancerModel"
      ]
    },
    {
      "page": "e22-rand-method",
      "title": "Method \"rand\"",
      "topics": [
        "rand",
        "rand,ANY-method",
        "rand-method"
      ]
    },
    {
      "page": "e11-SurvivalModel-class",
      "title": "The \"SurvivalModel\" Class",
      "topics": [
        "rand,SurvivalModel-method",
        "SurvivalModel",
        "SurvivalModel-class"
      ]
    },
    {
      "page": "e08-transforms",
      "title": "Transform functions",
      "topics": [
        "invGammaMultiple",
        "normalOffset"
      ]
    }
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      "title": "Umpire 2.0: Clinically Realistic Simulations",
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        "Simulating Mixed-Type Clinical Data",
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        "Apply Clinically Realistic Noise",
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