{
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  "Package": "Cyclops",
  "Type": "Package",
  "Title": "Cyclic Coordinate Descent for Logistic, Poisson and Survival\nAnalysis",
  "Version": "3.7.1",
  "Authors@R": "c(\nperson(\"Marc A.\", \"Suchard\", email = \"msuchard@ucla.edu\", role = c(\"aut\",\"cre\")),\nperson(\"Martijn J.\", \"Schuemie\", role = \"aut\"),\nperson(\"Trevor R.\", \"Shaddox\", role = \"aut\"),\nperson(\"Yuxi\", \"Tian\", role = \"aut\"),\nperson(\"Jianxiao\", \"Yang\", role = \"aut\"),\nperson(\"Eric\", \"Kawaguchi\", role = \"aut\"),\nperson(\"Sushil\", \"Mittal\", role =\"ctb\"),\nperson(\"Observational Health Data Sciences and Informatics\", role = \"cph\"),\nperson(\"Marcus\", \"Geelnard\", role = c(\"cph\", \"ctb\"),\ncomment = \"provided the TinyThread library\"),\nperson(\"Rutgers University\", role = c(\"cph\", \"ctb\"),\ncomment = \"provided the HParSearch routine\"),\nperson(\"R Development Core Team\", role = c(\"cph\", \"ctb\"),\ncomment = \"provided the ZeroIn routine\")\n)",
  "Description": "This model fitting tool incorporates cyclic coordinate\ndescent and majorization-minimization approaches to fit a\nvariety of regression models found in large-scale observational\nhealthcare data.  Implementations focus on computational\noptimization and fine-scale parallelization to yield efficient\ninference in massive datasets.  Please see: Suchard, Simpson,\nZorych, Ryan and Madigan (2013) <doi:10.1145/2414416.2414791>.",
  "License": "Apache License 2.0",
  "LazyData": "Yes",
  "Biarch": "true",
  "URL": "https://github.com/ohdsi/cyclops",
  "BugReports": "https://github.com/ohdsi/cyclops/issues",
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  "Repository": "https://ohdsi.r-universe.dev",
  "Date/Publication": "2026-05-26 15:23:19 UTC",
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  "Author": "Marc A. Suchard [aut, cre],\nMartijn J. Schuemie [aut],\nTrevor R. Shaddox [aut],\nYuxi Tian [aut],\nJianxiao Yang [aut],\nEric Kawaguchi [aut],\nSushil Mittal [ctb],\nObservational Health Data Sciences and Informatics [cph],\nMarcus Geelnard [cph, ctb] (provided the TinyThread library),\nRutgers University [cph, ctb] (provided the HParSearch routine),\nR Development Core Team [cph, ctb] (provided the ZeroIn routine)",
  "Maintainer": "Marc A. Suchard <msuchard@ucla.edu>",
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  "_exports": [
    "aconfint",
    "cacheCyclopsModelForJava",
    "clearCyclopsModelCache",
    "convertToCyclopsData",
    "convertToTimeVaryingCoef",
    "coverage",
    "createAutoGridCrossValidationControl",
    "createControl",
    "createCyclopsData",
    "createNonSeparablePrior",
    "createParameterizedPrior",
    "createPrior",
    "createWeightBasedSearchControl",
    "finalizeSqlCyclopsData",
    "fitCyclopsModel",
    "fitCyclopsSimulation",
    "getCovariateIds",
    "getCovariateTypes",
    "getCyclopsProfileLogLikelihood",
    "getFineGrayWeights",
    "getFloatingPointSize",
    "getHyperParameter",
    "getNumberOfCovariates",
    "getNumberOfRows",
    "getNumberOfStrata",
    "getUnivariableCorrelation",
    "getUnivariableSeparability",
    "gradient",
    "isInitialized",
    "listGPUDevices",
    "meanLinearPredictor",
    "mse",
    "Multitype",
    "readCyclopsData",
    "runBootstrap",
    "setOpenCLDevice",
    "simulateCyclopsData",
    "splitTime",
    "testProportionality"
  ],
  "_datasets": [
    {
      "name": "oxford",
      "title": "Oxford self-controlled case series data",
      "object": "oxford",
      "class": [
        "data.frame"
      ],
      "fields": [
        "indiv",
        "event",
        "interval",
        "agegr",
        "exgr",
        "loginterval"
      ],
      "rows": 38,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "cacheCyclopsModelForJava",
      "title": "Place Cyclops model fit object in a persistent cache",
      "topics": [
        "cacheCyclopsModelForJava"
      ]
    },
    {
      "page": "clearCyclopsModelCache",
      "title": "Clear the Cyclops persistent cache",
      "topics": [
        "clearCyclopsModelCache"
      ]
    },
    {
      "page": "coef.cyclopsFit",
      "title": "Extract model coefficients",
      "topics": [
        "coef.cyclopsFit"
      ]
    },
    {
      "page": "confint.cyclopsFit",
      "title": "Confidence intervals for Cyclops model parameters",
      "topics": [
        "confint.cyclopsFit"
      ]
    },
    {
      "page": "convertToCyclopsData",
      "title": "Convert data from two data frames or ffdf objects into a CyclopsData object",
      "topics": [
        "convertToCyclopsData",
        "convertToCyclopsData.data.frame",
        "convertToCyclopsData.tbl_dbi"
      ]
    },
    {
      "page": "convertToTimeVaryingCoef",
      "title": "Convert short sparse covariate table to long sparse covariate table for time-varying coefficients.",
      "topics": [
        "convertToTimeVaryingCoef"
      ]
    },
    {
      "page": "coverage",
      "title": "Coverage",
      "topics": [
        "coverage"
      ]
    },
    {
      "page": "createAutoGridCrossValidationControl",
      "title": "Create a Cyclops control object that supports multiple hyperparameters",
      "topics": [
        "createAutoGridCrossValidationControl"
      ]
    },
    {
      "page": "createControl",
      "title": "Create a Cyclops control object",
      "topics": [
        "createControl"
      ]
    },
    {
      "page": "createCyclopsData",
      "title": "Create a Cyclops data object",
      "topics": [
        "createCyclopsData"
      ]
    },
    {
      "page": "createNonSeparablePrior",
      "title": "Create a Cyclops prior object that returns the MLE of non-separable coefficients",
      "topics": [
        "createNonSeparablePrior"
      ]
    },
    {
      "page": "createParameterizedPrior",
      "title": "Create a Cyclops parameterized prior object",
      "topics": [
        "createParameterizedPrior"
      ]
    },
    {
      "page": "createPrior",
      "title": "Create a Cyclops prior object",
      "topics": [
        "createPrior"
      ]
    },
    {
      "page": "createWeightBasedSearchControl",
      "title": "Create a Cyclops control object that supports in- / out-of-sample hyperparameter search using weights",
      "topics": [
        "createWeightBasedSearchControl"
      ]
    },
    {
      "page": "cyclops",
      "title": "Cyclops: Cyclic coordinate descent for logistic, Poisson and survival analysis",
      "topics": [
        "Cyclops-package",
        "Cyclops",
        "cyclops"
      ]
    },
    {
      "page": "cyclopsLibraryFileName",
      "title": "Get full path to installed Cyclops library",
      "topics": [
        "cyclopsLibraryFileName"
      ]
    },
    {
      "page": "fitCyclopsModel",
      "title": "Fit a Cyclops model",
      "topics": [
        "fitCyclopsModel"
      ]
    },
    {
      "page": "fitCyclopsSimulation",
      "title": "Fit simulated data",
      "topics": [
        "fitCyclopsSimulation"
      ]
    },
    {
      "page": "getCovariateIds",
      "title": "Get covariate identifiers",
      "topics": [
        "getCovariateIds"
      ]
    },
    {
      "page": "getCovariateTypes",
      "title": "Get covariate types",
      "topics": [
        "getCovariateTypes"
      ]
    },
    {
      "page": "getCyclopsProfileLogLikelihood",
      "title": "Profile likelihood for Cyclops model parameters",
      "topics": [
        "getCyclopsProfileLogLikelihood"
      ]
    },
    {
      "page": "getFineGrayWeights",
      "title": "Creates a 'Surv' object that forces in competing risks and the IPCW needed for Fine-Gray estimation.",
      "topics": [
        "getFineGrayWeights"
      ]
    },
    {
      "page": "getFloatingPointSize",
      "title": "Get floating point size",
      "topics": [
        "getFloatingPointSize"
      ]
    },
    {
      "page": "getHyperParameter",
      "title": "Get hyperparameter",
      "topics": [
        "getHyperParameter"
      ]
    },
    {
      "page": "getNumberOfCovariates",
      "title": "Get total number of covariates",
      "topics": [
        "getNumberOfCovariates"
      ]
    },
    {
      "page": "getNumberOfRows",
      "title": "Get total number of rows",
      "topics": [
        "getNumberOfRows"
      ]
    },
    {
      "page": "getNumberOfStrata",
      "title": "Get number of strata",
      "topics": [
        "getNumberOfStrata"
      ]
    },
    {
      "page": "getUnivariableCorrelation",
      "title": "Get univariable correlation",
      "topics": [
        "getUnivariableCorrelation"
      ]
    },
    {
      "page": "getUnivariableSeparability",
      "title": "Get univariable linear separability",
      "topics": [
        "getUnivariableSeparability"
      ]
    },
    {
      "page": "gradient",
      "title": "Extract gradient",
      "topics": [
        "gradient"
      ]
    },
    {
      "page": "isInitialized",
      "title": "Check if a Cyclops data object is initialized",
      "topics": [
        "isInitialized"
      ]
    },
    {
      "page": "listGPUDevices",
      "title": "List available GPU devices",
      "topics": [
        "listGPUDevices"
      ]
    },
    {
      "page": "logLik.cyclopsFit",
      "title": "Extract log-likelihood",
      "topics": [
        "logLik.cyclopsFit"
      ]
    },
    {
      "page": "meanLinearPredictor",
      "title": "Calculates xbar*beta",
      "topics": [
        "meanLinearPredictor"
      ]
    },
    {
      "page": "mse",
      "title": "Mean squared error",
      "topics": [
        "mse"
      ]
    },
    {
      "page": "Multitype",
      "title": "Create a multitype outcome object",
      "topics": [
        "Multitype"
      ]
    },
    {
      "page": "oxford",
      "title": "Oxford self-controlled case series data",
      "topics": [
        "oxford"
      ]
    },
    {
      "page": "predict.cyclopsFit",
      "title": "Model predictions",
      "topics": [
        "predict.cyclopsFit"
      ]
    },
    {
      "page": "print.cyclopsData",
      "title": "Print a Cyclops data object",
      "topics": [
        "print.cyclopsData"
      ]
    },
    {
      "page": "print.cyclopsFit",
      "title": "Print a Cyclops model fit object",
      "topics": [
        "print.cyclopsFit"
      ]
    },
    {
      "page": "readCyclopsData",
      "title": "Read Cyclops data from file",
      "topics": [
        "readCyclopsData"
      ]
    },
    {
      "page": "residuals.cyclopsFit",
      "title": "Model residuals",
      "topics": [
        "residuals.cyclopsFit"
      ]
    },
    {
      "page": "runBootstrap",
      "title": "Run bootstrap for Cyclops model parameters",
      "topics": [
        "runBootstrap"
      ]
    },
    {
      "page": "setOpenCLDevice",
      "title": "Set GPU device",
      "topics": [
        "setOpenCLDevice"
      ]
    },
    {
      "page": "simulateCyclopsData",
      "title": "Simulation Cyclops dataset",
      "topics": [
        "simulateCyclopsData"
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