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  "Package": "OhdsiReportGenerator",
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  "Title": "Observational Health Data Sciences and Informatics Report\nGenerator",
  "Version": "2.2.0",
  "Date": "2026-05-15",
  "Authors@R": "c(\nperson(\"Jenna\", \"Reps\", email = \"jreps@its.jnj.com\", role = c(\"aut\", \"cre\")),\nperson(\"Anthony\", \"Sena\", email = \"sena@ohdsi.org\", role = c(\"aut\"))\n)",
  "Maintainer": "Jenna Reps <jreps@its.jnj.com>",
  "Description": "Extract results into R from the Observational Health Data\nSciences and Informatics result database (see\n<https://ohdsi.github.io/Strategus/results-schema/index.html>)\nand generate reports/presentations via 'quarto' that summarize\nresults in HTML format. Learn more about 'OhdsiReportGenerator'\nat <https://ohdsi.github.io/OhdsiReportGenerator/>.",
  "License": "Apache License 2.0",
  "URL": "https://ohdsi.github.io/OhdsiReportGenerator/,\nhttps://github.com/OHDSI/OhdsiReportGenerator",
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  "Date/Publication": "2026-05-15 19:05:34 UTC",
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    "addTarColumn",
    "createCharacterizationIndexes",
    "createCohortIndexes",
    "createIncidenceIndexes",
    "createPredictionReport",
    "createSccsIndexes",
    "formatBinaryCovariateName",
    "generateFullReport",
    "generateSummaryPredictionReport",
    "getAnalysisCohorts",
    "getBinaryCaseSeries",
    "getBinaryRiskFactors",
    "getBinaryTargetBaseline",
    "getCaseCounts",
    "getCaseTargetCounts",
    "getCharacterizationCohortBinary",
    "getCharacterizationCohortContinuous",
    "getCharacterizationDemographics",
    "getCharacterizationOutcomes",
    "getCharacterizationTargets",
    "getCmDiagnosticsData",
    "getCMEstimation",
    "getCmMetaEstimation",
    "getCmNegativeControlEstimates",
    "getCmOutcomes",
    "getCmPropensityModel",
    "getCmTable",
    "getCmTargets",
    "getCohortAttrition",
    "getCohortCounts",
    "getCohortDefinitions",
    "getCohortInclusionRules",
    "getCohortInclusionStats",
    "getCohortInclusionSummary",
    "getCohortMeta",
    "getCohortSubsetAttrition",
    "getCohortSubsetDefinitions",
    "getContinuousCaseSeries",
    "getContinuousRiskFactors",
    "getDatabaseDetails",
    "getDechallengeRechallenge",
    "getDechallengeRechallengeFails",
    "getEventDuration",
    "getExampleConnectionDetails",
    "getFullPredictionPerformances",
    "getIncidenceOutcomes",
    "getIncidenceRates",
    "getIncidenceTargets",
    "getOutcomeTable",
    "getPredictionAggregateTopPredictors",
    "getPredictionCohorts",
    "getPredictionCovariates",
    "getPredictionDiagnostics",
    "getPredictionDiagnosticTable",
    "getPredictionHyperParamSearch",
    "getPredictionIntercept",
    "getPredictionLift",
    "getPredictionModelDesigns",
    "getPredictionOutcomes",
    "getPredictionPerformances",
    "getPredictionPerformanceTable",
    "getPredictionTargets",
    "getPredictionTopPredictors",
    "getSccsDiagnosticsData",
    "getSccsEstimation",
    "getSccsMetaEstimation",
    "getSccsModel",
    "getSccsNegativeControlEstimates",
    "getSccsOutcomes",
    "getSccsTable",
    "getSccsTargets",
    "getSccsTimeToEvent",
    "getSubsetText",
    "getTargetBinaryFeatures",
    "getTargetContinuousFeatures",
    "getTargetTable",
    "getTimeToEvent",
    "getTreatmentPathways",
    "kableDark",
    "plotAgeDistributions",
    "plotCmEstimates",
    "plotSccsEstimates",
    "plotSexDistributions",
    "processCohortDefinitionsForQuarto",
    "processCohorts",
    "removeSpaces",
    "restrictCohortDefinitionsForQuarto",
    "viewIncidenceRate"
  ],
  "_help": [
    {
      "page": "dot-getCmVersion",
      "title": "An internal function to determine the version of CohortMethod used to store results",
      "concept": [
        "Estimation"
      ],
      "topics": [
        ".getCmVersion"
      ]
    },
    {
      "page": "dot-getSccsVersion",
      "title": "An internal function to determine the version of SCCS used to store results",
      "concept": [
        "Estimation"
      ],
      "topics": [
        ".getSccsVersion"
      ]
    },
    {
      "page": "addTarColumn",
      "title": "addTarColumn",
      "concept": [
        "helper"
      ],
      "topics": [
        "addTarColumn"
      ]
    },
    {
      "page": "createCharacterizationIndexes",
      "title": "A function to add indexes to the Characterization results",
      "concept": [
        "Indexes"
      ],
      "topics": [
        "createCharacterizationIndexes"
      ]
    },
    {
      "page": "createCohortIndexes",
      "title": "A function to add indexes to the Cohort Generator results",
      "concept": [
        "Indexes"
      ],
      "topics": [
        "createCohortIndexes"
      ]
    },
    {
      "page": "createIncidenceIndexes",
      "title": "A function to add indexes to the incidence results",
      "concept": [
        "Indexes"
      ],
      "topics": [
        "createIncidenceIndexes"
      ]
    },
    {
      "page": "createPredictionReport",
      "title": "createPredictionReport",
      "concept": [
        "Reporting"
      ],
      "topics": [
        "createPredictionReport"
      ]
    },
    {
      "page": "createSccsIndexes",
      "title": "A function to add indexes to the SCCS results",
      "concept": [
        "Indexes"
      ],
      "topics": [
        "createSccsIndexes"
      ]
    },
    {
      "page": "formatBinaryCovariateName",
      "title": "formatBinaryCovariateName",
      "concept": [
        "helper"
      ],
      "topics": [
        "formatBinaryCovariateName"
      ]
    },
    {
      "page": "generateFullReport",
      "title": "generateFullReport",
      "concept": [
        "Reporting"
      ],
      "topics": [
        "generateFullReport"
      ]
    },
    {
      "page": "generateSummaryPredictionReport",
      "title": "generateSummaryPredictionReport",
      "concept": [
        "Reporting"
      ],
      "topics": [
        "generateSummaryPredictionReport"
      ]
    },
    {
      "page": "getAnalysisCohorts",
      "title": "Extracts the different analyses ran for each target and event cohorts",
      "concept": [
        "TreatmentPatterns"
      ],
      "topics": [
        "getAnalysisCohorts"
      ]
    },
    {
      "page": "getBinaryCaseSeries",
      "title": "A function to extract case series characterization results",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getBinaryCaseSeries"
      ]
    },
    {
      "page": "getBinaryRiskFactors",
      "title": "A function to extract non-case and case binary characterization results",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getBinaryRiskFactors"
      ]
    },
    {
      "page": "getBinaryTargetBaseline",
      "title": "Extract the aggregate covariates for the target ids of interest",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getBinaryTargetBaseline"
      ]
    },
    {
      "page": "getCaseCounts",
      "title": "Extract the outcome cohort counts result",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getCaseCounts"
      ]
    },
    {
      "page": "getCaseTargetCounts",
      "title": "Extract the target cohort counts result",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getCaseTargetCounts"
      ]
    },
    {
      "page": "getCharacterizationCohortBinary",
      "title": "A function to extract cohort aggregate binary feature characterization results",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getCharacterizationCohortBinary"
      ]
    },
    {
      "page": "getCharacterizationCohortContinuous",
      "title": "A function to extract cohort aggregate continuous feature characterization results",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getCharacterizationCohortContinuous"
      ]
    },
    {
      "page": "getCharacterizationDemographics",
      "title": "Extract the binary age groups for the cases and targets",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getCharacterizationDemographics"
      ]
    },
    {
      "page": "getCharacterizationOutcomes",
      "title": "A function to extract the outcomes found in characterization",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getCharacterizationOutcomes"
      ]
    },
    {
      "page": "getCharacterizationTargets",
      "title": "A function to extarct the targets found in characterization",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getCharacterizationTargets"
      ]
    },
    {
      "page": "getCmDiagnosticsData",
      "title": "Extract the cohort method diagostic results",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "getCmDiagnosticsData"
      ]
    },
    {
      "page": "getCMEstimation",
      "title": "Extract the cohort method results",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "getCMEstimation"
      ]
    },
    {
      "page": "getCmMetaEstimation",
      "title": "Extract the cohort method meta analysis results",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "getCmMetaEstimation"
      ]
    },
    {
      "page": "getCmNegativeControlEstimates",
      "title": "Extract the cohort method negative controls",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "getCmNegativeControlEstimates"
      ]
    },
    {
      "page": "getCmOutcomes",
      "title": "A function to extract the outcomes found in cohort method",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "getCmOutcomes"
      ]
    },
    {
      "page": "getCmPropensityModel",
      "title": "Extract the cohort method model",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "getCmPropensityModel"
      ]
    },
    {
      "page": "getCmTable",
      "title": "Extract the cohort method table specified",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "getCmTable"
      ]
    },
    {
      "page": "getCmTargets",
      "title": "A function to extract the targets found in cohort method",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "getCmTargets"
      ]
    },
    {
      "page": "getCohortAttrition",
      "title": "Get cohort attrition",
      "concept": [
        "Cohorts"
      ],
      "topics": [
        "getCohortAttrition"
      ]
    },
    {
      "page": "getCohortCounts",
      "title": "Extract the cohort counts",
      "concept": [
        "Cohorts"
      ],
      "topics": [
        "getCohortCounts"
      ]
    },
    {
      "page": "getCohortDefinitions",
      "title": "Extract the cohort definition details",
      "concept": [
        "Cohorts"
      ],
      "topics": [
        "getCohortDefinitions"
      ]
    },
    {
      "page": "getCohortInclusionRules",
      "title": "Extract the cohort inclusion rules",
      "concept": [
        "Cohorts"
      ],
      "topics": [
        "getCohortInclusionRules"
      ]
    },
    {
      "page": "getCohortInclusionStats",
      "title": "Extract the cohort inclusion stats",
      "concept": [
        "Cohorts"
      ],
      "topics": [
        "getCohortInclusionStats"
      ]
    },
    {
      "page": "getCohortInclusionSummary",
      "title": "Extract the cohort inclusion summary",
      "concept": [
        "Cohorts"
      ],
      "topics": [
        "getCohortInclusionSummary"
      ]
    },
    {
      "page": "getCohortMeta",
      "title": "Extract the cohort meta",
      "concept": [
        "Cohorts"
      ],
      "topics": [
        "getCohortMeta"
      ]
    },
    {
      "page": "getCohortSubsetAttrition",
      "title": "Get cohort subset attrition",
      "concept": [
        "Cohorts"
      ],
      "topics": [
        "getCohortSubsetAttrition"
      ]
    },
    {
      "page": "getCohortSubsetDefinitions",
      "title": "Extract the cohort subset definition details",
      "concept": [
        "Cohorts"
      ],
      "topics": [
        "getCohortSubsetDefinitions"
      ]
    },
    {
      "page": "getContinuousCaseSeries",
      "title": "A function to extract case series continuous feature characterization results",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getContinuousCaseSeries"
      ]
    },
    {
      "page": "getContinuousRiskFactors",
      "title": "A function to extract non-case and case continuous characterization results",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getContinuousRiskFactors"
      ]
    },
    {
      "page": "getDatabaseDetails",
      "title": "Extract the database used in the analyses",
      "concept": [
        "Database"
      ],
      "topics": [
        "getDatabaseDetails"
      ]
    },
    {
      "page": "getDechallengeRechallenge",
      "title": "Extract the dechallenge rechallenge results",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getDechallengeRechallenge"
      ]
    },
    {
      "page": "getDechallengeRechallengeFails",
      "title": "A function to extract the failed dechallenge-rechallenge cases",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getDechallengeRechallengeFails"
      ]
    },
    {
      "page": "getEventDuration",
      "title": "Extracts summary of event duration",
      "concept": [
        "TreatmentPatterns"
      ],
      "topics": [
        "getEventDuration"
      ]
    },
    {
      "page": "getExampleConnectionDetails",
      "title": "create a connection detail for an example OHDSI results database",
      "concept": [
        "helper"
      ],
      "topics": [
        "getExampleConnectionDetails"
      ]
    },
    {
      "page": "getFullPredictionPerformances",
      "title": "Extract the model performances per evaluation",
      "concept": [
        "Prediction"
      ],
      "topics": [
        "getFullPredictionPerformances"
      ]
    },
    {
      "page": "getIncidenceOutcomes",
      "title": "A function to extract the outcomes found in incidence",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getIncidenceOutcomes"
      ]
    },
    {
      "page": "getIncidenceRates",
      "title": "Extract the cohort incidence result",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getIncidenceRates"
      ]
    },
    {
      "page": "getIncidenceTargets",
      "title": "A function to extract the targets found in incidence",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getIncidenceTargets"
      ]
    },
    {
      "page": "getOutcomeTable",
      "title": "Extract the outcome cohorts and where they are used in the analyses.",
      "concept": [
        "helper"
      ],
      "topics": [
        "getOutcomeTable"
      ]
    },
    {
      "page": "getPredictionAggregateTopPredictors",
      "title": "Extract the top N predictors across a set of models",
      "concept": [
        "Prediction"
      ],
      "topics": [
        "getPredictionAggregateTopPredictors"
      ]
    },
    {
      "page": "getPredictionCohorts",
      "title": "Extract a complete set of cohorts used in the prediction results",
      "concept": [
        "Prediction"
      ],
      "topics": [
        "getPredictionCohorts"
      ]
    },
    {
      "page": "getPredictionCovariates",
      "title": "Extract covariate summary details",
      "concept": [
        "Prediction"
      ],
      "topics": [
        "getPredictionCovariates"
      ]
    },
    {
      "page": "getPredictionDiagnostics",
      "title": "Extract the model design diagnostics for a specific development database",
      "concept": [
        "Prediction"
      ],
      "topics": [
        "getPredictionDiagnostics"
      ]
    },
    {
      "page": "getPredictionDiagnosticTable",
      "title": "Extract specific diagnostic table",
      "concept": [
        "Prediction"
      ],
      "topics": [
        "getPredictionDiagnosticTable"
      ]
    },
    {
      "page": "getPredictionHyperParamSearch",
      "title": "Extract hyper parameters details",
      "concept": [
        "Prediction"
      ],
      "topics": [
        "getPredictionHyperParamSearch"
      ]
    },
    {
      "page": "getPredictionIntercept",
      "title": "Extract model interception (for logistic regression)",
      "concept": [
        "Prediction"
      ],
      "topics": [
        "getPredictionIntercept"
      ]
    },
    {
      "page": "getPredictionLift",
      "title": "Extract model lift at given model sensitivity",
      "concept": [
        "Prediction"
      ],
      "topics": [
        "getPredictionLift"
      ]
    },
    {
      "page": "getPredictionModelDesigns",
      "title": "Extract the model designs from the prediction results",
      "concept": [
        "Prediction"
      ],
      "topics": [
        "getPredictionModelDesigns"
      ]
    },
    {
      "page": "getPredictionOutcomes",
      "title": "A function to extract the outcomes found in prediction",
      "concept": [
        "Prediction"
      ],
      "topics": [
        "getPredictionOutcomes"
      ]
    },
    {
      "page": "getPredictionPerformances",
      "title": "Extract the model performances",
      "concept": [
        "Prediction"
      ],
      "topics": [
        "getPredictionPerformances"
      ]
    },
    {
      "page": "getPredictionPerformanceTable",
      "title": "Extract specific results table",
      "concept": [
        "Prediction"
      ],
      "topics": [
        "getPredictionPerformanceTable"
      ]
    },
    {
      "page": "getPredictionTargets",
      "title": "A function to extarct the targets found in prediction",
      "concept": [
        "Prediction"
      ],
      "topics": [
        "getPredictionTargets"
      ]
    },
    {
      "page": "getPredictionTopPredictors",
      "title": "Extract the top N predictors per model",
      "concept": [
        "Prediction"
      ],
      "topics": [
        "getPredictionTopPredictors"
      ]
    },
    {
      "page": "getSccsDiagnosticsData",
      "title": "Extract the self controlled case series (sccs) diagostic results",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "getSccsDiagnosticsData"
      ]
    },
    {
      "page": "getSccsEstimation",
      "title": "Extract the self controlled case series (sccs) results",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "getSccsEstimation"
      ]
    },
    {
      "page": "getSccsMetaEstimation",
      "title": "Extract the self controlled case series (sccs) meta analysis results",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "getSccsMetaEstimation"
      ]
    },
    {
      "page": "getSccsModel",
      "title": "Extract the SCCS model table",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "getSccsModel"
      ]
    },
    {
      "page": "getSccsNegativeControlEstimates",
      "title": "Extract the SCCS negative controls",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "getSccsNegativeControlEstimates"
      ]
    },
    {
      "page": "getSccsOutcomes",
      "title": "A function to extract the outcomes found in self controlled case series",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "getSccsOutcomes"
      ]
    },
    {
      "page": "getSccsTable",
      "title": "Extract the SCCS table specified",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "getSccsTable"
      ]
    },
    {
      "page": "getSccsTargets",
      "title": "A function to extract the targets found in self controlled case series",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "getSccsTargets"
      ]
    },
    {
      "page": "getSccsTimeToEvent",
      "title": "Extract the SCCS time-to-event",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "getSccsTimeToEvent"
      ]
    },
    {
      "page": "getSubsetText",
      "title": "Function that converts a subsetDefinitionJson into text description",
      "concept": [
        "Cohorts"
      ],
      "topics": [
        "getSubsetText"
      ]
    },
    {
      "page": "getTargetBinaryFeatures",
      "title": "Extract aggregate statistics of binary feature analysis IDs of interest for targets (ignoring excluding people with prior outcome)",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getTargetBinaryFeatures"
      ]
    },
    {
      "page": "getTargetContinuousFeatures",
      "title": "Extract aggregate statistics of continuous feature analysis IDs of interest for targets",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getTargetContinuousFeatures"
      ]
    },
    {
      "page": "getTargetTable",
      "title": "Extract the target cohorts and where they are used in the analyses.",
      "concept": [
        "helper"
      ],
      "topics": [
        "getTargetTable"
      ]
    },
    {
      "page": "getTimeToEvent",
      "title": "Extract the time to event result",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "getTimeToEvent"
      ]
    },
    {
      "page": "getTreatmentPathways",
      "title": "Extracts treatment pathways",
      "concept": [
        "TreatmentPatterns"
      ],
      "topics": [
        "getTreatmentPathways"
      ]
    },
    {
      "page": "kableDark",
      "title": "output a nicely formatted html table",
      "concept": [
        "helper"
      ],
      "topics": [
        "kableDark"
      ]
    },
    {
      "page": "OhdsiReportGenerator",
      "title": "OhdsiReportGenerator",
      "topics": [
        "OhdsiReportGenerator-package",
        "OhdsiReportGenerator"
      ]
    },
    {
      "page": "plotAgeDistributions",
      "title": "Plots the age distributions using the binary age groups",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "plotAgeDistributions"
      ]
    },
    {
      "page": "plotCmEstimates",
      "title": "Plots the cohort method results for one analysis",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "plotCmEstimates"
      ]
    },
    {
      "page": "plotSccsEstimates",
      "title": "Plots the self controlled case series results for one analysis",
      "concept": [
        "Estimation"
      ],
      "topics": [
        "plotSccsEstimates"
      ]
    },
    {
      "page": "plotSexDistributions",
      "title": "Plots the sex distributions using the sex features",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "plotSexDistributions"
      ]
    },
    {
      "page": "processCohortDefinitionsForQuarto",
      "title": "Function processes the cohortDefinitions object ready for use in the main quarto report.",
      "concept": [
        "Cohorts"
      ],
      "topics": [
        "processCohortDefinitionsForQuarto"
      ]
    },
    {
      "page": "processCohorts",
      "title": "Extract the cohort parents and children cohorts (cohorts derieved from the parent cohort)",
      "concept": [
        "Cohorts"
      ],
      "topics": [
        "processCohorts"
      ]
    },
    {
      "page": "removeSpaces",
      "title": "removeSpaces",
      "concept": [
        "helper"
      ],
      "topics": [
        "removeSpaces"
      ]
    },
    {
      "page": "restrictCohortDefinitionsForQuarto",
      "title": "Function to figure out the target, comparator, outcome and indication ids of interest for the quarto report based on the user inputs",
      "concept": [
        "Cohorts"
      ],
      "topics": [
        "restrictCohortDefinitionsForQuarto"
      ]
    },
    {
      "page": "viewIncidenceRate",
      "title": "View the Incidence Rates",
      "concept": [
        "Characterization"
      ],
      "topics": [
        "viewIncidenceRate"
      ]
    }
  ],
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      "source": "ExampleCode.Rmd",
      "filename": "ExampleCode.html",
      "title": "Using Observational Health Data Sciences and Informatics (OHDSI) Report Generator",
      "author": "Jenna Reps, Anthony Sena",
      "engine": "knitr::knitr",
      "headings": [
        "Using the OhdsiReportGenerator Package",
        "Example Result Database",
        "Extracting Cohorts",
        "Extracting Characterization Results",
        "Extracting Prediction Results",
        "Extracting Estimation Results"
      ],
      "created": "2025-02-14 22:03:28",
      "modified": "2026-05-15 19:05:34",
      "commits": 4
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}