R: Observational Health Data Sciences and Informatics Report Generator

# Observational Health Data Sciences and Informatics Report Generator

## Documentation for package ‘OhdsiReportGenerator’ version 2.2.0

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

OhdsiReportGenerator-package | OhdsiReportGenerator
.getCmVersion | An internal function to determine the version of CohortMethod used to store results
.getSccsVersion | An internal function to determine the version of SCCS used to store results
addTarColumn | addTarColumn
createCharacterizationIndexes | A function to add indexes to the Characterization results
createCohortIndexes | A function to add indexes to the Cohort Generator results
createIncidenceIndexes | A function to add indexes to the incidence results
createPredictionReport | createPredictionReport
createSccsIndexes | A function to add indexes to the SCCS results
formatBinaryCovariateName | formatBinaryCovariateName
generateFullReport | generateFullReport
generateSummaryPredictionReport | generateSummaryPredictionReport
getAnalysisCohorts | Extracts the different analyses ran for each target and event cohorts
getBinaryCaseSeries | A function to extract case series characterization results
getBinaryRiskFactors | A function to extract non-case and case binary characterization results
getBinaryTargetBaseline | Extract the aggregate covariates for the target ids of interest
getCaseCounts | Extract the outcome cohort counts result
getCaseTargetCounts | Extract the target cohort counts result
getCharacterizationCohortBinary | A function to extract cohort aggregate binary feature characterization results
getCharacterizationCohortContinuous | A function to extract cohort aggregate continuous feature characterization results
getCharacterizationDemographics | Extract the binary age groups for the cases and targets
getCharacterizationOutcomes | A function to extract the outcomes found in characterization
getCharacterizationTargets | A function to extarct the targets found in characterization
getCmDiagnosticsData | Extract the cohort method diagostic results
getCMEstimation | Extract the cohort method results
getCmMetaEstimation | Extract the cohort method meta analysis results
getCmNegativeControlEstimates | Extract the cohort method negative controls
getCmOutcomes | A function to extract the outcomes found in cohort method
getCmPropensityModel | Extract the cohort method model
getCmTable | Extract the cohort method table specified
getCmTargets | A function to extract the targets found in cohort method
getCohortAttrition | Get cohort attrition
getCohortCounts | Extract the cohort counts
getCohortDefinitions | Extract the cohort definition details
getCohortInclusionRules | Extract the cohort inclusion rules
getCohortInclusionStats | Extract the cohort inclusion stats
getCohortInclusionSummary | Extract the cohort inclusion summary
getCohortMeta | Extract the cohort meta
getCohortSubsetAttrition | Get cohort subset attrition
getCohortSubsetDefinitions | Extract the cohort subset definition details
getContinuousCaseSeries | A function to extract case series continuous feature characterization results
getContinuousRiskFactors | A function to extract non-case and case continuous characterization results
getDatabaseDetails | Extract the database used in the analyses
getDechallengeRechallenge | Extract the dechallenge rechallenge results
getDechallengeRechallengeFails | A function to extract the failed dechallenge-rechallenge cases
getEventDuration | Extracts summary of event duration
getExampleConnectionDetails | create a connection detail for an example OHDSI results database
getFullPredictionPerformances | Extract the model performances per evaluation
getIncidenceOutcomes | A function to extract the outcomes found in incidence
getIncidenceRates | Extract the cohort incidence result
getIncidenceTargets | A function to extract the targets found in incidence
getOutcomeTable | Extract the outcome cohorts and where they are used in the analyses.
getPredictionAggregateTopPredictors | Extract the top N predictors across a set of models
getPredictionCohorts | Extract a complete set of cohorts used in the prediction results
getPredictionCovariates | Extract covariate summary details
getPredictionDiagnostics | Extract the model design diagnostics for a specific development database
getPredictionDiagnosticTable | Extract specific diagnostic table
getPredictionHyperParamSearch | Extract hyper parameters details
getPredictionIntercept | Extract model interception (for logistic regression)
getPredictionLift | Extract model lift at given model sensitivity
getPredictionModelDesigns | Extract the model designs from the prediction results
getPredictionOutcomes | A function to extract the outcomes found in prediction
getPredictionPerformances | Extract the model performances
getPredictionPerformanceTable | Extract specific results table
getPredictionTargets | A function to extarct the targets found in prediction
getPredictionTopPredictors | Extract the top N predictors per model
getSccsDiagnosticsData | Extract the self controlled case series (sccs) diagostic results
getSccsEstimation | Extract the self controlled case series (sccs) results
getSccsMetaEstimation | Extract the self controlled case series (sccs) meta analysis results
getSccsModel | Extract the SCCS model table
getSccsNegativeControlEstimates | Extract the SCCS negative controls
getSccsOutcomes | A function to extract the outcomes found in self controlled case series
getSccsTable | Extract the SCCS table specified
getSccsTargets | A function to extract the targets found in self controlled case series
getSccsTimeToEvent | Extract the SCCS time-to-event
getSubsetText | Function that converts a subsetDefinitionJson into text description
getTargetBinaryFeatures | Extract aggregate statistics of binary feature analysis IDs of interest for targets (ignoring excluding people with prior outcome)
getTargetContinuousFeatures | Extract aggregate statistics of continuous feature analysis IDs of interest for targets
getTargetTable | Extract the target cohorts and where they are used in the analyses.
getTimeToEvent | Extract the time to event result
getTreatmentPathways | Extracts treatment pathways
kableDark | output a nicely formatted html table
OhdsiReportGenerator | OhdsiReportGenerator
plotAgeDistributions | Plots the age distributions using the binary age groups
plotCmEstimates | Plots the cohort method results for one analysis
plotSccsEstimates | Plots the self controlled case series results for one analysis
plotSexDistributions | Plots the sex distributions using the sex features
processCohortDefinitionsForQuarto | Function processes the cohortDefinitions object ready for use in the main quarto report.
processCohorts | Extract the cohort parents and children cohorts (cohorts derieved from the parent cohort)
removeSpaces | removeSpaces
restrictCohortDefinitionsForQuarto | Function to figure out the target, comparator, outcome and indication ids of interest for the quarto report based on the user inputs
viewIncidenceRate | View the Incidence Rates