Package index • OhdsiReportGenerator

Database Extraction

These functions can be used to extract details about the databases.

getDatabaseDetails(): Extract the database used in the analyses

Cohort Extraction

These functions can be used to extract analyses cohort details.

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
getSubsetText(): Function that converts a subsetDefinitionJson into text description
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)
restrictCohortDefinitionsForQuarto(): Function to figure out the target, comparator, outcome and indication ids of interest for the quarto report based on the user inputs

Characterization Extractions and Plots

These functions can be used to extract results from characterization and cohort incidence analyses and plot results.

getBinaryCaseSeries(): A function to extract case series characterization results
getBinaryRiskFactors(): A function to extract non-case and case binary characterization results
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
getContinuousCaseSeries(): A function to extract case series continuous feature characterization results
getContinuousRiskFactors(): A function to extract non-case and case continuous characterization results
getDechallengeRechallenge(): Extract the dechallenge rechallenge results
getDechallengeRechallengeFails(): A function to extract the failed dechallenge-rechallenge cases
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
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
getTimeToEvent(): Extract the time to event result
plotAgeDistributions(): Plots the age distributions using the binary age groups
plotSexDistributions(): Plots the sex distributions using the sex features

Estimation Extractions and Plots

These functions can be used to extract results from estimation studies and plot results.

.getCmVersion(): An internal function to determine the version of CohortMethod used to store results
getCMEstimation(): Extract the cohort method results
getCmDiagnosticsData(): Extract the cohort method diagostic 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
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
plotCmEstimates(): Plots the cohort method results for one analysis
plotSccsEstimates(): Plots the self controlled case series results for one analysis

Prediction Extractions and Plots

These functions can be used to extract results from prediction studies and plot results.

getFullPredictionPerformances(): Extract the model performances per evaluation
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
getPredictionDiagnosticTable(): Extract specific diagnostic table
getPredictionDiagnostics(): Extract the model design diagnostics for a specific development database
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
getPredictionPerformanceTable(): Extract specific results table
getPredictionPerformances(): Extract the model performances
getPredictionTargets(): A function to extarct the targets found in prediction
getPredictionTopPredictors(): Extract the top N predictors per model

Treatment Patterns

These functions are used to help result extraction.

getAnalysisCohorts(): Extracts the different analyses ran for each target and event cohorts
getEventDuration(): Extracts summary of event duration
getTreatmentPathways(): Extracts treatment pathways

Reporting

These functions can be used to generate reports using quarto templates.

createPredictionReport(): createPredictionReport
generateFullReport(): generateFullReport
generatePresentation(): generatePresentation
generatePresentationMultiple(): generatePresentationMultiple
generateSummaryPredictionReport(): generateSummaryPredictionReport

Helpers

These functions are used to help result extraction.

addTarColumn(): addTarColumn
formatBinaryCovariateName(): formatBinaryCovariateName
getExampleConnectionDetails(): create a connection detail for an example OHDSI results database
getOutcomeTable(): Extract the outcome cohorts and where they are used in the analyses.
getTargetTable(): Extract the target cohorts and where they are used in the analyses.
kableDark(): output a nicely formatted html table
printReactable(): prints a reactable in a quarto document
removeSpaces(): removeSpaces

OhdsiReportGenerator

A package for extracting analyses results and generating reports.

OhdsiReportGenerator-package OhdsiReportGenerator: OhdsiReportGenerator