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.

getCohortCounts(): Extract the cohort counds

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

getCohortSubsetDefinitions(): Extract the cohort subset definition details

processCohorts(): Extract the cohort parents and children cohorts (cohorts derieved from the parent cohort)

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

getCaseBinaryFeatures(): Extract aggregate statistics of binary feature analysis IDs of interest for cases

getCaseContinuousFeatures(): Extract aggregate statistics of continuous feature analysis IDs of interest for targets

getCaseCounts(): Extract the outcome cohort counts result

getCaseTargetBinaryFeatures(): Extract aggregate statistics of binary feature analysis IDs of interest for targets

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.

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

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