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OhdsiReportGenerator (version 2.0.2)

Observational Health Data Sciences and Informatics Report Generator

Description

Extract results into R from the Observational Health Data Sciences and Informatics result database (see ) and generate reports/presentations via 'quarto' that summarize results in HTML format. Learn more about 'OhdsiReportGenerator' at .

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Install

install.packages('OhdsiReportGenerator')

Monthly Downloads

198

Version

2.0.2

License

Apache License 2.0

Issues

2

Pull Requests

4

Stars

0

Forks

3

Maintainer

Jenna Reps

Last Published

December 17th, 2025

Functions in OhdsiReportGenerator (2.0.2)

getCaseTargetCounts

Extract the target cohort counts result
getCaseBinaryFeatures

Extract aggregate statistics of binary feature analysis IDs of interest for cases
getCMEstimation

Extract the cohort method results
getCaseTargetBinaryFeatures

Extract aggregate statistics of binary feature analysis IDs of interest for targets
getCaseCounts

Extract the outcome cohort counts result
getCharacterizationCohortBinary

A function to extract cohort aggregate binary feature characterization results
getCharacterizationOutcomes

A function to extract the outcomes found in characterization
getCharacterizationDemographics

Extract the binary age groups for the cases and targets
getCaseContinuousFeatures

Extract aggregate statistics of continuous feature analysis IDs of interest for targets
getCharacterizationCohortContinuous

A function to extract cohort aggregate continuous feature characterization results
getCmOutcomes

A function to extract the outcomes found in cohort method
getCohortCounts

Extract the cohort counds
getCohortDefinitions

Extract the cohort definition details
getCmMetaEstimation

Extract the cohort method meta analysis results
getCmNegativeControlEstimates

Extract the cohort method negative controls
getCharacterizationTargets

A function to extarct the targets found in characterization
getCmDiagnosticsData

Extract the cohort method diagostic results
getCmPropensityModel

Extract the cohort method model
getDatabaseDetails

Extract the database used in the analyses
getContinuousRiskFactors

A function to extract non-case and case continuous characterization results
getCmTargets

A function to extract the targets found in cohort method
getCohortInclusionSummary

Extract the cohort inclusion summary
getCmTable

Extract the cohort method table specified
getExampleConnectionDetails

create a connection detail for an example OHDSI results database
getFullPredictionPerformances

Extract the model performances per evaluation
getOutcomeTable

Extract the outcome cohorts and where they are used in the analyses.
getCohortMeta

Extract the cohort meta
getIncidenceTargets

A function to extract the targets found in incidence
getIncidenceOutcomes

A function to extract the outcomes found in incidence
getIncidenceRates

Extract the cohort incidence result
getPredictionOutcomes

A function to extract the outcomes found in prediction
getPredictionPerformances

Extract the model performances
getPredictionPerformanceTable

Extract specific results table
getPredictionModelDesigns

Extract the model designs from the prediction results
getPredictionCohorts

Extract a complete set of cohorts used in the prediction results
getDechallengeRechallengeFails

A function to extract the failed dechallenge-rechallenge cases
getPredictionDiagnostics

Extract the model design diagnostics for a specific development database
getPredictionAggregateTopPredictors

Extract the top N predictors across a set of models
getPredictionHyperParamSearch

Extract hyper parameters details
getDechallengeRechallenge

Extract the dechallenge rechallenge results
getSccsTimeToEvent

Extract the SCCS time-to-event
getSccsDiagnosticsData

Extract the self controlled case series (sccs) diagostic results
getPredictionTopPredictors

Extract the top N predictors per model
getPredictionTargets

A function to extarct the targets found in prediction
getSccsMetaEstimation

Extract the self controlled case series (sccs) meta analysis results
getPredictionIntercept

Extract model interception (for logistic regression)
getCohortSubsetDefinitions

Extract the cohort subset definition details
getPredictionCovariates

Extract covariate summary details
getPredictionLift

Extract model lift at given model sensitivity
getContinuousCaseSeries

A function to extract case series continuous feature characterization results
getSccsEstimation

Extract the self controlled case series (sccs) results
getSccsTable

Extract the SCCS table specified
getTargetBinaryFeatures

Extract aggregate statistics of binary feature analysis IDs of interest for targets (ignoring excluding people with prior outcome)
getCohortInclusionRules

Extract the cohort inclusion rules
getPredictionDiagnosticTable

Extract specific diagnostic table
getCohortInclusionStats

Extract the cohort inclusion stats
getTargetContinuousFeatures

Extract aggregate statistics of continuous feature analysis IDs of interest for targets
getSccsTargets

A function to extract the targets found in self controlled case series
plotSccsEstimates

Plots the self controlled case series results for one analysis
getTargetTable

Extract the target cohorts and where they are used in the analyses.
getTimeToEvent

Extract the time to event result
removeSpaces

removeSpaces
getSccsOutcomes

A function to extract the outcomes found in self controlled case series
printReactable

prints a reactable in a quarto document
getSccsNegativeControlEstimates

Extract the SCCS negative controls
processCohorts

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

output a nicely formatted html table
plotAgeDistributions

Plots the age distributions using the binary age groups
plotCmEstimates

Plots the cohort method results for one analysis
getSccsModel

Extract the SCCS model table
plotSexDistributions

Plots the sex distributions using the sex features
addTarColumn

addTarColumn
OhdsiReportGenerator

OhdsiReportGenerator
getBinaryRiskFactors

A function to extract non-case and case binary characterization results
getBinaryCaseSeries

A function to extract case series characterization results
generateFullReport

generateFullReport
generatePresentation

generatePresentation
formatBinaryCovariateName

formatBinaryCovariateName
createPredictionReport

createPredictionReport
generatePresentationMultiple

generatePresentationMultiple
generateSummaryPredictionReport

generateSummaryPredictionReport