Observational Health Data Sciences and Informatics Report Generator

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Documentation for package ‘OhdsiReportGenerator’ version 2.0.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

OhdsiReportGenerator-package	OhdsiReportGenerator
addTarColumn	addTarColumn
createPredictionReport	createPredictionReport
formatBinaryCovariateName	formatBinaryCovariateName
generateFullReport	generateFullReport
generatePresentation	generatePresentation
generatePresentationMultiple	generatePresentationMultiple
generateSummaryPredictionReport	generateSummaryPredictionReport
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
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
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
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
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
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
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
printReactable	prints a reactable in a quarto document
processCohorts	Extract the cohort parents and children cohorts (cohorts derieved from the parent cohort)
removeSpaces	removeSpaces