Package index • OhdsiReportGenerator

Cohort Extraction

These functions can be used to extract analyses cohort details.

getCohortDefinitions(): Extract the cohort definition details

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

getCharacterizationDemographics(): Extract the binary age groups for the cases and targets

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

getIncidenceRates(): Extract the cohort incidence result

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

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

getTargetCounts(): Extract the target cohort counts result

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

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

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.

getPredictionCohorts(): Extract a complete set of cohorts used in the prediction results

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)

getPredictionModelDesigns(): Extract the model designs and aggregate performances for the prediction results

getPredictionPerformanceTable(): Extract specific results table

getPredictionPerformances(): Extract the model performances

getPredictionTopPredictors(): Extract the top N predictors per model

Reporting

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

generatePresentationMultiple(): generatePresentationMultiple

Helpers

These functions are used to help result extraction.

getExampleConnectionDetails(): create a connection detail for an example OHDSI results database

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