Package: OhdsiReportGenerator 2.2.0

Jenna Reps

OhdsiReportGenerator: Observational Health Data Sciences and Informatics Report Generator

Extract results into R from the Observational Health Data Sciences and Informatics result database (see <https://ohdsi.github.io/Strategus/results-schema/index.html>) and generate reports/presentations via 'quarto' that summarize results in HTML format. Learn more about 'OhdsiReportGenerator' at <https://ohdsi.github.io/OhdsiReportGenerator/>.

Authors:Jenna Reps [aut, cre], Anthony Sena [aut]

OhdsiReportGenerator_2.2.0.tar.gz
OhdsiReportGenerator_2.2.0.zip(r-4.7)OhdsiReportGenerator_2.2.0.zip(r-4.6)OhdsiReportGenerator_2.2.0.zip(r-4.5)
OhdsiReportGenerator_2.2.0.tgz(r-4.6-any)OhdsiReportGenerator_2.2.0.tgz(r-4.5-any)
OhdsiReportGenerator_2.2.0.tar.gz(r-4.7-any)OhdsiReportGenerator_2.2.0.tar.gz(r-4.6-any)
OhdsiReportGenerator_2.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
OhdsiReportGenerator/json (API)

# Install 'OhdsiReportGenerator' in R:

install.packages('OhdsiReportGenerator', repos = c('https://ohdsi.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ohdsi/ohdsireportgenerator/issues

Pkgdown/docs site:https://ohdsi.github.io

Uses libs:

openjdk– OpenJDK Java runtime, using Hotspot JIT

On CRAN:

quarto openjdk

5.00 score 5 scripts 691 downloads 88 exports 104 dependencies

Last updated from:f9de1b4b74. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	204
source / vignettes	OK	257
linux-release-x86_64	OK	222
macos-release-arm64	OK	231
macos-oldrel-arm64	OK	186
windows-devel	OK	180
windows-release	OK	185
windows-oldrel	OK	189
wasm-release	OK	178

Exports:addTarColumn createCharacterizationIndexes createCohortIndexes createIncidenceIndexes createPredictionReport createSccsIndexes formatBinaryCovariateName generateFullReport generateSummaryPredictionReport getAnalysisCohorts getBinaryCaseSeries getBinaryRiskFactors getBinaryTargetBaseline getCaseCounts getCaseTargetCounts getCharacterizationCohortBinary getCharacterizationCohortContinuous getCharacterizationDemographics getCharacterizationOutcomes getCharacterizationTargets getCmDiagnosticsData getCMEstimation getCmMetaEstimation getCmNegativeControlEstimates getCmOutcomes getCmPropensityModel getCmTable getCmTargets getCohortAttrition getCohortCounts getCohortDefinitions getCohortInclusionRules getCohortInclusionStats getCohortInclusionSummary getCohortMeta getCohortSubsetAttrition getCohortSubsetDefinitions getContinuousCaseSeries getContinuousRiskFactors getDatabaseDetails getDechallengeRechallenge getDechallengeRechallengeFails getEventDuration getExampleConnectionDetails getFullPredictionPerformances getIncidenceOutcomes getIncidenceRates getIncidenceTargets getOutcomeTable getPredictionAggregateTopPredictors getPredictionCohorts getPredictionCovariates getPredictionDiagnostics getPredictionDiagnosticTable getPredictionHyperParamSearch getPredictionIntercept getPredictionLift getPredictionModelDesigns getPredictionOutcomes getPredictionPerformances getPredictionPerformanceTable getPredictionTargets getPredictionTopPredictors getSccsDiagnosticsData getSccsEstimation getSccsMetaEstimation getSccsModel getSccsNegativeControlEstimates getSccsOutcomes getSccsTable getSccsTargets getSccsTimeToEvent getSubsetText getTargetBinaryFeatures getTargetContinuousFeatures getTargetTable getTimeToEvent getTreatmentPathways kableDark plotAgeDistributions plotCmEstimates plotSccsEstimates plotSexDistributions processCohortDefinitionsForQuarto processCohorts removeSpaces restrictCohortDefinitionsForQuarto viewIncidenceRate

Dependencies:backports base64enc bigD bit bit64 bitops blob bslib cachem checkmate CirceR cli clipr commonmark cpp11 crayon curl DatabaseConnector DBI dbplyr digest dplyr evaluate farver fastmap fontawesome forestploter fs generics ggplot2 glue gridExtra gt gtable gtExtras highr hms htmltools htmlwidgets isoband jquerylib jsonlite juicyjuice kableExtra knitr labeling later lifecycle litedown magrittr markdown memoise memuse mime paletteer ParallelLogger pillar pkgconfig prettyunits prismatic processx progress ps purrr quarto R6 rappdirs RColorBrewer Rcpp reactable reactR readr rematch2 rJava RJSONIO rlang rmarkdown rstudioapi S7 sass scales snow SqlRender stringi stringr svglite systemfonts textshaping tibble tidyr tidyselect tinytex triebeard tzdb urltools utf8 V8 vctrs viridisLite vroom withr xfun xml2 yaml

Using Observational Health Data Sciences and Informatics (OHDSI) Report Generator

Rendered fromExampleCode.Rmdusingknitr::knitr

Last update: 2026-05-15
Started: 2025-02-14

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
An internal function to determine the version of CohortMethod used to store results	.getCmVersion
An internal function to determine the version of SCCS used to store results	.getSccsVersion
addTarColumn	addTarColumn
A function to add indexes to the Characterization results	createCharacterizationIndexes
A function to add indexes to the Cohort Generator results	createCohortIndexes
A function to add indexes to the incidence results	createIncidenceIndexes
createPredictionReport	createPredictionReport
A function to add indexes to the SCCS results	createSccsIndexes
formatBinaryCovariateName	formatBinaryCovariateName
generateFullReport	generateFullReport
generateSummaryPredictionReport	generateSummaryPredictionReport
Extracts the different analyses ran for each target and event cohorts	getAnalysisCohorts
A function to extract case series characterization results	getBinaryCaseSeries
A function to extract non-case and case binary characterization results	getBinaryRiskFactors
Extract the aggregate covariates for the target ids of interest	getBinaryTargetBaseline
Extract the outcome cohort counts result	getCaseCounts
Extract the target cohort counts result	getCaseTargetCounts
A function to extract cohort aggregate binary feature characterization results	getCharacterizationCohortBinary
A function to extract cohort aggregate continuous feature characterization results	getCharacterizationCohortContinuous
Extract the binary age groups for the cases and targets	getCharacterizationDemographics
A function to extract the outcomes found in characterization	getCharacterizationOutcomes
A function to extarct the targets found in characterization	getCharacterizationTargets
Extract the cohort method diagostic results	getCmDiagnosticsData
Extract the cohort method results	getCMEstimation
Extract the cohort method meta analysis results	getCmMetaEstimation
Extract the cohort method negative controls	getCmNegativeControlEstimates
A function to extract the outcomes found in cohort method	getCmOutcomes
Extract the cohort method model	getCmPropensityModel
Extract the cohort method table specified	getCmTable
A function to extract the targets found in cohort method	getCmTargets
Get cohort attrition	getCohortAttrition
Extract the cohort counts	getCohortCounts
Extract the cohort definition details	getCohortDefinitions
Extract the cohort inclusion rules	getCohortInclusionRules
Extract the cohort inclusion stats	getCohortInclusionStats
Extract the cohort inclusion summary	getCohortInclusionSummary
Extract the cohort meta	getCohortMeta
Get cohort subset attrition	getCohortSubsetAttrition
Extract the cohort subset definition details	getCohortSubsetDefinitions
A function to extract case series continuous feature characterization results	getContinuousCaseSeries
A function to extract non-case and case continuous characterization results	getContinuousRiskFactors
Extract the database used in the analyses	getDatabaseDetails
Extract the dechallenge rechallenge results	getDechallengeRechallenge
A function to extract the failed dechallenge-rechallenge cases	getDechallengeRechallengeFails
Extracts summary of event duration	getEventDuration
create a connection detail for an example OHDSI results database	getExampleConnectionDetails
Extract the model performances per evaluation	getFullPredictionPerformances
A function to extract the outcomes found in incidence	getIncidenceOutcomes
Extract the cohort incidence result	getIncidenceRates
A function to extract the targets found in incidence	getIncidenceTargets
Extract the outcome cohorts and where they are used in the analyses.	getOutcomeTable
Extract the top N predictors across a set of models	getPredictionAggregateTopPredictors
Extract a complete set of cohorts used in the prediction results	getPredictionCohorts
Extract covariate summary details	getPredictionCovariates
Extract the model design diagnostics for a specific development database	getPredictionDiagnostics
Extract specific diagnostic table	getPredictionDiagnosticTable
Extract hyper parameters details	getPredictionHyperParamSearch
Extract model interception (for logistic regression)	getPredictionIntercept
Extract model lift at given model sensitivity	getPredictionLift
Extract the model designs from the prediction results	getPredictionModelDesigns
A function to extract the outcomes found in prediction	getPredictionOutcomes
Extract the model performances	getPredictionPerformances
Extract specific results table	getPredictionPerformanceTable
A function to extarct the targets found in prediction	getPredictionTargets
Extract the top N predictors per model	getPredictionTopPredictors
Extract the self controlled case series (sccs) diagostic results	getSccsDiagnosticsData
Extract the self controlled case series (sccs) results	getSccsEstimation
Extract the self controlled case series (sccs) meta analysis results	getSccsMetaEstimation
Extract the SCCS model table	getSccsModel
Extract the SCCS negative controls	getSccsNegativeControlEstimates
A function to extract the outcomes found in self controlled case series	getSccsOutcomes
Extract the SCCS table specified	getSccsTable
A function to extract the targets found in self controlled case series	getSccsTargets
Extract the SCCS time-to-event	getSccsTimeToEvent
Function that converts a subsetDefinitionJson into text description	getSubsetText
Extract aggregate statistics of binary feature analysis IDs of interest for targets (ignoring excluding people with prior outcome)	getTargetBinaryFeatures
Extract aggregate statistics of continuous feature analysis IDs of interest for targets	getTargetContinuousFeatures
Extract the target cohorts and where they are used in the analyses.	getTargetTable
Extract the time to event result	getTimeToEvent
Extracts treatment pathways	getTreatmentPathways
output a nicely formatted html table	kableDark
OhdsiReportGenerator	OhdsiReportGenerator-package OhdsiReportGenerator
Plots the age distributions using the binary age groups	plotAgeDistributions
Plots the cohort method results for one analysis	plotCmEstimates
Plots the self controlled case series results for one analysis	plotSccsEstimates
Plots the sex distributions using the sex features	plotSexDistributions
Function processes the cohortDefinitions object ready for use in the main quarto report.	processCohortDefinitionsForQuarto
Extract the cohort parents and children cohorts (cohorts derieved from the parent cohort)	processCohorts
removeSpaces	removeSpaces
Function to figure out the target, comparator, outcome and indication ids of interest for the quarto report based on the user inputs	restrictCohortDefinitionsForQuarto
View the Incidence Rates	viewIncidenceRate