Package: OhdsiReportGenerator 1.0.1

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_1.0.1.tar.gz
OhdsiReportGenerator_1.0.1.zip(r-4.5)OhdsiReportGenerator_1.0.1.zip(r-4.4)OhdsiReportGenerator_1.0.1.zip(r-4.3)
OhdsiReportGenerator_1.0.1.tgz(r-4.5-any)OhdsiReportGenerator_1.0.1.tgz(r-4.4-any)OhdsiReportGenerator_1.0.1.tgz(r-4.3-any)
OhdsiReportGenerator_1.0.1.tar.gz(r-4.5-noble)OhdsiReportGenerator_1.0.1.tar.gz(r-4.4-noble)
OhdsiReportGenerator_1.0.1.tgz(r-4.4-emscripten)OhdsiReportGenerator_1.0.1.tgz(r-4.3-emscripten)
OhdsiReportGenerator.pdf |OhdsiReportGenerator.html✨
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 site:https://ohdsi.github.io

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

On CRAN:

Conda:

openjdk

4.54 score 2 scripts 41 exports 126 dependencies

Last updated 11 days agofrom:876bfaac66. Checks:2 OK, 6 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 27 2025
R-4.5-winERRORFeb 27 2025
R-4.5-macERRORFeb 27 2025
R-4.5-linuxOKFeb 27 2025
R-4.4-winERRORFeb 27 2025
R-4.4-macERRORFeb 27 2025
R-4.3-winERRORFeb 27 2025
R-4.3-macERRORFeb 27 2025

Exports:generatePresentationMultiplegetBinaryCaseSeriesgetBinaryRiskFactorsgetCaseBinaryFeaturesgetCaseContinuousFeaturesgetCaseCountsgetCharacterizationDemographicsgetCmDiagnosticsDatagetCMEstimationgetCmMetaEstimationgetCohortDefinitionsgetCohortSubsetDefinitionsgetContinuousCaseSeriesgetContinuousRiskFactorsgetDechallengeRechallengegetExampleConnectionDetailsgetIncidenceRatesgetPredictionCohortsgetPredictionDiagnosticsgetPredictionDiagnosticTablegetPredictionHyperParamSearchgetPredictionInterceptgetPredictionModelDesignsgetPredictionPerformancesgetPredictionPerformanceTablegetPredictionTopPredictorsgetSccsDiagnosticsDatagetSccsEstimationgetSccsMetaEstimationgetTargetBinaryFeaturesgetTargetContinuousFeaturesgetTargetCountsgetTimeToEventkableDarkplotAgeDistributionsplotCmEstimatesplotSccsEstimatesplotSexDistributionsprintReactableprocessCohortsremoveSpaces

Dependencies:abindbackportsbase64encbitbit64blobbootbroombslibcachemcarcarDatacheckmateclicliprcolorspacecorrplotcowplotcpp11crayonDatabaseConnectorDBIdbplyrDerivdigestdoBydplyrevaluatefansifarverfastmapfontawesomeforestplotFormulafsgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehighrhmshtmltoolshtmlwidgetsisobandjquerylibjsonlitekableExtraknitrlabelinglaterlatticelifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivParallelLoggerpbkrtestpillarpkgconfigpolynomprettyunitsprocessxprogresspspurrrquantregquartoR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreactablereactRreadrreformulasrJavarlangrmarkdownrstatixrstudioapisassscalessnowSparseMSqlRenderstringistringrsurvivalsvglitesystemfontstibbletidyrtidyselecttinytextriebeardtzdburltoolsutf8vctrsviridisLitevroomwithrxfunxml2yaml

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

Jenna Reps, Anthony Sena

Rendered fromExampleCode.Rmdusingknitr::knitron Feb 27 2025.

Last update: 2025-02-18
Started: 2025-02-14

Readme and manuals

Help Manual

Help pageTopics
generatePresentationMultiplegeneratePresentationMultiple
A function to extract case series characterization resultsgetBinaryCaseSeries
A function to extract non-case and case binary characterization resultsgetBinaryRiskFactors
Extract aggregate statistics of binary feature analysis IDs of interest for casesgetCaseBinaryFeatures
Extract aggregate statistics of continuous feature analysis IDs of interest for targetsgetCaseContinuousFeatures
Extract the outcome cohort counts resultgetCaseCounts
Extract the binary age groups for the cases and targetsgetCharacterizationDemographics
Extract the cohort method diagostic resultsgetCmDiagnosticsData
Extract the cohort method resultsgetCMEstimation
Extract the cohort method meta analysis resultsgetCmMetaEstimation
Extract the cohort definition detailsgetCohortDefinitions
Extract the cohort subset definition detailsgetCohortSubsetDefinitions
A function to extract case series continuous feature characterization resultsgetContinuousCaseSeries
A function to extract non-case and case continuous characterization resultsgetContinuousRiskFactors
Extract the dechallenge rechallenge resultsgetDechallengeRechallenge
create a connection detail for an example OHDSI results databasegetExampleConnectionDetails
Extract the cohort incidence resultgetIncidenceRates
Extract a complete set of cohorts used in the prediction resultsgetPredictionCohorts
Extract the model design diagnostics for a specific development databasegetPredictionDiagnostics
Extract specific diagnostic tablegetPredictionDiagnosticTable
Extract hyper parameters detailsgetPredictionHyperParamSearch
Extract model interception (for logistic regression)getPredictionIntercept
Extract the model designs and aggregate performances for the prediction resultsgetPredictionModelDesigns
Extract the model performancesgetPredictionPerformances
Extract specific results tablegetPredictionPerformanceTable
Extract the top N predictors per modelgetPredictionTopPredictors
Extract the self controlled case series (sccs) diagostic resultsgetSccsDiagnosticsData
Extract the self controlled case series (sccs) resultsgetSccsEstimation
Extract the self controlled case series (sccs) meta analysis resultsgetSccsMetaEstimation
Extract aggregate statistics of binary feature analysis IDs of interest for targetsgetTargetBinaryFeatures
Extract aggregate statistics of continuous feature analysis IDs of interest for targetsgetTargetContinuousFeatures
Extract the target cohort counts resultgetTargetCounts
Extract the time to event resultgetTimeToEvent
output a nicely formatted html tablekableDark
OhdsiReportGeneratorOhdsiReportGenerator-package OhdsiReportGenerator
Plots the age distributions using the binary age groupsplotAgeDistributions
Plots the cohort method results for one analysisplotCmEstimates
Plots the self controlled case series results for one analysisplotSccsEstimates
Plots the sex distributions using the sex featuresplotSexDistributions
prints a reactable in a quarto documentprintReactable
Extract the cohort parents and children cohorts (cohorts derieved from the parent cohort)processCohorts
removeSpacesremoveSpaces