This package is considered a duplicate. The official version of this package is found at:https://ohdsi.r-universe.dev/OhdsiReportGenerator

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.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://cran.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:

openjdk

2.00 score 2 scripts 41 exports 126 dependencies

Last updated 11 days agofrom:b23dcaf2b5. Checks:2 OK. Indexed: no.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 26 2025
R-4.5-linux	OK	Feb 26 2025

Exports:generatePresentationMultiple getBinaryCaseSeries getBinaryRiskFactors getCaseBinaryFeatures getCaseContinuousFeatures getCaseCounts getCharacterizationDemographics getCmDiagnosticsData getCMEstimation getCmMetaEstimation getCohortDefinitions getCohortSubsetDefinitions getContinuousCaseSeries getContinuousRiskFactors getDechallengeRechallenge getExampleConnectionDetails getIncidenceRates getPredictionCohorts getPredictionDiagnostics getPredictionDiagnosticTable getPredictionHyperParamSearch getPredictionIntercept getPredictionModelDesigns getPredictionPerformances getPredictionPerformanceTable getPredictionTopPredictors getSccsDiagnosticsData getSccsEstimation getSccsMetaEstimation getTargetBinaryFeatures getTargetContinuousFeatures getTargetCounts getTimeToEvent kableDark plotAgeDistributions plotCmEstimates plotSccsEstimates plotSexDistributions printReactable processCohorts removeSpaces

Dependencies:abind backports base64enc bit bit64 blob boot broom bslib cachem car carData checkmate cli clipr colorspace corrplot cowplot cpp11 crayon DatabaseConnector DBI dbplyr Deriv digest doBy dplyr evaluate fansi farver fastmap fontawesome forestplot Formula fs generics ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable highr hms htmltools htmlwidgets isoband jquerylib jsonlite kableExtra knitr labeling later lattice lifecycle lme4 magrittr MASS Matrix MatrixModels memoise mgcv microbenchmark mime minqa modelr munsell nlme nloptr nnet numDeriv ParallelLogger pbkrtest pillar pkgconfig polynom prettyunits processx progress ps purrr quantreg quarto R6 rappdirs rbibutils RColorBrewer Rcpp RcppEigen Rdpack reactable reactR readr reformulas rJava rlang rmarkdown rstatix rstudioapi sass scales snow SparseM SqlRender stringi stringr survival svglite systemfonts tibble tidyr tidyselect tinytex triebeard tzdb urltools utf8 vctrs viridisLite vroom withr xfun xml2 yaml

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

Jenna Reps, Anthony Sena

Rendered fromExampleCode.Rmdusingknitr::knitron Feb 26 2025.

Last update: 2025-02-26
Started: 2025-02-26

Citation

Readme and manuals

Help Manual

Help page	Topics
generatePresentationMultiple	generatePresentationMultiple
A function to extract case series characterization results	getBinaryCaseSeries
A function to extract non-case and case binary characterization results	getBinaryRiskFactors
Extract aggregate statistics of binary feature analysis IDs of interest for cases	getCaseBinaryFeatures
Extract aggregate statistics of continuous feature analysis IDs of interest for targets	getCaseContinuousFeatures
Extract the outcome cohort counts result	getCaseCounts
Extract the binary age groups for the cases and targets	getCharacterizationDemographics
Extract the cohort method diagostic results	getCmDiagnosticsData
Extract the cohort method results	getCMEstimation
Extract the cohort method meta analysis results	getCmMetaEstimation
Extract the cohort definition details	getCohortDefinitions
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 dechallenge rechallenge results	getDechallengeRechallenge
create a connection detail for an example OHDSI results database	getExampleConnectionDetails
Extract the cohort incidence result	getIncidenceRates
Extract a complete set of cohorts used in the prediction results	getPredictionCohorts
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 the model designs and aggregate performances for the prediction results	getPredictionModelDesigns
Extract the model performances	getPredictionPerformances
Extract specific results table	getPredictionPerformanceTable
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 aggregate statistics of binary feature analysis IDs of interest for targets	getTargetBinaryFeatures
Extract aggregate statistics of continuous feature analysis IDs of interest for targets	getTargetContinuousFeatures
Extract the target cohort counts result	getTargetCounts
Extract the time to event result	getTimeToEvent
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
prints a reactable in a quarto document	printReactable
Extract the cohort parents and children cohorts (cohorts derieved from the parent cohort)	processCohorts
removeSpaces	removeSpaces