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Code to extract data from the OHDSI results structure and generate plots, presentations and reports

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OHDSI/OhdsiReportGenerator

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Build Statuscodecov.ioCRAN_Status_BadgeCRAN_Status_Badge

Introduction

This package contains functions for extracting characterization, estimation and prediction results from the OHDSI result database (seehttps://ohdsi.github.io/Strategus/results-schema/index.html).

It also contains codes to create useful plots, presentations templates and report templates.

Examples

Download this repository and using RStudio, install the package. Then you can make use of the report generator by running:

# Install OhdsiReportGenerator using remotes}install.packages('remotes')remotes::install_github('OHDSI/OhdsiReportGenerator')# Load the library to start using itlibrary(OhdsiReportGenerator)# to run the report generator with a demo set of resultsconDet<-OhdsiReportGenerator:::getExampleConnectionDetails()# render a quarto template report with the results in the# example database for targetId 1 and outcomeId 3.generatePresentation(server=conDet$server(),username=conDet$user(),password=conDet$password(),dbms=conDet$dbms,resultsSchema='main',dbDetails=NULL,lead='John Doe',team='name 1, name 2',trigger='A signal was found in spontaneous reports',safetyQuestion='',objective='',date= as.character(Sys.Date()),targetId=1,outcomeIds=3,cohortNames= c('target','outcome'),cohortIds= c(1,3),covariateIds=NULL,details=list(studyPeriod='All Time',restrictions="Age - None"  ),evaluationText='',includeCI=TRUE,includeCharacterization=TRUE,includeCM=TRUE,includeSCCS=TRUE,includePLP=FALSE,outputLocation= file.path(getwd(),"extras/reportTest"),outputName= paste0('presentation_', gsub(':','_',gsub('','_',as.character(date()))),'.html')intermediateDir= tempdir())

Technology

OhdsiReportGenerator is an R package.

System Requirements

Running the package requires R and Java.

License

OhdsiReportGenerator is licensed under Apache License 2.0.

Development

OhdsiReportGenerator is being developed in R Studio.

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Code to extract data from the OHDSI results structure and generate plots, presentations and reports

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