- A database in Common Data Model version 5 in one of these platforms: SQL Server, Oracle, PostgreSQL, IBM Netezza, Apache Impala, Amazon RedShift, Google BigQuery, or Microsoft APS.
- R version 4.0.0 or newer
- On Windows: RTools
- Java
- 25 GB of free disk space
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Follow these instructions for setting up your R environment, including RTools and Java.
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Open your study package in RStudio. Use the following code to install all the dependencies:
install.packages('devtools') install.packages('dplyr') install.packages('data.table') install.packages('R.utils') install.packages('rvg') install.packages('renv') install.packages('lubridate') devtools::install_github("OHDSI/DatabaseConnector",ref="v5.0.2") devtools::install_github("OHDSI/ParallelLogger",ref="v2.0.2")
Or use dockerfile in
DockerImage
Build Docker Image
$docker build --build-arg GIT_ACCESS_TOKEN=[insert-access-token-here] -t [image_name]:[image_tag] .
Run Docker Container
$docker run --name [conatainer_name] -e USER=user -e PASSWORD=password -p 8787:8787 [image_name]:[image_tag]
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In RStudio, select 'Build' then 'Install and Restart' to build the package.
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Once installed, you can execute the study by modifying and using the code below. For your convenience, this code is also provided under
extras/CodeToRun.R
:library(SAGE) # The folder where the study intermediate and result files will be written: outputFolder <- file.path("outputFolderDir") connectionDetails <- DatabaseConnector::createConnectionDetails( dbms = 'postgresql', server = 'myserver', user = 'joe', password = 'secret', pathToDriver = 'S:/jdbcDrivders' ) # The name of the database schema where the CDM data can be found: cdmDatabaseSchema<-'CDM_mydb.dbo' # The name of the database schema and table where the study-specific cohorts will be instantiated: cohortDatabaseSchema <- 'mydb.dbo' cohortTable <- "SAGE" # Some meta-information that will be used by the export function: databaseName <- 'MYDATABASE' execute(connectionDetails = connectionDetails, cdmDatabaseSchema = cdmDatabaseSchema, cohortDatabaseSchema = cohortDatabaseSchema, cohortTable = cohortTable, outputFolder = outputFolder, databaseName = databaseName, createCohorts = TRUE, runPrescriptionNum = TRUE, runDUR = TRUE, resultsToZip = TRUE, yearStartDate = as.Date("2006-01-01"), yearEndDate = as.Date("2022-12-31"), monthStartDate = as.Date("2006-01-01"), monthEndDate = as.Date("2022-12-31"))
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Share the file
drugCohort_<DatabaseId>.zip
in the output folder to the study coordinator
SAGE package is in development