extras/Eunomia_CodeToRun.R

In ohdsi-studies/Covid19VaccineAesiIncidenceRate: COVID-19 Vaccine AESI Incidence Characterization

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# PLEASE NOTE: This file is for testing purposes
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library(Covid19VaccineAesiIncidenceRate)

# Specify where the temporary files (used by the Andromeda package) will be created:
# andromedaTempFolder <- if (Sys.getenv('ANDROMEDA_TEMP_FOLDER') == '') '~/andromedaTemp' else
# Sys.getenv('ANDROMEDA_TEMP_FOLDER') options(andromedaTempFolder = andromedaTempFolder)

# Define a schema that can be used to emulate temp tables:
tempEmulationSchema <- NULL
connectionDetails <- Eunomia::getEunomiaConnectionDetails()

# Details specific to the database:
databaseId <- "Eunomia"
databaseName <- "Eunomia"
databaseDescription <- "Eunomia"

# Details for connecting to the CDM and storing the results
cdmDatabaseSchema <- "main"
cohortDatabaseSchema <- "main"
cohortTablePrefix <- "IRAESI"

minCellCount <- 5

# Set the folder for holding the study output
projectRootFolder <- "D:/TWT/Covid19VaccineAesiIncidenceRate/Runs"
outputFolder <- file.path(projectRootFolder, databaseId)
if (!dir.exists(outputFolder)) {
  dir.create(outputFolder, recursive = TRUE)
}
setwd(outputFolder)

# Use this to run the study. The results will be stored in a zip file called
# 'Results_<databaseId>.zip in the outputFolder.
runStudy(connectionDetails = connectionDetails,
         cdmDatabaseSchema = cdmDatabaseSchema,
         cohortDatabaseSchema = cohortDatabaseSchema,
         cohortTablePrefix = cohortTablePrefix,
         tempEmulationSchema = cohortDatabaseSchema,
         exportFolder = outputFolder,
         databaseId = databaseId,
         databaseName = databaseName,
         databaseDescription = databaseDescription,
         incremental = TRUE,
         minCellCount = minCellCount)


# # For uploading the results. You should have received the key file from the study coordinator:
# keyFileName <- 'E:/Covid19VaccineAesiIncidenceRate/study-data-site-covid19.dat'
# userName <- 'study-data-site-covid19'

# When finished with reviewing the diagnostics, use the next command to upload the diagnostic results
# uploadDiagnosticsResults(outputFolder, keyFileName, userName)


# When finished with reviewing the results, use the next command upload study results to OHDSI SFTP
# server: uploadStudyResults(outputFolder, keyFileName, userName)