Covid19Il6JakInhibitorsSccs/README.md

In ohdsi-studies/Covid19EstimationIl6JakInhibitors: A Package Skeleton for Comparative Effectiveness Studies

Self-Controlled Case Series Analysis of the Safety of IL-6 and JAK Inhibitors

IL-6 and JAK inhibitors are being considered for use in treatment and prophylaxis of COVID-19 in rapid clinical trials across the world. However, the full safety profiles of these drugs is unknown, and the current trials are unlikely to be powered or have sufficient follow-up time to evaluate most safety outcomes. The aim of this OHDSI study is to use existing retrospective data to evaluate the safety of IL-6 and JAK inhibitors, using the self-controlled case series (SCCS) design.

This study is part of the OHDSI 2020 COVID-19 study-a-thon.

Requirements

• A database in Common Data Model version 5 in one of these platforms: SQL Server, Oracle, PostgreSQL, IBM Netezza, Apache Impala, Amazon RedShift, or Microsoft APS.
• R version 3.5.0 or newer
• On Windows: RTools
• Java
• 25 GB of free disk space

See here for instructions on how to set up the R environment on Windows.

How to run

1. First, install the package: ```r # Prevents errors due to packages being built for other R versions: Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS" = TRUE)

# First, it probably is best to make sure you are up-to-date on all existing packages. # Important: This code is best run in R, not RStudio, as RStudio may have some libraries # (like 'rlang') in use. update.packages(ask = "graphics")

# When asked to update packages, select '3' ('none') (could be multiple times) # When asked whether to install from source, select 'No' (could be multiple times) install.packages("devtools") devtools::install_github("ohdsi/ParallelLogger", ref = "develop") devtools::install_github("ohdsi/Cyclops") devtools::install_github("ohdsi/EmpiricalCalibration") devtools::install_github("ohdsi/SelfControlledCaseSeries") devtools::install_github("ohdsi/OhdsiSharing") devtools::install_github("ohdsi-studies/Covid19EstimationHydroxychloroquine/Covid19Il6JakInhibitorsSccs") 2. Execute the study by modifying and executing the following code:r library(Covid19Il6JakInhibitorsSccs)

# Optional: specify where the temporary files (used by the ff package) will be created: options(fftempdir = "c:/fftemp")

# Maximum number of cores to be used: maxCores <- parallel::detectCores()

# The folder where the study intermediate and result files will be written: outputFolder <- "c:/Covid19Il6JakInhibitorsSccs"

# Details for connecting to the server: # See ?DatabaseConnector::createConnectionDetails for help connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "", server = "", user = "", password = "")

# The name of the database schema where the CDM data can be found: cdmDatabaseSchema <- ""

# The name of the database schema and table where the study-specific cohorts will be instantiated: cohortDatabaseSchema <- "" cohortTable <- ""

# Some meta-information that will be used by the export function: databaseId <- "" # A short name of the database, to be used to create file names. databaseName <- "" # The full name of the database databaseDescription <- "" # A paragraph describing the database

# If using Oracle, define a schema that can be used to emulate temp tables. Otherwise set as NULL: oracleTempSchema <- NULL

execute(connectionDetails = connectionDetails, cdmDatabaseSchema = cdmDatabaseSchema, cohortDatabaseSchema = cohortDatabaseSchema, cohortTable = cohortTable, oracleTempSchema = oracleTempSchema, outputFolder = outputFolder, databaseId = databaseId, databaseName = databaseName, databaseDescription = databaseDescription, createCohorts = TRUE, runSccs = TRUE, createCharacterization = TRUE, runSccsDiagnostics = TRUE, exportResults = TRUE, maxCores = maxCores) ```

1. Send the created zip file (and only the zip file) to the study coordinator. This can be done using the 'sccsIl6JakInhibitors' folder on the OHDSI SFTP server: ```r # For uploading the results. You should have received the key file from the study coordinator: keyFileName <- "c:/home/keyFiles/study-data-site-covid19.dat" userName <- "study-data-site-covid19"

# Upload results to OHDSI SFTP server: uploadResults(outputFolder, keyFileName, userName) ```

Support

• Developer questions/comments/feedback: OHDSI Forum
• We use the GitHub issue tracker for all bugs/issues/enhancements

License

The Covid19Il6JakInhibitorsSccs package is licensed under Apache License 2.0

ohdsi-studies/Covid19EstimationIl6JakInhibitors documentation built on June 28, 2020, 4:01 p.m.