RCRIValidationGP

• Analytics use case(s): Patient-Level Prediction
• Study type: Methods Research
• Tags: Prediction models
• Study lead: Alexander Saelmans
• Study lead forums tag: add
• Study start date: 02-25-2025
• Study end date: -
• Protocol: -
• Publications: -
• Results explorer: -

Code to run

# Set working directory to Renv file
#==========================================#
# Download the Renv lock file from the GitHub page

# Set working directory to the Renv lock file
setwd()
# Check whether the working directory was adjusted
.libPaths()

# Activate Renv
renv::activate()
# Restore R lock file
renv::restore()
# Restart R session
.rs.restartR()

# Usethis explanation
# The inputs have been filled in using the usethis package. This allows one to use
# inputs filled in the .Renviron file.
# More information on the usethis package can be found here:
# https://usethis.r-lib.org/reference/use_description.html
# You can also add you github token to the .Renviron file with
# GITHUB-PAT=your_token_here and retrieve it with Sys.getenv("GITHUB_PAT")

library(usethis)

# Inputs to run (edit these for your CDM):
# ========================================= #
# If your database requires temp tables being created in a specific schema
if (!Sys.getenv("DATABASE_TEMP_SCHEMA") == "") {
  options(sqlRenderTempEmulationSchema = Sys.getenv("DATABASE_TEMP_SCHEMA"))
}

# Where to save the output - a directory in your environment
outputFolder <- "./output/folder/"

# Fill in your connection details and path to driver
# See ?DatabaseConnector::createConnectionDetails for help for your 
# database platform
connectionDetails <- DatabaseConnector::createConnectionDetails(
  dbms = Sys.getenv("DBMS"), 
  server = Sys.getenv("DATABASE_SERVER"), 
  user = Sys.getenv("DATABASE_USER"),
  password = Sys.getenv("DATABASE_PASSWORD"),
  port = Sys.getenv("DATABASE_PORT"),
  connectionString = Sys.getenv("DATABASE_CONNECTION_STRING"),
  pathToDriver = Sys.getenv("DATABASE_DRIVER")
) 

# A schema with write access to store cohort tables
workDatabaseSchema <- Sys.getenv("WORK_SCHEMA")
  
# Name of cohort table that will be created for study
cohortTable <- Sys.getenv("COHORT_TABLE")

# Schema where the cdm data is
cdmDatabaseSchema <- Sys.getenv("CDM_SCHEMA")

# Aggregated statistics with cell count less than this are removed before sharing results.
minCellCount <- 5

# =========== END OF INPUTS ========== #

analysisSpecifications <- RCRIValidationGP::loadStudySpec()

executionSettings <- Strategus::createCdmExecutionSettings(
  workDatabaseSchema = workDatabaseSchema,
  cdmDatabaseSchema = cdmDatabaseSchema,
  cohortTableNames = CohortGenerator::getCohortTableNames(cohortTable = cohortTable),
  workFolder = file.path(outputFolder, "strategusWork"),
  resultsFolder = file.path(outputFolder, "strategusOutput"),
  minCellCount = minCellCount
)
  
Strategus::execute(
  analysisSpecifications = analysisSpecifications,
  executionSettings = executionSettings,
  connectionDetails = connectionDetails
)

#======================================#
# Don't forget to deactivate your Renv
renv::deactivate()

Submitting Results

To send the compressed folder results please message Alexander Saelmans (a.saelmans@erasmusmc.nl) and he will give you the privateKeyFileName and userName. You can then run the following R code to share the results:

# Please upload both the strategusWork and strategusOutput folders
 
# One time R package install
install_github("ohdsi/OhdsiSharing")
 
# Upload local files 'strategusWork.zip' and 'strategusOutput.zip to the sftp server study folder
library("OhdsiSharing")
 
privateKeyFileName <- "message us for this"
userName <- "message us for this"
remoteFolder <- "/"
fileName <- "example/strategusWork.zip"
sftpUploadFile(privateKeyFileName, userName, remoteFolder, fileName)

# Please send us the names given to the zip files in the sftp rcriv study folder, so we can access them