README.md

CohortDiagnosticsRenv

This project includes a renv.lock file to run the Darwin version of CohortDiagnostics.

1. Instructions

In this project you can find multiple scripts (extras folder) to run CohortDiagnostics. The scripts ending with "cdm.R" are using a CDMConnector object. In the R folder, there is a script with a helper function with the parameters adjusted for Darwin studies.

Install the latest version of renv:

install.packages("renv")

Restore the library

renv::restore()

2. Running the package

Edit the variables below to the correct values for your environment:

library(...)

# Login details
dbms <- Sys.getenv("dbms")
host <- Sys.getenv("host")
dbname <- Sys.getenv("dbname")
user <- Sys.getenv("user")
password <- Sys.getenv("password")
port <- Sys.getenv("port")

connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = dbms,
                                                                server = paste0(host, "/", dbname),
                                                                user = user,
                                                                password = password,
                                                                port = port)

connection <- DatabaseConnector::connect(connectionDetails)

# A folder on the local file system to store results:
outputDir <- "..."

# The database schema where the observational data in CDM is located.

cdmDatabaseSchema <- "..."

# The database schema where the cohorts can be instantiated.
cohortDatabaseSchema <- "..."


# The name of the table that will be created in the cohortDatabaseSchema.
cohortTable <- "..."

# The databaseId is a short (<= 20 characters)
databaseId <- "..."

# This statement instatiates the cohorts, performs the diagnostics, and writes the results to
# a zip file containing CSV files. This will probaby take a long time to run:
runDiagnostics(connectionDetails = connectionDetails,
               cdmDatabaseSchema = cdmDatabaseSchema,
               vocabularyDatabaseSchema = cdmDatabaseSchema,
               cohortDatabaseSchema = cohortDatabaseSchema,
               cohortTable = cohortTable,
               outputDir = outputDir,
               databaseId = databaseId)

# (Optionally) to view the results locally:
CohortDiagnostics::createMergedResultsFile(
  dataFolder = file.path(outputDir),
  sqliteDbPath = file.path(outputDir, "MergedCohortDiagnosticsData.sqlite")
)
CohortDiagnostics::launchDiagnosticsExplorer(sqliteDbPath = file.path(outputDir, "MergedCohortDiagnosticsData.sqlite"))