OHDSI NL Breast Cancer Study — Cohort Diagnostics

1. Instructions

A CodeToRun.R is provided in the extras folder.

Installation

1. See the instructions at https://ohdsi.github.io/Hades/rSetup.html for configuring your R environment, including Java and RStudio.

2. Download this project and run it in the same directory.

3. Execute the following R code for the environment:

Install the latest version of renv:

install.packages("renv")

Build the local library. This may take a while:

renv::init()

Restore the library

renv::restore()

2. Running the package

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

# 1. Open this project in RStudio and restore the R environment
renv::restore()

# 2. Edit the variables below to create a connection and run CohortDiagnostics

#  postgresql", "snowflake", "spark", and "redshift", "sql server"
dbms <- "..."
host <- Sys.getenv("...")
dbname <- Sys.getenv("...")
user <- Sys.getenv("...")
password <-  Sys.getenv("...")
port <- Sys.getenv("...")

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

connection <- DatabaseConnector::connect(connectionDetails)


# 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 <- paste0("tmp_cohort_", as.integer(Sys.time()) %% 10000)

# A folder with cohorts
cohortsFolder <- here::here("inst", "cohorts")

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

# A folder on the local file system to store results
outputDir <- here::here(paste("results", databaseId))

# test connection details ----
connection <- DatabaseConnector::connect(connectionDetails)

test <- DatabaseConnector::renderTranslateQuerySql(
  connection, 
  "select count(*) as n_persons from @cdmDatabaseSchema.person",
  cdmDatabaseSchema = cdmDatabaseSchema) |> dplyr::pull(1)

print(paste(test, "persons in the cdm database"))
DatabaseConnector::disconnect(connection)

# setup output folder and log -----
if (!file.exists(outputDir)) {
  dir.create(outputDir, recursive = TRUE)
}

source(here::here("runCohortDiagnostics.R"))

3. Upload the results to the DTZ

Please upload the zip file.