DrugUtilization

Introduction

This R package contains resources for the evaulation of drug exposures in the OMOP CDM for performing drug utilization studies.

Installation

1. On Windows, make sure RTools is installed.
2. The DatabaseConnector and SqlRender packages require Java. Java can be downloaded from http://www.java.com.
3. Download and open the R package using RStudio.
4. Create the file .Renviron in the root of the package to hold the settings for connecting to the CDM for performing the drug utilization summary.

# --------------------------------
# ------ CDM CONNECTION ----------
# --------------------------------
DBMS = "postgresql"
DB_SERVER = "myserver/db"
DB_PORT = 5432
DB_USER = databaseUserName
DB_PASSWORD = superSecretPassword
CDM_SCHEMA_LIST = "CDM_1,CDM_2,CDM_3"
RESULTS_SCHEMA_LIST = "CDM_1_results,CDM_2_results,CDM_3_results"
DATABASE_LIST = "CDM 1,CDM 2,CDM 3"
# --------------------------------
# -- NETWORK RESULTS CONNECTION --
# --------------------------------
NETWORK_DBMS = "postgresql"
NETWORK_DB_SERVER = "myserver/dus"
NETWORK_DB_PORT = 5432
NETWORK_DB_USER = dbUser
NETWORK_DB_PASSWORD = dbPassword
NETWORK_SCHEMA = "public"

The CDM_SCHEMA_LIST, RESULTS_SCHEMA_LIST, DATABASE_LIST can be used to specify a list of CDM schemas to use when generating the results if required.

5. Build the package.

Usage

The package provides functions to perform the drug exposure summary and for assembling results for sharing over the network.

Refer to the extras/TestCode.R code in the package to see working examples for each of these.

1. Create a drug exposure summary in the results schema of your CDM for a list of drugIngredientConceptIds:

DrugUtilization::createDrugExposureOverview(
    connectionDetails,
    cdmDatabaseSchema = cdmDatabaseSchema,
    resultsSchema = resultsSchema,
    drugIngredientConceptIds = drugConceptsOfInterest,
    debug = debug,
    debugSqlFile = "test.dsql"
  )

The debug setting is used when you'd like to emit the SQL to a file vs. running it directly on your CDM.

2. Export the results from the results schema to the local file system as CSVs:

    DrugUtilization::exportResultsToCSV(
      connectionDetails,
      cdmDatabaseSchema = cdmDatabaseSchema,
      resultsSchema = resultsSchema,
      outputFolder = outputFolder,
      sourceId = sourceId,
      sourceName = databaseName
    )

The sourceId and sourceName parameters are required but allow for users to define a list of sources for coordination across the network. When using the export, the assumption is that these results will be shared amongst the network of databases that are participating in a study and therefore the DBs will be uniquely identified by their sourceId and sourceName.

3. Create a PostgreSQL network database & schema to hold the results

networkDDLSql <- DrugUtilization::getNetworkResultsDDLSql(networkSchema = networkSchema)
DatabaseConnector::executeSql(connection = networkDbConnection, sql = networkDDLSql)

The code above will create the necessary tables & views in the PostgreSQL database. This will hold the results from across the network.

4. Load the data into the network schema

Refer to the extras/TestCode.R code in the package to see how this is scripted.

Development

DrugUtilization is being developed in R Studio.

Development Status

Alpha