Analyze FHIR Data in R

Access FHIR data with pure R script and standard SQL on any machine where R and Java can be installed. You can use the CData JDBC Driver for FHIR and the RJDBC package to work with remote FHIR data in R. By using the CData Driver, you are leveraging a driver written for industry-proven standards to access your data in the popular, open-source R language. This article shows how to use the driver to execute SQL queries to FHIR and visualize FHIR data by calling standard R functions.

Install R

You can match the driver's performance gains from multi-threading and managed code by running the multithreaded Microsoft R Open or by running open R linked with the BLAS/LAPACK libraries. This article uses Microsoft R Open 3.2.3, which is preconfigured to install packages from the Jan. 1, 2016 snapshot of the CRAN repository. This snapshot ensures reproducibility.

Load the RJDBC Package

To use the driver, download the RJDBC package. After installing the RJDBC package, the following line loads the package:

Connect to FHIR as a JDBC Data Source

You will need the following information to connect to FHIR as a JDBC data source:

• Driver Class: Set this to cdata.jdbc.fhir.FHIRDriver
• Classpath: Set this to the location of the driver JAR. By default this is the lib subfolder of the installation folder.

The DBI functions, such as dbConnect and dbSendQuery, provide a unified interface for writing data access code in R. Use the following line to initialize a DBI driver that can make JDBC requests to the CData JDBC Driver for FHIR:

You can now use DBI functions to connect to FHIR and execute SQL queries. Initialize the JDBC connection with the dbConnect function.

Set URL to the Service Base URL of the FHIR server. This is the address where the resources are defined in the FHIR server you would like to connect to. Set ConnectionType to a supported connection type. Set ContentType to the format of your documents. Set AuthScheme based on the authentication requirements for your FHIR server.

Generic, Azure-based, AWS-based, and Google-based FHIR server implementations are supported.

Sample Service Base URLs

• Generic: http://my_fhir_server/r4b/
• Azure: https://MY_AZURE_FHIR.azurehealthcareapis.com/
• AWS: https://healthlake.REGION.amazonaws.com/datastore/DATASTORE_ID/r4/
• Google: https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/fhirStores/FHIR_STORE_ID/fhir/

Generic FHIR Instances

The product supports connections to custom instances of FHIR. Authentication to custom FHIR servers is handled via OAuth (read more about OAuth in the Help documentation. Before you can connect to custom FHIR instances, you must set ConnectionType to Generic.

Built-in Connection String Designer

For assistance in constructing the JDBC URL, use the connection string designer built into the FHIR JDBC Driver. Either double-click the JAR file or execute the jar file from the command-line.

Fill in the connection properties and copy the connection string to the clipboard.

Below is a sample dbConnect call, including a typical JDBC connection string:

Schema Discovery

The driver models FHIR APIs as relational tables, views, and stored procedures. Use the following line to retrieve the list of tables:

Execute SQL Queries

You can use the dbGetQuery function to execute any SQL query supported by the FHIR API:

You can view the results in a data viewer window with the following command:

Plot FHIR Data

You can now analyze FHIR data with any of the data visualization packages available in the CRAN repository. You can create simple bar plots with the built-in bar plot function: