Reporting with R

This guide provides information about how to design reports with R over Opal data.

R being a programming language, any text editor could be used. In this guide we recommend to use the RStudio editor as it has reporting features integrated. RStudio is cross-platform, free of charge (Open Source Edition) and is available as a Desktop or a Server application. The Server flavor is more suitable for teams (shared development environment) and when restrictive security constraints apply (IP white-listing).

Prerequisites

In order to be able to interact with a Opal server, the prerequisites are the following:

  • having R installed both on client and on server sides
  • having R package opal installed
  • having access to a Opal server

Design of a Report Tutorial

A report in Opal is essentially a R script enhanced with presentation directives. This reporting capability is brought by the knitr R package. As the report IS a R script, it can be executed in different contexts:

  • R console
  • RStudio editor
  • Shell script
  • Opal

See more information about Report Execution Flows.

The following steps will walk you through the design of a report, tested in a development environment (R console/RStudio), then deployed in a production environment (Shell script/Opal).

First Step: Write a R Script

Report data are coming first, so start with writing a R script that:

  • connects to a Opal server
  • assign some Opal data to the remote R session
  • analyze, transform the data from the remote R session
  • end remote R session

Example

See an example of such a script: opal.R.

Run it in a R console or RStudio.

Second Step: Turn R script to R markdown

The R script can be enhanced with presentation directives as specified by knitr. We will chose the specific R report format based on Markdown. Detailed documentation can be found in the R Markdown article.

Example

See an example of such a report: opal-dev.Rmd.

You can run it in RStudio as described in the Using R Markdown article.

See the Opal Reporting with R output.

Third Step: Prepare for Deployment

As you might have noticed the opal-dev.Rmd contains the credentials of the user connecting to the Opal server. These can be externalized. Credentials will be provided by the context of execution as R options:

  • Shell script
  • Opal

See documentation about opal.login function for available R options.

Example

See an example of a production report opal-prod.Rmd. Note that no user credentials is provided. RStudio cannot execute it as usual as the editor does not knit the report in the current R session.

To execute this report you can use the opal.report helper function that will knit it for you. See an example of a R shell script running it: opal-exec.R.

For executing it in Opal, see instructions on how to specify the R options in the Reports Administration documentation.

Final Step: Schedule Report Execution

Once a report design is done, it is possible to register it in Opal in order to:

  • publish it so that it can be executed manually by other users,
  • execute it periodically,
  • archive and publish the reports generated.

For more details see Reports Administration.

If you have written a shell script, such as opal-exec.R example, it can be executed as any cron task.

Advanced Examples

See advanced examples in the table folder, where opal-table.Rmd features:

  • R Markdown sub-reports,
  • inline css-styling,
  • access to Opal variables description.

The result of this report is a document that presents the data dictionary of a Opal table with figures and summary statistics.

See Opal Data Dictionary with R output.

Report Execution Flows

Local R Session

When executed in the context of RStudio, R console or Shell script, the communication flow is:

../_images/report-local-r-session.png

Opal R Session

When executed by Opal the communication flow is:

../_images/report-remote-r-session.png