Generate Reports

After the analysis, we often would like to generate some reports. In SPR, we provide two types of reports: technical report and analysis report. Both of them would give you an interactive HTML file.

Technical report

systemPipeR compiles all the workflow execution logs in one central location, making it easier to check any standard output (stdout) or standard error (stderr) for any command-line tools used on the workflow or the R code stdout. Also, the workflow plot is appended at the beginning of the report, making it easier to click on the respective step.

sal <- renderLogs(sal)

An example log file can be viewed over here.

Analysis report

To communicate with researchers outside one’s field, text explanation is usually expected. When we design a workflow and import from a template, adding text description to help people understand the workflow is highly recommended. The template can also be used to display results. Remember only SPR chunks (spr=TRUE)
would be imported into the workflow. Therefore, other chunks are ignored until rendering the analysis report with renderReport. These non-SPR chunks will be evaluated (if they do not have eval=FALSE) in report rendering and all SPR chunks will all be muted. So these non-SPR chunks can be good places to add some images, tables, plots, or other light calculations.

sal <- renderReport(sal)

• Here the renderReport uses the copy of workflow template, which is stored in .SPRProject, as skeleton to generate the report. All text is copied over and all steps in current workflow are translated into reproducible code to the skeleton.
• If any step is added interactively, meaning they did not exist in the template when you used importWF, renderReport has an internal algorithm to find the right place to inject the translated code based on the order where they appear inside SYSargsList. However, there will be no text description of these new steps.
• The algorithm is smart but not 100%, so if any new step is been added interactively, we recommend you to add text description and code accordingly in the template and use importWF(..., update = TRUE) as discussed in import section to update.
• If all steps are added interactively, meaning you did not use importWF at all, sal2rmd will be called. We will discuss this function in the next section.

To have a glimpse of what the renderReport file look like, check out our pre-configed workflow templates rendered pages here.