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.
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
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.
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
would be imported into the workflow. Therefore, other chunks are ignored until rendering the analysis report with
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
renderReportuses 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
renderReporthas 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
importWF(..., update = TRUE)as discussed in import section to update.
- If all steps are added interactively, meaning you did not use
sal2rmdwill 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.