2 min read

reproducible abstract

A student asked me about how to include summary results in the abstract or executive summary at the top of an R Markdown report when they don’t get calculated until somewhere below.

I feel like I’ve seen a generally accepted solution to this, but I can’t find it. I thought maybe Keith Baggerly mentioned this in his slides about good reproducible reports, but he doesn’t seem to. I did find this RStudio Community discussion that is relevant, but it doesn’t have quite the solution I would want.

My suggestion was to include a code chunk something like this before the abstract:

```{r load_summary_results, echo=FALSE}
summary_file <- "_cache/summary_results.RData"
if(file.exists(summary_file)) {
} else {
  resultA <- NA
  resultB <- NA
  resultC <- NA

And then use resultA, resultB, and resultC in the abstract.

At the bottom of your document, save the results to a file with something like this:

```{r save_summary_results, echo=FALSE}
resultA <- [some calculation]
resultB <- [some other calculation]
resultC <- [a third calculation]

save(resultA, resultB, resultC, file=summary_file)

The first time you compile the report, your abstract would have a bunch of NA values in it. But then if you compile the report a second time, you’d pull in the results from the previous run.

Is there a better way? Let me know on twitter.