3.5 R Markdown Notebooks

As mentioned in Section 2.2 of the R Markdown Definitive Guide (Xie, Allaire, and Grolemund 2018), there are several ways to compile an Rmd document. One of them is to use R Markdown Notebooks, with the output format html_notebook, e.g.,

  1. ---
  2. title: An R Markdown Notebook
  3. output: html_notebook
  4. ---

When you use this output format in RStudio, the Knit button on the toolbar will become the Preview button.

The main advantage of using notebooks is that you can work on an Rmd document iteratively in the same R session. You can run one code chunk at a time by clicking the green arrow button on each chunk, and you will see the text or plot output in the editor. When you click the Preview button on the toolbar, it only renders the Rmd document to an HTML output document containing the output of all code chunks that you have already executed. The Preview button does not execute any code chunks. By comparison, when you use other output formats and hit the Knit button, RStudio launches a new R session to compile the whole document (hence all code chunks are executed at once), which usually takes more time.

If you do not like RStudio’s default behavior of showing the output of code chunks inline when you run them individually, you can uncheck the option “Show output inline for all R Markdown documents” from the menu Tools -> Global Options -> R Markdown. After that, when you run a code chunk, the output will be shown in the R console instead of inside the source editor. You can also set this option for an individual Rmd document in its YAML metadata:

  1. editor_options:
  2.   chunk_output_type: console

References

Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown.