Difference between R MarkDown and R NoteBook

Question

I am trying to understand at a high level what the differences between R Markdown and R NoteBook. I know they are interrelated but I would like to figu

Answer 1

Similarites: The R notebook and R Markdown document are pretty much similar. Markdown format works in both file types. Both the file formats can be used for communicating code along with results and commentary to others. One can choose to knit the created document to HTML, PDF and WORD output formats. If there is an error in the code, output will not be generated. To run the file: CTRL+SHIFT+K and to insert code chunk: CTRL+ALT+I.

R Markdown document: The Rmd document can be configured via a wizard and has options for reproducibilty document, presentation slides, shiny app etc and an option to create document from a template. If you change the code, the ouput is executed in the Rmd output. It does not offer the option to Preview the document. The YAML header has output format as: output: html_document

R Notebook Document: The R nb document is launched directly and no wizard (as in the case of .RMD) appears. Along with the notebook file, an additional html file that extension *.nb.html is generated. The notebook has the option for Preview. If any code is altered or edited, the new output is not shown. The output is shown in the code editor itself. Whatever the old output was it is only rendered. No new output is generated from the code change. In order to show the code output, we need to execute the chunk and then it will appear in the output. The YAML header has output as: output: html_notebook

YAML header : If we change the YAML header from one file to another, it will change the type of the document. For instance, you have a R notebook that has YAML header as html_notebook. If you change the YAML header, your R notebook will be converted to R Markdown document.

If you have to choose one, go with RMarkdown document as it offers more control and updates documents as soon as you knit it.

Answer 2

One of the most important differences is not completely clear from the above answers.

From Section 3.2.1.3 of the Bookdown book:

There is also a Restart R and Run All Chunks item in the Run menu on the editor toolbar, which gives you a fresh R session prior to running all the chunks. This is similar to the Knit button, which launches a separate R session to compile the document.

In other words, knitting creates a new environment and runs all the code there. By way of contrast, the R Notebook uses the Global Environment as is to render the HTML file. In fact, for an R Notebook, changes to the HTML file happen every time the .Rmd document is saved. The Preview button merely opens the HTML file in its current state. No code is run. Preview literally means what it says: it just shows you what has already been done.

Why does this matter? For example, if an R Notebook .Rmd file is opened, but no code chunks are run, then the HTML file will render all the markdown and input code just fine, but no output will appear. Or, suppose you define some variable x in the Console, but not in a code chunk. If you try to use x somewhere in an R Notebook, it will work just fine. Previewing the HTML document will also work just fine. On the other hand, knitting the document will generate an "unknown variable" error because knitting runs all the code in a new environment, and the variable x was never defined in the markdown file anywhere.