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An email which tries to make sense of the RMarkdown ecosystem

DATE: 2020-05-25

AUTHOR: John L. Godlee

I was asked by my supervisor to send out an email with some resources to get people started with writing RMarkdown documents, in preparation for a lab meeting on the subject later in the week. As well as the resources, I tried to shed some light on the confusing terminology behind the RMarkdown ecosystem.

Hi all,

I was asked to send out some links to resources on RMarkdown and Markdown. In addition to the Coding Club tutorial[1] which I sent a link to last week during lab meeting, here are some other links I've come across in the past:

1: https://ourcodingclub.github.io/tutorials/rmarkdown/

* A comprehensive Markdown syntax cheatsheet[2]

* RStudio's introduction to RMarkdown[3]

* The definitive RMarkdown Guide, by Yihui Xie, the lead dev on RMarkdown[4]

Here are some definitions of the various jargon terms:

2: https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet

3: https://rmarkdown.rstudio.com/articles_intro.html

4: https://bookdown.org/yihui/rmarkdown/

* Markdown - A text formatting standard to add structural elements to plain text documents, adding headers, lists, quotes etc.. Essentially Markdown is just a way of writing. Markdown documents can be written in any plain text editor. Markdown was designed to be read easily both by humans and machines.

* RMarkdown - An extension of the Markdown standard, adding many features which allow for writing scientific reports, including the embedding of executable R code. {rmarkdown} is also an R package that provides these extensions.

* HTML - The language of webpages. Every website you read (I think?) is written in HTML. RMarkdown can be converted to HTML webpages.

* LaTeX - Another text formatting standard which is specifically designed for creating high quality printable documents. RMarkdown uses LaTeX as a backend to convert RMarkdown documents to PDF.

* Knitr (knitting) - An R package which takes an RMarkdown document, executes the R code embedded within it, and 'knits' the results back into the document.

* Pandoc - A document conversion software which comes bundled with the {rmarkdown} R package. {rmarkdown} uses pandoc in the background to convert from RMarkdown to various output formats.

Finally, another article for those who are interested on the limitations of RMarkdown, by Yihui Xie: Markdown or LaTeX? - Yihui Xie

This email is written in markdown syntax.

See you at the lab meeting,

John