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 which I sent a link to last week during lab meeting, here are some other links I’ve come across in the past:
- A comprehensive Markdown syntax cheatsheet
- RStudio’s introduction to RMarkdown
- The definitive RMarkdown Guide, by Yihui Xie, the lead dev on RMarkdown
Here are some definitions of the various jargon terms:
- 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