TITLE: An email which tries to make sense of the RMarkdown ecosystem
DATE: 2020-05-25
AUTHOR: John L. Godlee
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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

  [Coding Club tutorial]: 
https://ourcodingclub.github.io/tutorials/rmarkdown/
  [A comprehensive Markdown syntax cheatsheet]: 
https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet
  [RStudio's introduction to RMarkdown]: 
https://rmarkdown.rstudio.com/articles_intro.html
  [The definitive RMarkdown Guide, by Yihui Xie, the lead dev on 
RMarkdown]: https://bookdown.org/yihui/rmarkdown/
  [Markdown or LaTeX? - Yihui Xie]: 
https://yihui.org/en/2013/10/markdown-or-latex/