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/
