R markdown allows connecting data, code, and text into reports, presentations, and other documents. It works with R, Python, and Bash code. The rmdformats package creates clean HTML documents from R markdown files using different template designs like "readthedown" and "docute". Templates allow formatting code and content into pages, tables of contents, and other features. Parameters control template features such as figure sizes and code folding. Resources for learning more about R markdown and rmdformats were also provided.

1. R markdown and
Rmdformats
Samantha L Wilson
Hoffman Lab Meeting
March 31st, 2021

2. R markdown
▪ R package
▪ Connects data, to code, and allows many outputs
▪ Allows you to save code, figures, text as reports, notebooks,
slide presentations, dashboards, websites, interactive
documents and more
▪ You can put this together in Rstudio or R*, but allows you to
specify and change to the language (You can use this with
python or bash code as well)

3. Installation

4. R markdown interface

5. Code chunk options

6. Coding languages

7. Tables

8. Some markdown basics
• R markdown will also process Latex
equations
• You can add bibliographies
• A more extensive r markdown cheat
sheet can be found here:
• https://rstudio.com/wp-
content/uploads/2015/02/rmarkdo
wn-cheatsheet.pdf

9. Outputs
available

10. Rmdformats
▪ An R package that creates clean, ready to use HTML
documents
▪ Many different templates available
▪ Easy to integrate code into documents

11. Example templates
• “readthedown”
• I have been using this template for my lab notebook
• Fully responsive with dynamic table of contents and
collapsible navigation

12. Example templates
▪ “docute”
▪ Responsive, with a dynamic table of
contents and a dark theme switcher

13. Example templates
▪ “material”
▪ Document is split into pages at
each <h1> header, and the table
of contents allows an animated
navigation between these pages
(you can use the cards:
false preamble parameter to
disable the splitting and display all
the cards at once).

14. Installation

15. Creating your document
Parameters
Specify the template design you want
Self_contained – in this case it’s refering to graphics.
I set as false as I want to upload figures I generate
from a local file
Specify figure size
Lightbox effect is added if true
Cold_folding – whether you want code blocks to be
hidden or shown
Highlight refers to syntax highlighting. You can
customize this per whatever syntax you prefer

16. Creating your document
Extras
You can also add custom fonts if you want with
embed_fonts
Can render with bookdown instead of rmarkdown
which will provide section numbering and cross
references
Can adjust table of content depth with toc_depth

17. Resources – R markdown
▪ https://rmarkdown.rstudio.com/

18. Resources - RmdFormats
▪ https://cran.r-
project.org/web/packages/rmdformats/rmdformats.pdf
▪ https://github.com/juba/rmdformats