21 R Markdown

21.1 Setup

See Setup/R Markdown.

21.2 Slides

October 21 2019 - Basic R Markdown



21.3 Basic markdown

Wrap a word with single asterisks for italics and double asterisks for bold.

Wrap a word with single asterisks for *italics* and double asterisks for **bold**.

Surround inline code chunks with single `backticks` or full code blocks with triple backticks:

yum <- is.delicious('gorgonzola')
[1] TRUE

Tables can be made with a markdown table generator (or by hand), or with functions, for example: knitr::kable.

carat cut color clarity depth table price x y z
0.23 Ideal E SI2 61.5 55 326 3.95 3.98 2.43
0.21 Premium E SI1 59.8 61 326 3.89 3.84 2.31
0.23 Good E VS1 56.9 65 327 4.05 4.07 2.31
0.29 Premium I VS2 62.4 58 334 4.20 4.23 2.63
0.31 Good J SI2 63.3 58 335 4.34 4.35 2.75

21.4 YAML

21.4.1 Rendering multiple output formats

To render multiple output formats from the same R Markdown document, use this example. We remap the knit button / shortcut to rendering all the output formats specified.

21.5 BibTeX

21.5.1 Setting italics in references

Setting italics in your .bibtex references is as simple as wrapping the words in \emph{}. For example:

\emph{Escherichia coli}

21.6 Tables

Lots of options are available for generating markdown tables from R objects, or text.


R packages

Note: differences between these packages are mainly in syntax but more importantly also in the possible output formats. Some only work with HTML output, some only PDF, etc.

21.7 Reflow lines

If this is a manuscript, and you are noticing (especially in Git) everything is on a few really long lines, simply reflow using the shortcut (CTRL+SHIFT+/) or remember to hit enter at the end of a line.

21.8 Presentations with xaringan

Yihui Xie made a great package for generating HTML presentations in R Markdown: xaringan.

All of Alec’s slides use this package, see Slides.

21.8.1 Incremental ggplot slides

An example for building your ggplots incrementally using this example xaringan document.