21 R Markdown

21.1 Setup

See Setup/R Markdown.

21.2 Slides

October 21 2019 - Basic R Markdown

Slides

Resources

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')
yum
[1] TRUE
```

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

knitr::kable(diamonds)

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.

Manually/copy-paste

• Tables Generator

R packages

• knitr::kable
• pander
• gt
• flextable
• xtable

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.