# 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

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.