R Markdown?

• Markdown is a lightweight markup language with plain text formatting syntax that can be converted to many formats, including HTML.
  It is completely independent from R.
  The extention is typically .md.

• R Markdown is an extension of the markdown syntax that enables R code to be executed. The extention is typically .Rmd.

• {rmarkdown} is an R package that proceses and converts .Rmd files into a number of different formats, including HTML, PDF and Word.

Create a new .Rmd in RStudio

New .Rmd

Compile .Rmd

Use the Knit button to produce a HTML file

Shortcut: Ctrl + Shift + K

Titles and text fonts in Markdown

# Big title
## Title
### Small title
_Italic_, *italic*, __bold__, **bold**, and `monospace`

Big title

Title

Small title

Italic, italic, bold, bold, and monospace

Lists in Markdown

1. This is
2. an ordered
3. list

 * This is
 * a bullet list
    * with indent

• You can enumerate only with '1.'; it will increment automatically

• You can also use '-' or '+' instead of '*'

More in Markdown

> You can insert quotes and $\LaTeX$ expressions

You can insert quotes and $\LaTeX$ expressions

$$ \frac{1}{n} \sum_{i=1}^n X_i $$

$$\frac{1}{n} \sum_{i=1}^n X_i$$

• Make an horizontal line with '***'

• Add 4 spaces at the end of your text in order to write to the next line

• You can write HTML in Markdown (e.g. use '<br>' to get a blank line)

Insert links and pictures

[Antoine's personal page](https://abichat.github.io/)

Antoine's personal page

![](https://slides.yihui.name/gif/impossible-parking.gif)

It also works directly with HTML syntax:

<a href="https://abichat.github.io/">Antoine's personal page</a>
<img src="https://slides.yihui.name/gif/impossible-parking.gif">

Basic chunk

```{r}
x <- 4
x
```

[1] 4

```{r, echo=FALSE}
x <- 5
x
```

```{r, eval=FALSE}
x <- 5
```

Figure options (1/2)

```{r, fig.align="center", out.width="60%"}
ggplot2::qplot(Sepal.Length, Sepal.Width, data = iris)
```

Figure options (2/2)

```{r, fig.align="center", out.width="80%", fig.asp=0.7, fig.width=4}
ggplot2::qplot(Sepal.Length, Sepal.Width, data = iris)
```

A better way to include pictures

```{r, fig.align="center", out.width="80%", echo=FALSE}
knitr::include_graphics(
  "https://slides.yihui.name/gif/impossible-parking.gif")
```

It allows you to use the chunk options for image size.

FAQ: two figures side-by-side

```{r, echo=FALSE, out.width="50%", fig.show="hold", fig.align="default"}
plot(iris)
plot(iris, pch = 20, col = iris$Species)
```

Supported languages in chunks

• R

• Python

• Shell

• SQL

• Rcpp

• Stan

• JavaScript

• CSS

• Julia

• C and Fortran

• many others...

Data frame printing and tables

You can play with YAML option df_print. For example, df_print: paged:

iris   ## or directly with `DT::datatable(iris)`

For more refined tables, you can use knitr::kable(), xtable::xtable(), kableExtra::kable().

Use R Markdown for..

• Reports (analysis, etc) with text, code and results in the same place! With many possible output formats including HTML, PDF, MS Word, etc.

• Notebooks (vs "Chunk Output in Console")

• Slides (like this one! -- see source code)

• Websites (such as the website of our R user group)

• Books (e.g. my online advanced R course or even a thesis)

• [WIP] {pagedown}: Paginate the HTML Output of R Markdown with CSS for Print

Slides formats

• ioslides (example)

• slidy (example)

• beamer (pdf)

• powerpoint (ppt)

• xaringan / remark.js (example: this presentation!)

• reveal.js

3 main reasons to make your slides with R Markdown:

1. Include code and results very easily

2. Make HTML presentations directly available online (easy to export them to PDF using "print to PDF" of Chrome)

3. Include fancy HTML widgets (like maps, searchable tables, interactive graphics, etc)

Include an interactive map with {leaflet}

library(leaflet)
leaflet(width = "100%") %>% 
  setView(lng = 5.767249, lat = 45.190590, zoom = 12) %>% 
  addTiles(options = providerTileOptions(minZoom = 2, maxZoom = 19))

+−

Leaflet | © OpenStreetMap contributors, CC-BY-SA

Websites

Example: webpage of the Grenoble RUG

How does it work?

• just multiple Rmd documents (one by page) rendered as HTML with a common navigation bar

• host the static HTML pages using e.g. GitHub pages

• make your own website in 20 minutes with this tutorial

You can also use {blogdown}. See the full documentation.

Books

Every R book is now written with {bookdown}.

See many of them at https://bookdown.org/.

Again, from our side, it is just a collection of R Markdown documents.

E.g. see my advanced R course and the associated GitHub repository.

Technical Documents

Formats in {bookdown} allows you to:

• number and reference equations, tables, figures, etc

• use special chunks such as theorems and proofs

• special headers such as "PART" and "APPENDIX"

• citations

• etc

To use this in single R Markdown documents (not books), you can use formats

• bookdown::html_document2()
• bookdown::pdf_document2()
• bookdown::word_document2()

Useful materials

• Official website

• R Markdown: The Definitive Guide

• Authoring Books and Technical Documents with R Markdown

• Reference guide

• Cheat sheet

• Tips for R Markdown

• For less problems with LaTeX distributions: {TinyTeX}

• Embed a File in the HTML Output of R Markdown

• Xaringan documentation

• Decouple Code and Output in xaringan slides

• Tips for making slides