Basics of Markdown

Here you have a summary guide of the main style syntax.

# H1
## H2
### H3
#### H4
##### H5
###### H6

Alternatively, for H1 and H2, an underline-ish style:

Alt-H1
======

Alt-H2
------

*italics* or _italics_.

**bold** or __bold__.

~~Strikethrough~~

1. First ordered list item
2. Another item

* Unordered list can use asterisks
- Or minuses
+ Or pluses

[I'm an inline-style link](https://www.google.com)

Inline-style: 
![alt text]("image")

Inline `code` has `back-ticks around` it.
```python
s = "Python syntax highlighting"
print s
```

> Blockquotes are very handy in emails to emulate reply text.

$-b \pm \sqrt{b^2 - 4ac} \over 2a$

Header

The header is the R Markdown document part where you can set the title, the author, the date, and the output as the image shows:

---
title: "Mastering R presentations"
author: "Paula LC"
date: "2019-09-24"
output: ioslides_document
---

But at the same time, other options can be determined as follows:

---
title: "Mastering R presentations"
author: "Paula LC"
date: "2019-09-24"
output: 
  ioslides_presentation:
    incremental: false
    self-included: true
---

Content

Once the header is completed, you can add any kind of content that you can practically imagine: R code, equations, charts, images, videos etc. In the next points we are going to see how to add each type of content.

---
title: "Example"
output:
  ioslides_document:
    mathjax: local
    self_contained: false
---

---
title: "Example"
output:
  ioslides_document:
    mathjax: "http://example.com/MathJax.js"
---

Colons can be used to align columns.

| Tables        | Are           | Cool  |
| ------------- |:-------------:| -----:|
| col 3 is      | right-aligned | $1600 |
| col 2 is      | centered      |   $12 |
| zebra stripes | are neat      |    $1 |

data <- faithful[1:4, ]
knitr::kable(data, caption = 'Table with kable')

data <- faithful[1:4, ]
print(xtable::xtable(data, caption = 'Table with xtable'), type = 'HTML', 
      HTML.table.attributes = 'border=0')

data <- faithful[1:4, ]
stargazer::stargazer(data, type = 'HTML', title = 'Table with stargazer')

library(highcharter)
highchart() %>% 
  hc_title(text = "Scatter chart with size and color") %>% 
  hc_add_series(mtcars, "point", hcaes(wt, mpg, size=drat, color=hp)) %>%
  widgetframe::frameWidget()

Ioslides

Ioslides is a nice R presentation format characterized by the simplicity of the result. There are some features specific from ioslides, such as the display mode

• f: enable fullscreen mode
• w: toggle widescreen mode
• o: enable overview mode
• h: enable code highlight mode
• p: show presenter notes

or the incremental bullets:

---
output:
  ioslides_presentation:
    incremental: true
---

Moreover, you can change the presentation size, the text size, or even the transition speed in the header of the document. Specifically, for the transition speed you can set the number of seconds for each slide or use the standard options: default, slower, faster.

---
output:
  ioslides_presentation:
    widescreen: true
    smaller: true
    transition: slower
---

For another hand, there is a quick way to add a background image without editing the CSS file,

## {data-background="my_background.png"}

But if you want to add specific style changes to your presentation, I recommend you to edit the CSS file and add it to the header of the RMarkdown document:

---
output:
  ioslides_presentation:
    css: styles.css
---

One of the disadvantages of ioslides is that customization is limited compared with other output formats. At the end of this tutorial we explain how to modify by your own a CSS file.

Slidy

Slidy has more flexibility than ioslides as to appearance and style. Now we are going to see some of the main special features that slidy has.

There is the chance to change the display mode with the next shortcuts;

• c: Show table of contents
• c: Toggles the display of the footer
• a: Toggles display of current vs all slides (useful for printing handouts)
• s: Make fonts smaller
• b: Make fonts larger

And we can adjust the font directly in the header of the document without editing the CSS file:

---
output:
  slidy_presentation:
    font_adjustment: -1
---

You will find other interesting features of slidy such as the countdown timer in the footer or the customized footer text that can be easily added with the options duration and footer.

Beamer

Beamer is a \(\LaTeX\) class to produce presentations and slides. It is so common in academia and so useful to add mathematical formulas and expressions. You can create your own Beamer presentations from R without a deep knowledge of \(\LaTeX\) (only Markdown).

So the first step is to install tex. Tex is a typesetting for complex mathematical formulae used in \(\LaTeX\). To install it, download tone of the next programs, depending on your OS system: - MikTeX on Windows - MacTeX 2013+ on OS X - TeX Live 2013+ on Linux

Beamer themes are the same that you can find in \(\LaTeX\). In the next link https://hartwork.org/beamer-theme-matrix/ you have the list of the different available header options related to the appearance and style:

---
output:
  beamer_presentation:
    theme: "AnnArbor"
    colortheme: "dolphin"
    fonttheme: "structurebold"
---

Reveal.js

There are other interesting options to create presentations in R such as reveal.js and xaringan. Reveal is very well-known because of the flexibility in the themes and transitions by default, the vertical slides or the possibility to include a web site inside a slide. In this part, we are going to explain how to generate a revealjs file and the main features of this awesome library.

First of all, it is required to install revealjs package

install.packages("revealjs")

Then, you can directly change in the R Markdown document header the output argument to revealjs_presentation or go to menu File -> New File -> R Markdown -> From template and select reveal.js presentation.

There are some amazing keyboard shortcuts:

-f for fullscreen - o or ESC for overview mode - alt or (ctrl in Linux) and click an element, to zoom this element - s for speaker view (so pretty!) - B or . to pause the presentation

And there is a lot of variety about appearance and styles. If you want to change how the presentation looks like, you can choose any of the next theme options: default, simple, sky, beige, serif, solarized, blood, moon, night, black, league, and white. And for the syntax highlighting style: default, tango, pygments, kate, monochrome, espresso, zenburn, and haddock. Pass null to prevent syntax highlighting. The way to specify it is the same than the previous presentation types.

---
output:
  revealjs::revealjs_presentation:
    theme: black
    highlight: pygments
---

In revealjs you can center the text of the slides changing the center option to true, which by default is false, as well as the possibility of modifying the transitions and backgrounds, i.e. how the slide is going to move to the next one. Available transitions and background_transitions are default, fade, slide, convex, concave, zoom or none. Any of these global options can be overriden specifying the data-transition attribute in the header of the slide:

## Use a zoom transition {data-transition="zoom"}

Moreover, Revealjs lets add different backgrounds like color, image, video, and iframe:

## CSS color background {data-background=#ff0000}

## Full size image background {data-background="background.jpeg"}

## Video background {data-background-video="background.mp4"}

## A background page {data-background-iframe="https://example.com"}

Finally, you can specify the level of heading will be used with the slide_level option. For example, if the slide_level is 2, the level-1 headers will be built horizontally and level-2 headers, vertically.

Other interesting features are the great look on touch devices, the fragmented slides, easy to export to pdf, keyboard bindings, or the parallax scrolling background.

References https://CRAN.R-project.org/package=revealjs.

Ninja presentation

The last type of presentations that we are going to see is the xaringan library. It is an R Markdown extension based on the JavaScript library remark.js (https://remarkjs.com). This package was originally designed for “ninja”, so it is recommended to people that have a well-known of CSS. For another hand, if you need slides to be self-contained, then xaringan it is not a good option because needs a webserver to run. Another bad news is that xaringan doesn’t work well with HTML widgets.

To install the library type

install.packages("xaringan")

or install it directly from GitHub to ensure that you are downloading the last version

devtools::install_github('yihui/xaringan')

Once you get installed, go to the menu File -> New File -> R Markdown -> From template and click on ninja presentation.

Note: If you understand chinese you can select the last option ;).

The header is going to look like this

---
title: "Presentation Ninja"
subtitle: "⚔<br/>with xaringan"
author: "Yihui Xie"
institute: "RStudio, Inc."
date: "2016/12/12 (updated: 2019-09-23)"
output:
  xaringan::moon_reader:
    lib_dir: libs
    nature:
      highlightStyle: github
      highlightLines: true
      countIncrementalSlides: false
---

A lit bit more complicated than others and as you will see, there are some funny arguments that make this library really different.

• css: to add your own CSS file,
• self_contained: to produce a self-contained HTML file
• seal: to generate a title slide automatically using the YAML metadata of the R Markdown document (if FALSE, you should write the title slide by yourself)
• yolo: to insert the Mustache Karl (TM) randomly in the slides. Using TRUE, a number between 0-1 to insert the Mustache Karl in a percentage of the slides, or even a list(times = n, img = path)
• chakra: path to the remark.js library (can be either local or remote).
• nature: (Nature transformation) A list of configurations to be passed to remark.create(), e.g. list(ratio = ‘16:9’, navigation = list(click = TRUE)); see https://github.com/gnab/remark/wiki/Configuration

Besides the options provided by remark.js, there are others such interesting like autoplay the slides or the countdown timer. Slides can be automatically played setting the autoplay option under nature (in milliseconds). For example, to display slides every 30 seconds and see the countdown timer:

---
output:
  xaringan::moon_reader:
    nature:
      autoplay: 30000
      countdown: 30000
---

It is possible to highlight code lines turning the option highlightLines to true or to extend the markdown syntax defining custom macros with the beforeInit option under the option nature.