HTML5 Documents or Slides with R Markdown

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Last term I taught Data Analysis at UNAB and I had to find a way to combine slides and R code.


You can write but you can’t run R code from TeXShop or other editor. LaTeX Beamer is a good option but it has that big flaw. In addition, some of my students used to study from their tablets and smartphones and they complained about missing characters when reading pdf presentations.


R Markdown allows you to create Rmd documents where you can write text and add both LaTeX and R code with html or pdf output. You can also embed Google Fonts to your presentation and missing characters won’t be an issue anymore.

Building a document/presentation

In RStudio is quite easy and with 2-3 clicks you are ready to go but here I’m presenting some additional steps that will do the magic.

Basic Steps

Create a new document, edit the content and you are ready to go. The first time you do this RStudio will ask you to download some libraries. img1 img2

After you create your document the first lines are like these:

title: "DOCUMENT"
author: "Pachamaltese"
date: "December 2, 2015"
output: html_document

To insert LaTeX equations just use \( (e.g. $a+b$=\)a+b$) and to insert R code click “chunks” img3

R Markdown chunks contain options

  • eval = TRUE/FALSE to run (do not run) code
  • echo = TRUE/FALSE to display/hide the involved code

Here is an example. I show you the result and the code using eval=FALSE.

Using echo=TRUE

{r, echo=TRUE}

Results in


plot of chunk plot-1

Using echo=FALSE

{r, echo=FALSE}

Results in

plot of chunk plot-2

To obtain the output click on Knit HTML (or Knit PDF)

img4 img5

What you’ll obtain will be something like this

img6 img7

Adjusting images

Figure width and height can be configured as you wish. For example

{r, echo=FALSE, fig.height=3, fig.width=4}

plot of chunk plot-3

Creating lightweight documents

If you want your html file to be as light as possible one option is to use vignette_html. To to that you need to modify the first lines of your Rmd file like this:

title: "DOCUMENT"
author: "Pachamaltese"

Creating customized presentations

I saw a good design from the excellent Regression Models unit on Coursera by Brian Caffo and team. I adapted that design allowing several authors and more customization to produce my course material (the Rmd and style files are available here). To obtain the same result you need to change the first lines of your Rmd file like this:

author: "AUTHOR 1"
hitheme: tomorrow
framework: io2012
knit : slidify::knit2slides

Further reading

  • Knitr – chunks options
  • Slidify – changing styles and animations

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