# # RMarkdown and knitr presentation

Adding a footer is not natively possible. Luckily, we can make use of jQuery and CSS to add a footer to the slides of an ioslides presentation rendered with knitr. First of all we have to include the jQuery plugin. This is done by the line

<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.2/jquery.min.js"></script>



Now we can use jQuery to alter the DOM (document object model) of our presentation. In other words: we alter the HTML structure of the document. As soon as the presentation is loaded ($(document).ready(function() { ... })), we select all slides, that do not have the class attributes .title-slide, .backdrop, or .segue and add the tag <footer></footer> right before each slide is 'closed' (so before </slide>). The attribute label carries the content that will be displayed later on. All we have to do now is to layout our footer with CSS: After each <footer> (footer::after): • display the content of the attribute label • use font size 12 • position the footer (20 pixels from the bottom of the slide and 60 pxs from the left) (the other properties can be ignored but might have to be modified if the presentation uses a different style template). --- title: "Adding a footer to presentaion slides" author: "Martin Schmelzer" date: "26 Juli 2016" output: ioslides_presentation --- r{r setup, include=FALSE} knitr::opts_chunk$set(echo = FALSE)
r

<script>
$(document).ready(function() {$('slide:not(.title-slide, .backdrop, .segue)').append('<footer label=\"My amazing footer!\"></footer>');
})
</script>

<style>
footer:after {
content: attr(label);
font-size: 12pt;
position: absolute;
bottom: 20px;
left: 60px;
line-height: 1.9;
}
</style>

## Slide 1

This is slide 1.

## Slide 2

This is slide 2

# Test

## Slide 3

And slide 3.



The result will look like this:

(opens new window)

## # Rstudio example

This is a script saved as .Rmd, on the contrary of r scripts saved as .R.

To knit the script, either use the render function or use the shortcut button in Rstudio.

---
title: "Rstudio exemple of a rmd file"
author: 'stack user'
date: "22 July 2016"
output: html_document
---

The header is used to define the general parameters and the metadata.

## R Markdown

This is an R Markdown document.
It is a script written in markdown with the possibility to insert chunk of R code in it.
To insert R code, it needs to be encapsulated into inverted quote.

Like that for a long piece of code:

r{r cars}
summary(cars)
r

And like r cat("that") for small piece of code.

## Including Plots

You can also embed plots, for example:

r{r echo=FALSE}
plot(pressure)
r



#### # Syntax

- YAML format, used when the script is compile to define general parameter and metadata

#### # Parameters

Parameter definition
title the title of the document
author The author of the document
date The date of the document: Can be "r format(Sys.time(), '%d %B, %Y')"
author The author of the document
output The output format of the document: at least 10 format available. For html document, html_output. For PDF document, pdf_document, ..

### # Sub options parameters:

sub-option description html pdf word odt rtf md github ioslides slidy beamer
citation_package The LaTeX package to process citations, natbib, biblatex or none X X X
code_folding Let readers to toggle the display of R code, "none", "hide", or "show" X
colortheme Beamer color theme to use X
css CSS file to use to style document X X X
dev Graphics device to use for figure output (e.g. "png") X X X X X X X
duration Add a countdown timer (in minutes) to footer of slides X
fig_caption Should figures be rendered with captions? X X X X X X X
fig_height, fig_width Default figure height and width (in inches) for document X X X X X X X X X X
highlight Syntax highlighting: "tango", "pygments", "kate","zenburn", "textmate" X X X X X
includes File of content to place in document (in_header, before_body, after_body) X X X X X X X X
incremental Should bullets appear one at a time (on presenter mouse clicks)? X X X
keep_md Save a copy of .md file that contains knitr output X X X X X X
keep_tex Save a copy of .tex file that contains knitr output X X
latex_engine Engine to render latex, or ""pdflatex", "xelatex", lualatex" X X
lib_dir Directory of dependency files to use (Bootstrap, MathJax, etc.) X X X
mathjax Set to local or a URL to use a local/URL version of MathJax to render X X X
md_extensions Markdown extensions to add to default definition or R Markdown X X X X X X X X X X