Rmd Syntax

Syntax

Italics

Can be producted by either _text1_ or *text1* which will look this text1 or text2.

Bold

Produced using a pair of double asterisks **text3** or __text4__ which will look like this text3 or text4.

Headers

# Header 1
## Header 2
### Header 3
etc...

Numbered list

1. Item 1
2. Item 2
3. Item 3
    + part a
    + part b

Item 1
Item 2
Item 3
- part a
- part b

Unnumbered list

* Item 1
* Item 2
* Item 3
    + part a
    + part b

Item 1
Item 2
Item 3
- part a
- part b

Script

A pair of tildes (~) turn text to a subscript (e.g., H~3~PO~4~ renders H₃PO₄). A pair of carets (^) produce a superscript (e.g., Cu^2+^ renders Cu²⁺). To get strike through ~~strike~~ renders to this ~~strike~~

Images

![](http://example.com/logo.png)
![optional caption text](figures/img.png)

Hyperlinks

http://example.com
[linked phrase](http://example.com)

Horizontal rule

Three or more asterisks or dashes *** or ---

Tables

First Header  | Second Header
------------- | -------------
Content Cell  | Content Cell
Content Cell  | Content Cell

Math and symbols

Math in RMarkdown

$x = y $ $x = y $ $x < y $ $x < y $ $x \le y $ $x y $ $x^{n}$ $x^{n}$ $\hat{x}$ $\hat{x}$ $\tilde{x}$ $\tilde{x}$ $\frac{a}{b}$ $\frac{a}{b}$ $\mu M$ $\mu M$ $\alpha A$ $\alpha A$ $\beta B$ $\beta B$ $\pi \Pi$ $\pi \Pi$ $^\circ C$ $^\circ C$

Code chunks & output

here

Text colour

Below are some useful bits of code that you can use to change font. For basic Rmd syntax see offical Reference Guide.

It is also handy to have colour guides/convertors at the ready, checkout the my section on colour in Plot Aesthetics & Colour.

For `Rmd` -> `PDF` docs

Font colour

The quickest option is this \textcolor{olive}{This text is olive}. It will look like this “This text is olive” in your PDF document.

If you want a more customisable option you can use the following to first choose your font colour, and then apply it. Define text colour (this won’t appear in your Knitted PDF)

\definecolor{fancyTextColor}{HTML}{FF0000}

Then use the following syntax to change font colour \colorbox{hightlightColor}{This text is red} It will look like this “This text is red” in your PDF document.

For `Rmd` -> `html` docs

Font colour and text

the following html code

Roses are <span style="color:red; font-family:Georgia; font-size:2em;">red.</span>

Will give you this output

Roses are red.

For coloured text blocks.

<style>
div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;}
</style>
<div class = "blue">

- This is my first conclusion
- This is my second conclusion

</div>

This is my first conclusion
This is my second conclusion

Custom Fonts in R Markdown PDF Font Formatting - coloring and emphasis

Hyperlinks

Underlink links in PDF documents By default hyperlinks on PDF knitted documents are not underlined. Use the following to underlink the link.

[\underline{R Markdown: The Definitive Guide}](https://bookdown.org/yihui/rmarkdown/)

R Markdown: The Definitive Guide

Images, Figures and videos

Tips and tricks for working with images and figures in R Markdown documents.

Simple add for image

![image caption](path/to/image.png)

Videos

Embed video

vebmedr is a package that makes embedding video into Rmarkdown simple.

Install the package from CRAN

install.packages("vembedr")

Example

library("htmltools")
library("vembedr")

embed_url("https://www.youtube.com/watch?v=uV4UpCq2azs")

Fun stuff

Icons

Depending on the type of RMarkdown document you are working with (i.e. what are you “knitting” to), will depend on which code works for you. As always there is more than one way to this.

To start with the most commonly used icons are from font awesome suite - so head here to pick your (free) icons.

HTML docs

For HTML docs (including webpages), I have found the following works best <i class="fab fa-r-project"></i> this will give you a beautiful RStudio icon .

If you want to use Ionicons then include you will first need to make sure the following line appears within your Rmarkdown doc (don’t worry it wont appear in the knitted product) <script src="https://unpkg.com/ionicons@5.0.0/dist/ionicons.js"></script>. Then use the following code to insert your icons, for example this <ion-icon name="bug-outline"></ion-icon> produces a lovely bug for you . You can customise the icons, see here.

This code <span class="badge badge-info">Info</span> will produce this badge Info in html document, more details found here

Webpages (HTML) - nav bar

You can add icons to the nav bar on your webpage, just like on this one. In the YAML doc add the following bit of code under the relevent section icon: fa-icon e.g. for the rstudio icon use fa-r-project for this icon

Example - partial YAML doc, for more info on RMarkdown webpages/YAML head to RMarkdown Webpages section

navbar:
  title: "Code"
  left:
  - text: "Home"
    href: index.html
  - text: "RStudio"
    icon: fa-file-alt

PDF docs

When knitting to PDF I have found the easiest way using the icon package.

Install developer version from github

# install.packages("devtools")
devtools::install_github("ropenscilabs/icon")

Then add the following bit of code in your RMarkdown document.

library(icon)
icon::fa("rocket") # equivalent to icon::fa_rocket()

and you’ll get this . Got some extra tips and trick see here.

Some more info on icon available here and here.

Download button

The downloadthis package is to implement download buttons in HTML outputs from RMarkdown without need for runtime::shiny

Install

install.packages("downloadthis")

Then add the following to your Rmarkdown document - this example will give you a red download button with a link to the downloadthis pdf manual (remember to hide the code so only the output appears using {r echo=FALSE} at the start of your code chunk).

library(downloadthis)
download_link(
  link = "https://github.com/fmmattioni/downloadthis/raw/master/inst/example/file_1.pdf",
  button_label = "Download pdf file",
  button_type = "danger",
  has_icon = TRUE,
  icon = "fa fa-save",
  self_contained = FALSE
)

Diagram

diagrams

Table

In additional to using basic RMarkdown syntax for tables

First Header  | Second Header
------------- | -------------
Content Cell  | Content Cell
Content Cell  | Content Cell

Which look like this

First Header	Second Header
Content Cell	Content Cell
Content Cell	Content Cell

You can use KableExtra

Themes

RMarkdown theme gallery

Headings and navigation

bookdown includes tabbed sections

This code here will created heading with tabbed sections:

### Quarterly Results {.tabset}

#### By Product

Content on tabbed section 1 here

#### By Region

Maybe insert a short list here:

* item 1
* item 2
* item 3

It will look like this:

Quarterly Results

By Product

Content on tabbed section 1 here

By Region

Maybe insert a short list here:

item 1
item 2
item 3

Work by Siobhon Egan

siobhon.egan@murdoch.edu.au