RMarkdown basics

rstudio

rmarkdown

The basics of RMarkdown

Author

Siobhon Egan

Published

February 13, 2021

🔗 Links

Italics

Can be produced 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

Unnumbered list

* 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

[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

Resource link here

Text colour

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

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

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 When you knit a document to PDF the hyperlinks are not underlined or colour, although they still work just fine. If you prefer to have your hyperlinks underlined as the following to the header section

header-includes:
  - \hypersetup{colorlinks=false,
     allbordercolors={0 0 0},
     pdfborderstyle={/S/U/W 1}}

Another way is to use the following latex command, however this does not knit well to html. [\underline{R Markdown: The Definitive Guide}](https://bookdown.org/yihui/rmarkdown/) will give the following: 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

emojis

You can add emojis into Rmarkdown html docs with the following code: :bowling: which will give you this 🎳 A full list of emoji short cuts available here.

You could also use unicode formatting - see here for more info.

You can also use emojis in plotting, see here.

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

<script src="https://unpkg.com/ionicons@5.0.0/dist/ionicons.js"></script>

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 navigation bar on your webpage, just like on this one. In the YAML doc add the following bit of code under the relevant 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: 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.

Buttons

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
)

This code words when knitting to HTML, that opens a link when you click on it

    <article>
    <h3><a href="https://www.researchgate.net/publication/327174678_What's_in_a_tick_Meta-analysis_of_microbial_diversity_in_Australian_ticks">What’s in a tick? Meta-analysis of microbial diversity in Australian ticks</a></h3>
    <div class="summary">
    <span><i class="fa fa-calendar"></i> _2018-08_</span>
    <p>Global Microbiome II 2018 (West Coast Microbiome Network) | Perth, Western Australia</p>
    <a class="btn btn-outline-primary btn-sm" href="https://www.researchgate.net/publication/327174678_What's_in_a_tick_Meta-analysis_of_microbial_diversity_in_Australian_ticks" role="button">Poster</a>
    </div>

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 create headings 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

Headings

In addition to info in the Rmarkdown page some extra bits.

Add sections to the book using the following at the start of a RMarkdown page

# (PART) Section A {-}

# Page 1

This will section will appear until it recognises another section.

Call out note

:::{.callout-note}
Note that there are five types of callouts, including: 
`note`, `tip`, `warning`, `caution`, and `important`.
:::

Gives this:

Note

Note that there are five types of callouts, including: note, tip, warning, caution, and important.

Math and symbols

Code chunks & output

Text colour

For Rmd -> PDF docs

For Rmd -> html docs

Hyperlinks

Images, Figures and videos

Videos

Fun stuff

emojis

Icons

Buttons

Diagram

Table

Themes

Headings and navigation

Quarterly Results

By Product

By Region

Headings

Call out note

For `Rmd` -> `PDF` docs

For `Rmd` -> `html` docs