R Markdown Workshop

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# <span style="text-shadow: 2px 2px 30px white;">R Markdown Workshop</span>

<br><br>
## <span style="color:yellow;text-shadow: 2px 2px 30px black;">The Basics</span>

:::

::: center shade_black animated bounceInUp slower

Presented by Emi Tanaka

School of Mathematics and Statistics

<img src="assets/USydLogo-white.svg" style="width:200px"><br>
<span><i class="fas  fa-envelope faa-float animated "></i></span>  dr.emi.tanaka@gmail.com
<span><i class="fab  fa-twitter faa-float animated faa-fast "></i></span>  @statsgen

.bottom_abs.width100.bg-black[
19th Nov 2019 @ SSA Vic | Melbourne, Australia
]

:::

::::::::::

::: { .shade_black .pos .font_small width:20%;right:10px;bottom:20%;padding:5px;border: solid 5px white;}

<i class="fas fa-exclamation-circle"></i> These slides are viewed best by Chrome and occasionally need to be refreshed if elements did not load properly. See here for <a href=session1.pdf style="color:white!important"/>PDF <i class="fas fa-file-pdf"></i></a>.

:::

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<br>

<div class="circle-image">
<center>
<img src="images/avatar.png" width = "150px"/>
</center>
</div>

**Emi Tanaka** <br>
*Lecturer in Statistics*<br>
The University of Sydney

<br>

<i class="fas fa-globe"></i> https://emitanaka.org/

<i class="fas fa-envelope"></i> dr.emi.tanaka@gmail.com

<i class="fab fa-twitter"></i> @statsgen

:::

::: item

# About your instructor

* I'm moving to Monash University starting January 2020
* I teach R at university courses as well as use it daily for research and hobby
* If you ever wonder who answers those stackoverflow questions, I'm one of those magic fairies

<center>
<a href="https://stackexchange/users/10113966/emi"><img src="https://stackoverflow.com/users/flair/10113966.png" width="208" height="58" alt="profile for Emi at Stack Overflow, Q&amp;A for professional and enthusiast programmers" title="profile for Emi at Stack Overflow, Q&amp;A for professional and enthusiast programmers" style="border:solid 2px black;"></a>
</center>

.blue[**Introduce yourself to someone you don't know!**]

:::

:::

<div class="countdown" id="timer_5dd23e9b" style="right:0;bottom:0;font-size:1em;" data-warnwhen="0">
<code class="countdown-time"><span class="countdown-digits minutes">03</span><span class="countdown-digits colon">:</span><span class="countdown-digits seconds">00</span></code>
</div>

---

# What you can do with R Markdown?

--

<br>
<center>
<iframe src="session1.html" width="80%" height="450px" style="border: solid 3px black;"></iframe>
</center>

<div class="color-box">
These <b>slides</b> are made using R Markdown.
</div>

---

# What you can do with R Markdown?

<br>
<center>
<iframe src="output/html/html_template_paper.html" width="80%" height="450px" style="border: solid 3px black;"></iframe>
</center>

<div class="color-box">
This <b>dynamic report</b> is made using R Markdown.
</div>

---

# What you can do with R Markdown?

<br>
<center>
<object data="output/articles/article_template_pnas_article.pdf" type="application/pdf" width="80%" height="450px" style="border: solid 3px black;">
<embed src="output/articles/article_template_pnas_article.pdf" type="application/pdf" />
</object>
</center>

<div class="color-box">
This <b>manuscript</b> is made using R Markdown.
</div>

---

# What you can do with R Markdown?

<br>
<center>
<iframe src="https://otexts.com/fpp2/" width="80%" height="450px" style="border: solid 3px black;"></iframe>
</center>

<div class="color-box">
This <b>online book</b> is made using R Markdown.<br>
Available at https://otexts.com/fpp2/ <br>

The <b>pdf book</b> version is also made using R Markdown. 
</div>

---

# What you can do with R Markdown?

<br>
<div class="grid" style="grid: 1fr / 1fr 1fr;">
<div class="item">
<center>
<iframe src="https://thesis.earo.me/" width="80%" height="450px" style="border: solid 3px black;"></iframe>
</center>
</div>

<div class="item">
<center>
<a href="https://github.com/earowang/thesis/blob/master/_thesis/thesis.pdf"><img src="images/earothesis.png" width="60%" style="border: solid 3px black;"/></a>
</center>
</div>
</div>

<div class="color-box">
This <b>thesis</b> (online and pdf) is made using R Markdown.<br>
Available at https://thesis.earo.me/ <br>

</div>

---

# What you can do with R Markdown?

<br>
<div class="grid" style="grid: 1fr / 1fr 1fr;">
<div class="item">
<center>
<iframe src="https://emitanaka.org/r/posts/2018-12-12-scientific-and-technical-blogging-radix-vs-blogdown/" width="80%" height="450px" style="border: solid 3px black;"></iframe>
</center>
</div>

<div class="item">
<center>
<iframe src="https://emitanaka.rbind.io/post/scientific-and-technical-blogging-radix-vs-blogdown-remix/" width="80%" height="450px" style="border: solid 3px black;"></iframe>
</center>
</div>
</div>

<div class="color-box">
These <b>blog posts</b> are made using R Markdown.

</div>

---

# What you can do with R Markdown?

::: { .grid .grid: 1fr / 2.5fr 1fr; }

::: item

Possibilities are endless...

* Microsoft Word document (.doc, .docx)
* Open Document Text (.odt)
* Rich text format (.rtf)
* Power point slides (.ppt, .pptx)
* Posters (as .html or .pdf)
* Resume (as .html or .pdf)
* Interactive R Notebooks (.html)
* Markdown documents (.md)
* Dashboard (.html)

:::

::: item

<br>
<center>
<img src="images/rmarkdown-book-cover.png" width = "50%">
</center>

.font_small[Check out [Xie et al. (2018) R Markdown: The Definite Guide](https://bookdown.org/yihui/rmarkdown/).]

:::

:::

---

# Schedule

<br>

Time | Activity 
:----|:-----
1:30PM - 3.00PM | 📜 *Session 1: R Markdown Basics* 
3.00PM - 3.30PM | ☕ *Afternoon Tea* 
3.30PM - 4.30pm | 📖 *Session 2: Reproducible Reports* 
4.30PM - 5.00pm | 🦋 *Session 3: Pretty Presentations*

---

# Get Started

::: paddings

Find slides at<br><Br>

.center[
.blue[<i class="fas fa-link"></i>  https://rmd-ssavic-2019.netlify.com/]
]

<br>

Open <br><Br>

.center[
.blue[<i class="fas fa-link"></i>  http://bit.ly/rmd-ssavic-2019]
]

<br>

and save a permanent copy to your RStudio Cloud account for the R exercises.

<br><Br>

:::

---

# Before R Markdown (and Sweave)

<br>
<center>
<img src="images/rmd-motivation.png" width  = "90%"/>
</center>

---

# R Markdown in a nutshell 🥜

::: paddings

R Markdown integrates .blue[**text**] + .blue[`code`] in one source document with ability to knit *to many output formats* (via Pandoc).

<img src="images/rmd-overview.png" width  = "100%"/>

:::

---

class: center middle

.font_large[🔍 Open and inspect the file]

.font_large[`first-rmarkdown.Rmd`]

---

# R Markdown Basics

<img src="images/demo-first-rmd.png" width="80%" />

---

# Knitting: <code>Rmd</code> <i class="far fa-file"></i>&nbsp; <i class="fas fa-arrow-right"></i>&nbsp;<code>md</code> <i class="far fa-file"></i>&nbsp;<i class="fas fa-arrow-right"></i> &nbsp;<code>html</code> <i class="far fa-file"></i>

<img src="images/demo-knit-html.png" width="100%" />

---

# Knitting: <code>Rmd</code> <i class="far fa-file"></i>&nbsp; <i class="fas fa-arrow-right"></i>&nbsp;<code>md</code> <i class="far fa-file"></i>&nbsp;<i class="fas fa-arrow-right"></i> &nbsp;<code>pdf</code> <i class="far fa-file"></i>

<img src="images/demo-knit-pdf.png" width="100%" />

---

class: center middle

.font_large[How does it all work?]

<br>

<img src="images/rmd-magic.png" width = "700px"/>

---

class: font_small

# R Markdown under the hood: .blue[`html_document`]

.indigo[`knitr`] 📦 does the hard work of converting <code>Rmd</code> <i class="far fa-file"></i>&nbsp; <i class="fas fa-arrow-right"></i>&nbsp;<code>md</code> <i class="far fa-file"></i>
::: grid

::: item

````markdown
---
title: "My Report"
output: html_document
---

# Hello

```{r}
1 + 1
```

````
<p></p>

:::

::: item

````markdown
---
title: "My Report"
output: html_document
---

# Hello

```r
1 + 1
```

```
## [1] 2
```

````

<p></p>

:::

:::

::: {.pos top:20%;left:20%;}
`Rmd` <i class="far fa-file"></i>
:::
::: {.pos top:20%;left:70%;}
`md` <i class="far fa-file"></i>
:::

---

class: font_small

# R Markdown under the hood: .blue[`html_document`]

Then .indigo[`rmarkdown`] 📦 prepares <code>md</code> <i class="far fa-file"></i> for .indigo[`pandoc`] to convert to html <i class="far fa-file"></i>.
::: grid

::: item

````markdown
---
title: "My Report"
output: html_document
---

# Hello

```r
1 + 1
```

```
## [1] 2
```

````

<p></p>

:::

::: item

```html

<body>
<div class="container-fluid main-container">
<div class="fluid-row" id="header">
<h1 class="title toc-ignore">My Report</h1>
</div>
<div id="hello" class="section level1">
<h1>Hello</h1>
<pre class="r"><code>1 + 1</code></pre>
<pre><code>## [1] 2</code></pre>
</div>
</div>
</body>
```

:::

:::

::: {.white .font_small .pos bottom:60px; right:10%; width:200px;padding:5px;background-color:rgb(0,0,0, 0.3);border: solid 3px black;	}
<i class="fas  fa-exclamation-triangle"></i> This html file is missing some elements due to restriction of space.
:::

::: {.pos top:20%;left:20%;}
`md` <i class="far fa-file"></i>
:::
::: {.pos top:20%;left:70%;}
`html` <i class="far fa-file"></i>
:::

---

class: font_small

# R Markdown under the hood: .blue[`pdf_document`]

Same as before: `knitr` 📦 converts <code>Rmd</code> <i class="far fa-file"></i>&nbsp; <i class="fas fa-arrow-right"></i>&nbsp;<code>md</code> <i class="far fa-file"></i>
::: grid

::: item

````markdown
---
title: "My Report"
output: pdf_document
---

# Hello

```{r}
1 + 1
```

````
<p></p>

:::

::: item

````markdown
---
title: "My Report"
output: pdf_document
---

# Hello

```r
1 + 1
```

```
## [1] 2
```

````

<p></p>

:::

:::

::: { .pos top:20%;left:20%; }
`Rmd` <i class="far fa-file"></i>
:::
::: { .pos top:20%;left:70%; }
`md` <i class="far fa-file"></i>
:::

---

class: font_small

# R Markdown under the hood: .blue[`pdf_document`]

Then `rmarkdown` 📦 prepares <code>md</code> <i class="far fa-file"></i> for `pandoc` to convert to .indigo[`tex`] <i class="far fa-file"></i> <i class="fas fa-arrow-right"></i> pdf <i class="fas fa-file-pdf"></i>.
::: grid

::: item

````markdown
---
title: "My Report"
output: html_document
---

# Hello

```r
1 + 1
```

```
## [1] 2
```

````

<p></p>

:::

::: item

```latex
\begin{document}
\maketitle
\hypertarget{hello}{%
\section{Hello}\label{hello}}
\begin{Shaded}
\begin{Highlighting}[]
\DecValTok{1} \OperatorTok{+}\StringTok{ }\DecValTok{1}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
## [1] 2
\end{verbatim}
\end{document}
```

:::

:::

::: {.pos top:20%;left:10%;}
`md` <i class="far fa-file"></i>
:::
::: {.pos top:20%;right:40%;}
`tex` <i class="far fa-file"></i>
:::

::: {.white .font_small .pos bottom:7%; right:10%; width:200px;padding:5px;background-color:rgb(0,0,0, 0.3);border: solid 3px black;	}
<i class="fas  fa-exclamation-triangle"></i> This tex document is missing elements before `\begin{document}` due to restriction of space.
:::

---

class: center middle

.font_large[Meta data with YAML]

<br>

<img src="images/metadata.png" width = "300px"/>

---

# YAML - YAML Ain't Markup Language

:::: { .grid grid: 1fr / 1fr 2fr; }

::: item

Basic format
```markdown
---
key: value
---
```
:::

::: item

Example

```
---
title: "R Markdown Workshop"
subtitle: "The Basics"
author: "Emi Tanaka"
date: "`r Sys.Date()`"
output: html_document
---
```

There must be a space after "`:`"!
<p></p>
:::

:::

---

class: font_small

# Default (minimal) html output

```
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">

<head>
<meta name="author" content="Emi Tanaka" />
<meta name="date" content="2019-11-19" />
<title>R Markdown Workshop</title>
</head>

<body>
<h1 class="title toc-ignore">R Markdown Workshop</h1>
<h3 class="subtitle">The Basics</h3>
<h4 class="author">Emi Tanaka</h4>
<h4 class="date">2019-11-19</h4>
</body>
</html>
```
<p></p>

::: { .info-box .pos width:200px;left:30%;top:48%;}

html meta data

:::

::: { .info-box .pos width:420px;left:47%;top:70%;}

Default html template add special YAML key values to file automatically

:::

::: {.output .pos top:80px; right:20px; width: 450px;}

<img src = "images/minimal-html-output.png" width = "400px"/>

:::

---

# YAML structure

::: paddings

* White spaces indicate structure in YAML - don't use tabs though!
* Same as R, you can comment lines by starting with `#`.
* YAML is case sensitive.
* A `key` can hold multiple values.

```markdown
key: 
  - value1
  - value2
```

```markdown
key: [value1, value2]
```

<p></p>

:::

---

class: font_small

# YAML with multiple key values

```
---
title: "R Package & R Markdown Workshop"
author: 
* - "Damjan Vukcevic"
* - "Emi Tanaka"
output: html_document
---
```

.output[

html raw file

```
<body>
<h1 class="title toc-ignore">R Package & R Markdown Workshop</h1>
*<h4 class="author">Damjan Vukcevic</h4>
*<h4 class="author">Emi Tanaka</h4> 
</body>
```

<p></p>

]

::: {.output .pos top:100px; right:20px; width:470px;}

<img src = "images/minimal-html-output2.png" width = "450px"/>

:::

---

class: font_small

# Values spanning multiple lines

```markdown
---
title: >
  this is a  
  **single line**
  
abstract: |
  this value spans  
  *many lines* and  
  appears as it is  
  
output: pdf_document
---

```

Note that there are **two spaces** after each line in the above YAML values. 
This is necessary to create a new line for markdown.

::: {.output .pos top:80px; right:20px;}

<img src = "images/minimal-pdf-output.png" width = "500px"/>

:::

---

class: center middle

.font_large[🔎 Open and inspect the file]

.font_large[`second-rmarkdown.Rmd`]

---

# `key` can contain `key`s

::: paddings

```
---
output: 
  html_document:
    toc: true
    toc_float: true 
    code_download: true 
    code_folding: "hide"
---
```

.font_large[What does each of the above keys do?]

:::

<div class="countdown" id="timer_5dd23ee2" style="right:0;bottom:0;font-size:1em;" data-warnwhen="0">
<code class="countdown-time"><span class="countdown-digits minutes">04</span><span class="countdown-digits colon">:</span><span class="countdown-digits seconds">00</span></code>
</div>

---

# `ymlthis` 📦

::: grid

::: item

<img src="images/ymlthis.png" height = "550px" style="border: solid 1px black;"/>

:::

::: item

* If you installed `ymlthis` then go to RStudio > Addins > YMLTHIS 
* It will launch a shiny app with various YAML options
* See also helper functions at https://ymlthis.r-lib.org/

:::

:::

---

class: center middle

.font_large[🔧 Open and inspect the file]

.font_large[`challenge-01-yaml.Rmd`]

---

class: middle center

.font_large[Text]

<br>

<img src="images/text.png" width = "300px"/>

---

# Text in Markdown: Headers

::: grid

::: item

<br>

.text[

```markdown
# Header 1
## Header 2
### Header 3
#### Header 4
##### Header 5
###### Header 6

```

<p></p>

]

:::

::: item

<Br>

.output[

# Header 1
## Header 2
### Header 3
#### Header 4
##### Header 5
###### Header 6

]

:::

:::

::: footnote
Go to RStudio > Help > Markdown Quick Reference
:::

---

# Text in Markdown: Formatting

::: grid

::: item

<br>

.text[

```markdown
 **This text is bold** 
 
 __This text is also bold__  
 
 *This text is italic* 
 
 _This text is also italic_  
 
 **_You can combine both_** 
```

<p></p>

]

:::

::: item

<p><Br></p>

.output[

**This text is bold** 
 
__This text is also bold__  
 
*This text is italic* 
 
_This text is also italic_  
 
**_You can combine both_**

]

:::

:::

::: footnote
Go to RStudio > Help > Markdown Quick Reference
:::

---

# Text in Markdown: Lists

::: grid

::: item

.text[

```markdown
 1. Breakfast
   * Cereal
   * Milk
 1. Lunch
   * Pizza
 * Tissue box 
   * Soft 
   * Hard
 * Soy sauce

```

<p></p>

]

:::

::: item

.output[

1. Breakfast
  * Cereal
  * Milk
1. Lunch
   * Pizza
* Tissue box 
   * Soft 
   * Hard
* Soy sauce

]

:::

:::

::: footnote
Go to RStudio > Help > Markdown Quick Reference
:::

---

# Markdown: lightweight markup language<br> *Focus on writing - add flair later*

::: {.grid grid: 270px 1fr / 1fr 1fr; }

::: { .item border: double 10px #005ab3; }

.blue[`markdown`]

```markdown
# Section 
Bla bla.
Then **bold**.
```

:::

::: item bg-grey

.blue[`html`]

```html
<h1>Section</h1>
Bla bla.
Then <b>bold</b>.

```
:::

::: item  bg-grey

.blue[`latex`]

```latex
\section{Section}
Bla bla.
Then \textbf{bold}.

```

:::

::: item

.blue[`docx`]

# Section 
Bla bla.  
Then **bold**.

:::

:::

---

class: center middle

.font_large[🔧 Open and go through:]

.font_large[`challenge-02-table.Rmd`]

<div class="countdown" id="timer_5dd23e99" style="right:0;bottom:0;font-size:1em;" data-warnwhen="0">
<code class="countdown-time"><span class="countdown-digits minutes">05</span><span class="countdown-digits colon">:</span><span class="countdown-digits seconds">00</span></code>
</div>

---

class: middle center

.font_large[Code chunk]

<br>

<img src="images/code-chunk.png" width = "300px"/>

---

# Keyboard shortcut for inserting code chunk

::: paddings

<br>

In RStudio .Rmd <i class="far fa-file"></i> press

<br>

* Mac: <kbd>⌘</kbd> + <kbd>⌥</kbd> + <kbd>i</kbd>

* PC: <kbd>Ctrl</kbd> + <kbd>Alt</kbd> + <kbd>i</kbd>

<br>

to insert a chunk of R code

::: font_large

````markdown
```{r}

```
````

:::

---

# Chunk options: <code>echo</code> & <code>eval</code>

::: grid 
::: item

````markdown
```{r, echo = FALSE}
plot(speed ~ dist, cars)
```
````
<center>
<i class="fas fa-arrow-down"></i>
</center>

<img src="figure/unnamed-chunk-1-1.svg" width="288" style="display: block; margin: auto;" />

<p></p>

:::

::: item

````markdown
```{r, eval = FALSE}
plot(speed ~ dist, cars)
```
````

<center>
<i class="fas fa-arrow-down"></i>
</center>

```r
plot(speed ~ dist, cars)
```

<p></p>

:::

:::

---

# Valid chunk options

<Br>

::: paddings

* Chunk options must be written in **one line**, i.e. no line break.

* All option values must be **valid R expressions**. Exception is the chunk name. E.g.
   * `fig.path = figures/` is not valid but <br>`fig.path = "figures/"` is valid
   * `eval = true` is not valid but<br> `eval = runif(1) > 0.5` is valid
   
:::

---

# Chunk names (or labels)

<br>

::: paddings

The chunk below is called `plot1`.
````markdown
```{r plot1}
ggplot(cars, aes(dist, speed)) + geom_point()
```
````

All chunks have a label regardless of whether it is explicitly supplied or not.

<i class="fa fa-exclamation-triangle"></i> Do not include spaces, "_" or punctuation marks in your chunk name!

:::

---

class: center middle

.font_large[🔧 Pick your challenge:]

<br>

* `challenge-03-include.Rmd`
* `challenge-04-global-option.Rmd`
* `challenge-05-figures.Rmd`
* `challenge-06-cache.Rmd`
* `challenge-07-names.Rmd`

<div class="countdown" id="timer_5dd23df7" style="right:0;bottom:0;font-size:1em;" data-warnwhen="0">
<code class="countdown-time"><span class="countdown-digits minutes">25</span><span class="countdown-digits colon">:</span><span class="countdown-digits seconds">00</span></code>
</div>

---

class: middle center

.font_large[Inline code]

<br>

<img src="images/inline-code.png" width = "300px"/>

---

# Inline R Commands

<Br>

::: paddings

Text can contain inline R commands where output is `eval`uated but code is not `echo`ed.

:::

<br><br>

::: grid

::: {.item border-right: dashed 3px black; }

.label[Text]

```markdown
Updated last: `r Sys.Date()`
```

.label[Output]

Updated last: 2019-11-18

:::

::: item

.label[Text]

```markdown
The value of $\pi$ is `r pi`.
```

.label[Output]

The value of `\(\pi\)` is 3.1415927.

:::

:::

---

# Accessing YAML meta data inline

::: grid

::: item

All YAML meta data are stored in `rmarkdown::metadata` as a list.

```
---
title: "R Markdown Workshop"
output: html_document
---
```
---

```r
rmarkdown::metadata$title
```

```
  [1] "R Markdown Workshop"
```

<p></p>

:::

::: item

All key values of `params` is stored as a list in `params`.

```
---
params: 
   data: datav1.csv
output: pdf_document
---
```

---

```r
params$data
```

```
  [1] "datav1.csv"
```
<p></p>
:::

:::

---

class: center middle white
background-color: #0a2631

.font_large[Stack your Rmd components as you want but only one YAML piece and it needs to be on the top!]

<br>

<img src="images/lego-stack.png" width = "600px"/>

For workflow, you'd probably want to keep your tower's height manageable.

---

# R Markdown is not just for R

::: grid

::: item

````markdown
```{python, echo = FALSE}
a = [1, 2, 3]
a[0]
```
````

<center>
<i class="fas fa-arrow-down"></i>
</center>

```
  1
```
<p></p>

:::

::: item

````markdown
```{bash, echo = FALSE}
date +%B
```
````
<center>
<i class="fas fa-arrow-down"></i>
</center>

```
  November
```
<p></p>
::::

::::

---

class: center middle

.font_large[Sharing your html documents]

---

# RPubs

::: paddings

After knitting, find this Publish button:

<center>
<img src="images/publish.png" width = "170px" style = "border: solid 1px black;"/>
</center>

and select RPubs if there is a choice:

<center>
<img src="images/rpub.png" width = "600px" style = "border: solid 1px black;"/>
</center>

:::

---

# Netlify: without Git

::: paddings

* Rename your output html file as `index.html`
* Go to https://app.netlify.com/
* If you are logged in, go to the bottom of Sites to find

<center>
<img src="images/netlify.png" width = "400px"/>
</center>

* Drag and drop the folder that contains the `index.html` 
* 🎉 it's alive!
* You probably want to change the site name - to do this go to site > site settings > change site name.

:::

---

# Netlify: with Git

::: paddings

* Rename your output html file as `index.html`
* Git commit your folder (or html file alone if no dependency)
* Host it on GitHub (my preference), GitLab or Bitbucket
* Go to https://app.netlify.com/ and create a new site from the repo
* 🎉🎉🎉🎉🎉 
* Again, you probably want to change the site name - to do this go to site > site settings > change site name.

:::

---

class: middle center

.font_large[

Happy sharing!

That's it for the basics!

]

---

background-color: #e5e5e5

# Session Information

:::: scroll-350

```r
devtools::session_info()
```

```
  ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   setting  value                       
   version  R version 3.6.1 (2019-07-05)
   os       macOS Mojave 10.14.4        
   system   x86_64, darwin15.6.0        
   ui       X11                         
   language (EN)                        
   collate  en_AU.UTF-8                 
   ctype    en_AU.UTF-8                 
   tz       Australia/Sydney            
   date     2019-11-18                  
  
  ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   package     * version    date       lib source                              
   anicon        0.1.0      2019-11-07 [1] Github (emitanaka/anicon@0b756df)   
   assertthat    0.2.1      2019-03-21 [1] CRAN (R 3.6.0)                      
   backports     1.1.5      2019-10-02 [1] CRAN (R 3.6.0)                      
   broom         0.5.2      2019-04-07 [1] CRAN (R 3.6.0)                      
   callr         3.3.2      2019-09-22 [1] CRAN (R 3.6.0)                      
   cellranger    1.1.0      2016-07-27 [1] CRAN (R 3.6.0)                      
   cli           1.1.0      2019-03-19 [1] CRAN (R 3.6.0)                      
   colorspace    1.4-1      2019-03-18 [1] CRAN (R 3.6.0)                      
   countdown     0.3.3      2019-11-18 [1] Github (gadenbuie/countdown@5c895d9)
   crayon        1.3.4      2017-09-16 [1] CRAN (R 3.6.0)                      
   desc          1.2.0      2018-05-01 [1] CRAN (R 3.6.0)                      
   devtools      2.2.1      2019-09-24 [1] CRAN (R 3.6.0)                      
   digest        0.6.22     2019-10-21 [1] CRAN (R 3.6.0)                      
   dplyr       * 0.8.3      2019-07-04 [1] CRAN (R 3.6.0)                      
   ellipsis      0.3.0      2019-09-20 [1] CRAN (R 3.6.0)                      
   emo           0.0.0.9000 2019-11-11 [1] Github (hadley/emo@02a5206)         
   evaluate      0.14       2019-05-28 [1] CRAN (R 3.6.0)                      
   forcats     * 0.4.0      2019-02-17 [1] CRAN (R 3.6.0)                      
   fs            1.3.1      2019-05-06 [1] CRAN (R 3.6.0)                      
   generics      0.0.2      2018-11-29 [1] CRAN (R 3.6.0)                      
   ggplot2     * 3.2.1      2019-08-10 [1] CRAN (R 3.6.0)                      
   glue          1.3.1      2019-03-12 [1] CRAN (R 3.6.0)                      
   gtable        0.3.0      2019-03-25 [1] CRAN (R 3.6.0)                      
   haven         2.1.1      2019-07-04 [1] CRAN (R 3.6.0)                      
   hms           0.5.2      2019-10-30 [1] CRAN (R 3.6.0)                      
   htmltools     0.4.0      2019-10-04 [1] CRAN (R 3.6.0)                      
   httr          1.4.1      2019-08-05 [1] CRAN (R 3.6.0)                      
   icon          0.1.0      2019-11-07 [1] Github (emitanaka/icon@8458546)     
   jsonlite      1.6        2018-12-07 [1] CRAN (R 3.6.0)                      
   knitr         1.25       2019-09-18 [1] CRAN (R 3.6.0)                      
   lattice       0.20-38    2018-11-04 [1] CRAN (R 3.6.1)                      
   lazyeval      0.2.2      2019-03-15 [1] CRAN (R 3.6.0)                      
   lifecycle     0.1.0      2019-08-01 [1] CRAN (R 3.6.0)                      
   lubridate     1.7.4      2018-04-11 [1] CRAN (R 3.6.0)                      
   magrittr      1.5        2014-11-22 [1] CRAN (R 3.6.0)                      
   Matrix        1.2-17     2019-03-22 [1] CRAN (R 3.6.1)                      
   memoise       1.1.0      2017-04-21 [1] CRAN (R 3.6.0)                      
   modelr        0.1.5      2019-08-08 [1] CRAN (R 3.6.0)                      
   munsell       0.5.0      2018-06-12 [1] CRAN (R 3.6.0)                      
   nlme          3.1-140    2019-05-12 [1] CRAN (R 3.6.1)                      
   pillar        1.4.2      2019-06-29 [1] CRAN (R 3.6.0)                      
   pkgbuild      1.0.6      2019-10-09 [1] CRAN (R 3.6.0)                      
   pkgconfig     2.0.3      2019-09-22 [1] CRAN (R 3.6.0)                      
   pkgload       1.0.2      2018-10-29 [1] CRAN (R 3.6.0)                      
   prettyunits   1.0.2      2015-07-13 [1] CRAN (R 3.6.0)                      
   processx      3.4.1      2019-07-18 [1] CRAN (R 3.6.0)                      
   ps            1.3.0      2018-12-21 [1] CRAN (R 3.6.0)                      
   purrr       * 0.3.3      2019-10-18 [1] CRAN (R 3.6.0)                      
   R6            2.4.0      2019-02-14 [1] CRAN (R 3.6.0)                      
   Rcpp          1.0.2      2019-07-25 [1] CRAN (R 3.6.0)                      
   readr       * 1.3.1      2018-12-21 [1] CRAN (R 3.6.0)                      
   readxl        1.3.1      2019-03-13 [1] CRAN (R 3.6.0)                      
   remotes       2.1.0      2019-06-24 [1] CRAN (R 3.6.0)                      
   reticulate    1.13       2019-07-24 [1] CRAN (R 3.6.0)                      
   rlang         0.4.1      2019-10-24 [1] CRAN (R 3.6.0)                      
   rmarkdown     1.16       2019-10-01 [1] CRAN (R 3.6.0)                      
   rprojroot     1.3-2      2018-01-03 [1] CRAN (R 3.6.0)                      
   rstudioapi    0.10       2019-03-19 [1] CRAN (R 3.6.0)                      
   rvest         0.3.4      2019-05-15 [1] CRAN (R 3.6.0)                      
   scales        1.0.0      2018-08-09 [1] CRAN (R 3.6.0)                      
   sessioninfo   1.1.1      2018-11-05 [1] CRAN (R 3.6.0)                      
   stringi       1.4.3      2019-03-12 [1] CRAN (R 3.6.0)                      
   stringr     * 1.4.0      2019-02-10 [1] CRAN (R 3.6.0)                      
   testthat      2.2.1      2019-07-25 [1] CRAN (R 3.6.0)                      
   tibble      * 2.1.3      2019-06-06 [1] CRAN (R 3.6.0)                      
   tidyr       * 1.0.0      2019-09-11 [1] CRAN (R 3.6.0)                      
   tidyselect    0.2.5      2018-10-11 [1] CRAN (R 3.6.0)                      
   tidyverse   * 1.2.1      2017-11-14 [1] CRAN (R 3.6.0)                      
   usethis       1.5.1      2019-07-04 [1] CRAN (R 3.6.0)                      
   vctrs         0.2.0      2019-07-05 [1] CRAN (R 3.6.0)                      
   whisker       0.4        2019-08-28 [1] CRAN (R 3.6.0)                      
   withr         2.1.2      2018-03-15 [1] CRAN (R 3.6.0)                      
   xaringan      0.13       2019-10-30 [1] CRAN (R 3.6.0)                      
   xfun          0.10       2019-10-01 [1] CRAN (R 3.6.0)                      
   xml2          1.2.2      2019-08-09 [1] CRAN (R 3.6.0)                      
   yaml          2.2.0      2018-07-25 [1] CRAN (R 3.6.0)                      
   zeallot       0.1.0      2018-01-28 [1] CRAN (R 3.6.0)                      
  
  [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library
```

<p></p>
:::

These slides are licensed under <br><center><a href="https://creativecommons.org/licenses/by-sa/3.0/au/"><img src="images/cc.svg" style="height:2em;"/><img src="images/by.svg" style="height:2em;"/><img src="images/sa.svg" style="height:2em;"/></a></center>