Communicating with Data via R markdown

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# Communicating with Data via R Markdown

## R Markdown Basics

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Presented by Emi Tanaka

School of Mathematics and Statistics

<img src="assets/USydLogo-white.svg" style="width:200px"> 
 dr.emi.tanaka@gmail.com
 @statsgen

4th October 2019 | COMBINE | Sydney, Australia

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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 </a>.

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**Hi! I'm Emi! 👋**

I'm a .yellow[lecturer in statistics] at The University of Sydney (soon moving to .yellow[Monash University]).

**Introduce yourself to someone you don't know!**

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# HELP!

Please send SOS signal by attaching sticky note on your laptop.

Please help your neighbours 🙏

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Open

http://bit.ly/rmd-combine-2019

and save a permanent copy to your RStudio Cloud account.

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# Schedule

| Time          | Activity                                |
|:--------------|:----------------------------------------|
| 1:00PM - 1:25PM | Session 1: R Markdown Basics          |
| 1:25PM - 1:30PM | *Break* 🍵           |
| 1:30PM - 3:00PM | Session 2A: Reproducible Reports I           |
| 3:00PM - 3:30PM | *Afternoon Tea* ☕🍰              |
| 3:30PM - 4:10PM | Session 2B: Reproducible Reports II  |
| 4:10PM - 4:15PM | *Break* 🚽           |
| 4:15PM - 5:00PM | Session 3: Pretty Presentations  |

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# R Markdown Basics

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# Knitting: <code>Rmd</code> &nbsp; &nbsp;<code>md</code> &nbsp; &nbsp;<code>html</code>

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There are many other .yellow[output formats] possible with R Markdown via Pandoc.

Can you name another 3?

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# R Markdown under the hood: `html_document`

.indigo[`knitr`] 📦 does the hard work of converting <code>Rmd</code> &nbsp; &nbsp;<code>md</code> 
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````markdown
---
title: "My Report"
output: html_document
---

# Hello

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

````

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

# Hello

```r
1 + 1
```

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

````

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`Rmd` 
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`md` 
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# R Markdown under the hood: `html_document`

Then .indigo[`rmarkdown`] 📦 prepares <code>md</code> for .indigo[`pandoc`] to convert to html .
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````markdown
---
title: "My Report"
output: html_document
---

# Hello

```r
1 + 1
```

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

````

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```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>
```

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 This html file is missing some elements due to restriction of space.
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`md` 
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`html` 
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# R Markdown under the hood: .red[`pdf_document`]

Same as before: `knitr` 📦 converts <code>Rmd</code> &nbsp; &nbsp;<code>md</code> 
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````markdown
---
title: "My Report"
output: pdf_document
---

# Hello

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

````

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

# Hello

```r
1 + 1
```

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

````

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`Rmd` 
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`md` 
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# R Markdown under the hood: .red[`pdf_document`]

Then `rmarkdown` 📦 prepares <code>md</code> for `pandoc` to convert to .indigo[`tex`] pdf .
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````markdown
---
title: "My Report"
output: html_document
---

# Hello

```r
1 + 1
```

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

````

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```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}
```

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`md` 
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`tex` 
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 This tex document is missing elements before `\begin{document}` due to restriction of space.
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#Get started with

`challenge-01.Rmd`

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# Advanced question

How do you render different output formats at once?

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# That's it!

These slides are made using `xaringan` R-package.

The workshop materials are licensed under [<img src="images/cc.svg" style="height:1em"/><img src="images/by.svg" style="height:1em"/><img src="images/sa.svg" style="height:1em"/>](https://creativecommons.org/licenses/by-sa/3.0/au/).

Emi Tanaka

dr.emi.tanaka@gmail.com 
 @statsgen

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# Check that you can:

<ul>
<li>Make a html document from .Rmd</li><li>Make a pdf document from .Rmd</li><li>Have some understanding of how R Markdown works under the hood.</li><li>Have some understanding of how some R Markdown components works only in specific output formats.</li>
</ul>

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