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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="" xml:lang="">
<head>
<title>Communicating with Data via R markdown</title>
<meta charset="utf-8" />
<meta name="author" content="Emi Tanaka" />
<link href="libs/remark-css-0.0.1/ninjutsu.css" rel="stylesheet" />
<link href="libs/font-awesome-animation-1.0/font-awesome-animation-emi.css" rel="stylesheet" />
<script src="libs/fontawesome-5.0.13/js/fontawesome-all.min.js"></script>
<link href="libs/countdown-0.2.0/countdown.css" rel="stylesheet" />
<script src="libs/countdown-0.2.0/countdown.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
<link rel="stylesheet" href="assets/animate.css" type="text/css" />
<link rel="stylesheet" href="assets/cssgrid.css" type="text/css" />
<link rel="stylesheet" href="assets/custom.css" type="text/css" />
</head>
<body>
<textarea id="source">
background-image: url(images/bg2.jpg)
background-size: cover
class: hide-slide-number
:::::::::: { .grid grid: 50% 50% / 1fr;}
::: item center
# <span style="text-shadow: 2px 2px 30px white;">Communicating with Data <br> via R Markdown</span>
<br><br>
## <span style="color:white;text-shadow: 2px 2px 30px black;">R Markdown Basics</span>
:::
::: item 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> [email protected]
<span><i class="fab fa-twitter faa-float animated faa-fast "></i></span> @statsgen
4th October 2019 | COMBINE | Sydney, 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>.
:::
---
class: question
::: {.item text-align:left; }
**Hi! I'm Emi! 👋**
<br>
I'm a .yellow[lecturer in statistics] at The University of Sydney (soon moving to .yellow[Monash University]).
<br>
**Introduce yourself to someone you don't know!**
:::
<div class="countdown" id="timer_5d95a45f" style="right:0;bottom:0;font-size:1.3em;">
<code><span class="digits minutes">03</span><span class="digits colon">:</span><span class="digits seconds">00</span></code>
</div>
---
class: question
# HELP!
<img src="images/sticky-note.png" width="150px"/>
Please send SOS signal by attaching sticky note on your laptop.
<br>
Please help your neighbours 🙏
---
class: challenge font_smaller middle
Open
<br>
http://bit.ly/rmd-combine-2019
<br>
and save a permanent copy to your RStudio Cloud account.
---
class: center
# Schedule
<br>
| 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 |
---
# R Markdown Basics
<img src="images/demo-first-rmd.png" width="70%" />
---
# 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: middle question
There are many other .yellow[output formats] possible with R Markdown via Pandoc.
Can you name another 3?
---
class: font_small
# R Markdown under the hood: `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: `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(256,160,160, 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: .red[`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: .red[`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%;left:40%;}
`tex` <i class="far fa-file"></i>
:::
::: {.white .font_small .pos bottom:7%; right:10%; width:200px;padding:5px;background-color:rgb(256,160,160, 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: challenge middle
#Get started with
`challenge-01.Rmd`
<div class="countdown" id="timer_5d95a3b9" style="right:0;bottom:0;font-size:1.5em;">
<code><span class="digits minutes">05</span><span class="digits colon">:</span><span class="digits seconds">00</span></code>
</div>
---
class: challenge middle
# Advanced question
How do you render different output formats at once?
---
background-image: url(images/bg2.jpg)
background-size: cover
class: hide-slide-number
::: grid
::: {.item .shade_black .animated .slideInLeft border-right-style:solid; border-right-color:white; }
# 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/).
<br><br>
Emi Tanaka
<i class="fas fa-envelope faa-float animated"></i> [email protected]<br>
<i class="fab fa-twitter faa-float animated faa-fast"></i> @statsgen
:::
::: {.item .shade_black .checklist .animated .slideInRight border-left-style: solid; border-right-color: white;}
# 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>
:::
:::
</textarea>
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