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:::::::::: { .grid grid: 50% 50% / 1fr;} 
::: item center

# &lt;span style="text-shadow: 2px 2px 30px white;"&gt;Communicating with Data &lt;br&gt; via R Markdown&lt;/span&gt;

&lt;br&gt;&lt;br&gt;
## &lt;span style="color:#f9af2b;text-shadow: 2px 2px 30px black;"&gt;Reproducible Reports&lt;/span&gt;

:::

::: item center shade_black animated bounceInUp slower

Presented by Emi Tanaka

School of Mathematics and Statistics

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

&lt;i class="fas fa-exclamation-circle"&gt;&lt;/i&gt; These slides are viewed best by Chrome and occasionally need to be refreshed if elements did not load properly. See here for &lt;a href=session2.pdf style="color:white!important"/&gt;PDF &lt;i class="fas fa-file-pdf"&gt;&lt;/i&gt;&lt;/a&gt;. 

:::


---

class: info 

# In a nutshell 🥜

&lt;br&gt;&lt;br/&gt;


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

]

---


::: grid 

::: item 
# Text in Markdown

```markdown
# Header 1
## Header 2

- Unordered list 1 
- Unordered list 2
 
1. Ordered list 1
1. Ordered list 2
 
_This is italic._ *This too.*
__This is bold.__ **This too.**
_**This is bold &amp; italic.**_
```

&lt;p&gt;&lt;/p&gt;

::: 

::: item 

[Output]{.header .bg-blue .white padding:10px; border: solid 2px black;}

# Header 1
## Header 2

* Unordered list 1 
* Unordered list 2

1. Ordered list 1
1. Ordered list 2
 
_This is italic._ *This too.*
__This is bold.__ **This too.**
_**This is bold &amp; italic.**_

:::

:::

::: {.bottom_abs .width100 .bg-indigo .white padding-left:10px;}
Go to RStudio &gt; Help &gt; Markdown Quick Reference
:::


---

class: info

# Shortcut for inserting code chunk  

::: grid 

::: item

In RStudio .Rmd &lt;i class="far fa-file"&gt;&lt;/i&gt; press

* Mac: &lt;kbd&gt;⌘&lt;/kbd&gt; + &lt;kbd&gt;⌥&lt;/kbd&gt; + &lt;kbd&gt;i&lt;/kbd&gt; 


* PC: &lt;kbd&gt;Ctrl&lt;/kbd&gt; + &lt;kbd&gt;Alt&lt;/kbd&gt; + &lt;kbd&gt;i&lt;/kbd&gt; 

to insert a chunk of R code

::: font_large

````markdown
```{r}

```
````

:::
:::

::: item 

:::

:::

---

# Chunk options: &lt;code&gt;echo&lt;/code&gt; &amp; &lt;code&gt;eval&lt;/code&gt;

::: grid 
::: item 

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

&lt;img src="session2_files/figure-html/unnamed-chunk-1-1.png" style="display: block; margin: auto;" /&gt;

&lt;p&gt;&lt;/p&gt;

::: 

::: item 

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

&lt;center&gt;
&lt;i class="fas fa-arrow-down"&gt;&lt;/i&gt;
&lt;/center&gt;


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

&lt;p&gt;&lt;/p&gt;

:::

:::

---

class: question middle

There are many more .yellow[chunk options].

Can you name 5 other ones?

Hint: https://yihui.name/knitr/options/

(We'll explore some later.)


---

class: info

# Valid chunk options

* 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 &lt;br&gt;`fig.path = "figures/"` is valid
   * `eval = true` is not valid but&lt;br&gt; `eval = runif(1) &gt; 0.5` is valid

---

class: info

# Chunk names (or labels)

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.

&lt;i class="fa fa-exclamation-triangle"&gt;&lt;/i&gt; Do not include spaces, "_" or punctuation marks in your chunk name!

---


::: pad10

# Inline R Commands


```markdown
Today's date is `r Sys.Date()`.
```

Today's date is 2019-10-03.

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

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

* Note: the inline command needs to be R commands.


* Inline command does *not* `echo` and always `eval`uates.

&lt;p&gt;&lt;/p&gt;

:::


---

class: challenge middle

# Go through 

* `challenge-02.Rmd`
* `challenge-03.Rmd`
* `challenge-04.Rmd`
* `challenge-05.Rmd`
* `challenge-06.Rmd`


<div class="countdown" id="timer_5d95d6bf" style="right:0;bottom:0;font-size:1.5em;">
<code><span class="digits minutes">25</span><span class="digits colon">:</span><span class="digits seconds">00</span></code>
</div>

---

# R Markdown is not just for R

::: grid 

::: item 

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

&lt;center&gt;
&lt;i class="fas fa-arrow-down"&gt;&lt;/i&gt;
&lt;/center&gt;


```
## 1
```
&lt;p&gt;&lt;/p&gt;

:::

::: item 

````markdown
```{bash, echo = FALSE}
date +%B
```
````
&lt;center&gt;
&lt;i class="fas fa-arrow-down"&gt;&lt;/i&gt;
&lt;/center&gt;


```
## October
```
&lt;p&gt;&lt;/p&gt;
::::

::::

---

class: question middle

Can you name some other engines?

Hint: https://yihui.name/knitr/demo/engines/


---


# YAML - YAML Ain't Markup Language

:::: grid

::: item 

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

::: item 

Example

```
---
title: "Communicating with Data via R Markdown"
subtitle: "Reproducible Reports"
author: "Emi Tanaka"
date: "`r Sys.Date()`"
output: html_document
---
```

There must be a space after "`:`"!
&lt;p&gt;&lt;/p&gt;
:::

:::

---

# Metadata

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


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

```
## [1] "Communicating with Data via R markdown"
```

```r
rmarkdown::metadata$author
```

```
## [1] "Emi Tanaka"
```

---

class: font_small

# Default (minimal) html output

```
&lt;!DOCTYPE html&gt;
&lt;html xmlns="http://www.w3.org/1999/xhtml"&gt;

&lt;head&gt;
&lt;meta name="author" content="Emi Tanaka" /&gt;
&lt;meta name="date" content="2019-10-04" /&gt;
&lt;title&gt;Communicating with Data via R Markdown&lt;/title&gt;
&lt;/head&gt;

&lt;body&gt;
&lt;h1 class="title toc-ignore"&gt;Communicating with Data via R Markdown&lt;/h1&gt;
&lt;h3 class="subtitle"&gt;Reproducible Reports&lt;/h3&gt;
&lt;h4 class="author"&gt;Emi Tanaka&lt;/h4&gt;
&lt;h4 class="date"&gt;2019-10-04&lt;/h4&gt;
&lt;/body&gt;
&lt;/html&gt;
```
&lt;p&gt;&lt;/p&gt;

::: { .bubble1 .pos width:300px;left:70%;top:48%;}

html meta data

:::

::: { .bubble1 .pos width:650px;left:43%;top:75%;}

Default html template add special YAML key values to file automatically

:::

::: {.pos top:10px; right:20px;}
output&lt;br&gt;
&lt;img src = "images/minimal-html-output.png" width = "250px" style="border: solid 3px black;"/&gt;

:::

---

::: pad10

# YAML structure

* 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: 
  - value 1
  - value 2
```

```markdown
key: [value 1, value 2]
```

:::

---

class: font_small

# YAML with multiple key values

```
---
title: "Communicating with Data via R Markdown"
author: 
 - "Emi Tanaka"
 - "Accomplice"
output: html_document
---
```

```
&lt;body&gt;
&lt;h1 class="title toc-ignore"&gt;Communicating with Data via R Markdown&lt;/h1&gt;
&lt;h4 class="author"&gt;Emi Tanaka&lt;/h4&gt;
*&lt;h4 class="author"&gt;Accomplice&lt;/h4&gt; 
&lt;/body&gt;
```

&lt;p&gt;&lt;/p&gt;

::: {.pos top:10px; right:20px;}
output&lt;br&gt;
&lt;img src = "images/minimal-html-output2.png" width = "250px" style="border: solid 3px black;"/&gt;

:::


---

class: question


::: {text-align: left;}

# `key` can contain `key`s


```
---
output: 
  html_document:
    toc: true
    toc_float: true
---
```
&lt;p&gt;&lt;/p&gt;
What does this do?

:::

(Note: white space is important)

---

class: font_small

# Values spanning multiple lines

```markdown
---
title: &gt;
  this is a\ 
  single line\
  
abstract: |
  this value spans\
  many lines and\
  appears as it is\
  
output: pdf_document
---

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

::: {.pos top:80px; right:20px;}
output&lt;br&gt;
&lt;img src = "images/minimal-pdf-output.png" width = "800px" style="border: solid 3px black;"/&gt;

:::

---

class: challenge middle

# Go through

`challenge-07.Rmd`

<div class="countdown" id="timer_5d95d590" style="right:0;bottom:0;font-size:1.5em;">
<code><span class="digits minutes">10</span><span class="digits colon">:</span><span class="digits seconds">00</span></code>
</div>

---

class: font_small

# Parametrized Report

````markdown
---
title: "Parameterized Report"
params:
  species: setosa
output: html_document
---

```{r, message = FALSE, fig.dim = c(3,2)}
library(tidyverse)
iris %&gt;% 
*  filter(Species==params$species) %&gt;% 
   ggplot(aes(Sepal.Length, Sepal.Width)) +
   geom_point(aes(color=Species))
```
````

::: {.pos top:10px; right:10px;}
output&lt;br&gt;
&lt;img src = "images/parameterised-report-eg1.png" width = "550px" style="border: solid 3px black;"/&gt;

:::

---

class: font_smaller

::: grid
::: item 
# Knit with Parameters
```markdown
---
title: "Parameterized Report"
params:
  species: 
    label: "Species"
    value: setosa
    input: select
    choices: [setosa, versicolor, virginica]
  color: red
  max:
    label: "Maximum Sepal Width"
    value: 4
    input: slider
    min: 4
    max: 5
    step: 0.1
output: html_document
---
```

:::

::: item 

&lt;img src = "images/knit-with-params.png" width = "300px" style="border: solid 3px black;"/&gt;

````markdown
```{r, message = params$printmsg, fig.dim = c(3,2)}
library(tidyverse)
iris %&gt;% 
  filter(Species==params$species) %&gt;% 
  filter(Sepal.Width &lt; params$max) %&gt;% 
  ggplot(aes(Sepal.Length, Sepal.Width)) +
  geom_point(aes(color=Species), 
             color = params$color)
```
````


:::

:::

---

class: font_smaller

# Shiny Report Generator
::: grid
::: item 
```markdown
---
title: "Parameterized Report"
params:
  species: 
    label: "Species"
    value: setosa
    input: select
    choices: [setosa, versicolor, virginica]
  color: red
  max:
    label: "Maximum Sepal Width"
    value: 5
    input: slider
    min: 4
    max: 5
    step: 0.05
output: html_document
---
```

:::

::: item 

# &amp;nbsp;

&lt;img src = "images/shiny-params.png" width = "100%" style="border: solid 3px black;"/&gt;


:::

:::

---

class: font_smaller

# R Markdown via Command Line

::: grid 

::: item 

`demo-render.Rmd`

````markdown
---
title: "Parameterized Report"
params:
  species: setosa
output: html_document
---

```{r, message = FALSE, fig.dim = c(3,2)}
library(tidyverse)
iris %&gt;% 
*  filter(Species==params$species) %&gt;% 
   ggplot(aes(Sepal.Length, Sepal.Width)) +
   geom_point(aes(color=Species))
```
````

:::

::: item 

You can knit this file via R command by using `render` function:


```r
library(rmarkdown)
render("demo-render.Rmd")
```

You can overwrite the YAML values by supplying arguments to `render`:


```r
library(rmarkdown)
render("demo-render.Rmd", 
       output_format = "pdf_document",
       params = list(species = "virginica"))
```


:::

:::


---

class: challenge middle

# Go through

`challenge-08.Rmd` and `challenge-09.Rmd`

<div class="countdown" id="timer_5d95d4ff" style="right:0;bottom:0;font-size:1.5em;">
<code><span class="digits minutes">10</span><span class="digits colon">:</span><span class="digits seconds">00</span></code>
</div>

---

# Themes: `html_document`  

&lt;!-- The Modal --&gt;
&lt;div id="myModal" class="modal"&gt;
  &lt;div id="caption"&gt;&lt;/div&gt;
  &lt;span class="close" onclick="document.getElementById('myModal').style.display='none'"&gt;&amp;times;&lt;/span&gt;
  &lt;iframe class="modal-content" id="img01"&gt;&lt;/iframe&gt;&lt;br&gt;
&lt;/div&gt;

You can change the look of the html document by specifying themes:
::: grid 

::: item 

* `default` &lt;img class="modalImg" alt="default"/&gt; 
* `cerulean` &lt;img class="modalImg" alt="cerulean"/&gt; 
* `journal`  &lt;img class="modalImg" alt="journal"/&gt; 
* `flatly` &lt;img class="modalImg" alt="flatly"/&gt; 
* `darkly` &lt;img class="modalImg" alt="darkly"/&gt; 
* `readable` &lt;img class="modalImg" alt="readable"/&gt; 
* `spacelab` &lt;img class="modalImg" alt="spacelab"/&gt; 
* `united` &lt;img class="modalImg" alt="united"/&gt; 

:::

::: item 


* `cosmo` &lt;img class="modalImg" alt="cosmo"/&gt; 
* `lumen` &lt;img class="modalImg" alt="lumen"/&gt; 
* `paper` &lt;img class="modalImg" alt="paper"/&gt; 
* `sandstone` &lt;img class="modalImg" alt="sandstone"/&gt; 
* `simplex` &lt;img class="modalImg" alt="simplex"/&gt; 
* `yeti` &lt;img class="modalImg" alt="yeti"/&gt; 
* `NULL`  &lt;img class="modalImg" alt="null"/&gt; 

:::

::: item 


```markdown
output: 
  html_document:
    theme: cerulean
```

These [bootswatch](https://bootswatch.com/) themes attach the whole bootstrap library which makes your html file size larger.

:::

:::

---

# `prettydoc` 

&lt;!-- The Modal --&gt;
&lt;div id="myModal2" class="modal"&gt;
  &lt;div id="caption2"&gt;&lt;/div&gt;
  &lt;span class="close" onclick="document.getElementById('myModal2').style.display='none'"&gt;&amp;times;&lt;/span&gt;
  &lt;iframe class="modal-content" id="img02"&gt;&lt;/iframe&gt;&lt;br&gt;
&lt;/div&gt;

::: grid 

::: item 

`prettydoc` 📦 is a community contributed `theme` that is light-weight:

* `cayman` &lt;img class="modalImg2" alt="cayman"/&gt; 
* `tactile` &lt;img class="modalImg2" alt="tactile"/&gt; 
* `architect` &lt;img class="modalImg2" alt="architect"/&gt; 
* `leonids` &lt;img class="modalImg2" alt="leonids"/&gt; 
* `hpstr` &lt;img class="modalImg2" alt="hpstr"/&gt; 


:::

::: item 


```markdown
output: 
  prettydoc::html_pretty:
    theme: cayman
```

See more about it below:

https://prettydoc.statr.me/

:::

:::


---

# `rmdformats`

&lt;!-- The Modal --&gt;
&lt;div id="myModal3" class="modal"&gt;
  &lt;div id="caption3"&gt;&lt;/div&gt;
  &lt;span class="close" onclick="document.getElementById('myModal3').style.display='none'"&gt;&amp;times;&lt;/span&gt;
  &lt;iframe class="modal-content" id="img03"&gt;&lt;/iframe&gt;&lt;br&gt;
&lt;/div&gt;


::: grid 

::: item 

`rmdformats` 📦 contains four built-in `html` formats: 


* `readthedown` &lt;img class="modalImg3" alt="readthedown"/&gt; 
* `html_clean` &lt;img class="modalImg3" alt="html_clean"/&gt; 
* `html_docco` &lt;img class="modalImg3" alt="html_docco"/&gt; 
* `material` &lt;img class="modalImg3" alt="material"/&gt; 

:::

::: item 

You can use these formats by simply specifying the output in YAML as below:


```markdown
output: rmdformats::readthedown
```

See more about it below:

https://github.com/juba/rmdformats

:::

:::

---

# `rticles` - LaTeX Journal Article Templates

&lt;!-- The Modal --&gt;
&lt;div id="myModal4" class="modal"&gt;
  &lt;div id="caption4"&gt;&lt;/div&gt;
  &lt;span class="close" onclick="document.getElementById('myModal4').style.display='none'"&gt;&amp;times;&lt;/span&gt;
  &lt;iframe class="modal-content" id="img04"&gt;&lt;/iframe&gt;&lt;br&gt;
&lt;/div&gt;
::: grid
::: item 
* `acm` &lt;img class='modalPdf' alt='acm_article'/&gt;
* `acs` &lt;img class='modalPdf' alt='acs_article'/&gt;
* `aea` &lt;img class='modalPdf' alt='aea_article'/&gt;
* `agu` &lt;img class='modalPdf' alt='agu_article'/&gt;
* `amq` &lt;img class='modalPdf' alt='amq_article'/&gt;
* `ams` &lt;img class='modalPdf' alt='ams_article'/&gt;
* `asa` &lt;img class='modalPdf' alt='asa_article'/&gt;
* `biometrics` &lt;img class='modalPdf' alt='biometrics_article'/&gt;
* `copernicus` &lt;img class='modalPdf' alt='copernicus_article'/&gt;


:::

::: item 

* `elsevier` &lt;img class='modalPdf' alt='elsevier_article'/&gt;
* `frontiers` &lt;img class='modalPdf' alt='frontiers_article'/&gt;
* `ieee` &lt;img class='modalPdf' alt='ieee_article'/&gt;
* `jss` &lt;img class='modalPdf' alt='jss_article'/&gt;
* `mdpi` &lt;img class='modalPdf' alt='mdpi_article'/&gt;
* `mnras` &lt;img class='modalPdf' alt='mnras_article'/&gt;
* `peerj` &lt;img class='modalPdf' alt='peerj_article'/&gt;
* `plos` &lt;img class='modalPdf' alt='plos_article'/&gt;

:::

::: item 
* `pnas` &lt;img class='modalPdf' alt='pnas_article'/&gt;
* `rjournal` &lt;img class='modalPdf' alt='rjournal_article'/&gt;
* `rsos` &lt;img class='modalPdf' alt='rsos_article'/&gt;
* `rss` &lt;img class='modalPdf' alt='rss_article'/&gt;
* `sage` &lt;img class='modalPdf' alt='sage_article'/&gt;
* `sim` &lt;img class='modalPdf' alt='sim_article'/&gt;
* `springer` &lt;img class='modalPdf' alt='springer_article'/&gt;
* `tf` &lt;img class='modalPdf' alt='tf_article'/&gt;

::::

::::


::: {.bottom_abs .width100 .bg-indigo .white padding-left:10px;}
Go to RStudio &gt; File &gt; New File &gt; R Markdown ... &gt; From Template
:::


---


# External Files in Templating

::: grid

::: item 

* When using `rticles`, each journal usually require external files (e.g. `cls` or image files).
* These external components are stored within the package.
* If you are drafting an Rmd template with external components then you need to extract these to your folder first. 

::: 

::: item bg-gray

**GUI**

* `RStudio &gt; File &gt; New File &gt; R Markdown ... &gt; From Template`

**Command line**


```r
rmarkdown::draft("file.Rmd", 
 template = "biometrics_article",
 package = "rticles")
```


:::

:::


---

class: info

# More customisation needed?

&lt;br&gt;

Default templates for many output are found at

&lt;br&gt;

&lt;center&gt;

&lt;a href="https://github.com/jgm/pandoc-templates"&gt;https://github.com/jgm/pandoc-templates&lt;/a&gt;

&lt;/center&gt;

&lt;br&gt;

We'll go through the latex template.

---

I found this nice latex template online. 

::: grid 

::: item 

You can see it at `main.pdf`.

&lt;center&gt;
&lt;iframe src="exercises/demo/main.pdf" width = "90%", height = "500px"&gt;&lt;/iframe&gt;
&lt;/center&gt;

:::

::: item 

It was compiled from `main.tex`.

&lt;center&gt;
&lt;iframe src="exercises/demo/main.tex" width = "90%", height = "500px"&gt;&lt;/iframe&gt;
&lt;/center&gt;

:::

::::

::: {.bottom_abs .width100 .bg-indigo .white padding-left:10px;}
Find `main.tex` and `main.pdf` in `demo` folder.
:::

---

class: middle question

How do I use this template so that I can write contents from an Rmd file instead?

---

# Templating 

We will use 

```markdown 
---
output: 
  pdf_document: 
    template: main.tex
---

But nothing written in the body shows up in the output!
```

--

You need to add `$body$` in the latex template file where you want the body of the md file to appear. 

---

class: font_smaller pad10

# Templating: few more tweaks

* R Markdown needs a few more special tweaks before `\begin{document}` in latex template:

```latex
\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
$if(highlighting-macros)$
$highlighting-macros$
$endif$
```

* These are *minimum* tweaks needed for a LaTeX template.
* You can find common tweaks (including for beamer) at 
&lt;a href="https://github.com/jgm/pandoc-templates"&gt;https://github.com/jgm/pandoc-templates&lt;/a&gt;
* You can define your own tweaks but it is better practice to use the ones defined in pandoc template rather than trying to reinvent the wheel.

---

class: font_smaller

# How pandoc template works: `key`

::: grid 

::: item 

`Rmd` &lt;i class="fas fa-file"&gt;&lt;/i&gt;

```markdown
---
title: "COMBINE 2019"
author: "Emi Tanaka"
output:
  pdf_document: 
    template: "template.tex"
---
```

YAML meta data can be used by surrounding `key` with $.

:::

::: item 

`template.tex` &lt;i class="fas fa-file"&gt;&lt;/i&gt;

```latex

\documentclass{article}
\title{$title$}
\author{$author$}
\date{}

\begin{document}

\maketitle

\end{document}

```

::: {.center font-family:"Computer Modern"!important;}

.font_medium[COMBINE 2019]&lt;br&gt;
Emi Tanaka

:::

:::

:::

---

class: font_smaller

# How pandoc template works: if statements

::: grid 

::: item 

`Rmd` &lt;i class="fas fa-file"&gt;&lt;/i&gt;

```markdown
---
title: "COMBINE 2019"
author: "Emi Tanaka"
output:
  pdf_document: 
    template: "template.tex"
---
```

Simple "if null statements".

:::

::: item 

`template.tex` &lt;i class="fas fa-file"&gt;&lt;/i&gt;

```latex

\documentclass[
$if(fontsize)$
$fontsize$,
$endif$
]{article}
\title{$title$}
\author{$author$}
\date{}

\begin{document}

\maketitle

\end{document}

```


:::

:::

---

class: font_smaller

# How pandoc template works: accessing list

::: grid 

::: item 

`Rmd` &lt;i class="fas fa-file"&gt;&lt;/i&gt;

```markdown
---
title: "COMBINE 2019"
author:
 - name: "Rachel Wang"
   email: "rachel.wang@sydney.edu.au"
 - name: "Connor Smith"
   email: "connor.smith@sydney.edu.au"
output:
  pdf_document: 
    template: "template.tex"
---
```

Here it will become 

.font_small[`\author{Rachel Wang \and Connor Smith}`]

:::

::: item 

`template.tex` &lt;i class="fas fa-file"&gt;&lt;/i&gt;

```latex

\documentclass{article}
\title{$title$}
\author{
$for(author)$
$author.name$$sep$ \and 
$endfor$
}
\date{}

\begin{document}

\maketitle

\end{document}

```


:::

:::


---

class: challenge middle

# Go through

`challenge-10.Rmd`

<div class="countdown" id="timer_5d95d48a" 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: pad10

# Cross Reference


::: grid 

::: item 

* When you make a header via Rmd
```
# Some Header
```
 an id is created automatically.
* The id is created by replacing .red[space with `-`] and making it .red[all lower case].
* Now you can link to this header by `[some text](#some-header)`.
* Cross references work for both pdf and html outputs.

::: 

::: item 

&lt;center&gt;
&lt;iframe src="exercises/demo/demo-header.html" width = "90%", height = "500px"&gt;&lt;/iframe&gt;
&lt;/center&gt;

:::

:::


---


class: pad10

# Direct Reference for `html`


::: grid 

::: item 

* For `html` output, you can also give a link directly to the relevant section.
* E.g. open `demo-header.html` in the `demo` folder in a web browser. 
* Append say `#chicken-data` to the url. It should look like 
.center[
`demo-header.html#chicken-data`
]
* It should have taken you to straight to the corresponding header.

::: 

::: item 

:::

:::

---

class: pad10

# User-defined id


::: grid 

::: item 

* You can define your own id by appending `{#your-id}`.

```markdown
# Some header {#header1}
```
* Now you can link to this header with the id `header1`.
* Note there should be no space in the id name!

::: 

::: item 

:::

:::


---

class: pad10 font_smaller

# Bibliography

* BibTeX citation style format is used to store references in `.bib` files.
* Remember that you can get most BibTeX citation for R packages `citation` function. (Scroll below to see the BibTeX citation).

.scroll-350[

```r
citation("xaringan")
```

```
## 
## To cite package 'xaringan' in publications use:
## 
##   Yihui Xie (2019). xaringan: Presentation Ninja. R package
##   version 0.9. https://CRAN.R-project.org/package=xaringan
## 
## A BibTeX entry for LaTeX users is
## 
##   @Manual{,
##     title = {xaringan: Presentation Ninja},
##     author = {Yihui Xie},
##     year = {2019},
##     note = {R package version 0.9},
##     url = {https://CRAN.R-project.org/package=xaringan},
##   }
```
]

---

# Citations


::: grid 

::: item 

* You can include BibTeX by specifying the `bib` file at YAML as:

```markdown
bibliography: bibliography.bib
```


[@bibtex-key] &lt;i class="fas fa-arrow-right"&gt;&lt;/i&gt; (Author et al. 2019)

or 

@bibtex-key &lt;i class="fas fa-arrow-right"&gt;&lt;/i&gt; Author et al. 2019

* See `demo-citation.Rmd` in the demo folder.


::: 

::: item 

:::

:::


---

class: question middle 

.yellow[R Markdown] is such an *indispensible tool* for making documents, especially if you have plan to *include statistical output*.


How do you use (or plan to use) &lt;br&gt;R Markdown?

---

class: info

# People that made R Markdown possible

The development of R Markdown is largely thanks to


* .yellow[Yihui Xie] &lt;br&gt;*Software Engineer at RStudio*&lt;br&gt; for `knitr`


* .yellow[John MacFarlane] &lt;br&gt;*Professor of Philosophy at UC Berkeley*&lt;br&gt; for `pandoc`


* and .yellow[many contributors] behind the development of these tools.


---


background-image: url(images/bg1.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 [&lt;img src="images/cc.svg" style="height:1em"/&gt;&lt;img src="images/by.svg" style="height:1em"/&gt;&lt;img src="images/sa.svg" style="height:1em"/&gt;](https://creativecommons.org/licenses/by-sa/3.0/au/).

&lt;br&gt;&lt;br&gt;

Emi Tanaka

&lt;i class="fas fa-envelope faa-float animated"&gt;&lt;/i&gt; dr.emi.tanaka@gmail.com&lt;br&gt;
&lt;i class="fab fa-twitter faa-float animated faa-fast"&gt;&lt;/i&gt;  @statsgen


:::

::: {.item .shade_black .checklist .animated .slideInRight border-left-style: solid; border-right-color: white;}

# Check that you can:

&lt;ul&gt;
&lt;li&gt;Understand how YAML changes .Rmd&lt;/li&gt;&lt;li&gt;Understand how to manipulate chunks in .Rmd&lt;/li&gt;&lt;li&gt;Understand how to change the template in .Rmd&lt;/li&gt;&lt;li&gt;Understand how to cross-reference and do citations&lt;/li&gt;
&lt;/ul&gt;

:::

:::
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