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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title>xaringan Theme Presentation Title</title>
<meta charset="utf-8" />
<meta name="date" content="2020-11-22" />
<script src="libs/header-attrs/header-attrs.js"></script>
<link href="libs/remark-css/default.css" rel="stylesheet" />
<script src="libs/htmlwidgets/htmlwidgets.js"></script>
<script src="libs/jquery/jquery.min.js"></script>
<link href="libs/leaflet/leaflet.css" rel="stylesheet" />
<script src="libs/leaflet/leaflet.js"></script>
<link href="libs/leafletfix/leafletfix.css" rel="stylesheet" />
<script src="libs/Proj4Leaflet/proj4-compressed.js"></script>
<script src="libs/Proj4Leaflet/proj4leaflet.js"></script>
<link href="libs/rstudio_leaflet/rstudio_leaflet.css" rel="stylesheet" />
<script src="libs/leaflet-binding/leaflet.js"></script>
<link href="libs/datatables-css/datatables-crosstalk.css" rel="stylesheet" />
<script src="libs/datatables-binding/datatables.js"></script>
<link href="libs/dt-core/css/jquery.dataTables.min.css" rel="stylesheet" />
<link href="libs/dt-core/css/jquery.dataTables.extra.css" rel="stylesheet" />
<script src="libs/dt-core/js/jquery.dataTables.min.js"></script>
<link href="libs/crosstalk/css/crosstalk.css" rel="stylesheet" />
<script src="libs/crosstalk/js/crosstalk.min.js"></script>
<link rel="stylesheet" href="css/MiR.css" type="text/css" />
<link rel="stylesheet" href="css/MiR-fonts.css" type="text/css" />
</head>
<body>
<textarea id="source">
class: title-slide, center, middle
<img src="img/mir_logo.png" width="200" />
<div>
<style type="text/css">.xaringan-extra-logo {
width: 80px;
height: 128px;
z-index: 0;
background-image: url(https://mircommunity.com/images/mir_logo.png);
background-size: contain;
background-repeat: no-repeat;
position: absolute;
top:1em;right:1em;
}
</style>
<script>(function () {
let tries = 0
function addLogo () {
if (typeof slideshow === 'undefined') {
tries += 1
if (tries < 10) {
setTimeout(addLogo, 100)
}
} else {
document.querySelectorAll('.remark-slide-content:not(.title-slide):not(.inverse):not(.hide_logo)')
.forEach(function (slide) {
const logo = document.createElement('div')
logo.classList = 'xaringan-extra-logo'
logo.href = null
slide.appendChild(logo)
})
}
}
document.addEventListener('DOMContentLoaded', addLogo)
})()</script>
</div>
# xaringan Theme Presentation Title
----
## **MiR Community**
###
### November 22, 2020
---
background-image: url(https://upload.wikimedia.org/wikipedia/commons/b/be/Sharingan_triple.svg)
???
Image credit: [Wikimedia Commons](https://commons.wikimedia.org/wiki/File:Sharingan_triple.svg)
---
class: center, middle
# xaringan
### /ʃaː.'riŋ.ɡan/
---
class: inverse, center, middle
# Get Started
---
# Hello World
Install the **xaringan** package from [Github](https://github.com/yihui/xaringan):
--
You are recommended to use the [RStudio IDE](https://www.rstudio.com/products/rstudio/), but you do not have to.
- Create a new R Markdown document from the menu `File -> New File -> R Markdown -> From Template -> Ninja Presentation`;<sup>1</sup>
--
- Click the `Knit` button to compile it;
--
- or use the [RStudio Addin](https://rstudio.github.io/rstudioaddins/)<sup>2</sup> "Infinite Moon Reader" to live preview the slides (every time you update and save the Rmd document, the slides will be automatically reloaded in RStudio Viewer.
.footnote[
[1] 中文用户请看[这份教程](http://slides.yihui.org/xaringan/zh-CN.html)
[2] See [#2](https://github.com/yihui/xaringan/issues/2) if you do not see the template or addin in RStudio.
]
---
background-image: url(https://github.com/yihui/xaringan/releases/download/v0.0.2/karl-moustache.jpg)
background-position: 50% 50%
class: center, bottom, inverse
# You only live once!
---
# Hello Ninja
As a presentation ninja, you certainly should not be satisfied by the "Hello World" example. You need to understand more about two things:
1. The [remark.js](https://remarkjs.com) library;
1. The **xaringan** package;
Basically **xaringan** injected the chakra of R Markdown (minus Pandoc) into **remark.js**. The slides are rendered by remark.js in the web browser, and the Markdown source needed by remark.js is generated from R Markdown (**knitr**).
---
# remark.js
You can see an introduction of remark.js from [its homepage](https://remarkjs.com). You should read the [remark.js Wiki](https://github.com/gnab/remark/wiki) at least once to know how to
- create a new slide (Markdown syntax<sup>*</sup> and slide properties);
- format a slide (e.g. text alignment);
- configure the slideshow;
- and use the presentation (keyboard shortcuts).
It is important to be familiar with remark.js before you can understand the options in **xaringan**.
.footnote[[*] It is different with Pandoc's Markdown! It is limited but should be enough for presentation purposes. Come on... You do not need a slide for the Table of Contents! Well, the Markdown support in remark.js [may be improved](https://github.com/gnab/remark/issues/142) in the future.]
---
background-image: url(https://github.com/yihui/xaringan/releases/download/v0.0.2/karl-moustache.jpg)
background-size: cover
class: center, bottom, inverse
# I was so happy to have discovered remark.js!
---
class: inverse, middle, center
# Using xaringan
---
# xaringan
Provides an R Markdown output format `xaringan::moon_reader` as a wrapper for remark.js, and you can use it in the YAML metadata, e.g.
```yaml
---
title: "A Cool Presentation"
output:
xaringan::moon_reader:
yolo: true
nature:
autoplay: 30000
---
```
See the help page `?xaringan::moon_reader` for all possible options that you can use.
---
# remark.js vs xaringan
Some differences between using remark.js (left) and using **xaringan** (right):
.pull-left[
1. Start with a boilerplate HTML file;
1. Plain Markdown;
1. Write JavaScript to autoplay slides;
1. Manually configure MathJax;
1. Highlight code with `*`;
1. Edit Markdown source and refresh browser to see updated slides;
]
.pull-right[
1. Start with an R Markdown document;
1. R Markdown (can embed R/other code chunks);
1. Provide an option `autoplay`;
1. MathJax just works;<sup>*</sup>
1. Highlight code with `{{}}`;
1. The RStudio addin "Infinite Moon Reader" automatically refreshes slides on changes;
]
.footnote[[*] Not really. See next page.]
---
# Math Expressions
You can write LaTeX math expressions inside a pair of dollar signs, e.g. &#36;\alpha+\beta$ renders `\(\alpha+\beta\)`. You can use the display style with double dollar signs:
```
$$\bar{X}=\frac{1}{n}\sum_{i=1}^nX_i$$
```
`$$\bar{X}=\frac{1}{n}\sum_{i=1}^nX_i$$`
Limitations:
1. The source code of a LaTeX math expression must be in one line, unless it is inside a pair of double dollar signs, in which case the starting `$$` must appear in the very beginning of a line, followed immediately by a non-space character, and the ending `$$` must be at the end of a line, led by a non-space character;
1. There should not be spaces after the opening `$` or before the closing `$`.
1. Math does not work on the title slide (see [#61](https://github.com/yihui/xaringan/issues/61) for a workaround).
---
# R Code
```
# Estimate Std. Error t value Pr(>|t|)
# (Intercept) -17.579095 6.7584402 -2.601058 1.231882e-02
# speed 3.932409 0.4155128 9.463990 1.489836e-12
```
```
# [1] "地爆天星" "天照"
```
---
# R Plots
<img src="MiR_files/figure-html/cars-1.svg" width="504" />
---
# Tables
If you want to generate a table, make sure it is in the HTML format (instead of Markdown or other formats), e.g.,
<table>
<thead>
<tr>
<th style="text-align:right;"> Sepal.Length </th>
<th style="text-align:right;"> Sepal.Width </th>
<th style="text-align:right;"> Petal.Length </th>
<th style="text-align:right;"> Petal.Width </th>
<th style="text-align:left;"> Species </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:right;"> 5.1 </td>
<td style="text-align:right;"> 3.5 </td>
<td style="text-align:right;"> 1.4 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 4.9 </td>
<td style="text-align:right;"> 3.0 </td>
<td style="text-align:right;"> 1.4 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 4.7 </td>
<td style="text-align:right;"> 3.2 </td>
<td style="text-align:right;"> 1.3 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 4.6 </td>
<td style="text-align:right;"> 3.1 </td>
<td style="text-align:right;"> 1.5 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 5.0 </td>
<td style="text-align:right;"> 3.6 </td>
<td style="text-align:right;"> 1.4 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 5.4 </td>
<td style="text-align:right;"> 3.9 </td>
<td style="text-align:right;"> 1.7 </td>
<td style="text-align:right;"> 0.4 </td>
<td style="text-align:left;"> setosa </td>
</tr>
</tbody>
</table>
---
# HTML Widgets
I have not thoroughly tested HTML widgets against **xaringan**. Some may work well, and some may not. It is a little tricky.
Similarly, the Shiny mode (`runtime: shiny`) does not work. I might get these issues fixed in the future, but these are not of high priority to me. I never turn my presentation into a Shiny app. When I need to demonstrate more complicated examples, I just launch them separately. It is convenient to share slides with other people when they are plain HTML/JS applications.
See the next page for two HTML widgets.
---
<div id="htmlwidget-b1bec933df3124cf0404" style="width:100%;height:432px;" class="leaflet html-widget"></div>
<script type="application/json" data-for="htmlwidget-b1bec933df3124cf0404">{"x":{"options":{"crs":{"crsClass":"L.CRS.EPSG3857","code":null,"proj4def":null,"projectedBounds":null,"options":{}}},"calls":[{"method":"addTiles","args":["//{s}.tile.openstreetmap.org/{z}/{x}/{y}.png",null,null,{"minZoom":0,"maxZoom":18,"tileSize":256,"subdomains":"abc","errorTileUrl":"","tms":false,"noWrap":false,"zoomOffset":0,"zoomReverse":false,"opacity":1,"zIndex":1,"detectRetina":false,"attribution":"© <a href=\"http://openstreetmap.org\">OpenStreetMap<\/a> contributors, <a href=\"http://creativecommons.org/licenses/by-sa/2.0/\">CC-BY-SA<\/a>"}]}],"setView":[[42.0285,-93.65],17,[]]},"evals":[],"jsHooks":[]}</script>
---
<div id="htmlwidget-9c64b3718aeea1c58444" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-9c64b3718aeea1c58444">{"x":{"filter":"none","fillContainer":false,"data":[["1","2","3","4","5","6","7","8","9","10"],[5.1,4.9,4.7,4.6,5,5.4,4.6,5,4.4,4.9],[3.5,3,3.2,3.1,3.6,3.9,3.4,3.4,2.9,3.1],[1.4,1.4,1.3,1.5,1.4,1.7,1.4,1.5,1.4,1.5],[0.2,0.2,0.2,0.2,0.2,0.4,0.3,0.2,0.2,0.1],["setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa"]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>Sepal.Length<\/th>\n <th>Sepal.Width<\/th>\n <th>Petal.Length<\/th>\n <th>Petal.Width<\/th>\n <th>Species<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"pageLength":8,"columnDefs":[{"className":"dt-right","targets":[1,2,3,4]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false,"lengthMenu":[8,10,25,50,100]}},"evals":[],"jsHooks":[]}</script>
---
# Some Tips
- When you use the "Infinite Moon Reader" addin in RStudio, your R session will be blocked by default. You can click the red button on the right of the console to stop serving the slides, or use the _daemonized_ mode so that it does not block your R session. To do the latter, you can set the option
```r
options(servr.daemon = TRUE)
```
in your current R session, or in `~/.Rprofile` so that it is applied to all future R sessions. I do the latter by myself.
To know more about the web server, see the [**servr**](https://github.com/yihui/servr) package.
--
- Do not forget to try the `yolo` option of `xaringan::moon_reader`.
```yaml
output:
xaringan::moon_reader:
yolo: true
```
---
# Some Tips
- Slides can be automatically played if you set the `autoplay` option under `nature`, e.g. go to the next slide every 30 seconds in a lightning talk:
```yaml
output:
xaringan::moon_reader:
nature:
autoplay: 30000
```
--
- A countdown timer can be added to every page of the slides using the `countdown` option under `nature`, e.g. if you want to spend one minute on every page when you give the talk, you can set:
```yaml
output:
xaringan::moon_reader:
nature:
countdown: 60000
```
Then you will see a timer counting down from `01:00`, to `00:59`, `00:58`, ... When the time is out, the timer will continue but the time turns red.
---
# Some Tips
- The title slide is created automatically by **xaringan**, but it is just another remark.js slide added before your other slides.
The title slide is set to `class: center, middle, inverse, title-slide` by default. You can change the classes applied to the title slide with the `titleSlideClass` option of `nature` (`title-slide` is always applied).
```yaml
output:
xaringan::moon_reader:
nature:
titleSlideClass: [top, left, inverse]
```
--
- If you'd like to create your own title slide, disable **xaringan**'s title slide with the `seal = FALSE` option of `moon_reader`.
```yaml
output:
xaringan::moon_reader:
seal: false
```
---
# Some Tips
- There are several ways to build incremental slides. See [this presentation](https://slides.yihui.org/xaringan/incremental.html) for examples.
- The option `highlightLines: true` of `nature` will highlight code lines that start with `*`, or are wrapped in `{{ }}`, or have trailing comments `#<<`;
```yaml
output:
xaringan::moon_reader:
nature:
highlightLines: true
```
See examples on the next page.
---
# Some Tips
.pull-left[
An example using a leading `*`:
```r
if (TRUE) {
** message("Very important!")
}
```
Output:
```r
if (TRUE) {
* message("Very important!")
}
```
This is invalid R code, so it is a plain fenced code block that is not executed.
]
.pull-right[
An example using `{{}}`:
````
```{r tidy=FALSE}
if (TRUE) {
*{{ message("Very important!") }}
}
```
````
Output:
```
## Very important!
```
It is valid R code so you can run it. Note that `{{}}` can wrap an R expression of multiple lines.
]
---
# Some Tips
An example of using the trailing comment `#<<` to highlight lines:
````markdown
```{r tidy=FALSE}
library(ggplot2)
ggplot(mtcars) +
aes(mpg, disp) +
geom_point() + #<<
geom_smooth() #<<
```
````
Output:
---
# Some Tips
When you enable line-highlighting, you can also use the chunk option `highlight.output` to highlight specific lines of the text output from a code chunk. For example, `highlight.output = TRUE` means highlighting all lines, and `highlight.output = c(1, 3)` means highlighting the first and third line.
````md
```{r, highlight.output=c(1, 3)}
head(iris)
```
````
```
*## Sepal.Length Sepal.Width Petal.Length Petal.Width Species
## 1 5.1 3.5 1.4 0.2 setosa
*## 2 4.9 3.0 1.4 0.2 setosa
## 3 4.7 3.2 1.3 0.2 setosa
## 4 4.6 3.1 1.5 0.2 setosa
## 5 5.0 3.6 1.4 0.2 setosa
## 6 5.4 3.9 1.7 0.4 setosa
```
Question: what does `highlight.output = c(TRUE, FALSE)` mean? (Hint: think about R's recycling of vectors)
---
# Some Tips
- To make slides work offline, you need to download a copy of remark.js in advance, because **xaringan** uses the online version by default (see the help page `?xaringan::moon_reader`).
- You can use `xaringan::summon_remark()` to download the latest or a specified version of remark.js. By default, it is downloaded to `libs/remark-latest.min.js`.
- Then change the `chakra` option in YAML to point to this file, e.g.
```yaml
output:
xaringan::moon_reader:
chakra: libs/remark-latest.min.js
```
- If you used Google fonts in slides (the default theme uses _Yanone Kaffeesatz_, _Droid Serif_, and _Source Code Pro_), they won't work offline unless you download or install them locally. The Heroku app [google-webfonts-helper](https://google-webfonts-helper.herokuapp.com/fonts) can help you download fonts and generate the necessary CSS.
---
# Macros
- remark.js [allows users to define custom macros](https://github.com/yihui/xaringan/issues/80) (JS functions) that can be applied to Markdown text using the syntax `![:macroName arg1, arg2, ...]` or ``. For example, before remark.js initializes the slides, you can define a macro named `scale`:
```js
remark.macros.scale = function (percentage) {
var url = this;
return '<img src="' + url + '" style="width: ' + percentage + '" />';
};
```
Then the Markdown text
```markdown
```
will be translated to
```html
<img src="image.jpg" style="width: 50%" />
```
---
# Macros (continued)
- To insert macros in **xaringan** slides, you can use the option `beforeInit` under the option `nature`, e.g.,
```yaml
output:
xaringan::moon_reader:
nature:
beforeInit: "macros.js"
```
You save your remark.js macros in the file `macros.js`.
- The `beforeInit` option can be used to insert arbitrary JS code before `remark.create()`. Inserting macros is just one of its possible applications.
---
# CSS
Among all options in `xaringan::moon_reader`, the most challenging but perhaps also the most rewarding one is `css`, because it allows you to customize the appearance of your slides using any CSS rules or hacks you know.
You can see the default CSS file [here](https://github.com/yihui/xaringan/blob/master/inst/rmarkdown/templates/xaringan/resources/default.css). You can completely replace it with your own CSS files, or define new rules to override the default. See the help page `?xaringan::moon_reader` for more information.
---
# CSS
For example, suppose you want to change the font for code from the default "Source Code Pro" to "Ubuntu Mono". You can create a CSS file named, say, `ubuntu-mono.css`:
```css
@import url(https://fonts.googleapis.com/css?family=Ubuntu+Mono:400,700,400italic);
.remark-code, .remark-inline-code { font-family: 'Ubuntu Mono'; }
```
Then set the `css` option in the YAML metadata:
```yaml
output:
xaringan::moon_reader:
css: ["default", "ubuntu-mono.css"]
```
Here I assume `ubuntu-mono.css` is under the same directory as your Rmd.
See [yihui/xaringan#83](https://github.com/yihui/xaringan/issues/83) for an example of using the [Fira Code](https://github.com/tonsky/FiraCode) font, which supports ligatures in program code.
---
# Themes
Don't want to learn CSS? Okay, you can use some user-contributed themes. A theme typically consists of two CSS files `foo.css` and `foo-fonts.css`, where `foo` is the theme name. Below are some existing themes:
```
## [1] "chocolate-fonts" "chocolate" "default-fonts" "default"
## [5] "duke-blue" "fc-fonts" "fc" "hygge-duke"
## [9] "hygge" "ki-fonts" "ki" "kunoichi"
## [13] "lucy-fonts" "lucy" "metropolis-fonts" "metropolis"
## [17] "middlebury-fonts" "middlebury" "ninjutsu" "rladies-fonts"
## [21] "rladies" "robot-fonts" "robot" "rutgers-fonts"
## [25] "rutgers" "shinobi" "tamu-fonts" "tamu"
## [29] "uio-fonts" "uio" "uo-fonts" "uo"
## [33] "uol-fonts" "uol" "useR-fonts" "useR"
```
---
# Themes
To use a theme, you can specify the `css` option as an array of CSS filenames (without the `.css` extensions), e.g.,
```yaml
output:
xaringan::moon_reader:
css: [default, metropolis, metropolis-fonts]
```
If you want to contribute a theme to **xaringan**, please read [this blog post](https://yihui.org/en/2017/10/xaringan-themes).
---
class: inverse, middle, center
background-image: url(https://upload.wikimedia.org/wikipedia/commons/3/39/Naruto_Shiki_Fujin.svg)
background-size: contain
# Naruto
---
background-image: url(https://upload.wikimedia.org/wikipedia/commons/b/be/Sharingan_triple.svg)
background-size: 100px
background-position: 90% 8%
# Sharingan
The R package name **xaringan** was derived<sup>1</sup> from **Sharingan**, a dōjutsu in the Japanese anime _Naruto_ with two abilities:
- the "Eye of Insight"
- the "Eye of Hypnotism"
I think a presentation is basically a way to communicate insights to the audience, and a great presentation may even "hypnotize" the audience.<sup>2,3</sup>
.footnote[
[1] In Chinese, the pronounciation of _X_ is _Sh_ /ʃ/ (as in _shrimp_). Now you should have a better idea of how to pronounce my last name _Xie_.
[2] By comparison, bad presentations only put the audience to sleep.
[3] Personally I find that setting background images for slides is a killer feature of remark.js. It is an effective way to bring visual impact into your presentations.
]
---
# Naruto terminology
The **xaringan** package borrowed a few terms from Naruto, such as
- [Sharingan](http://naruto.wikia.com/wiki/Sharingan) (写輪眼; the package name)
- The [moon reader](http://naruto.wikia.com/wiki/Moon_Reader) (月読; an attractive R Markdown output format)
- [Chakra](http://naruto.wikia.com/wiki/Chakra) (查克拉; the path to the remark.js library, which is the power to drive the presentation)
- [Nature transformation](http://naruto.wikia.com/wiki/Nature_Transformation) (性質変化; transform the chakra by setting different options)
- The [infinite moon reader](http://naruto.wikia.com/wiki/Infinite_Tsukuyomi) (無限月読; start a local web server to continuously serve your slides)
- The [summoning technique](http://naruto.wikia.com/wiki/Summoning_Technique) (download remark.js from the web)
You can click the links to know more about them if you want. The jutsu "Moon Reader" may seem a little evil, but that does not mean your slides are evil.
---
class: center
# Hand seals (印)
Press `h` or `?` to see the possible ninjutsu you can use in remark.js.
---
class: center, middle
# Thanks!
Slides created via the R package [**xaringan**](https://github.com/yihui/xaringan).
The chakra comes from [remark.js](https://remarkjs.com), [**knitr**](http://yihui.org/knitr), and [R Markdown](https://rmarkdown.rstudio.com).
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