• Preface
• HTML Documents
• Markdown Basics
• R Code Chunks
• Deployment
• Miscellaneous
• Appendix
  • R Presentation
  • ioslides

A convenient tool to generate reproducible document.

• Markdown
  • Remove HTML tag for higher readibility.
  • Inline HTML is avaliable.
• R markdown
  • Markdown + embedded R code chunks
  • Rmd -> md -> html(docx, pdf)
• Why R Markdown
  • Consolidate your code and document into single file.
  • Easy for version control.

• v1: based on package knitr and markdown
• v2: based on knitr and pandoc, intergrated into RStudio v0.98.932 or later
  • default bootstrap template
  • docx and pdf
  • slides with ioslides and Beamer
  • embedded shiny apps
• keep using R Markdown v1:

<!-- rmarkdown v1 -->

• RStudio — Install the latest version of RStudio

• Other environments — Install the rmarkdown package.

• YAML Metadata: YAML document options
• Markdown: Article text
• R Code Chunk: Executible R code

• RStudio: "Knit" command (Ctrl+Shift+K)

• Command line: rmarkdown::render function

  rmarkdown::render("input.Rmd")

Currently YAML doesn't work well with Chinese on Windows. Don't use Chinese title if you are a Windows guy.

With Rstudio, You can edit various output options with friendly UI.

---
title: "R Markdown Exercise"
author: "Mansun Kuo"
date: "July 24, 2014"
output:
  html_document:
    css: assets/css/custom.css
    fig_caption: no
    fig_height: 5
    fig_width: 7
    highlight: default
    keep_md: no
    number_sections: no
    theme: default
    toc: yes
---

CSS:

#nextsteps {
   color: blue;
}

.emphasized {
   font-size: 1.2em;
}

Apply to Whole Section:

### Apply to Whole Section {#nextsteps .emphasized}

使用RStudio產生一個HTML文件:

• 標題為R Markdown Exercise。

• include table of contents

*italic*   **bold**

_italic_   __bold__

I am italic

I am bold

Setext:

Header 1
=============

Header 2
-------------

atx:

# Header 1

## Header 2

### Header 3

加上報告的段落標題：

## 油電業薪資近9萬，是教服業的4倍?

### 行業別每人每月薪資 - Top 3 & Last 3

### 行業別每人每月薪資總表

End a line with two or more spaces:

Roses are red,  
Violets are blue.

Subsequent paragraphs must be preceded by a blank line and indented four spaces or a tab.

* fruits

    delicious!!!
    + apples
        - macintosh
        - red delicious
    + pears
    + peaches
* vegetables  
  healthy!!!
    + broccoli
    + chard

A plain http address or add a link to a phrase.

Inline Link:

[2014台灣資料科學愛好者年會](http://twconf.data-sci.org/)

2014台灣資料科學愛好者年會

Reference Link:

[2014台灣資料科學愛好者年會][dsc]

[dsc]: http://twconf.data-sci.org/

2014台灣資料科學愛好者年會

在「油電業薪資近9萬，是教服業的4倍?」標題下加上新聞來源連結的Lists：

• 自由時報
• 經濟部

新聞連結：

- [自由時報](https://tw.news.yahoo.com/%E6%B2%B9%E9%9B%BB%E6%A5%AD%E8%96%AA%E8%B3%87%E8%BF%919%E8%90%AC-%E6%95%99%E6%9C%8D%E6%A5%AD%E7%9A%844%E5%80%8D-221333602.html)
- [經濟部](http://www.moea.gov.tw/Mns/populace/news/News.aspx?kind=1&menu_id=40&news_id=35719)

A friend once said:

> It's always better to give
> than to receive.

• Plain code blocks are displayed in a fixed-width font but not evaulated.

  ```
  This text is displayed verbatim / preformatted
  ```
  

• Specify the language of the block is avaliable

  ```r
  x = rnorm(10)
  ```

  x = rnorm(10)

• LaTeX
  • Inline equation: $equation$
    

  • Display equation: $$ equation $$

  • Useful Resources
    • Daum Equation Editor: Chrome Plugin
    • Online LaTeX Equation Editor
• MathML
  • <math ...> </math> for equations.

Three or more asterisks or dashes:

******

------

R code will be evaluated and printed

```{r}
summary(cars$dist)
```

summary(cars$dist)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##       2      26      36      43      56     120

```{r plot}
summary(cars)
plot(cars)
```

• Easy Navigation in RStudio

  

• echo(TRUE): whether to include R source code in the output file
• eval(TRUE): whether to evaluate the code chunk
• message(TRUE): whether to preserve messages emitted by message()
• include(TRUE): if include=FALSE, nothing will be written into the output document, but the code is still evaluated and plot files are generated
• warning(TRUE): whether to preserve warnings in the output

Set global chunk options:

knitr::opts_chunk$set()

在「油電業薪資近9萬，是教服業的4倍?」之前設定Global Chunk Options：

```{r, include=FALSE}
# load("data/salary.RData")
data(salary, package="DSC2014Tutorial")
knitr::opts_chunk$set(warning = FALSE,
                      echo = FALSE,
                      message = FALSE)
```

• dev('png'): figure format(png, jpeg, tiff, svg, …)
• fig.path('figure/'): figure path
• fig.width(7): figure width
• fig.height(7): figure height
• dpi(72): DPI (dots per inch)

```{r dev='svg', fig.path='myplot', fig.height=8}
plot(iris)
```

將前面課程練習過的圖加在「行業別每人每月薪資 - Top 3 & Last 3」之下：

```{r plot, dpi=75, fig.width=10}
a = order(salary_2013$每人每月薪資)
salary_news = matrix(salary_2013$每人每月薪資[c(head(a,3),tail(a,3))],ncol = 6)
colnames(salary_news) = salary_2013$行業[c(head(a,3),tail(a,3))]

# Mac顯示中文需設置字型
# http://equation85.github.io/blog/graph-font-of-r-in-mac-os-x/
par(family='STKaiti')
mp = barplot(salary_news) #x軸座標
text(mp,10000,salary_news) #標註薪資
```

Set results='asis' to write raw results from R into the output document

在「行業別每人每月薪資總表」下加上表格：

```{r results='asis'}
index = order(salary_2013$每人每月薪資, decreasing = TRUE)
knitr::kable(salary_2013[index, c("行業", "每人每月薪資")], 
             row.names=FALSE)
```

• cache(FALSE): whether to cache a code chunk to improve proformance for expensive computing

• If you run into problems with cached output, you can always clear the knitr cache by removing the folder named with a _cache suffix.

• engine('R'): the language name of the code chunk
  • 'bash'
  • 'python'
  • 'Rcpp'

```{r engine='bash'}
whoami
```

I counted 2 red trucks on the highway.

使用Inline R Code在圖形下方加上一些基本的敘述：

從上方圖表可以清楚地看到，`r colnames(salary_news)[which.max(salary_news)]`每人每月薪資為
`r salary_news[which.max(salary_news)]`元，
是所有行業別中最高的，
第二名`r colnames(salary_news)[length(salary_news)-1]`也有
`r salary_news[length(salary_news)-1]`，
第三名`r colnames(salary_news)[length(salary_news)-2]`較第二名少了
`r salary_news[length(salary_news)-1]  - salary_news[length(salary_news)-2]`，但還是有
`r salary_news[length(salary_news)-2]`元。

整體薪資水準較為不佳則是`r colnames(salary_news)[1]`
、`r colnames(salary_news)[2]`和`r colnames(salary_news)[3]`，
其中`r colnames(salary_news)[1]`每人每月薪資是
`r salary_news[1]`，
約僅有`r colnames(salary_news)[which.max(salary_news)]`的
`r round(salary_news[1] / salary_news[length(salary_news)] * 100)`%。

• Report
• Rmd File

Extra: Generate word document with Knit Word

There are various way to publish your document on the web.

• RPubs
  • RPubs
  • markdown::rpubsUpload
• File hosting services
  • Dropbox
  • Google Drive

Deploy your HTML document on the web.

• Using R markdown to generate reproducible report
• Slides + R Markdown
• Config file + R Markdown

You can add R Markdown and HTML in the YAML content.

```{r results='asis', echo=FALSE}
library(whisker)
temp = '<span class="{{color}}{{number}}">{{color}}{{number}}</span>'
numbers = c("", "2", "3")
colors = c("red", "blue", "green", "yellow", "gray")
for (color in colors){
    cat("- ")
    for (number in numbers){
        out = whisker.render(temp)
        cat(out)
    }
    cat("\n")
}
```

• iframe: displaying a web page within a web page

  <iframe src="http://twconf.data-sci.org/" height=600 width=800></iframe>

• img: inserting images into an HTML document.

  Much easier for adjusting width and height.

  <img src="assets/img/Taiwan-R-logo.png" alt="logo" height="42" width="42">

library(knitr)
library(ggvis)
mtcars %>%
    ggvis(x = ~wt, y = ~mpg) %>%
    layer_smooths(se=TRUE, opacity := 0.5, opacity.hover := 0.75) %>% 
    layer_points(fill = ~factor(cyl), size := 50, size.hover := 200) %>%
    set_options(hover_duration = 250)

It’s possible to embed a Shiny application within a document.

• R Markdown Cheat Sheet
• R Markdown
• knitr
• RStudio Documentation
• Reproducible Research
• Shiny Articles
• Slides GitHub Page
• googleVis簡介

• A feature of RStudio that enable easy authoring of HTML5 presentations based on R Markdown.
• Special Feature
  • Extensive support for authoring and previewing presentations within the RStudio IDE
  • Flexible two column layouts
• Getting Started

Set global option in first slide.

R Presentation
========================================================
author: Mansun Kuo
date: June 22, 2014

Slides automatically display their titles unless title: false is specified.

Slide 1
====================================
title: false

- Bullet 1
- Bullet 2
- Bullet 3

• Every time you save your presentation the preview is refreshed and navigated to whatever slide you were editing.
• Within the preview pane, you can press the Edit button on the toolbar to jump immediately to it's location in the source file.

Two-Column Slide
====================================
left: 70%

First column
***
Second column

• transition: transition style
  • none, linear, rotate, fade, zoom, concave
• transition-speed: transition speed
  • default, slow, fast

R Presentation
========================================================
author: Mansun Kuo
date: June 22, 2014
transition: rotate
transition-speed: fast

• type: slide appearance
  • section, sub-section, prompt, alert

Type
========================================================
type: sub-section
incremental: true

• incremental: display content incrementally
  • true, false

Incremental Display
========================================================
incremental: true

- Bullet 1
- Bullet 2
- Bullet 3

• Clear Knitr Cache: clear knitr cache for this presentation
• View in Browser: view the presentation in an external web browser
• Save AS Web Page: save the presentation as a standalone web page
• Publish to RPubs: publish the presentation to RPubs

R Presentation
========================================================
author: Mansun Kuo
date: June 22, 2014
css: assets/css/rpres.css

Apply to individual slides:

My Slide
===================================
class: illustration

Apply to spans of text:

My Slide
================================== 
<span class="emphasized">Pay attention to this!</span>

• A feature of RStudio that create an ioslides presentation.
• Special Feature
  • Code Highlighting
  • Presenter mode
• Getting Started

• #: create a section
• ##: create a new slide
• ---: create a new slide without a header(horizontal rule)
• |: add a subtitle

# section

## slide 1

---

## slide 2 | with subtitle

• 'f' enable fullscreen mode

• 'w' toggle widescreen mode

• 'o' enable overview mode

• 'h' enable code highlight mode

• 'p' show presenter notes

• 'Esc' exits all of these modes.

---
output:
  ioslides_presentation:
    incremental: true
---

Render bullets incrementally for specific slide:

> - Eat eggs
> - Drink coffee

• Eat eggs
• Drink coffee

• widescreen: widescreen mode
• smaller: smaller text

---
output:
  ioslides_presentation:
    widescreen: true
    smaller: true
---

Set smaller text for specific slide:

## Getting up {.smaller}

transition: default, slower, faster

---
output:
  ioslides_presentation:
    transition: slower
---

Add a 128x128 logo:

---
output:
  ioslides_presentation:
    logo: logo.png
---

Using ### <b> and ### </b> to enclose the lines you want to highlight.

x <- 10
y <- 20

Note that the content will flow across the columns.

<div class="columns-2">
  ![Image](assets/img/Taiwan-R-logo.png)

  - Bullet 1
  - Bullet 2
  - Bullet 3
</div>

You can color content using base color classes red, blue, green, yellow, and gray (or variations of them e.g. red2, red3, blue2, blue3, etc.).

<div class="red2">
This text is red
</div>

• red red2 red3
• blue blue2 blue3
• green green2 green3
• yellow yellow2 yellow3
• gray gray2 gray3

mypresentation.html?presentme=true

mypresentation.html?presentme=false

To add presenter notes:

<div class="notes">
This is my note.
- It can contain markdown
- like this list
</div>