R for data science||R Markdown

话要说起来，我接触到的第一门现代语言就是Markdown了。起因是自己年轻的时候，喜欢写作，在网上了解到阳志平、李笑来等写作用Markdown。然后就开始用火狐浏览器的Markdown Here ，大概花了两个小时，搞出了自己喜欢的Markdown主题。后来才知道R是可以用markdown来写作的，然后是简书也可以，然后是有道笔记对Markdown的支持。

当然并不是说现在我的Markdown用的有多深，还是和一开始一样只是会一些基本的语法，这正是使用它的原因：简单。我也不会在这里介绍很多markdown语法，网上并不缺少这类资料。

R Markdown 基础

R Markdown 速查表 在Rstudio中很容易找到：

help中有这多好东西呢！

有了速查表可以开始了：

---
title: "Untitled"
author: "zhouyunlai"
date: "2019年8月6日"
output: html_document
---
\```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
\```

## R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

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


## Including Plots

You can also embed plots, for example:

\```{r pressure, echo=FALSE}
plot(pressure)
\```

Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

新建的文件基本包含了RMarkdown的基本结构了：

• 两个--- 之间YAML文件头
• ``` 之间的 R代码段
• 一些具有简单格式的文文本

如果想要生成包含所有文本代码的报告可以点击 Kint 或者按组合键Ctrl+ Shift+ K ,还可以使用rmarkdown::render("1-example.Rmd") 在R中生成。

使用Markdown 格式化文本

.Rmd文件中的文本是使用Markdown语言写的，Markdown适用于格式化纯文本文件的一种轻量级语法，其设计思想是使得文本极容易书写又容易阅读。Markdown学习起来非常容易。

Text formatting

*italic* or italic
*bold* bold
`code`
\superscript^2^ and subscript~2~

Headings

---

# 1st Level Header

## 2nd Level Header

### 3rd Level Header

Lists

---

* Bulleted list item 1
* Item 2
* Item 2a
* Item 2b
\1. Numbered list item 1
\1. Item 2. The numbers are incremented automatically in the output.

Links and images

---

<http://example.com>

[linked phrase](http://example.com)

!optional caption text

Tables

---

First Header | Second Header
------------- | -------------
Content Cell | Content Cell
Content Cell | Content Cell

代码段

插入代码段：

• Cmd/Ctrl + Alt + I
• The “Insert” button icon in the editor toolbar.
• By manually typing the chunk delimiters```{r} and ```

代码段名称

我们可以赋予一个代码段一个名称，这样做有三个好处：

• 方便浏览特定的代码段
• 可以使代码生成的图形具有特定的名称
• 可以建立代码段网络

代码段选项

用选项results=选择文本型结果的类型。 取值有：

• markup, 这是缺省选项， 会把文本型结果变成HTML的原样文本格式。
• hide, 运行了代码后不显示运行结果。
• hold, 一个代码块所有的代码都显示完， 才显示所有的结果。
• asis, 文本型输出直接进入到HTML文件中， 这需要R代码直接生成HTML标签， knitr包的kable()函数可以把数据框转换为HTML代码的表格。

表格

knitr::kable(
  mtcars[1:5, ], 
  caption = "A knitr kable."
)

|                  |  mpg| cyl| disp|  hp| drat|    wt|  qsec| vs| am| gear| carb|
|:-----------------|----:|---:|----:|---:|----:|-----:|-----:|--:|--:|----:|----:|
|Mazda RX4         | 21.0|   6|  160| 110| 3.90| 2.620| 16.46|  0|  1|    4|    4|
|Mazda RX4 Wag     | 21.0|   6|  160| 110| 3.90| 2.875| 17.02|  0|  1|    4|    4|
|Datsun 710        | 22.8|   4|  108|  93| 3.85| 2.320| 18.61|  1|  1|    4|    1|
|Hornet 4 Drive    | 21.4|   6|  258| 110| 3.08| 3.215| 19.44|  1|  0|    3|    1|
|Hornet Sportabout | 18.7|   8|  360| 175| 3.15| 3.440| 17.02|  0|  0|    3|    2|

	mpg	cyl	disp	hp	drat	wt	qsec	vs	am	gear	carb
Mazda RX4	21.0	6	160	110	3.90	2.620	16.46	0	1	4	4
Mazda RX4 Wag	21.0	6	160	110	3.90	2.875	17.02	0	1	4	4
Datsun 710	22.8	4	108	93	3.85	2.320	18.61	1	1	4	1
Hornet 4 Drive	21.4	6	258	110	3.08	3.215	19.44	1	0	3	1
Hornet Sportabout	18.7	8	360	175	3.15	3.440	17.02	0	0	3	2

值得学习的R Markdown 包： xtable, stargazer, pander, tables, and ascii packages.

书中还讨论了，缓存、全局选项，内联代码、排错、YAML文件头，文档参数和参考文献引用等主题。

R Markdown 输出类型

• 文档

pdf_documentmakes a PDF with LaTeX (an open source document layout system), which you’ll need to install. RStudio will prompt you if you don’t already have it.

word_document for Microsoft Word documents (.docx).

odt_document for OpenDocument Text documents (.odt).

rtf_documentfor Rich Text Format (.rtf) documents.

md_document for a Markdown document. This isn’t typically useful by itself, but you might use it if, for example, your corporate CMS or lab wiki uses markdown.

github_document: this is a tailored version of md_document designed for sharing on GitHub.

For html_documents another option is to make the code chunks hidden by default, but visible with a click:

output:
  html_document:
    code_folding: hide

• 笔记本

output:
  html_notebook: default
  github_document: default

• 演示文稿

1. ioslides_presentation - HTML presentation with ioslides

2. slidy_presentation - HTML presentation with W3C Slidy

3. beamer_presentation - PDF presentation with LaTeX Beamer.

Two other popular formats are provided by packages:

1. revealjs::revealjs_presentation - HTML presentation with reveal.js. Requires the revealjspackage.

2. rmdshower, https://github.com/MangoTheCat/rmdshower, provides a wrapper around the shower, https://github.com/shower/shower, presentation engine

• 仪表盘
  ---
  title: "Diamonds distribution dashboard"
  output: flexdashboard::flex_dashboard
  ---

  
  图片.png

• 交互元素

  htmlwidgets

library(leaflet)
leaflet() %>%
  setView(117.0425, 39.40777777777778 , zoom = 10) %>% 
  addTiles() %>%
  addMarkers(117.0425, 39.40777777777778 , popup = "zhouyunlai@") 

There are many packages that provide htmlwidgets, including:

• dygraphs, http://rstudio.github.io/dygraphs/, for interactive time series visualisations.

• DT, http://rstudio.github.io/DT/, for interactive tables.

• threejs, https://github.com/bwlewis/rthreejs for interactive 3d plots.

• DiagrammeR, http://rich-iannone.github.io/DiagrammeR/ for diagrams (like flow charts and simple node-link diagrams).

To learn more about htmlwidgets and see a more complete list of packages that provide them visit http://www.htmlwidgets.org/.

shiny

---
title: "Shiny Web App"
output: html_document
runtime: shiny
---

```{r setup, include = FALSE}
library(ggplot2)
library(dplyr)
knitr::opts_chunk$set(fig.width = 5, fig.asp = 1/3)
```

```{r}
library(shiny)

textInput("name", "What is your name?")
numericInput("age", "How old are you?", NA, min = 0, max = 150)
```

• 网站

With a little additional infrastructure you can use R Markdown to generate a complete website:

• Put your .Rmd files in a single directory. index.Rmd will become the home page.

• Add a YAML file named _site.yml provides the navigation for the site. For example:

  name: "my-website"
  navbar:
    title: "My Website"
    left:
      - text: "Home"
        href: index.html
      - text: "Viridis Colors"
        href: 1-example.html
      - text: "Terrain Colors"
        href: 3-inline.html
  

Execute rmarkdown::render_site() to build _site, a directory of files ready to deploy as a standalone static website, or if you use an RStudio Project for your website directory. RStudio will add a Build tab to the IDE that you can use to build and preview your site.

Read more at http://rmarkdown.rstudio.com/rmarkdown_websites.html.

---

Other packages provide even more output formats:

• The bookdown package, https://github.com/rstudio/bookdown, makes it easy to write books, like this one. To learn more, read Authoring Books with R Markdown, by Yihui Xie, which is, of course, written in bookdown. Visit http://www.bookdown.org to see other bookdown books written by the wider R community.

• The prettydoc package, https://github.com/yixuan/prettydoc/, provides lightweight document formats with a range of attractive themes.

• The rticles package, https://github.com/rstudio/rticles, compiles a selection of formats tailored for specific scientific journals.

See http://rmarkdown.rstudio.com/formats.html for a list of even more formats. You can also create your own by following the instructions at http://rmarkdown.rstudio.com/developer_custom_formats.html.

---

r4ds
R Markdown 简介
R_文档输出_rmarkdown