2017-06-22 20:38:24

简介

什么是markdown?

Markdown is a text-to-HTML conversion tool for web writers. Markdown allows you to write using an easy-to-read, easy-to-write plain text format, then convert it to structurally valid XHTML (or HTML).

– John Gruber

作者: John Gruber 和 Aaron Swartz
目标: 成为一种适用于网络的书写语言，实现“易读、易写”
优点: 轻量、易学(半小时上手)，让写作者能更关注内容本身(而非排版)
应用广泛: GitHub、reddit、Stack Exchange、简书、…

markup vs markdown

其实markdown也是一种markup(标记)语言

常用的markup: HTML/XML

<h1>Title 1</h1>

<p>Bla <b>bla</b> bla.</p>
<hr>

<ul>
    <li>Item 1</li>
    <li>Item 2</li>
</ul>

<img src="image.png"></img>

对应的markdown

# Title 1

Bla **bla** bla.

* * *

- Item 1
- Item 2

![](image.png)

本地编辑器: StackEdit

GitHub

基本语法

标题 (h1 - h6)

# Header 1

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

## Header 2

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

### Header 3

#### Header 4

##### Header 5

###### Header 6

Header 1

Header 2

Header 3

Header 4

Header 5

Header 6

编号

无序

* Item 1
* Item 2
    + Item 2a
    + Item 2b
        - Item 2b1
        - Item 2b2

Item 1
Item 2
- Item 2a
- Item 2b
  - Item 2b1
  - Item 2b2

有序

1. Item 1
1. Item 2
1. Item 3
1. Item 4
    + Item 4a
    + Item 4b

Item 1
Item 2
Item 3
Item 4
- Item 4a
- Item 4b

强调

斜体

*italic*

_italic_*_

italic

粗体

**bold**

__bold__

bold

断行、分割

断行

行末加两个以上空格

Roses are red,   
Violets are blue.

Roses are red,
Violets are blue.

如行末不多加空格

Roses are red, 
Violets are blue.

Roses are red, Violets are blue.

分割线

三个或以上星号/短横杠

---

***

链接、图片

链接

<http://www.google.com>
[Google](http://www.google.com)

http://www.google.com

Google

图片

![Fig: logo](A05_04_markdown_files/logo.png)

Fig: logo

引文

A friend once said:

> ###### Rule No.1
> - It's always better to give 
> than to receive.   
> - Refer to the above.

A friend once said:

Rule No.1

It's always better to give than to receive.

Refer to the above.

代码

行内代码

功能性

There were `r nrow(cars)` cars studied

There were 50 cars studied

无功能性

Let's use dataset `cars`.

Let's use dataset cars.

代码块

功能性

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

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   2.00   26.00   36.00   42.98   56.00  120.00

无功能性

```
summary(cars$speed)
```

表格

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

First Header	Second Header
Content Cell	Content Cell
Content Cell	Content Cell
Content Cell	Content Cell

| First Header | Second Header |
|:-------------+--------------:|
| Content `Cell` | Content *Cell* |
| Content Cell | [Content](google.com) Cell |
| Content Cell  | Content **Cell** |

First Header	Second Header
Content `Cell`	Content Cell
Content Cell	Content Cell
Content Cell	Content Cell

$\LaTeX$公式

行内公式

$\LaTeX$ grammar for
 $\delta=(\alpha+\beta)/\gamma$

$\LaTeX$ grammar for $\delta=(\alpha+\beta)/\gamma$

成块公式

Bayes Equation:
$$P(B|A)=\frac{P(A|B)P(B)}{P(A)}$$

Bayes Equation: \[P(B|A)=\frac{P(A|B)P(B)}{P(A)}\]

注释

注释型链接

I spend so much time reading [R bloggers][1] and [Simply Statistics][2]!  

[1]: http://www.r-bloggers.com/   "R bloggers"  
[2]: http://simplystatistics.org/ "Simply Statistics"

I spend so much time reading R bloggers and Simply Statistics!

脚注

I spend so much time reading R bloggers[^rb]

[^rb]: R-bloggers "R-bloggers is a sets of blogs for R users."

I spend so much time reading R bloggers¹

锚点

Go back to [Page 5](#5).

Go back to Page 5.

<p id="anchor-1">bla bla</p>
Go to [anchor1](#anchor-1)

bla bla

Go to anchor1

其他

上下标

superscript^2^

superscript²

subscript~2~

subscript₂

删除线

~~strikethrough~~

~~strikethrough~~

rmarkdown

在Rstudio中创建RMarkdown(.Rmd)文档

开发方: RStudio Inc.
基于markdown语法，支持R、Python、SQL等程序语言
工作界面支持notebook
支持Word/HTML/PDF静态文档、交互文档、仪表盘、手册、图书、网站等
可安装rticles包，基于内置模板生成报告

rmarkdown文档的结构

YAML头

YAML: 主要用于编写配置文件的标记语言，较XML、json等更简洁
基本语法规则
- 大小写敏感
- 使用缩进而非嵌套表示层级关系
- 缩进时不允许使用Tab键，只允许使用空格。
- 缩进的空格数目不重要，只要相同层级的元素左侧对齐即可
rmarkdown头部YAML
- 以三连横杠起始、结束
- 记录配置参数: title、author、date、output、reference、params等
- 通过配置output的主要参数，即可将文档转成相应格式

文档体

文档体包括文字和代码
文字部分支持markdown和LaTeX语法
代码支持R、Python、SQL、SAS等
- 以 ```{r} 或 ```{python} …起始
- 以 ``` 结束
一个r, engine=python的例子

x="Hello, python world!"
print(x.split(' '))

## ['Hello,', 'python', 'world!']

参考文献 - 外部法

将文献导入Zotero，再导出为.bib
在YAML头定义bibliography和csl

bibliography: example.bib
csl: the-lancet.csl

在正文中@<文献id>引用某条文献,或
- 例子 1
[@<文献1id>;@<文献2id>]引用文献
- 例子¹
文献会列表显示在文档末尾

参考文献 - 内部法

直接将各条文献按YAML语法写入YAML头
引用方法同外部法^1,2

---
references:
- id: fenner2012a
  title: One-click science marketing
  author:
  - family: Fenner
    given: Martin
  container-title: Nature Materials
  volume: 11
  URL: 'http://dx.doi.org/10.1038/nmat3283'
  DOI: 10.1038/nmat3283
  issue: 4
  publisher: Nature Publishing Group
  page: 261-263
  type: article-journal
  issued:
    year: 2012
    month: 3
---

`params`

在YAML头指定参数列表
文档代码块中直接以 params$<对象> 引用这些参数
提高文档的复用性

---
title: Sample
output: html_document
params:
    data: "iris"
---

```{r}
summary(params$data)
```

生成文档

.Rmd文档 –[knit]–> .md文档 –[Pandoc]–> 最终文档

Pandoc是一个开源工具，当生成pdf时，需要调用MikTeX、TexLive等组件

1. `Knit`按钮

2. `render`函数

render(input, output_format = NULL, 
       output_file = NULL, output_dir = NULL,
       output_options = NULL, 
       intermediates_dir = NULL,
       knit_root_dir = NULL,
       runtime = c("auto", "static", "shiny", 
            "shiny_prerendered"),
       clean = TRUE, params = NULL, 
       knit_meta = NULL, envir = parent.frame(),
       run_pandoc = TRUE, quiet = FALSE, 
       encoding = getOption("encoding"))

Thank you!

回到主目录

参考文献

1 Williams TA, Lenders JWM, Mulatero P et al. Outcomes after adrenalectomy for unilateral primary aldosteronism: An international consensus on outcome measures and analysis of remission rates in an international cohort. Lancet Diabetes Endocrinol 2017; published online May. DOI:10.1016/S2213-8587(17)30135-3.

2 Fenner M. One-click science marketing. Nature Materials 2012; 11: 261–3.

目录

简介