Introductory RMarkdown

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90 second video for an introduction to R

• Markdown, who R you?
• 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).
• Thus, Markdown is two things:

1. a plain text formatting syntax;
2. a software tool, written in Perl, that converts the plain text formatting to HTML.

• Markdown's syntax is intended for one purpose: to be used as a format for writing for the web.
• Markdown is not a replacement for HTML, or even close to it. Its syntax is very small.
• For any markup that is not covered by Markdown's syntax, you simply use HTML itself.

For example, to add an HTML table to a Markdown article:

This is a regular paragraph.

<table>
    <tr>
        <td>Foo</td>
    </tr>
</table>

This is another regular paragraph.

Markdown Syntax (English Version)

Markdown Syntax (Chinese Version)

Block Elements

• Paragraphs and Line Breaks
• Headers
• Blockquotes
• Lists
• Code Blocks
• Horizontal Rules)

Span Elements

• Links
• Emphasis
• Code
• Images

Miscellaneous

• Backslash Escapes
• Automatic Links

A paragraph is simply one or more consecutive lines of text, separated by one or more blank lines. Markdown supports “hard-wrapped” text paragraphs.

When you want to insert a <br /> break tag using Markdown, you end a line with two or more spaces, then type return.

Setext-style headers are “underlined” using equal signs and dashes. For example:

This is an H1
=============
This is an H2
-------------

Atx-style headers use 1-6 hash characters at the start of the line, corresponding to header levels 1-6. For example:

# This is an H1
## This is an H2
###### This is an H6

Markdown uses email-style > characters for blockquoting.

> This is the first level of quoting.
>
> > This is nested blockquote.
>
> Back to the first level.

It looks like

This is the first level of quoting.

This is nested blockquote.

Back to the first level.

Markdown supports ordered (numbered) and unordered (bulleted) lists. Unordered lists use *, +, and - followed by at least one space – interchangably – as list markers. Such as

- Red
- Green
- Blue

It looks like

• Red
• Green
• Blue

Ordered lists use numbers followed by periods:

1. Bird
3. McHale
2. Parish

It looks like

1. Bird
2. McHale
3. Parish

The number doesn't matter.

To produce a code block in Markdown, simply indent every line of the block by at least 4 spaces or 1 tab. For example:

Here is an example of AppleScript:

    tell application "Foo"
        beep
    end tell

One level of indentation – 4 spaces or 1 tab – is removed.

Here is an example of AppleScript:

tell application "Foo"
    beep
end tell

You can produce a horizontal rule tag (<hr />) by placing three or more hyphens, asterisks, or underscores on a line by themselves. If you wish, you may use spaces between the hyphens or asterisks. Each of the following lines will produce a horizontal rule:

* * *

***

*****

- - -

---------------------------------------

Markdown supports two style of links: inline and reference. To create an inline link, use a set of regular parentheses immediately after the link text's closing square bracket. For example:

This is [an example](http://example.com/ "Title") inline link.

[This link](http://example.net/) has no title attribute.

And

[WISE](http://www.wise.xmu.edu.cn/index.asp)

will creates link to WISE

Reference-style links use a second set of square brackets, inside which you place a label of your choosing to identify the link:

This is [an example][id] reference-style link.

Then, anywhere in the document, you define your link label like this, on a line by itself:

[id]: http://example.com/  "Optional Title Here"

Here's an example of reference links in action:

I get 10 times more traffic from [Google] [1] than from
[Yahoo] [2] or [MSN] [3].

[1]: http://google.com/        "Google"
[2]: http://search.yahoo.com/  "Yahoo Search"
[3]: http://search.msn.com/    "MSN Search"

Using the implicit link name shortcut, you could instead write:

I get 10 times more traffic from [Google][] than from
[Yahoo][] or [MSN][].

[google]: http://google.com/        "Google"
[yahoo]:  http://search.yahoo.com/  "Yahoo Search"
[msn]:    http://search.msn.com/    "MSN Search"

Both give you:

I get 10 times more traffic from Google than from Yahoo or MSN.

Markdown treats asterisks (*) and underscores (_) as indicators of emphasis. E.g., this input:

*single asterisks*

_single underscores_

**double asterisks**

__double underscores__

They will produce:

single asterisks

single underscores

double asterisks

double underscores

To indicate a span of code, wrap it with backtick quotes (`). Unlike a pre-formatted code block, a code span indicates code within a normal paragraph. For example:

Use the `read.table()` function.

will produce:

Use the read.table() function.

To include a literal backtick character within a code span,

``There is a literal backtick (`) here.``

There is a literal backtick (`) here.

Markdown uses an image syntax that is intended to resemble the syntax for links, allowing for two styles: inline and reference.

Inline image syntax looks like this:

![Alt text](/path/to/img.jpg)

![Alt text](/path/to/img.jpg "Optional title")

Reference-style image syntax looks like this:

![Alt text][id]

Where “id” is the name of a defined image reference. Image references are defined using syntax identical to link references:

[id]: url/to/image  "Optional title attribute"

Markdown supports a shortcut style for creating “automatic” links for URLs and email addresses: simply surround the URL or email address with angle brackets.

You can do this:

<http://www.xmu.edu.cn/>

Markdown will turn this: http://www.xmu.edu.cn/

Markdown allows you to use backslash escapes to generate literal characters which would otherwise have special meaning in Markdown's formatting syntax.

If you wanted to surround a word with literal asterisks, you can use backslashes before the asterisks, like this:

\*literal asterisks\*

It gives you:

*literal asterisks*

R Markdown is an authoring format that enables easy creation of dynamic documents, presentations, and reports from R. It combines the core syntax of markdown with embedded R code chunks that are run so their output can be included in the final document. R Markdown documents are fully reproducible (they can be automatically regenerated whenever underlying R code or data changes).

This is what I want to show you!

• Markdown Basics
• R Code Chunks
• Inline R Code
• Embedding Equations
• Output Options
• Shiny
• knitr package

summary(cars)

     speed           dist    
 Min.   : 4.0   Min.   :  2  
 1st Qu.:12.0   1st Qu.: 26  
 Median :15.0   Median : 36  
 Mean   :15.4   Mean   : 43  
 3rd Qu.:19.0   3rd Qu.: 56  
 Max.   :25.0   Max.   :120  

You can also evaluate R expressions inline by enclosing the expression within a single back-tick qualified with r. For example,

x=2
y=45

Then the following code:

I get ` r x` jobs and each pays me ` r y` a day. Then I earn $ ` r x*y` a day.

(remove the space before r) gives you:

I get 2 jobs and each pays me $ 45 a day. Then I earn $ 90 a day.

You can embed LaTeX or MathML equations in R Markdown files using the following syntax:

• $equation$ for inline equations (note there must not be white space adjacent to the $ delimiters)
• $$ equation $$ for display equations
• <math ...> </math> for MathML equations.

The combined forecast is:
$$Y_{t,1}^{c}=kY_{t,1}^{1}+(1-k)Y_{t,1}^{2}$$

It gives you:

The combined forecast is: \[ Y_{t,1}^{c}=kY_{t,1}^{1}+(1-k)Y_{t,1}^{2} \]

The Arithmetic mean is equal to $\frac{1}{n} \sum_{i=1}^{n} x_{i}$.

will give you:

The Arithmetic mean is equal to \( \frac{1}{n} \sum_{i=1}^{n} x_{i} \).

R Markdown documents can contain a metadata section that includes both title, author, and date information as well as options for customizing output.

---
title: "Sample Document"
output:
  html_document:
    toc: true
    theme: united
  pdf_document:
    toc: true
    highlight: zenburn
---

Elegant, flexible and fast dynamic report generation with R

The knitr package was designed to be a transparent engine for dynamic report generation with R.

knitr package options

You needn't know all of them.

StackEdit

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RStudio

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