Introduction

This is a style guide to help in formatting Markdown content for the site. This page is very similar to the style cheatsheet on Trevor Bedford’s site. In general, I’ve tried to adhere to GitHub style, with the intention that anything that renders on GitHub will render here as well. The following isn’t meant to be exhaustive, just a reminder of what’s possible with Markdown.

Headings

# Heading 1
## Heading 2
### Heading 3
#### Heading 4
##### Heading 5
###### Heading 6

Heading 1

Heading 2

Heading 3

Heading 4

Heading 5

Heading 6

Text styling

Italicize text by surrounding it in *asterisks* or _underscores_.
Bold text by surrounding it with **double asterisks** or __double underscores__.
Combine with **_double asterisks plus underscores_**.
Strike-through text with ~~double tildes~~.
Superscript contiguous text with carrots like x^2y, surround with parentheses for more complex expressions like x^(2y + 3z).

Italicize text by surrounding it in asterisks or underscores.

Bold text by surrounding it with double asterisks or double underscores.

Combine with double asterisks plus underscores.

Strike-through text with double tildes.

Superscript contiguous text with carrots like 7^th or x^2y, surround with parentheses for more complex expressions like x^(2y + 3z) or x^(2y + 5(x-y)).

Lists

* Thing one with an asterisk
+ Thing two with a plus
- Thing three with a minus

1. The first order of business
2. The second order of business
  * The first part of the 2nd order
  * The second part of the 2nd order
3. The third order of business

• Thing one with an asterisk
• Thing two with a plus
• Thing three with a minus

1. The first order of business
2. The second order of business
   • The first part of the 2nd order
   • The second part of the 2nd order
3. The third order of business

Images

Images work like links, but with a prefaced !. This supports SVG as well PNG, JPG, etc…

![](http://octodex.github.com/images/minion.png)
![An image with alt text](http://octodex.github.com/images/dojocat.jpg)

Can always drop in HTML, so sizing adjustments can be done with:

<img style="width:50px;" src="/images/logo_bw.svg"/>

To add a caption to an image use the figure tag, like so:

<figure>
  <img src="/images/logo_bw.svg" alt="">
  <a id="beastie"/></a>
  <figcaption>A rat in a cage.</figcaption>
</figure>

</a>

A bit of inline monospaced font can be made `by surrounding text with backticks`.

```java
public class HelloWorld {

    public static void main(String[] args) {
        // Prints "Hello, World" to the terminal window.
        System.out.println("Hello, World");
    }

}
``` results in:

public class HelloWorld {

    public static void main(String[] args) {
        // Prints "Hello, World" to the terminal window.
        System.out.println("Hello, World");
    }

}

```xml
<BirthDeathSkylineModel spec="BirthDeathSkylineModel" id="birthDeath" tree="@tree" contemp="true">
      <parameter name="origin" id="origin" value ="100" lower="0."/>    
      <parameter name="R0" id="R0" value="2" lower="0." dimension ="10"/>
      <parameter name="becomeUninfectiousRate" id="becomeUninfectiousRate" value="1" lower="0." dimension ="10"/>
      <parameter name="samplingProportion" id="samplingProportion" value="0."/>
      <parameter name="rho" id="rho" value="1e-6" lower="0." upper="1."/>
</BirthDeathSkylineModel>
``` results in:

<BirthDeathSkylineModel spec="BirthDeathSkylineModel" id="birthDeath" tree="@tree" contemp="true">
      <parameter name="origin" id="origin" value ="100" lower="0."/>    
      <parameter name="R0" id="R0" value="2" lower="0." dimension ="10"/>
      <parameter name="becomeUninfectiousRate" id="becomeUninfectiousRate" value="1" lower="0." dimension ="10"/>
      <parameter name="samplingProportion" id="samplingProportion" value="0."/>
      <parameter name="rho" id="rho" value="1e-6" lower="0." upper="1."/>
</BirthDeathSkylineModel>

    > myString <- "Hello, World!"
    > print ( myString)
    [1] "Hello, World!"
    ```
results in:

```R
> myString <- "Hello, World!"
> print (myString)
[1] "Hello, World!"

Inline equations: {`% eqinline \dot{x} = \sigma(y-x) %`}

Displayed equations: 
{`% eq \left( \sum_{k=1}^n a_k b_k \right)^2 \leq \left( \sum_{k=1}^n a_k^2 \right) \left( \sum_{k=1}^n b_k^2 \right) %`}

Except remove the ` from between { and %.

> The data we have is not the data we want, and the data we need is not the data we have.

> We can input **any** formatted text in here:
 
> - Even
> - Lists
 
> or equations:
 
> {`% eq (x_1, \ldots, x_n) \left( \begin{array}{ccc}
      \phi(e_1, e_1) & \cdots & \phi(e_1, e_n) \\
      \vdots & \ddots & \vdots \\
      \phi(e_n, e_1) & \cdots & \phi(e_n, e_n)
    \end{array} \right)
  \left( \begin{array}{c}
      y_1 \\
      \vdots \\
      y_n
    \end{array} \right) %`}

[This is an external link to Google](http://www.google.com/)

[This is a relative link to elsewhere in the site](/projects/)

[This is a link to a figure on the same page](#fig:beastie)

This is an external link to Google

This is a relative link to elsewhere in the site

This is a link to a figure on the same page

Horizontal rule

Use more than three hyphens, asterisks or underscores. Using only three hyphens will still draw a line, but may cause interference with the yaml header in some parsers.

****
----
____

Line breaks

Here's a line for us to start with.

This line is separated by two newlines, so it will be a separate paragraph.

This line is also a separate paragraph, though...
Adding a single line break does not create a new paragraph.

For multiple line breaks use `<br>` tags: 

<br>
<br>
like above.

Here’s a line for us to start with.

This line is separated by two newlines, so it will be a separate paragraph.

This line is also a separate paragraph, though… Adding a single line break does not create a new paragraph.

For multiple line breaks use <br> tags:

like above.