*Note: This is an expanded version of the default R Markdown tutorial* 


# Basics 
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>.

Note the figure options set in the opening "YAML" header. The YAML header is a group of value pairs that tells the compiler what you want your output to look like. Begin and end your YAML with three dashes. (Note: The R Markdown template pre-builds this for you!)

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:


[//]: (comments can be added to the document like this.) 

```{r}
summary(iris)
```

You can also embed plots, for example:

```{r, echo=FALSE}
plot(iris)
```

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

# Formatting 
You can write code in line, using \` , e.g. `r 1+3` or `r mean(cars$speed)`.

Also, you can write equations inline using the dollar sign, e.g., $\pi \approx \frac{22}{7}$. Note that this will only be "pretty print" in the PDF, and may show up as LaTeX code in the HTML. 

Math can be in display mode as well, with the double dollar sign $$ e = mc^2 $$

You can get superscript with carets (^) like^this^, strikethrough with tildes (\~) like ~~this~~, and subscripts with tildes as well, like~this~. In order to print out any ["special" characters][3], you must preface them with a backslash, like so: "\textbackslash \#", which prints "\#".

Block quotes are done with \>, 

> Love all, trust a few,
> do wrong to none. -- Shakespeare

You can create links in [phrases][1]!

Another formatting point is with asterisks. You can make text *italic* and **bold**, as well as adding a horizontal rule, with three or more astericks, as below.

*****

Unordered lists are made with asterisks and plus signs,

* Item 1
    + Item 1A
    + Item 1B
* Item 2
* Item 3

Ordered lists are made with numbers 

1. Item 1
    a. Item 1A
    b. Item 1B
2. Item 2 
    + Item 2A
    + Item 2B
3. Item 3


R plots can be as fancy as you'd like. 

##
```{r}
library(ggplot2)
qplot(speed, dist, data = cars) + geom_smooth()

```
If there is an error in R code, you need to install ggplot2 package.

If you want verbatim text, use the \`\`\` command without the bracketed r.

```
Then the text will come out in fixed-width font
```

It can also be done in-line to make the name of a `function` obvious.


*****

Tables can be made easily in Markdown, like the following

Blah  | BlahBlah
----- | -----
Stuff  | Stuff
Stuff | Stuff


# More Advanced content

A table of content can be added by setting `toc:true` in the preamble. The theme can be changed there as well. To see this content, look [here][2]. Shiny is an extremely interesting interactive document that can be produced within R Markdown, while it is out of our scope for today, I suggest you look into it.



The reference guides linked [here][4] are very helpful with figuring out R Markdown nuances.


[1]: http://lmgtfy.com/?q=R+Markdown+Tutorial
[2]: http://rmarkdown.rstudio.com/html_document_format.html#appearance-and-style
[3]: https://en.wikibooks.org/wiki/LaTeX/Special_Characters#Other_symbols
[4]: https://sites.google.com/site/riceorientationrtutorial/home/reproducible-homework/usn