---
title: "R Markdown Tutorial"
subtitle: "Psych 640 Lab"
author: "Andrew Cohen and William Hopper"
date: "November 29, 2015"
output: html_document
---

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

### 1) Text

This is an R Markdown document. 

Hit the **Knit HTML** button and watch the magic happen.

Plain text is written like this. You can also make text *italic* or **bold**.

You can include urls like this <http://rmarkdown.rstudio.com> or like this [click here](http://rmarkdown.rstudio.com).

Headers are included by prefixing text with # (large header), ## (medium), or ### (small), as in the "Text" header above.

You can also make unordered lists...

- Item 1 (must be separated from text by a blank line)
- Item 2
- Item 3
    - Item 3a (needs to be indented 4 spaces)
    - Item 3b

...or ordered lists...

1. Item 1 (must be separated from text by a blank line)
2. Item 2
3. Item 3
    a. Item 3a (needs to be indented 4 spaces)
    b. Item 3b

If you want to include a manual line break,   
end the line with 2 spaces.  

> Blockquotes are a useful way to present information when you want something to stand out from the rest of the text like quotes. -Andrew Cohen

If you want to make text look like R code you can surround it with backticks like this: `R code looking stuff`.

```
You can also make code blocks with 3 backticks.
This code is pre-formatted.
This font is fixed width.
```

Here is a superscript 2^2^.   
Here is a subscript H~0~.

You can separate regions with horizontal lines made of dashes or equal signs.

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

### 2) Extenal Images

Here is how you include an image from the web.  
![puppy](http://greatinspire.com/wp-content/uploads/2012/11/Cute-puppy-photos-582.jpg)

Here is how you include an image from a file on your computer.  
<!-- ![kitten]('filepath/kitten.jpeg') -->
filepath would need to be updated to the location of the file.   
Because we don't know the right path on your computer, this line is commented out using \<!-- -->.

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

### 3) Equations

Here is how to create an inline equation: $1 + 1 = 2$. Don't include whitespace next to the $ and the equation.

You can have R compute inline equations like this: `r 1 + 1`. Notice that it prints `2` not `1 + 1`. You need to put the lowercase r there.

Use two dollar signs and LaTex syntax for equations you want to show in their own "paragraph".
$$SEM=\frac{s}{\sqrt{n}}$$ 

LaTex allows you to produce any mathematical symbol for formula you can think of.
LaTex syntax can be found [here](ftp://ftp.ams.org/pub/tex/doc/amsmath/short-math-guide.pdf).

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

### 4) Tables

Header 1 | Header 2 
---------|---------
info 11 | info 21
info 12 | info 22
info 13 | info 23
info 14 | info 24

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

### 5) Chunks

You can include R code chunks like the one below. This R code will be evaluated like in a normal R session and the results will be printed out in the final document. 

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

I named this chunk 'Car summary' (optional).

If you want to prevent printing the code that generated the output, add `echo = FALSE`. Notice that the `summary(cars)` bit went away.

```{r Car summary no echo, echo=FALSE}
summary(cars)
```

You can also prevent R from evaluating the code.

```{r Car summary no evaluation, eval=FALSE}
summary(cars)
```

We can convert R data structures into Markdown tables for prettier formatting. 
Here we use the `kable` function from the knitr package.

```{r Car summary with knitr, echo=FALSE}
library(knitr)
kable(summary(cars), row.names=FALSE, caption="With Knitr")
```

You can also embed plots:

```{r Car plot, echo=FALSE, fig.height=6, fig.width=6, fig.align='left'}
par(pty='s')
plot(cars)
```

Notice the fig.height, fig.width, and fig.align options. There are lots of other chunk options.

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

### 6) Other

RStudio allows you to run chunks of code as normal R code. Put the cursor in the previous code chunk. From the upper right 'Chunks' menu select `Run Current Chunk`.

You can also jump to a chunk by selecting `Jump To...`

Notice the little arrows to the left of some lines of code (e.g., headers, code blocks, chunks, etc). You can click on them to collapse or expand a region.