---
title: "RMarkdown"
author: "James L. Adams"
output:
  html_document: default
  pdf_document: default
  word_document: default
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## Installation

```{r installation, eval=FALSE}
install.packages("rmarkdown")

## This one's just for making plots later
install.packages("gapminder")
```

# Syntax
## Headers

# Header 1

```
# Header 1
```

## Header 2

```
## Header 2
```

### Header 3

```
### Header 3
```

#### Header 4

```
#### Header 4
```

##### Header 5

```
##### Header 5
```

###### Header 6

```
###### Header 6
```

## Text Styles

> block quote

```
> block quote
```

**Bold**

```
**Bold**
```

*Italic*

```
*Italic*
```

endash: --

```
endash: --
```

emdash: ---

```
emdash: ---
```

inline equation (using $LaTeX$): $A = \pi*r^{2}$

```
inline equation (using $LaTeX$): $A = \pi*r^{2}$
```

Subscripts ~Hello!~ and superscripts ^Hello!^ are easy.

```
Subscripts ~Hello!~ and superscripts ^Hello!^ are easy.
```

[Here's a link](https://www.google.com)

```
[Here's a link](https://www.google.com)
```

## Images

image: ![](https://s-media-cache-ak0.pinimg.com/originals/1d/96/13/1d96138537ae93c28554fa623f56a527.gif)

```
image: ![](https://s-media-cache-ak0.pinimg.com/originals/1d/96/13/1d96138537ae93c28554fa623f56a527.gif)
```

## Lists

* unordered list
* number 2
    + sub-item (four spaces)


```
* unordered list
* number 2
  + sub-item (four spaces)
```

1. ordered list
2. item 2
    + sub-item (four spaces)


```
1. ordered list
2. item 2
    + sub-item (four spaces)
```

## Tables

The default rendering is as you would see in the R terminal:
```{r}
head(mtcars)
```


You can use other styles, including interactive tables when knitting to HTML. Here's one using a knitr kable:
```{r}
knitr::kable(head(mtcars))
```


## Code    

Here's a piece of `inline code` to look at.

```
Here's a piece of `inline code` to look at.
```

Here is a piece of inline R code: `r sum(3, 7)`

```{r eval = FALSE}
Here is a piece of inline R code: `r sum(3, 7)`
```


    ```
    Code chunks are delineated by three backticks
    ```

```{r}
# R Code goes here!!
```

```{r echo = FALSE}
# This won't show up
```

```{r}
# This will generate output
summary(cars)
```


```{r eval = FALSE}
# Including "eval = FALSE" means this code will not run
summary(cars)
```

## Plots
```{r}
# Throw some plots in:
library(ggplot2)
library(gapminder)

ggplot(gapminder, aes(x = gdpPercap, y = lifeExp)) +
  geom_point(aes(color = continent))

```


```{r}
# Reproducible reports for when your data changes:
library(MASS)
library(ggplot2)
set.seed(42)

df <- data.frame(mvrnorm(500, mu = c(0,0), Sigma = matrix(c(1,0.56,0.56,1), ncol = 2),
               empirical = TRUE))

head(df)

ggplot(df, aes(x = X1, y = X2)) +
  geom_point() +
  geom_smooth(method = "lm")

```

```{r}
set.seed(500)

df <- data.frame(mvrnorm(500, mu = c(0,0), Sigma = matrix(c(1,0.56,0.56,1), ncol = 2),
               empirical = TRUE))

head(df)

ggplot(df, aes(x = X1, y = X2)) +
  geom_point() +
  geom_smooth(method = "lm")
```


## Other Languages
Code chunks can be in other languages including:

* Python
* SQL
* Bash
* Rcpp
* Stan
* JavaScript
* CSS

### Python
```{python}
x = 'hello, world!'
print(x.split(' '))
```


## Footnotes

Here's a footnote,[^1] and a second one. [^longnamednote]

[^1]: Here's the first footnote.

[^longnamednote]: Here's the other.

```
Here's a footnote,[^1] and a second one. [^longnamednote]

[^1]: Here's the first footnote.

[^longnamednote]: Here's the other.
```

## Source
The Rmd used to produce this can be found [here](https://raw.githubusercontent.com/jladams/parker/master/Rmd/RMarkdown.Rmd).