Iris_Example.Rmd

---
title: "Iris Example"
author: "DSI Workshop"
output: 
  html_document:
    toc: true
    theme: spacelab
  pdf_document: default
---

***

# First Section: Iris Violin Plot

## Subsection: Original Code

* Let's revisit the violin plot of the Iris data from the `ggplot2` section of the workshop.

* The code can be embedded in the R Markdown document.  When the document is compiled, the code will be executed (`eval = TRUE` in the Rmd source) and the resulting plot will be included in the document.

* The code itself is also printed because of the option `echo = TRUE` (also in the Rmd source).

* The original code from Lingge was:

```{r echo = TRUE, eval = TRUE, warning = FALSE, fig.width = 5, fig.height = 2.5, fig.align = 'center'}
library(ggplot2)
ggplot(data = iris, aes(x = Species, y = Petal.Width)) +
  geom_violin(aes(fill = Species)) +
  labs(title = 'Iris Petal Width')
```

## Using Chunk Options

Some important chunk options and [default values] are:

* `eval [TRUE]`: Should the chunk be evaluated
* `echo [TRUE]`: Should the chunk be printed
* `warning [TRUE]`: Should warnings be printed
* `error [FALSE]`: Should messages be printed
* `tidy [FALSE]`: Should the code be reformatted for ease of display
* `results ["markup"]`: Possible values are "markup", "asis", "hold", "hide"
* `cache [FALSE]`: Should results be cached for future render
* `comment ["##"]`: Prefix character when displaying results
* `fig.width [7]`: Width in inches for plots from chunk
* `fig.height [7]`: Height in inches for plots from chunk
* `fig.align ["right"]`: Alignment of figures

<small>[Adapted from the R Markdown Cheat Sheet](https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf)</small>

### Subsubsection: Violin Plot

Change the code chunk options so that the code is not displayed and the plot is larger.

```{r echo = FALSE, eval = TRUE, warning = FALSE, fig.width = 7, fig.height = 4.5}
library(ggplot2)
ggplot(data = iris, aes(x = Species, y = Petal.Width)) +
  geom_violin(aes(fill = Species)) +
  labs(title = 'Iris Petal Width')
```

***

# Images

#### Format to embed images: `![](path/to/smallorb.png)`

![](Figures/iris.png)

<br><br>

#### To have more control over display options, we can use a code chunk:

```{r iris_image, out.width = "100px"}
knitr::include_graphics('Figures/iris.png')
```

<br><br>

#### Alternatively, we could use HTML to embed the image.

`<img src="Figures/iris.png" alt="Iris" style="align:right;width:604px;height:128px;">`

<img src="Figures/iris.png" alt="Iris" style="align:right;width:604px;height:128px;">
<br><br>

***

# Some Other R Markdown Features

## Displaying Math

We can easily display mathematical symbols and equations using $\LaTeX$ style formating:

* Here's an example of an inline equation: $x^2 + y^2 = z^2$.

* We can use many nice $\LaTeX$ options such as Greek letters ($\phi, \alpha, \Sigma$) and math notation ($\int, \infty, \|\cdot\|, \nabla$)

* We can also use display math formats: 

$$\sum_{i = 0}^{\infty} \frac{\lambda^x e^{-\lambda}}{x!} = 1$$

***

<br><br>

## Inline Code

Similar to math, code can be included inline as well: Two plus two equals `r 2 + 2`.

* The language must be specified for the code to be executed,

  + Displayed only: `levels(iris$Species)`
  
  + Evaluated: `r levels(iris$Species)`
  
  
***

<br><br>

## Displaying Data

#### Display data as it would be printed from the `R` console:

```{r display_raw}
head(iris)
```

#### Display data in Table format

##### Using `knitr` and `kable`

```{r knitr_table}
knitr::kable(
  head(iris), 
  caption = "A knitr kable."
)
```

##### Using `xtable` package

```{r results = "asis"}
print(xtable::xtable(head(iris), caption = "Table with xtable"), type = "html", html.table.attributes = "border=1")
```

##### Using `stargazer` package

```{r results = "asis"}
stargazer::stargazer(head(iris), type = "html", title = "Stargazer Table")
```

***

<br><br>

## Other Tips and Tools

* Can choose a theme for the page style or can provide your own css file

* Can use inline <strong>HTML</strong> to <i>format text</i> and include things like links: <a href="https://http://rmarkdown.rstudio.com/rmarkdown_websites.html#overview">More on Building Websites with R Markdown</a>

* The `bookdown` package can be used to typeset a book using R Markdown.

* Presentations can be created in R Markdown as well using the output document types: `ioslides_presentation`, `slidy_presentation`, `beamer_presentation`, or `xaringan`