Intro_to_RMarkdown.Rmd

---
title: "Intro to R Markdown"
subtitle: "UCI Data Science Initiative"
author: "Dustin Pluta"
date: "May 12, 2017"
output: 
  xaringan::moon_reader:
    seal: yes
    
    nature:
      highlightStyle: github
---

```{r setup, include=FALSE}
options(htmltools.dir.version = FALSE)
```

# Needed Packages

- `dplyr`

- `ggplot2`

- `shiny`

- `flexdashboard`

- `plotly`

- `stargazer`

## Optional Packages

- `biclust`

- `xaringan`

---

# Topics


1. Intro to R Markdown

2. Basic Syntax and Formatting

4. Advanced Formatting

5. Interactive Markdown Documents


---

# Some Resources for R

* [`dplyr` Cheat Sheet](https://www.rstudio.com/wp-content/uploads/2015/02/data-wrangling-cheatsheet.pdf)

* [R Markdown Cheat Sheet](https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf)

* [R Markdown Tutorial](http://www.jacolienvanrij.com/Tutorials/tutorialMarkdown.html)

* [knitr](https://yihui.name/knitr/)

* [Data Carpentry Lessons for R](http://www.datacarpentry.org/R-ecology-lesson/)

* [dplyr Tutorial](http://genomicsclass.github.io/book/pages/dplyr_tutorial.html)

* [Advanced R (by Hadley Wickham)](http://adv-r.had.co.nz/)

* [R for Data Science (by Grolemund and Wickham)](http://r4ds.had.co.nz/)

---

# Intro to R Markdown

* __R Markdown__ is an implementation of the _Markdown_ markup language 

* Markdown is a versatile tool that makes it easy to make readable scientific documents in a variety of formats

* R markdown is actively developed and supported by the RStudio team, which means:

  + RStudio has many tools and features to make R Markdown flexible and easy to use

  + New R Markdown features and packages are frequently released
  
---

# Intro to R Markdown

* __R For Data Science__ on the intent of R Markdown:

_R Markdown files are designed to be used in three ways:_

1. _For communicating to decision makers, who want to focus on the conclusions, not the code behind the analysis._

2. _For collaborating with other data scientists (including future you!), who are interested in both your conclusions, and how you reached them (i.e. the code)._

3. _As an environment in which to do data science, as a modern day lab notebook where you can capture not only what you did, but also what you were thinking._

---

# Getting Started with R Markdown

* R Markdown files end in `.Rmd`

* Create a new R markdown document in RStudio:

  + `File > New File > R Markdown...`
  
.center[<img src="Figures/Open_New_RMarkdown.png" height="400">]
  
---

# Getting Started with R Markdown

.center[<img src="Figures/Open_New_RMarkdown2.png" height="400">]

  
---

# Getting Started with R Markdown

* The default R Markdown template gives some examples of basic R Markdown features

.center[<img src="Figures/Open_New_RMarkdown3.png" height="500">]


---

# Getting Started with R Markdown

.center[<img src="Figures/EDIT1_Open_New_RMarkdown3.png" height="600">]


---

# Getting Started with R Markdown

.center[<img src="Figures/EDIT2_Open_New_RMarkdown3.png" height="600">]


---

# Getting Started with R Markdown

.center[<img src="Figures/EDIT3_Open_New_RMarkdown3.png" height="600">]


---

# Getting Started with R Markdown

.center[<img src="Figures/EDIT4_Open_New_RMarkdown3.png" height="600">]


---

# Getting Started with R Markdown

.center[<img src="Figures/EDIT5_Open_New_RMarkdown3.png" height="600">]


---

# Getting Started with R Markdown

.center[<img src="Figures/EDIT6_Open_New_RMarkdown3.png" height="600">]


---

# Getting Started with R Markdown

.center[<img src="Figures/EDIT7_Open_New_RMarkdown3.png" height="600">]


---

# Getting Started with R Markdown

* Compile or "knit" the R Markdown document to the desired format (either html, pdf, or Word document)

.center[<img src="Figures/EDIT_Open_New_RMarkdown4.png" height="300">]



---

# Getting Started with R Markdown

.center[<img src="Figures/Practice_First_Knit.png" height="500">]

---

# Getting Started with R Markdown

* Let's modify the plot to include a title, and make the points blue.

.center[<img src="Figures/EDIT_Open_New_RMarkdown5.png" height="400">]


---

# Getting Started with R Markdown

```{r pressure}
plot(pressure, main = "Plot Title", pch = 23, col = "blue", bg = "blue")
```

---

# Practice With R Markdown


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

1. R Markdown Basic Example: Shows simple plot with `cars` data set.

2. R Markdown Exercise Set 1: More examples and some exercises to try on the Iris and IMDB data sets.

---

# More R Markdown Features

1. Presentations: beamer, ioslides, slidy, xaringan

2. knitr

3. Blogdown

4. Bookdown

5. Interactive Documents 


---

# Presentations

- You can easily create academic presentations using 4 different formats

    + beamer (pdf)
    
    + ioslides (html)
    
    + slidy (html)
    
    + xaringan (html)
    
.center[<img src="Figures/RMarkdown_Presentation.png" height="300">]


---

# knitr

- R Markdown can make full use of Latex through the `knitr` package

- `knitr` lets you easily display mathematical formulas and other Latex formatting in your Markdown document

- For example, math can be inserted inline like $\alpha^2 + \beta^2 = \gamma^2$ or in display mode:

$$Y = X \beta + \varepsilon$$

$$\int_{\mathbb{R}} \sum_{i = 1}^n \nabla \ell_i d\mu$$

---

# Blogdown

[Making a Website Using Blogdown, Hugo, and GitHub pages](https://proquestionasker.github.io/blog/Making_Site)/

[Example Blogdown Blog: Simply Statistics](https://simplystatistics.org)