---
title: "Tutorial 4: Introduction to R Markdown"
output: github_document
---

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

This tutorial will introduce the basics of R Markdown. R Markdown is an extension in RStudio which allows you to create word documents, pdfs and presentations within RStudio. It allows you to seamlessly incorporate data analysis and visualistions created in R into a professionally looking report.

It allows you to create a report template which can be easily updated in response to changes in data by simply altering a single line of code.  

## Getting Started

-   To create your first R Markdown document open up RStudio.

- If you haven't already installed markdown you will first have to run 
```{r, eval=FALSE}
install.packages("rmarkdown")`
```


-   Once the R Markdown package is installed click on **File > New File > R Markdown...**

-   The following box will appear:

![](images/r_markdown_open.png)

-   Enter **First R Markdown Document** into the title box and your name in the author box.

-   Click ok.

### The YAML Header

-   At the top of the R Markdown document you just created you will notice the following lines of code:

```{r, eval=FALSE}
---
title: "HTML_example"
author: "Jane Doe"
date: "3/25/2019"
output: html_document
---
```

-   This is known as the YAML header.

-   The `output: html_document` line of code states that the output type of the document is html. This line can be changed to `pdf_document`, `word_document` or `ioslides_presentation` etc depending on the document output preference.

### Global Settings

-   You will also notice the following code chunk:

<!-- ![](images/global%20chunk.png) -->


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


-   The `knitr::opts_chunk$set()` function means that any format specified between the brackets will automatically apply to all code chunks in the document. Any defaults set can be overidden in the individual code chunks in the document.

### Including Code in an R Markdown Document

-   The R Markdown Document you have created already contains a brief description of how to include code in an R Markdown Document.

-   Note that each code chunk is given a name. The name for the individual code chunks can be found between the curly brackets and after the letter `r`.

-   It is possible to write code in languages other than R within R Markdown, for example Python and SQL.

-   To insert a new code chunk select the following button which can be found at the top of your R Script box: ![](images/insert_r_code.png)


**Exercise 1: Read through the writing code information already contained in the R Markdown document. How would you ensure that only the output of a code chunk appeared in the final document and not the code chunk itself? Edit the global options so that code chunks are automatically hidden in the final document.**

### Knitting the R Markdown Document

-   To generate a report from an R Markdown file you simply need to click the knit button at the top of the R Script box: ![](images/knit.png)

-   A preview of the document will automatically open which shows how the final document looks.

-   If you decide you want to make changes to the document you can then do so in RStudio and the final document will be updated when the knit button is selected again.

-   The actual document created can be found in the working directory where the file is saved.


**Exercise 2: Knit First R Markdown Document as a html document.**



# Markdown Syntax 

- Text in markdown can be formatted using certain markdown commands.
- For presentations each sub-section is a new slide.

<br>


```markdown

*italic text*  

**bold text**  



# Section heading  

## Sub-section heading

```

*italic text*  

**bold text**  

<br>

# Section heading  

## Sub-section heading

<br>


### Lists

- Lists are created as follows.

<br>

```markdown

Unordered List:

* Item 1
* Item 2
    - Item 2a
    - Item 2b

Ordered List:

1. Item 1
1. Item 2
    i. Item 3a
    i. Item 3b
    
```
<br>

Unordered List:

* Item 1
* Item 2
    + Item 2a
    - Item 2b

Ordered List:

1. Item 1
2. Item 2
    i. Item 2a
    i. Item 2b


**Exercise 3: Add an ordered list to your document.**

<br>

### Figures

- Figures can be added using.

```markdown
![](images/Edge_Logo.png)
```
or for html files
```markdown
<img src="images/Edge_Logo.png" alt="logo" height="100">
```

<br>

![](images/Edge_Logo.png)
<br>
<div class="centered">
<img src="images/Edge_Logo.png" alt="logo" height="80">

### Links

URL hyperlinks can be added using
```markdown
[click here](www.google.com)
```
[click here](www.google.com)

## References 

### Cheatsheets
  - This [R Markdown cheatsheet](https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf) is a concise document outlining the basics of R Markdown
  - The [R Markdown reference](https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf) document is a more detailed version of the cheatsheet.
    
### In-depth references   
  - For more tips on getting started with R Markdown, the [R Markdown site](https://rmarkdown.rstudio.com) contains easy to follow tutorials on the basic use of the package.  
  - If you want an in-depth comprehensive look at R Markdown then try reading [R Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/) which is a free online book.
    
    
    
    

<br>
<br>

## Knitting PDFs (optional)

- In order to generate PDF's, you will need to have to install LaTeX.
- If you have not heard of or installed LaTeX before, it is recommended that you install TinyTeX (https://yihui.name/tinytex/):

```{r , eval=FALSE}
install.packages("tinytex")
tinytex::install_tinytex()  # install TinyTeX
```

The output type in the YAML header can then be changed to `pdf_document`. Alternatively, you can select pdf from the dropdown box beside the Knit button.

```{r, eval=FALSE}
---
title: "Untitled"
author: "Aidan Boland"
date: "3/28/2019"
output: pdf_document
---
```