Essentials 04: R Markdown Recap

# Essentials 04: R Markdown Recap

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# Setup & Suggested Workflow

- Create one R project file for all seminR sessions, create an r_docs & data folder & save all Rmds and datasets to these folders respectively

- Make a cheat sheet of useful functions and .orange[#] comment their meaning and usage as you go through seminRs, practicals, tutorials etc.

- Use the [Padlet](https://uofsussex.padlet.org/de84/seminrs) to suggest seminR topics

### .orange[Task]: 
Open/create your seminRs project

#### .orange[Reminder]:

File > New Project... New Directory > New Project > *Give your project a name & location*

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# Session Objectives

### Writing Pretty Reports with R Markdown

- Recap R Markdown Basics  
- YAML  
- Code Chunks  
- Formatting Text
- Good Practice & Common Errors

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# R Markdown

- Package for executing code & writing reports

- Makes our work reproducible & dynamic

- One file that renders to multiple file types (html, doc, pdf..)

## 3 Main Components

- YAML (metadata)

- Code (chunks or inline)

- Text

To create our nicely formatted report, we use the Knit button 
<img src="./images/knit.png" width="7%" />
 which renders our document based on the YAML & includes any code/text in the output

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# YAML

- First part of an Rmd, enclosed by ---  
- Contains metadata about your document, i.e. title, author, output type...
- Most common cause of errors are forgotten "" or incorrect indentation

<br>

### .orange[Task]:

Open a new Rmd file

Change the YAML so that

1. The author is your name
1. The title is "Essentials 04: Writing Pretty Reports with R Markdown"

Save this file to the r_docs folder of your seminRs project (shortcut: ctrl/cmd + s)

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# Code

Code Chunks

Inline Code (today's level up topic)

### Demo

- Chunk structure

- The 'setup' chunk

- How to insert, name & run chunks

- Other ways to run chunks

- Chunk options

- The Knit button

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# Code

### .orange[Tasks]:

- Delete out the unnecessary code chunks (i.e keep 'setup')  
- Load tidyverse & palmerpenguins in the setup chunk  
- Insert a chunk, rename it to be called data  
- Copy the below code into your data chunk & knit your doc:

```r
data <- palmerpenguins::penguins
```

- Change the chunk options so the data chunk is not included in the knitted doc & knit again  
- Insert a chunk, rename it to be called plot  
- Copy the below code into your plot chunk & knit your doc:

```r
plot(data$body_mass_g)
```

- Change the chunk options so that the code from the plot chunk is not shown & knit again

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# Formatting Text

We have to 'mark up' our text

- Headings specified by #

- Emphasis (bold/italic) by enclosing in 1 or 2 * or _

- For new paragraphs/lines end the line with two spaces

- For lists, use numbers or hyphens for each line (remember to double space)

- Superscript by enclosing in ^, subscript by enclosing in ~

- Equations enclosed by $

If you're super confused with formatting, check out the .italic[Visual Editor] in RStudio for a MS Word-like interface or use the R Markdown [cheat sheet](https://rmarkdown.rstudio.com/lesson-15.html)

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# Formatting Text

Try out your formatting skills by downloading the [R Markdown file](https://and.netlify.app/seminr/04/essentials/essentials_04.Rmd)

.bold.orange[Task]: Edit the extract from Field et al. (2019) to match the one below when it is knitted

</p>

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# Top Tips

### Good Practice (IMO)

- Use # comments in your code chunks for future reference/to aid readability  
- Keep your code chunks nice & tidy  
- Break down super long code chunks into smaller chunks  
- Relatedly, don't use one code chunk per line of code  
- When naming code chunks, avoid spaces (use - instead)  
- Give your chunks useful names to help organise your analyses easier  
- For assignments, set your global chunk options to echo = F to hide code by default   
- Search the R Markdown cheat sheet for additional options

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# Top Tips

### Most Common Mistakes & Errors

- Using install.packages() in a chunk  
- Using View() in a chunk  
- Duplicate code chunk labels  
- Forgetting an empty line above a heading #  
- Forgetting two spaces at the end of a line (e.g. lists, new paragraphs)  
- Incorrect indentation in the YAML

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