index.Rmd

---
title: "Fundamentals of RMarkdown"
author: "Mike Frank & Chris Hartgerink"
date: "July 31st, 2017"
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bibliography: library.bib
---

## Workshop

1. Short intro to Markdown (this!)
2. A document you can work through to get started
3. Exercises along the way where we'll highlight how to make useful documents (e.g. APA manuscript)
4. No need to stay until end if you feel you've got what you wanted

## Learning goals

By the end of this workshop you should:

* Know what Markdown is and how the syntax works, 
* See how to integrate code and data with RMarkdown, 
* Understand the different output formats from RMarkdown and how to generate them
* Know about generating APA format files with [`papaja`](https://github.com/crsh/papaja) and bibtex.

## RMarkdown = R + Markdown

1. It combines the magic of R with the simplicity of Markdown documents
1. The purpose: write your manuscripts and automatically insert results!
1. Use cases (amongst others):
  * prevent rounding errors
  * promote computational reproducibility
  * encourage error correction by minimizing manual work

## The Markdown

- Markdown is the simplest document language!
- Open standard, convertable into `.tex`, `.docx`, `.html`, `.pdf`, etc
- You can [learn Markdown in five (!) minutes](https://learnxinyminutes.com/docs/markdown/)
- Despite being simple, very powerful and used on many web platforms

## Basic Markdown: headings

- `# Header 1` creates a heading of the first level
- `## Header 2` creates a heading of the _second_ level
- `### Header 3` ...
- etc

## Basic Markdown: letter styles

- `**bold**` creates **bold**
- `*italic*` creates *italic*
- `***bold and italic!***` creates ***bold and italic!***

## The R

- If you're here, you probably know R
- Programming language for statistics
- Packages to add functionality
- Everything open-source!

## Combining R and Rmarkdown

- Can write text, include code
- We can include both code and its outputs, or just one of the two
- "Literate programming": mix code and explanation so that it's easier to figure out what's going on.

## Example code chunk

```{r}
x <- rnorm(100, 50, 20)
y <- rnorm(143, 51, 20)

t.test(x, y)
```

## Example in line

1. However, we can also evaluate code in text, and replace text with output
1. For example, let's round $\pi$ to four decimal places, using the code `round(pi, 4)`
  * `r round(pi, 4)`

<!-- ## RMarkdown is more powerful -->

<!-- - It's not just about individual results.  -->
<!-- - Ensures data preparation, analysis code is IN the manuscript -->
<!-- - Plus: Don't make all those tables and figures manually! :-) -->

## Output formats

- HTML - easy to share results on the web 
- PDF - for manuscripts/reports (requires installing `latex`)
- Word - for editing with non-R collaborators, journals

## Templates

- Nicely formatted handouts / reports
- APA manuscripts using `papaja` (we'll get into this in depth)
- Specialized styles like PNAS or Cognitive Science
- Don't waste time reformatting - just change the template

## RMarkdown presentations

- If you want to go overboard, you can render slides from code too
- This is not always perfect, but it's great for course notes, especially teaching stats.
- This presentation also written in Rmarkdown!

## Workshop

Work through the handout accompanying these slides, which you can find at [http://bit.ly/rmarkdown-pdf](https://bit.ly/rmarkdown-pdf) and [http://bit.ly/rmarkdown-html](https://bit.ly/rmarkdown-html)