The Reproducibility Crisis

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# The Reproducibility Crisis

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# The "Reproducibility Crisis"

*Note: It's not just Psychology! Neuroscience, Political Science, Public Health, etc... Nearly every scientific discipline has issues!*

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# The "Reproducibility Crisis"

How did the authors actually do their analyses?
  - Did they transform their variables? If so, how?
  - How did they handle missing data?
  - Did they do what they said they were going to do in the Methods section of the paper?
  
Can we check that they did everything correctly? 
  - We need to be able to *reproduce* their findings
  - In order to reproduce a figure, you need the data and the code!
    - Code needs to be in a format that **other humans** can read!

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# Make Your Life Prettier

- Format code and text so that it's easier to read
  - Comments in a script are great, but it can get cumbersome
- This is great for homework assignments, showing your research advisor or boss your findings, and publishing code along with your manuscripts!
- Some examples:

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# How do we do this?
To make our code pretty and readable, we're going to use something called **Markdown**. It's a way to take plain text and convert it into a pretty, formatted document like HTML, PDF, or even MS Word.

- Specifically, it's a way to write formatted text without writing full-blown HTML.
  - It is not specific to `R`! Lots of things use Markdown! For example, the [.url[README files on Github like this one]](https://github.com/facebook/react) (scroll down to formatted text). Learning this will help even if you decide to leave academia. 
  - **RMarkdown** is simply Markdown but within `R`. This will, obvs, be our focus.

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# Why use RMarkdown?
...but my script has lots of comments and it's fine, right?

NO!

- .R scripts are monotonous
  - Make a professional document or report
    - Headers
    - Bullet lists
    - **Clearly differentiate between text and code**
    - Link to websites, insert pictures etc. 
  - MUCH easier to read!
  - MUCH easier to reproduce!

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name: check

# Before we begin
You will need the following packages. I'm 95% sure that `R` automatically installs the first two packages when you install `R`. The third package you should have already intalled as part of one of the practice sets. However, please check your Packages tab now -- if you do not have any of these, please install them!

- `rmarkdown`
  - `knitr`
  - `kableExtra`

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# Before we bgin
When you go to `File > New File >` you will see options for RMarkdown & RNotebook.

We are going to work with RNotebook.

- Frankly, they are nearly identical, including having the same file extension (`.Rmd`), so it doesn't matter much tbh
  - It's slightly easier to preview an RNotebook, so we'll stick to that.
  - *I will use RMarkdown and RNotebook interchangably from here on out, because they are seriously that similar!*
  - .small[Those of you coming from Python 🐍, this is the equivalent of a Jupyter notebook]

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name: fwd

# This section
There are 2 sections (in addition to this one) spanning reproducibility with RMarkdown.

1. The first will introduce you to the skeleton of a `.Rmd` document. This is a way to get familiar with the basics.
  
  2. The second will show you all the paramters you can change to make your document even prettier. This is to give you a taste of all of the flexibility available at your fingertips.