Meet the Toolkit

# Meet the Toolkit
### Yue Jiang
### Duke University

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## Reproducible data analysis

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## Reproducibility checklist

**Near-term goals:**

- Are the tables and figures reproducible from the code and data?

- Does the code actually do what you think it does?

- In addition to what was done, is it clear **why** it was done?

<br>

**Long-term goals:**

- Can the code be used for other data?

- Can you extend the code to do other things?
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## Toolkit

- **Scriptability** `$\rightarrow$` R

- **Literate programming** (code, narrative, output in one place) `$\rightarrow$` 
R Markdown

- **Version control** `$\rightarrow$` Git / GitHub

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# The toolkit in detail

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## What is R and RStudio?

- R is a statistical programming language

- RStudio is a convenient interface for R (an integrated development 
environment, IDE)

- At its simplest:<sup>*</sup>
    - R is like a car’s engine
    - RStudio is like a car’s dashboard

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## R essentials (a short list)

- **Functions** are (most often) verbs, followed by what they will be applied to 
in parentheses:

```r
do_this(to_this)
do_that(to_this, to_that, with_those)
```

- **Columns** (variables) in data frames are accessed with `$`:

```r
dataframe$var_name
```

- **Packages** are installed with the `install.packages` function and loaded 
with the `library` function, once per session:

```r
install.packages("package_name")
library(package_name)
```

---

## tidyverse

- The [tidyverse](https://www.tidyverse.org/) is an **opinionated** collection 
of R packages designed for data science.

- All packages share an underlying philosophy and a common grammar.

.footnote[
Image from [Teaching in the Tidyverse 2020](https://education.rstudio.com/blog/2020/07/teaching-the-tidyverse-in-2020-part-1-getting-started/)
]

---

## R Markdown

What is R Markdown?

- Fully reproducible reports -- the analysis is run from the beginning each time 
you knit

- [Markdown cheat sheet](https://github.com/rstudio/cheatsheets/raw/master/rmarkdown-2.0.pdf)

- Code goes in chunks, defined by three backticks, narrative goes outside of 
chunks

- **Remember**: the workspace of the R Markdown document is *separate* from the 
Console

How will we use R Markdown?

- Every assignment / lab / project / etc. is an R Markdown document

- You'll always have a template R Markdown document to start with

- The amount of scaffolding in the template will decrease over the semester

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## Why do we need version control?

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## What is versioning?

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## Git and GitHub

- **Git** is a version control system -- like “Track Changes” features from 
Microsoft Word.

- **GitHub** is the home for your Git-based projects on the internet (like 
DropBox but much better).

- There are a lot of Git commands and very few people know them all. 99% of the 
time you will use git to add, commit, push, and pull.

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## Git and GitHub tips

- We will be doing git things and interfacing with GitHub through RStudio

- If you Google for help, skip any methods for using git through the command 
line.

- There is a great resource for working with git and R: 
[happygitwithr.com](http://happygitwithr.com/). Some of the content in there is 
beyond the scope of this course, but it's a good place to look for help.

---

## Recap

Can you answer these questions?

- What is a reproducible data analysis, and why is it important?
- What is version control, and why is it important?
- What is R vs. RStudio? 
- What is git vs. GitHub?

---

## The Flint Water Crisis

The Flint Water Crisis was a public health emergency that started in 2014. Before 
class, please read the short article linked
[here](https://www2.stat.duke.edu/courses/Fall20/sta199.001/reading/flint-water-story.pdf).

Keep the following things in mind from the article:

- The "action" level for lead is 15 parts per billion (ppb)
- The MDEQ recommended flushing of pipes for at least five minutes

---

## Integrating RStudio with GitHub

Each assignment, application exercise, and lab in this course will have an 
associated link used to create a private **repository** on the class 
organization page. Today's link is given at 
[https://classroom.github.com/a/qPa2wG39](https://classroom.github.com/a/qPa2wG39).

In class, we will use R Markdown to make a reproducible report regarding the 
Flint Water Crisis.