Reproducible Reporting with R Markdown

class: title-slide, center, middle

# Reproducible Reporting with R Markdown

---

.footnote[Slide adapted from [R Markdown for Medicine](https://rmd4medicine.netlify.app/) by [Alison Hill](https://alison.rbind.io/project/rmd4medicine/), [CC BY 4.0](https://rmd4medicine.netlify.app/license/)]

# What is R Markdown?

1. An authoring framework for data science.

1. A document format (`.Rmd`).

1. An R package named `rmarkdown`.

1. A file format for making dynamic documents with R.

1. A tool for integrating prose, code, and results.

1. A computational document.

1. Wizardry.

---
# What is R Markdown?

1. ["An authoring framework for data science."](https://rmarkdown.rstudio.com/lesson-1.html) (✔️)

1. [A document format (`.Rmd`).](https://bookdown.org/yihui/rmarkdown/) (✔️)

1. [An R package named `rmarkdown`.](https://rmarkdown.rstudio.com/docs/) (✔️)

1. ["A file format for making dynamic documents with R."](https://rmarkdown.rstudio.com/articles_intro.html) (✔️)

1. ["A tool for integrating text, code, and results."](https://r4ds.had.co.nz/communicate-intro.html) (✔️)

1. ["A computational document."](http://radar.oreilly.com/2011/07/wolframs-computational-documen.html) (✔️)

1. Wizardry. (🧙)

---
# Replication/reproducibility crisis?

<br><br>
.center[
![](https://media.giphy.com/media/11fDMHAzihB8D6/source.gif))
]

---
# How does R Markdown work?

.center[
<img src="images/rmarkdown/Knit-to-html.jpg" width="85%" />
]

---
# How does R Markdown work?

.center[
<img src="images/rmarkdown/doc-live.jpg" width="85%" />
]

---
# What is inside?

.center[
<img src="images/rmarkdown_wizards.png" width="5303" />
]

.footnote[Artwork by [@allison_horst](https://twitter.com/allison_horst)]

---
# What is inside?

.center[
<img src="images/rmarkdown/doc-make.jpg" width="1061" />
]

---
# R Markdown Tutorial

🔗 Click [here](09-rmarkdown_handout.html) to access the tutorial.

---
# General advice

✔️ **Document your document:** use YAML to set up meaningful metadata

✔️ **Style your document:** use YAML to add options to your chosen output format

✔️ **Organize your text:** use markdown headers with `#`

✔️ **Organize your code:** use `knitr` chunk labels

✔️ **Style your text:** use markdown **bold**, _italics_, bullets <i class="fas  fa-list "></i> and lists <i class="fas  fa-list-ol "></i>

✔️ **Style your output:** use `knitr` chunk options

✔️ 🧶 early, 🧶 often

---
class: inverse, center, middle
# Q & A

---
class: inverse, center, middle
# That's a wrap!

## Don't forget to check out [resources](https://uopsych-r-bootcamp-2020.netlify.app/resources/) 💡

![](https://media.giphy.com/media/OZbGrdp7FiDiE/giphy.gif)