The basics

class: title-slide, left, middle
background-image: url("images/renoir.jpg")
background-position: right
background-size: contain
background-color: #0071B8

.pull-left[

# The basics

## R / Medicine 2021

### Alison Hill &#183; RStudio

#### [r3-rmedicine.netlify.app](https://r3-rmedicine.netlify.app)
]

---
class: middle, center

# <i class="fas fa-cloud"></i>

# Go here and log in (free):

https://rstd.io/r3-cloud

---
layout: true

<div class="my-footer"><span>https://rstd.io/r3-cloud</span></div>

---
class: middle, center

# Who we are

.columns[

.left-col[
### Alison Hill

[<svg aria-hidden="true" role="img" viewBox="0 0 496 512" style="height:1em;width:0.97em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg> @apreshill](https://github.com/apreshill)    
[<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"/></svg> @apreshill](https://twitter.com/apreshill)   
[<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M326.612 185.391c59.747 59.809 58.927 155.698.36 214.59-.11.12-.24.25-.36.37l-67.2 67.2c-59.27 59.27-155.699 59.262-214.96 0-59.27-59.26-59.27-155.7 0-214.96l37.106-37.106c9.84-9.84 26.786-3.3 27.294 10.606.648 17.722 3.826 35.527 9.69 52.721 1.986 5.822.567 12.262-3.783 16.612l-13.087 13.087c-28.026 28.026-28.905 73.66-1.155 101.96 28.024 28.579 74.086 28.749 102.325.51l67.2-67.19c28.191-28.191 28.073-73.757 0-101.83-3.701-3.694-7.429-6.564-10.341-8.569a16.037 16.037 0 0 1-6.947-12.606c-.396-10.567 3.348-21.456 11.698-29.806l21.054-21.055c5.521-5.521 14.182-6.199 20.584-1.731a152.482 152.482 0 0 1 20.522 17.197zM467.547 44.449c-59.261-59.262-155.69-59.27-214.96 0l-67.2 67.2c-.12.12-.25.25-.36.37-58.566 58.892-59.387 154.781.36 214.59a152.454 152.454 0 0 0 20.521 17.196c6.402 4.468 15.064 3.789 20.584-1.731l21.054-21.055c8.35-8.35 12.094-19.239 11.698-29.806a16.037 16.037 0 0 0-6.947-12.606c-2.912-2.005-6.64-4.875-10.341-8.569-28.073-28.073-28.191-73.639 0-101.83l67.2-67.19c28.239-28.239 74.3-28.069 102.325.51 27.75 28.3 26.872 73.934-1.155 101.96l-13.087 13.087c-4.35 4.35-5.769 10.79-3.783 16.612 5.864 17.194 9.042 34.999 9.69 52.721.509 13.906 17.454 20.446 27.294 10.606l37.106-37.106c59.271-59.259 59.271-155.699.001-214.959z"/></svg> alison.rbind.io](https://alison.rbind.io)
]

.middle-col[
### Stephan Kadauke

.right-col[
### Paul Villanueva

[<svg aria-hidden="true" role="img" viewBox="0 0 496 512" style="height:1em;width:0.97em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg> @pommevilla](https://github.com/pommevilla)    
[<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"/></svg> @pommevilla](https://twitter.com/pommevilla)  
[<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M326.612 185.391c59.747 59.809 58.927 155.698.36 214.59-.11.12-.24.25-.36.37l-67.2 67.2c-59.27 59.27-155.699 59.262-214.96 0-59.27-59.26-59.27-155.7 0-214.96l37.106-37.106c9.84-9.84 26.786-3.3 27.294 10.606.648 17.722 3.826 35.527 9.69 52.721 1.986 5.822.567 12.262-3.783 16.612l-13.087 13.087c-28.026 28.026-28.905 73.66-1.155 101.96 28.024 28.579 74.086 28.749 102.325.51l67.2-67.19c28.191-28.191 28.073-73.757 0-101.83-3.701-3.694-7.429-6.564-10.341-8.569a16.037 16.037 0 0 1-6.947-12.606c-.396-10.567 3.348-21.456 11.698-29.806l21.054-21.055c5.521-5.521 14.182-6.199 20.584-1.731a152.482 152.482 0 0 1 20.522 17.197zM467.547 44.449c-59.261-59.262-155.69-59.27-214.96 0l-67.2 67.2c-.12.12-.25.25-.36.37-58.566 58.892-59.387 154.781.36 214.59a152.454 152.454 0 0 0 20.521 17.196c6.402 4.468 15.064 3.789 20.584-1.731l21.054-21.055c8.35-8.35 12.094-19.239 11.698-29.806a16.037 16.037 0 0 0-6.947-12.606c-2.912-2.005-6.64-4.875-10.341-8.569-28.073-28.073-28.191-73.639 0-101.83l67.2-67.19c28.239-28.239 74.3-28.069 102.325.51 27.75 28.3 26.872 73.934-1.155 101.96l-13.087 13.087c-4.35 4.35-5.769 10.79-3.783 16.612 5.864 17.194 9.042 34.999 9.69 52.721.509 13.906 17.454 20.446 27.294 10.606l37.106-37.106c59.271-59.259 59.271-155.699.001-214.959z"/></svg> pommevilla.rbind.io](https://pommevilla.rbind.io/)
]
]

---
background-image: url(images/deardata.jpg)
background-size: 50%

.footnote[https://www.dear-data.com/]

---
class: center
background-image: url(https://media.giphy.com/media/11fDMHAzihB8D6/source.gif)

# Reproducibility crisis?

???

We are not here today to solve science or medicine's reproducibility crisis.

What I do think R Markdown can help you with today when you leave here is to tackle two other crises: one I think of as the confidence crisis...

---
class: center
background-image: url(https://media.giphy.com/media/OPZZ6KWJOZ3AA/source.gif)

# Confidence crisis

---
class: center
background-image: url(https://dickbrouwer.com/img/meeting_cheese.png)
background-size: contain

# 🧀 Cheese crisis 🧀

.footnote[https://dickbrouwer.com/blog/a-guide-to-better-meetings/]

---
class: middle, center

# Change your mental model

.pull-left[

### Source &harr; output

]

.pull-right[

### Source &rarr; output

]

---
class: middle

.pull-left[

| Time (PDT)      | Activity                                |
|:----------------|:----------------------------------------|
| 12:30 - 01:20pm | Session 1 (Basics)                      |
| 01:20 - 01:30pm | *Break* ☕           |
| 01:30 - 02:20pm | Session 2 (Authoring)                   |
| 02:20 - 02:30pm | *Break* 🍵              |
| 02:30 - 03:20pm | Session 3 (Projects & Workflows)        |
| 03:20 - 03:30pm | *Break* 🚰    |
| 03:30 - 04:00pm | Wrap-up / Q & A                         |
]

.pull-right[
Format:

+ Live demos / slides
+ Solo activities called "Your Turns" (with timer)
+ No group activities
+ Video on or off
+ Choose your own adventure style

]

---
class: middle, left, inverse
background-image: url(images/01-explore.png)
background-position: right
background-size: contain

# Live demo:

### RStudio Cloud

---
class: your-turn

# Your turn

Open up the file `01-explore.qmd`.

Try to identify these parts in the source:

1. The **metadata**

1. The **text**

1. The **code**

**If this was easy**, try to find all code that produces a *plot*.

_psst...`01-explore-alison-params.qmd` is also there..._

---
class: inverse

# Basic anatomy: source

We look at the source anatomy for `01-explore.qmd` together:

1. The **metadata**

1. The **text**

1. The **code**

---
background-image: url(https://media.giphy.com/media/L2qukNXGjccyuAYd3W/giphy.gif?cid=790b76111a5dd3955457a4d3d0e9af2155a499ed56980b4e&rid=giphy.gif&ct=g)

---
class: inverse, center, middle

# We are using Quarto

---
background-image: url(https://media.giphy.com/media/d3mlPd7WETdWajCg/giphy.gif?cid=790b76116f9fa682cadbdd5172881710096d429f49efc369&rid=giphy.gif&ct=g)

---
class: middle, center, inverse

---
background-image: url(https://media.giphy.com/media/26gs6ASI0ExbUXq0g/giphy.gif?cid=790b7611b5a33442a8ef1fb752428b0364020b5606646756&rid=giphy.gif&ct=g)

---
background-image: url(https://media.giphy.com/media/26Do4GhHgmdCR0Uq4/giphy.gif?cid=790b7611938d81930e55cd8f0b4b88b6dd9d4827d9fca53c&rid=giphy.gif&ct=g)

---
class: middle, center
background-image: url(images/Pandoc.jpg)
background-size: contain
background-position: right
background-color: #fff

.columns[

.left-col[

## What is Quarto?

]
]

---
background-image: url(images/hexes.png)
background-size: contain
background-position: left
class: left, middle
background-color: #fff

.pull-right[
# What is Quarto?

+ A command line interface (CLI) installed at your terminal (not an R package!)
    + <https://quarto.org/docs/getting-started/installation.html>
    
+ Built in RStudio support with a daily version build
    + <https://quarto.org/docs/tools/rstudio.html>
]

---
background-image: url(images/py-alone.png)
background-size: contain

# Why Quarto?

---
class: middle, center
background-image: url(images/py-together.png)
background-size: contain

---
background-image: url(images/quarto-how.png)
background-size: contain
background-position: bottom
class: center, top
background-color: #fff

# How does it work?

---
background-image: url(images/render.png)
class: middle center
background-position: 50% 60%

# Hello, Quarto!

---
class: middle, left, inverse
background-image: url(images/01-explore-html.png)
background-position: right
background-size: contain

# Live demo:

### We render together

---
class: inverse

# Basic anatomy: output

We look at the output anatomy for `01-explore.qmd` together:

1. The **metadata**

1. The **text**

1. The **code**

1. The **output**

---
name: card0
background-image: url(images/card0.png)
background-size: contain

.footnote[https://www.dear-data.com/]

---
name: card1
background-image: url(images/card1.png)
background-size: contain

.footnote[https://www.dear-data.com/]

---
name: card2
background-image: url(images/card2.png)
background-size: contain

.footnote[https://www.dear-data.com/]

---
name: card3
background-image: url(images/card3.png)
background-size: contain

---
background-image: url(images/card4.png)
background-size: contain

---
class: middle, center
background-color: #fff

# What is inside?

![](images/doc-make.jpg)

---
class: inverse, center, middle

# Text

---
class: middle, left, inverse
background-image: url(https://quarto.org/docs/visual-editor/images/visual-editing.png)
background-position: right
background-size: contain

# Live demo:

### Quarto visual editor (Paul V)

https://quarto.org/docs/visual-editor/

---

# <center>Headers</center>

.pull-left[
```markdown
# HEADER 1

## HEADER 2

### HEADER 3

#### HEADER 4

##### HEADER 5

###### HEADER 6
```
]

.pull-right[
# HEADER 1

## HEADER 2

### HEADER 3

#### HEADER 4

##### HEADER 5

###### HEADER 6
]

---

![](images/rmd-nav.png)

---

# <center>Text</center>

.pull-left[
```markdown
Childhood **vaccines**  
are one of the  
_great triumphs_  
of modern medicine. 
```
]

.pull-right[

Childhood **vaccines**  
are one of the  
_great triumphs_  
of modern medicine.

]

---
class: top

# <center>Bulleted Lists</center>

.pull-left[

```markdown
Indeed, parents whose children are  
vaccinated no longer have to worry about  
their child's death or disability from:

- whooping cough, 
- polio, 
- diphtheria, 
- hepatitis, or 
- a host of other infections.
```

]

.pull-right[

Indeed, parents whose children are  
vaccinated no longer have to worry about  
their child's death or disability from:

- whooping cough, 
- polio, 
- diphtheria, 
- hepatitis, or 
- a host of other infections.

]

---
class: top

# <center>Numbered Lists</center>

.pull-left[

```markdown
Vaccines are the most cost-effective  
health care interventions there are.  
We have three new, extremely effective  
vaccines to roll out in developing  
countries:

1. pneumonia
1. rotavirus
1. meningitis A
```

]

.pull-right[

Vaccines are the most cost-effective  
health care interventions there are.  
We have three new, extremely effective  
vaccines to roll out in developing  
countries:

1. pneumonia
1. rotavirus
1. meningitis A

]

---

# <center>Images</center>

.pull-left[
```markdown
Receiving rubella vaccination, Brazil, 2008.
![](http://bit.ly/VaccineBySandraRugio)
```
]

.pull-right[
Receiving rubella vaccination, Brazil, 2008.
![](http://bit.ly/VaccineBySandraRugio)
]

---

# <center>Links</center>

.pull-left[
```markdown
[Photo](https://en.wikipedia.org/wiki/Vaccine)

Receiving rubella vaccination, Brazil, 2008.
![](http://bit.ly/VaccineBySandraRugio)
```
]

.pull-right[
[Photo](https://en.wikipedia.org/wiki/Vaccine)

Receiving rubella vaccination, Brazil, 2008.
![](http://bit.ly/VaccineBySandraRugio)
]

---
class: middle

# Check-in

.pull-left[

How do you add headers in Markdown?

`! Header`

`- Header`

`# Header`

`1. Header`

]

.pull-right[

What about lists? Bulleted? Numbered?

`! Item 1`

`- Item 1`

`# Item 1`

`1. Item 1`

]

---

# Your turn

Find this section:

```markdown
<--TODO: add markdown table of treatment arms here-->
```

Using the visual markdown editor, make this table:

| Arm | Drug   |
|:----|:-------|
| A   | IFL    |
| F   | FOLFOX |
| G   | IROX   |

_psst...markdown on the next slide..._

---

# Your turn

## Markdown versions

.pull-left[
```markdown
| Arm | Drug   |
|:----|:-------|
| A   | IFL    |
| F   | FOLFOX |
| G   | IROX   |
```
]

.pull-right[
```markdown
|Arm|Drug|
|:---|:---|
|A|IFL|
|F|FOLFOX|
|G|IROX|
```
]

Spacing actually doesn't matter - it mainly helps your eyeballs.

---
class: inverse, center, middle

# <i class="fab fa-r-project"></i> code

---

# Code chunks

.pull-left[

````
```{r}
mockdata %>% 
  distinct(arm)
```
````

What is the fate of this chunk?

]

.pull-right[

```r
mockdata %>% 
  distinct(arm)
#> # A tibble: 3 x 1
#>   arm      
#>   <chr>    
#> 1 A: IFL   
#> 2 F: FOLFOX
#> 3 G: IROX
```

]

---

# Code chunks

.pull-left[

````
```{r}
n_sites <- n_distinct(mockdata$site)
```
````

What fate do you predict here?

]

.pull-right[

```r
n_sites <- n_distinct(mockdata$site)
```

]

---

# Code chunks

.pull-left[

````
```{r}
n_sites <- n_distinct(mockdata$site)
n_sites
```
````

]

.pull-right[

```r
n_sites <- n_distinct(mockdata$site)
n_sites
#> [1] 1
```

]

---

# Code chunks

.pull-left[

````
```{r}
ggplot(mockdata, aes(x = arm, 
                     y = n, 
                     fill = arm)) +
  geom_col()
```
````

What about this one?

]

.pull-right[

```r
ggplot(mockdata, aes(x = arm, 
                     y = n, 
                     fill = arm)) +
  geom_col()
```

]

---

# Add chunks

button or

Command (or Cmd) `⌘` + Option (or Alt) `⌥` +  `i` (Mac)

Ctrl + Alt + `i` (Windows/Linux)

---

# Run chunks

.pull-left[
interactively (show button)
]

.pull-right[
whole doc (knit button or run all chunks or )
]

---
class: inverse, center, middle

# Output

---

# Chunk options

.pull-left[

````
```{r}
glimpse(mockdata)
```
````

]

.pull-right[

```r
glimpse(mockdata)
#> Rows: 3
#> Columns: 5
#> $ arm      <chr> "A: IFL", "F: FOLFOX", "G: IROX"
#> $ site     <chr> "Boston", "Boston", "Boston"
#> $ country  <chr> "USA", "USA", "USA"
#> $ n_target <dbl> 34, 34, 34
#> $ n        <dbl> 20, 13, 17
```

]

---

# echo

.pull-left[

````
```{r}
#| echo: FALSE
glimpse(mockdata)
```
````

Same as:

````
```{r echo=FALSE}
glimpse(mockdata)
```
````

]

.pull-right[

```
#> Rows: 3
#> Columns: 5
#> $ arm      <chr> "A: IFL", "F: FOLFOX", "G: IROX"
#> $ site     <chr> "Boston", "Boston", "Boston"
#> $ country  <chr> "USA", "USA", "USA"
#> $ n_target <dbl> 34, 34, 34
#> $ n        <dbl> 20, 13, 17
```

]

---

# eval

.pull-left[

````
```{r}
#| eval: FALSE
glimpse(mockdata)
```
````

Same as:

````
```{r eval=FALSE}
glimpse(mockdata)
```
````

]

.pull-right[

```r
glimpse(mockdata)
```

]

---

# include

.pull-left[

````
```{r}
#| include: FALSE
glimpse(mockdata)
```
````

Same as:

````
```{r include=FALSE}
glimpse(mockdata)
```
````

]

.pull-right[

]

---

# Combining chunk options

.pull-left[

````
```{r}
#| echo: TRUE
#| results: 'hide'
glimpse(mockdata)
```
````

Same as:

````
```{r echo=TRUE, results='hide'}
glimpse(mockdata)
```
````

Careful! The `r` part is the **code engine** (other engines possible)

]

.pull-right[

```r
glimpse(mockdata)
```

]

---

# message / warning

![](https://www.tidyverse.org/images/tidyverse_1.2.0/tidyverse_1-2-0_pkg_load.gif)

---

# message / warning

.pull-left[

````
```{r}
#| message: FALSE
#| warning: FALSE
library(tidyverse)
```
````

]

.pull-right[

```r
library(tidyverse)
```

]

---

# Combining chunk options

.pull-left[

````
```{r}
#| echo: TRUE
#| results: 'hide'
glimpse(mockdata)
```
````

+ Place after a hash-pipe <br>`#|`

+ Stack multiples

+ Uses colon `:`

]

.pull-right[
````
```{r echo=TRUE, results='hide'}
glimpse(mockdata)
```
````

+ Place between curly braces<br>`{r option=value}`

+ List multiples separated by commas<br>`{r option1=value, option2=value}`

+ Uses equal sign `=`

]

---

.left-column[
# Default options
]

.right-column[

```r
str(knitr::opts_chunk$get())
#> List of 53
#>  $ eval         : logi TRUE
#>  $ echo         : logi TRUE
#>  $ results      : chr "markup"
#>  $ tidy         : logi FALSE
#>  $ tidy.opts    : NULL
#>  $ collapse     : logi TRUE
#>  $ prompt       : logi FALSE
#>  $ comment      : chr "#>"
#>  $ highlight    : logi TRUE
#>  $ strip.white  : logi TRUE
#>  $ size         : chr "normalsize"
#>  $ background   : chr "#F7F7F7"
#>  $ cache        : logi FALSE
#>  $ cache.path   : chr "01-basics_cache/html/"
#>  $ cache.vars   : NULL
#>  $ cache.lazy   : logi TRUE
#>  $ dependson    : NULL
#>  $ autodep      : logi FALSE
#>  $ cache.rebuild: logi FALSE
#>  $ fig.keep     : chr "high"
#>  $ fig.show     : chr "asis"
#>  $ fig.align    : chr "default"
#>  $ fig.path     : chr "01-basics_files/figure-html/"
#>  $ dev          : chr "png"
#>  $ dev.args     : NULL
#>  $ dpi          : num 72
#>  $ fig.ext      : NULL
#>  $ fig.width    : num 7
#>  $ fig.height   : num 7
#>  $ fig.env      : chr "figure"
#>  $ fig.cap      : NULL
#>  $ fig.scap     : NULL
#>  $ fig.lp       : chr "fig:"
#>  $ fig.subcap   : NULL
#>  $ fig.pos      : chr ""
#>  $ out.width    : NULL
#>  $ out.height   : NULL
#>  $ out.extra    : NULL
#>  $ fig.retina   : num 1
#>  $ external     : logi TRUE
#>  $ sanitize     : logi FALSE
#>  $ interval     : num 1
#>  $ aniopts      : chr "controls,loop"
#>  $ warning      : logi TRUE
#>  $ error        : logi FALSE
#>  $ message      : logi TRUE
#>  $ render       : NULL
#>  $ ref.label    : NULL
#>  $ child        : NULL
#>  $ engine       : chr "R"
#>  $ split        : logi FALSE
#>  $ include      : logi TRUE
#>  $ purl         : logi TRUE
```

]

---
class: middle, center, inverse

# Metadata

---

# metadata: YAML

.pull-left[

_"YAML Ain't Markup Language"_

```yaml
---
key: value
---
```

]

.pull-right[

]

---
class: middle, center

# Execution options

---

# Execution options

Set globally for the whole document.

.pull-left[

```.yaml
---
execute:
  echo: false
  messages: false
  warning: false
  out.width: "100%" 
---
```

]

.pull-right[

+ Use `execute` in your YAML to cement

+ You can (and should) use individual chunk options too

+ No need for a `knitr` setup chunk!

]

---
class: middle, center

# Output formats

---
class: your-turn

# Your turn

## Use a different built-in format

Inside `01-explore.qmd`, edit the YAML to include Word `docx`:

```yaml
---
format:
  docx: default
  html: default
---
```

Render, and follow the steps to preview it.

Note: Our version of RStudio here is not updating the Render button properly. This *does* happen on desktop!

---
class: middle, center

# Output options

---

# Save output options in your YAML

.pull-left[

```.yaml
---
title: 'Explore mockstudy data'
author: Paul Villanueva
format: html
---
```

```.yaml
---
title: 'Explore mockstudy data'
author: Paul Villanueva
format: 
  html:
    toc: true
---
```

]

.pull-right[

]
---
class: middle

# Check-in

.pull-left[
How do you use a **single** format?

(a)
```yaml
format: html
```
(b)
```yaml
output: html_document
```

]

.pull-right[
How do you set **options** for a format?

(a)
```yaml
format: 
  html: 
    toc: true
```

(b)
```yaml
output: 
  html_document(toc=true)
```

]

---
class: middle

# Check-in

.pull-left[
How do you add another output **format**?

(a)
```yaml
format: 
  html: default
  docx: default
```
(b)
```
output: 
  html_document()
  word_document()
```

]

.pull-right[
How do you add output **options** to one format?

(a)
```yaml
format: 
  html: 
    toc: true
  docx: default
```
(b)
```
output: 
  html_document(toc=true)
  word_document(default)
```

]

---

# Your turn: Edit your YAML

Move the `html` format to the top (above `docx`), then use the linked Quarto docs to:

1. Add a [table of contents](https://quarto.org/docs/output-formats/html-basics.html#table-of-contents)

1. Add [commenting](https://quarto.org/docs/output-formats/html-basics.html#commenting)

1. Add a [theme](https://quarto.org/docs/output-formats/html-themes.html)

1. Add [code tools](https://quarto.org/docs/output-formats/html-code.html#code-tools)

**Render** to HTML to see the output.

**If this was all easy**, try adding [code folding](https://quarto.org/docs/output-formats/html-code.html#folding-code) (*hint: make sure `echo: true` *)

_psst...answers on the next slide..._

---

# Answers

```yaml
---
execute:
  echo: true
  messages: false
  warning: false
format: 
  html:
    theme: "lux"
    toc: true
    code-fold: true
    code-summary: "Show the code"
    code-tools: true
---
```

---

# What is hard about YAML?

.pull-left[
![](https://media.giphy.com/media/Nt2cPxzpKhbCE/giphy.gif)
]

.pull-right[
+ Indentations matter

+ Rarely informative error messages

+ Knowing which output options are relevant for different formats (i.e., Word, PDF, HTML, etc.)

+ Easy to forget the right `key`

+ Easy to forget the possible `values` for a given `key`
]

---
class: your-turn

# Your turn:New data dump! 📰

Data from more sites just came in &mdash; we now have data for Boston, Seattle, and Denver.

1. Replace `mockboston` in the file `mockbsd`.

1. **Render** to HTML. Do you see data for all 3 sites?

1. Clean up the chunks (split, combine, use options as you see fit)

1. Use the RStudio outline pane; rejoice!

**If this was easy**, try to use a parameter for the data file.

_psst...`01-explore-alison-params.qmd` is still there..._

---
class: middle, center

# Take-aways

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

✔️ **Style your document:** use YAML to add formats and options

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

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

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

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

Render early, render often

---
class: middle, center

# ⏱

# Time for a break!