slides

Creating a Quarto Document I

File -> New File -> Quarto Document...

Outputs:
- Document (what you’ll use for most things)
- Presentation (for making slides in various formats)
- Interactive (an html and R based web app, advanced)

Creating a Quarto Document I

html: renders a webpage, viewable in any browser
- default, easiest to produce and share
- can have interactive elements (gifs, animations, web apps)
- requires internet connection to host and share (you can view offline)
pdf: renders a PDF document
- most common document format around
- requires LaTeX distribution to render (more on that soon)
word: create a Micosoft Word document
- …if you must

Structure of a Quarto Document

Entire document is written in a single file with three types of content:

YAML header for metadata

---
title: "Title"
format: html
---

Text of the document written with markdown

# Header 1
**Bold** and *italic* text.

R chunks for data analysis, plots, figures, tables, statistics, as necessary

2+2

[1] 4

YAML Header I

Top of a document contains the YAML¹ separated by three dashes --- above and below
Contains the metadata of the document, such as:

---
title: "My Document"
author: "Ryan Safner"
date: "`r Sys.Date()`" # here I'm using R code to generate today's date!
format: html
---

format must be specified, everything else can be left blank, and other options can be added as necessary
In most cases, you can safely ignore other things in the yaml until you are ready

YAML Header Example I

Example from these slides

---
format:
  revealjs:
    theme: [default, custom.scss]
    logo: "../images/metrics_hex.png"
    footer: "[ECON 480 — Econometrics](https://metricsF22.classes.ryansafner.com)"
    height: 900
    width: 1600
    #df-print: paged
    slide-number: c
overview: true
execute:
  echo: false
  warning: false
  freeze: auto
---

YAML Header Example II

Example from one of my papers:

---
title: Distributing Patronage^[I would like to thank the Board of Associates of Hood College...]
subtitle: Intellectual Property in the Transition from Natural State to Open Access Order
date: \today
author: 
- Ryan Safner^[Hood College, Department of Economics and Business Administration; safner@hood.edu]

abstract: |
  | "This paper explores the emergence of the modern forms of copyright and patent in ...
  | *JEL Classification:* O30, O43, N43
  | *Keywords:* Copyright, intellectual property, economic history, freedom of the press, economic development

bibliography: patronage.bib
geometry: margin = 1in
fontsize: 12pt
mainfont: Fira Sans Condensed
output: 
  pdf_document:
    latex_engine: xelatex
    number_sections: true
    fig_caption: yes

header-includes:
    - \usepackage{booktabs}
---

R Chunks

You can create a “chunk” of R code with three backticks¹ above and below your code
After the first pair of backticks, signify the language of the code² inside braces, e.g:

Input

```{r}
2+2 # code goes here!
```

Output

[1] 4

R Chunks

Input

```{r}
gapminder %>%
  head()
```

Output

# A tibble: 6 × 6
  country     continent  year lifeExp      pop gdpPercap
  <fct>       <fct>     <int>   <dbl>    <int>     <dbl>
1 Afghanistan Asia       1952    28.8  8425333      779.
2 Afghanistan Asia       1957    30.3  9240934      821.
3 Afghanistan Asia       1962    32.0 10267083      853.
4 Afghanistan Asia       1967    34.0 11537966      836.
5 Afghanistan Asia       1972    36.1 13079460      740.
6 Afghanistan Asia       1977    38.4 14880372      786.

R Chunks

Input

```{r}
library("ggplot2") # load ggplot2
ggplot(data = mpg)+
  aes(x = displ,
      y = hwy)+
  geom_point(aes(color = class))
```

Output

R Chunk Options

Chunks can have options with the “hash pipe” #| at the top of the chunk

#| label: my_chunk_title # give chunk a name
#| eval: true # run the code?
#| echo: true # display code?
#| warning: true # display warnings?
#| message: false # display messages?
#| fig.width: 6 # width for figures

In R Markdown (the predecessor to Quarto…that I know better), you put options inside the braces at the top of a chunk. This is still valid in Quarto:

```{r my_chunk_title, eval = T, echo = F, warning = F, message = F, fig.width = 6}
```

Global Chunk Options

You can set default options for all chunks in the YAML header:

execute:
  echo: false # hide all input code
  warning: false # hide all output warnings
  message: false # hide all output messages

Learn more here and here

R Inline Code

If you just want to display some code (or at least format it like code) in the middle of a sentence, place between a single backtick on either side.
- e.g. if I mention `tidyverse` or `gapminder`, it formats the text as in-line code.
To actually execute R code to output something in the middle of a sentence, put r as the first character inside the backticks, and then run the actual code such as pi is equal to 3.1415927.

Input

pi is equal to `r pi`.

Output

pi is equal to 3.1415927.

Or Like This

Input

The average GDP per capita is ` r dollar(mean(gapminder$gdpPercap)) ` with a standard deviation of ` r dollar(sd(gapminder$gdpPercap)) `.

Output

The average GDP per capita is $7,215.33 with a standard deviation of $9,857.45.

Writing Text with Markdown: Formatting

Markdown is a lightweight markup language geared towards HTML (i.e. the internet)
- Markup languages used to add commands about how to display plain text

Markdown Syntax	Output
`italics and bold`	italics and bold
`superscript^2^ / subscript~2~`	superscript² / subscript₂
`~~strikethrough~~`	~~strikethrough~~
`verbatim code`	`verbatim code`

Comment your document with  (will not print in output; this comes from html)

Writing Text with Markdown: Lists

Markdown Syntax	Output
`* unordered list + sub-item 1 + sub-item 2 - sub-sub-item 1`	unordered list sub-item 1 sub-item 2 sub-sub-item 1
`* item 2 Continued (indent 4 spaces)`	item 2 Continued (indent 4 spaces)
`1. ordered list 2. item 2 i) sub-item 1 A. sub-sub-item 1`	ordered list item 2 sub-item 1 sub-sub-item 1

Writing Text with Markdown: Headings

Markdown Syntax	Output
`# Header 1`	Header 1
`## Header 2`	Header 2
`### Header 3`	Header 3
`#### Header 4`	Header 4
`##### Header 5`	Header 5
`###### Header 6`	Header 6

Writing Text with Markdown: Links

Markdown

You can embed
[named hyperlinks](https://metricsF22.classes.ryansafner.com/),
direct urls like <https://metricsF22.classes.ryansafner.com/>,
and links to 
[other places — like the previous slide](#writing-text-with-markdown-headings)
in the document.

Output

You can embed named hyperlinks, direct urls like https://metricsF22.classes.ryansafner.com/, and links to other places — like the previous slide in the document.

Writing Text with Markdown: Images

Markdown

![Caption: tidyverse](images/tidyverse1.png)

![](https://dplyr.tidyverse.org/logo.png)

Output

dplyr logo

Read the Quarto Documentation on figures for more.

Writing Text with Markdown: Making Tables

Markdown

| Right | Left | Default | Center |
|------:|:-----|---------|:------:|
|   12  |  12  |    12   |    12  |
|  123  |  123 |   123   |   123  |
|    1  |    1 |     1   |     1  |

: Table Example {tbl-colwidths="[25,25,25,25]"}

Output

Table Example
Right	Left	Default	Center
12	12	12	12
123	123	123	123
1	1	1	1

See the Quarto Documentation for more help on tables

Writing Text with Markdown: Printing Tables

Sometimes we want to print tables from our data
The kableExtra package is great for this see Documentation

library(kableExtra)
mtcars %>%
  head() %>%
  kbl()

	mpg	cyl	disp	hp	drat	wt	qsec	vs	am	gear	carb
Mazda RX4	21.0	6	160	110	3.90	2.620	16.46	0	1	4	4
Mazda RX4 Wag	21.0	6	160	110	3.90	2.875	17.02	0	1	4	4
Datsun 710	22.8	4	108	93	3.85	2.320	18.61	1	1	4	1
Hornet 4 Drive	21.4	6	258	110	3.08	3.215	19.44	1	0	3	1
Hornet Sportabout	18.7	8	360	175	3.15	3.440	17.02	0	0	3	2
Valiant	18.1	6	225	105	2.76	3.460	20.22	1	0	3	1

Writing Text with Markdown: Printing Tables

Sometimes we want to print tables from our data
The kableExtra package is great for this see Documentation

library(kableExtra)
mtcars %>%
  head() %>%
  kbl()

	mpg	cyl	disp	hp	drat	wt	qsec	vs	am	gear	carb
Mazda RX4	21.0	6	160	110	3.90	2.620	16.46	0	1	4	4
Mazda RX4 Wag	21.0	6	160	110	3.90	2.875	17.02	0	1	4	4
Datsun 710	22.8	4	108	93	3.85	2.320	18.61	1	1	4	1
Hornet 4 Drive	21.4	6	258	110	3.08	3.215	19.44	1	0	3	1
Hornet Sportabout	18.7	8	360	175	3.15	3.440	17.02	0	0	3	2
Valiant	18.1	6	225	105	2.76	3.460	20.22	1	0	3	1

Writing Text with Markdown: Printing Tables

mtcars %>%
  head() %>%
  rmarkdown::paged_table()

Writing Math

Add beautifully-formatted math with the $ tag before and after the math, two $$ before/after for a centered equation

In-line math example: $1^2=\frac{\sqrt{16}}{4}$ produces in my text

Centered-equation example:

Input

$$ \hat{\beta_1}=\frac{\displaystyle \sum_{i=1}^n (X_i-\bar{X})(Y_i-\bar{Y})}{\displaystyle \sum_{i=1}^n (X_i-\bar{X})^2} $$

Output

Writing Math

Math uses a (much older) language called , used by mathematicians, economists, and others to write papers and slides with perfect math and formatting
- I used to use for everything before I found R and markdown
- Producing pdf output actually converts markdown files into first!
- Much steeper learning curve, a good cheatsheet
- An extensive library of mathematical symbols, notation, formats, and ligatures, e.g.
A great resource: Wikibooks LaTeX Mathematics chapter

Writing Math

Input	Output
$\alpha$
$\pi$
$\frac{1}{2}$
$\hat{x}$
$\bar{y}$
$x_{1,2}$
`x^{a-1}$`
$\lim_{x \to \infty}$
$A=\begin{bmatrix} a_{1,1} & a_{1,2} \\ a_{2,1} & a_{2,2} \\ \end{bmatrix}$

Citations, References, & Bibliography

Manage your citations and bibliography automatically with .bib files
First create a .bib file to list all of your references in
- You can do this in R via: File -> New File -> Text File (and save with .bib at the end)
- See examplebib.bib in this repository used in this document
- At the top of your YAML header in the main document, add bibliography: examplebib.bib so R knows to pull references from this file
- For each reference, add information to a .bib file, like so:

An Example `.bib` File

@article{safner2016,
  author = {Ryan Safner},
  year = {2016},
  journal = {Journal of Institutional Economics},
  title = {Institutional Entrepreneurship, Wikipedia, 
           and the Opportunity of the Commons},
  volume = {12},
  number = {4},
  pages = {743-771}
}

A .bib file is a plain text file with entries like this
Classes for @article, @book, @collectedwork, @unpublished, etc.
- Each will have different keys needed (e.g. editor, publisher, address)
First input after the @article is your citation key (e.g. safner2016)
- Whenever you want to cite this article, you’ll invoke this key

Citations

Whenever you want to cite a work in your text, call up the citation key with @, like so: @safner2016[], which produces (Safner, 2016)
You can customize citations, e.g.:

Write	Produces
`[@Safner2016]`	(Safner, 2016)
`@Safner2016`	Safner 2016
`-@Safner2016`	(2016)
`@Safner2016[p. 743-744]`	(Safner, 2016, p.743-744)

BibTeX will automatically collect all works cited at the end and produce a bibliography according to a style you can choose

Reference Management Software

For more information and examples, see Quarto’s Documentation on Citations
Lot of programs can help you manage references and export complete .bib files to use with R Markdown
- Mendeley and Zotero are free and cross-platform
- I use Papers (Paid and Mac only)
- Simplest program (what I use) that makes .bib files is Bibdesk

Plain-Text Editors

Markdown files are plain text files and can be edited in any text editor
- something as basic (and boring!) as “Notepad,” for example
- many good text editors out there: Typora; Ulysses
Any good editor will have syntax highlighting and coloring when you use tags (like bold, italic, code, and code #comments).
VS Code; Notepad++; Sublime

VS Code

RStudio is My Text Editor of Choice

Honestly, I write everything in R Studio’s text editor
- Syntax highlighting
- Actually can run R code, autocomplete, etc
- Can render the markdown to an output format: html, pdf, etc.
You can write R code in other text editors, but you can’t execute them outside of R Studio (or the command line, but that’s too advanced.) Same with actually rendering your markdown to an output (pdf, html, etc)

Tips with Markdown

Empty space is very important in markdown
Lines that begin with a space may not render properly
Math that contains spaces between the dollar-signs may not render properly
Moving from one type of content to another (e.g. a heading to a list to text to an equation to text) requires blank lines between them to work
Here is a great general tutorial on markdown syntax