Articles

Session 1: Getting to know Quarto

Cynthia Huang

Tuesday, July 18, 2023

Scholarly Writing

Article Features

Quarto supports

a standardized schema for key details like authors and affiliations that can be expressed once in the source document,
cross-referencing of figures, tables, equations etc., and
the use of Citation Style Language (CSL) to automate the formatting of citations and bibliographies,
outputting to pdf, html, and docx with custom formatting,

Components of an Article

---
title: "Toward a Unified Theory of High-Energy Metaphysics: Silly String Theory"
date: 2008-02-29
author:
  - name: Josiah Carberry
    id: jc
    orcid: 0000-0002-1825-0097
    email: josiah@psychoceramics.org
    affiliation: 
      - name: Brown University
        city: Providence
        state: RI
        url: www.brown.edu
abstract: > 
  The characteristic theme of the works of Stone is 
  the bridge between culture and society. ...
keywords:
  - Metaphysics
  - String Theory
license: "CC BY"
copyright: 
  holder: Josiah Carberry
  year: 2008
citation: 
  container-title: Journal of Psychoceramics
  volume: 1
  issue: 1
  doi: 10.5555/12345678
funding: "The author received no specific funding for this work."
---

Metadata: Extended YAML front matter fields
Content: markdown text, tables, figures, raw LaTex, citations
Code: executed by knitr (R) or jupyter (python)

Metadata

Front Matter

Quarto pre-defines useful metadata keys for scholarly writing:
- authors, affiliations, roles
- article abstract and keywords
- acknowledgements and thanks
- citation, license, copyright, funding

but not all formats use every metadata field.

File Includes

The following include-in-* options allow you to include contents of a file (e.g. file.tex) verbatim at certain positions:

Option Position Use Cases

Option	Position	Use Cases
`include-in-header`	end of the header before `\begin{document}` or `<body>`	Inject commands into the LaTeX preamble
`include-before-body`	beginning of the document body after `\begin{document}` or `<body>`	Include navigation bars or banners in HTML
`include-after-body`	end of the document body before `\end{document}` or `</body>`

include-in-header

end of the header

before \begin{document} or <body>

Inject commands into the LaTeX preamble

include-before-body

beginning of the document body

after \begin{document} or <body>

Include navigation bars or banners in HTML

include-after-body

end of the document body

before \end{document} or </body>

LaTex Output

There are two ways to produce a LaTex file (.tex) using options specificed in the YAML header:

Option 1: Use the latex format instead of pdf

format:
  latex:
    documentclass: report
    classoption: [twocolumn, landscape]
    lof: true
    lot: true

Option 2: Use the keep-tex option in the pdf format

format:
  pdf:
    documentclass: report
    keep-tex: true

Content

Equations

or just use Visual Mode!

Figures

Markdown:

![Penguins playing with a Quarto ball](images/penguins-quarto-ball.png){fig-align="left" height="200px"}

Output (HTML):

Figures

Markdown:

![Penguins playing with a Quarto ball](images/penguins-quarto-ball.png){fig-align="right" height="200px"}

Output (HTML):

Subfigures

Markdown:

::: {#fig-penguins layout-ncol=2}

![Blue penguin](images/blue-penguin.png){#fig-blue width="250px"}

![Orange penguin](images/orange-penguin.png){#fig-orange width="250px"}

Two penguins

:::

Subfigures

Output (LaTex):

\begin{figure}

\begin{minipage}[t]{0.50\linewidth}

{\centering 

\raisebox{-\height}{

\includegraphics[width=2.60417in,height=\textheight]{images/blue-penguin.png}

}

}

\subcaption{\label{fig-blue}Blue penguin}
\end{minipage}%
%
\begin{minipage}[t]{0.50\linewidth}

{\centering 

\raisebox{-\height}{

\includegraphics[width=2.60417in,height=\textheight]{images/orange-penguin.png}

}

}

\subcaption{\label{fig-sleep}Orange penguin}
\end{minipage}%

\caption{\label{fig-penguins}Two penguins}

\end{figure}

Subfigures

Output (PDF):

LaTex Figure Options

Quarto can some options specific to LaTex output such as figure position and environments

---
title: "Sidenotes"
format:
  pdf:
    fig-pos: 'h'
    include-in-header: 
      text: |
        \usepackage{mdframed}
---

![Elephant](elephant.png){fig-env="mdframed"}

See PDF Reference > Figures for available options

Raw LaTex Commands

Pandoc (and thus Quarto) allows for mixing raw LaTex with markdown when creating PDF documents. For example:

\begin{tabular}{|l|l|}\hline
Age & Frequency \\ \hline
18--25  & 15 \\
26--35  & 33 \\
36--45  & 22 \\ \hline
\end{tabular}

Warning

Note that raw LaTex will not be rendered in HTML format. However, if you have existing LaTex content (e.g. from STATA) that can’t be re-exported or re-written in markdown this is a useful option.

Your Turn: my_first_article.qmd

Open my_first_article.qmd inside your last Rproject.
Follow the PDF exercise instructions

10:00

Journal Articles

Submit straight from Quarto

Journal Article extensions offer templates to adapt an existing .qmd document

according to the styles required for various journals,

and create the LaTeX required for submission to multiple journals.

Journal formats

github.com/quarto-journals

Journal / Publisher	Name
Association of Computing Machinery	acm
American Chemical Society	acs
American Geophysical Union	agu
Biophysical journal	biophysical-journal
Elsevier Journals*	elsevier
American Statistical Association Journals	jasa
Journal of Statistical Software	jss
Public Library of Science	plos

Getting started with a journal article

The quarto use template command can be used to create an article from one these formats, e.g. for Elsevier:

Terminal

quarto use template quarto-journals/elsevier

Our Turn: Journal Article Templates

Let’s write an article together for Elsevier and showcase the following features of Quarto journal articles:

PDF output
Extended YAML front matter
Reference management