Data Rich Reports

Session 7–PDF Documents

Overview

Code for Today

Download the Quarto files for this session and the previous one here

Quarto for PDF Documents

  • Make sure you have the tinytex package installed
    • quarto install tinytex
  • Open the session-2.3.qmd file
  • Try renderingthe document

LaTex and Quarto

::: - Quarto uses LaTex to render standard PDFs - LaTex is a typesetting system that is widely used for technical and scientific documents - Quarto uses LaTex to create PDFs from your markdown files - Uses knitr to do the conversion - There is also something called typst that we will explore later :::

PDF YAML Code

What is All of This Code?

---
title: "My Paper"
subtitle: "An Example of a Quarto Paper"
author:
  - name: Bullwinkle J. Moose
  - name: Rocky the Flying Squirrel 
format: 
  pdf:
    documentclass: article
date: today
date-format: long
abstract: |
  Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. More Latin.
link-citations: true
#link-bibliography: false
colorlinks: true
linkcolor: Blue4
fig-width: 6.5
fig-height: 4.5
fig-cap-location: top
block-headings: false   # so that titlesec package works
geometry: margin = 1in
fontsize: 12pt
mainfont: Times New Roman
mathfont: STIX Two Math
linestretch: 2
indent: true
bibliography: references.bib
#cite-method: biblatex
#biblio-style: apa
#csl: american-political-science-association.csl
reference-section-title: References
execute:
  echo: false
  message: false
  warning: false
include-in-header: header.tex
---

Let’s Start with What we Know


title: "My Paper"
subtitle: "An Example of a Quarto Paper"
author:
  - name: Bullwinkle J. Moose
  - name: Rocky the Flying Squirrel 
format: 
  pdf:
    documentclass: article
date: today
date-format: long

Let’s Start with What we Know


execute:
  echo: false
  message: false
  warning: false

Abstract


abstract: |
  Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. More Latin.

Figure Specifications


fig-width: 6.5
fig-height: 4.5
fig-cap-location: top
block-headings: false   # so that titlesec package works

Font and Spacing


Note that fonts are defined by system fonts. System fonts are defined by the operating system and differ across Macs and PCs.

geometry: margin = 1in
fontsize: 12pt
mainfont: Times New Roman
mathfont: STIX Two Math
linestretch: 2
indent: true

References


bibliography: references.bib
#cite-method: biblatex
#biblio-style: apa
#csl: american-political-science-association.csl
reference-section-title: References

Header


What is in the header.tex file?

%%% Setup for frontmatter and spacing %%%

\usepackage{indentfirst} % indent first para
\setlength{\parindent}{0.5in} % set indent length
\setlength{\parskip}{0em} % no extra space between paras
\usepackage{titlesec} % to set spacing of section titles
\titlespacing\section{0pt}{0pt plus 2pt minus 2pt}{0pt plus 2pt minus 2pt}
\titlespacing\subsection{0pt}{0pt plus 2pt minus 2pt}{0pt plus 2pt minus 2pt}
\titlespacing\subsubsection{0pt}{0pt plus 2pt minus 2pt}{0pt plus 2pt minus 2pt}

Header


What is in the header.tex file?

%%% Captions %%%
          
\usepackage{caption}
\captionsetup{
  %captionskip = 0pt,   % eliminate space bw capiton and figure
  %labelformat = empty, % eliminate caption label
  %font = bf,
  justification = raggedright, % left justify the caption 
  singlelinecheck = true,      % but only if it is more than one line
  font = footnotesize,         % make font smaller
  labelfont = bf               % make the caption label bold
}

Try This


  • Starting with what you don’t know…
    • Comment out different lines in the YAML header
    • Rerender the document
    • What is the result?
  • Try to find a different font for the document
    • On a Mac, look in the Font Book app
    • On a PC, look in the settings under “Personalization”
10:00

References

.bib files


  • .bib files are a way to store references
  • They are a plain text file used by LaTex
  • Quarto needs them to compile the list of references at the end
  • They are a bit tricky to write by hand
  • Which is why we use a reference manager like Zotero or Mendeley

Zotero Demo


  • Let’s install Zotero
  • Then we need the Zotero plugin to grab references from the web
  • Then we also need the Better BibTex plugin to export the .bib file
    • Produces a .bib file that is easier to read and edit
    • Along with that produces a citation key that is easy to use
  • Next we need to export our .bib file to our project folder
  • Then we can insert the citaion with [@authorXXXX]
  • Note that we can also do this in HTML documents, but we highlight it here because research manuscripts tend to still be produced mainly as PDFs

Changing Reference Style


  • There are two ways to change the reference style
    • The csl file in the YAML header
    • The biblio-style in the YAML header
  • The csl file is a style file that can be found here
  • The biblio-style is a style that can be found here
    • Mostly we are going to use apa, mla or chicago-authordate in the social science
    • But default for Quarto is already Chicago author-date

Your Turn!


  • Do everything I just did
  • I’ll come around to make sure you are caught up
10:00

Advanced PDFs

Extensions

  • Quarto extensions are an easy way to style your documents
  • A list of extensions is here
  • For PDFs the journal and custom format extensions are most relevant
  • Use an extension for a new document: quarto use template repo-name/extension-name
  • To add it to an existing document: quarto add repo-name/extension-name

Typst


  • Typst is a modern typesetting system
  • Check out their webiste
  • Typst is pretty new but it shows a lot of promise
  • A lot of elements are very similar to Quarto PDFs
  • Let’s have a look at the documentation
  • And see if we can produce a Typst document!

DRR Website