References at top level in TOC after appendices

[fzenk]

Description

Thanks for your awesome work on this project! I am writing a thesis in Quarto, and I am currently having trouble getting the references to print after the appendices while still being listed as a top-level heading in the table of contents (TOC).

First, I tried this in the _quarto.yml file of my Quarto book project:

project:
  type: book
book:
  title: ""
  chapters:
    - index.qmd
    - chapter1.qmd
    - chapter2.qmd
    - chapter3.qmd
  appendices: 
    - appendices.qmd
    - references.qmd # I put the references here
bibliography: references.bib
csl: apa.csl
toc: true
format:
  pdf:
    documentclass: report

The references were printed after the appendices, but they were included in the TOC as a final appendix (only obvious when looking at the "document outline" pane in the pdf output).

Then I tried this:

project:
  type: book
book:
  title: ""
  chapters:
    - index.qmd
    - chapter1.qmd
    - chapter2.qmd
    - chapter3.qmd
  appendices: 
    - appendices.qmd
  references: references.qmd # I put the references here
bibliography: references.bib
csl: apa.csl
toc: true
format:
  pdf:
    documentclass: report

Although the references were included as a top-level heading in the TOC/document outline this time, they were also printed before the appendices (which is undesirable for me).

The contents of references.qmd are as follows:

# References {.unnumbered}

::: {#refs}
:::

Is there anything I can do in the _quarto.yml file or elsewhere to achieve the desired result?

BTW, the same question has been asked before on the following page (but as far as I can tell it was never fully answered either there or here in the GitHub discussions): https://community.rstudio.com/t/quarto-references-chapter-section-at-top-level-in-toc-after-appendices/144332

Thank you for your assistance with this.

[mcanouil]

Linking to @cderv answer of another thread as it should also work here.

• How do I include "References" and "Citation" section in the TOC? #6021 (comment)

[fzenk]

Thanks for the question, @cscheid! I found a way to achieve the desired result in a latex report HERE.

Here's my MWE:

\documentclass[12pt]{report}

\usepackage[hidelinks]{hyperref}
\usepackage{bookmark} % Step 1: Load bookmark package after hyperref package

\begin{document}

\tableofcontents

\chapter*{List of Abbreviations}
\addcontentsline{toc}{chapter}{List of Abbreviations}

\addcontentsline{toc}{part}{Chapters}
\chapter{First Chapter}
\chapter{Second Chapter}
\chapter{Third Chapter}

\addcontentsline{toc}{part}{Appendices}
\appendix
\chapter{First Appendix}
\chapter{Second Appendix}
\chapter{Third Appendix}

\bookmarksetup{startatroot} % Step 2: Add this line right before the references
\chapter*{References}
\addcontentsline{toc}{chapter}{References}

\end{document}

The TOC looks like this:

And the bookmarks/outline looks like this:

If I make the references a numbered chapter, then it's clear that they are still part of the appendices because they are listed as "D References" (i.e., a 4th appendix) in the TOC. However, I'm not too concerned about that since the reader won't be able to tell as long as we keep the references as an unnumbered chapter.

I was hopeful that the same approach might work in my Quarto book project, but unfortunately it didn't. The references are still nested under the appendices in the bookmarks/outline, even after I load the bookmark package and call the \bookmarksetup{startatroot} command right before the references chapter. I also tried removing the link-citations: true line from the _quarto.yml file and loading the hyperref package just before the bookmark package in the latex header, but that didn't help. Here's the result:

[cscheid]

One thing you can try to do is to add keep-tex: true to your YAML metadata. This way, quarto will generate your PDF file as usual, but will not remove the .tex file it used.

From there, you can try to first tweak the .tex file manually (so that you understand what's causing the issue), and then work backwards to where you want to be. In general, situations where substantial .tex work needs to happen are better handled in quarto with a custom format, which can include a custom .tex template.

[fzenk]

Thank you for the advice, @cscheid! To be clear, are you suggesting that I tweak an existing document class to make a custom class that meets my formatting requirements? I am already customizing pieces of the report class in my include-in-header .sty file (between the \makeatletter and \makeatother commands), mostly to make changes to the formatting of the headings (for some reason none of my Quarto files or book projects compile successfully when I try to load the titlesec package, which would be the easier way to do that). Since I'm new to all of this, would you mind giving me a hint as to where I can find a copy of the report class source file to modify, and how to load the completed custom class into my Quarto book project? I found THIS page on CTAN, and I suspect the file I want is there somewhere, but there are so many files in the download that I don't know where to start looking (maybe classes.dtx?). I'd greatly appreciate any pointers you might have to offer on this.

[mcanouil]

See:

• documentation on templates/partials: https://quarto.org/docs/journals/templates.html#template-partials.
• documentation on extension formats/templates: https://quarto.org/docs/extensions/listing-journals.html and https://quarto.org/docs/journals/formats.html.

[fzenk]

Thanks for sending me these links, @mcanouil. I see now that what is being suggested is that I modify the Pandoc LaTeX template (either the entire template or one of the template partials). I'll take a whack at this approach when I get a chance and report back if I have any success or if I have additional questions. Thanks again to you and the rest of the Quarto team for the prompt responses.