Which tool to write a PhD thesis/manuscript: quarto Book or quarto Manuscript? Pro&cons based on your experience

[KleinWurm]

Description

Good morning Quarto community!

I would like to open a discussion about the use of Quarto to write a PhD thesis/manuscript. If it has already been answered please point me to the right direction because I was not able to find guidance elsewhere. I am very new to this exercice so please, do not hesitate to share your feedback and experience on the things that are very much needed when writing a PhD thesis, I might have overlooked at least some of them.

Quarto makes it possible to write plain text, possibly complex, documents without overcrowding the writing with divs and spans. It is possible to use templates (css, others?) to customize the appearence, it supports cross-referencing, caching, etc. Thus it holds the promise to be good tool for writing long and complex documents such as a PhD manuscript.

From what I have seen, a PhD manuscripts require the following:

1. a robust tool that can handle possibly hundreds of pages with an imposed layout (for example a LaTeX template provided by the university),
2. connection to reference management tool (Zotero) and cross-referencing
3. execute code from side-files, reason is, sometimes the code can be very long and it seems better to keep it on a separated file to enhance the readability of the main text.
4. keeps the writing process simple and clean to focus on the content (Markdown here you are), and support equations

Quarto Manuscripts, Books and the extension Journal article appear as relevant candidates for this task. But the first item of the previous list makes me a bit affraid of jumping into Quarto for this project as I do not know how to twist the layout to make things appear and look like the template from the university.

Then, I am not certain about the limitations of Manuscripts, Books and Journal articles and would like to avoid discovering a breaking problem after months of redactions.

Have you already used Manuscripts or Books or Journal articles projects to write your PhD thesis? Are you using it currently maybe? Do you know useful ressources that can help future readers to make their mind? What are the pro and cons of using one of them? Which type is the most relevant in your opinion?

Have a great day,

Edit: I am aware that Extension for a PhD thesis with Quarto exists but, if I am not mistaken, it was before Manuscripts was released.

[cscheid]

A manuscript is really intended as a journal manuscript, and not for the length of a thesis. A thesis is much closer to a book, so I would use that.

But the first item of the previous list makes me a bit affraid of jumping into Quarto for this project as I do not know how to twist the layout to make things appear and look like the template from the university.

That's a very good worry to have. I'm the main Quarto dev now but I was a tenured academic professor in a US university before joining the project. So, if you allow me to put my professor hat back on for three minutes: your job to write a thesis will be hard enough as it is. If you're not already familiar with templates, etc, I would use whatever tool your current colleagues are using, and focus on the thesis itself rather than the tech around it!

[baptiste]

I would use whatever tool your current colleagues are using

I don't disagree, but when I give this advice to students I also tell them to consider a few other factors:

• how far along are you in your PhD? If you're close to finishing, or already have substantial parts written, it's probably best to stick to the tools you know best
• how strict are your supervisors when it comes to using specific tools? Some of my colleagues insist that their students use MS Word, so that they can annotate and review with that program themselves. I don't approve – I think PhD candidates should have the freedom to choose their own tools, especially when there are better options – but this kind of situation does happen.
• how invested are you in typography/presentation/reproducible documents? It sounds like you've recognised some strengths in a quarto-like system, and this is a useful skill to master in itself.

To be honest, thesis formatting is usually pretty basic, and there are many templates available (tex or even quarto) that would likely need only minimal changes to match your university's requirements. I'm sure you'd get enough tips from this forum to make it work if something's not available out of the box. And, you can always produce a word or latex file from your plain markdown content if you decide to stick to one of those two formats after all.

[KleinWurm]

First, many thanks @cscheid and @baptiste for your insights!

I understand that if I choose to write the thesis using Quarto, I should use a Book project. My main supervisor is open to use Markdown editing for this project and we already faced the limit of MS Word in terms of stability when it comes to big documents in a previous work.

It is very good to know that worrying about the time-consumming aspect of templating and you are very right to say that the job is to write a thesis and not showcase a writing tech (even though it is addictive to learn them).

I will give Quarto Book a try and add feeback in this discussion as soon as possible.