Instructions

Quarto Chapters

• Quarto is an open-source document preparation system.
• If you are using the latest version of Rstudio, quarto is included. Otherwise, follow the link to download the standalone version. There is also a VS Code extension.
• Each chapter is written using quarto in Rstudio.
• These .qmd files are stored in chapters_quarto.
• Quarto features markdown syntax, and can mix and match code chunks from a range of languages.
• Figures can be dynamically generated with quarto, which also controls all figure options.
• Models can be built and cached using quarto, which saves you time.

Rendering

• The project is set up to render only latex, but you can change this to render individual pdf/html instances of chapters.
• Once you have finished writing a chapter, go into main.tex and edit the CHAPTERS section to include all your chapters.
• Authorship, declarations, and abstracts are also handled by main.tex.
• Once all chapters are finished, you are ready to knit your final thesis.
• I am an R user, so I have written an R script that renders each .qmd chapter, reformats the .tex of each chapter, and then produces the thesis using the .cls file included.
• NB: reformatting the .tex is important. Pandoc adds preamables which main.tex does not want.
• (Feel free to create a PR to contribute scripts in other languages that achieve this.)
• My R script uses TinyTex to produce the final thesis, but this is not necessary - uploading a .zip of the thesis to overleaf also works perfectly.
• Please read the finalise_thesis.R script comments before using it, as you may need to manually install additional fonts.

Quirks

• Due to the fonts used, LuaLatex must be used to compile.
• If you use TinyTex like me, you will need to additionally install the luatex85 package (there is a line in finalise.r that does this). Overleaf might need you to select this option via the menu.
• Biber (not BibLatex) must also be used. Overleaf does this automatically, but I had to specify this for TinyTex.

Using Trackdown for Collaborative Editing

• I have used the Trackdown package to enable collaborative editing. Set up is relatively involved. In short:
  • Follow instructions to create Google drive API to sync with local qmd files
  • Authorise using client id and secret from Google drive API
  • I have provided helper_functions.R to automate up and down sync between qmds and google docs

Housekeeping

• This template is based on the UoM thesis template found on Overleaf and written by Alex Casson.
• Additional improvements for functionality were made by David Petrescu.
• Justification for not using Quarto books: this implementation keeps each chapter (potentially including Docker containers etc) separate, and lets Latex (via a pre-existing thesis template) handle the formatting. IMO this is simpler and more language-agnostic. NB this means that most formatting options (margins, fonts etc) are dealt with by main.tex or the .cls file.
• I use Rstudio, but there is no reason why this would not work with any IDE that supports quarto (however I won't be much help re issues for other IDEs).
• To-Do:
  • Write guide to Dockerising chapters/entire thesis.
  • Write more scripts for finalising thesis