README.md

Notes on adapting oxforddown for GitLab

See this repo's commit history for details on how the oxforddown template has been adapted for use with GitLab CI. My motivation was that for free tier subscriptions, GitLab pages are allowed for private repositories, where as GitHub pages are for public repositories only.

To summarise the main changes I have made:

• Added renv.
• Added a .gitlab-ci.yml file which builds the thesis on every push to GitLab.
• Enabled use of the RStudio 'Build' tab and convenient 'cmd/ctrl+shift+b' keyboard shortcut for local builds.
• Added notes and basic setup steps for using the flextable package for creating tables.

A huge thanks to Ulrik Lyngs for this amazing template!

How to cite

If you use this template to write your thesis, please cite it! 🥰

@misc{lyngsOxforddown2019,
  author = {Lyngs, Ulrik},
  title = {oxforddown: An Oxford University Thesis Template for R Markdown},
  year = {2019},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/ulyngs/oxforddown}},
  doi = {10.5281/zenodo.3484681},
}

Contents

• Requirements
• How to use
  • How-to chapters
  • Video tutorials
  • Writing your thesis
  • Building your entire thesis
    • PDF output
    • Gitbook output
    • BS4 book output
    • Word output
  • Building a single chapter
• Customisations and extensions
• Limitations
  • Gotchas
  • Output formats

Oxforddown

A template for writing an Oxford University thesis in R Markdown. The template uses the bookdown R package together with the OxThesis LaTeX template, plus lots of inspiration from thesisdown.

• Sample PDF output
• Sample BS4 book output

Examples of theses written with oxforddown (see also Google Scholar):

• Ulysses in Cyberspace: Examining the Effectiveness of Design Patterns for Digital Self-Control by Ulrik Lyngs
• The Psychology of Managerial Capital Allocation by Shir Dekel
• Teens, Screens and Wellbeing: An Improved Approach by Amy Orben
• Interpreting Neural Language Models for Linguistic Complexity Assessment by Gabriele Sarti
• Modeling of nutrient dynamics in an urbanized tropical estuary and application to eutrophication risk management by Nguyen Truong An

NOTE: If you've used this template to write your thesis, drop me a line at [email protected] and I'll add a link showcasing it!

Requirements

• R and RStudio version 1.2 or higher

• The R packages rmarkdown, bookdown, tidyverse, kableExtra, and here

• a LaTeX installation

  • Option 1: Use TinyTeX (a minimal LaTeX installation intended for use with R Markdown)

    • the development version of TinyTex is currently required. Install from R with

    remotes::install_github('yihui/tinytex')
    tinytex::install_tinytex()

    • Then install the LaTeX packages used by oxforddown (diskspace taken up by TinyTex with the required packages installed is about 280 Mb)

    missing_packages <- c(
      "appendix", "babel-english", "babel-greek", "babel-latin", 
      "biber", "biblatex", "caption", "cbfonts-fd", "colortbl", "csquotes", 
      "enumitem", "environ", "eso-pic", "fancyhdr", "greek-fontenc", 
      "grfext", "hyphen-greek", "hyphen-latin", "lineno", "logreq", 
      "makecell", "microtype", "minitoc", "multirow", "notoccite", 
      "oberdiek", "pdflscape", "pdfpages", "quotchap", "soul", "tabu", 
      "threeparttable", "threeparttablex", "titlesec", "tocbibind", 
      "trimspaces", "ulem", "units", "utopia", "varwidth", "wrapfig",
      "fvextra", "xurl"
      )
    tinytex::tlmgr_install(missing_packages)

  • Option 2: Use an ordinary LaTeX distribution

    • Mac: download and install MacTeX from tug.org/mactex/ (~4 gigs)
    • Windows: download and install MikTex from miktex.org

• If on Mac

  • Command line developer tools. If you haven't got these installed already, your mac will probably automatically prompt you to install them. Otherwise, you can install them by opening a terminal and typing xcode-select --install

How to use

• download the ulyngs/oxforddown repo as a zip
• open oxforddown.Rproj in RStudio

How-to chapters

Read the 'How to use' chapter to understand the structure of oxforddown and how to do the basic things like building your thesis.

For how to use R Markdown syntax in general and in oxforddown in particular, read the dedicated chapters on this (R Markdown basics, Citations, cross-references, and collaboration, and Tables).

See also the general, official R Markdown resources R Markdown: The Definitive Guide and the R Markdown Cookbook.

Video tutorials

I am in the process of updating the tutorial videos to v3 - I've noted below which have yet to be updated, but are still informative, and struck out those that no longer apply:

• Part 1: Building the entire thesis
• Part 2: Building a single chapter
• (old but informative) Part 3: Understanding the file structure
• (old but informative) Part 4: A walk-through example of creating your thesis
• Part 5: The content included in index.Rmd (or: why the introduction chapter is special)
• (old but informative) Part 6: Adjusting the order of chapters
• (old but informative) Part 7: _bookdown.yml: Adjusting build settings
• Part 8: Makefile: Adjusting build settings
• (old but informative) Part 9: The LaTeX templates

Writing your thesis

• update the YAML header (the stuff at the top between '---') in index.Rmd with your name, college, etc.
• write the individual chapters as .Rmd files in the root folder
• write the front matter (abstract, acknowledgements, abbreviations) and back matter (appendices) by adjusting the .Rmd files in the front-and-back-matter/ folder

.Rmd files you don't want included in the body text must be given file names that begin with an underscore (e.g. front-and-back-matter/_abstract.Rmd and front-and-back-matter/_acknowledgements.Rmd). (Alternatively, specify manually in _bookdown.yml which files should be merged into the body text.)

Building your entire thesis

• Build the entire thesis by opening index.Rmd and clicking the 'knit' button.
• The generated thesis files are saved in the docs/ folder
• To choose output formats, go to the top of index.Rmd's YAML header and edit the line thesis_formats <- "pdf"; to the format(s) you want (options are "pdf", "bs4", "gitbook", and "word")
• You can build to multiple formats simultaneously with, e.g., thesis_formats <- c("pdf", "bs4", "word")
• If you want to customise the build function, edit scripts_and_filters/knit-functions.R

PDF output

knit: (function(input, ...) {
    thesis_formats <- "pdf";
    ...

When you build the entire thesis to PDF, Latex generates a whole bunch of auxillary files - these are automatically removed after the build process end by the custom knit function that is used when you knit index.Rmd.

To change how this removal is done, edit scripts_and_filters/knit-functions.R. The line file.remove(list.files(pattern = "*\\.(log|mtc\\d*|maf|aux|bcf|lof|lot|out|toc)$")) within if ("pdf" %in% output_format){ is the one that removes files after PDF output is generated.

BS4 book output (HTML)

knit: (function(input, ...) {
    thesis_formats <- "bs4";
    ...

• NOTE: the bs4 book output requires the downlit and bslib R packages (install them with install.packages)
• Note also that to deploy a BS4 book on GitHub Pages, there must be a .nojekyll file in the docs/ folder, otherwise GitHub does some voodoo that causes some filepaths not to work. This file is generated automatically by oxforddown's knitting function.

Gitbook output (HTML)

knit: (function(input, ...) {
    thesis_formats <- "gitbook";
    ...

• Note that to deploy a gitbook on GitHub Pages, there must be a .nojekyll file in the docs/ folder, otherwise GitHub does some voodoo that causes some filepaths not to work. This file is generated automatically by oxforddown's knitting function.

Word output

knit: (function(input, ...) {
    thesis_formats <- "word";
    ...

• Note that the Word output has no templates behind it, and many things do not work (e.g. image rotation, highlighting corrections). I encourage pull requests that optimise the Word output, e.g. by using tools from the officer package.

Building a single chapter

To knit an individual chapter without compiling the entire thesis:

1. open the .Rmd file of a chapter
2. add a YAML header specifying the output format(s) (e.g. bookdown::word_document2 for a word document you might want to upload to Google Docs for feedback from collaborators)
3. click the knit button (the output file is then saved in the root folder)

As shown in the sample chapters' YAML headers, to output a single chapter to PDF, use e.g.:

output:
  bookdown::pdf_document2:
    template: templates/brief_template.tex
    citation_package: biblatex
documentclass: book
bibliography: references.bib

The file templates/brief_template.tex formats the chapter in the OxThesis style but without including the front matter (table of contents, abstract, etc).

NOTE: The bibliography path in your individual chapters' YAML headers needs to be identical to the one in index.Rmd - otherwise your individual chapters' bibliography path may override the path in index.Rmd and cause trouble when you knit the entire thesis.

Customisations and extensions

• for common things you might want to do in your thesis, read through the sample content
• the 'Customisations and extensions' chapter (thanks @bmvandoren!) has tips on how to include PDF pages from a published typeset article in your thesis, and much more!

Limitations

Gotchas

• don't use underscores (_) in your YAML front matter or code chunk labels! (underscores have special meaning in LaTeX, so therefore you are likely to get an error, cf. https://yihui.org/en/2018/03/space-pain/)

  • bad YAML: bibliography: bib_final.bib
  • good YAML: bibliography: bib-final.bib
  • bad chunk label: {r my_plot}
  • good chunk label: {r my-plot}

Output formats

• at the moment only PDF and HTML output have been properly implemented; I may improve on the Word output further down the line

Enjoy!