York Thesis Class in LyX

This is an example repository used for building thesis (Masters or PhD) in LyX, derived from the instructions located on the technical requirements page. When compiled, the bare-bones of this thesis template will look like this, which gives you a general outline of how to start writting your thesis or disseration.

LyX, like LaTeX, is a document preparation system built around the concept of defining the structure of your document. For larger documents, such as a dissertation, this is incredibly useful because the document is much easier to keep internally consistent (e.g., figure and table labels will always be correct, even if you add or remove others at a later time). E.g., see this blog post for a discussion.

As well, it's very easy to turn a thesis written in LyX into published articles because the labels will always be consistent in new documents. Hence, you could create a new apa6 manuscript file in LyX to copy-and-paste your way towards your next manuscript and publication. It really is that simple.

If you need some material to help understand the fundamentals of LyX, here are a few sources:

• Visual Tour from the main LyX website
• Some fundamental elements in pdf form
• 5-part YouTube video primarily focused on making math in LyX (if you know any LaTeX math commands, you are way ahead of the game here because typing math in LyX with a LaTeX flavor will make you extremely efficient)

Installation

To use this template you'll need to meet the following requirements:

Requirements:

• Install the LyX program for your OS
• Install the york-thesis class through whatever TeX system you are using (e.g., TeX-Live, MiKTeX, MacTeX)
• Follow the configuration instructions below

As well, if you want to go the extra mile (and you should!)

• Obtain a decent bibliography manager to edit .bib files. You could just use a text editor but a dedicated .bib manager is much nicer. If you installed Jabref when installing LyX, it has support to push references directly to LyX, and is overall a good reference manager
• Install R and the 'knitr' package. This is only required if you want to integrate LyX with R to evaluate R code within your document

Configuration:

• Move the 'york-thesis.layout' file in the LyX_files/ directory to LyX's ~/layouts directory
  • On Ubuntu, mine was located in ~/home/phil/.lyx/layouts
  • Windows is probably in C:/Program Files/LyX/layouts
  • On Mac OS X, it is preferred to place this file in ~/Library/Application\ Support/LyX-2.2/layouts (note: the Library directory is hidden by default in recent versions of OS X. Use the "Go To Folder" shortcut, Command+Shift+G, to navigate there quickly).
• Open the LyX program and go to 'Tools -> Reconfigure'. Now restart LyX.

Finally, pat yourself on the back because it should work now LyX! You can open .lyx files directly, or open them with 'File -> Open' if you open LyX first.

How To Use LyX

The way to understand how LyX (and LaTeX) behave is to think of files, figures, references, etc, as objects being 'pointed to' within some LyX file. A LyX file points to a figure, and this is included when the document is compiled to a PDF. Any external changes to said file will be included in the document the next time it is compiled; this has huge benefits when things have to be edited at a later time (unlike document systems like MS Word, in which if a figure has to be changed it has to be changed in the document itself.....which can have horrible repercussions and overall is quite cumbersome). This same philosophy works for references, chapters, appendices, etc, and helps to keep different document elements isolated and manageable.

The design of the LyX files for this York Thesis template is fairly simply:

• There is one master file, york-thesis.lyx, which points to independent files (styles, front-matter, chapters, etc). This is the main file which links all the material together, and essentially declares the structure of the final product.
• Chapters go into their own separate files in the main directory, and are included in the master file as 'Children' using the LyX insert commands.
• Front-matter material has been put into the front/ directory, containing LyX and LaTeX files. Edit these as you see fit. The only LaTeX file that you should edit directly (with a standard text editor) is the preamble.tex file, which contains information about your degree, committee, defense date, etc.
• Extra material, such as customized figures, tables, appendices, etc, go into other directories and are inserted with LyX Input methods. This goes for the bibliography as well, which is included in a bibliography/ directory by default.

Finally, to compile the LyX file to a PDF, click on Document -> View Master Document, or use a suitable keyboard shortcut (e.g., Ctrl + Shift + R).

Additionally, some stylistic things to help keep you organized and efficient:

• In LyX, turn on things like continuous spell-checking and word completion. These are off by default.
• Frequently label sections, tables, figures, etc, with meaningful labels. This will help you reference content later on, and are dynamically updated as you add more material. Create a label with Insert -> Label, and reference any label with Insert -> Cross-Reference
• Use external PDF's files for figures. PDFs are extremely high quality (vector graphics), and look the best in the final product.
• Break additional content up into folders. If it turns out you have lots of figures and tables, you may want to break these up by chapter. So instead of putting all figures into figures/, create new directories such as figures/chapter-1/, figures/chapter-2/, and so on, and put files in there.
• Use BibTeX to manage your references. If you need tools to convert your previous references into something more suitable, here is a good start

Extra

When compling the document to a pdf, if you are do not have the master file active (e.g., you currently have Chapter 3 active) then using Ctrl + r will not compile the entire document. Instead, use Ctrl + Alt + r, which for Linux and Windows is the compile master document keyboard hotkey. Note that this can be used to update the pdf file if it is already open, so use it as often as you like.