Editing LaTeX Dissertation Formatting Tips (section)

= LaTeX tips for building an electronic thesis or dissertation at the University of Washington =

''Note: these notes are based on [[User:groceryheist|Nathan TeBlunthuis’s]] experience dissertating in 2021. As time goes on, rules and policies might change and render all or part of this advice obsolete.''

''I use a Makefile and some Linux utilities to build my documents. If you’re on a different operating system and want to reproduce my workflow, you might have to install some additional software like [https://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/ <code>pdftk</code>] a <code>make</code> utility compatible with <code>GNU make</code> and [https://www.ctan.org/pkg/latexmk/ <code>latekmk</code>]. The source code for my dissertation is available to CDSC members and is located in the <code>cdsc_examples_repository</code>.''

== Front matter ==

The only hard [https://grad.uw.edu/for-students-and-post-docs/thesisdissertation/etd-formatting-guidelines/ formatting requirements] for the electronic thesis or dissertation (ETD) are the copyright, title, and abstract pages. You can get Microsoft Word templates for each these pages from the graduate school or, as I did, you can use a [http://www2.ee.washington.edu/people/faculty/mamishev/word/ template in a single Word File] maintained by Alex Mamishev, Professor in Electrical Engineering.

I filled out the template and then exported the copyright, title_page, and abstract as separate <code>.pdf</code> files. I build a single pdf with all of my chapters and then use <code>pdftk</code> to staple on the front matter:

<pre>pdftk copyright_page.pdf title_page.pdf abstract.pdf ETD_version.pdf cat output diss_ecology_of_online_communities.pdf</pre>
== Project Organization ==

You probably want to break your dissertation up into several different <code>.tex</code> files. Although I prefer to work on paper-length projects of 8,000 to 14,000 words or so in a single file, for a book or dissertation-length project it clearly makes more sense to keep each chapter in a different file. Building a very large <code>.tex</code> project can take too long. Very long files are more cumbersome to edit, even when using a powerful editor like Emacs. You are likely to publish different chapters as stand-alone articles. Indeed, the central 3 chapters of my dissertation were composed as stand-alone research articles, and two of them were under review when I defended.

To synchronize the publication and dissertation versions of these articles, I created a special <code>git</code> branch in the repositories for each project. The sole purpose of these branches was to make it convenient to merge any changes I made to the articles into the dissertation.<br />
I added the <code>.tex</code> files from these project-repositories into my dissertation project using a [https://en.wikipedia.org/wiki/Symbolic_link symbolic links].<br />
I used [https://yihui.org/knitr/ <code>knitr</code>] to build my tables and figures in these projects, but I did not find it necessary to include the knitr source code in my dissertation project. So when I edited these chapters, I worked on the <code>knitr</code> files (<code>.Rtex</code>) in the project repositories. To bring these changes into the dissertation, I ran knitr and then, in a manual step, edited the resulting <code>*.tex</code> files to turn them from stand-alone LaTeX projects into <code>memoir</code> chapters, as described below. I then used the <code>\input</code> LaTeX command to insert the contents of <code>.tex</code> files into the main document.  I used the git branches to track these versions of the <code>.tex</code> files.

I realize I could have used a more careful organization of my LaTeX projects to avoid the manual step. ''C’est la vie.'' For simplicity, I didn’t include all the project-specific stuff in <code>cdsc_examples_repositories</code> and just copied the final <code>.tex</code> files instead.<br />
If you need some help reproducing this workflow in your project, please reach out to [[User:groceryheist|Nate]].

== Using the <code>Memoir</code> Package ==

I use the [https://ctan.org/pkg/memoir <code>memoir</code>] LaTeX package to format my dissertation as a book. You may have encountered <code>memoir</code> before if you’ve used the latex templates in the <code>cdsc_tex</code> repository that [[User:Mako|Mako]] maintains. Memoir really shines for book length projects such as your dissertation, and like a book, it is aware of when pages are on the right or the left side of the book. It comes with some attractive formatting styles, creates a fancy table of contents and lets you insert section-specific bibliographies.

Following the required front matter, my dissertation opens like an academic book, with a table of contents, a list of tables and a list of figures. Memoir generates these automatically with the spell:

<pre>\tableofcontents
\listoffigures
\listoftables</pre>
Following these tables and lists, I have an “Acknowledgments” section and a “Dedication.” I created these with the <code>\chapter*</code> command. <code>\chapter</code> starts a new chapter on the next right-hand page and adds the chapter to the table of contents. <code>\chapter*</code> does the same, but leaves the chapter out of the table of contents. I also used <code>\chapter*</code> to insert prefaces for each chapter that note if the chapter is published, has been presented and credit my collaborators.

=== Converting Articles into <code>Memoir</code> Chapters ===

As described above, I used the <code>\input</code> command to insert a <code>.tex</code> file for chapter into the main document. Each stand-alone article has its own LaTeX preamble, which begins with a <code>\documentclass</code> command and ends with <code>\begin{document}.</code> Since I built my dissertation as a single document, I stripped the preambles from each chapter file and added any dependencies from any of my projects to the preamble of the main file (<code>ETD_version.tex</code>). I also removed <code>\end{document}</code> and <code>\printbibliography</code> commands from the end of the file.

Finally, chapters don’t normally have abstracts, and the <code>\abstract</code> command doesn’t work to insert an abstract in each chapter. Fortunately, you can use the <code>\chapterprecishere</code> command provided by <code>memoir</code> to insert an abstract at the beginning of the chapters.

=== References ===

Normally, a dissertation or other book-length project has a single bibliography at the end. So even though your articles will have their own bibliographies, you’ll want to consolidate them. Fortunately, LaTeX will do this be default. You’ll just need a single <code>\printbibliography</code> command after your last chapter.

To help show off all the work I did during my PhD that’s related to my dissertation project, I included some papers as appendices. Since these were stand-alone papers that weren’t really part of the dissertation, I printed separate bibliographies for each using the <code>\refsection</code> command. Putting an appendix in a separate <code>\refsection</code> makes <code>\printbibliography</code> print only the citations that were used within the appendix.

I didn’t bother creating a new <code>.bib</code> file for the dissertation. I just added symbolic links to the <code>.bib</code> files for my different articles to the project and used the <code>\addbibresource</code> command. I get a lot of <code>Duplicate entry key</code> warnings from <code>biblatex</code> this way, but it’s doesn’t affect the <code>.pdf</code> output.