TeX’n Your Diss

Based upon the old page here

This page is devoted to comments from various students that have written their dissertations in LaTeX. The UO grad school has discontinued any support for writing in LaTeX, so this is a place for students to share information regarding issues that may have come up for them during the process.

 

Tyler Harvey (June 2017)

  • Read all the advice past physgrads have issued before you start or not long after
  • Start with the latest uothesis.cls (currently Ryan’s, with one new line from Roger; attached below) and possibly replace it as soon as somebody sends a new one out. I started with Matt Jemielita’s a while ago, and it turns out Ryan and Roger’s updates solved some of the complaints the dissertation editor raised.
  • Write your dissertation in a day with this one weird trick: write up and publish all of your work, early and often, so that the actual dissertation “writing” is just formatting and an introduction and a conclusion, which, yes, could take as little as one day
  • Do turn in a content and style request form a quarter before you intend to graduate, because I think that takes some of the heat off as far as adherence to arbitrary formatting guidelines from the dissertation editor (also you theoretically have to if you want to include any data that anyone helped you take). if you do this, I think you can basically ignore all of the guidelines in the ETD style manual that relate only to the body of the dissertation and focus on formatting the preface correctly. the UO recently retired out the local dissertation editor position, and whoever does it now probably doesn’t read past page 1 if you’ve turned in a content and style request form. the manual says to put supplementary material in appendices at the very end of the dissertation, but that makes the dissertation really disjointed to read, so I just put it right after the respective paper and got no complaints. in retrospect, I probably also would have just kept abstracts with the respective papers, too, rather than putting them all in the introduction. because that’s “journal format”, right? I did, on the other hand, get like 5 complaints per page on the preface.
  • Don’t actually try to preserve the formats of all your nice previously published papers. you will fail. the grad school has some formatting requirements that the form above doesn’t free you from, so you can’t just literally staple the PDFs together, and you really don’t want to hack together the style files from multiple journals into one. I’ve attached an example of a neutered paper where I hacked together a table to make the title and authors list, as well as the original paper for comparison.
  • Publish open-access when possible. if you can convince your advisor to shell out $1.5k-$5k for open access for every paper you intend to include in your dissertation, it makes acquiring the copyright permissions to re-use material from already-published papers really easy (i.e. you already paid for that right, so you don’t need to do anything).
  • Make sure all your section names are short. Ryan’s updates to uothesis.cls allow for longer-than-one-line figure and table names in the Table of Contents, but section names longer than one line will cause you as-yet-unsolvable formatting issues. just don’t do it. if you really want to keep your long section names, prepare to learn some really low-level LaTeX macros and consider self-flagellation and short section names as more fun alternative.
  • The grad school may eventually change their formatting guidelines in a way that breaks the last best physgrad’s uothesis.cls. if this happens, seek help and alternative class files. This one could be good in that situation. whoever maintains it added an option for subsections in the table of contents, which could be nice.

 

Roger Smith (August 2016)

In addition to all the things below, I found some issues with the references cited. More specifically, I did not particularly like the “unsrtnat” style within the natbib package. Instead, I chose the OSA Journals bib style, “osajnl.bst” from the OSA publishing website.

A general comment: to force LaTeX to make bibliography entries have capitalization, enclose the proper noun in curly brackets, for example:[ title = {Quantum cryptography based on {Bell’s} theorem},]

After submitting my dissertation to the graduate school, I was informed that my title was not reverse pyramid (uothesis.cls does not have this as a default), my CV did not have the proper spaces after certain headings (I commented out some vertical space lines in my .cls file on accident), and I did not have enough leading dots for my table of contents pages. The first two were easy fixes – I introduced a line skip in the title (\\ in LaTeX) and uncommented the commands to put in extra paces. The dots were a bit more challenging to figure out after having no experience with class files.

The graduate school requires that you have at least 3 dots between a title and the page number in the ToC, ToF, and ToT. In the class file, the command that puts all the dots in is \dottedtocline{level}{indent}{numwidth}{text}{page} The text and page arguments should follow from your document when you put in a section, figure, or table. The level is the nesting level. The indent is the total indent from the left margin. The numwidth is the width of the box if there is a \numberline command in text. You can adjust the numwidth to shorten the word box and make a larger separation between the number and the words – when my figures went to double digits (i.e. Figure 2.10), the word and the numbers ran together.

To make it so that the titles go to the next line (which the graduate school mandates if there are less than 3 leader dots), then include the following command

\renewcommand{\@tocrmarg}{6.5em}

This changes the Table of Contents right margin to the final argument. For me, 6.5em made it so that the section headings that were too long went to the next line, but the figures that had the proper number of leading dots were preserved (I changed a bunch of headings to make them shorter after the first round of comments).

 

Ryan Quitzow-James (July 2016)

Continuing the long tradition of recently graduated students passing on their modified uothesis class file, I’m sending my modified version!

The main thing this class file fixed is the alignment in the list of tables and the list of figures at the beginning. Previously the text would often invade the page number column if there were more then one line in the (often shortened) caption in the list. In addition I removed the hanging indent on the descriptions in these lists, but that should be pretty easy to add back in if you want.

I also did some minor work on improving the consistency of how dots were added to subsections etc. Previously there were some cases where there were either missing or added dots at some part in the hierarchy. Another adjustment was to the horizontal position of the chapter names in the Table of contents. The chapter number was overlapping with the chapter title for some of my titles, so I changed the horizontal positioning to fix that. There is also an adjustment I made to the dedication portion, mainly making it raggedright.

That’s all I remember for now. Main thing was really the fix to the alignment in the list of figures and list of tables. That was the big issue the graduate school wanted me to fix when I submitted it to them.

 

Matt Jemielita’s comments (sometime in 2015)

  • University of Oregon thesis class
    • There are numerous University of Oregon thesis classes floating around on the internet. The copy of this class available on CTAN is unfortunately out of date and doesn’t conform to the standards set out by the Graduate School. Below I’ve included a copy of a University of Oregon thesis class that worked in the summer of 2015. Additionally, I’ve included all the files that you need to assemble your dissertation. When downloading this file make sure to save over the uothesis.cls that may have come with your distribution of Tex. The biggest difference, as far as I can tell, between the version on CTAN and the one they currently accept is that the most up-to-date version has dots after all the figure numbers in the table of contents. The graduate school really cares about these dots.
    • Below I’ve attached template files for your dissertation.
    • With this thesis class there are a handful of small problems that I had:
      • When adding \label{} to any section of the dissertation the space between the header and the subsequent text was single instead of double spaced. While not elegant, my solution was to add \vspace{24pt} immediately after any time I used \label{}.
      • The roman numerals on the prefatory pages sometimes are not all at the same height. This problem goes away if you use all the commands in the thesis.tex file linked to above.
  • Make captions for figures like this:
    • \caption{Short text that additionally goes into table of figures}{Longer, more explanatory text}
  • Bibliography style. The graduate school claims on their thesis submission form that only a certain range of bibliography styles are accepted (APA, ACS, MLA, Chicago, or Turabian) and that you need to provide an example if you use anything else. I used unsrt, a default bibtex style, without providing any other examples and the thesis editor was okay with this. There’s no guarantee of course that this will be the case in the future.
  • Version tracking
    • If you use some type of software for version control you can keep track of changes you and your adviser have made without going too crazy. Git is currently the most popular version control software. Various companies provide online hosting for version controlled software-two popular ones are GitHub and BitBucket. This online service can additionally function as a backup of your dissertation. If using version control, put every new sentence on it’s own line otherwise the changes will not be tracked appropriately.
    • Alternatively, if you’re okay with having slightly less control over your version you can use Dropbox for storing your thesis. Dropbox has a nice feature where you can access previous versions of every document in your folder (this may only be the case on the paid version of Dropbox). This is what I used and it provides a great deal of peace of mind with basically no work on your part.
  • Depending on the number of images in your dissertation the tex’d version may be rather larger. Compress the file by running on the command line:
    gs -sDEVICE=pdfwrite -dCompatabilityLevel=1.4 -dPDFSETTINGS=/prepress -dNOPAUSE -dQUIET -dBATCH -sOutputFile=out.pdf in.pdf
    This command (which I don’t understand at all) compresses the document to the resolution used in whatever readers are used for previewing so you’re not really down-sampling the pdf.
  • XeLeTeX/LuaTeX: These other Tex distributions provide additional font support not provided in LaTex.
  • Software for Latex (Max OSX only)
    • TeXShop is a quite good free editor that works without a lot of fuss.
    • I used Texpad ($25) for writing my dissertation. It was well worth the money and gives additional features like auto-compile and a dual screen mode (tex and pdf).
  • The package ‘todonotes’ provides nice support for adding notes into the pdf about changes you still need to make.
  • It’s possible to make an appointment to talk with the thesis editor. I did this and it was well worth my time.

 

Mike Taormina (sometime in 2014)

Mike left these notes for Matt J. above. I (RAS) have added in my comments on what I believe the notes mean in italics.

  • draftcopy  – this can be fed into the header to change the look of the dissertation for editing purposes. This is documented in the uothesis.pdf file.
  • \ednote, \needref, \here – These comments can be used in draft copy as comments for the writer to remember later. These commands put marks into the draft pdf as reminders
  • natbib options: sort&compress, numbers – These two options can be put into the header as well and are good to use for the dissertation. They are documented in the pdf as well.
  • numsections – This header command numbers the individual sections in a particular way, in contrast to gsmodern.
  • TexShop: (I believe these commands are specific to TexShop, but I didn’t use it and am not completely sure.)
    • %! TEX root =    (for chapters)
    • %! TEX TS-program =
    • %! TEX encoding =
    • Overpic (overlay figure labels)