2025-dotson-dissertation

This repository holds my preliminary exam document. The style guide comes from the University of Illinois Urbana-Champaign Graduate College. A link to the resources may be found here.

Reproducing the Analysis

Many of the plots that were present in the original preliminary document were produced using a juptyer notebook. The analyses new to this thesis were developed using a snakemake workflow. This repository includes an environment.yaml file to facilitate reproducibility of this work.

Prerequisites

This workflow assumes users have a working installation of the following

• mamba/conda (package dependency and environment management tools)
• LaTeX
• biber (per the recommendation from the UIUC Graduate College)

Setting up the environment

To set up the mamba environment, run the following commands in either command prompt or terminal.

bash cd 2025-dotson-dissertation mamba create mamba activate 2025-dotson-thesis

Running the workflow

The snakemake workflow used here is shown by the DAG below.

To run execute the snakemake workflow run the following commands in either command prompt or terminal.

bash cd analysis snakemake --cores=1

[!NOTE] Why use snakemake to build the dissertation when there is already a Make file in the docs directory?

Primarily because Windows can't execute make. There are additional advantages as well. snakemake is arguably easier to understand and produces a nice DAG model of the workflow itself. Further, the analysis is meant to be run sequentially.

Compiling the dissertation

If you only want to reproduce the document itself without running any analysis, here are the following instructions.

Windows

The document style must be compiled using biber. Doing this from the command line is more reliable than modifying TeXworks or other editor (I have experienced issues with Windows blocking a biber.exe call from TeXworks). Make sure your LaTeX installation is up-to-date.

bash C:\Users\samgd\Research\2025-dotson-dissertation\docs>pdflatex -shell-escape 2025-dotson-thesis.tex C:\Users\samgd\Research\2025-dotson-dissertation\docs>biber 2025-dotson-thesis # This is not a typo. Do not include a file extension. C:\Users\samgd\Research\2025-dotson-dissertation\docs>pdflatex -shell-escape 2025-dotson-thesis.tex C:\Users\samgd\Research\2025-dotson-dissertation\docs>pdflatex -shell-escape 2025-dotson-thesis.tex

Unix

bash $ cd 2025-dotson-dissertation/docs $ make

From the template repository

uiucthesis class

A LaTeX package for formatting theses in the format required by the University of Illinois at Urbana-Champaign.

Update Notes

• 3.1a (Samuel G Dotson)
  • Adds prelim macro
• 3.1 (Zachary J Weiner)
  • Format table of contents entries with titletoc, prepend "Chapter" and "Appendix"
  • Place appendices after references, returning to \mainmatter so that appendices are still numbered
  • Add copyright and licensing information
• 3.0 (Zachary J Weiner)
  • Significant revision, obsolete options removed and source simplified
• 2.25b (Stephen Mayhew)
  • Removed the Vita Section
  • Added a Makefile
  • Changed all dates from 2009 -> 2014
  • Be careful when updating the date in the first line of uiucthesis2021.dtx! All numbers must be two digits, including month and day.