When I was writing my dissertation back in 2010, I was peripherally aware of LaTeX but not so much that I felt like investing the time required to learn how to make a complex document with it, so I ultimately wrote my dissertation in MS-Word and compiled it in a very ugly and sloppy way into what was ultimately reduced to a single file called old-dissertation.doc, written in the old MS-Word document format before they were XML-based. This archive is intended to simplify the process of creating a dissertation using LaTeX that complies with the JHU formatting requirements found here.

1. to make a LaTeX conversion of my MS-Word dissertation (produced in 2010), along with all the LaTeX bells and whistles of internal document links and references as well as integrated bookmarks in the final PDF file.

2. to produce the template I wish I had available to me when I was writing my dissertation back in 2010; a more or less complete minimal working example (mwe) of a JHU-compliant dissertation using LaTeX with all the required parts in the required order.

1. Install a major LaTeX distribution such as TeX Live (multi-platform), MiKTeX (Windows) or MacTeX (Mac OS). The output produced by these files contains dummytext by default from the lipsum package provided in most LaTeX distributions.

2. To compile the included sample document, type latex mwe. If you want to test the references and everything, use the usual magic sequence of commands:

pdflatex mwe
biber mwe # or bibtex mwe
pdflatex mwe
pdflatex mwe

Extra compiles may be needed for and accurate Table of Contents, List of Figures, etc.

I use the outstanding latexmk (Version 4.65) program by by John Collins which can be obtained from CTAN or from the author's website to automate the process of compiling .tex files and cleaning up the unwanted files produced in the compilation process.

I added a bash function to my ~/.bash_profile dotfile of the form

latex-make-and-clean () {
  time latexmk -pdf -pdflatex='pdflatex -file-line-error -synctex=1' "$@" && latexmk -c
  rm *.bbl pdfa.xmpi text/*.aux
  }

which will run pdflatex and biber (or bibtex) as many times as necessary to properly compile the file with references, a table of contents, appendices and so forth. Synctex is incorporated as well. Finally, the current directory and subdirectory text/ are cleaned of superfluous files, while reporting the time elapsed at the end.

As single commands, this looks like

time latexmk -pdf -pdflatex='pdflatex -file-line-error -synctex=1' mwe
latexmk -c
rm *.bbl pdfa.xmpi text/*.aux

I opted for a reductionist approach, seeking to minimize the number and type of files required to produce a document of the desired complexity that compiles without modification, mainly because I remember feeling overwhelmed by the apparent complexity of some LaTeX repos I came across when I was trying to put my own dissertation together. Bearing that in of mind, we have

• mwe.tex – The root LaTeX file containing the LaTeX preamble as well as the "include" statements for each part of the dissertation

• mwe.pdf – A compiled version of the sample document

• classics.bib – A sample BibTeX file containing references to a number of classic scientific works

• figures/ – directory for figure images

• text/ – directory for content files

• jrc-dissertation.pdf - the LaTeX version of John Clayton's dissertation (upon which the mwe was modeled)

• README.md - this document

Figures should be generated as such:

\begin{figure}[p]
  \centering
  \includegraphics[width=\columnwidth]{myfigure}
  \caption{My caption}
  \label{fig:myfig}
\end{figure}

Where the figure myfigure.EXT can be located in the directory designated by the \graphicspath command in the mwe.tex file.

Note that no file extension is given in the includegraphicx command; this makes the code maximally portable for different graphics drivers. For pdflatex, there are many allowable extensions, including .pdf and .jpg among others. For plain LaTeX, you generally have to use .eps files. But, if you hard-code the extension in your LaTeX code, then you will not be able to switch between latex and pdflatex.

I started with old-dissertation.doc, an old 2009-ish MS-Word file (26MB or so) and converted it first to old-dissertation.htm (along with a directory of extracted images figures) with the native Word Version in which it was created. The resulting html file was converted to rich text with textutil -convert rtf and the resulting old-dissertation.rtf file was converted to a LaTeX file with the rtf2latex2e command line tool. Finally, the contents of old-dissertation.tex were split according to line number with sed, as in:

sed -n '47,94p' old-dissertation.tex > abstract.tex
sed -n '97,121p' old-dissertation.tex > thesis-readers.tex
sed -n '122,200p' old-dissertation.tex > preface.tex
sed -n '201,441p' old-dissertation.tex > contents.tex
sed -n '443,582p' old-dissertation.tex > list-of-figures.tex
sed -n '584,599p' old-dissertation.tex > list-of-appendices.tex
sed -n '601,1108p' old-dissertation.tex > chapter-1.tex
sed -n '1110,1779p' old-dissertation.tex > chapter-2.tex
sed -n '1781,2380p' old-dissertation.tex > chapter-3.tex
sed -n '2382,2921p' old-dissertation.tex > chapter-4.tex
sed -n '2923,3020p' old-dissertation.tex > general-discussions-conclusions.tex
sed -n '3022,4122p' old-dissertation.tex > references.tex
sed -n '4124,4523p' old-dissertation.tex > appendix-i.tex
sed -n '4525,5010p' old-dissertation.tex > appendix-ii.tex
sed -n '5012,10950p' old-dissertation.tex > appendix-iii.tex
sed -n '10953,11342p' old-dissertation.tex > cv.tex
sed -n '11344,11373p' old-dissertation.tex > biographical-sketch.tex

The line numbers were manually derived from old-dissertation.tex in vim

• Added each .tex file split from old-dissertation.tex to text/ directory

• These files were then integrated into the project and modified as necessary to compile

• Added bib file generated from the BibDesk reference manager and tweaked as necessary

• removed rnw_chapter directory

• removed color profile

• incorporated link color from RJournal_nogeom.sty

• removed RJournal style file

• adjusted title page to JHU specifications based on example files and pointsize while removing most vspace calls in favor of adding space after forced line breaks as a multiple of baselineskip.

• incorporated thesis readers into abstract.tex

• The original thesis.cls class file was authored by Ian Goh (in 1999, based on the .clo files) and primarily based on the UCTHESIS document class for LaTeX version 2e by Blaise B. Frederick and Ethan Munson from 1994
• format.tex was created independently of thesis.cls by Chuanfa Guo in the Biostatistics department of JHPSH on October 26, 1998
• The thesis.cls class file for JHU was updated by Matt Clapp on November 11, 2005
• The report-class based template was created by R. Jacob Vogelstein in May, 2007
  • Updated by Noah J. Cowan on March 1, 2010
  • Updated by Brian D. Weitzner on April 29, 2014 as available at GitHub
  • Updated by John Muschelli on January 29, 2016 and now uses a makefile as available here
  • Updated by Leonardo Collado Torres on April 13, 2016 as available at this repo
  • Forked by John Clayton in December, 2019 as available at this repo