JHU Unofficial Thesis Readme

Author: R. Jacob Vogelstein
Updated by Noah J. Cowan, March 1, 2010
Updated by Brian D. Weitzner, April 29, 2014 as available at GitHub and as an Overleaf template as uploaded by Karla Hernandez (see how to support PDF/A files at the end of this README)
Updated by John Muschelli, 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 or as an Overleaf template (The template is missing this small change).

This archive is intended to simplify the process of creating a thesis in LaTeX that complies with the JHU formatting requirements found here.

Makefile version

Muschelli added a makefile and Rnw files to his thesis. Collado Torres simply took Muschelli's thesis, made it into a template and submitted it to Overleaf. The rest of the README is as-is from the time Weitzner modified. To use this version you will have to modify the main.tex file and add chapters as necessary. Then you will have to update the makefile with the names of the new chapters.

If you want to reproduce the current PhD_Thesis.pdf file, simply run

make

To clean the files that you won't need, run

make clean

To open the PDF file run

make open

Finally to start editing main.tex run

make edit

The file RJournal_nogeom.sty is used to change the color of some links and other style changes.

It might be best to simply clone this repository, start editing and committing your changes in case you want to rollback or remember why you changed something.

If you want to check a complete PhD Thesis see John Muschelli's. It contains more LaTeX tricks that you might need to use.

Use at Overleaf

If you don't want to install LaTeX simply use Overleaf or ShareLaTeX. You won't need the makefile in that case.

In particular, you might want to see this read-only version at Overleaf. It doesn't have a makefile because they are currently not supported (see this tweet). Also, the Rnw chapter is basically a regular chapter when using Overleaf since you have to create the tex file yourself using knitr::knit() and upload the resulting tex file and figures to Overleaf.

To go ahead and use this template in Overleaf, go to the Overleaf template and click on open as template.

Previous information

The files described below are still available under the unused_files directory. Some of the previous information is still valid. You might be interested in using either the files last edited by Brian D. Weitzner at weitzner/jhu-thesis-template under commit d8ba0a or the original JHU-Biostats template included here as unused_files/OLD_FORMAT.tex.

Quick Start

Install LaTeX and a decent editor (ideally emacs+AUCTeX+RefTeX) on your computer.
To compile the included sample document, type "latex root". If you want to test the references and everything, use the usual magic sequence of commands:

pdflatex root
bibtex root
pdflatex root
pdflatex root

Extra compiles may be needed for accurate TOC, List of Figures, etc.

What's Included?

thesis.cls – The TeX class file that contains many of the formatting commands.
jhu12.clo – The 12pt font "class option" file that contains the specific formatting commands for a 12-point font JHU thesis document.
IEEEtran.bst – A recent version (as of May 2007) of the BibTeX style file for formatting citations in the style used by IEEE Transactions journals.
thesis.bib – A sample bibliography file in BibTeX format.
root.tex – The "root" LaTeX file that contains the LaTeX preamble as well as "include" statements for each of your thesis chapters.
chapter0.tex – A sample chapter with some formatting/header options.
chapter1.tex – Another sample chapter with some different formatting/header options.
rjvheadshot.jpg – A sample graphic with the right dimesions for the headshot used on the Vita page.
root.pdf – A compiled version of the sample document.
jhu10.clo – USE AT YOUR OWN RISK – An old version of a 10pt font "class option" file that DOES NOT FULLY COMPLY with the JHU thesis formatting requirements, but is better than nothing if you want to use a smaller font.
jhu11.clo – USE AT YOUR OWN RISK – An old version of an 11pt font "class option" file that DOES NOT FULLY COMPLY with the JHU thesis formatting requirements, but is better than nothing if you want to use a smaller font.

Figures

Figures should be generated as such:

\begin{figure}[htbp]
  \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 root.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.

Use at Overleaf

The version by Brian D. Weitzner is available as an Overleaf template that Karla Hernandez uploaded. View it here. Note that it does not include support for PDF/A files as of the version available on April 13, 2016. However, you can add PDF/A file support by following the instructions available here.