This project provides a template for writing a PhD thesis in R Markdown, and rendering those files into a PDF formatted according to the requirements of the University of Washington. It uses the University of Washington Thesis class to convert R Markdown files into a PDF formatted ready for submission at UW. This project was inspired by the thesisdown and bookdown packages.
Currently, the PDF and gitbook versions are fully-functional. The word and epub versions are developmental, have no templates behind them, and are essentially calls to the appropriate functions in bookdown.
If you are new to working with bookdown and rmarkdown, please read over the documentation available in huskydown PDF template and the bookdown book.
Under the hood, the University of Washington Thesis LaTeX template is used to ensure that documents conform precisely to submission standards. At the same time, composition and formatting can be done using lightweight markdown syntax, and R code and its output can be seamlessly included using rmarkdown.
Using huskydown has some prerequisites which are described below. To compile PDF documents using R, you need to have LaTeX installed. It can be downloaded for Windows at http://http://miktex.org/download and for OSX at http://tug.org/mactex/mactex-download.html. Follow the instructions to install the necessary packages after downloading the (somewhat large) installer files. You may need to install a few extra LaTeX packages on your first attempt to knit as well.
We use some fonts, EB Garamond, Source Code Pro and Lato, that all are freely available online if you don't have them already. You should install these before proceeding.
On a Linux system, this should give you what you need:
sudo apt-get update
sudo apt-get install texlive-xetex -y
sudo apt-get install texlive-bibtex-extra biber -y
sudo apt-get install fonts-ebgaramond -y
wget https://github.com/adobe-fonts/source-code-pro/archive/1.017R.zip
unzip 1.017R.zip
sudo cp source-code-pro-1.017R/OTF/*.otf /usr/local/share/fonts/
sudo apt-get install fonts-lato -y
On an OSX system, assuming MacTeX and homebrew are installed and updated, this will get you the fonts and other LaTeX packages needed for this template:
brew update
brew tap caskroom/fonts
brew cask install font-eb-garamond font-source-code-pro font-lato
sudo tlmgr update --self
sudo tlmgr install biblatex titling titlesec quotchap lettrine appendix units tocloft draftwatermark everypage wasysym logreq xstring collection-fontsrecommended texliveonfly
On Windows the usual pointing and clicking is required to download and install LaTeX and the fonts listed above.
To use huskydown from RStudio:
-
Assuming you have already installed LaTeX and the fonts described above, install the latest version of RStudio. You can use huskydown without RStudio. For example, you can write the Rmd files in your favourite text editor (e.g. Atom, Notepad++). But RStudio is probably the easiest tool for writing both R code and text in your thesis.
-
Install the bookdown and huskydown packages:
if (!require("devtools")) install.packages("devtools", repos = "http://cran.rstudio.org")
devtools::install_github("rstudio/bookdown")
devtools::install_github("benmarwick/huskydown")
- Use the New R Markdown dialog to select Thesis, here are the steps, and a screenshot below:
File -> New File -> R Markdown... then choose 'From template', then choose 'UW-Thesis, and enter index as the Name. Note that this will currently only Knit if you name the directory index at this step.
Or if you're not using RStudio, run this line to create a new PhD thesis from the template:
rmarkdown::draft('index.Rmd', template = 'thesis', package = 'huskydown', create_dir = TRUE)- Edit the individual chapter R Markdown files to write your thesis.
To render your thesis, open index.Rmd in RStudio and then hit the
"knit" button. To change the output formats between PDF, gitbook and Word ,
look at the output: field in index.Rmdand comment-out the formats
you don't want.
Alternatively, if you're not using RStudio, you can use this from the R console:
bookdown::render_book('index.Rmd', huskydown::thesis_pdf(latex_engine = 'xelatex'))Your thesis will be deposited in the _book/ directory.
The following components are ones you should edit to customize your thesis:
This is the main configuration file for your thesis. Arrange the order of your chapters in this file and ensure that the names match the names in your folders.
This file contains all the meta information that goes at the beginning of your document. You'll need to edit this to put your name in, the title of your thesis, etc.
These are the Rmd files for each chapter in your dissertation. Write your thesis in these. If you're writing in RStudio, you may find the wordcount addin useful for getting word counts and readability statistics in R markdown documents.
Store your bibliography (as bibtex files) here. We recommend using the citr addin and Zotero to efficiently manage and insert citations.
Specific style files for bibliographies should be stored here. A good source for citation styles is https://github.com/citation-style-language/styles#readme
Store your figures and data here and reference them in your R Markdown files.
This project has drawn directly on code and ideas in the following:
- https://github.com/UWIT-IAM/UWThesis
- https://github.com/stevenpollack/ucbthesis
- https://github.com/suchow/Dissertate
- https://github.com/SeungkiKwak/Kwak_S_PhD_thesis
- https://github.com/dhalperi/uwthesis-tweaked
Other relevant projects:
- Ed Berry's blog post 'Writing your thesis with bookdown', Posted on September 25, 2017
- thesisdowndss by Mine Cetinkaya-Rundel at Duke University
- beaverdown by Zhian Kamvar at Oregon State University
If you would like to contribute to this project, please start by reading our Guide to Contributing. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.