README.md

In SeungkiKwak/Kwak_S_PhD_thesis: Sungki Kwak's PhD Thesis

Seungki Kwak's PhD Thesis

This research compendium contains the source files for my PhD. It is organised as an R package that contains a function that will render the R markdown files into a single attractive PDF that conforms to the UW Graduate School requirements for thesis formatting. The thesis chapters, figures and raw data files are in the inst/rmarkdown_template directory.

Installation

The most convinent way to access the files in this compendium is to download the zip file and unzip on your computer, or clone this repository to your computer with this line at the terminal:

git clone https://github.com/SeungkiKwak/Kwak_S_PhD_thesis/

Then open the Kwak_S_PhD_Thesis.RProj file in RStudio to explore the compendium. The PDF file of the thesis, along with other supporting material, is in the inst/rmarkdown_template directory .

To install this as an R package, and access the thesis files, use devtools with the following lines at the R prompt:

install.packages("devtools")
library(devtools)
devtools::install_github("ropensci/dependencies") # non-CRAN dependency
devtools::install_github("SeungkiKwak/Kwak_S_PhD_thesis")
library(kwakthesis)

Build the thesis

If you want to rebuild the PDF file of the thesis, you'll need to make a copy of this repository as indicated above, then change the working directory in R to inst/rmarkdown_template and use the function rmd2pdf to make a PDF file of the thesis, like this:

rmd2pdf("thesis.Rmd")

Dependencies

You may need to install some additional software before you can build the PDF. In particular, the process depends on Xelatex and pandoc. You can check to see if you have these by running these lines at a shell prompt:

which pandoc
which xelatex
which biber

If you don't have one of these, you can install from the shell prompt like so (these instructions are for Linux, if you're using Windows or OSX, go to Google for instructions specific to your system and Xelatex installation):

# for pandoc
wget https://github.com/jgm/pandoc/releases/download/1.13.2/pandoc-1.13.2-1-amd64.deb
sudo gdebi pandoc-1.13.2-1-amd64.deb
# for biber
sudo apt-get install biber
# for xelatex
sudo apt-get install texlive-full
# for font EB Garamond
sudo apt-get install fonts-ebgaramond
# for font Source Code Pro
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/
# for font Lato regular

Acknowledgements

For acknowledgements relating to the PhD project, please see the PDF in inst/rmarkdown_template. Here I acknowledge projects that I have drawn from to create this repository (and not the PhD thesis). This compedium contains source code and formatting ideas from the following sources:

• Latex, Knitr, and RMarkdown templates for UC Berkeley's graduate thesis
• Jim Fox's LaTeX Class file for University of Washington thesis formatting
• Dissertate: a LaTeX dissertation template to support the production and typesetting of a PhD dissertation at Harvard, Princeton, and NYU

SeungkiKwak/Kwak_S_PhD_thesis documentation built on May 9, 2019, 1:22 p.m.