Warning

This package was last updated on May 22, 2014. Before submitting the final draft of your thesis, double check with the Graduate Division that everything is kosher (e.g., the margins are properly sized, the front page is properly spaced, etc.).

To access these templates, by themselves, just download (or clone) this repo, and check out the templates in the inst/ directory.

Installation

xelatex

The package functions rnw2pdf and rmd2pdf make system calls to xelatex (and biber). These normally come installed on OS X and Linux systems. Double check that they are accessible by running the following at the command line:

which xelatex
which biber

pandoc

This package uses pandoc to convert markdown (.md) files to latex (.tex) files. rmd2pdf will not run unless pandoc is accesible via the command-line. I.e., which pandoc returns a non-null string.

This version was tested on pandoc version 1.12.4, however the version available in the ubuntu software center (1.12.3) should suffice. If it doesn’t you’ll have to manually install pandoc and create system links via

sudo ln -s /full/path/to/.cabal/.bin /usr/local/bin

And then double check that everything works with

which pandoc

the actual package

To install this as an R package, and therefore access the templates, as well as the helper functions rnw2pdf and rmd2pdf, you can either clone this repo, and build the package manually, or use devtools via:

library(devtools)
devtools::install_github(repo = "ucbthesis", username = "stevenpollack")

I don’t forsee this package every making it to CRAN (though it passes all the checks), so this is your best means of obtaining this code.

Usage

Latex

If you know latex, the R code in this package is worthless. You’ll want to pull down the files in inst/latex and modify those files accordingly.

Knitr

If knitr is your bag, the templates in inst/knitr are what you need. The files chap1.Rnw, chap2.Rnw and abstract.Rnw demonstrate the parent-child document model implemented by knitr. Be warned: child documents are sensititve to white space at their head’s, so make sure there are no lines ahead of the code chunk:

<<cache=FALSE, echo=FALSE>>
set_parent("parent-document.Rnw")
@

in the child document.

Once you’ve written your .Rnw and want to compile it into a .pdf to see that everything’s a-okay you have two options:

  1. If you’re using RStudio: just hit the compile button (CTRL+SHIFT+I).
  2. If you’re not using RStudio: change your working directory to the location of your .Rnw (yourFile.Rnw) file and run rnw2pdf('yourFile.Rnw'). See the help documentation for rnw2pdf for more details.

R Markdown

If you’re using R Markdown (and I don’t necessarily suggest you do, as this is your thesis), then you’ll want to check out the use case in inst/rmarkdown.

This package includes the function rmd2pdf which performs the following:

.Rmd
  \
   ----- knitr ---> .md
                    /
.tex <-- pandoc ---
 \
 xelatex + biber 
            \
             --> .pdf

inst/rmarkdown includes a file, thesis_template.latex which is a pandoc template to facilitation the conversion from .md to .tex. This template is how you specify the latex preamble to that xelatex processes to make the final .pdf. Modify the preamble in this document as you would with any latex document. For example, if you need the amsmath package for your dissertation, add \usepackage{amsmath} somewhere before \begin{document} in the .latex template.