thesis-template-with-knitr

Thesis template with individual chapters as different Sweave/knitr

I used Sweave/knitr to generate (majority of ) analyses and the figures in my thesis. I used the style files in https://github.com/weitzner/jhu-thesis-template

Each chapter is a separate Rnw file. The Rnw files include R code chunks which are run with knitr ( http://yihui.name/knitr/ ), and the tex files are generated with the figures as outputs of the R chunks. For fast simulations/analyses this works nicely, as you don’t need to remember which R script you used to generate a figure. For simulations that take a long amount of time, there is a cache option, so that the R code chunk is not run unless you made a change.
I would suggest using RStudio so that you can do version control, running simulations and building a pdf in one software tool.

A non-complete list of requirements:

*Latex (Miktex can install them automatically)
These are some Latex packages that are required for building a pdf (available in MikTex distribution).
media9
\usepackage{cmbright} %clean look
\usepackage{cite}
\usepackage{amssymb,amsmath,amsthm,amscd}
\usepackage{pgfplots}
\usepackage{graphicx}
\usepackage{subcaption}
\usepackage{ mathrsfs, bm}
\usepackage[pdfa]{hyperref}
\usepackage{algorithm2e}
\usepackage{url}
\usepackage{ragged2e}
\usepackage{fixltx2e}
\usepackage{array}

\usepackage{wrapfig}
\usepackage[T1]{fontenc}
\usepackage[latin1]{inputenc}
\usepackage{verbatim}
\usepackage{multirow}
\usepackage{fancyhdr} % Use nice looking headers along with the required footer page numbers

\usepackage{lscape}
\usepackage[refpage]{nomencl}
\usepackage{makeidx}

%shorthand commands
\input{common.tex}

\usepackage{hyperxmp}
%\usepackage[T1]{fontenc}
%SA: This package is not necessary unless you want to create a slideshow-like plot window like I did.
\usepackage{animate}

ggplot2