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}
*R
ggplot2