📘 PhD dissertation Appendix A online reference: R code 📘

R functions and code for the PhD dissertation of Tyman Stanford @ github.com/tystan/thesis/.

Statistical analysis of proteomic mass spectrometry data for the identification of biomarkers and disease diagnosis. The University of Adelaide, 2015.

📙 Navigation 📙

The files referenced below are hyperlinked for ease of navigation.

• A PDF version of the R code used and referenced throughout the dissertation is available in AppendixRCode.pdf.
  • This contains all the relevant R code in one syntax highlighted self-contained document.
• The individual R files are available in the R/ directory.
  • The files are numbered so as to be ordered in sequence of appearance in the dissertation and AppendixRCode.pdf.

---

---

---

📗 The information below is unlikely to be of interest unless attempting to reproduce AppendixRCode.pdf using LaTeX 📗

• The top-level file AppendixRCode.tex is the TeX file required to generate AppendixRCode.pdf.
  • The directory tex/ contains the source files referenced in AppendixRCode.tex.

Pygments

The Pygments command-line tool was used to perform syntax highlighting and mathematical notation markup from source code comment text. Pygments can convert R files (and many other programming languages) into syntax highlighted Verbatimenvironment LaTeX markup as .tex files. Many thanks to the authors and maintainers of this freely available software.

• The file perform_pygmentisation.sh is the command-line input (for unix-alike platforms) used to convert the files in R/ to the files in tex/. This requires Pygments to be installed.

Installing pygments

The following steps were required to install Pygments:

#### download `get-pip.py' from: https://bootstrap.pypa.io/get-pip.py

#### then in terminal/shell, move to the location of get-pip.py
cd ~/{dir-location-of-get-pip.py}
#### and run get-pip.py in python: (use `sudo' for admin access)
sudo python get-pip.py

#### now to install pygments, type:
sudo pip install pygments
#### how'd it go? (there should be files listed here)
pip show --files pygments

A more thorough treatment is available at the download pages of Pygments and pip should it be required.