Markdown

Since I used the Markdown language for the first time, I do all my notes in this particular style, because I think it is very easy and it just makes sence.

The structure of your thesis may look like this:

# Introduction

# First Chapter

## First Sub Chapter

## Second Sub Chapter

# Second Chapter

# Third Chapter

# Discussion

The command \tableofcontents builds the table of contents out of your headers and sub headers and looks really clean. Furthermore you can include number_sections = true in the YAML header to number the sections of your thesis, which is a good idea.

Besides the headers Markdown also handles the format of text.

*italic* **bold** different font

If you have many variables, the readability of your thesis may profit if you to make them italic or in a different font. My variables had indices, therefore I could not use pure Markdown, but a \(\LaTeX\) command, which may look like this: $variable_{it}$ and results in \(variable_{it}\).