# Markdown for Manuscripts: Enhancements

Today was my first time using markdown for a manuscript methods section (see previous post on getting set up in markdown). It had lots of equations so using LaTeX to write the equations was quite nice. Here’s an example of the markdown code:

\$\mu_{s,h,d,y} = \left\{ \begin{array}{1 1} \omega_{s,h,d,y} + \delta_{s}(t_{s,h,d-1,y} - \omega_{s,h,d-1,y}) & \quad \text{for t_{s,h,d-1,y} is real} \\ \omega_{s,h,d,y} & \quad \text{for t_{s,h,d-1,y} is not real} \end{array} \right. \$

where $\delta_{s}$ is an autoregressive [AR(1)] coefficient
that varies randomly by site and $\omega_{s,h,d,y}$
is the expected temperature before accounting for temporal
autocorrelation in the error structure.


which nicely renders in HTML (or PDF) as seen in this screenshot. This was quite refreshing as I always have headaches with MS Word Equation Editor. Mostly, I just wanted to write a quick post to share some of the tools I found useful while doing this. In the screenshot above I was editing in Sublime Text and doing the automatic preview in Marked 2. It’s the first time I’ve moved away from Mou, which was a nice editor with built-in preview but I wanted to take advantage of some of the higher end features of Sublime Text and Marked 2. I’m glad I did. I’m using trial versions but will definitely buy them this week. Great software!

## Automate pandoc

pandoc-watch Makefile to convert all markdown files in a directory to PDF

## LaTeX Symbols and Math

http://martinkeefe.com/math/mathjax3 (fantastic resource)

http://en.wikibooks.org/wiki/LaTeX/Mathematics

http://www.artofproblemsolving.com/Wiki/index.php/LaTeX:Symbols