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. latex_example 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

Editors

Karthik Ram’s list: https://github.com/karthik/markdown_science/wiki/Tools-to-support-your-markdown-authoring GNU Emacs Emacs for Mac OS X Sublime Text 3 – $70 at time of writing

Table Support/Generator

Sublime Table Editor – Table Editor is a ST2 and ST3 package for edit simple text tables in text mode, markdown mode, textile mode, reStructuredText mode etc. Table Editor is very similar to Emacs-org mode table editor with almost the same keys. Emacs as table mode for this Tables Generator is a web-based tool for generating markdown tables Create Tables with knitr

Preview

Mou previews automatically and is simple and clean, but has few extra tools Marked is a markdown previewer for OS X ($13.99 at time of writing)

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

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