So, first I will say a little bit about the general problem, and then I will tell you something specific: how to take the draft of a scholarly paper, typically including bibliographical references, figures, and the results of some data analysis, and turn it into nice-looking PDF and HTML output. The hopefully redeeming thing about this discussion is that it will help you use the various resources I make available for doing this.
Update (2014-01-28): Dr. Drang:
The Markdown file is processed by a shell script,
md2report, which spits out a LaTeX version of the report. Most of the time this file is ready to be processed by
pdflatex, which also gathers in all the images files and creates the PDF output. If the report needs a particularly complex table, or if I need to tweak the spacing somewhere, I’ll go in and edit the LaTeX file directly. This is pretty rare, which is why I’ve grayed out my input to the LaTeX file. The great majority of my reports need no direct LaTeX input from me.
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