Moved the Rmd file over from the aboted Sweave file.  Added more references to the bibtex file in preparation to programmatically add them in.  Compiled the paper.
Moved the funciton `compile_it` into the R directory, will add it to the base neotoma package at some point though.

Roughly finished Russ' example.
Moved the markdown branch header over.
Merged the markdown branch back into the master.  I'm going to try to manage branches better, we'll see how it goes.

Merge branch 'markdown'

Conflicts:
	Neotoma_paper.Rmd
Ran a trial of Pandoc to PDF using the (improperly named) file `ToDocX_knit.R`.  Seems to run well, but some problems with the citations and the `kable`s.  Otherwise, things look good.  Analysis is basically done, so it's just text at this point.
Merged with master