Revisions to address the reviewer comments:
1.  `revision_notes.md`: Added the reviewer comments to an md file to allow us to provide markdown responses inline.  Added responses.
2.  `Neotoma_paper.Rmd`:
*  changed the csl file so that software, entered in the bibtex file as 'Manual' will also show version number.
* Modified abstract in reference to reviewer 1's comments.  In particular revising the last sentence/paragraph to be more explicit.
* Split pgh 2 of introduction, added a link to the Neotoma Manual and clarified the API link.
* Added link to the paleodbR package.
*  Fleshed out the Figure 1 caption.
* Clarified the reference to Alnus pollen arounf Figure 3.
3. Modified the `csl` file and re-saved as `harvard1_mod.csl` so that "manual" type objects provide version numbers.
4.  Added the Neotoma Manual, Cathy Barnowsky's paper and the paleodbR package to the bib file.
5.  Modified `ToDocX_knit.R` to pull from ropensci not SimonGoring.
6.  The alnus-data-plot was updated, but I'm not sure why.  Generally ignorable.
Removed the TODO file, it's old and out of date.  Added the docx and PDF files submitted and somewhat out of date.  Will recompile once I've pulled & pushed.
Changes reflect general cleanup elsewhere.
* Resolved conflict around Figure 1.
* Updated Makefile from `pull`.
* Lots of local changes being resolved.

Merge branch 'master' of https://github.com/SimonGoring/neotoma_paper

Conflicts:
	Neotoma_paper.Rmd
	ToDocX_knit.R
	neotoma_bib.bib
	neotoma_paper.docx
Resolved conflick.  Not sure why it appeared suddenly.  Re-resolves the Figure 1 conflict.