Update Neotoma_paper.md

Removed some messages that should have been supressed.
merge latest upstream; fix a conflict in .Rmd
Merge pull request #1 from gavinsimpson/master

In-text edits to draft Simon circulated in early July
made a few changes to Neotoma_paper.Rmd, see html escaped comments
Merge pull request #6 from sckott/master

made a few changes to Neotoma_paper.Rmd, see html escaped comments
Cleaning up the directory based on issue #7 from @karthik.  Also includes some changes to the mapping to try to fix issue #4, resolved the issue with changes to the neotoma package, but also changed mapping.
Resolved conflicts caused by my forgetting to pull before I edit.

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

Conflicts:
	Neotoma_paper.Rmd
Fixed bib issues

@Simongoring
I fixed a few issues with the bib file. The ??? you see here:
"These findings basically echo those of Graham et al. (???) who showed that taxon response is largely individualistic."
is because that reference does not exist in Neotoma.bib. You just need to add it in.
Rendered output files

@Simongoring: Make sure these look ok.
Added a Makefile

From the command line, you can type make all to render the PDF and word documents. If nothing in `Neotoma_paper.Rmd` has changed, then it wont unnecessarily rerun things.

With some editors like Sublime Text, it will automatically detect the Makefile and set the build system so a command + B will build all 3 output files (md, docx and pdf)
Working through JWilliams' revisions.  Cleaning code to reflect recent changes to the `neotoma` package that helped clean up the code.

Also recompiled & re-pandoc'd
Added Grimm to bib file.
Text changes up until the Pinus section.  Added Word docs to an alternate directory and created a flag for the locked word docs (~$ files).  Most code changes reflect recent changes to `neotoma`.
Modified files
Meging conflicts
A few comments re:packages
Some changes following a discussion between @andydawson and I.

* minor code revisions to get rid of ggmap, this needs to be finished (i.e., ggmap not completely gone)
* changed if/else statement in top.pine to ifelse.
* reknit the document to make sure some things are working
* removed multiplot and returned the statement to cut out far western sites.
* commented use of reshape2.
Fixed the render file `ToDocX_knit.R`: deleted old copies of the pdf, html and docx files.
* Modified the `top.pinus` function to account for new sites in Neotoma that are short (i.e., only span the last century or two) that were causing problems with the loess smooth.
Deleting unused files
switch some bits of the code to analogue functions as per suggestion in #3