update simmap example in manuscript
embed image
Update manuscript.md
Update manuscript.md
Fixed capitalization screwup in some code examples

Sorry, I did a search and replace s/nexus/NEXUS/i but it messed up `read.nexus` and such. Fixed now.
fix notation in simmap test
Merge branch 'devel' of github.com:ropensci/RNeXML into devel
add contributing guidelines
handle image generation automatically
notes on caching
just use imgur, since flickr uploading isn't portable across users
cannot use $ in Rscript -e command in makefile. oh well
updated readme
updated manuscript.Rmd with @rvosa's edits, regenerate manuscript.md