Merge pull request #172 from EDiLD/dev_ms

Dev ms
removed all R packaging files, not needed for manuscript
removed tests folder
moved doc folder to root, and added readme
edited readme, making changes in ms according to reviews from naim and karthik, still working
incorporated changes from karthik and naim, fixes #170, should be close to submit
moved misc files to new folder
a few spelling changes to ms, added cover letter
a few changes before submission to plos, submission to plosone done
a few changes to references
changed to ms and appendix
added some figures
small edit to fix references in appendix
added Appendix C for info on api keys and installingn rom github, fell free to edit, issue # 178
added nfew version of ms to f1000_rev folder, folded in changes from reviewers, issue #178