Updated resilience matrix and weights after discussion with Katie, Liz, and Ben.  Ben added some notes to function.R file.
Latest run with full data!
Changes to the High Seas data
Merge pull request #3 from OHI-Science/master

including high seas and fixes in bbest repo
Mostly these reflect changes in file names (hd_subtidal_sb pressure changed to exclude subtidal portion).  There were also some very small changes to the UV pressure.  This did not alter the final data to any real extent (2nd/3rd decimal place changes)
Changing FIS so that median score is used as the starting estimate for b_bmsy for unevaluated taxa (rather than the minimum)
New scores when median is used as starting b_bmsy estimate for unevaluated taxa
Testing out changing pressure variable call
since problems with ohicore::Conf class not being found, ran build check and discovered errors with NAMESPACE unnecessarily calling stringr and sqldf. So removed dependencies (TODO: migrate sqldf() calls to dplyr), ran document() and trying with new NAMESPACE.
commented out Conf_write documentation and inserted blank line after export of classes
moved TODO comment at top to bottom, so starts with class name
cleaning up files based on check() messages
iterating over previous commits to find culprit to #80. strangely, now Conf.Rd and Conf-class.Rd showing up as new files. Added automated test to check for existence of key classes Conf and Layers.
updated rate limiting sleep and output of log.txt
export(Conf) export(Layers) added back to NAMESPACE since iterate_commits.R showing this as difference between the following most recent commit which didn't load Conf and the prior one which did.

committed: 2014-04-02T22:40:43Z
sha: 9733a842916547d74afc37a27a563896e04a4ac9
Conf exists: FALSE

----

committed: 2014-04-02T01:42:40Z
sha: 1d2d58c0cf2f5c8e3dd976c2d220d60a0678e05a
Conf exists: TRUE

hopefully this will do the trick for ohi-science/ohicore#80
added explicit @export and @exportClass to Conf and Layers fixing ohi-science/ohicore#80 by ensuring further devtools::document() calls include the needed export() in the NAMESPACE file. For more see

http://stackoverflow.com/questions/21532365/roxygen2-how-to-export-reference-class-generator
adding sqldf dependancy back for now to ensure AggreegateLayers.R and CalculatePressuresAll.R work.
Merge pull request #82 from bbest/master

getting Conf and Layers classes to load
Merge pull request #79 from Melsteroni/master

General pull request for addition of AQ, changes to HS, and one change to CalculateAll.R
Merge pull request #4 from OHI-Science/master

fetching Mel's CalculateAll pressures fix, plus Antarctica and High Seas