saves plots of initial ensemble forecast to PDF files for each site
save output plot to PDF
save raw output to csv file so that it can be appended to for iterations
adding functions that will be used to update the forecast
found bug in initial conditions...using X from state space model for r input!
Yet another update to get.site.data and friends. Seems to be working well now.
Merge pull request #44 from dgianotti/master

Yet another update to get.site.data and friends. Seems to be working wel...
Added shell script. Commented out currently non-functioning parts of Operations.
Updated Operations.R and .sh.
Merge pull request #45 from dgianotti/master

Updated Operations.R and added Operations shell script.
Merge pull request #10 from EcoForecast/master

Update Dan's fork
made some fairly major structural changes to get this running operationally for the last step of the project (needs a bit more work on the particle filter update function)
Myrge branch 'master' of https://github.com/EcoForecast/PhenologyForecast

trying to resolve conflicts!
Conflicts:
	Operations.R
	get.site.data.R
making some fairly major changes to make the forecast operational. the particle filter function for the "update forecast" step needs a bit of work still (this is the new  update.particle.filter.forecast function)
Fixed check.for.complete.SS.model
Merge pull request #46 from dgianotti/master

Fixed check.for.complete.SS.model bug
Fixed bug in run.SS.model
Merge pull request #47 from dgianotti/master

Fixed bug in run.SS.model
Cleaned up run.SS.model, no longer depends on HistoricalData (can probably remove that now). Added a few things to global_input_parameters.
Cleaned up run.SS.model, no longer depends on HistoricalData (can probably remove that now). Added a few things to global_input_parameters.
Merge pull request #48 from dgianotti/master

Cleaned up run.SS.model, no longer depends on HistoricalData (can remove that from the project at this point).