Delete output.pdf

Accidentally pushed
Create Particle Filter model.
Delete .Rapp.history
Function to set ensemble size in operations script
fixed bugs in particle code and made notes on what needs to be done next
Merge pull request #25 from dgianotti/master

Updates to Operations.R, RunJAGS.R, make.SS.plots.R, run.SS.model.R.  Created new file, get.site.data.R.
Delete RunJAGS_detroyV1.R

This is for testing purposes only.  Not needed in Repo

-Dan
Merge pull request #8 from EcoForecast/master

Add in beginings of particle filter code