Merge pull request #3 from EcoForecast/master

Getting updated project
fixed output so that output for each site is saving as a different element in a list
made note re past changes
fixed multiple bugs in code, added plots of output and correlations. need to add MCMC diagnostics and check distributions and priors
added MCMC diagnostics
Merge pull request #18 from AngelaRigden/master

Merge pull request #3 from EcoForecast/master
Merge pull request #5 from EcoForecast/master

Update all files, specifically for Diana's new JAGS code