Parameter collections

Provide parameter collection pattern for easier model definition
Fix failing EM test

I erased one of Brian's changes in my previous commit. This broke some
of the EM tests. I also updated parts of the tests where deprecated
classes were still being used. Lastly, I increased the number of MH
iterations for a couple of tests which seemed to be failing more often
than their counterparts with BP and Importance.
Merge pull request #316 from mhoward2718/DEV2.5.0

Parameter collections