Changes to the convergence checks

The main changes in the most recent updates are:

- an attempt to stop the resetting of the parameters during convergence checks in cedric.convergence.r
- testing for convergence on log_10(S_phi) instead of S_phi
- testing for convergence on log_10(phi) instead of phi
- added ability to turn off estimation of S_phi and phi bias/noise
- Fixing some small typos