documentation for CmdStanPy optimization

Summary:

A bunch of suggestions for making the optimization doc easier to understand.

• User's Guide: Maximum Likelihood Estimation

  • we should indicate that (a) we get penalized MLEs as well as MLE in the title and description, (b) explain that this means turning the Jacobian adjustment off, and (c) that with Jacobian adjustment off we do not get the posterior mode, aka the max a posteriori (MAP) estimate a Bayesian is likely to expect
  • we should indicate _np suffix is NumPy ndarray and _pd is a pandas data frame
  • we should break the output for running optimize, printing the _dict, printing the _np, and printing the _pd values
  • we should indicate the result is on the constrained scale

• API Docs

  • indicate that results are on the constrained scale in CmdStanMLE
  • replace forward apostrophes with back ticks to get rendered quotes (both here and above)

Current Version:

1.0.7

Start with the User's Guide section titled “Maximum Likelihood Estimation” and the API documentation for CmdStanMLE. Review each checklist item against the current wording and examples, including the NumPy and pandas result descriptions. Done means the guide and API docs explain the requested scales, estimates, suffixes, output steps, and rendered quotes.