clean up and add comments for mat_fec calcs

[Rick-Methot-NOAA]

What issue(s) does this PR address?

resolves #348

Describe the issue, if not included in the PR

some aspects of maturity and fecundity were being calculated even in not used; calculated values could be nonsensical if user provided placeholder rather than realistic parameter values. Solution: replace output in these situations with a constant vector of 0.5. Augment comments in code to describe the relevant situations.

What tests have been done? Upload any model input files created for testing in a zip file, if possible.

minimal

What tests/review still need to be done? Who can do it, and by when is it needed (ideally)?

try it out with the setup identified in issue #348

is there an input change for users to Stock Synthesis?

no
If so, please provide an example of the new inputs needed.

[New example stock synthesis input goes here]

Check which is true. This PR requires:

• no further changes to r4ss
• no further changes to the manual
• no further changes to SSI (the SS3 GUI)
• no further changes to the stock synthesis change log (new features, bug reports)

Describe any changes in r4ss/SS3 manual/SSI that are needed (if not checked):

r4ss needs to adjust headers for the biology_report (no. 42)

If changes are needed in the change log, please fill in the table here:

Version	Date	Description	Issue	Input change	Action	Topic	Type
3.30.20	[Add date]	[add concise description]	#[add issue]	[yes or no]	[fix, new, or revise]	[e.g., biology. Use issue label options.]	[input, output, and/or calc, or ALL]

Additional information (optional):

[Rick-Methot-NOAA]

@iantaylor-NOAA looks like this change has created a plot issue for r4ss.

[k-doering-NOAA]

Thanks @iantaylor-NOAA for starting the re-run! Looks like it passed, so there is no issue with r4ss.

@iantaylor-NOAA , if you have the time, maybe you can review Rick's changes (or maybe you already have?) and "approve" the pull request if it is ready to merge in?

[iantaylor-NOAA]

Looks good. In addition to the automated tests, I ran the r4ss::SS_plots() function on models that had fecundity method 1 and 4 to confirm that things don't just run but look OK, which they do. I still need to turn off the length-based maturity and fecundity plots for the models that don't use those values, but for now the constant 0.5 value will make it clear that this isn't connected to the parameter lines.

I appreciate the extra message in the ss_new file about parameter lines needed.

[iantaylor-NOAA]

Since I requested no changed, I went ahead and merged and deleted the branch. Does that make sense or is it better to leave it to @Rick-Methot-NOAA to merge after the review is complete?

[Rick-Methot-NOAA]

On a small item like this, I think it is fine for either the initiator or the reviewer to do the merge.
For a big feature, I think it best to have the initiator be the one who says "done"

[iantaylor-NOAA]

Sounds good. I got carried away clicking through things after completing the review.