improve Fdetail info in ssnew for Fmethod 4

[Rick-Methot-NOAA]

Concisely describe what has been changed/addressed in the pull request.

Information on use of F_detail needed improvement for F method 4.

• Resolves issue #
  no linked issue

What tests have been done?

The revised control.ss_new now looks like:

4 # F_Method:  1=Pope midseason rate; 2=F as parameter; 3=F as hybrid; 4=fleet-specific parm/hybrid (#4 is superset of #2 and #3 and is recommended)
2.95 # max F (methods 2-4) or harvest fraction (method 1)
 # Read list of fleets that do F as parameter; unlisted fleets stay hybrid, bycatch fleets must be included with start_PH=1, high F fleets should switch early
 # (A) fleet;
 # (B) F_starting_value (ignored if start_PH=1 or reading from ss3.par);
 # (C) start_PH for fleet's Fparms (99 to stay in hybrid, <0 to stay at starting value)
 # Terminate list with -9999 for fleet
 # or terminate with -9998 to invoke reading fleet-time specific F values after first reading N hybrid tune loops)
 # (A) (B) (C)
 1 0.05 99 # FISHERY
-9998 1 1 # end of list, triggers reading F_detail
4 #_number of loops for hybrid tuning; 4 precise; 3 faster; 2 enough if switching to parms is enabled
# F_detail:  List of fleet-time specific F related values to read; enter -Yr to fill remaining years&seasons; -999 for phase or catch_se keeps base value for the run
#fleet year seas F_value catch_se phase
 1 2000 1 0.05 0.01 1
 1 1999 1 0.04 0.01 1
-9999 1 1 1 1 1  # end of F_detail
#

and the info in echoinput is:

4 F_Method as read
2.95 max_harvest_rate 
read list of fleet ID, starting F, and phase to transition to parameters
 1 0.05 99
 -9998 1 1
now read N tuning loops while in hybrid phases (2 is OK if switching to parm later, 3 OK, 4 more precise with many fleets)
hybrid tuning loops as read: 4
# now read List of fleet-time specific F related values to read; enter -Yr to fill remaining years&seasons; -999 for phase or catch_se keeps base value for the run; end that list with -1 for fleet
#Fleet Yr Seas F_value catch_se phase
 1 2000 1 0.05 0.01 1
 1 1999 1 0.04 0.01 1
 -1 1 1 1 1 1
 detailed F_setups 
 1 2000 1 0.05 0.01 1
 1 1999 1 0.04 0.01 1

Where are the relevant files?

What tests/review still need to be done?

• update Manual accordingly

Is there an input change for users to Stock Synthesis?

Additional information (optional).

[e-perl-NOAA]

@Rick-Methot-NOAA In the manual, it has the following:
https://github.com/nmfs-ost/ss3-doc/blob/d1bd6e2dd5d3c4ed3ff45724405673eccb30844d/9control.tex#L1455-L1457

Does this mean that for F method 2 you DON'T need the fleet number and DO need the number of detail setup lines to read but for F method 4 you DO need the fleet number and you DON'T need the number of detail setup lines to read?

[Rick-Methot-NOAA]

fleet number is needed for both. Where does it say otherwise for Fmethod 2?

[e-perl-NOAA]

In the example I liked above, it doesn't have to fleet number in that string of values. It has an example string of values of:

0.10 1 0 Initial F value, phase, and number of F detail setup lines to read

Then the additional entry option if F method is 2 and N for F detail is > 0 which does include fleet.
Example from user manual is
1 1980 1 0.20 0.05 4 (fleet, year, season, F, SE, phase)

[Rick-Methot-NOAA]

Correct. So, within the entry of F details the format is the same. What is different between FMethod 2 and 4 is how you invoke the need to read any F detail lines.
For FMethod 2, you do it by entering a value >0 in the N F detail spot.
For FMethod 4, you do it by using -9998 to terminate the previous list.

[e-perl-NOAA]

Yes, but in F method 4 that first list of values appears to be fleet, F value, phase, and with F method 2 (according to those linked lines in a previous comment above in the user manual) the first list of values is F value, phase, number of F detail setup lines to read (no fleet is entered there, it's just entered in with the F detail setup lines). I just want to make sure this is correct in the user manual.

[Rick-Methot-NOAA]

for FMethod 2, the "Initial F value" is the starting F value for all fishing fleets.
Let's rename it to "Starting F value for all fishing fleets".
control.ss_new already uses that language:

  else if (F_Method == 2)
  {
    report4 << F_parm_intval(1) << " # overall start F value (all fleets; used if start phase = 1 and not reading parfile)" << endl;
    report4 << F_Method_PH(1) << " # start phase for parms (does hybrid in early phases)" << endl;
    report4 << F_detail << " # N detailed inputs to read" << endl;
    report4 << "# detailed setup for F_Method=2; -Yr to fill remaining years; -999 for phase or se ignores keeps default for those fields " << endl;
    report4 << "#_fleet year seas F_value se phase" << endl;

[Rick-Methot-NOAA]

The pdf is showing an extraneous "3" or "2" at beginning of several fields:

The line:
If F_Method = 2 and N for detail is > 0
can be reduced to:
If N for detail is > 0

[e-perl-NOAA]

Latex in the github action is somehow struggling with the multicolumn specification. When I run it locally it doesn't produce that. I'll have to look into that tomorrow to see why the latex in the GitHub action has now decided to not recognize that.