Add text about how to use new spawner-recruitment option when there is time-varying biology

[e-perl-NOAA]

See issue #191 and PR #640.

List of things that need to be added to the user manual thus far:

• Add the following to the spawner recruit input in the control file section

  "SR_LN(R0)_derived"
  "SR_BH_steep_derived";
  "SR_BH_ln(alpha)";
  "SR_BH_ln(beta)";
  

• Add in starter section:
  • about new option 6 for depletion basis 6=Bmark_SSB_unf
  • init SPR_reporting option 5=SPR
  • 1 #_Compatibility: flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs >=3.30.24
• Add a link to the control file spawner recruit section and time-varying biology section to the vignette/ppt about the changes made and what the impacts are.
• Add text about using the last line in the following code to the forecast file section

  1 # Control rule method (0: none; 1: ramp does catch=f(SSB), buffer on F; 2: ramp does F=f(SSB), buffer on F; 3: ramp does catch=f(SSB), buffer on catch; 4: ramp does F=f(SSB), buffer on catch) 
  # values for top, bottom and buffer exist, but not used when Policy=0
  0.4 # Control rule inflection for constant F (as frac of Bzero, e.g. 0.40); must be > control rule cutoff, or set to -1 to use Bmsy/SSB_unf 
  # Also see HCR_anchor below
  0.1 # Control rule cutoff for no F (as frac of Bzero, e.g. 0.10) 
  0.75 # Buffer:  enter Control rule target as fraction of Flimit (e.g. 0.75), negative value invokes list of [year, scalar] with filling from year to YrMax 
  #
  3 #_N forecast loops (1=OFL only; 2=ABC; 3=get F from forecast ABC catch with allocations applied)
  3 # First forecast loop with stochastic recruitment
  1 # Forecast base recruitment:  0= spawn_recr; 1=mult*spawn_recr_fxn; 2=mult*VirginRecr; 3=deprecated; 4=mult*mean_over_yr_range
  # for option 4, set phase for fore_recr_devs to -1 in control to get constant mean in MCMC, else devs will be applied
  1 # multiplier on base recruitment 
  2 # HCR_anchor: 0 or 1 uses unfished benchmark SSB (old hardwired approach), 2 = virgin SSB
  

• Update report section to include any relevant changes to SPAWN_RECRUIT report:19

@Rick-Methot-NOAA Are there any other changes to the input files regarding the spawner-recruit update that I am missing here? This is all I got from reading the 191 issue in terms of inputs/outputs in the user manual

[Rick-Methot-NOAA]

I'll plan to get this updated right after webinar; there are changes

[e-perl-NOAA]

@Rick-Methot-NOAA I added what was in the presentation but please feel free to edit/add or suggest changes

[Rick-Methot-NOAA]

I will refresh the list. the first item at top of of original list no longer exists.

starter file
-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1749058407
1 #_Compatibility: flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs >=3.30.24
3.30 #_final: check value for end of file and for version control

new option 6:
6 #_depl_basis: Depletion denom is: 0=skip; 1=X*SSB_virgin; 2=X*SSB_msy; 3=X*SSB_styr; 4=X*SSB_endyr; 5=X*dyn_Bzero; 6=X*SSB_unf_bmark; values>=11 invoke N multiyr with 10s & 100s digit; append .1 to invoke log(ratio); e.g. 122.1 produces log(12 yr trailing average of B/Bmsy)
Note that option 1 will also affect interpretation of Biomass target in the forecast.ss file.

new option 5:
5 #_SPR_basis: 0 (skip); 1 (1-SPR)/(1-SPR_tgt); 2 (1-SPR)/(1-SPR_MSY); 3 (1-SPR)/(1-SPR_Btarget); 4 (1-SPR); 5 (SPR)

control file:
Add option for alpha, beta parameterization of Beverton-Holt. No other S-R forms have the explicit alpha, beta option. Note that ln(alpha) and ln(beta) are the estimated parameters. The parameter lines for ln(R0) and steepness must exist. Their values are derived from alpha and beta. It is permissible to place a prior on steepness.

10 #_Spawner-Recruitment; Options: 1=NA; 2=Ricker; 3=std_B-H; 4=SCAA; 5=Hockey; 6=B-H_flattop; 7=survival_3Parm; 8=Shepherd_3Parm; 9=RickerPower_3parm
0  # 0/1 to use steepness in initial equ recruitment calculation
 0 #  not_used
#_          LO            HI          INIT         PRIOR         PR_SD       PR_type      PHASE    env-var    use_dev   dev_mnyr   dev_mxyr     dev_PH      Block    Blk_Fxn #  parm_name
             3            31       8.76855          10.3            10             0         -1          0          0          0          0          0          0          0 # SR_LN(R0)_derived
           0.2             1      0.749996           0.7          0.05             1         -4          0          0          0          0          0          0          0 # SR_BH_steep_derived
         0.001            31      0.576742          10.3            10             0         -1          0          0          0          0          0          0          0 # SR_BH_ln(alpha)
           -30            30      -8.27882           0.7          0.05             1         -4          0          0          0          0          0          0          0 # SR_BH_ln(beta)

forecast file:
0.244952 # Biomass target (e.g. 0.40) as fraction of SSB_virgin if depletion basis = 1, else as fraction of SSB_unfished in benchmark
explicit mention of HCR_anchor here:
1 # Control rule inflection for constant F (as frac of HCR_anchor, see below); must be > control rule cutoff

Then the selection of HCR_anchor occurs here:

1 # multiplier on base recruitment 
3 # HCR_anchor: 0 or 2 uses unfished benchmark SSB (old hardwired approach); 1 = virgin SSB; 3 = BMSY
#
2010  # FirstYear for caps and allocations (should be after years with fixed inputs) 

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