From 1fb37cd86908edb4dab9c6dad28e7e6697897ad7 Mon Sep 17 00:00:00 2001
From: RickMethot <richard.methot@noaa.gov>
Date: Wed, 8 Feb 2023 16:24:40 -0800
Subject: [PATCH 01/22] first commit for B-H with ab

add S-R option 10 for a,b formulation
---
 SS_benchfore.tpl              | 12 ++---
 SS_param.tpl                  |  1 +
 SS_popdyn.tpl                 | 33 +++++++++++---
 SS_readcontrol_330.tpl        | 11 ++++-
 SS_recruit.tpl                | 85 ++++++++++++++++++-----------------
 SS_write_report.tpl           |  8 +++-
 StockSynthesis.code-workspace |  1 +
 7 files changed, 94 insertions(+), 57 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index d2e5025e..d95f5171 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -902,7 +902,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     }
 
     //  SPAWN-RECR:   calc equil spawn-recr in YPR; need to make this area-specific
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work(2), SR_parm_work(3), SSB_unf, Recr_unf, SSB_equil); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSB_equil); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
 
     Bspr = Equ_SpawnRecr_Result(1);
     Bspr_rec = Equ_SpawnRecr_Result(2);
@@ -1017,7 +1017,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     if (rundetail > 0 && mceval_counter == 0 && show_MSY == 1)
       echoinput << "Calculated F0.1: " << Btgt_Fmult << endl;
     SPR_temp = SSB_equil;
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work(2), SR_parm_work(3), SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
     Btgt = Equ_SpawnRecr_Result(1);
     Btgt_Rec = Equ_SpawnRecr_Result(2);
     YPR_Btgt_enc = YPR_enc; //  total encountered yield per recruit
@@ -1111,7 +1111,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         SPR_Btgt = SSB_equil / SPR_unfished;
         //  SPAWN-RECR:   calc equil spawn-recr for Btarget calcs;  need to make area-specific
         SPR_temp = SSB_equil;
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work(2), SR_parm_work(3), SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         yld1(ii) = Equ_SpawnRecr_Result(1);
       }
 
@@ -1331,7 +1331,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       //  SPAWN-RECR:   calc spawn-recr for MSY calcs;  need to make area-specific
       MSY_SPR = SSB_equil / SPR_unfished;
       SPR_temp = SSB_equil;
-      Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work(2), SR_parm_work(3), SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+      Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
       Bmsy = Equ_SpawnRecr_Result(1);
       Recr_msy = Equ_SpawnRecr_Result(2);
       yld1(1) = YPR_opt * Recr_msy;
@@ -1424,7 +1424,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
           //  SPAWN-RECR:   calc spawn-recr for MSY calcs;  need to make area-specific
           MSY_SPR = SSB_equil / SPR_unfished;
           SPR_temp = SSB_equil;
-          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work(2), SR_parm_work(3), SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
           Bmsy = Equ_SpawnRecr_Result(1);
           Recr_msy = Equ_SpawnRecr_Result(2);
           Profit = (PricePerF * YPR_val_vec) * Recr_msy - Cost;
@@ -1718,7 +1718,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         SPR_Btgt2 = SSB_equil / SPR_unfished;
         //  SPAWN-RECR:   calc equil spawn-recr for Btarget calcs;  need to make area-specific
         SPR_temp = SSB_equil;
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work(2), SR_parm_work(3), SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         yld1(ii) = Equ_SpawnRecr_Result(1);
       }
 
diff --git a/SS_param.tpl b/SS_param.tpl
index 9ddf9a86..da7d0d5e 100644
--- a/SS_param.tpl
+++ b/SS_param.tpl
@@ -416,6 +416,7 @@ PARAMETER_SECTION
    //  note that bycatch_F(1,Nfleet,1,nseas) has similar role  
    number alpha;
    number beta;
+   number steepness;
    number GenTime;
    number Yield;
    number Adj4010;
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index e6c64a53..1548b7d4 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -337,17 +337,38 @@ FUNCTION void get_initial_conditions()
   Fishon = 0;
   virg_fec = fec;
   Recr.initialize(); //  will store recruitment by area
+
+  //  SPAWN-RECR:   get expected recruitment globally or by area
+  if (recr_dist_area == 1 || pop == 1) //  do global spawn_recruitment calculations
+  {
+    equ_Recr = 1.0;
+    Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation.  Returns SPR because R = 1.0
+    SPR_virgin = SSB_equil; //  spawners per recruit.  Needed for Sr_fxn = 10
+
+    if(SR_fxn == 10)  // B-H with a,b
+    {
+      alpha = mfexp(SR_parm(3));
+      beta = mfexp(SR_parm(4));
+      steepness = alpha * SPR_virgin / (4.00 + alpha * SPR_virgin);
+      Recr_virgin = 1.0 / beta * (alpha - ( 1.0 / SPR_virgin));
+      SR_parm(1) = log(Recr_virgin);
+      SR_parm(2) = steepness;
+      // warning<< SR_parm(1) << " Ln(R0) " << mfexp(SR_parm(1)) << endl
+      //     << " alpha_beta: "<<alpha<<" "<<beta<<endl
+      //   << " spr: "<<SPR_virgin<<endl
+      //    << " der_steep: "<< alpha * SPR_virgin / (4.00 + alpha * SPR_virgin)<<endl
+      //    << "der_R0: "<<  1.0 / beta * (alpha - ( 1.0 / SPR_virgin))<<endl;
+    }
+    else {
+      Recr_virgin = mfexp(SR_parm(1));
+    }
+  
   for (int i = 1; i <= N_SRparm2; i++)
   {
     SR_parm_byyr(eq_yr, i) = SR_parm(i);
     SR_parm_virg(i) = SR_parm(i);
     SR_parm_work(i) = SR_parm(i);
   }
-
-  //  SPAWN-RECR:   get expected recruitment globally or by area
-  if (recr_dist_area == 1 || pop == 1) //  do global spawn_recruitment calculations
-  {
-    Recr_virgin = mfexp(SR_parm(1));
     equ_Recr = Recr_virgin;
     exp_rec(eq_yr, 1) = Recr_virgin; //  expected Recr from s-r parms
     exp_rec(eq_yr, 2) = Recr_virgin;
@@ -507,7 +528,7 @@ FUNCTION void get_initial_conditions()
     CrashPen += Equ_penalty;
     SPR_temp = SSB_equil / equ_Recr; //  spawners per recruit at initial F
     //  get equilibrium SSB and recruitment from SPR_temp, Recr_virgin and virgin steepness
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm(2), SR_parm(3), SSB_virgin, Recr_virgin, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm, SSB_virgin, Recr_virgin, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
 
     R1_exp = Equ_SpawnRecr_Result(2); //  set the expected recruitment equal to this equilibrium
     exp_rec(eq_yr, 1) = R1_exp;
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index e33d5173..e7042c6c 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1937,13 +1937,13 @@
 !!//  SS_Label_Info_4.6 #Read setup for Spawner-Recruitment parameters
   //  SPAWN-RECR: read setup for SR parameters:  LO, HI, INIT, PRIOR, PRtype, CV, PHASE
   init_int SR_fxn
-!!echoinput<<SR_fxn<<" #_SR_function: 1=NA; 2=Ricker(2 parms); 3=BevHolt(2); 4=SCAA(2); 5=Hockey(3); 6=B-H_flattop(2); 7=Survival(3); 8=Shepherd(3); 9=Ricker_Power(3) "<<endl;
+!!echoinput<<SR_fxn<<" #_SR_function: 1=NA; 2=Ricker(2 parms); 3=BevHolt(2); 4=SCAA(2); 5=Hockey(3); 6=B-H_flattop(2); 7=Survival(3); 8=Shepherd(3); 9=Ricker_Power(3); 10=B-H_a,b(4)"<<endl;
   init_int init_equ_steepness;
 !!echoinput<<init_equ_steepness<<"  # 0/1 to use steepness in initial equ recruitment calculation"<<endl;
   init_int sigmaR_dendep;
 !! echoinput<<sigmaR_dendep<<"  #  future feature:  0/1 to make realized sigmaR a function of SR curvature"<<endl;
   ivector N_SRparm(1,10)
-!!N_SRparm.fill("{0,2,2,2,3,2,3,3,3,3}");
+!!N_SRparm.fill("{0,2,2,2,3,2,3,3,3,4}");
   int N_SRparm2
   int N_SRparm3  //  with timevary links included
 !!N_SRparm2=N_SRparm(SR_fxn)+3;
@@ -2026,6 +2026,13 @@
       ParmLabel += "SR_RkrPower_gamma";
       break;
     }
+    case 10: // Bev-Holt a,b
+    {
+      ParmLabel += "SR_BH_steep_derived";
+      ParmLabel += "SR_BH_ln(alpha)";
+      ParmLabel += "SR_BH_ln(beta)";
+      break;
+    }
   }
   ParmLabel += "SR_sigmaR";
   ParmLabel += "SR_regime";
diff --git a/SS_recruit.tpl b/SS_recruit.tpl
index 93d3fe73..f6a58c32 100644
--- a/SS_recruit.tpl
+++ b/SS_recruit.tpl
@@ -49,25 +49,14 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
     case 3: // Beverton-Holt
     {
       steepness = SR_parm_work(2);
-      alpha = 4.0 * steepness * Recr_virgin / (5. * steepness - 1.);
-      beta = (SSB_virgin_adj * (1. - steepness)) / (5. * steepness - 1.);
+      dvariable SPR = SSB_virgin_adj / Recr_virgin;
+      alpha = ((4.0 * steepness) / (1. - steepness)) / SPR ;
+      beta = (1.0 / Recr_virgin) * (alpha - (1.0 / SPR));
       NewRecruits = (4. * steepness * Recr_virgin_adj * SSB_curr_adj) /
           (SSB_virgin_adj * (1. - steepness) + (5. * steepness - 1.) * SSB_curr_adj);
       break;
     }
 
-    // Beverton-Holt with alpha beta
-    /*
-      case 3: // Beverton-Holt
-      {
-        steepness=SR_parm_work(2);
-        alpha = 4.0 * steepness*Recr_virgin / (5.*steepness-1.);
-        beta = (SSB_virgin_adj*(1.-steepness)) / (5.*steepness-1.);
-        NewRecruits =  (alpha*SSB_curr_adj) / (beta+SSB_curr_adj);
-        break;
-      }
-   */
-
     //  SS_Label_43.3.4  constant expected recruitment
     case 4: // none
     {
@@ -88,8 +77,9 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
     case 6: //Beverton-Holt constrained
     {
       steepness = SR_parm_work(2);
-      alpha = 4.0 * steepness * Recr_virgin / (5. * steepness - 1.);
-      beta = (SSB_virgin_adj * (1. - steepness)) / (5. * steepness - 1.);
+      dvariable SPR = SSB_virgin_adj / Recr_virgin;
+      alpha = ((4.0 * steepness) / (1. - steepness)) / SPR ;
+      beta = (1.0 / Recr_virgin) * (alpha - (1.0 / SPR));
       if (SSB_curr_adj > SSB_virgin_adj)
       {
         SSB_BH1 = SSB_virgin_adj;
@@ -167,6 +157,14 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
       NewRecruits = Recr_virgin_adj * temp * mfexp(RkrTop);
       break;
     }
+
+      case 10: // Beverton-Holt with alpha beta
+      {
+        alpha = mfexp(SR_parm_work(3));
+        beta = mfexp(SR_parm_work(4));
+        NewRecruits =  (alpha*SSB_curr_adj) / (1.0 + beta * SSB_curr_adj);
+        break;
+      }
   }
   RETURN_ARRAYS_DECREMENT();
   return NewRecruits;
@@ -270,7 +268,7 @@ FUNCTION void apply_recdev(prevariable& NewRecruits, const prevariable& Recr_vir
 //********************************************************************
  /*  SS_Label_FUNCTION 44 Equil_Spawn_Recr_Fxn */
 //  SPAWN-RECR:   function  Equil_Spawn_Recr_Fxn
-FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const prevariable& SRparm2, const prevariable& SRparm3,
+FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
     const prevariable& SSB_virgin, const prevariable& Recr_virgin, const prevariable& SPR_temp)
   {
   RETURN_ARRAYS_INCREMENT();
@@ -286,7 +284,7 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const prevariable& SRparm2, const prev
   dvariable srz_min;
   dvariable SRZ_surv;
 
-  steepness = SRparm2; //  common usage but some different
+  steepness = SRparm(2); //  common usage but some different
   //  SS_Label_44.1  calc equilibrium SpawnBio and Recruitment from input SPR_temp, which is spawning biomass per recruit at some given F level
   switch (SR_fxn)
   {
@@ -296,16 +294,7 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const prevariable& SRparm2, const prev
       write_message (FATAL, 0); // EXIT!
       break;
     }
-    //  SS_Label_44.1.1  Beverton-Holt with flattop beyond Bzero
-    case 6: //Beverton-Holt
-    {
-      alpha = 4.0 * steepness * Recr_virgin / (5. * steepness - 1.);
-      beta = (SSB_virgin * (1. - steepness)) / (5. * steepness - 1.);
-      B_equil = alpha * SPR_temp - beta;
-      B_equil = posfun(B_equil, 0.0001, temp);
-      R_equil = (4. * steepness * Recr_virgin * B_equil) / (SSB_virgin * (1. - steepness) + (5. * steepness - 1.) * B_equil);
-      break;
-    }
+
     //  SS_Label_44.1.2  Ricker
     case 2: // Ricker
     {
@@ -314,17 +303,32 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const prevariable& SRparm2, const prev
 
       break;
     }
-    //  SS_Label_44.1.3  Beverton-Holt
+      //  SS_Label_44.1.1  Beverton-Holt 
+    case 6: //Beverton-Holt with flattop beyond Bzero, but no flattop in equil calcs
+    {
+    }
+  //  SS_Label_44.1.3  Beverton-Holt
     case 3: // same as case 6
     {
-      alpha = 4.0 * steepness * Recr_virgin / (5. * steepness - 1.);
-      beta = (SSB_virgin * (1. - steepness)) / (5. * steepness - 1.);
+      dvariable SPR = SSB_virgin / Recr_virgin;
+      alpha = ((4.0 * steepness) / (1. - steepness)) / SPR ;
+      beta = (1.0 / Recr_virgin) * (alpha - (1.0 / SPR));
       B_equil = alpha * SPR_temp - beta;
       B_equil = posfun(B_equil, 0.0001, temp);
       R_equil = (4. * steepness * Recr_virgin * B_equil) / (SSB_virgin * (1. - steepness) + (5. * steepness - 1.) * B_equil); //Beverton-Holt
       break;
     }
 
+    case 10: // Beverton-Holt with alpha and beta parameterization
+    {
+      alpha = mfexp(SRparm(3));
+      beta = mfexp(SRparm(4));
+      B_equil = alpha * SPR_temp - beta;
+      B_equil = posfun(B_equil, 0.0001, temp);
+      R_equil =  (alpha * Recr_virgin * B_equil) / (1.0 + beta * Recr_virgin * B_equil);
+      break;
+    }
+
     //  SS_Label_44.1.4  constant recruitment
     case 4: // constant; no bias correction
     {
@@ -335,7 +339,7 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const prevariable& SRparm2, const prev
     //  SS_Label_44.1.5  Hockey Stick
     case 5: // hockey stick
     {
-      alpha = SRparm3 * Recr_virgin; // min recruitment level
+      alpha = SRparm(3) * Recr_virgin; // min recruitment level
       //        temp=SSB_virgin/R0*steepness;  // spawners per recruit at inflection
       beta = (Recr_virgin - alpha) / (steepness * SSB_virgin); //  slope of recruitment on spawners below the inflection
       B_equil = Join_Fxn(0.0 * SSB_virgin / Recr_virgin, SSB_virgin / Recr_virgin, SSB_virgin / Recr_virgin * steepness, SPR_temp, alpha / ((1. / SPR_temp) - beta), SPR_temp * Recr_virgin);
@@ -347,9 +351,8 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const prevariable& SRparm2, const prev
     {
       SRZ_0 = log(1.0 / (SSB_virgin / Recr_virgin));
       srz_min = SRZ_0 * (1.0 - steepness);
-      B_equil = SSB_virgin * (1. - (log(1. / SPR_temp) - SRZ_0) / pow((srz_min - SRZ_0), (1. / SRparm3)));
-      B_equil = posfun(B_equil, 0.0001, temp);
-      SRZ_surv = mfexp((1. - pow((B_equil / SSB_virgin), SRparm3)) * (srz_min - SRZ_0) + SRZ_0); //  survival
+      B_equil = SSB_virgin * (1. - (log(1. / SPR_temp) - SRZ_0) / pow((srz_min - SRZ_0), (1. / SRparm(3))));
+      SRZ_surv = mfexp((1. - pow((B_equil / SSB_virgin), SRparm(3))) * (srz_min - SRZ_0) + SRZ_0); //  survival
       R_equil = B_equil * SRZ_surv;
       break;
     }
@@ -367,14 +370,14 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const prevariable& SRparm2, const prev
       //       REC = (TOP/BOT)**(1.0/POWER)*SPRF0/SPR
       // Power = exp(logC);
       // Hupper = 1.0/(5.0 * pow(0.2,Power));
-      Shepherd_c = SRparm3;
-      Shepherd_c2 = pow(0.2, SRparm3);
+      Shepherd_c = SRparm(3);
+      Shepherd_c2 = pow(0.2, SRparm(3));
       Hupper = 1.0 / (5.0 * Shepherd_c2);
-      steepness = 0.2 + (SRparm2 - 0.2) / (0.8) * (Hupper - 0.2);
+      steepness = 0.2 + (SRparm(2) - 0.2) / (0.8) * (Hupper - 0.2);
       Shep_top = 5.0 * steepness * (1.0 - Shepherd_c2) * (SPR_temp * Recr_virgin) / SSB_virgin - (1.0 - 5.0 * steepness * Shepherd_c2);
       Shep_bot = 5.0 * steepness - 1.0;
       Shep_top2 = posfun(Shep_top, 0.001, temp);
-      R_equil = (SSB_virgin / SPR_temp) * pow((Shep_top2 / Shep_bot), (1.0 / SRparm3));
+      R_equil = (SSB_virgin / SPR_temp) * pow((Shep_top2 / Shep_bot), (1.0 / SRparm(3)));
       B_equil = R_equil * SPR_temp;
       break;
     }
@@ -382,8 +385,8 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const prevariable& SRparm2, const prev
     //  SS_Label_43.3.8  Ricker-power
     case 9: // Ricker power 3-parameter SRR.  per Punt & Cope 2017
     {
-      steepness = SRparm2;
-      dvariable RkrPower = SRparm3;
+      steepness = SRparm(2);
+      dvariable RkrPower = SRparm(3);
       temp = SSB_virgin / (SPR_temp * Recr_virgin);
       dvariable RkrTop = pow(0.8, RkrPower) * log(temp) / log(5.0 * steepness);
       RkrTop = posfun(RkrTop, 0.000001, CrashPen);
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index ed3af3bc..17a54ff3 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -1783,8 +1783,12 @@ FUNCTION void write_bigoutput()
            << pick_report_name(19);
     SS2out << "  Function: " << SR_fxn << "  RecDev_method: " << do_recdev << "   sum_recdev: " << sum_recdev << endl
            << SR_parm(1) << " Ln(R0) " << mfexp(SR_parm(1)) << endl
-           << steepness << " steepness" << endl
+           << steepness << " steepness " << "#_derived_alpha_beta: "<<alpha<<" "<<beta<<endl
            << Bmsy / SSB_virgin << " Bmsy/Bzero ";
+        SS2out << " spr: "<<SPR_virgin<<endl;
+         SS2out << " der_steep: "<< alpha * SPR_virgin / (4.00 + alpha * SPR_virgin)<<endl;
+         SS2out << "der_R0: "<<  1.0 / beta * (alpha - ( 1.0 / SPR_virgin))<<endl;;
+
     if (SR_fxn == 8)
     {
       dvariable Shepherd_c;
@@ -4793,7 +4797,7 @@ FUNCTION void SPR_profile()
         Do_Equil_Calc(equ_Recr);
         //  SPAWN-RECR:   calc equil spawn-recr in the SPR loop
         SPR_temp = SSB_equil;
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work(2), SR_parm_work(3), SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         Btgt_prof = Equ_SpawnRecr_Result(1);
         Btgt_prof_rec = Equ_SpawnRecr_Result(2);
         if (Btgt_prof < 0.001 || Btgt_prof_rec < 0.001)
diff --git a/StockSynthesis.code-workspace b/StockSynthesis.code-workspace
index 2bfc56e8..cdd30489 100644
--- a/StockSynthesis.code-workspace
+++ b/StockSynthesis.code-workspace
@@ -10,6 +10,7 @@
 			"\"*.extension\":": "\"tpl\"",
 			"*.htp": "c",
 			"ostream": "c",
+			"xlocale": "c",
 			"iosfwd": "c"
 		},
 		"explorer.excludeGitIgnore": true

From 8981777d772d6df49b4c3ae1007b6e6dba2fd268 Mon Sep 17 00:00:00 2001
From: RickMethot <richard.methot@noaa.gov>
Date: Mon, 13 Feb 2023 17:36:35 -0800
Subject: [PATCH 02/22] revise to use WHAM syntax

---
 SS_benchfore.tpl    |  5 ++++-
 SS_popdyn.tpl       |  5 ++---
 SS_recruit.tpl      | 43 ++++++++++++++++++++++++++++---------------
 SS_write_report.tpl | 23 +++++++++++++++++------
 4 files changed, 51 insertions(+), 25 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index d95f5171..badaeb38 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -748,6 +748,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   Recr_unf = mfexp(SR_parm_work(1));
   Do_Equil_Calc(Recr_unf);
   SSB_unf = SSB_equil;
+  report5<<" calc SSBunf "<<SSB_unf<<" recr "<<Recr_unf<<" work "<<SR_parm_work<<" parm "<<SR_parm<<endl;
   SR_parm_work(N_SRparm2 + 1) = SSB_unf;
   if (show_MSY == 1)
     report5 << "SR_parm for benchmark: " << SR_parm_work << endl
@@ -902,7 +903,8 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     }
 
     //  SPAWN-RECR:   calc equil spawn-recr in YPR; need to make this area-specific
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSB_equil); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    SPR_temp = SSB_equil;  //  based on most recent call to Do_Equil_Calc
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
 
     Bspr = Equ_SpawnRecr_Result(1);
     Bspr_rec = Equ_SpawnRecr_Result(2);
@@ -1111,6 +1113,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         SPR_Btgt = SSB_equil / SPR_unfished;
         //  SPAWN-RECR:   calc equil spawn-recr for Btarget calcs;  need to make area-specific
         SPR_temp = SSB_equil;
+    
         Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         yld1(ii) = Equ_SpawnRecr_Result(1);
       }
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 1548b7d4..766486c6 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -349,8 +349,8 @@ FUNCTION void get_initial_conditions()
     {
       alpha = mfexp(SR_parm(3));
       beta = mfexp(SR_parm(4));
-      steepness = alpha * SPR_virgin / (4.00 + alpha * SPR_virgin);
-      Recr_virgin = 1.0 / beta * (alpha - ( 1.0 / SPR_virgin));
+      alpha = 4.0 * steepness / (SPR_virgin * (1. - steepness));
+      beta = (5.0 * steepness - 1.0) / ((1 - steepness) * SSB_virgin);
       SR_parm(1) = log(Recr_virgin);
       SR_parm(2) = steepness;
       // warning<< SR_parm(1) << " Ln(R0) " << mfexp(SR_parm(1)) << endl
@@ -529,7 +529,6 @@ FUNCTION void get_initial_conditions()
     SPR_temp = SSB_equil / equ_Recr; //  spawners per recruit at initial F
     //  get equilibrium SSB and recruitment from SPR_temp, Recr_virgin and virgin steepness
     Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm, SSB_virgin, Recr_virgin, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-
     R1_exp = Equ_SpawnRecr_Result(2); //  set the expected recruitment equal to this equilibrium
     exp_rec(eq_yr, 1) = R1_exp;
 
diff --git a/SS_recruit.tpl b/SS_recruit.tpl
index f6a58c32..3b2affb4 100644
--- a/SS_recruit.tpl
+++ b/SS_recruit.tpl
@@ -49,9 +49,10 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
     case 3: // Beverton-Holt
     {
       steepness = SR_parm_work(2);
-      dvariable SPR = SSB_virgin_adj / Recr_virgin;
-      alpha = ((4.0 * steepness) / (1. - steepness)) / SPR ;
-      beta = (1.0 / Recr_virgin) * (alpha - (1.0 / SPR));
+//      dvariable SPR = SSB_virgin_adj / Recr_virgin;
+//      dvariable alpha = (4.0 * steepness) / ( SPR * (1. - steepness)) ;
+//      dvariable beta = (5.0 * steepness - 1.0 )/((1.0 - steepness ) * Recr_virgin * SPR );
+//      beta = (1.0 / Recr_virgin) * (alpha - (1.0 / SPR));
       NewRecruits = (4. * steepness * Recr_virgin_adj * SSB_curr_adj) /
           (SSB_virgin_adj * (1. - steepness) + (5. * steepness - 1.) * SSB_curr_adj);
       break;
@@ -77,9 +78,9 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
     case 6: //Beverton-Holt constrained
     {
       steepness = SR_parm_work(2);
-      dvariable SPR = SSB_virgin_adj / Recr_virgin;
-      alpha = ((4.0 * steepness) / (1. - steepness)) / SPR ;
-      beta = (1.0 / Recr_virgin) * (alpha - (1.0 / SPR));
+//      dvariable SPR = SSB_virgin_adj / Recr_virgin;
+//      alpha = ((4.0 * steepness) / (1. - steepness)) / SPR ;
+//      beta = (1.0 / Recr_virgin) * (alpha - (1.0 / SPR));
       if (SSB_curr_adj > SSB_virgin_adj)
       {
         SSB_BH1 = SSB_virgin_adj;
@@ -162,7 +163,7 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
       {
         alpha = mfexp(SR_parm_work(3));
         beta = mfexp(SR_parm_work(4));
-        NewRecruits =  (alpha*SSB_curr_adj) / (1.0 + beta * SSB_curr_adj);
+        NewRecruits =  (alpha * SSB_curr_adj) / (beta + SSB_curr_adj);
         break;
       }
   }
@@ -310,22 +311,34 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
   //  SS_Label_44.1.3  Beverton-Holt
     case 3: // same as case 6
     {
-      dvariable SPR = SSB_virgin / Recr_virgin;
-      alpha = ((4.0 * steepness) / (1. - steepness)) / SPR ;
-      beta = (1.0 / Recr_virgin) * (alpha - (1.0 / SPR));
-      B_equil = alpha * SPR_temp - beta;
+  // from WHAM per Tim Miller:
+  //  WHAM based on R = A*S/(1+B*S)
+  //  log_SR_a = log(4 * SR_h/(exp(log_SPR0)*(1 - SR_h)));
+  //  log_SR_b = log((5*SR_h - 1)/((1-SR_h)*SR_R0*exp(log_SPR0)));
+  //  SR_h = 0.2 * exp(0.8*log(exp(log_SR_a) * exp(log_SPR0)));
+  //  SR_R0 = log(exp(log_SR_a + log_SPR0))/(exp(log_SR_b + log_SPR0));
+
+  //  SS3 previously used alternative formulation: R = A*S/(B+S)
+  //  converting SS3 to align with WHAM
+      alpha = 4.0 * steepness / (SPR_virgin * (1. - steepness));
+      beta = (5.0 * steepness - 1.0) / ((1 - steepness) * SSB_virgin);
+      B_equil = (alpha * SPR_temp - 1.0) / beta;
       B_equil = posfun(B_equil, 0.0001, temp);
-      R_equil = (4. * steepness * Recr_virgin * B_equil) / (SSB_virgin * (1. - steepness) + (5. * steepness - 1.) * B_equil); //Beverton-Holt
+      R_equil = alpha * B_equil / (1.0 + beta * B_equil);
+//      report5<<" WHAM Beq "<<B_equil<<" Req "<<R_equil<<" alpha "<<alpha<<" beta "<<beta<<" SSB_unf "<<SSB_unf<<endl;
+//      R_equil = (4. * steepness * Recr_virgin * B_equil) / (SSB_virgin * (1. - steepness) + (5. * steepness - 1.) * B_equil); //Beverton-Holt
+//      report5<<" SS3 Beq "<<B_equil<<" Req "<<R_equil<<" alpha "<<alpha<<" beta "<<beta<<" SSB_unf "<<SSB_unf<<endl;
       break;
     }
 
-    case 10: // Beverton-Holt with alpha and beta parameterization
+    case 10: // Beverton-Holt with alpha and beta parameterization using  R = A*S/(B+S) approach
     {
       alpha = mfexp(SRparm(3));
       beta = mfexp(SRparm(4));
-      B_equil = alpha * SPR_temp - beta;
+      B_equil = (alpha * SPR_temp - 1.0) / beta;
       B_equil = posfun(B_equil, 0.0001, temp);
-      R_equil =  (alpha * Recr_virgin * B_equil) / (1.0 + beta * Recr_virgin * B_equil);
+      R_equil = alpha * B_equil / (1.0 + beta * B_equil);
+//      report5<<SPR_temp<<" Beq "<<B_equil<<" Req "<<R_equil<<" alpha "<<alpha<<" beta "<<beta<<" SSB_unf "<<SSB_unf<<endl;
       break;
     }
 
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 17a54ff3..136b0675 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -1783,13 +1783,24 @@ FUNCTION void write_bigoutput()
            << pick_report_name(19);
     SS2out << "  Function: " << SR_fxn << "  RecDev_method: " << do_recdev << "   sum_recdev: " << sum_recdev << endl
            << SR_parm(1) << " Ln(R0) " << mfexp(SR_parm(1)) << endl
-           << steepness << " steepness " << "#_derived_alpha_beta: "<<alpha<<" "<<beta<<endl
+           << steepness << " steepness " << endl
            << Bmsy / SSB_virgin << " Bmsy/Bzero ";
-        SS2out << " spr: "<<SPR_virgin<<endl;
-         SS2out << " der_steep: "<< alpha * SPR_virgin / (4.00 + alpha * SPR_virgin)<<endl;
-         SS2out << "der_R0: "<<  1.0 / beta * (alpha - ( 1.0 / SPR_virgin))<<endl;;
-
-    if (SR_fxn == 8)
+    SS2out << " SPR_virgin "<<SPR_virgin<<endl;
+    if (SR_fxn == 10)
+    {
+  //  SR_h = 0.2 * exp(0.8*log(exp(log_SR_a) * exp(log_SPR0)));
+  //  SR_R0 = log(exp(log_SR_a + log_SPR0))/(exp(log_SR_b + log_SPR0));
+      SS2out << " derived_steepness "<< 0.2 * mfexp( 0.8 * log( alpha ) * SPR_virgin)<<" using_virgin_SPR; will be time-varying if biology is time-varying"<<endl;
+      SS2out << "derived_R0 "<<  log( alpha * SPR_virgin ) / ( beta * SPR_virgin)<endl;
+    }
+    else if (SR_fxn == 3)
+    {
+      alpha = 4.0 * steepness / (SPR_virgin * (1. - steepness));
+      beta = (5.0 * steepness - 1.0) / ((1 - steepness) * SSB_virgin);
+      SS2out << " derived_alpha " << alpha << " using_virgin_SPR" << endl;
+      SS2out << "derived_beta " <<  beta <<endl;
+    }
+    else if (SR_fxn == 8)
     {
       dvariable Shepherd_c;
       dvariable Shepherd_c2;

From 5351bb622ca8ddbd33dbf712365d023f2956fbb1 Mon Sep 17 00:00:00 2001
From: RickMethot <richard.methot@noaa.gov>
Date: Mon, 13 Feb 2023 17:43:58 -0800
Subject: [PATCH 03/22] Update .gitignore

---
 .gitignore | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/.gitignore b/.gitignore
index 7036b5eb..7dfad946 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,10 +7,9 @@
 *.htp
 *.obj
 *.log
-ss.tpl
-ss3.tpl
-ss_opt.tpl
-ss_trans.tpl
+Compile/ss.tpl
+Compile/ss_opt.tpl
+Compile/ss_trans.tpl
 ~$*.*
 Compile/ss.log
 Compile/ss3.log

From cc71b493c7c93d17e8fb6640836e58d5d4f6adcf Mon Sep 17 00:00:00 2001
From: RickMethot <richard.methot@noaa.gov>
Date: Fri, 19 May 2023 11:14:13 -0700
Subject: [PATCH 04/22] Srr=10 now matching SRR=3

---
 SS_popdyn.tpl          | 15 ++++++++-------
 SS_readcontrol_330.tpl |  2 +-
 SS_recruit.tpl         |  5 ++---
 SS_write_report.tpl    | 10 ++++------
 4 files changed, 15 insertions(+), 17 deletions(-)

diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 766486c6..724ee024 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -347,17 +347,18 @@ FUNCTION void get_initial_conditions()
 
     if(SR_fxn == 10)  // B-H with a,b
     {
+  //  WHAM based on R = A*S/(1+B*S)
+  //  log_SR_a = log(4 * SR_h/(exp(log_SPR0)*(1 - SR_h)));
+  //  log_SR_b = log((5*SR_h - 1)/((1-SR_h)*SR_R0*exp(log_SPR0)));
+  //  h = a * SPR0 / (4. + a * SPR0)
+  //  R0 = 1/b * (a-1/SPR0)
+
       alpha = mfexp(SR_parm(3));
       beta = mfexp(SR_parm(4));
-      alpha = 4.0 * steepness / (SPR_virgin * (1. - steepness));
-      beta = (5.0 * steepness - 1.0) / ((1 - steepness) * SSB_virgin);
+      steepness = alpha * SPR_virgin / (4. + alpha * SPR_virgin);
+      Recr_virgin = 1. / beta * (alpha - (1. / SPR_virgin));
       SR_parm(1) = log(Recr_virgin);
       SR_parm(2) = steepness;
-      // warning<< SR_parm(1) << " Ln(R0) " << mfexp(SR_parm(1)) << endl
-      //     << " alpha_beta: "<<alpha<<" "<<beta<<endl
-      //   << " spr: "<<SPR_virgin<<endl
-      //    << " der_steep: "<< alpha * SPR_virgin / (4.00 + alpha * SPR_virgin)<<endl
-      //    << "der_R0: "<<  1.0 / beta * (alpha - ( 1.0 / SPR_virgin))<<endl;
     }
     else {
       Recr_virgin = mfexp(SR_parm(1));
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index e7042c6c..725eecc4 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1972,7 +1972,7 @@
   SR_parm_timevary.initialize();
   SR_env_link = 0;
   SR_env_target = 0;
-  //#_SR_function: 1=null; 2=Ricker; 3=std_B-H; 4=SCAA; 5=Hockey; 6=B-H_flattop; 7=Survival_3Parm "<<endl;
+  //#_SR_function: 1=null; 2=Ricker; 3=std_B-H; 4=SCAA; 5=Hockey; 6=B-H_flattop; 7=Survival_3Parm; 10=B-H with a,b "<<endl;
   ParmLabel += "SR_LN(R0)";
   switch (SR_fxn)
   {
diff --git a/SS_recruit.tpl b/SS_recruit.tpl
index 3b2affb4..86604f67 100644
--- a/SS_recruit.tpl
+++ b/SS_recruit.tpl
@@ -161,9 +161,10 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
 
       case 10: // Beverton-Holt with alpha beta
       {
+  //  WHAM based on R = A*S/(1+B*S)
         alpha = mfexp(SR_parm_work(3));
         beta = mfexp(SR_parm_work(4));
-        NewRecruits =  (alpha * SSB_curr_adj) / (beta + SSB_curr_adj);
+        NewRecruits =  (alpha * SSB_curr_adj) / (1.0 + beta * SSB_curr_adj);
         break;
       }
   }
@@ -315,8 +316,6 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
   //  WHAM based on R = A*S/(1+B*S)
   //  log_SR_a = log(4 * SR_h/(exp(log_SPR0)*(1 - SR_h)));
   //  log_SR_b = log((5*SR_h - 1)/((1-SR_h)*SR_R0*exp(log_SPR0)));
-  //  SR_h = 0.2 * exp(0.8*log(exp(log_SR_a) * exp(log_SPR0)));
-  //  SR_R0 = log(exp(log_SR_a + log_SPR0))/(exp(log_SR_b + log_SPR0));
 
   //  SS3 previously used alternative formulation: R = A*S/(B+S)
   //  converting SS3 to align with WHAM
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 136b0675..10b9b6a3 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -1788,17 +1788,15 @@ FUNCTION void write_bigoutput()
     SS2out << " SPR_virgin "<<SPR_virgin<<endl;
     if (SR_fxn == 10)
     {
-  //  SR_h = 0.2 * exp(0.8*log(exp(log_SR_a) * exp(log_SPR0)));
-  //  SR_R0 = log(exp(log_SR_a + log_SPR0))/(exp(log_SR_b + log_SPR0));
-      SS2out << " derived_steepness "<< 0.2 * mfexp( 0.8 * log( alpha ) * SPR_virgin)<<" using_virgin_SPR; will be time-varying if biology is time-varying"<<endl;
-      SS2out << "derived_R0 "<<  log( alpha * SPR_virgin ) / ( beta * SPR_virgin)<endl;
+      SS2out << " Ln_alpha_parameter: " << SR_parm(3) << " alpha " << mfexp(SR_parm(3)) << endl;
+      SS2out << " Ln_beta_parameter: " << SR_parm(4) << " beta " << mfexp(SR_parm(4)) << endl;
     }
     else if (SR_fxn == 3)
     {
       alpha = 4.0 * steepness / (SPR_virgin * (1. - steepness));
       beta = (5.0 * steepness - 1.0) / ((1 - steepness) * SSB_virgin);
-      SS2out << " derived_alpha " << alpha << " using_virgin_SPR" << endl;
-      SS2out << "derived_beta " <<  beta <<endl;
+      SS2out << " Ln_alpha_derived: " << log(alpha) << " alpha " << alpha << endl;
+      SS2out << " Ln_beta_derived: " << log(beta) << " beta " << beta;
     }
     else if (SR_fxn == 8)
     {

From 03b1420ebaf1cf97480a74dcb55e5e796cc09c9a Mon Sep 17 00:00:00 2001
From: RickMethot <richard.methot@noaa.gov>
Date: Fri, 19 May 2023 17:06:15 -0700
Subject: [PATCH 05/22] adding reporting for timevary growth

---
 SS_benchfore.tpl              |  8 ++++++++
 SS_popdyn.tpl                 |  8 ++++++++
 SS_write_report.tpl           | 14 ++++++++------
 StockSynthesis.code-workspace |  3 ++-
 4 files changed, 26 insertions(+), 7 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index badaeb38..ecafcd8c 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -3650,6 +3650,14 @@ FUNCTION void Get_Forecast()
 
         Smry_Table(y, 11) = SSB_equil;
         Smry_Table(y, 13) = GenTime;
+        if( SR_fxn == 10 )
+        {
+          temp = SSB_equil / equ_Recr;  //  current year's SPB/R with current biology at age
+          alpha = mfexp(SR_parm_work(3));
+          beta = mfexp(SR_parm_work(4));
+          SR_parm_byyr(y, 2) =  alpha * temp / (4. + alpha * temp);  //  implied steepness
+          SR_parm_byyr(y, 1) = log( 1. / beta * (alpha - (1. / temp)));  //  implied ln_R0
+        }
         Fishon = 1;
         Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation
         if (STD_Yr_Reverse_Ofish(y) > 0)
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 724ee024..58476d6c 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -1785,6 +1785,14 @@ FUNCTION void get_time_series()
       Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation with current year's biology
       Smry_Table(y, 11) = SSB_equil;
       Smry_Table(y, 13) = GenTime;
+      if( SR_fxn == 10 )
+      {
+        temp = SSB_equil / Recr_virgin;  //  current year's SPB/R with current biology at age
+        alpha = mfexp(SR_parm_work(3));
+        beta = mfexp(SR_parm_work(4));
+        SR_parm_byyr(y, 2) =  alpha * temp / (4. + alpha * temp);  //  implied steepness
+        SR_parm_byyr(y, 1) = log( 1. / beta * (alpha - (1. / temp)));  //  implied ln_R0
+      }
       Fishon = 1;
       Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation with current year's biology and F
       if (STD_Yr_Reverse_Ofish(y) > 0)
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 10b9b6a3..00e27e89 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -1789,7 +1789,7 @@ FUNCTION void write_bigoutput()
     if (SR_fxn == 10)
     {
       SS2out << " Ln_alpha_parameter: " << SR_parm(3) << " alpha " << mfexp(SR_parm(3)) << endl;
-      SS2out << " Ln_beta_parameter: " << SR_parm(4) << " beta " << mfexp(SR_parm(4)) << endl;
+      SS2out << " Ln_beta_parameter: " << SR_parm(4) << " beta " << mfexp(SR_parm(4));
     }
     else if (SR_fxn == 3)
     {
@@ -1813,9 +1813,7 @@ FUNCTION void write_bigoutput()
     {
       SS2out << " Ricker_Power: " << SR_parm(3);
     }
-
-    SS2out << endl;
-    SS2out << sigmaR << " sigmaR" << endl;
+    SS2out << endl << sigmaR << " sigmaR" << endl;
     SS2out << init_equ_steepness << "  # 0/1 to use steepness in initial equ recruitment calculation" << endl;
 
     SS2out << SR_parm(N_SRparm2 - 1) << " init_eq:  see below" << endl
@@ -1848,7 +1846,7 @@ FUNCTION void write_bigoutput()
     }
     SS2out << endl;
 
-    SS2out << "Yr SpawnBio exp_recr with_regime bias_adjusted pred_recr dev biasadjuster era mature_bio mature_num raw_dev" << endl;
+    SS2out << "Yr SpawnBio exp_recr with_regime bias_adjusted pred_recr dev biasadjuster era mature_bio mature_num raw_dev SPR0 h R0" << endl;
     SS2out << "S/Rcurve " << SSB_virgin << " " << Recr_virgin << endl;
     y = styr - 2;
     SS2out << "Virg " << SSB_yr(y) << " " << exp_rec(y) << " - " << 0.0 << " Virg " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " 0.0 " << endl;
@@ -1899,7 +1897,11 @@ FUNCTION void write_bigoutput()
       {
         SS2out << " _ _ Fixed";
       }
-      SS2out << endl;
+      temp = Smry_Table(y,11) / Recr_virgin;
+      alpha = mfexp(SR_parm_byyr(y,3));
+      beta = mfexp(SR_parm_byyr(y,4));
+      SS2out << " " << temp << " " << alpha * temp / (4. + alpha * temp) << " " << 1. / beta * (alpha - (1. / temp));
+      SS2out << SR_parm_byyr(y)(1,4) << endl;
     }
 
     // REPORT_KEYWORD SPAWN_RECR_CURVE
diff --git a/StockSynthesis.code-workspace b/StockSynthesis.code-workspace
index cdd30489..14159ac5 100644
--- a/StockSynthesis.code-workspace
+++ b/StockSynthesis.code-workspace
@@ -11,7 +11,8 @@
 			"*.htp": "c",
 			"ostream": "c",
 			"xlocale": "c",
-			"iosfwd": "c"
+			"iosfwd": "c",
+			"cmath": "c"
 		},
 		"explorer.excludeGitIgnore": true
 	}

From 63c8681015a082be98608b94609111a06ee6580c Mon Sep 17 00:00:00 2001
From: RickMethot <richard.methot@noaa.gov>
Date: Wed, 31 May 2023 09:40:07 -0700
Subject: [PATCH 06/22] WIP

---
 SS_benchfore.tpl | 19 ++++++++++++-------
 SS_recruit.tpl   |  5 ++++-
 2 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index ecafcd8c..b8e232f6 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -748,18 +748,22 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   Recr_unf = mfexp(SR_parm_work(1));
   Do_Equil_Calc(Recr_unf);
   SSB_unf = SSB_equil;
-  report5<<" calc SSBunf "<<SSB_unf<<" recr "<<Recr_unf<<" work "<<SR_parm_work<<" parm "<<SR_parm<<endl;
-  SR_parm_work(N_SRparm2 + 1) = SSB_unf;
+  SPR_unfished = SSB_unf / Recr_unf; //  this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
   if (show_MSY == 1)
+  {
     report5 << "SR_parm for benchmark: " << SR_parm_work << endl
-            << "for years: " << Bmark_Yr(9) << " " << Bmark_Yr(10) << "  SSB_virgin was: " << SSB_virgin << endl;
-  if (show_MSY == 1)
-    report5 << "Repro_output_by_age_for_morph_1: " << fec(1) << endl;
+            << "mean from years: " << Bmark_Yr(9) << " " << Bmark_Yr(10) << endl;
+    SPR_virgin = SSB_virgin / Recr_virgin;
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_virgin); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    report5 << " Virgin SPR0, SSB, R: " << SPR_virgin << " " << Equ_SpawnRecr_Result << endl;
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_unfished); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    report5 << " Benchmark SPR0, SSB, R: " << SPR_unfished << " " << Equ_SpawnRecr_Result << endl;
+  }
+  SR_parm_work(N_SRparm2 + 1) = SSB_unf;
   Mgmt_quant(1) = SSB_unf;
   Mgmt_quant(2) = totbio;
   Mgmt_quant(3) = smrybio;
   Mgmt_quant(4) = Recr_unf;
-
   // find Fspr             SS_Label_710
   {
     if (show_MSY == 1)
@@ -905,6 +909,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     //  SPAWN-RECR:   calc equil spawn-recr in YPR; need to make this area-specific
     SPR_temp = SSB_equil;  //  based on most recent call to Do_Equil_Calc
     Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+         report5<<SPR_temp<<" " << Equ_SpawnRecr_Result<<endl;
 
     Bspr = Equ_SpawnRecr_Result(1);
     Bspr_rec = Equ_SpawnRecr_Result(2);
@@ -1113,8 +1118,8 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         SPR_Btgt = SSB_equil / SPR_unfished;
         //  SPAWN-RECR:   calc equil spawn-recr for Btarget calcs;  need to make area-specific
         SPR_temp = SSB_equil;
-    
         Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+         report5<<SPR_temp<<" " << Equ_SpawnRecr_Result<<endl;
         yld1(ii) = Equ_SpawnRecr_Result(1);
       }
 
diff --git a/SS_recruit.tpl b/SS_recruit.tpl
index 86604f67..c24509c0 100644
--- a/SS_recruit.tpl
+++ b/SS_recruit.tpl
@@ -319,12 +319,15 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
 
   //  SS3 previously used alternative formulation: R = A*S/(B+S)
   //  converting SS3 to align with WHAM
+      SPR_virgin = SSB_virgin / Recr_virgin;
       alpha = 4.0 * steepness / (SPR_virgin * (1. - steepness));
       beta = (5.0 * steepness - 1.0) / ((1 - steepness) * SSB_virgin);
+      report5<<" alpha "<<alpha<<" beta "<<beta<<" SSB_unf "<<SSB_virgin<<" SPR "<<SPR_virgin<<" steep "<<steepness<<endl;
       B_equil = (alpha * SPR_temp - 1.0) / beta;
+//      report5<<" spr "<<SPR_temp<<"  Beq "<<B_equil<<endl;
       B_equil = posfun(B_equil, 0.0001, temp);
       R_equil = alpha * B_equil / (1.0 + beta * B_equil);
-//      report5<<" WHAM Beq "<<B_equil<<" Req "<<R_equil<<" alpha "<<alpha<<" beta "<<beta<<" SSB_unf "<<SSB_unf<<endl;
+//      report5<<"  Beq "<<B_equil<<" Req "<<R_equil<<endl;
 //      R_equil = (4. * steepness * Recr_virgin * B_equil) / (SSB_virgin * (1. - steepness) + (5. * steepness - 1.) * B_equil); //Beverton-Holt
 //      report5<<" SS3 Beq "<<B_equil<<" Req "<<R_equil<<" alpha "<<alpha<<" beta "<<beta<<" SSB_unf "<<SSB_unf<<endl;
       break;

From 9201cee9ee21c19b9da7b49bf1bd1a7b57bf6e95 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Wed, 22 May 2024 16:11:03 -0700
Subject: [PATCH 07/22] working version with a,b

---
 SS_recruit.tpl      | 41 +++++++++++++++++++----------------------
 SS_write_report.tpl |  8 ++++----
 2 files changed, 23 insertions(+), 26 deletions(-)

diff --git a/SS_recruit.tpl b/SS_recruit.tpl
index c24509c0..5553dd26 100644
--- a/SS_recruit.tpl
+++ b/SS_recruit.tpl
@@ -49,15 +49,19 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
     case 3: // Beverton-Holt
     {
       steepness = SR_parm_work(2);
-//      dvariable SPR = SSB_virgin_adj / Recr_virgin;
-//      dvariable alpha = (4.0 * steepness) / ( SPR * (1. - steepness)) ;
-//      dvariable beta = (5.0 * steepness - 1.0 )/((1.0 - steepness ) * Recr_virgin * SPR );
-//      beta = (1.0 / Recr_virgin) * (alpha - (1.0 / SPR));
       NewRecruits = (4. * steepness * Recr_virgin_adj * SSB_curr_adj) /
           (SSB_virgin_adj * (1. - steepness) + (5. * steepness - 1.) * SSB_curr_adj);
       break;
     }
 
+      case 10: // Beverton-Holt with alpha beta  per WHAM:  R = A*S/(1+B*S)
+      {
+        alpha = mfexp(SR_parm_work(3));
+        beta = mfexp(SR_parm_work(4));
+        NewRecruits =  (alpha * SSB_curr_adj) / (1.0 + beta * SSB_curr_adj);
+        break;
+      }
+
     //  SS_Label_43.3.4  constant expected recruitment
     case 4: // none
     {
@@ -159,14 +163,6 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
       break;
     }
 
-      case 10: // Beverton-Holt with alpha beta
-      {
-  //  WHAM based on R = A*S/(1+B*S)
-        alpha = mfexp(SR_parm_work(3));
-        beta = mfexp(SR_parm_work(4));
-        NewRecruits =  (alpha * SSB_curr_adj) / (1.0 + beta * SSB_curr_adj);
-        break;
-      }
   }
   RETURN_ARRAYS_DECREMENT();
   return NewRecruits;
@@ -322,18 +318,19 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
       SPR_virgin = SSB_virgin / Recr_virgin;
       alpha = 4.0 * steepness / (SPR_virgin * (1. - steepness));
       beta = (5.0 * steepness - 1.0) / ((1 - steepness) * SSB_virgin);
-      report5<<" alpha "<<alpha<<" beta "<<beta<<" SSB_unf "<<SSB_virgin<<" SPR "<<SPR_virgin<<" steep "<<steepness<<endl;
+
+//      report5 <<" SSB_unf "<<SSB_virgin<<" SPR_unf "<<SPR_virgin<<" steep: "<<steepness<<" R0: "<<Recr_virgin << endl;
+//      report5 <<" derive_alpha "<<alpha<<" derive_beta "<<beta << endl;
+//      report5 << " deriv_h: " << alpha * SPR_virgin / (4. + alpha * SPR_virgin) << " derive_R0: " << 1. / beta * (alpha - (1. / SPR_virgin))<<endl;
       B_equil = (alpha * SPR_temp - 1.0) / beta;
-//      report5<<" spr "<<SPR_temp<<"  Beq "<<B_equil<<endl;
       B_equil = posfun(B_equil, 0.0001, temp);
       R_equil = alpha * B_equil / (1.0 + beta * B_equil);
-//      report5<<"  Beq "<<B_equil<<" Req "<<R_equil<<endl;
-//      R_equil = (4. * steepness * Recr_virgin * B_equil) / (SSB_virgin * (1. - steepness) + (5. * steepness - 1.) * B_equil); //Beverton-Holt
-//      report5<<" SS3 Beq "<<B_equil<<" Req "<<R_equil<<" alpha "<<alpha<<" beta "<<beta<<" SSB_unf "<<SSB_unf<<endl;
+//      report5 << "SPR_input: " << SPR_temp << " B_equil: " << B_equil << " R_equil: "<<R_equil << endl<<endl;
+
       break;
     }
 
-    case 10: // Beverton-Holt with alpha and beta parameterization using  R = A*S/(B+S) approach
+    case 10: // Beverton-Holt with alpha and beta parameterization using  R = A*S/(1+B*S) approach; same as WHAM
     {
       alpha = mfexp(SRparm(3));
       beta = mfexp(SRparm(4));
@@ -354,11 +351,11 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
     //  SS_Label_44.1.5  Hockey Stick
     case 5: // hockey stick
     {
-      alpha = SRparm(3) * Recr_virgin; // min recruitment level
+      dvariable hockey_min = SRparm(3) * Recr_virgin; // min recruitment level
       //        temp=SSB_virgin/R0*steepness;  // spawners per recruit at inflection
-      beta = (Recr_virgin - alpha) / (steepness * SSB_virgin); //  slope of recruitment on spawners below the inflection
-      B_equil = Join_Fxn(0.0 * SSB_virgin / Recr_virgin, SSB_virgin / Recr_virgin, SSB_virgin / Recr_virgin * steepness, SPR_temp, alpha / ((1. / SPR_temp) - beta), SPR_temp * Recr_virgin);
-      R_equil = Join_Fxn(0.0 * SSB_virgin, SSB_virgin, SSB_virgin * steepness, B_equil, alpha + beta * B_equil, Recr_virgin);
+      dvariable hockey_slope = (Recr_virgin - hockey_min) / (steepness * SSB_virgin); //  slope of recruitment on spawners below the inflection
+      B_equil = Join_Fxn(0.0 * SSB_virgin / Recr_virgin, SSB_virgin / Recr_virgin, SSB_virgin / Recr_virgin * steepness, SPR_temp, hockey_min / ((1. / SPR_temp) - hockey_slope), SPR_temp * Recr_virgin);
+      R_equil = Join_Fxn(0.0 * SSB_virgin, SSB_virgin, SSB_virgin * steepness, B_equil, hockey_min + hockey_slope * B_equil, Recr_virgin);
       break;
     }
     //  SS_Label_44.1.7  3 parameter survival based
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 00e27e89..fbba7bd2 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -1794,7 +1794,7 @@ FUNCTION void write_bigoutput()
     else if (SR_fxn == 3)
     {
       alpha = 4.0 * steepness / (SPR_virgin * (1. - steepness));
-      beta = (5.0 * steepness - 1.0) / ((1 - steepness) * SSB_virgin);
+      beta = (5.0 * steepness - 1.0) / ((1. - steepness) * SSB_virgin);
       SS2out << " Ln_alpha_derived: " << log(alpha) << " alpha " << alpha << endl;
       SS2out << " Ln_beta_derived: " << log(beta) << " beta " << beta;
     }
@@ -1846,7 +1846,7 @@ FUNCTION void write_bigoutput()
     }
     SS2out << endl;
 
-    SS2out << "Yr SpawnBio exp_recr with_regime bias_adjusted pred_recr dev biasadjuster era mature_bio mature_num raw_dev SPR0 h R0" << endl;
+    SS2out << "Yr SpawnBio exp_recr with_regime bias_adjusted pred_recr dev biasadjuster era mature_bio mature_num raw_dev SSBe/R0 h R0" << endl;
     SS2out << "S/Rcurve " << SSB_virgin << " " << Recr_virgin << endl;
     y = styr - 2;
     SS2out << "Virg " << SSB_yr(y) << " " << exp_rec(y) << " - " << 0.0 << " Virg " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " 0.0 " << endl;
@@ -1897,10 +1897,10 @@ FUNCTION void write_bigoutput()
       {
         SS2out << " _ _ Fixed";
       }
-      temp = Smry_Table(y,11) / Recr_virgin;
+      dvariable SPR = Smry_Table(y, 11) / Recr_virgin;
       alpha = mfexp(SR_parm_byyr(y,3));
       beta = mfexp(SR_parm_byyr(y,4));
-      SS2out << " " << temp << " " << alpha * temp / (4. + alpha * temp) << " " << 1. / beta * (alpha - (1. / temp));
+      SS2out << " " << SPR << " " << alpha * SPR / (4. + alpha * SPR) << " " << 1. / beta * (alpha - (1. / SPR));
       SS2out << SR_parm_byyr(y)(1,4) << endl;
     }
 

From 2bb4301bdb0dd4c27cad2118a5ebd7a097c5d387 Mon Sep 17 00:00:00 2001
From: "Richard.Methot" <1365818351113302@mil>
Date: Tue, 28 May 2024 14:39:34 -0700
Subject: [PATCH 08/22] Update .gitignore

---
 .gitignore | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.gitignore b/.gitignore
index 7dfad946..a602a79c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,6 +10,8 @@
 Compile/ss.tpl
 Compile/ss_opt.tpl
 Compile/ss_trans.tpl
+Compile/ss3.tpl
+Compile/Make_SS_warn.bat
 ~$*.*
 Compile/ss.log
 Compile/ss3.log

From d01422e9739e4f8a22d4e406dc72def7b4678a32 Mon Sep 17 00:00:00 2001
From: Rick-Methot-NOAA <richard.methot@noaa.gov>
Date: Wed, 12 Jun 2024 14:50:29 -0700
Subject: [PATCH 09/22] augment spawn_recr report and use to test time-vary
 SR_parm approach

---
 SS_benchfore.tpl       |  12 ++--
 SS_popdyn.tpl          |  18 ++++--
 SS_readcontrol_330.tpl |   9 +++
 SS_recruit.tpl         |  13 ++--
 SS_write_report.tpl    | 139 ++++++++++++++++++++++++++++++++++-------
 5 files changed, 156 insertions(+), 35 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index b8e232f6..69dd8ffc 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -753,7 +753,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   {
     report5 << "SR_parm for benchmark: " << SR_parm_work << endl
             << "mean from years: " << Bmark_Yr(9) << " " << Bmark_Yr(10) << endl;
-    SPR_virgin = SSB_virgin / Recr_virgin;
+    //  SPR_virgin = SSB_virgin / Recr_virgin;  // already defined
     Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_virgin); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
     report5 << " Virgin SPR0, SSB, R: " << SPR_virgin << " " << Equ_SpawnRecr_Result << endl;
     Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_unfished); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
@@ -1906,15 +1906,15 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   }
   else if (show_MSY == 2) //  do brief output
   {
-    SS2out << SPR_actual / 100. << " " << SPR_Fmult << " " << Mgmt_quant(10) << " " << YPR_spr_dead / Vbio1_spr << " " << Bspr_rec << " "
+    report5 << SPR_actual / 100. << " " << SPR_Fmult << " " << Mgmt_quant(10) << " " << YPR_spr_dead / Vbio1_spr << " " << Bspr_rec << " "
            << Bspr << " " << YPR_spr_dead * Bspr_rec << " " << YPR_spr_ret * Bspr_rec
            << " " << Vbio1_spr * Bspr_rec << " # ";
 
-    SS2out << SPR_Btgt << " " << Btgt / SSB_unf << " " << Btgt_Fmult << " " << Mgmt_quant(7) << " " << YPR_Btgt_dead / Vbio1_Btgt << " " << Btgt_Rec << " "
+    report5 << SPR_Btgt << " " << Btgt / SSB_unf << " " << Btgt_Fmult << " " << Mgmt_quant(7) << " " << YPR_Btgt_dead / Vbio1_Btgt << " " << Btgt_Rec << " "
            << Btgt << " " << YPR_Btgt_dead * Btgt_Rec << " " << YPR_Btgt_ret * Btgt_Rec
            << " " << Vbio1_Btgt * Btgt_Rec << " # ";
 
-    SS2out << MSY_SPR << " " << Bmsy / SSB_unf << " " << MSY_Fmult << " " << Mgmt_quant(14) << " " << MSY / (Vbio1_MSY * Recr_msy) << " " << Recr_msy << " "
+    report5 << MSY_SPR << " " << Bmsy / SSB_unf << " " << MSY_Fmult << " " << Mgmt_quant(14) << " " << MSY / (Vbio1_MSY * Recr_msy) << " " << Recr_msy << " "
            << Bmsy << " " << MSY << " " << YPR_msy_dead * Recr_msy << " " << YPR_msy_ret * Recr_msy
            << " " << Vbio1_MSY * Recr_msy << " # " << endl;
   }
@@ -2578,6 +2578,7 @@ FUNCTION void Get_Forecast()
               }
             }
             //  SPAWN-RECR:   get recruitment in forecast;  needs to be area-specific
+            // SR_fxn
             if (SR_parm_timevary(1) == 0) //  R0 is not time-varying
             {
               R0_use = Recr_virgin;
@@ -3216,7 +3217,8 @@ FUNCTION void Get_Forecast()
               }
             }
             //  SS_Label_Info_24.3.4.1 #Get recruitment from this spawning biomass
-            //  SPAWN-RECR:   calc recruitment in time series; need to make this area-specififc
+            //  SPAWN-RECR:   calc recruitment in time series; need to make this area-specific
+            // SR_fxn
             if (SR_parm_timevary(1) == 0) //  R0 is not time-varying
             {
               R0_use = Recr_virgin;
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 58476d6c..265e2c37 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -357,6 +357,7 @@ FUNCTION void get_initial_conditions()
       beta = mfexp(SR_parm(4));
       steepness = alpha * SPR_virgin / (4. + alpha * SPR_virgin);
       Recr_virgin = 1. / beta * (alpha - (1. / SPR_virgin));
+//      warning << " before AB_calcs " << "parm " << SR_parm(1) << " calc " << log(Recr_virgin) << endl;
       SR_parm(1) = log(Recr_virgin);
       SR_parm(2) = steepness;
     }
@@ -370,6 +371,8 @@ FUNCTION void get_initial_conditions()
     SR_parm_virg(i) = SR_parm(i);
     SR_parm_work(i) = SR_parm(i);
   }
+//  if (SR_fxn == 3) warning << "tester_A: " << SR_parm_work(1) << " base: " << SR_parm(1) << endl;
+//  if (SR_fxn == 10) warning << "tester_A: " << SR_parm_work(4) << " base: " << SR_parm(4) << endl;
     equ_Recr = Recr_virgin;
     exp_rec(eq_yr, 1) = Recr_virgin; //  expected Recr from s-r parms
     exp_rec(eq_yr, 2) = Recr_virgin;
@@ -476,6 +479,9 @@ FUNCTION void get_initial_conditions()
     else
     {
       SR_parm_work(f) = parm_timevary(SR_parm_timevary(f), eq_yr);
+//      warning << "tester_B: " << SR_parm_work(f) << " timevary " << " base " << SR_parm(f) <<endl;
+//      warning << parm_timevary(2) << endl;
+
     }
     SR_parm_byyr(eq_yr, f) = SR_parm_work(f);
   }
@@ -529,7 +535,7 @@ FUNCTION void get_initial_conditions()
     CrashPen += Equ_penalty;
     SPR_temp = SSB_equil / equ_Recr; //  spawners per recruit at initial F
     //  get equilibrium SSB and recruitment from SPR_temp, Recr_virgin and virgin steepness
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm, SSB_virgin, Recr_virgin, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
     R1_exp = Equ_SpawnRecr_Result(2); //  set the expected recruitment equal to this equilibrium
     exp_rec(eq_yr, 1) = R1_exp;
 
@@ -725,6 +731,7 @@ FUNCTION void get_time_series()
       else
       {
         SR_parm_work(f) = parm_timevary(SR_parm_timevary(f), y);
+//        warning << "tester_C: " << SR_parm_work(f) << " timevary_year " << endl;
       }
       SR_parm_byyr(y, f) = SR_parm_work(f);
     }
@@ -1019,6 +1026,7 @@ FUNCTION void get_time_series()
 
         //  SS_Label_Info_24.2.3 #Get the total recruitment produced by this spawning biomass
         //  SPAWN-RECR:   calc recruitment in time series; need to make this area-specific
+        //  SR_Fxn  relevant keyword
         if (SR_parm_timevary(1) == 0) //  R0 is not time-varying
         {
           R0_use = Recr_virgin;
@@ -1027,6 +1035,7 @@ FUNCTION void get_time_series()
         else
         {
           R0_use = mfexp(SR_parm_work(1));
+          warning << y << " set R0use to SRparm_work " << R0_use << " vir: " << Recr_virgin << endl;
           equ_Recr = R0_use;
           Fishon = 0;
           eq_yr = y;
@@ -1478,14 +1487,15 @@ FUNCTION void get_time_series()
         }
         //  SS_Label_Info_24.3.4.1 #Get recruitment from this spawning biomass
         //  SPAWN-RECR:   calc recruitment in time series; need to make this area-specific
-        if (SR_parm_timevary(1) == 0) //  R0 is not time-varying
+        //  SR_fxn
+        if (SR_update_SPR0 == 0) //  SR parms are not time-varying
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
         }
-        else
+        else  //  update SSB_use and R0_use where will update SPR0 inside the Spawn_recr fxn
         {
-          R0_use = mfexp(SR_parm_work(1));
+          R0_use = mfexp(SR_parm_work(1));  //  check to be sure this works when R0 is derived from B-H with alpha, beta parameters
           equ_Recr = R0_use;
           Fishon = 0;
           eq_yr = y;
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 725eecc4..2a5925ca 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1656,6 +1656,7 @@
 
 !!//  SS_Label_Info_4.5.4 #Set up time-varying parameters for MG parms
   int timevary_used;
+  int timevary_MG_firstyr;
   int timevary_parm_cnt_MG;
   int timevary_parm_start_MG;
 
@@ -1704,6 +1705,7 @@
   timevary_parm_start_MG = 0;
   timevary_parm_cnt_MG = 0;
   timevary_used = 0;
+  timevary_MG_firstyr = YrMax;
   MGparm_timevary.initialize();
   ivector block_design_null(1, 1);
   block_design_null.initialize();
@@ -1804,6 +1806,7 @@
       {
         MG_active(f) = 1;
         timevary_MG(y, 0) = 1; // tracks active status for all MG types
+        if(timevary_MG_firstyr == YrMax) timevary_MG_firstyr = y;  // save for reporting in MSY and spawn_recruit output
       }
     }
     //  timevary growth or maturity and Maunder M refers to that maturity
@@ -1961,6 +1964,7 @@
   int timevary_parm_cnt_SR;
   ivector timevary_SRparm(styr-3,YrMax+1);
   ivector SR_parm_timevary(1,N_SRparm2);
+  int SR_update_SPR0  // 0/1 flag to control updating of SPR0 for timevary biology 
 
  LOCAL_CALCS
   // clang-format on
@@ -1972,6 +1976,8 @@
   SR_parm_timevary.initialize();
   SR_env_link = 0;
   SR_env_target = 0;
+  SR_update_SPR0 = 0;
+
   //#_SR_function: 1=null; 2=Ricker; 3=std_B-H; 4=SCAA; 5=Hockey; 6=B-H_flattop; 7=Survival_3Parm; 10=B-H with a,b "<<endl;
   ParmLabel += "SR_LN(R0)";
   switch (SR_fxn)
@@ -2118,6 +2124,9 @@
         for (y = styr - 3; y <= YrMax + 1; y++) {
           timevary_SRparm(y) = timevary_pass(y);
         } // year vector for this category og MGparm
+        // special consideration for impact on spawner-recruitment SPR0 calculations
+        if (SR_fxn == 10 && (SR_parm_timevary(3) > 0 || SR_parm_timevary(4) > 0) )  {SR_update_SPR0 = 1;}  //  alpha or beta is time-varying
+        else if ((SR_parm_timevary(1) > 0 || SR_parm_timevary(2) > 0) )  {SR_update_SPR0 = 1;}  //  R0 or steepness is time-varying
       }
     }
   N_SRparm3 = N_SRparm2;
diff --git a/SS_recruit.tpl b/SS_recruit.tpl
index 5553dd26..2065b277 100644
--- a/SS_recruit.tpl
+++ b/SS_recruit.tpl
@@ -22,6 +22,7 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
   dvariable SRZ_0;
   dvariable srz_min;
   dvariable SRZ_surv;
+//  warning << y << "  Tester_R0 " <<  Recr_virgin_adj << " SSB0 " << SSB_virgin_adj << " SSB_curr: " << SSB_current << endl;
 
   //  SS_Label_43.1  add 0.1 to input spawning biomass value to make calculation more rebust
   SSB_curr_adj = SSB_current + 0.100; // robust
@@ -56,8 +57,8 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
 
       case 10: // Beverton-Holt with alpha beta  per WHAM:  R = A*S/(1+B*S)
       {
-        alpha = mfexp(SR_parm_work(3));
-        beta = mfexp(SR_parm_work(4));
+        dvariable alpha = mfexp(SR_parm_work(3));
+        dvariable beta = mfexp(SR_parm_work(4));
         NewRecruits =  (alpha * SSB_curr_adj) / (1.0 + beta * SSB_curr_adj);
         break;
       }
@@ -315,10 +316,12 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
 
   //  SS3 previously used alternative formulation: R = A*S/(B+S)
   //  converting SS3 to align with WHAM
-      SPR_virgin = SSB_virgin / Recr_virgin;
+  //    SPR_virgin = SSB_virgin / Recr_virgin;  //  this is already defined
       alpha = 4.0 * steepness / (SPR_virgin * (1. - steepness));
       beta = (5.0 * steepness - 1.0) / ((1 - steepness) * SSB_virgin);
 
+      // " h " << steepness << " derive "  << alpha * SPR_virgin / (4. + alpha * SPR_virgin) << " " << endl;
+      // " R0 " << Recr_virgin << " derive "  << 1. / beta * (alpha - 1./SPR_virgin) << endl;
 //      report5 <<" SSB_unf "<<SSB_virgin<<" SPR_unf "<<SPR_virgin<<" steep: "<<steepness<<" R0: "<<Recr_virgin << endl;
 //      report5 <<" derive_alpha "<<alpha<<" derive_beta "<<beta << endl;
 //      report5 << " deriv_h: " << alpha * SPR_virgin / (4. + alpha * SPR_virgin) << " derive_R0: " << 1. / beta * (alpha - (1. / SPR_virgin))<<endl;
@@ -332,8 +335,8 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
 
     case 10: // Beverton-Holt with alpha and beta parameterization using  R = A*S/(1+B*S) approach; same as WHAM
     {
-      alpha = mfexp(SRparm(3));
-      beta = mfexp(SRparm(4));
+      dvariable alpha = mfexp(SRparm(3));
+      dvariable beta = mfexp(SRparm(4));
       B_equil = (alpha * SPR_temp - 1.0) / beta;
       B_equil = posfun(B_equil, 0.0001, temp);
       R_equil = alpha * B_equil / (1.0 + beta * B_equil);
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index fbba7bd2..a550c756 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -1779,26 +1779,14 @@ FUNCTION void write_bigoutput()
     var /= (n_rmse(1) + 1.0e-09);
 
     dvariable steepness = SR_parm(2);
+
     SS2out << endl
            << pick_report_name(19);
     SS2out << "  Function: " << SR_fxn << "  RecDev_method: " << do_recdev << "   sum_recdev: " << sum_recdev << endl
            << SR_parm(1) << " Ln(R0) " << mfexp(SR_parm(1)) << endl
-           << steepness << " steepness " << endl
+           << steepness << " steepness" << endl
            << Bmsy / SSB_virgin << " Bmsy/Bzero ";
-    SS2out << " SPR_virgin "<<SPR_virgin<<endl;
-    if (SR_fxn == 10)
-    {
-      SS2out << " Ln_alpha_parameter: " << SR_parm(3) << " alpha " << mfexp(SR_parm(3)) << endl;
-      SS2out << " Ln_beta_parameter: " << SR_parm(4) << " beta " << mfexp(SR_parm(4));
-    }
-    else if (SR_fxn == 3)
-    {
-      alpha = 4.0 * steepness / (SPR_virgin * (1. - steepness));
-      beta = (5.0 * steepness - 1.0) / ((1. - steepness) * SSB_virgin);
-      SS2out << " Ln_alpha_derived: " << log(alpha) << " alpha " << alpha << endl;
-      SS2out << " Ln_beta_derived: " << log(beta) << " beta " << beta;
-    }
-    else if (SR_fxn == 8)
+    if (SR_fxn == 8)
     {
       dvariable Shepherd_c;
       dvariable Shepherd_c2;
@@ -1813,7 +1801,9 @@ FUNCTION void write_bigoutput()
     {
       SS2out << " Ricker_Power: " << SR_parm(3);
     }
-    SS2out << endl << sigmaR << " sigmaR" << endl;
+
+    SS2out << endl;
+    SS2out << sigmaR << " sigmaR" << endl;
     SS2out << init_equ_steepness << "  # 0/1 to use steepness in initial equ recruitment calculation" << endl;
 
     SS2out << SR_parm(N_SRparm2 - 1) << " init_eq:  see below" << endl
@@ -1846,7 +1836,114 @@ FUNCTION void write_bigoutput()
     }
     SS2out << endl;
 
-    SS2out << "Yr SpawnBio exp_recr with_regime bias_adjusted pred_recr dev biasadjuster era mature_bio mature_num raw_dev SSBe/R0 h R0" << endl;
+    SS2out << endl << "#New_Expanded_Spawn_Recr_report" << endl << pick_report_name(19) << endl;
+    SS2out << "SR_Function: " << SR_fxn << endl;
+    SS2out << "#" << endl << "parm  parm_label value phase" << endl;
+    for (int j = 1; j <=N_SRparm2; j++)
+    {
+      SS2out << j << " " << ParmLabel(firstSRparm + j) << " " << SR_parm(j) << " " << SR_parm_PH(j);
+      if (SR_parm_timevary(j) > 0 && j <= 4 ) //  timevary SRparm exists
+      {SS2out << " #_is_time_vary,_so_SRR_updates_base_SPR_annually";} 
+  if (j == (N_SRparm2 - 1) && SR_parm_timevary(j) > 0) //  timevary regime exists
+    {SS2out << " #_Persistent_deviations_from_SRR_(e.g.regimes)_exist";}
+      SS2out << endl;
+    }
+
+    SS2out << "# " <<endl;
+    SS2out << "sigmaR: "<< sigmaR  << endl;
+    SS2out << "SPR_virgin: " << SPR_virgin << " #_uses_biology_from_start_year: " << styr <<endl;
+
+    switch (SR_fxn)
+    {
+      case 3: // Beverton-Holt with steepness
+    {
+      alpha = 4.0 * steepness / (SPR_virgin * (1. - steepness));
+      beta = (5.0 * steepness - 1.0) / ((1. - steepness) * SSB_virgin);
+      SS2out << "Ln(R0): " << SR_parm(1) << endl << "R0: " << mfexp(SR_parm(1)) << endl;
+      SS2out << "steepness: " << steepness << endl;
+      SS2out << "Ln(alpha)_derived: " << log(alpha) << " alpha " << alpha << endl;
+      SS2out << "Ln(beta)_derived: " << log(beta) << " beta " << beta;
+      break;
+    }
+      case 10: // Beverton-Holt with alpha, beta
+    {
+      SS2out << "Ln(alpha): " << SR_parm(3) << " alpha " << mfexp(SR_parm(3)) << endl;
+      SS2out << "Ln(beta): " << SR_parm(4) << " beta " << mfexp(SR_parm(4)) << endl;
+      SS2out << "steepness_derived: " << alpha * SPR_virgin / (4. + alpha * SPR_virgin) << " " << SR_parm(3) << endl;  // steepness virgin
+      SS2out << "R0_derived: " << 1. / beta * (alpha - (1. / SPR_virgin)) << " " << SR_parm(1) << endl;  //  virgin R0
+      break;
+    }
+    case 8:
+    {
+      dvariable Shepherd_c;
+      dvariable Shepherd_c2;
+      dvariable Hupper;
+      Shepherd_c = SR_parm(3);
+      Shepherd_c2 = pow(0.2, Shepherd_c);
+      Hupper = 1.0 / (5.0 * Shepherd_c2);
+      temp = 0.2 + (SR_parm(2) - 0.2) / (0.8) * (Hupper - 0.2);
+      SS2out << " Shepherd_c: " << Shepherd_c << " steepness_limit: " << Hupper << " Adjusted_steepness: " << temp << endl;
+      break;
+    }
+    case 9:
+    {
+      SS2out << " Ricker_Parm1: " << SR_parm(1) << endl;
+      SS2out << " Ricker_Parm2: " << SR_parm(2) << endl;
+      SS2out << " Ricker_Power: " << SR_parm(3) << endl;
+      break;
+    }
+    default:
+    {
+      SS2out << "default output needed " << endl;
+      break;
+    }
+    }
+
+    SS2out << endl << "#" << endl << "Quantities for MSY and other benchmark calculations " << endl << "Benchmark_years: 1_beg_bio 2_end_bio 3_beg_selex 4_end_selex 5_beg_relF 6_end_relF 7_beg_recr_dist 8_end_recr_dist 9_beg_SRparm 10_end_SRparm" << endl;
+    SS2out << "Benchmark_years: " << Bmark_Yr << endl;
+    if( timevary_MG_firstyr == YrMax)
+    { SS2out << "No_timevary_biology " << endl; }
+    else
+    { SS2out << "First_year_with_timevary_MG: " << timevary_MG_firstyr << endl; }
+    for ( int k = 1; k <=9; k+=2) 
+    { if (Bmark_Yr(k+1) > Bmark_Yr(k))
+      {SS2out << "#_range_of_years_is_averaged,_so_reduces_standard_error_of_result;_do_this_only_when_timevarying_makes_necessary:  " << k << " "<< k+1 << endl;}
+    }
+    SS2out << "SPR_unfished_benchmark: " << Mgmt_quant(1) / Mgmt_quant(4) << "  #_based_on_averaging_biology_over_benchmark_year_range " << endl;
+    SS2out << "Bmsy/Bzero: "<< Bmsy / SSB_virgin  << " # using styr bio for Bzero" << endl;
+    SS2out << "Bmsy/Bunf: "<< Bmsy / Mgmt_quant(1)  << " # using MSY's averaged bio for Bunf" << endl;
+
+    SS2out << "#" << endl << "RecDev_method: " << do_recdev << endl << "sum_recdev: " << sum_recdev << endl << "recr_logL: " << recr_like << endl;
+    SS2out << recdev_start << " " << recdev_end << " main_recdev:start_end" << endl
+           << recdev_adj(1) << " " << recdev_adj(2, 5) << " breakpoints_for_bias_adjustment_ramp " << endl;
+
+    temp = sigmaR * sigmaR; //  sigmaR^2
+    SS2out << "ERA    N    RMSE  RMSE^2/sigmaR^2  mean_BiasAdj est_rho Durbin-Watson" << endl;
+    SS2out << "main  " << n_rmse(1) << " " << rmse(1) << " " << square(rmse(1)) / temp << " " << rmse(2) << " " << cross / var << " " << Durbin;
+    if (wrote_bigreport == 0) //  first time writing bigreport
+    {
+      if (rmse(1) < 0.5 * sigmaR && rmse(2) > (0.01 + 2.0 * square(rmse(1)) / temp))
+      {
+        warnstream << "Main recdev biasadj is >2 times ratio of rmse to sigmaR";
+        SS2out << " # " << warnstream.str() ;
+        write_message (WARN, 0);
+      }
+    }
+    SS2out << endl;
+
+    SS2out << "early " << n_rmse(3) << " " << rmse(3) << " " << square(rmse(3)) / temp << " " << rmse(4);
+    if (wrote_bigreport == 0) //  first time writing bigreport
+    {
+      if (rmse(3) < 0.5 * sigmaR && rmse(4) > (0.01 + 2.0 * square(rmse(3)) / temp))
+      {
+        warnstream << "Early recdev biasadj is >2 times ratio of rmse to sigmaR";
+        SS2out << " # " << warnstream.str();
+        write_message (WARN, 0);
+      }
+    }
+    SS2out << endl  << "#" << endl << "Initial_equilibrium: " << init_equ_steepness << "  # 0/1_to_use_spawner-recruitment_in_initial_equ_recruitment_calculation" << endl << "#" << endl;
+
+    SS2out << "Yr SpawnBio exp_recr with_regime bias_adjusted pred_recr dev biasadjuster era mature_bio mature_num raw_dev SPR0_curr h_curr R0_curr P1 P2 P3 P4" << endl;
     SS2out << "S/Rcurve " << SSB_virgin << " " << Recr_virgin << endl;
     y = styr - 2;
     SS2out << "Virg " << SSB_yr(y) << " " << exp_rec(y) << " - " << 0.0 << " Virg " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " 0.0 " << endl;
@@ -1897,10 +1994,10 @@ FUNCTION void write_bigoutput()
       {
         SS2out << " _ _ Fixed";
       }
-      dvariable SPR = Smry_Table(y, 11) / Recr_virgin;
-      alpha = mfexp(SR_parm_byyr(y,3));
-      beta = mfexp(SR_parm_byyr(y,4));
-      SS2out << " " << SPR << " " << alpha * SPR / (4. + alpha * SPR) << " " << 1. / beta * (alpha - (1. / SPR));
+      dvariable SPR_curr = Smry_Table(y, 11) / Recr_virgin;
+      SS2out << " " << SPR_curr << " ";
+      SS2out << alpha * SPR_curr / (4. + alpha * SPR_curr) << " ";  // steepness with current SPR
+      SS2out << 1. / beta * (alpha - (1. / SPR_curr)) << " ";  //  R0 with current SPR
       SS2out << SR_parm_byyr(y)(1,4) << endl;
     }
 

From 92208d49846353ba47287c5351e3034c782e5e05 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Wed, 26 Jun 2024 15:05:50 -0700
Subject: [PATCH 10/22] adding benchmark change

---
 SS_benchfore.tpl    | 4 ++--
 SS_write_report.tpl | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 69dd8ffc..3801e082 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -1340,7 +1340,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       MSY_SPR = SSB_equil / SPR_unfished;
       SPR_temp = SSB_equil;
       Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-      Bmsy = Equ_SpawnRecr_Result(1);
+      Bmsy = Equ_SpawnRecr_Result(1);  //  with MSY set to SPR, not directly estimated
       Recr_msy = Equ_SpawnRecr_Result(2);
       yld1(1) = YPR_opt * Recr_msy;
       YPR_msy_enc = YPR_enc;
@@ -1433,7 +1433,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
           MSY_SPR = SSB_equil / SPR_unfished;
           SPR_temp = SSB_equil;
           Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-          Bmsy = Equ_SpawnRecr_Result(1);
+          Bmsy = Equ_SpawnRecr_Result(1);  //  MSY is directly estimated
           Recr_msy = Equ_SpawnRecr_Result(2);
           Profit = (PricePerF * YPR_val_vec) * Recr_msy - Cost;
           if (Do_MSY == 2) //  dead catch without excluded bycatch fleets
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index a550c756..cee1ba29 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -1851,7 +1851,7 @@ FUNCTION void write_bigoutput()
 
     SS2out << "# " <<endl;
     SS2out << "sigmaR: "<< sigmaR  << endl;
-    SS2out << "SPR_virgin: " << SPR_virgin << " #_uses_biology_from_start_year: " << styr <<endl;
+    SS2out << "SPR0_(virgin): " << SPR_virgin << " #_uses_biology_from_start_year: " << styr <<endl;
 
     switch (SR_fxn)
     {
@@ -1869,8 +1869,8 @@ FUNCTION void write_bigoutput()
     {
       SS2out << "Ln(alpha): " << SR_parm(3) << " alpha " << mfexp(SR_parm(3)) << endl;
       SS2out << "Ln(beta): " << SR_parm(4) << " beta " << mfexp(SR_parm(4)) << endl;
-      SS2out << "steepness_derived: " << alpha * SPR_virgin / (4. + alpha * SPR_virgin) << " " << SR_parm(3) << endl;  // steepness virgin
-      SS2out << "R0_derived: " << 1. / beta * (alpha - (1. / SPR_virgin)) << " " << SR_parm(1) << endl;  //  virgin R0
+      SS2out << "steepness_derived: " << alpha * SPR_virgin / (4. + alpha * SPR_virgin) << endl;  // steepness virgin
+      SS2out << "ln(R0)_derived: " << log( 1. / beta * (alpha - (1. / SPR_virgin))) << endl;  //  virgin R0
       break;
     }
     case 8:

From 93eb385c9d05acd7801a0c25951a3962105422d1 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Wed, 3 Jul 2024 15:30:57 -0700
Subject: [PATCH 11/22] format changes for spawn_recr report

---
 SS_readcontrol_330.tpl |  6 +++++-
 SS_write_report.tpl    | 40 ++++++++++++++++++++++++----------------
 2 files changed, 29 insertions(+), 17 deletions(-)

diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 2a5925ca..338de133 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1979,7 +1979,11 @@
   SR_update_SPR0 = 0;
 
   //#_SR_function: 1=null; 2=Ricker; 3=std_B-H; 4=SCAA; 5=Hockey; 6=B-H_flattop; 7=Survival_3Parm; 10=B-H with a,b "<<endl;
-  ParmLabel += "SR_LN(R0)";
+  if (SR_fxn == 10)
+  {ParmLabel += "SR_LN(R0)_derived";}
+  else
+  {ParmLabel += "SR_LN(R0)";}
+  
   switch (SR_fxn)
   {
     case 1: // previous placement for B-H constrained
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index cee1ba29..9317d147 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -1838,6 +1838,7 @@ FUNCTION void write_bigoutput()
 
     SS2out << endl << "#New_Expanded_Spawn_Recr_report" << endl << pick_report_name(19) << endl;
     SS2out << "SR_Function: " << SR_fxn << endl;
+    SS2out << "N_SRparms: " << N_SRparm2 << endl;
     SS2out << "#" << endl << "parm  parm_label value phase" << endl;
     for (int j = 1; j <=N_SRparm2; j++)
     {
@@ -1845,7 +1846,7 @@ FUNCTION void write_bigoutput()
       if (SR_parm_timevary(j) > 0 && j <= 4 ) //  timevary SRparm exists
       {SS2out << " #_is_time_vary,_so_SRR_updates_base_SPR_annually";} 
   if (j == (N_SRparm2 - 1) && SR_parm_timevary(j) > 0) //  timevary regime exists
-    {SS2out << " #_Persistent_deviations_from_SRR_(e.g.regimes)_exist";}
+    {SS2out << " #_Regime_parameter_used_to_offset_from_SRR";}
       SS2out << endl;
     }
 
@@ -1869,8 +1870,8 @@ FUNCTION void write_bigoutput()
     {
       SS2out << "Ln(alpha): " << SR_parm(3) << " alpha " << mfexp(SR_parm(3)) << endl;
       SS2out << "Ln(beta): " << SR_parm(4) << " beta " << mfexp(SR_parm(4)) << endl;
-      SS2out << "steepness_derived: " << alpha * SPR_virgin / (4. + alpha * SPR_virgin) << endl;  // steepness virgin
       SS2out << "ln(R0)_derived: " << log( 1. / beta * (alpha - (1. / SPR_virgin))) << endl;  //  virgin R0
+      SS2out << "steepness_derived: " << alpha * SPR_virgin / (4. + alpha * SPR_virgin) << endl;  // steepness virgin
       break;
     }
     case 8:
@@ -1882,19 +1883,12 @@ FUNCTION void write_bigoutput()
       Shepherd_c2 = pow(0.2, Shepherd_c);
       Hupper = 1.0 / (5.0 * Shepherd_c2);
       temp = 0.2 + (SR_parm(2) - 0.2) / (0.8) * (Hupper - 0.2);
-      SS2out << " Shepherd_c: " << Shepherd_c << " steepness_limit: " << Hupper << " Adjusted_steepness: " << temp << endl;
-      break;
-    }
-    case 9:
-    {
-      SS2out << " Ricker_Parm1: " << SR_parm(1) << endl;
-      SS2out << " Ricker_Parm2: " << SR_parm(2) << endl;
-      SS2out << " Ricker_Power: " << SR_parm(3) << endl;
+      SS2out << "Shepherd_c: " << Shepherd_c << endl << "Shepard_steepness_limit: " << Hupper << endl << "Shepard_adjusted_steepness: " << temp << endl;
       break;
     }
     default:
     {
-      SS2out << "default output needed " << endl;
+      SS2out << "other_SRR " << endl;
       break;
     }
     }
@@ -1914,8 +1908,8 @@ FUNCTION void write_bigoutput()
     SS2out << "Bmsy/Bunf: "<< Bmsy / Mgmt_quant(1)  << " # using MSY's averaged bio for Bunf" << endl;
 
     SS2out << "#" << endl << "RecDev_method: " << do_recdev << endl << "sum_recdev: " << sum_recdev << endl << "recr_logL: " << recr_like << endl;
-    SS2out << recdev_start << " " << recdev_end << " main_recdev:start_end" << endl
-           << recdev_adj(1) << " " << recdev_adj(2, 5) << " breakpoints_for_bias_adjustment_ramp " << endl;
+    SS2out << "main_recdev:start_end: " << recdev_start << " " << recdev_end << endl
+           << "breakpoints_for_bias_adjustment_ramp: " <<recdev_adj(1,4) << endl << "max_bias_adj: " << recdev_adj(5) <<  endl;
 
     temp = sigmaR * sigmaR; //  sigmaR^2
     SS2out << "ERA    N    RMSE  RMSE^2/sigmaR^2  mean_BiasAdj est_rho Durbin-Watson" << endl;
@@ -1942,8 +1936,17 @@ FUNCTION void write_bigoutput()
       }
     }
     SS2out << endl  << "#" << endl << "Initial_equilibrium: " << init_equ_steepness << "  # 0/1_to_use_spawner-recruitment_in_initial_equ_recruitment_calculation" << endl << "#" << endl;
-
-    SS2out << "Yr SpawnBio exp_recr with_regime bias_adjusted pred_recr dev biasadjuster era mature_bio mature_num raw_dev SPR0_curr h_curr R0_curr P1 P2 P3 P4" << endl;
+    if (SR_fxn == 10) SS2out << "#_Note:_h_curr_and_R0_curr_are_for_info_only;_calculated_from_alpha_beta_and_current_SPR0" << endl;
+    SS2out << "#_columns_with_P_will_show_time_vary_SR_parameters" << endl << "#" << endl;
+    SS2out << "Yr SpawnBio exp_recr with_regime bias_adjusted pred_recr dev biasadjuster era mature_bio mature_num raw_dev SPR0_curr ";
+    if(SR_fxn == 10)
+    {SS2out << "h_curr R0_curr ";}
+    else
+    {SS2out << "NA1 NA2 ";}
+;
+    for (j = 1; j <= N_SRparm2; j++) 
+    {SS2out << "P" << j << " ";}
+    SS2out << endl;
     SS2out << "S/Rcurve " << SSB_virgin << " " << Recr_virgin << endl;
     y = styr - 2;
     SS2out << "Virg " << SSB_yr(y) << " " << exp_rec(y) << " - " << 0.0 << " Virg " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " 0.0 " << endl;
@@ -1996,9 +1999,14 @@ FUNCTION void write_bigoutput()
       }
       dvariable SPR_curr = Smry_Table(y, 11) / Recr_virgin;
       SS2out << " " << SPR_curr << " ";
+      if (SR_fxn == 10)
+      {
       SS2out << alpha * SPR_curr / (4. + alpha * SPR_curr) << " ";  // steepness with current SPR
       SS2out << 1. / beta * (alpha - (1. / SPR_curr)) << " ";  //  R0 with current SPR
-      SS2out << SR_parm_byyr(y)(1,4) << endl;
+      }
+      else
+      {SS2out << " - - ";}
+      SS2out << SR_parm_byyr(y)(1,N_SRparm2) << endl;
     }
 
     // REPORT_KEYWORD SPAWN_RECR_CURVE

From 38ae9ee9d3f3c7cb551fd66838ec704c4449af8d Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Tue, 9 Jul 2024 15:13:53 -0700
Subject: [PATCH 12/22] fixes to ss_warn

---
 Compile/Make_SS_warn.bat | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Compile/Make_SS_warn.bat b/Compile/Make_SS_warn.bat
index f53510ee..af9b1430 100644
--- a/Compile/Make_SS_warn.bat
+++ b/Compile/Make_SS_warn.bat
@@ -28,6 +28,6 @@ tpl2cpp ss3
 
 g++ -c -std=c++17 -O2 -D_FILE_OFFSET_BITS=64  -DUSE_ADMB_CONTRIBS -D_USE_MATH_DEFINES -I. -I"C:\ADMB-13.2\include" -I"C:\ADMB-13.2\include\contrib" -Wall -Wextra -o ss3.obj ss3.cpp
 
-g++ -static -o ss3.exe ss3.obj "C:\ADMB-13.2\lib\libadmb-contrib-mingw64-g++12.a"
+g++ -static -o ss3.exe ss3.obj "C:\ADMB-13.2\lib\libadmb-contrib-mingw64-g++13.a"
 
 dir *.exe

From f0342232a69d99e3081393dfee725e4979345b43 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Tue, 13 Aug 2024 20:06:06 -0700
Subject: [PATCH 13/22] WIP-more work needed on benchmark calcs

---
 SS_benchfore.tpl    | 30 ++++++++++++++++++++------
 SS_param.tpl        |  1 +
 SS_popdyn.tpl       | 21 +++++++++---------
 SS_recruit.tpl      | 52 ++++++++++++++++++++++-----------------------
 SS_write_report.tpl |  6 +++---
 5 files changed, 63 insertions(+), 47 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 3801e082..9b7fcd2f 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -744,6 +744,18 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       SR_parm_work(j) = temp / (Bmark_Yr(10) - Bmark_Yr(9) + 1.);
     }
   }
+
+  if(SR_fxn == 10)  //  B-H with alpha, beta
+  {
+      alpha = mfexp(SR_parm_work(3));
+      beta = mfexp(SR_parm_work(4));
+      Fishon = 0;
+      Recr_unf = 1.0;
+      Do_Equil_Calc(Recr_unf);
+      SPR_virgin_adj = SSB_equil / 1.0;
+      SR_parm_work(2) = alpha * SPR_virgin_adj / (4. + alpha * SPR_virgin_adj);  // steepness
+      SR_parm_work(1) = log(1. / beta * (alpha - (1. / SPR_virgin_adj)));  // ln(R0)
+  }
   Fishon = 0;
   Recr_unf = mfexp(SR_parm_work(1));
   Do_Equil_Calc(Recr_unf);
@@ -751,13 +763,17 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   SPR_unfished = SSB_unf / Recr_unf; //  this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
   if (show_MSY == 1)
   {
-    report5 << "SR_parm for benchmark: " << SR_parm_work << endl
+    report5 << "SR_parms for benchmark: " << SR_parm_work << endl
             << "mean from years: " << Bmark_Yr(9) << " " << Bmark_Yr(10) << endl;
     //  SPR_virgin = SSB_virgin / Recr_virgin;  // already defined
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_virgin); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    report5 << " Virgin SPR0, SSB, R: " << SPR_virgin << " " << Equ_SpawnRecr_Result << endl;
+    report5 << " Virgin SSB, R0: " << SSB_virgin << " " << Recr_virgin << " "  << SPR_virgin_adj << endl;
+    report5 << " unfished SSB, R0: " << SSB_unf << " " << Recr_unf << " "  << SPR_unfished << " with current biology " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl;
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SPR_virgin_adj); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    report5 << " Virgin SPR0, result_SSB, R: " << SPR_virgin_adj << " " << Equ_SpawnRecr_Result << endl << endl;
     Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_unfished); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    report5 << " Benchmark SPR0, SSB, R: " << SPR_unfished << " " << Equ_SpawnRecr_Result << endl;
+    report5 << " Benchmark SPR0, result_SSB, R: " << SPR_unfished << " " << Equ_SpawnRecr_Result << endl << endl;
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SPR_unfished); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    report5 << " Benchmark SPR0, result_SSB, R: " << SPR_unfished << " " << Equ_SpawnRecr_Result << " with virgin spawn-recr " << endl;
   }
   SR_parm_work(N_SRparm2 + 1) = SSB_unf;
   Mgmt_quant(1) = SSB_unf;
@@ -1930,7 +1946,7 @@ FUNCTION void Get_Forecast()
   dvariable OFL_catch;
   dvariable Fcast_Crash;
   dvariable totcatch;
-  dvariable R0_use;
+  dvariable R0_use;  // annually updated variable if SR_update_SPR0 == 1
   dvariable SSB_use;
   dvar_matrix catage_w(1, gmorph, 0, nages);
   dvar_vector tempcatch(1, Nfleet);
@@ -2579,7 +2595,7 @@ FUNCTION void Get_Forecast()
             }
             //  SPAWN-RECR:   get recruitment in forecast;  needs to be area-specific
             // SR_fxn
-            if (SR_parm_timevary(1) == 0) //  R0 is not time-varying
+            if (SR_update_SPR0 == 0) //  R0 is not time-varying
             {
               R0_use = Recr_virgin;
               SSB_use = SSB_virgin;
@@ -3219,7 +3235,7 @@ FUNCTION void Get_Forecast()
             //  SS_Label_Info_24.3.4.1 #Get recruitment from this spawning biomass
             //  SPAWN-RECR:   calc recruitment in time series; need to make this area-specific
             // SR_fxn
-            if (SR_parm_timevary(1) == 0) //  R0 is not time-varying
+            if (SR_update_SPR0 == 0) //  R0 is not time-varying
             {
               R0_use = Recr_virgin;
               SSB_use = SSB_virgin;
diff --git a/SS_param.tpl b/SS_param.tpl
index da7d0d5e..06c280ea 100644
--- a/SS_param.tpl
+++ b/SS_param.tpl
@@ -166,6 +166,7 @@ PARAMETER_SECTION
   number half_sigmaRsq;
   number sigmaR;
   number SPR_virgin;
+  number SPR_virgin_adj;
   number regime_change;
   number rho;
   number dirichlet_Parm;
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 265e2c37..3aa6d549 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -344,7 +344,7 @@ FUNCTION void get_initial_conditions()
     equ_Recr = 1.0;
     Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation.  Returns SPR because R = 1.0
     SPR_virgin = SSB_equil; //  spawners per recruit.  Needed for Sr_fxn = 10
-
+    SPR_virgin_adj = SSB_equil;
     if(SR_fxn == 10)  // B-H with a,b
     {
   //  WHAM based on R = A*S/(1+B*S)
@@ -355,8 +355,8 @@ FUNCTION void get_initial_conditions()
 
       alpha = mfexp(SR_parm(3));
       beta = mfexp(SR_parm(4));
-      steepness = alpha * SPR_virgin / (4. + alpha * SPR_virgin);
-      Recr_virgin = 1. / beta * (alpha - (1. / SPR_virgin));
+      steepness = alpha * SPR_virgin_adj / (4. + alpha * SPR_virgin_adj);
+      Recr_virgin = 1. / beta * (alpha - (1. / SPR_virgin_adj));
 //      warning << " before AB_calcs " << "parm " << SR_parm(1) << " calc " << log(Recr_virgin) << endl;
       SR_parm(1) = log(Recr_virgin);
       SR_parm(2) = steepness;
@@ -380,7 +380,7 @@ FUNCTION void get_initial_conditions()
     exp_rec(eq_yr, 4) = Recr_virgin;
     Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation
     SSB_virgin = SSB_equil;
-    SPR_virgin = SSB_equil / Recr_virgin; //  spawners per recruit
+//    SPR_virgin = SSB_equil / Recr_virgin; //  spawners per recruit already calculated
     if(Do_Benchmark==0)
     {
       Mgmt_quant(1)=SSB_virgin;
@@ -696,7 +696,7 @@ FUNCTION void get_time_series()
   dvariable crashtemp1;
   dvariable interim_tot_catch;
   dvariable Z_adjuster;
-  dvariable R0_use;
+  dvariable R0_use;  // annually updated variable if SR_update_SPR0 == 1; gets passed to Spawn_Recr() function
   dvariable SSB_use;
 
   if (Do_Morphcomp > 0)
@@ -1024,10 +1024,10 @@ FUNCTION void get_time_series()
           }
         }
 
-        //  SS_Label_Info_24.2.3 #Get the total recruitment produced by this spawning biomass
+        //  SS_Label_Info_24.2.3 #Get the total recruitment produced by this spawning biomass at the beginning of the season
         //  SPAWN-RECR:   calc recruitment in time series; need to make this area-specific
         //  SR_Fxn  relevant keyword
-        if (SR_parm_timevary(1) == 0) //  R0 is not time-varying
+        if (SR_update_SPR0 == 0) //  SRparm are not time-varying
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
@@ -1035,12 +1035,12 @@ FUNCTION void get_time_series()
         else
         {
           R0_use = mfexp(SR_parm_work(1));
-          warning << y << " set R0use to SRparm_work " << R0_use << " vir: " << Recr_virgin << endl;
           equ_Recr = R0_use;
           Fishon = 0;
           eq_yr = y;
           bio_yr = y;
           Do_Equil_Calc(R0_use); //  call function to do equilibrium calculation
+          SSB_use = SSB_equil;
           if (fishery_on_off == 1)
           {
             Fishon = 1;
@@ -1049,7 +1049,6 @@ FUNCTION void get_time_series()
           {
             Fishon = 0;
           }
-          SSB_use = SSB_equil;
         }
         Recruits = Spawn_Recr(SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr
         if (SR_fxn != 7) apply_recdev(Recruits, R0_use); //  apply recruitment deviation
@@ -1485,7 +1484,7 @@ FUNCTION void get_time_series()
             SSB_yr(y) = SSB_current;
           }
         }
-        //  SS_Label_Info_24.3.4.1 #Get recruitment from this spawning biomass
+        //  SS_Label_Info_24.3.4.1 #Get recruitment from this spawning biomass at some time during the season
         //  SPAWN-RECR:   calc recruitment in time series; need to make this area-specific
         //  SR_fxn
         if (SR_update_SPR0 == 0) //  SR parms are not time-varying
@@ -1501,6 +1500,7 @@ FUNCTION void get_time_series()
           eq_yr = y;
           bio_yr = y;
           Do_Equil_Calc(R0_use); //  call function to do equilibrium calculation
+          SSB_use = SSB_equil;
           if (fishery_on_off == 1)
           {
             Fishon = 1;
@@ -1509,7 +1509,6 @@ FUNCTION void get_time_series()
           {
             Fishon = 0;
           }
-          SSB_use = SSB_equil;
         }
 
         Recruits = Spawn_Recr(SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr
diff --git a/SS_recruit.tpl b/SS_recruit.tpl
index 2065b277..179ecd6e 100644
--- a/SS_recruit.tpl
+++ b/SS_recruit.tpl
@@ -268,7 +268,7 @@ FUNCTION void apply_recdev(prevariable& NewRecruits, const prevariable& Recr_vir
  /*  SS_Label_FUNCTION 44 Equil_Spawn_Recr_Fxn */
 //  SPAWN-RECR:   function  Equil_Spawn_Recr_Fxn
 FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
-    const prevariable& SSB_virgin, const prevariable& Recr_virgin, const prevariable& SPR_temp)
+    const prevariable& SSB_temp, const prevariable& RECR_temp, const prevariable& SPR_temp)
   {
   RETURN_ARRAYS_INCREMENT();
   dvar_vector Equil_Spawn_Recr_Calc(1, 2); // values to return 1 is B_equil, 2 is R_equil
@@ -297,8 +297,8 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
     //  SS_Label_44.1.2  Ricker
     case 2: // Ricker
     {
-      B_equil = SSB_virgin * (1. + (log(Recr_virgin / SSB_virgin) + log(SPR_temp)) / steepness);
-      R_equil = Recr_virgin * B_equil / SSB_virgin * mfexp(steepness * (1. - B_equil / SSB_virgin));
+      B_equil = SSB_temp * (1. + (log(RECR_temp / SSB_temp) + log(SPR_temp)) / steepness);
+      R_equil = RECR_temp * B_equil / SSB_temp * mfexp(steepness * (1. - B_equil / SSB_temp));
 
       break;
     }
@@ -316,14 +316,14 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
 
   //  SS3 previously used alternative formulation: R = A*S/(B+S)
   //  converting SS3 to align with WHAM
-  //    SPR_virgin = SSB_virgin / Recr_virgin;  //  this is already defined
-      alpha = 4.0 * steepness / (SPR_virgin * (1. - steepness));
+  //    SPR_virgin = SSB_temp / RECR_temp;  //  this is already defined
+      alpha = 4.0 * steepness / (SPR_virgin_adj * (1. - steepness));
       beta = (5.0 * steepness - 1.0) / ((1 - steepness) * SSB_virgin);
 
       // " h " << steepness << " derive "  << alpha * SPR_virgin / (4. + alpha * SPR_virgin) << " " << endl;
-      // " R0 " << Recr_virgin << " derive "  << 1. / beta * (alpha - 1./SPR_virgin) << endl;
-//      report5 <<" SSB_unf "<<SSB_virgin<<" SPR_unf "<<SPR_virgin<<" steep: "<<steepness<<" R0: "<<Recr_virgin << endl;
-//      report5 <<" derive_alpha "<<alpha<<" derive_beta "<<beta << endl;
+      // " R0 " << RECR_temp << " derive "  << 1. / beta * (alpha - 1./SPR_virgin) << endl;
+//      report5 <<" SSB_unf "<<SSB_temp<<" SPR_unf "<<SPR_virgin<<" steep: "<<steepness<<" R0: "<<RECR_temp << endl;
+      report5 <<" derive_alpha "<<alpha<<" derive_beta "<<beta << endl;
 //      report5 << " deriv_h: " << alpha * SPR_virgin / (4. + alpha * SPR_virgin) << " derive_R0: " << 1. / beta * (alpha - (1. / SPR_virgin))<<endl;
       B_equil = (alpha * SPR_temp - 1.0) / beta;
       B_equil = posfun(B_equil, 0.0001, temp);
@@ -347,27 +347,27 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
     //  SS_Label_44.1.4  constant recruitment
     case 4: // constant; no bias correction
     {
-      B_equil = SPR_temp * Recr_virgin;
-      R_equil = Recr_virgin;
+      B_equil = SPR_temp * RECR_temp;
+      R_equil = RECR_temp;
       break;
     }
     //  SS_Label_44.1.5  Hockey Stick
     case 5: // hockey stick
     {
-      dvariable hockey_min = SRparm(3) * Recr_virgin; // min recruitment level
-      //        temp=SSB_virgin/R0*steepness;  // spawners per recruit at inflection
-      dvariable hockey_slope = (Recr_virgin - hockey_min) / (steepness * SSB_virgin); //  slope of recruitment on spawners below the inflection
-      B_equil = Join_Fxn(0.0 * SSB_virgin / Recr_virgin, SSB_virgin / Recr_virgin, SSB_virgin / Recr_virgin * steepness, SPR_temp, hockey_min / ((1. / SPR_temp) - hockey_slope), SPR_temp * Recr_virgin);
-      R_equil = Join_Fxn(0.0 * SSB_virgin, SSB_virgin, SSB_virgin * steepness, B_equil, hockey_min + hockey_slope * B_equil, Recr_virgin);
+      dvariable hockey_min = SRparm(3) * RECR_temp; // min recruitment level
+      //        temp=SSB_temp/R0*steepness;  // spawners per recruit at inflection
+      dvariable hockey_slope = (RECR_temp - hockey_min) / (steepness * SSB_temp); //  slope of recruitment on spawners below the inflection
+      B_equil = Join_Fxn(0.0 * SSB_temp / RECR_temp, SSB_temp / RECR_temp, SSB_temp / RECR_temp * steepness, SPR_temp, hockey_min / ((1. / SPR_temp) - hockey_slope), SPR_temp * RECR_temp);
+      R_equil = Join_Fxn(0.0 * SSB_temp, SSB_temp, SSB_temp * steepness, B_equil, hockey_min + hockey_slope * B_equil, RECR_temp);
       break;
     }
     //  SS_Label_44.1.7  3 parameter survival based
     case 7: // survival
     {
-      SRZ_0 = log(1.0 / (SSB_virgin / Recr_virgin));
+      SRZ_0 = log(1.0 / (SSB_temp / RECR_temp));
       srz_min = SRZ_0 * (1.0 - steepness);
-      B_equil = SSB_virgin * (1. - (log(1. / SPR_temp) - SRZ_0) / pow((srz_min - SRZ_0), (1. / SRparm(3))));
-      SRZ_surv = mfexp((1. - pow((B_equil / SSB_virgin), SRparm(3))) * (srz_min - SRZ_0) + SRZ_0); //  survival
+      B_equil = SSB_temp * (1. - (log(1. / SPR_temp) - SRZ_0) / pow((srz_min - SRZ_0), (1. / SRparm(3))));
+      SRZ_surv = mfexp((1. - pow((B_equil / SSB_temp), SRparm(3))) * (srz_min - SRZ_0) + SRZ_0); //  survival
       R_equil = B_equil * SRZ_surv;
       break;
     }
@@ -389,10 +389,10 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
       Shepherd_c2 = pow(0.2, SRparm(3));
       Hupper = 1.0 / (5.0 * Shepherd_c2);
       steepness = 0.2 + (SRparm(2) - 0.2) / (0.8) * (Hupper - 0.2);
-      Shep_top = 5.0 * steepness * (1.0 - Shepherd_c2) * (SPR_temp * Recr_virgin) / SSB_virgin - (1.0 - 5.0 * steepness * Shepherd_c2);
+      Shep_top = 5.0 * steepness * (1.0 - Shepherd_c2) * (SPR_temp * RECR_temp) / SSB_temp - (1.0 - 5.0 * steepness * Shepherd_c2);
       Shep_bot = 5.0 * steepness - 1.0;
       Shep_top2 = posfun(Shep_top, 0.001, temp);
-      R_equil = (SSB_virgin / SPR_temp) * pow((Shep_top2 / Shep_bot), (1.0 / SRparm(3)));
+      R_equil = (SSB_temp / SPR_temp) * pow((Shep_top2 / Shep_bot), (1.0 / SRparm(3)));
       B_equil = R_equil * SPR_temp;
       break;
     }
@@ -402,10 +402,10 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
     {
       steepness = SRparm(2);
       dvariable RkrPower = SRparm(3);
-      temp = SSB_virgin / (SPR_temp * Recr_virgin);
+      temp = SSB_temp / (SPR_temp * RECR_temp);
       dvariable RkrTop = pow(0.8, RkrPower) * log(temp) / log(5.0 * steepness);
       RkrTop = posfun(RkrTop, 0.000001, CrashPen);
-      R_equil = temp * Recr_virgin * (1.0 - pow(RkrTop, 1.0 / RkrPower));
+      R_equil = temp * RECR_temp * (1.0 - pow(RkrTop, 1.0 / RkrPower));
       B_equil = R_equil * SPR_temp;
       break;
     }
@@ -428,10 +428,10 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
         Hupper=1.0/(5.0*Shepherd_c2);
         steepness=0.20001+((0.8)/(1.0+exp(-SRparm2))-0.2)/(0.8)*(Hupper-0.2);
 //        steep2=0.20001+(steepness-0.2)/(0.8)*(Hupper-0.2);
-        Shep_top=5.0*steepness*(1.0-Shepherd_c2)*(SPR_temp*Recr_virgin)/SSB_virgin-(1.0-5.0*steepness*Shepherd_c2);
+        Shep_top=5.0*steepness*(1.0-Shepherd_c2)*(SPR_temp*RECR_temp)/SSB_temp-(1.0-5.0*steepness*Shepherd_c2);
         Shep_bot=5.0*steepness-1.0;
         Shep_top2=posfun(Shep_top,0.001,temp);
-        R_equil=(SSB_virgin/SPR_temp) * pow((Shep_top2/Shep_bot),(1.0/Shepherd_c));
+        R_equil=(SSB_temp/SPR_temp) * pow((Shep_top2/Shep_bot),(1.0/Shepherd_c));
         B_equil=R_equil*SPR_temp;
         break;
       }
@@ -448,10 +448,10 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
 //   if (Recs < 0) Rec2 = 0; else Rec2 = Recs;
         steepness = 0.2 + (10.0 - 0.2)/(1+exp(-SR_parm_work(2)));
         dvariable RkrPower=exp(SR_parm_work(3));
-        temp=SSB_virgin/(SPR_temp*Recr_virgin);
+        temp=SSB_virgin/(SPR_temp*RECR_temp);
         dvariable RkrTop =  pow(0.8,RkrPower)*log(temp)/log(5.0*steepness);
         RkrTop = posfun(RkrTop,0.000001,CrashPen);
-        R_equil = temp *Recr_virgin * (1.0 - pow(RkrTop,1.0/RkrPower));
+        R_equil = temp *RECR_temp * (1.0 - pow(RkrTop,1.0/RkrPower));
         B_equil=R_equil*SPR_temp;
         break;
       }
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 9317d147..5413697b 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -1858,7 +1858,7 @@ FUNCTION void write_bigoutput()
     {
       case 3: // Beverton-Holt with steepness
     {
-      alpha = 4.0 * steepness / (SPR_virgin * (1. - steepness));
+      alpha = 4.0 * steepness / (SPR_virgin_adj * (1. - steepness));
       beta = (5.0 * steepness - 1.0) / ((1. - steepness) * SSB_virgin);
       SS2out << "Ln(R0): " << SR_parm(1) << endl << "R0: " << mfexp(SR_parm(1)) << endl;
       SS2out << "steepness: " << steepness << endl;
@@ -1870,8 +1870,8 @@ FUNCTION void write_bigoutput()
     {
       SS2out << "Ln(alpha): " << SR_parm(3) << " alpha " << mfexp(SR_parm(3)) << endl;
       SS2out << "Ln(beta): " << SR_parm(4) << " beta " << mfexp(SR_parm(4)) << endl;
-      SS2out << "ln(R0)_derived: " << log( 1. / beta * (alpha - (1. / SPR_virgin))) << endl;  //  virgin R0
-      SS2out << "steepness_derived: " << alpha * SPR_virgin / (4. + alpha * SPR_virgin) << endl;  // steepness virgin
+      SS2out << "ln(R0)_derived: " << log( 1. / beta * (alpha - (1. / SPR_virgin_adj))) << endl;  //  virgin R0
+      SS2out << "steepness_derived: " << alpha * SPR_virgin_adj / (4. + alpha * SPR_virgin_adj) << endl;  // steepness virgin
       break;
     }
     case 8:

From 0d6d3b613b5e7332462ac7dfad4aa78d695732c3 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Thu, 15 Aug 2024 17:02:43 -0700
Subject: [PATCH 14/22] WIP2-need-to-fix-SPR-passing_to_benchmark

---
 SS_benchfore.tpl | 36 ++++++++++++++++++------------------
 SS_popdyn.tpl    | 17 ++++++++---------
 2 files changed, 26 insertions(+), 27 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 9b7fcd2f..37bc9758 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -536,7 +536,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   dvariable last_F1;
   dvariable Closer;
   dvariable Vbio1_unfished;
-  dvariable SPR_unfished;
+  dvariable SPR_unf;
   dvariable Vbio_MSY;
   dvariable Vbio1_MSY;
   dvariable junk;
@@ -751,7 +751,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       beta = mfexp(SR_parm_work(4));
       Fishon = 0;
       Recr_unf = 1.0;
-      Do_Equil_Calc(Recr_unf);
+      Do_Equil_Calc(Recr_unf);  // 
       SPR_virgin_adj = SSB_equil / 1.0;
       SR_parm_work(2) = alpha * SPR_virgin_adj / (4. + alpha * SPR_virgin_adj);  // steepness
       SR_parm_work(1) = log(1. / beta * (alpha - (1. / SPR_virgin_adj)));  // ln(R0)
@@ -759,21 +759,21 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   Fishon = 0;
   Recr_unf = mfexp(SR_parm_work(1));
   Do_Equil_Calc(Recr_unf);
-  SSB_unf = SSB_equil;
-  SPR_unfished = SSB_unf / Recr_unf; //  this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
+  SSB_unf = SSB_equil;  // equilibrium unfished SSB using the benchmark averaged Recr_unf and benchmark averaged biology
+  SPR_unf = SSB_unf / Recr_unf; //  this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
   if (show_MSY == 1)
   {
     report5 << "SR_parms for benchmark: " << SR_parm_work << endl
             << "mean from years: " << Bmark_Yr(9) << " " << Bmark_Yr(10) << endl;
     //  SPR_virgin = SSB_virgin / Recr_virgin;  // already defined
     report5 << " Virgin SSB, R0: " << SSB_virgin << " " << Recr_virgin << " "  << SPR_virgin_adj << endl;
-    report5 << " unfished SSB, R0: " << SSB_unf << " " << Recr_unf << " "  << SPR_unfished << " with current biology " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl;
+    report5 << " unfished SSB, R0: " << SSB_unf << " " << Recr_unf << " "  << SPR_unf << " with current biology " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl;
     Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SPR_virgin_adj); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
     report5 << " Virgin SPR0, result_SSB, R: " << SPR_virgin_adj << " " << Equ_SpawnRecr_Result << endl << endl;
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_unfished); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    report5 << " Benchmark SPR0, result_SSB, R: " << SPR_unfished << " " << Equ_SpawnRecr_Result << endl << endl;
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SPR_unfished); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    report5 << " Benchmark SPR0, result_SSB, R: " << SPR_unfished << " " << Equ_SpawnRecr_Result << " with virgin spawn-recr " << endl;
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_unf); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    report5 << " Benchmark SPR0, result_SSB, R: " << SPR_unf << " " << Equ_SpawnRecr_Result << endl << endl;
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SPR_unf); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    report5 << " Benchmark SPR0, result_SSB, R: " << SPR_unf << " " << Equ_SpawnRecr_Result << " with virgin spawn-recr " << endl;
   }
   SR_parm_work(N_SRparm2 + 1) = SSB_unf;
   Mgmt_quant(1) = SSB_unf;
@@ -808,7 +808,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     SPR_target100 = SPR_target * 100.;
 
     Do_Equil_Calc(equ_Recr);
-    SPR_unfished = SSB_unf / Recr_unf; //  this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
+    SPR_unf = SSB_unf / Recr_unf; //  this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
     Vbio1_unfished = smrybio; // gets value from equil_calc
     if (show_MSY == 1)
     {
@@ -854,7 +854,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
 
         Fishon = 1;
         Do_Equil_Calc(equ_Recr);
-        yld1(ii) = 100. * SSB_equil / SPR_unfished; //  spawning potential ratio
+        yld1(ii) = 100. * SSB_equil / SPR_unf; //  spawning potential ratio
       }
       SPR_actual = yld1(1); //  spawning potential ratio
 
@@ -1008,7 +1008,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       last_F1 = F1(1);
       if (show_MSY == 1)
       {
-        report5 << j << " " << F1(1) << " " << equ_F_std << " " << SSB_equil / SPR_unfished << " " << YPR_opt << " " << F01_actual << " " << F01_second << " last F1 " << last_F1 << " Closer " << Closer << " delta " << (F01_origin * 0.1 - F01_actual) / (F01_second) << endl;
+        report5 << j << " " << F1(1) << " " << equ_F_std << " " << SSB_equil / SPR_unf << " " << YPR_opt << " " << F01_actual << " " << F01_second << " last F1 " << last_F1 << " Closer " << Closer << " delta " << (F01_origin * 0.1 - F01_actual) / (F01_second) << endl;
       }
       F1(1) += (F01_origin * 0.1 - F01_actual) / (F01_second);
       F1(1) = (1. - Closer) * F1(1) + Closer * last_F1;
@@ -1051,7 +1051,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     YPR_Btgt_revenue = (PricePerF * YPR_val_vec) * Btgt_Rec; //  vector*vector*scalar
     //    YPR_Btgt_revenue = Price*YPR_ret*Btgt_Rec;
     YPR_Btgt_profit = YPR_Btgt_revenue - Cost;
-    SPR_Btgt = SSB_equil / SPR_unfished;
+    SPR_Btgt = SSB_equil / SPR_unf;
     Vbio_Btgt = totbio;
     Vbio1_Btgt = smrybio;
     Mgmt_quant(7) = equ_F_std;
@@ -1131,7 +1131,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
           //  else  Hrate for bycatch fleets already set
         }
         Do_Equil_Calc(equ_Recr); //  where equ_Recr=1.0, so returned SSB_equil is a SSB/R,
-        SPR_Btgt = SSB_equil / SPR_unfished;
+        SPR_Btgt = SSB_equil / SPR_unf;
         //  SPAWN-RECR:   calc equil spawn-recr for Btarget calcs;  need to make area-specific
         SPR_temp = SSB_equil;
         Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
@@ -1353,7 +1353,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
 
       Do_Equil_Calc(equ_Recr);
       //  SPAWN-RECR:   calc spawn-recr for MSY calcs;  need to make area-specific
-      MSY_SPR = SSB_equil / SPR_unfished;
+      MSY_SPR = SSB_equil / SPR_unf;
       SPR_temp = SSB_equil;
       Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
       Bmsy = Equ_SpawnRecr_Result(1);  //  with MSY set to SPR, not directly estimated
@@ -1446,7 +1446,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
           }
           Do_Equil_Calc(equ_Recr);
           //  SPAWN-RECR:   calc spawn-recr for MSY calcs;  need to make area-specific
-          MSY_SPR = SSB_equil / SPR_unfished;
+          MSY_SPR = SSB_equil / SPR_unf;
           SPR_temp = SSB_equil;
           Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
           Bmsy = Equ_SpawnRecr_Result(1);  //  MSY is directly estimated
@@ -1739,7 +1739,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
           //  else  Hrate for bycatch fleets already set
         }
         Do_Equil_Calc(equ_Recr);
-        SPR_Btgt2 = SSB_equil / SPR_unfished;
+        SPR_Btgt2 = SSB_equil / SPR_unf;
         //  SPAWN-RECR:   calc equil spawn-recr for Btarget calcs;  need to make area-specific
         SPR_temp = SSB_equil;
         Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
@@ -1947,7 +1947,7 @@ FUNCTION void Get_Forecast()
   dvariable Fcast_Crash;
   dvariable totcatch;
   dvariable R0_use;  // annually updated variable if SR_update_SPR0 == 1
-  dvariable SSB_use;
+  dvariable SSB_use;  // selected version of SSB that gets passes to Spawn_Recr
   dvar_matrix catage_w(1, gmorph, 0, nages);
   dvar_vector tempcatch(1, Nfleet);
   imatrix Do_F_tune(t_base, TimeMax_Fcast_std, 1, Nfleet); //  flag for doing F from catch
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 3aa6d549..f4600932 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -344,7 +344,7 @@ FUNCTION void get_initial_conditions()
     equ_Recr = 1.0;
     Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation.  Returns SPR because R = 1.0
     SPR_virgin = SSB_equil; //  spawners per recruit.  Needed for Sr_fxn = 10
-    SPR_virgin_adj = SSB_equil;
+    SPR_virgin_adj = SSB_equil;  //  also needed for Sr_fxn 10.  Will get revised in benchmark to use averaged biology if requested.
     if(SR_fxn == 10)  // B-H with a,b
     {
   //  WHAM based on R = A*S/(1+B*S)
@@ -381,14 +381,14 @@ FUNCTION void get_initial_conditions()
     Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation
     SSB_virgin = SSB_equil;
 //    SPR_virgin = SSB_equil / Recr_virgin; //  spawners per recruit already calculated
-    if(Do_Benchmark==0)
+    if(Do_Benchmark==0)  // assign values that would be created in benchmark section
     {
-      Mgmt_quant(1)=SSB_virgin;
-      SSB_unf=SSB_virgin;
-      Recr_unf=Recr_virgin;
-      Mgmt_quant(2)=totbio;  //  from equil calcs
-      Mgmt_quant(3)=smrybio;  //  from equil calcs
-      Mgmt_quant(4)=Recr_virgin;
+      Mgmt_quant(1) = SSB_virgin;
+      SSB_unf = SSB_virgin;
+      Recr_unf = Recr_virgin;
+      Mgmt_quant(2) = totbio;  //  from equil calcs
+      Mgmt_quant(3) = smrybio;  //  from equil calcs
+      Mgmt_quant(4) = Recr_virgin;
     }
     Smry_Table(styr - 2, 1) = totbio; //  from equil calcs
     Smry_Table(styr - 2, 2) = smrybio; //  from equil calcs
@@ -1495,7 +1495,6 @@ FUNCTION void get_time_series()
         else  //  update SSB_use and R0_use where will update SPR0 inside the Spawn_recr fxn
         {
           R0_use = mfexp(SR_parm_work(1));  //  check to be sure this works when R0 is derived from B-H with alpha, beta parameters
-          equ_Recr = R0_use;
           Fishon = 0;
           eq_yr = y;
           bio_yr = y;

From b4ee3f638ed2ef5973e355b26a434bda6ce78794 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Fri, 13 Sep 2024 16:27:52 -0700
Subject: [PATCH 15/22] WIP: add switch in benchmark to use correct SPR0

---
 SS_benchfore.tpl       |  42 +++++++--------
 SS_popdyn.tpl          |   5 +-
 SS_readcontrol_330.tpl |   2 +-
 SS_recruit.tpl         | 116 ++++++++++++++++++++---------------------
 4 files changed, 80 insertions(+), 85 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 37bc9758..572c7d73 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -745,35 +745,30 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     }
   }
 
-  if(SR_fxn == 10)  //  B-H with alpha, beta
+  if (SR_update_SPR0 == 0)  //  use virgin biology for the spawner-recruitment R0,h calculations
   {
-      alpha = mfexp(SR_parm_work(3));
-      beta = mfexp(SR_parm_work(4));
-      Fishon = 0;
-      Recr_unf = 1.0;
-      Do_Equil_Calc(Recr_unf);  // 
-      SPR_virgin_adj = SSB_equil / 1.0;
-      SR_parm_work(2) = alpha * SPR_virgin_adj / (4. + alpha * SPR_virgin_adj);  // steepness
-      SR_parm_work(1) = log(1. / beta * (alpha - (1. / SPR_virgin_adj)));  // ln(R0)
+     Recr_unf = Recr_virgin;
+     SSB_unf = SSB_virgin;
+     SPR_unf = SSB_unf / Recr_unf;
+  }
+  else  // use benchmark biology in the spawner-recruitment R0,h calculations
+  {
+    Fishon = 0;
+    Recr_unf = mfexp(SR_parm_work(1));
+    Do_Equil_Calc(Recr_unf);
+    SSB_unf = SSB_equil;  // equilibrium unfished SSB using the benchmark averaged Recr_unf and benchmark averaged biology
+    SPR_unf = SSB_unf / Recr_unf; //  this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
   }
-  Fishon = 0;
-  Recr_unf = mfexp(SR_parm_work(1));
-  Do_Equil_Calc(Recr_unf);
-  SSB_unf = SSB_equil;  // equilibrium unfished SSB using the benchmark averaged Recr_unf and benchmark averaged biology
-  SPR_unf = SSB_unf / Recr_unf; //  this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
   if (show_MSY == 1)
   {
     report5 << "SR_parms for benchmark: " << SR_parm_work << endl
-            << "mean from years: " << Bmark_Yr(9) << " " << Bmark_Yr(10) << endl;
-    //  SPR_virgin = SSB_virgin / Recr_virgin;  // already defined
-    report5 << " Virgin SSB, R0: " << SSB_virgin << " " << Recr_virgin << " "  << SPR_virgin_adj << endl;
-    report5 << " unfished SSB, R0: " << SSB_unf << " " << Recr_unf << " "  << SPR_unf << " with current biology " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl;
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SPR_virgin_adj); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    report5 << " Virgin SPR0, result_SSB, R: " << SPR_virgin_adj << " " << Equ_SpawnRecr_Result << endl << endl;
+            << "Benchmark biology averaged over years: " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl;
+    if ( SR_update_SPR0 == 1) report5 << "SPR0 for equilibrium spawner-recruit based on benchmark biology, not virgin biology" << endl;
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SPR_virgin); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    report5 << " Virgin SSB, R0, SPR0: " << SSB_virgin << " " << Recr_virgin << " "  << SPR_virgin << " equil: " << Equ_SpawnRecr_Result << endl;
+
     Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_unf); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    report5 << " Benchmark SPR0, result_SSB, R: " << SPR_unf << " " << Equ_SpawnRecr_Result << endl << endl;
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SPR_unf); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    report5 << " Benchmark SPR0, result_SSB, R: " << SPR_unf << " " << Equ_SpawnRecr_Result << " with virgin spawn-recr " << endl;
+    report5 << " Benchmark SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << SPR_unf << " equil: " << Equ_SpawnRecr_Result << endl;
   }
   SR_parm_work(N_SRparm2 + 1) = SSB_unf;
   Mgmt_quant(1) = SSB_unf;
@@ -925,7 +920,6 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     //  SPAWN-RECR:   calc equil spawn-recr in YPR; need to make this area-specific
     SPR_temp = SSB_equil;  //  based on most recent call to Do_Equil_Calc
     Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-         report5<<SPR_temp<<" " << Equ_SpawnRecr_Result<<endl;
 
     Bspr = Equ_SpawnRecr_Result(1);
     Bspr_rec = Equ_SpawnRecr_Result(2);
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index f4600932..a93be215 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -535,6 +535,7 @@ FUNCTION void get_initial_conditions()
     CrashPen += Equ_penalty;
     SPR_temp = SSB_equil / equ_Recr; //  spawners per recruit at initial F
     //  get equilibrium SSB and recruitment from SPR_temp, Recr_virgin and virgin steepness
+    //  this is the initial year, so no time-vary effects available, so uses _virgin quantities for spawner-recruitment
     Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
     R1_exp = Equ_SpawnRecr_Result(2); //  set the expected recruitment equal to this equilibrium
     exp_rec(eq_yr, 1) = R1_exp;
@@ -1039,7 +1040,7 @@ FUNCTION void get_time_series()
           Fishon = 0;
           eq_yr = y;
           bio_yr = y;
-          Do_Equil_Calc(R0_use); //  call function to do equilibrium calculation
+          Do_Equil_Calc(R0_use); //  call function to do equilibrium calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
           if (fishery_on_off == 1)
           {
@@ -1050,7 +1051,7 @@ FUNCTION void get_time_series()
             Fishon = 0;
           }
         }
-        Recruits = Spawn_Recr(SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr
+        Recruits = Spawn_Recr(SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr using either virgin or adjusted R0 and SSB0
         if (SR_fxn != 7) apply_recdev(Recruits, R0_use); //  apply recruitment deviation
         // distribute Recruitment of age 0 fish among the current and future settlements; and among areas and morphs
         //  use t offset for each birth event:  Settlement_offset(settle)
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 338de133..a6ed423a 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -6473,7 +6473,7 @@
       active_parm(CoVar_Count) = j;
       if (y == styr - 2)
       {
-        ParmLabel += "Recr_Virgin";
+        ParmLabel += "Recr_virgin";
       }
       else if (y == styr - 1)
       {
diff --git a/SS_recruit.tpl b/SS_recruit.tpl
index 179ecd6e..5766efce 100644
--- a/SS_recruit.tpl
+++ b/SS_recruit.tpl
@@ -6,7 +6,7 @@
 //********************************************************************
  /*  SS_Label_FUNCTION 43 Spawner-recruitment function */
 //  SPAWN-RECR:   function: to calc R from S
-FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariable& Recr_virgin_adj, const prevariable& SSB_current)
+FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_use, const prevariable& Recr_virgin_use, const prevariable& SSB_current)
   {
   RETURN_ARRAYS_INCREMENT();
   dvariable NewRecruits;
@@ -22,7 +22,7 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
   dvariable SRZ_0;
   dvariable srz_min;
   dvariable SRZ_surv;
-//  warning << y << "  Tester_R0 " <<  Recr_virgin_adj << " SSB0 " << SSB_virgin_adj << " SSB_curr: " << SSB_current << endl;
+//  warning << y << "  Tester_R0 " <<  Recr_virgin_use << " SSB0 " << SSB_virgin_use << " SSB_curr: " << SSB_current << endl;
 
   //  SS_Label_43.1  add 0.1 to input spawning biomass value to make calculation more rebust
   SSB_curr_adj = SSB_current + 0.100; // robust
@@ -30,7 +30,7 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
   regime_change = SR_parm_work(N_SRparm2 - 1); //  this is a persistent deviation off the S/R curve
 
   //  SS_Label_43.3  calculate expected recruitment from the input spawning biomass and the SR curve
-  // functions below use Recr_virgin_adj,SSB_virgin_adj which could have been adjusted adjusted above from R0,SSB_virgin
+  // functions below use Recr_virgin_use,SSB_virgin_use which could have been adjusted adjusted above from R0,SSB_virgin
   switch (SR_fxn)
   {
     case 1: // previous placement for B-H constrained
@@ -43,15 +43,15 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
     case 2: // ricker
     {
       steepness = SR_parm_work(2);
-      NewRecruits = Recr_virgin_adj * SSB_curr_adj / SSB_virgin_adj * mfexp(steepness * (1. - SSB_curr_adj / SSB_virgin_adj));
+      NewRecruits = Recr_virgin_use * SSB_curr_adj / SSB_virgin_use * mfexp(steepness * (1. - SSB_curr_adj / SSB_virgin_use));
       break;
     }
     //  SS_Label_43.3.3  Beverton-Holt
     case 3: // Beverton-Holt
     {
       steepness = SR_parm_work(2);
-      NewRecruits = (4. * steepness * Recr_virgin_adj * SSB_curr_adj) /
-          (SSB_virgin_adj * (1. - steepness) + (5. * steepness - 1.) * SSB_curr_adj);
+      NewRecruits = (4. * steepness * Recr_virgin_use * SSB_curr_adj) /
+          (SSB_virgin_use * (1. - steepness) + (5. * steepness - 1.) * SSB_curr_adj);
       break;
     }
 
@@ -66,7 +66,7 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
     //  SS_Label_43.3.4  constant expected recruitment
     case 4: // none
     {
-      NewRecruits = Recr_virgin_adj;
+      NewRecruits = Recr_virgin_use;
       break;
     }
     //  SS_Label_43.3.5  Hockey stick
@@ -74,8 +74,8 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
       //  the 3rd parameter allows for a minimum recruitment level
       {
         steepness = SR_parm_work(2);
-        temp = SR_parm_work(3) * Recr_virgin_adj + SSB_curr_adj / (steepness * SSB_virgin_adj) * (Recr_virgin_adj - SR_parm_work(3) * Recr_virgin_adj); //  linear decrease below steepness*SSB_virgin_adj
-        NewRecruits = Join_Fxn(0.0 * SSB_virgin_adj, SSB_virgin_adj, steepness * SSB_virgin_adj, SSB_curr_adj, temp, Recr_virgin_adj);
+        temp = SR_parm_work(3) * Recr_virgin_use + SSB_curr_adj / (steepness * SSB_virgin_use) * (Recr_virgin_use - SR_parm_work(3) * Recr_virgin_use); //  linear decrease below steepness*SSB_virgin_use
+        NewRecruits = Join_Fxn(0.0 * SSB_virgin_use, SSB_virgin_use, steepness * SSB_virgin_use, SSB_curr_adj, temp, Recr_virgin_use);
         break;
       }
 
@@ -83,32 +83,32 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
     case 6: //Beverton-Holt constrained
     {
       steepness = SR_parm_work(2);
-//      dvariable SPR = SSB_virgin_adj / Recr_virgin;
+//      dvariable SPR = SSB_virgin_use / Recr_virgin;
 //      alpha = ((4.0 * steepness) / (1. - steepness)) / SPR ;
 //      beta = (1.0 / Recr_virgin) * (alpha - (1.0 / SPR));
-      if (SSB_curr_adj > SSB_virgin_adj)
+      if (SSB_curr_adj > SSB_virgin_use)
       {
-        SSB_BH1 = SSB_virgin_adj;
+        SSB_BH1 = SSB_virgin_use;
       }
       else
       {
         SSB_BH1 = SSB_curr_adj;
       }
-      NewRecruits = (4. * steepness * Recr_virgin_adj * SSB_BH1) / (SSB_virgin_adj * (1. - steepness) + (5. * steepness - 1.) * SSB_BH1);
+      NewRecruits = (4. * steepness * Recr_virgin_use * SSB_BH1) / (SSB_virgin_use * (1. - steepness) + (5. * steepness - 1.) * SSB_BH1);
       break;
     }
 
     //  SS_Label_43.3.7  survival based
     case 7: // survival based, so constrained such that recruits cannot exceed fecundity
     {
-      // PPR_0=SSB_virgin_adj/Recr_virgin_adj;  //  pups per recruit at virgin
+      // PPR_0=SSB_virgin_use/Recr_virgin_use;  //  pups per recruit at virgin
       // Surv_0=1./PPR_0;   //  recruits per pup at virgin
-      // Pups_0=SSB_virgin_adj;  //  total population fecundity is the number of pups produced
+      // Pups_0=SSB_virgin_use;  //  total population fecundity is the number of pups produced
       // Sfrac=SR_parm(2);
-      SRZ_0 = log(1.0 / (SSB_virgin_adj / Recr_virgin_adj));
+      SRZ_0 = log(1.0 / (SSB_virgin_use / Recr_virgin_use));
       steepness = SR_parm_work(2);
       srz_min = SRZ_0 * (1.0 - steepness);
-      SRZ_surv = mfexp((1. - pow((SSB_curr_adj / SSB_virgin_adj), SR_parm_work(3))) * (srz_min - SRZ_0) + SRZ_0); //  survival
+      SRZ_surv = mfexp((1. - pow((SSB_curr_adj / SSB_virgin_use), SR_parm_work(3))) * (srz_min - SRZ_0) + SRZ_0); //  survival
       NewRecruits = SSB_curr_adj * SRZ_surv;
       exp_rec(y, 1) = NewRecruits; // expected arithmetic mean recruitment
       //  SS_Label_43.3.7.1  Do variation in recruitment by adjusting survival
@@ -145,8 +145,8 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
       Shepherd_c2 = pow(0.2, SR_parm_work(3));
       Hupper = 1.0 / (5.0 * Shepherd_c2);
       steepness = 0.2 + (SR_parm_work(2) - 0.2) / (0.8) * (Hupper - 0.2);
-      temp = (SSB_curr_adj) / (SSB_virgin_adj);
-      NewRecruits = (5. * steepness * Recr_virgin_adj * (1. - Shepherd_c2) * temp) /
+      temp = (SSB_curr_adj) / (SSB_virgin_use);
+      NewRecruits = (5. * steepness * Recr_virgin_use * (1. - Shepherd_c2) * temp) /
           (1.0 - 5.0 * steepness * Shepherd_c2 + (5. * steepness - 1.) * pow(temp, Shepherd_c));
       break;
     }
@@ -156,11 +156,11 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
     {
       steepness = SR_parm_work(2);
       dvariable RkrPower = SR_parm_work(3);
-      temp = SSB_curr_adj / SSB_virgin_adj;
+      temp = SSB_curr_adj / SSB_virgin_use;
       temp2 = posfun(1.0 - temp, 0.0000001, temp3);
       temp = 1.0 - temp2; //  Rick's new line to stabilize recruitment at R0 if B>B0
       dvariable RkrTop = log(5.0 * steepness) * pow(temp2, RkrPower) / pow(0.8, RkrPower);
-      NewRecruits = Recr_virgin_adj * temp * mfexp(RkrTop);
+      NewRecruits = Recr_virgin_use * temp * mfexp(RkrTop);
       break;
     }
 
@@ -169,7 +169,7 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_adj, const prevariab
   return NewRecruits;
   } //  end spawner_recruitment
 
-FUNCTION void apply_recdev(prevariable& NewRecruits, const prevariable& Recr_virgin_adj)
+FUNCTION void apply_recdev(prevariable& NewRecruits, const prevariable& Recr_virgin_use)
   {
   RETURN_ARRAYS_INCREMENT();
   //  SS_Label_43.4  For non-survival based SRR, get recruitment deviations by adjusting recruitment itself
@@ -196,7 +196,7 @@ FUNCTION void apply_recdev(prevariable& NewRecruits, const prevariable& Recr_vir
     {
       if (do_recdev >= 3)
       {
-        NewRecruits = Recr_virgin_adj * mfexp(recdev(y)); //  recruitment deviation
+        NewRecruits = Recr_virgin_use * mfexp(recdev(y)); //  recruitment deviation
       }
       else if (SR_fxn != 7)
       {
@@ -228,7 +228,7 @@ FUNCTION void apply_recdev(prevariable& NewRecruits, const prevariable& Recr_vir
       }
       case 2: //  use multiplier of R0
       {
-        exp_rec(y, 2) = Recr_virgin_adj * Fcast_Loop_Control(4); //  apply fcast multiplier to the virgin recruitment
+        exp_rec(y, 2) = Recr_virgin_use * Fcast_Loop_Control(4); //  apply fcast multiplier to the virgin recruitment
         NewRecruits = exp_rec(y, 2);
         if (SR_fxn != 4)
           NewRecruits *= mfexp(-biasadj(y) * half_sigmaRsq); // bias adjustment
@@ -268,7 +268,7 @@ FUNCTION void apply_recdev(prevariable& NewRecruits, const prevariable& Recr_vir
  /*  SS_Label_FUNCTION 44 Equil_Spawn_Recr_Fxn */
 //  SPAWN-RECR:   function  Equil_Spawn_Recr_Fxn
 FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
-    const prevariable& SSB_temp, const prevariable& RECR_temp, const prevariable& SPR_temp)
+    const prevariable& SSB_virgin_use, const prevariable& Recr_virgin_use, const prevariable& SPR_current)
   {
   RETURN_ARRAYS_INCREMENT();
   dvar_vector Equil_Spawn_Recr_Calc(1, 2); // values to return 1 is B_equil, 2 is R_equil
@@ -284,7 +284,7 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
   dvariable SRZ_surv;
 
   steepness = SRparm(2); //  common usage but some different
-  //  SS_Label_44.1  calc equilibrium SpawnBio and Recruitment from input SPR_temp, which is spawning biomass per recruit at some given F level
+  //  SS_Label_44.1  calc equilibrium SpawnBio and Recruitment from input SPR_current, which is spawning biomass per recruit at some given F level
   switch (SR_fxn)
   {
     case 1: // previous placement for B-H constrained
@@ -297,8 +297,8 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
     //  SS_Label_44.1.2  Ricker
     case 2: // Ricker
     {
-      B_equil = SSB_temp * (1. + (log(RECR_temp / SSB_temp) + log(SPR_temp)) / steepness);
-      R_equil = RECR_temp * B_equil / SSB_temp * mfexp(steepness * (1. - B_equil / SSB_temp));
+      B_equil = SSB_virgin_use * (1. + (log(Recr_virgin_use / SSB_virgin_use) + log(SPR_current)) / steepness);
+      R_equil = Recr_virgin_use * B_equil / SSB_virgin_use * mfexp(steepness * (1. - B_equil / SSB_virgin_use));
 
       break;
     }
@@ -316,19 +316,19 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
 
   //  SS3 previously used alternative formulation: R = A*S/(B+S)
   //  converting SS3 to align with WHAM
-  //    SPR_virgin = SSB_temp / RECR_temp;  //  this is already defined
+  //    SPR_virgin = SSB_virgin_use / Recr_virgin_use;  //  this is already defined
       alpha = 4.0 * steepness / (SPR_virgin_adj * (1. - steepness));
       beta = (5.0 * steepness - 1.0) / ((1 - steepness) * SSB_virgin);
 
       // " h " << steepness << " derive "  << alpha * SPR_virgin / (4. + alpha * SPR_virgin) << " " << endl;
-      // " R0 " << RECR_temp << " derive "  << 1. / beta * (alpha - 1./SPR_virgin) << endl;
-//      report5 <<" SSB_unf "<<SSB_temp<<" SPR_unf "<<SPR_virgin<<" steep: "<<steepness<<" R0: "<<RECR_temp << endl;
-      report5 <<" derive_alpha "<<alpha<<" derive_beta "<<beta << endl;
+      // " R0 " << Recr_virgin_use << " derive "  << 1. / beta * (alpha - 1./SPR_virgin) << endl;
+//      report5 <<" SSB_unf "<<SSB_virgin_use<<" SPR_unf "<<SPR_virgin<<" steep: "<<steepness<<" R0: "<<Recr_virgin_use << endl;
+//      report5 <<" derive_alpha "<<alpha<<" derive_beta "<<beta << endl;
 //      report5 << " deriv_h: " << alpha * SPR_virgin / (4. + alpha * SPR_virgin) << " derive_R0: " << 1. / beta * (alpha - (1. / SPR_virgin))<<endl;
-      B_equil = (alpha * SPR_temp - 1.0) / beta;
+      B_equil = (alpha * SPR_current - 1.0) / beta;
       B_equil = posfun(B_equil, 0.0001, temp);
       R_equil = alpha * B_equil / (1.0 + beta * B_equil);
-//      report5 << "SPR_input: " << SPR_temp << " B_equil: " << B_equil << " R_equil: "<<R_equil << endl<<endl;
+//      report5 << "SPR_input: " << SPR_current << " B_equil: " << B_equil << " R_equil: "<<R_equil << endl<<endl;
 
       break;
     }
@@ -337,37 +337,37 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
     {
       dvariable alpha = mfexp(SRparm(3));
       dvariable beta = mfexp(SRparm(4));
-      B_equil = (alpha * SPR_temp - 1.0) / beta;
+      B_equil = (alpha * SPR_current - 1.0) / beta;
       B_equil = posfun(B_equil, 0.0001, temp);
       R_equil = alpha * B_equil / (1.0 + beta * B_equil);
-//      report5<<SPR_temp<<" Beq "<<B_equil<<" Req "<<R_equil<<" alpha "<<alpha<<" beta "<<beta<<" SSB_unf "<<SSB_unf<<endl;
+//      report5<<SPR_current<<" Beq "<<B_equil<<" Req "<<R_equil<<" alpha "<<alpha<<" beta "<<beta<<" SSB_unf "<<SSB_unf<<endl;
       break;
     }
 
     //  SS_Label_44.1.4  constant recruitment
     case 4: // constant; no bias correction
     {
-      B_equil = SPR_temp * RECR_temp;
-      R_equil = RECR_temp;
+      B_equil = SPR_current * Recr_virgin_use;
+      R_equil = Recr_virgin_use;
       break;
     }
     //  SS_Label_44.1.5  Hockey Stick
     case 5: // hockey stick
     {
-      dvariable hockey_min = SRparm(3) * RECR_temp; // min recruitment level
-      //        temp=SSB_temp/R0*steepness;  // spawners per recruit at inflection
-      dvariable hockey_slope = (RECR_temp - hockey_min) / (steepness * SSB_temp); //  slope of recruitment on spawners below the inflection
-      B_equil = Join_Fxn(0.0 * SSB_temp / RECR_temp, SSB_temp / RECR_temp, SSB_temp / RECR_temp * steepness, SPR_temp, hockey_min / ((1. / SPR_temp) - hockey_slope), SPR_temp * RECR_temp);
-      R_equil = Join_Fxn(0.0 * SSB_temp, SSB_temp, SSB_temp * steepness, B_equil, hockey_min + hockey_slope * B_equil, RECR_temp);
+      dvariable hockey_min = SRparm(3) * Recr_virgin_use; // min recruitment level
+      //        temp=SSB_virgin_use/R0*steepness;  // spawners per recruit at inflection
+      dvariable hockey_slope = (Recr_virgin_use - hockey_min) / (steepness * SSB_virgin_use); //  slope of recruitment on spawners below the inflection
+      B_equil = Join_Fxn(0.0 * SSB_virgin_use / Recr_virgin_use, SSB_virgin_use / Recr_virgin_use, SSB_virgin_use / Recr_virgin_use * steepness, SPR_current, hockey_min / ((1. / SPR_current) - hockey_slope), SPR_current * Recr_virgin_use);
+      R_equil = Join_Fxn(0.0 * SSB_virgin_use, SSB_virgin_use, SSB_virgin_use * steepness, B_equil, hockey_min + hockey_slope * B_equil, Recr_virgin_use);
       break;
     }
     //  SS_Label_44.1.7  3 parameter survival based
     case 7: // survival
     {
-      SRZ_0 = log(1.0 / (SSB_temp / RECR_temp));
+      SRZ_0 = log(1.0 / (SSB_virgin_use / Recr_virgin_use));
       srz_min = SRZ_0 * (1.0 - steepness);
-      B_equil = SSB_temp * (1. - (log(1. / SPR_temp) - SRZ_0) / pow((srz_min - SRZ_0), (1. / SRparm(3))));
-      SRZ_surv = mfexp((1. - pow((B_equil / SSB_temp), SRparm(3))) * (srz_min - SRZ_0) + SRZ_0); //  survival
+      B_equil = SSB_virgin_use * (1. - (log(1. / SPR_current) - SRZ_0) / pow((srz_min - SRZ_0), (1. / SRparm(3))));
+      SRZ_surv = mfexp((1. - pow((B_equil / SSB_virgin_use), SRparm(3))) * (srz_min - SRZ_0) + SRZ_0); //  survival
       R_equil = B_equil * SRZ_surv;
       break;
     }
@@ -389,11 +389,11 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
       Shepherd_c2 = pow(0.2, SRparm(3));
       Hupper = 1.0 / (5.0 * Shepherd_c2);
       steepness = 0.2 + (SRparm(2) - 0.2) / (0.8) * (Hupper - 0.2);
-      Shep_top = 5.0 * steepness * (1.0 - Shepherd_c2) * (SPR_temp * RECR_temp) / SSB_temp - (1.0 - 5.0 * steepness * Shepherd_c2);
+      Shep_top = 5.0 * steepness * (1.0 - Shepherd_c2) * (SPR_current * Recr_virgin_use) / SSB_virgin_use - (1.0 - 5.0 * steepness * Shepherd_c2);
       Shep_bot = 5.0 * steepness - 1.0;
       Shep_top2 = posfun(Shep_top, 0.001, temp);
-      R_equil = (SSB_temp / SPR_temp) * pow((Shep_top2 / Shep_bot), (1.0 / SRparm(3)));
-      B_equil = R_equil * SPR_temp;
+      R_equil = (SSB_virgin_use / SPR_current) * pow((Shep_top2 / Shep_bot), (1.0 / SRparm(3)));
+      B_equil = R_equil * SPR_current;
       break;
     }
 
@@ -402,11 +402,11 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
     {
       steepness = SRparm(2);
       dvariable RkrPower = SRparm(3);
-      temp = SSB_temp / (SPR_temp * RECR_temp);
+      temp = SSB_virgin_use / (SPR_current * Recr_virgin_use);
       dvariable RkrTop = pow(0.8, RkrPower) * log(temp) / log(5.0 * steepness);
       RkrTop = posfun(RkrTop, 0.000001, CrashPen);
-      R_equil = temp * RECR_temp * (1.0 - pow(RkrTop, 1.0 / RkrPower));
-      B_equil = R_equil * SPR_temp;
+      R_equil = temp * Recr_virgin_use * (1.0 - pow(RkrTop, 1.0 / RkrPower));
+      B_equil = R_equil * SPR_current;
       break;
     }
 
@@ -428,11 +428,11 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
         Hupper=1.0/(5.0*Shepherd_c2);
         steepness=0.20001+((0.8)/(1.0+exp(-SRparm2))-0.2)/(0.8)*(Hupper-0.2);
 //        steep2=0.20001+(steepness-0.2)/(0.8)*(Hupper-0.2);
-        Shep_top=5.0*steepness*(1.0-Shepherd_c2)*(SPR_temp*RECR_temp)/SSB_temp-(1.0-5.0*steepness*Shepherd_c2);
+        Shep_top=5.0*steepness*(1.0-Shepherd_c2)*(SPR_current*Recr_virgin_use)/SSB_virgin_use-(1.0-5.0*steepness*Shepherd_c2);
         Shep_bot=5.0*steepness-1.0;
         Shep_top2=posfun(Shep_top,0.001,temp);
-        R_equil=(SSB_temp/SPR_temp) * pow((Shep_top2/Shep_bot),(1.0/Shepherd_c));
-        B_equil=R_equil*SPR_temp;
+        R_equil=(SSB_virgin_use/SPR_current) * pow((Shep_top2/Shep_bot),(1.0/Shepherd_c));
+        B_equil=R_equil*SPR_current;
         break;
       }
 
@@ -448,11 +448,11 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
 //   if (Recs < 0) Rec2 = 0; else Rec2 = Recs;
         steepness = 0.2 + (10.0 - 0.2)/(1+exp(-SR_parm_work(2)));
         dvariable RkrPower=exp(SR_parm_work(3));
-        temp=SSB_virgin/(SPR_temp*RECR_temp);
+        temp=SSB_virgin/(SPR_current*Recr_virgin_use);
         dvariable RkrTop =  pow(0.8,RkrPower)*log(temp)/log(5.0*steepness);
         RkrTop = posfun(RkrTop,0.000001,CrashPen);
-        R_equil = temp *RECR_temp * (1.0 - pow(RkrTop,1.0/RkrPower));
-        B_equil=R_equil*SPR_temp;
+        R_equil = temp *Recr_virgin_use * (1.0 - pow(RkrTop,1.0/RkrPower));
+        B_equil=R_equil*SPR_current;
         break;
       }
    */

From 18fcf7df1821fb27f1a98bf3e7f67ae0fa7844ac Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Mon, 16 Sep 2024 18:22:06 -0700
Subject: [PATCH 16/22] refactor SPR to SSBpR; clean-up reference to timevary
 biology

---
 SS_benchfore.tpl    | 73 ++++++++++++++++++++++++---------------------
 SS_param.tpl        |  6 ++--
 SS_popdyn.tpl       | 18 ++++++-----
 SS_recruit.tpl      | 54 ++++++++++++++++-----------------
 SS_write_report.tpl | 14 ++++-----
 5 files changed, 85 insertions(+), 80 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 572c7d73..39f9e044 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -536,7 +536,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   dvariable last_F1;
   dvariable Closer;
   dvariable Vbio1_unfished;
-  dvariable SPR_unf;
+  dvariable SSBpR_unf;
   dvariable Vbio_MSY;
   dvariable Vbio1_MSY;
   dvariable junk;
@@ -749,7 +749,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   {
      Recr_unf = Recr_virgin;
      SSB_unf = SSB_virgin;
-     SPR_unf = SSB_unf / Recr_unf;
+     SSBpR_unf = SSB_unf / Recr_unf;
   }
   else  // use benchmark biology in the spawner-recruitment R0,h calculations
   {
@@ -757,18 +757,21 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     Recr_unf = mfexp(SR_parm_work(1));
     Do_Equil_Calc(Recr_unf);
     SSB_unf = SSB_equil;  // equilibrium unfished SSB using the benchmark averaged Recr_unf and benchmark averaged biology
-    SPR_unf = SSB_unf / Recr_unf; //  this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
+    SSBpR_unf = SSB_unf / Recr_unf; //  this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
+    SSBpR_virgin_adj = SSB_unf / Recr_unf;  //  update 
   }
   if (show_MSY == 1)
   {
     report5 << "SR_parms for benchmark: " << SR_parm_work << endl
             << "Benchmark biology averaged over years: " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl;
     if ( SR_update_SPR0 == 1) report5 << "SPR0 for equilibrium spawner-recruit based on benchmark biology, not virgin biology" << endl;
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SPR_virgin); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    report5 << " Virgin SSB, R0, SPR0: " << SSB_virgin << " " << Recr_virgin << " "  << SPR_virgin << " equil: " << Equ_SpawnRecr_Result << endl;
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SSBpR_virgin); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    report5 << " Virgin SSB, R0, SPR0: " << SSB_virgin << " " << Recr_virgin << " "  << SSBpR_virgin << " equil: " << Equ_SpawnRecr_Result << endl;
+
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_unf); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    report5 << " Benchmark SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << SSBpR_unf << " equil: " << Equ_SpawnRecr_Result << endl;
+    report5 << "Repro_output_by_age_for_morph_1: " << fec(1) << endl;
 
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_unf); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    report5 << " Benchmark SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << SPR_unf << " equil: " << Equ_SpawnRecr_Result << endl;
   }
   SR_parm_work(N_SRparm2 + 1) = SSB_unf;
   Mgmt_quant(1) = SSB_unf;
@@ -803,7 +806,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     SPR_target100 = SPR_target * 100.;
 
     Do_Equil_Calc(equ_Recr);
-    SPR_unf = SSB_unf / Recr_unf; //  this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
+    SSBpR_unf = SSB_unf / Recr_unf; //  this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
     Vbio1_unfished = smrybio; // gets value from equil_calc
     if (show_MSY == 1)
     {
@@ -849,7 +852,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
 
         Fishon = 1;
         Do_Equil_Calc(equ_Recr);
-        yld1(ii) = 100. * SSB_equil / SPR_unf; //  spawning potential ratio
+        yld1(ii) = 100. * SSB_equil / SSBpR_unf; //  spawning potential ratio
       }
       SPR_actual = yld1(1); //  spawning potential ratio
 
@@ -918,8 +921,8 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     }
 
     //  SPAWN-RECR:   calc equil spawn-recr in YPR; need to make this area-specific
-    SPR_temp = SSB_equil;  //  based on most recent call to Do_Equil_Calc
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    SSBpR_temp = SSB_equil;  //  based on most recent call to Do_Equil_Calc
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
 
     Bspr = Equ_SpawnRecr_Result(1);
     Bspr_rec = Equ_SpawnRecr_Result(2);
@@ -1002,7 +1005,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       last_F1 = F1(1);
       if (show_MSY == 1)
       {
-        report5 << j << " " << F1(1) << " " << equ_F_std << " " << SSB_equil / SPR_unf << " " << YPR_opt << " " << F01_actual << " " << F01_second << " last F1 " << last_F1 << " Closer " << Closer << " delta " << (F01_origin * 0.1 - F01_actual) / (F01_second) << endl;
+        report5 << j << " " << F1(1) << " " << equ_F_std << " " << SSB_equil / SSBpR_unf << " " << YPR_opt << " " << F01_actual << " " << F01_second << " last F1 " << last_F1 << " Closer " << Closer << " delta " << (F01_origin * 0.1 - F01_actual) / (F01_second) << endl;
       }
       F1(1) += (F01_origin * 0.1 - F01_actual) / (F01_second);
       F1(1) = (1. - Closer) * F1(1) + Closer * last_F1;
@@ -1033,8 +1036,8 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     Btgt_Fmult = F1(1);
     if (rundetail > 0 && mceval_counter == 0 && show_MSY == 1)
       echoinput << "Calculated F0.1: " << Btgt_Fmult << endl;
-    SPR_temp = SSB_equil;
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    SSBpR_temp = SSB_equil;
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
     Btgt = Equ_SpawnRecr_Result(1);
     Btgt_Rec = Equ_SpawnRecr_Result(2);
     YPR_Btgt_enc = YPR_enc; //  total encountered yield per recruit
@@ -1045,7 +1048,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     YPR_Btgt_revenue = (PricePerF * YPR_val_vec) * Btgt_Rec; //  vector*vector*scalar
     //    YPR_Btgt_revenue = Price*YPR_ret*Btgt_Rec;
     YPR_Btgt_profit = YPR_Btgt_revenue - Cost;
-    SPR_Btgt = SSB_equil / SPR_unf;
+    SPR_Btgt = SSB_equil / SSBpR_unf;
     Vbio_Btgt = totbio;
     Vbio1_Btgt = smrybio;
     Mgmt_quant(7) = equ_F_std;
@@ -1060,9 +1063,12 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     // ******************************************************
     if (show_MSY == 1)
     {
-      report5 << "#" << endl
-              << "Find_target_SSB/Bzero; where Bzero is for Bmark years, not Virgin" << endl
-              << "Iter Fmult ann_F SPR Catch SSB Recruits SSB/Bzero Tot_catch";
+      report5 << "#" << endl;
+  if (SR_update_SPR0 == 0)  //  use virgin biology for the spawner-recruitment R0,h calculations
+    {report5 << "Find_target_SSB/Bzero; where Bzero is Virgin SSB:" << SSB_unf << " where SSBpR_unf = " << SSBpR_unf << endl;}
+  else
+    {report5 << "Find_target_SSB/Bzero; where Bzero is for Bmark biology and updated SPR0: " << SSB_unf << " where SSBpR_unf = " << SSBpR_unf << endl;}
+  report5  << "Iter Fmult ann_F SPR Catch SSB Recruits SSB/Bzero Tot_catch";
       for (p = 1; p <= pop; p++)
         for (gp = 1; gp <= N_GP; gp++)
         {
@@ -1088,8 +1094,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       Nloops = 28;
     }
 
-    //    Btgttgt=BTGT_target*SSB_virgin;   //  this is relative to virgin, not to the average biology from benchmark years
-    Btgttgt = BTGT_target * SSB_unf; //  now relative to Bmark
+    Btgttgt = BTGT_target * SSB_unf;
 
     for (j = 0; j <= Nloops; j++) // loop find Btarget
     {
@@ -1124,12 +1129,11 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
           }
           //  else  Hrate for bycatch fleets already set
         }
-        Do_Equil_Calc(equ_Recr); //  where equ_Recr=1.0, so returned SSB_equil is a SSB/R,
-        SPR_Btgt = SSB_equil / SPR_unf;
+        Do_Equil_Calc(equ_Recr); //  where equ_Recr=1.0, so returned SSB_equil is in units of SSB/R,
+        SSBpR_temp = SSB_equil;
+        SPR_Btgt = SSBpR_temp / SSBpR_unf;  //  where SSBpR_unf = SSB_unf / Recr_unf so units of SSB/R; so result is SPR_Btgt = (fished SSB/R) / (unfished SSB/R)
         //  SPAWN-RECR:   calc equil spawn-recr for Btarget calcs;  need to make area-specific
-        SPR_temp = SSB_equil;
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-         report5<<SPR_temp<<" " << Equ_SpawnRecr_Result<<endl;
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         yld1(ii) = Equ_SpawnRecr_Result(1);
       }
 
@@ -1169,6 +1173,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
             report5 << " " << SSB_equil_pop_gp(p, gp) * Equ_SpawnRecr_Result(2);
           }
         report5 << endl;
+//        " SSB_unf " << SSB_unf << " recr " <<Recr_unf<< " SSB_equil " << SSB_equil << " ssbpr_virginadj: " << SSBpR_virgin_adj << " Btgt " << Btgt << endl;
       }
     } // end search loop
 
@@ -1347,9 +1352,9 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
 
       Do_Equil_Calc(equ_Recr);
       //  SPAWN-RECR:   calc spawn-recr for MSY calcs;  need to make area-specific
-      MSY_SPR = SSB_equil / SPR_unf;
-      SPR_temp = SSB_equil;
-      Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+      MSY_SPR = SSB_equil / SSBpR_unf;
+      SSBpR_temp = SSB_equil;
+      Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
       Bmsy = Equ_SpawnRecr_Result(1);  //  with MSY set to SPR, not directly estimated
       Recr_msy = Equ_SpawnRecr_Result(2);
       yld1(1) = YPR_opt * Recr_msy;
@@ -1440,9 +1445,9 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
           }
           Do_Equil_Calc(equ_Recr);
           //  SPAWN-RECR:   calc spawn-recr for MSY calcs;  need to make area-specific
-          MSY_SPR = SSB_equil / SPR_unf;
-          SPR_temp = SSB_equil;
-          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+          MSY_SPR = SSB_equil / SSBpR_unf;
+          SSBpR_temp = SSB_equil;
+          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
           Bmsy = Equ_SpawnRecr_Result(1);  //  MSY is directly estimated
           Recr_msy = Equ_SpawnRecr_Result(2);
           Profit = (PricePerF * YPR_val_vec) * Recr_msy - Cost;
@@ -1733,10 +1738,10 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
           //  else  Hrate for bycatch fleets already set
         }
         Do_Equil_Calc(equ_Recr);
-        SPR_Btgt2 = SSB_equil / SPR_unf;
+        SPR_Btgt2 = SSB_equil / SSBpR_unf;
         //  SPAWN-RECR:   calc equil spawn-recr for Btarget calcs;  need to make area-specific
-        SPR_temp = SSB_equil;
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        SSBpR_temp = SSB_equil;
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         yld1(ii) = Equ_SpawnRecr_Result(1);
       }
 
diff --git a/SS_param.tpl b/SS_param.tpl
index 06c280ea..43a4206c 100644
--- a/SS_param.tpl
+++ b/SS_param.tpl
@@ -165,8 +165,8 @@ PARAMETER_SECTION
   number two_sigmaRsq;
   number half_sigmaRsq;
   number sigmaR;
-  number SPR_virgin;
-  number SPR_virgin_adj;
+  number SSBpR_virgin;
+  number SSBpR_virgin_adj;
   number regime_change;
   number rho;
   number dirichlet_Parm;
@@ -249,7 +249,7 @@ PARAMETER_SECTION
 
   number SPR_trial
   number SPR_actual;
-  number SPR_temp;  //  used to pass quantity into Equil_SpawnRecr
+  number SSBpR_temp;  //  SSB per Recruit; used to pass quantity into Equil_SpawnRecr
   number Recruits;                            // Age0 Recruits
   number equ_mat_bio
   number equ_mat_num
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index a93be215..c42f907e 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -343,8 +343,8 @@ FUNCTION void get_initial_conditions()
   {
     equ_Recr = 1.0;
     Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation.  Returns SPR because R = 1.0
-    SPR_virgin = SSB_equil; //  spawners per recruit.  Needed for Sr_fxn = 10
-    SPR_virgin_adj = SSB_equil;  //  also needed for Sr_fxn 10.  Will get revised in benchmark to use averaged biology if requested.
+    SSBpR_virgin = SSB_equil; //  spawners per recruit.  Needed for Sr_fxn = 10
+    SSBpR_virgin_adj = SSB_equil;  //  also needed for Sr_fxn 10.  Will get revised in benchmark to use averaged biology if requested.
     if(SR_fxn == 10)  // B-H with a,b
     {
   //  WHAM based on R = A*S/(1+B*S)
@@ -355,8 +355,8 @@ FUNCTION void get_initial_conditions()
 
       alpha = mfexp(SR_parm(3));
       beta = mfexp(SR_parm(4));
-      steepness = alpha * SPR_virgin_adj / (4. + alpha * SPR_virgin_adj);
-      Recr_virgin = 1. / beta * (alpha - (1. / SPR_virgin_adj));
+      steepness = alpha * SSBpR_virgin_adj / (4. + alpha * SSBpR_virgin_adj);
+      Recr_virgin = 1. / beta * (alpha - (1. / SSBpR_virgin_adj));
 //      warning << " before AB_calcs " << "parm " << SR_parm(1) << " calc " << log(Recr_virgin) << endl;
       SR_parm(1) = log(Recr_virgin);
       SR_parm(2) = steepness;
@@ -380,7 +380,7 @@ FUNCTION void get_initial_conditions()
     exp_rec(eq_yr, 4) = Recr_virgin;
     Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation
     SSB_virgin = SSB_equil;
-//    SPR_virgin = SSB_equil / Recr_virgin; //  spawners per recruit already calculated
+//    SSBpR_virgin = SSB_equil / Recr_virgin; //  spawners per recruit already calculated
     if(Do_Benchmark==0)  // assign values that would be created in benchmark section
     {
       Mgmt_quant(1) = SSB_virgin;
@@ -533,10 +533,10 @@ FUNCTION void get_initial_conditions()
 
     Do_Equil_Calc(equ_Recr);
     CrashPen += Equ_penalty;
-    SPR_temp = SSB_equil / equ_Recr; //  spawners per recruit at initial F
-    //  get equilibrium SSB and recruitment from SPR_temp, Recr_virgin and virgin steepness
+    SSBpR_temp = SSB_equil / equ_Recr; //  spawners per recruit at initial F
+    //  get equilibrium SSB and recruitment from SSBpR_temp, Recr_virgin and virgin steepness
     //  this is the initial year, so no time-vary effects available, so uses _virgin quantities for spawner-recruitment
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
     R1_exp = Equ_SpawnRecr_Result(2); //  set the expected recruitment equal to this equilibrium
     exp_rec(eq_yr, 1) = R1_exp;
 
@@ -1042,6 +1042,7 @@ FUNCTION void get_time_series()
           bio_yr = y;
           Do_Equil_Calc(R0_use); //  call function to do equilibrium calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
+          SSBpR_virgin_adj = SSB_use / R0_use;  //  update 
           if (fishery_on_off == 1)
           {
             Fishon = 1;
@@ -1501,6 +1502,7 @@ FUNCTION void get_time_series()
           bio_yr = y;
           Do_Equil_Calc(R0_use); //  call function to do equilibrium calculation
           SSB_use = SSB_equil;
+          SSBpR_virgin_adj = SSB_use / R0_use;  //  update 
           if (fishery_on_off == 1)
           {
             Fishon = 1;
diff --git a/SS_recruit.tpl b/SS_recruit.tpl
index 5766efce..645dbcf3 100644
--- a/SS_recruit.tpl
+++ b/SS_recruit.tpl
@@ -268,7 +268,7 @@ FUNCTION void apply_recdev(prevariable& NewRecruits, const prevariable& Recr_vir
  /*  SS_Label_FUNCTION 44 Equil_Spawn_Recr_Fxn */
 //  SPAWN-RECR:   function  Equil_Spawn_Recr_Fxn
 FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
-    const prevariable& SSB_virgin_use, const prevariable& Recr_virgin_use, const prevariable& SPR_current)
+    const prevariable& SSB_virgin_use, const prevariable& Recr_virgin_use, const prevariable& SSBpR_current)
   {
   RETURN_ARRAYS_INCREMENT();
   dvar_vector Equil_Spawn_Recr_Calc(1, 2); // values to return 1 is B_equil, 2 is R_equil
@@ -284,7 +284,7 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
   dvariable SRZ_surv;
 
   steepness = SRparm(2); //  common usage but some different
-  //  SS_Label_44.1  calc equilibrium SpawnBio and Recruitment from input SPR_current, which is spawning biomass per recruit at some given F level
+  //  SS_Label_44.1  calc equilibrium SpawnBio and Recruitment from input SSBpR_current, which is spawning biomass per recruit at some given F level
   switch (SR_fxn)
   {
     case 1: // previous placement for B-H constrained
@@ -297,7 +297,7 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
     //  SS_Label_44.1.2  Ricker
     case 2: // Ricker
     {
-      B_equil = SSB_virgin_use * (1. + (log(Recr_virgin_use / SSB_virgin_use) + log(SPR_current)) / steepness);
+      B_equil = SSB_virgin_use * (1. + (log(Recr_virgin_use / SSB_virgin_use) + log(SSBpR_current)) / steepness);
       R_equil = Recr_virgin_use * B_equil / SSB_virgin_use * mfexp(steepness * (1. - B_equil / SSB_virgin_use));
 
       break;
@@ -316,19 +316,17 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
 
   //  SS3 previously used alternative formulation: R = A*S/(B+S)
   //  converting SS3 to align with WHAM
-  //    SPR_virgin = SSB_virgin_use / Recr_virgin_use;  //  this is already defined
-      alpha = 4.0 * steepness / (SPR_virgin_adj * (1. - steepness));
-      beta = (5.0 * steepness - 1.0) / ((1 - steepness) * SSB_virgin);
-
-      // " h " << steepness << " derive "  << alpha * SPR_virgin / (4. + alpha * SPR_virgin) << " " << endl;
-      // " R0 " << Recr_virgin_use << " derive "  << 1. / beta * (alpha - 1./SPR_virgin) << endl;
-//      report5 <<" SSB_unf "<<SSB_virgin_use<<" SPR_unf "<<SPR_virgin<<" steep: "<<steepness<<" R0: "<<Recr_virgin_use << endl;
+      alpha = 4.0 * steepness / (SSBpR_virgin_adj * (1. - steepness));
+      beta = (5.0 * steepness - 1.0) / ((1 - steepness) * SSB_virgin_use);
+      // " h " << steepness << " derive "  << alpha * SSBpR_virgin / (4. + alpha * SSBpR_virgin) << " " << endl;
+      // " R0 " << Recr_virgin_use << " derive "  << 1. / beta * (alpha - 1./SSBpR_virgin) << endl;
+//      report5 <<" SSB_unf "<<SSB_virgin_use<<" SSBpR_unf "<<SSBpR_virgin<<" steep: "<<steepness<<" R0: "<<Recr_virgin_use << endl;
 //      report5 <<" derive_alpha "<<alpha<<" derive_beta "<<beta << endl;
-//      report5 << " deriv_h: " << alpha * SPR_virgin / (4. + alpha * SPR_virgin) << " derive_R0: " << 1. / beta * (alpha - (1. / SPR_virgin))<<endl;
-      B_equil = (alpha * SPR_current - 1.0) / beta;
+//      report5 << " deriv_h: " << alpha * SSBpR_virgin / (4. + alpha * SSBpR_virgin) << " derive_R0: " << 1. / beta * (alpha - (1. / SSBpR_virgin))<<endl;
+      B_equil = (alpha * SSBpR_current - 1.0) / beta;
       B_equil = posfun(B_equil, 0.0001, temp);
       R_equil = alpha * B_equil / (1.0 + beta * B_equil);
-//      report5 << "SPR_input: " << SPR_current << " B_equil: " << B_equil << " R_equil: "<<R_equil << endl<<endl;
+//      report5 << "SPR_input: " << SSBpR_current << " B_equil: " << B_equil << " R_equil: "<<R_equil << endl<<endl;
 
       break;
     }
@@ -337,17 +335,17 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
     {
       dvariable alpha = mfexp(SRparm(3));
       dvariable beta = mfexp(SRparm(4));
-      B_equil = (alpha * SPR_current - 1.0) / beta;
+      B_equil = (alpha * SSBpR_current - 1.0) / beta;
       B_equil = posfun(B_equil, 0.0001, temp);
       R_equil = alpha * B_equil / (1.0 + beta * B_equil);
-//      report5<<SPR_current<<" Beq "<<B_equil<<" Req "<<R_equil<<" alpha "<<alpha<<" beta "<<beta<<" SSB_unf "<<SSB_unf<<endl;
+//      report5<<SSBpR_current<<" Beq "<<B_equil<<" Req "<<R_equil<<" alpha "<<alpha<<" beta "<<beta<<" SSB_unf "<<SSB_unf<<endl;
       break;
     }
 
     //  SS_Label_44.1.4  constant recruitment
     case 4: // constant; no bias correction
     {
-      B_equil = SPR_current * Recr_virgin_use;
+      B_equil = SSBpR_current * Recr_virgin_use;
       R_equil = Recr_virgin_use;
       break;
     }
@@ -357,7 +355,7 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
       dvariable hockey_min = SRparm(3) * Recr_virgin_use; // min recruitment level
       //        temp=SSB_virgin_use/R0*steepness;  // spawners per recruit at inflection
       dvariable hockey_slope = (Recr_virgin_use - hockey_min) / (steepness * SSB_virgin_use); //  slope of recruitment on spawners below the inflection
-      B_equil = Join_Fxn(0.0 * SSB_virgin_use / Recr_virgin_use, SSB_virgin_use / Recr_virgin_use, SSB_virgin_use / Recr_virgin_use * steepness, SPR_current, hockey_min / ((1. / SPR_current) - hockey_slope), SPR_current * Recr_virgin_use);
+      B_equil = Join_Fxn(0.0 * SSB_virgin_use / Recr_virgin_use, SSB_virgin_use / Recr_virgin_use, SSB_virgin_use / Recr_virgin_use * steepness, SSBpR_current, hockey_min / ((1. / SSBpR_current) - hockey_slope), SSBpR_current * Recr_virgin_use);
       R_equil = Join_Fxn(0.0 * SSB_virgin_use, SSB_virgin_use, SSB_virgin_use * steepness, B_equil, hockey_min + hockey_slope * B_equil, Recr_virgin_use);
       break;
     }
@@ -366,7 +364,7 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
     {
       SRZ_0 = log(1.0 / (SSB_virgin_use / Recr_virgin_use));
       srz_min = SRZ_0 * (1.0 - steepness);
-      B_equil = SSB_virgin_use * (1. - (log(1. / SPR_current) - SRZ_0) / pow((srz_min - SRZ_0), (1. / SRparm(3))));
+      B_equil = SSB_virgin_use * (1. - (log(1. / SSBpR_current) - SRZ_0) / pow((srz_min - SRZ_0), (1. / SRparm(3))));
       SRZ_surv = mfexp((1. - pow((B_equil / SSB_virgin_use), SRparm(3))) * (srz_min - SRZ_0) + SRZ_0); //  survival
       R_equil = B_equil * SRZ_surv;
       break;
@@ -389,11 +387,11 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
       Shepherd_c2 = pow(0.2, SRparm(3));
       Hupper = 1.0 / (5.0 * Shepherd_c2);
       steepness = 0.2 + (SRparm(2) - 0.2) / (0.8) * (Hupper - 0.2);
-      Shep_top = 5.0 * steepness * (1.0 - Shepherd_c2) * (SPR_current * Recr_virgin_use) / SSB_virgin_use - (1.0 - 5.0 * steepness * Shepherd_c2);
+      Shep_top = 5.0 * steepness * (1.0 - Shepherd_c2) * (SSBpR_current * Recr_virgin_use) / SSB_virgin_use - (1.0 - 5.0 * steepness * Shepherd_c2);
       Shep_bot = 5.0 * steepness - 1.0;
       Shep_top2 = posfun(Shep_top, 0.001, temp);
-      R_equil = (SSB_virgin_use / SPR_current) * pow((Shep_top2 / Shep_bot), (1.0 / SRparm(3)));
-      B_equil = R_equil * SPR_current;
+      R_equil = (SSB_virgin_use / SSBpR_current) * pow((Shep_top2 / Shep_bot), (1.0 / SRparm(3)));
+      B_equil = R_equil * SSBpR_current;
       break;
     }
 
@@ -402,11 +400,11 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
     {
       steepness = SRparm(2);
       dvariable RkrPower = SRparm(3);
-      temp = SSB_virgin_use / (SPR_current * Recr_virgin_use);
+      temp = SSB_virgin_use / (SSBpR_current * Recr_virgin_use);
       dvariable RkrTop = pow(0.8, RkrPower) * log(temp) / log(5.0 * steepness);
       RkrTop = posfun(RkrTop, 0.000001, CrashPen);
       R_equil = temp * Recr_virgin_use * (1.0 - pow(RkrTop, 1.0 / RkrPower));
-      B_equil = R_equil * SPR_current;
+      B_equil = R_equil * SSBpR_current;
       break;
     }
 
@@ -428,11 +426,11 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
         Hupper=1.0/(5.0*Shepherd_c2);
         steepness=0.20001+((0.8)/(1.0+exp(-SRparm2))-0.2)/(0.8)*(Hupper-0.2);
 //        steep2=0.20001+(steepness-0.2)/(0.8)*(Hupper-0.2);
-        Shep_top=5.0*steepness*(1.0-Shepherd_c2)*(SPR_current*Recr_virgin_use)/SSB_virgin_use-(1.0-5.0*steepness*Shepherd_c2);
+        Shep_top=5.0*steepness*(1.0-Shepherd_c2)*(SSBpR_current*Recr_virgin_use)/SSB_virgin_use-(1.0-5.0*steepness*Shepherd_c2);
         Shep_bot=5.0*steepness-1.0;
         Shep_top2=posfun(Shep_top,0.001,temp);
-        R_equil=(SSB_virgin_use/SPR_current) * pow((Shep_top2/Shep_bot),(1.0/Shepherd_c));
-        B_equil=R_equil*SPR_current;
+        R_equil=(SSB_virgin_use/SSBpR_current) * pow((Shep_top2/Shep_bot),(1.0/Shepherd_c));
+        B_equil=R_equil*SSBpR_current;
         break;
       }
 
@@ -448,11 +446,11 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
 //   if (Recs < 0) Rec2 = 0; else Rec2 = Recs;
         steepness = 0.2 + (10.0 - 0.2)/(1+exp(-SR_parm_work(2)));
         dvariable RkrPower=exp(SR_parm_work(3));
-        temp=SSB_virgin/(SPR_current*Recr_virgin_use);
+        temp=SSB_virgin/(SSBpR_current*Recr_virgin_use);
         dvariable RkrTop =  pow(0.8,RkrPower)*log(temp)/log(5.0*steepness);
         RkrTop = posfun(RkrTop,0.000001,CrashPen);
         R_equil = temp *Recr_virgin_use * (1.0 - pow(RkrTop,1.0/RkrPower));
-        B_equil=R_equil*SPR_current;
+        B_equil=R_equil*SSBpR_current;
         break;
       }
    */
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 5413697b..a6accdd4 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -1852,13 +1852,13 @@ FUNCTION void write_bigoutput()
 
     SS2out << "# " <<endl;
     SS2out << "sigmaR: "<< sigmaR  << endl;
-    SS2out << "SPR0_(virgin): " << SPR_virgin << " #_uses_biology_from_start_year: " << styr <<endl;
+    SS2out << "SPR0_(virgin): " << SSBpR_virgin << " #_uses_biology_from_start_year: " << styr <<endl;
 
     switch (SR_fxn)
     {
       case 3: // Beverton-Holt with steepness
     {
-      alpha = 4.0 * steepness / (SPR_virgin_adj * (1. - steepness));
+      alpha = 4.0 * steepness / (SSBpR_virgin_adj * (1. - steepness));
       beta = (5.0 * steepness - 1.0) / ((1. - steepness) * SSB_virgin);
       SS2out << "Ln(R0): " << SR_parm(1) << endl << "R0: " << mfexp(SR_parm(1)) << endl;
       SS2out << "steepness: " << steepness << endl;
@@ -1870,8 +1870,8 @@ FUNCTION void write_bigoutput()
     {
       SS2out << "Ln(alpha): " << SR_parm(3) << " alpha " << mfexp(SR_parm(3)) << endl;
       SS2out << "Ln(beta): " << SR_parm(4) << " beta " << mfexp(SR_parm(4)) << endl;
-      SS2out << "ln(R0)_derived: " << log( 1. / beta * (alpha - (1. / SPR_virgin_adj))) << endl;  //  virgin R0
-      SS2out << "steepness_derived: " << alpha * SPR_virgin_adj / (4. + alpha * SPR_virgin_adj) << endl;  // steepness virgin
+      SS2out << "ln(R0)_derived: " << log( 1. / beta * (alpha - (1. / SSBpR_virgin_adj))) << endl;  //  virgin R0
+      SS2out << "steepness_derived: " << alpha * SSBpR_virgin_adj / (4. + alpha * SSBpR_virgin_adj) << endl;  // steepness virgin
       break;
     }
     case 8:
@@ -1903,7 +1903,7 @@ FUNCTION void write_bigoutput()
     { if (Bmark_Yr(k+1) > Bmark_Yr(k))
       {SS2out << "#_range_of_years_is_averaged,_so_reduces_standard_error_of_result;_do_this_only_when_timevarying_makes_necessary:  " << k << " "<< k+1 << endl;}
     }
-    SS2out << "SPR_unfished_benchmark: " << Mgmt_quant(1) / Mgmt_quant(4) << "  #_based_on_averaging_biology_over_benchmark_year_range " << endl;
+    SS2out << "SSBpR_unfished_benchmark: " << Mgmt_quant(1) / Mgmt_quant(4) << "  #_based_on_averaging_biology_over_benchmark_year_range " << endl;
     SS2out << "Bmsy/Bzero: "<< Bmsy / SSB_virgin  << " # using styr bio for Bzero" << endl;
     SS2out << "Bmsy/Bunf: "<< Bmsy / Mgmt_quant(1)  << " # using MSY's averaged bio for Bunf" << endl;
 
@@ -4912,8 +4912,8 @@ FUNCTION void SPR_profile()
 
         Do_Equil_Calc(equ_Recr);
         //  SPAWN-RECR:   calc equil spawn-recr in the SPR loop
-        SPR_temp = SSB_equil;
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SPR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        SSBpR_temp = SSB_equil;
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         Btgt_prof = Equ_SpawnRecr_Result(1);
         Btgt_prof_rec = Equ_SpawnRecr_Result(2);
         if (Btgt_prof < 0.001 || Btgt_prof_rec < 0.001)

From f6744984d21e00ee244acc48082e455c2c258741 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Fri, 20 Sep 2024 09:58:02 -0700
Subject: [PATCH 17/22] create new switch to control updating of SSBpR0

---
 SS_benchfore.tpl       | 12 +++++-----
 SS_popdyn.tpl          |  8 +++----
 SS_readcontrol_330.tpl | 53 +++++++++++++++++++++++++++++++++++++-----
 SS_write_ssnew.tpl     |  6 ++++-
 4 files changed, 62 insertions(+), 17 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 39f9e044..63d9475b 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -745,7 +745,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     }
   }
 
-  if (SR_update_SPR0 == 0)  //  use virgin biology for the spawner-recruitment R0,h calculations
+  if (SR_update_SSBpR0_bmark == 0)  //  use virgin biology for the spawner-recruitment R0,h calculations in bmark
   {
      Recr_unf = Recr_virgin;
      SSB_unf = SSB_virgin;
@@ -764,7 +764,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   {
     report5 << "SR_parms for benchmark: " << SR_parm_work << endl
             << "Benchmark biology averaged over years: " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl;
-    if ( SR_update_SPR0 == 1) report5 << "SPR0 for equilibrium spawner-recruit based on benchmark biology, not virgin biology" << endl;
+    if ( SR_update_SSBpR0_bmark == 1) report5 << "SPR0 for equilibrium spawner-recruit based on benchmark biology, not virgin biology" << endl;
     Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SSBpR_virgin); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
     report5 << " Virgin SSB, R0, SPR0: " << SSB_virgin << " " << Recr_virgin << " "  << SSBpR_virgin << " equil: " << Equ_SpawnRecr_Result << endl;
 
@@ -1064,7 +1064,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     if (show_MSY == 1)
     {
       report5 << "#" << endl;
-  if (SR_update_SPR0 == 0)  //  use virgin biology for the spawner-recruitment R0,h calculations
+  if (SR_update_SSBpR0_bmark == 0)  //  use virgin biology for the spawner-recruitment R0,h calculations
     {report5 << "Find_target_SSB/Bzero; where Bzero is Virgin SSB:" << SSB_unf << " where SSBpR_unf = " << SSBpR_unf << endl;}
   else
     {report5 << "Find_target_SSB/Bzero; where Bzero is for Bmark biology and updated SPR0: " << SSB_unf << " where SSBpR_unf = " << SSBpR_unf << endl;}
@@ -1945,7 +1945,7 @@ FUNCTION void Get_Forecast()
   dvariable OFL_catch;
   dvariable Fcast_Crash;
   dvariable totcatch;
-  dvariable R0_use;  // annually updated variable if SR_update_SPR0 == 1
+  dvariable R0_use;  // annually updated value if SR_update_SSBpR0_timeseries == 1
   dvariable SSB_use;  // selected version of SSB that gets passes to Spawn_Recr
   dvar_matrix catage_w(1, gmorph, 0, nages);
   dvar_vector tempcatch(1, Nfleet);
@@ -2594,7 +2594,7 @@ FUNCTION void Get_Forecast()
             }
             //  SPAWN-RECR:   get recruitment in forecast;  needs to be area-specific
             // SR_fxn
-            if (SR_update_SPR0 == 0) //  R0 is not time-varying
+            if (SR_update_SSBpR0_timeseries == 0) //  R0 is not time-varying
             {
               R0_use = Recr_virgin;
               SSB_use = SSB_virgin;
@@ -3234,7 +3234,7 @@ FUNCTION void Get_Forecast()
             //  SS_Label_Info_24.3.4.1 #Get recruitment from this spawning biomass
             //  SPAWN-RECR:   calc recruitment in time series; need to make this area-specific
             // SR_fxn
-            if (SR_update_SPR0 == 0) //  R0 is not time-varying
+            if (SR_update_SSBpR0_timeseries == 0) //  R0 is not time-varying
             {
               R0_use = Recr_virgin;
               SSB_use = SSB_virgin;
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index c42f907e..79b1d59f 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -697,7 +697,7 @@ FUNCTION void get_time_series()
   dvariable crashtemp1;
   dvariable interim_tot_catch;
   dvariable Z_adjuster;
-  dvariable R0_use;  // annually updated variable if SR_update_SPR0 == 1; gets passed to Spawn_Recr() function
+  dvariable R0_use;  // annually updated variable if SR_update_SSBpR0_timeseries == 1; gets passed to Spawn_Recr() function
   dvariable SSB_use;
 
   if (Do_Morphcomp > 0)
@@ -1028,7 +1028,7 @@ FUNCTION void get_time_series()
         //  SS_Label_Info_24.2.3 #Get the total recruitment produced by this spawning biomass at the beginning of the season
         //  SPAWN-RECR:   calc recruitment in time series; need to make this area-specific
         //  SR_Fxn  relevant keyword
-        if (SR_update_SPR0 == 0) //  SRparm are not time-varying
+        if (SR_update_SSBpR0_timeseries == 0) //  SRparm are not time-varying
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
@@ -1489,12 +1489,12 @@ FUNCTION void get_time_series()
         //  SS_Label_Info_24.3.4.1 #Get recruitment from this spawning biomass at some time during the season
         //  SPAWN-RECR:   calc recruitment in time series; need to make this area-specific
         //  SR_fxn
-        if (SR_update_SPR0 == 0) //  SR parms are not time-varying
+        if (SR_update_SSBpR0_timeseries == 0) //  SR parms are not time-varying
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
         }
-        else  //  update SSB_use and R0_use where will update SPR0 inside the Spawn_recr fxn
+        else  //  update SSB_use and R0_use where will update SSBpR0 inside the Spawn_recr fxn
         {
           R0_use = mfexp(SR_parm_work(1));  //  check to be sure this works when R0 is derived from B-H with alpha, beta parameters
           Fishon = 0;
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index a6ed423a..2299f346 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1943,8 +1943,21 @@
 !!echoinput<<SR_fxn<<" #_SR_function: 1=NA; 2=Ricker(2 parms); 3=BevHolt(2); 4=SCAA(2); 5=Hockey(3); 6=B-H_flattop(2); 7=Survival(3); 8=Shepherd(3); 9=Ricker_Power(3); 10=B-H_a,b(4)"<<endl;
   init_int init_equ_steepness;
 !!echoinput<<init_equ_steepness<<"  # 0/1 to use steepness in initial equ recruitment calculation"<<endl;
-  init_int sigmaR_dendep;
-!! echoinput<<sigmaR_dendep<<"  #  future feature:  0/1 to make realized sigmaR a function of SR curvature"<<endl;
+  init_int SR_update_SSBpR0_rd;
+//  SR_update_SSBpR0_rd values
+//  1 best:  update SSBpR0 for benchmark and for time series only if SRparm R0 or h (not regime) is set to have time-varying property
+//  2 incorrect, relic:  always update SSBpR0 for benchmark's use of spawner-recruitment (old, incorrect SS3 approach), but only for the time series if there is a timevary SR parm
+//  3 option:  do not update SSBpR0 (do keep start year SPR0), even if R0 or h is set to have time-varying property
+  int SR_update_SSBpR0_bmark
+  int SR_update_SSBpR0_timeseries
+ LOCAL_CALCS
+  SR_update_SSBpR0_bmark = 0;
+  SR_update_SSBpR0_timeseries = 0;
+  echoinput<<SR_update_SSBpR0_rd<<"  #  controls effect of time-varying biology on spawner-recruitment updating" << endl;
+ END_CALCS
+
+//   echoinput<<sigmaR_dendep<<"  #  future feature:  0/1 to make realized sigmaR a function of SR curvature"<<endl;
+
   ivector N_SRparm(1,10)
 !!N_SRparm.fill("{0,2,2,2,3,2,3,3,3,4}");
   int N_SRparm2
@@ -1964,7 +1977,7 @@
   int timevary_parm_cnt_SR;
   ivector timevary_SRparm(styr-3,YrMax+1);
   ivector SR_parm_timevary(1,N_SRparm2);
-  int SR_update_SPR0  // 0/1 flag to control updating of SPR0 for timevary biology 
+  int SR_update_parm  // 0/1 flag to control updating of SPR0 for timevary biology 
 
  LOCAL_CALCS
   // clang-format on
@@ -1976,7 +1989,7 @@
   SR_parm_timevary.initialize();
   SR_env_link = 0;
   SR_env_target = 0;
-  SR_update_SPR0 = 0;
+  SR_update_parm = 0;
 
   //#_SR_function: 1=null; 2=Ricker; 3=std_B-H; 4=SCAA; 5=Hockey; 6=B-H_flattop; 7=Survival_3Parm; 10=B-H with a,b "<<endl;
   if (SR_fxn == 10)
@@ -2129,8 +2142,8 @@
           timevary_SRparm(y) = timevary_pass(y);
         } // year vector for this category og MGparm
         // special consideration for impact on spawner-recruitment SPR0 calculations
-        if (SR_fxn == 10 && (SR_parm_timevary(3) > 0 || SR_parm_timevary(4) > 0) )  {SR_update_SPR0 = 1;}  //  alpha or beta is time-varying
-        else if ((SR_parm_timevary(1) > 0 || SR_parm_timevary(2) > 0) )  {SR_update_SPR0 = 1;}  //  R0 or steepness is time-varying
+        if (SR_fxn == 10 && (SR_parm_timevary(3) > 0 || SR_parm_timevary(4) > 0) )  {SR_update_parm = 1;}  //  alpha or beta is time-varying
+        else if ((SR_parm_timevary(1) > 0 || SR_parm_timevary(2) > 0) )  {SR_update_parm = 1;}  //  R0 or steepness is time-varying
       }
     }
   N_SRparm3 = N_SRparm2;
@@ -2142,6 +2155,34 @@
     echoinput << " SR timevary_parm_cnt start and end " << timevary_parm_start_SR << " " << timevary_parm_cnt_SR << endl;
     echoinput << "link to timevary parms:  " << SR_parm_timevary << endl;
   }
+
+//  SR_update_SSBpR0_rd values
+//  1 best:  update SSBpR0 for benchmark and for time series only if SRparm R0 or h (not regime) is set to have time-varying property
+//  2 incorrect, relic:  always update SSBpR0 for benchmark's use of spawner-recruitment (old, incorrect SS3 approach), but only for the time series if there is a timevary SR parm
+//  3 option:  do not update SSBpR0 (do keep start year SPR0), even if R0 or h is set to have time-varying property
+
+  switch (SR_update_SSBpR0_rd)
+  {
+  case 0:
+    if(timevary_MG_firstyr < YrMax)  // timevary biology exists and SR_update not set
+    {
+      warnstream << "user must select 1, 2, or 3 for updating SPR0 flag (formerly labelled future feature in SR input) because there is time-varying biology";
+      write_message (FATAL, 0); // EXIT!
+    }
+    break;
+  case 1:
+    SR_update_SSBpR0_bmark = 1 * SR_update_parm;  //  but conditional on SRparm_timevary, so update value there
+    SR_update_SSBpR0_timeseries = 1 * SR_update_parm;
+    break;
+  case 2:
+    SR_update_SSBpR0_bmark = 1;
+    SR_update_SSBpR0_timeseries = 0;
+    break;
+  case 3:
+    SR_update_SSBpR0_bmark = 0;
+    SR_update_SSBpR0_timeseries = 0;
+    break;
+  }
   echoinput << "SR_Npar and N_SRparm2 and N_SRparm3:  " << N_SRparm(SR_fxn) << " " << N_SRparm2 << " " << N_SRparm3 << endl;
   // clang-format off
  END_CALCS
diff --git a/SS_write_ssnew.tpl b/SS_write_ssnew.tpl
index 38a9a5ec..fdd984be 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -2136,7 +2136,11 @@ FUNCTION void write_nucontrol()
   report4 << "#" << endl;
   report4 << SR_fxn << " #_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" << endl;
   report4 << init_equ_steepness << "  # 0/1 to use steepness in initial equ recruitment calculation" << endl;
-  report4 << sigmaR_dendep << "  #  future feature:  0/1 to make realized sigmaR a function of SR curvature" << endl;
+  report4 << SR_update_SSBpR0_rd <<  "#  SR_update_SSBpR0" << endl <<
+  "#  0 - OK, but only if no timevary biology or SR parm" << endl <<
+  "#  1 - best: update SSBpR0 for benchmark and for time series only if SRparm R0 or h (not regime) is set to have time-varying property" << endl <<
+  "#  2 - incorrect (old, incorrect SS3 approach):  always update SSBpR0 for benchmark's use of spawner-recruitment, but only for the time series if there is a timevary SR parm" << endl <<
+  "#  3 - option:  do not update SSBpR0 (do keep start year SSBpR0), even if R0 or h is set to have time-varying property" << endl << "#" << endl;
   report4 << "#_          LO            HI          INIT         PRIOR         PR_SD       PR_type      PHASE    env-var    use_dev   dev_mnyr   dev_mxyr     dev_PH      Block    Blk_Fxn #  parm_name" << endl;
   report4.unsetf(std::ios_base::fixed);
   report4.unsetf(std::ios_base::floatfield);

From e9b838d4472651266c61e4f1e7f415ffd2af5b26 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Fri, 4 Oct 2024 14:58:13 -0700
Subject: [PATCH 18/22] too many changes

---
 SS_benchfore.tpl       |   82 +--
 SS_global.tpl          |    4 +-
 SS_param.tpl           |  250 ++++----
 SS_popdyn.tpl          | 1229 +++++++++++++++-----------------------
 SS_proced.tpl          |    6 +-
 SS_readcontrol_330.tpl |   21 +-
 SS_readdata_330.tpl    |    4 +-
 SS_write.tpl           |    2 +-
 SS_write_report.tpl    |   44 +-
 SS_write_ssnew.tpl     | 1267 +++++++++++++++-------------------------
 10 files changed, 1154 insertions(+), 1755 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 63d9475b..9bcb1edb 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -4,6 +4,15 @@
 // SS_Label_file  # * <u>get_forecast()</u>  //  calculates forecast quantities, includes all popdy characteristics of the time series, writes forecast-report.sso
 // SS_Label_file  #
 
+// Terminology
+// SSB refers to spawning stock biomass, calculated from reproductive output at age (fec()) and numbers-at-age at spawn_month in spawn_seas
+// SSBpR refers to SSB per recruit calculated with equilibrium age composition in equil_calc
+// SPR refers to spawner potential ratio which is the ratio of SSBpR at some level of F to SSBpR with F = 0
+
+// SSBpR_virgin  calculated and reported, but never used
+// SSBpR_virgin_adj  used only in the alpha-beta spawner-recruitment.  _adj means could be updated if SR_update_SSBpR0_timeseries == 1.  Also used to get alpha in equil_spawn_recr B-H
+//  but note that also uses SSB_virgin_use.  So need to align _use with _adj
+
 FUNCTION void setup_Benchmark()  // and forecast
   {
   //  SS_Label_Info_7.5 #Get averages from selected years to use in forecasts
@@ -113,12 +122,7 @@ FUNCTION void setup_Benchmark()  // and forecast
         }
     }
     t = styr + (endyr + 1 - styr) * nseas + spawn_seas - 1;
-    fec = Wt_Age_t(t, -2);
-    //        for (g=1;g<=gmorph;g++)
-    //        if(use_morph(g)>0 && sx(g)==1)
-    //        {
-    //          fec(g)=save_sel_num(t,0,g);
-    //       }
+//    fec = Wt_Age_t(t, -2);  this will always be overwritten, so deleting
 
     if (Fcast_Loop_Control(3) == 3) //  using mean recr_dist from range of years
     {
@@ -569,7 +573,6 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   eq_yr = y;
   t_base = y + (y - styr) * nseas - 1;
   bio_t_base = styr + (bio_yr - styr) * nseas - 1;
-
   //  set the Hrate for bycatch fleets so not scaled with other fleets
   //  bycatch_F(f,s) is created here for use in forecast
   for (f = 1; f <= Nfleet; f++)
@@ -643,6 +646,8 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       Make_AgeLength_Key(s, subseas);
 
       //  SPAWN-RECR:   call make_fecundity for benchmarks
+      //  this means that any calculation of SSB in benchmark will use the updated fec
+      //  but SSBpR0 will only use that updated fec if SR_update_SSBpR0_bmark == 1
       if (s == spawn_seas)
       {
         {
@@ -744,7 +749,6 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       SR_parm_work(j) = temp / (Bmark_Yr(10) - Bmark_Yr(9) + 1.);
     }
   }
-
   if (SR_update_SSBpR0_bmark == 0)  //  use virgin biology for the spawner-recruitment R0,h calculations in bmark
   {
      Recr_unf = Recr_virgin;
@@ -763,14 +767,17 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   if (show_MSY == 1)
   {
     report5 << "SR_parms for benchmark: " << SR_parm_work << endl
-            << "Benchmark biology averaged over years: " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl;
-    if ( SR_update_SSBpR0_bmark == 1) report5 << "SPR0 for equilibrium spawner-recruit based on benchmark biology, not virgin biology" << endl;
+            << "Benchmark biology averaged over years: " << Bmark_Yr(1) << " " << Bmark_Yr(2) << " flag for updating SSBpR0 = " << SR_update_SSBpR0_bmark << endl;
     Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SSBpR_virgin); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
     report5 << " Virgin SSB, R0, SPR0: " << SSB_virgin << " " << Recr_virgin << " "  << SSBpR_virgin << " equil: " << Equ_SpawnRecr_Result << endl;
-
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_unf); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    report5 << " Benchmark SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << SSBpR_unf << " equil: " << Equ_SpawnRecr_Result << endl;
-    report5 << "Repro_output_by_age_for_morph_1: " << fec(1) << endl;
+    if ( SR_update_SSBpR0_bmark == 1)
+    {
+      report5 << "SPR0 for equilibrium spawner-recruit based on benchmark biology, not virgin biology" << endl;
+      Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_unf); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+      report5 << " Benchmark SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << SSBpR_unf << " equil: " << Equ_SpawnRecr_Result << endl;
+    }
+    report5 << 0 << " y: " << y << " Repro_output_by_age_for_morph_1 bench " << fec(1) << endl;
+//    report5 << "Repro_output_by_age_for_morph_1: " << fec(1) << endl;
 
   }
   SR_parm_work(N_SRparm2 + 1) = SSB_unf;
@@ -1849,7 +1856,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     report5 << "ann_F " << Mgmt_quant(10) << endl;
     report5 << "Exploit(Catch_dead/B_smry) " << YPR_spr_dead / Vbio1_spr << endl;
     report5 << "Recruits " << Bspr_rec << endl;
-    report5 << "SPBio " << Bspr << " " << Bspr / Bspr_rec << endl;
+    report5 << "SSBio " << Bspr << " " << Bspr / Bspr_rec << endl;
     report5 << "Catch_encountered " << YPR_spr_enc * Bspr_rec << " " << YPR_spr_enc << endl;
     report5 << "Catch_dead " << YPR_spr_dead * Bspr_rec << " " << YPR_spr_dead << endl;
     report5 << "Catch_retain " << YPR_spr_ret * Bspr_rec << " " << YPR_spr_ret << endl;
@@ -1869,7 +1876,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       report5 << "ann_F " << Mgmt_quant(7) << endl;
       report5 << "Exploit(Catch_dead/B_smry) " << YPR_Btgt_dead / Vbio1_Btgt << endl;
       report5 << "Recruits@F0.1 " << Btgt_Rec << endl;
-      report5 << "SPBio " << Btgt << " " << Btgt / Btgt_Rec << endl;
+      report5 << "SSBio " << Btgt << " " << Btgt / Btgt_Rec << endl;
       report5 << "Catch_encountered " << YPR_Btgt_enc * Btgt_Rec << " " << YPR_Btgt_enc << endl;
       report5 << "Catch_dead " << YPR_Btgt_dead * Btgt_Rec << " " << YPR_Btgt_dead << endl;
       report5 << "Catch_retain " << YPR_Btgt_ret * Btgt_Rec << " " << YPR_Btgt_ret << endl;
@@ -1889,7 +1896,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       report5 << "ann_F " << Mgmt_quant(7) << endl;
       report5 << "Exploit(Catch_dead/B_smry) " << YPR_Btgt_dead / Vbio1_Btgt << endl;
       report5 << "Recruits " << Btgt_Rec << endl;
-      report5 << "SPBio " << Btgt << " " << Btgt / Btgt_Rec << endl;
+      report5 << "SSBio " << Btgt << " " << Btgt / Btgt_Rec << endl;
       report5 << "Catch_encountered " << YPR_Btgt_enc * Btgt_Rec << " " << YPR_Btgt_enc << endl;
       report5 << "Catch_dead " << YPR_Btgt_dead * Btgt_Rec << " " << YPR_Btgt_dead << endl;
       report5 << "Catch_retain " << YPR_Btgt_ret * Btgt_Rec << " " << YPR_Btgt_ret << endl;
@@ -1906,9 +1913,9 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     report5 << "ann_F " << Mgmt_quant(14) << endl;
     report5 << "Exploit(Catch/Bsmry) " << MSY / (Vbio1_MSY * Recr_msy) << endl;
     report5 << "Recruits@MSY " << Recr_msy << endl;
-    report5 << "SPBmsy " << Bmsy << " " << Bmsy / Recr_msy << endl;
-    report5 << "SPBmsy/SPB_virgin " << Bmsy / SSB_virgin << endl;
-    report5 << "SPBmsy/SPB_unfished " << Bmsy / SSB_unf << endl;
+    report5 << "SSBmsy " << Bmsy << " " << Bmsy / Recr_msy << endl;
+    report5 << "SSBmsy/SSB_virgin " << Bmsy / SSB_virgin << endl;
+    report5 << "SSBmsy/SSB_unfished " << Bmsy / SSB_unf << endl;
     report5 << "MSY_for_optimize " << MSY << " " << MSY / Recr_msy << endl;
     report5 << "MSY_encountered " << YPR_msy_enc * Recr_msy << " " << YPR_msy_enc << endl;
     report5 << "MSY_dead " << YPR_msy_dead * Recr_msy << " " << YPR_msy_dead << endl;
@@ -1934,6 +1941,8 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
            << " " << Vbio1_MSY * Recr_msy << " # " << endl;
   }
   write_bodywt = write_bodywt_save;
+    report5 << 0 << " y: " << y << " Repro_output_by_age_for_morph_1 end_bench: " << fec(1) << endl;
+//    report5 << "Repro_output_by_age_for_morph_1_after_benchmark: " << fec(1) << endl;
   } //  end benchmarks
 
 FUNCTION void Get_Forecast()
@@ -1945,8 +1954,6 @@ FUNCTION void Get_Forecast()
   dvariable OFL_catch;
   dvariable Fcast_Crash;
   dvariable totcatch;
-  dvariable R0_use;  // annually updated value if SR_update_SSBpR0_timeseries == 1
-  dvariable SSB_use;  // selected version of SSB that gets passes to Spawn_Recr
   dvar_matrix catage_w(1, gmorph, 0, nages);
   dvar_vector tempcatch(1, Nfleet);
   imatrix Do_F_tune(t_base, TimeMax_Fcast_std, 1, Nfleet); //  flag for doing F from catch
@@ -2220,6 +2227,8 @@ FUNCTION void Get_Forecast()
 
   for (int Fcast_Loop1 = 1; Fcast_Loop1 <= jloop; Fcast_Loop1++) //   for different forecast conditions
   {
+    report5 << Fcast_Loop1 << " y: " << 0 << " Repro_output_by_age_for_morph_1 top_forecast: " << fec(1) << endl;
+
     switch (Fcast_Loop1) //  select which ABC_loops to use
     {
       case 1: // do OFL only
@@ -2290,7 +2299,7 @@ FUNCTION void Get_Forecast()
           get_growth3(y, t, s, subseas); //  in case needed for Lorenzen M
           Make_AgeLength_Key(s, subseas); //  which also updates Wt_Age_beg, etc.
         }
-        if (s == spawn_seas)
+//        if (s == spawn_seas)  //  
         {
           if (WTage_rd == 1)
           {
@@ -2301,12 +2310,12 @@ FUNCTION void Get_Forecast()
           }
           else
           {
-            get_mat_fec();
+            get_mat_fec();  // does spawnseas and stores in wt_Age_t(t, -2)
           }
         }
       }
     }
-
+    report5 << Fcast_Loop1 << " y: " << y << " updated_Repro_output_by_age_for_morph_1 endyr: " << fec(1) << endl;
     for (y = endyr + 1; y <= YrMax; y++)
     {
       t_base = styr + (y - styr) * nseas - 1;
@@ -2496,6 +2505,7 @@ FUNCTION void Get_Forecast()
                   Wt_Age_mid(s, g) = ALK(ALK_idx, g) * wt_len(s, GP(g)); // use for fisheries with no size selectivity
                 }
             }
+    report5 << Fcast_Loop1 << " y: " << y << " updated_Repro_output_by_age_for_morph_1 annual: " << fec(1) << endl;
             Wt_Age_t(t, 0) = Wt_Age_beg(s);
             for (g = 1; g <= gmorph; g++)
               if (use_morph(g) > 0)
@@ -2577,18 +2587,18 @@ FUNCTION void Get_Forecast()
 
             if (Hermaphro_Option != 0) // get male biomass
             {
-              MaleSPB(y).initialize();
+              MaleSSB(y).initialize();
               for (p = 1; p <= pop; p++)
               {
                 for (g = 1; g <= gmorph; g++)
                   if (sx(g) == 2 && use_morph(g) > 0) //  male; all assumed to be mature
                   {
-                    MaleSPB(y, p, GP4(g)) += Wt_Age_t(t, 0, g) * natage(t, p, g); // accumulates SSB by area and by growthpattern
+                    MaleSSB(y, p, GP4(g)) += Wt_Age_t(t, 0, g) * natage(t, p, g); // accumulates SSB by area and by growthpattern
                   }
               }
-              if (Hermaphro_maleSPB > 0.0) // add MaleSPB to female SSB
+              if (Hermaphro_maleSSB > 0.0) // add MaleSSB to female SSB
               {
-                SSB_current += Hermaphro_maleSPB * sum(MaleSPB(y));
+                SSB_current += Hermaphro_maleSSB * sum(MaleSSB(y));
                 SSB_yr(y) = SSB_current;
               }
             }
@@ -2617,7 +2627,6 @@ FUNCTION void Get_Forecast()
               }
               SSB_use = SSB_equil;
             }
-
             Recruits = Spawn_Recr(SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr
             if (SR_fxn != 7) apply_recdev(Recruits, R0_use); //  apply recruitment deviation
             if (Fcast_Loop1 < Fcast_Loop_Control(2)) //  use expected recruitment  this should include environ effect - CHECK THIS
@@ -3216,18 +3225,18 @@ FUNCTION void Get_Forecast()
 
             if (Hermaphro_Option != 0) // get male biomass
             {
-              MaleSPB(y).initialize();
+              MaleSSB(y).initialize();
               for (p = 1; p <= pop; p++)
               {
                 for (g = 1; g <= gmorph; g++)
                   if (sx(g) == 2 && use_morph(g) > 0) //  male; all assumed to be mature
                   {
-                    MaleSPB(y, p, GP4(g)) += Wt_Age_t(t, 0, g) * elem_prod(natage(t, p, g), mfexp(-Z_rate(t, p, g) * spawn_time_seas)); // accumulates SSB by area and by growthpattern
+                    MaleSSB(y, p, GP4(g)) += Wt_Age_t(t, 0, g) * elem_prod(natage(t, p, g), mfexp(-Z_rate(t, p, g) * spawn_time_seas)); // accumulates SSB by area and by growthpattern
                   }
               }
-              if (Hermaphro_maleSPB > 0.0) // add MaleSPB to female SSB
+              if (Hermaphro_maleSSB > 0.0) // add MaleSSB to female SSB
               {
-                SSB_current += Hermaphro_maleSPB * sum(MaleSPB(y));
+                SSB_current += Hermaphro_maleSSB * sum(MaleSSB(y));
                 SSB_yr(y) = SSB_current;
               }
             }
@@ -3666,7 +3675,7 @@ FUNCTION void Get_Forecast()
         Smry_Table(y, 4) = Mgmt_quant(Fcast_catch_start + y - endyr);
         eq_yr = y;
         equ_Recr = Recr_unf;
-        bio_yr = endyr;
+        bio_yr = y;
         Fishon = 0;
         Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation
 
@@ -3674,7 +3683,7 @@ FUNCTION void Get_Forecast()
         Smry_Table(y, 13) = GenTime;
         if( SR_fxn == 10 )
         {
-          temp = SSB_equil / equ_Recr;  //  current year's SPB/R with current biology at age
+          temp = SSB_equil / equ_Recr;  //  current year's SSB/R with current biology at age
           alpha = mfexp(SR_parm_work(3));
           beta = mfexp(SR_parm_work(4));
           SR_parm_byyr(y, 2) =  alpha * temp / (4. + alpha * temp);  //  implied steepness
@@ -3682,6 +3691,7 @@ FUNCTION void Get_Forecast()
         }
         Fishon = 1;
         Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation
+//             warning <<y<<"  SSB_virgin: " << SSB_virgin<< "SSB_use: "<<SSB_use<<" SSB_unf: "<<SSB_unf<<" fec(15): "<<fec(1,15)<<endl;
         if (STD_Yr_Reverse_Ofish(y) > 0)
           SPR_std(STD_Yr_Reverse_Ofish(y)) = SSB_equil / Smry_Table(y, 11);
         Smry_Table(y, 9) = totbio;
diff --git a/SS_global.tpl b/SS_global.tpl
index 4fa5dcfb..c18dc5af 100644
--- a/SS_global.tpl
+++ b/SS_global.tpl
@@ -1270,10 +1270,10 @@ REPORT_SECTION
     if (Do_TG > 0)
       report << " TG-fleetcomp " << TG_like1 << endl
              << " TG-negbin " << TG_like2 << endl;
-    report << " -log(L): " << obj_fun << "  Spbio: " << value(SSB_yr(styr)) << " " << value(SSB_yr(endyr)) << endl;
+    report << " -log(L): " << obj_fun << "  SSBio: " << value(SSB_yr(styr)) << " " << value(SSB_yr(endyr)) << endl;
 
     report << endl
-           << "Year Spbio Recruitment" << endl;
+           << "Year SSBio Recruitment" << endl;
     report << "Virg " << SSB_yr(styr - 2) << " " << exp_rec(styr - 2, 4) << endl;
     report << "Init " << SSB_yr(styr - 1) << " " << exp_rec(styr - 1, 4) << endl;
     for (y = styr; y <= endyr; y++)
diff --git a/SS_param.tpl b/SS_param.tpl
index 43a4206c..ed5e5a29 100644
--- a/SS_param.tpl
+++ b/SS_param.tpl
@@ -13,53 +13,52 @@ INITIALIZATION_SECTION
 PARAMETER_SECTION
 //  {
 //  SS_Label_Info_5.0.1 #Setup convergence critera and max func evaluations
- LOCAL_CALCS
-  // clang-format on
-  // set the filename to all ADMB output files to "base_modelname.[ext]"
-  //  where base_modelname can be read from command line with command modelname followed by text
-  //  e.g.  ss3_win.exe -nohess -stopph 3  modelname ss4you
-  //  if requested modelname.par is not found, then will attempt to read from ss3.par then ss.par
-  //  whatever name is read, the write will be to modelname.par.  Which has default of ss3.par
-  ad_comm::adprogram_name = base_modelname;
-  echoinput << "Begin setting up parameters" << endl;
-  cout << "Begin setting up parameters ... ";
-  if (readparfile >= 1)
-  {
-    anystring = base_modelname + ".par";
-    cout << " read parm file: " << anystring << endl;
-
+LOCAL_CALCS
+// clang-format on
+// set the filename to all ADMB output files to "base_modelname.[ext]"
+//  where base_modelname can be read from command line with command modelname followed by text
+//  e.g.  ss3_win.exe -nohess -stopph 3  modelname ss4you
+//  if requested modelname.par is not found, then will attempt to read from ss3.par then ss.par
+//  whatever name is read, the write will be to modelname.par.  Which has default of ss3.par
+ad_comm::adprogram_name = base_modelname;
+echoinput << "Begin setting up parameters" << endl;
+cout << "Begin setting up parameters ... ";
+if (readparfile >= 1) {
+  anystring = base_modelname + ".par";
+  cout << " read parm file: " << anystring << endl;
+
+  ifstream fin(anystring);
+  if (fin.fail()) {
+    cout << " no find, try ss3.par" << endl;
+    anystring = "ss3.par";
     ifstream fin(anystring);
-    if(fin.fail() ) {
-      cout << " no find, try ss3.par" << endl;
-      anystring = "ss3.par";
-      ifstream fin(anystring);
-      if(fin.fail() ) {
+    if (fin.fail()) {
       cout << " no find, try ss.par" << endl;
       anystring = "ss.par";
       ifstream fin(anystring);
-      if(fin.fail() ) {
-    	  warnstream << "could not find ss3.par, ss.par, or requested parfile " << base_modelname << ".par";
-    	  write_message(FATAL, 0);
+      if (fin.fail()) {
+        warnstream << "could not find ss3.par, ss.par, or requested parfile " << base_modelname << ".par";
+        write_message(FATAL, 0);
       }
-    }}
-    cout << " found "<<anystring<<endl;
-
-    ad_comm::change_pinfile_name(anystring);
+    }
   }
-
-  maximum_function_evaluations.allocate(func_eval.indexmin(), func_eval.indexmax());
-  maximum_function_evaluations = func_eval;
-  convergence_criteria.allocate(func_conv.indexmin(), func_conv.indexmax());
-  convergence_criteria = func_conv;
-  if (do_ageK == 1) //  need for age-specific K
-  {
-    k = nages;
-  } // use for dimension of VBK()
-  else
-  {
-    k = 0;
-  }
-  // clang-format off
+  cout << " found " << anystring << endl;
+
+  ad_comm::change_pinfile_name(anystring);
+}
+
+maximum_function_evaluations.allocate(func_eval.indexmin(), func_eval.indexmax());
+maximum_function_evaluations = func_eval;
+convergence_criteria.allocate(func_conv.indexmin(), func_conv.indexmax());
+convergence_criteria = func_conv;
+if (do_ageK == 1) //  need for age-specific K
+{
+  k = nages;
+} // use for dimension of VBK()
+else {
+  k = 0;
+}
+// clang-format off
  END_CALCS
 
 !! //  SS_Label_Info_5.0.2 #Create dummy_parm that will be estimated even if turn_off_phase is set to 0
@@ -112,23 +111,25 @@ PARAMETER_SECTION
   4darray Save_PopBio(styr-3*nseas,TimeMax_Fcast_std+nseas,1,2*pop,1,gmorph,0,nages)
 
  LOCAL_CALCS
-  // clang-format on
-  // If empirical wt-at-age is used, maturity and fecundity vectors are set to a distinctive value of 0.5
-  // If parameters are used, then the calcs could be age-based or length-based or both, so start with default value of 1.0
-  // These calculations happen in function get_mat_fec() in file SS_biofxn.tpl
-   if (WTage_rd == 1 || Maturity_Option == 4 || Maturity_Option == 5 ) {
-     mat_len = 0.5;
-     mat_age = 0.5;
-     mat_fec_len = 0.5;
-     fec_len = 0.5;
-   }
-   else {
-     mat_len = 1.0;
-     mat_age = 1.0;
-     mat_fec_len = 1.0;
-     fec_len = 1.0;
-   }    
-  // clang-format off
+    // clang-format on
+    // If empirical wt-at-age is used, maturity and fecundity vectors are set to a distinctive value of 0.5
+    // If parameters are used, then the calcs could be age-based or length-based or both, so start with default value of 1.0
+    // These calculations happen in function get_mat_fec() in file SS_biofxn.tpl
+    if (WTage_rd == 1 || Maturity_Option == 4 || Maturity_Option == 5)
+{
+  mat_len = 0.5;
+  mat_age = 0.5;
+  mat_fec_len = 0.5;
+  fec_len = 0.5;
+}
+else
+{
+  mat_len = 1.0;
+  mat_age = 1.0;
+  mat_fec_len = 1.0;
+  fec_len = 1.0;
+}
+// clang-format off
  END_CALCS
 
   3darray age_age(0,N_ageerr+store_agekey_add,1,n_abins2,0,gender*nages+gender-1)
@@ -159,7 +160,7 @@ PARAMETER_SECTION
   3darray recr_dist_endyr(1,N_GP*gender,1,N_settle_timings,1,pop);
 !!//  SS_Label_Info_5.1.2 #Create SR_parm vector, recruitment vectors
   init_bounded_number_vector SR_parm(1,N_SRparm3,SR_parm_LO,SR_parm_HI,SR_parm_PH)
-  matrix SR_parm_byyr(styr-3,YrMax,1,N_SRparm2+1)  //  R0, steepness, parm3, sigmar, rec_dev_offset, R1, rho, SPB   Time_vary implementation of spawner-recruitment
+  matrix SR_parm_byyr(styr-3,YrMax,1,N_SRparm2+1)  //  R0, steepness, parm3, sigmar, rec_dev_offset, R1, rho, SSB   Time_vary implementation of spawner-recruitment
   vector SR_parm_virg(1,N_SRparm2+1)
   vector SR_parm_work(1,N_SRparm2+1)
   number two_sigmaRsq;
@@ -171,31 +172,28 @@ PARAMETER_SECTION
   number rho;
   number dirichlet_Parm;
  LOCAL_CALCS
-  // clang-format on
-  Ave_Size.initialize();
-  //  if(SR_parm(N_SRparm2)!=0.0 || SR_parm_PH(N_SRparm2)>0) {SR_autocorr=1;} else {SR_autocorr=0;}  // flag for recruitment autocorrelation
-  if (do_recdev == 1)
-  {
-    k = recdev_start;
-    j = recdev_end;
-    s = 1;
-    p = -1;
-  }
-  else if (do_recdev >= 2)
-  {
-    s = recdev_start;
-    p = recdev_end;
-    k = 1;
-    j = -1;
-  }
-  else
-  {
-    s = 1;
-    p = -1;
-    k = 1;
-    j = -1;
-  }
-  // clang-format off
+// clang-format on
+Ave_Size.initialize();
+//  if(SR_parm(N_SRparm2)!=0.0 || SR_parm_PH(N_SRparm2)>0) {SR_autocorr=1;} else {SR_autocorr=0;}  // flag for recruitment autocorrelation
+if (do_recdev == 1) {
+  k = recdev_start;
+  j = recdev_end;
+  s = 1;
+  p = -1;
+}
+else if (do_recdev >= 2) {
+  s = recdev_start;
+  p = recdev_end;
+  k = 1;
+  j = -1;
+}
+else {
+  s = 1;
+  p = -1;
+  k = 1;
+  j = -1;
+}
+// clang-format off
  END_CALCS
 
 //  vector biasadj(styr-nages,YrMax)  // biasadj as used; depends on whether a recdev is estimated or not
@@ -211,26 +209,22 @@ PARAMETER_SECTION
   vector recdev(recdev_first,YrMax);
 
  LOCAL_CALCS
-  // clang-format on
-  if (do_recdev == 0)
-  {
-    s = -1;
-  }
-  else
-  {
-    s = YrMax;
-  }
-  if (Do_Impl_Error > 0)
-  {
-    k = Fcast_recr_PH2;
-    j = YrMax;
-  }
-  else
-  {
-    k = -1;
-    j = -1;
-  }
-  // clang-format off
+// clang-format on
+if (do_recdev == 0) {
+  s = -1;
+}
+else {
+  s = YrMax;
+}
+if (Do_Impl_Error > 0) {
+  k = Fcast_recr_PH2;
+  j = YrMax;
+}
+else {
+  k = -1;
+  j = -1;
+}
+// clang-format off
  END_CALCS
   init_bounded_vector Fcast_recruitments(recdev_end+1,s,recdev_LO,recdev_HI,Fcast_recr_PH2)
   init_bounded_vector Fcast_impl_error(endyr+1,j,-1,1,k)
@@ -241,9 +235,12 @@ PARAMETER_SECTION
   number Recr_virgin
   number SSB_vir_LH
 
-  number SSB_unf
+  number SSB_unf //  SSB unfished, based on benchmark biology
   number Recr_unf
+  number SSB_use
+  number R0_use;  // annually updated value if SR_update_SSBpR0_timeseries == 1
 
+  number SSB_deplete //  SSB that will be used as denominator for depletion calculations and as basis for control rule inflection
   number SSB_current;                            // Spawning biomass
   number SSB_equil;
 
@@ -322,7 +319,7 @@ PARAMETER_SECTION
 !!k=0;
 !!if(Hermaphro_Option!=0) k=1;
 
-  3darray MaleSPB(styr-3,YrMax*k,1,pop,1,N_GP)         //Male Spawning biomass
+  3darray MaleSSB(styr-3,YrMax*k,1,pop,1,N_GP)         //Male Spawning biomass
 
   matrix SSB_equil_pop_gp(1,pop,1,N_GP);
   matrix MaleSSB_equil_pop_gp(1,pop,1,N_GP);
@@ -388,16 +385,15 @@ PARAMETER_SECTION
 
 
  LOCAL_CALCS
-  // clang-format on
-  if (N_Fparm > 0) // continuous F
-  {
-    k = N_Fparm;
-  }
-  else
-  {
-    k = -1;
-  }
-  // clang-format off
+// clang-format on
+if (N_Fparm > 0) // continuous F
+{
+  k = N_Fparm;
+}
+else {
+  k = -1;
+}
+// clang-format off
  END_CALCS
  //  defining F_rate as number_vector allows for Fparm_PH to be element specific
   init_bounded_number_vector F_rate(1,k,0.,max_harvest_rate,Fparm_PH_dim)
@@ -493,9 +489,9 @@ PARAMETER_SECTION
   number overdisp     // overdispersion
 
  LOCAL_CALCS
-   // clang-format on
-   k = Do_TG * (3 * N_TG + 2 * Nfleet1);
-  // clang-format off
+        // clang-format on
+        k = Do_TG * (3 * N_TG + 2 * Nfleet1);
+// clang-format off
  END_CALCS
 
   init_bounded_number_vector TG_parm(1,k,TG_parm_LO,TG_parm_HI,TG_parm_PH);
@@ -508,12 +504,12 @@ PARAMETER_SECTION
   matrix parm_timevary(1,timevary_cnt,styr-1,YrMax);  //  time series of adjusted parm values for block and trend
 
  LOCAL_CALCS
-  // clang-format on
-  if (Do_Forecast > 0)
-    k = TimeMax_Fcast_std + nseas;
-  else
-    k = TimeMax + nseas;
-  // clang-format off
+// clang-format on
+if (Do_Forecast > 0)
+  k = TimeMax_Fcast_std + nseas;
+else
+  k = TimeMax + nseas;
+// clang-format off
  END_CALCS
 
 !!//  SS_Label_Info_5.1.7 #Create arrays for storing derived selectivity quantities for use in mortality calculations
@@ -599,8 +595,8 @@ PARAMETER_SECTION
   number equ_M_std
   
 !!//  SS_Label_Info_5.1.8 #Create matrix called smry to store derived quantities of interest
-  matrix Smry_Table(styr-3,YrMax,1,17);
-  // 1=totbio, 2=smrybio, 3=smrynum, 4=enc_catch, 5=dead_catch, 6=ret_catch, 7=spbio, 8=recruit,
+  matrix Smry_Table(styr-3,YrMax,1,20+2*gmorph);
+  // 1=totbio, 2=smrybio, 3=smrynum, 4=enc_catch, 5=dead_catch, 6=ret_catch, 7=SSBio, 8=recruit,
   // 9=equ_totbio, 10=equ_smrybio, 11=equ_SSB_virgin, 12=equ_S1, 13=Gentime, 14=YPR, 15=meanage_spawners, 16=meanage_smrynums, 17=meanage_catch
  
 
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 79b1d59f..1004e9ab 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -6,7 +6,7 @@
 // SS_Label_file  #
 
 FUNCTION void setup_recdevs()
-  {
+{
   //  SS_Label_Info_7.1 #Set up recruitment bias_adjustment vector
   sigmaR = SR_parm(N_SRparm(SR_fxn) + 1);
   two_sigmaRsq = 2.0 * sigmaR * sigmaR;
@@ -14,45 +14,35 @@ FUNCTION void setup_recdevs()
 
   biasadj.initialize();
 
-  if (SR_fxn == 4 || do_recdev == 0)
-  {
+  if (SR_fxn == 4 || do_recdev == 0) {
     // keep all at 0.0 if not using SR fxn
   }
   //    else if (mceval_phase() || initial_params::mc_phase==1 || recdev_adj(5)<0.0)
-  else if (mceval_phase() || initial_params::mc_phase == 1)
-  {
+  else if (mceval_phase() || initial_params::mc_phase == 1) {
     //      biasadj=1.0;
     biasadj = recdev_doit; //  sets to 1.0 for the years or initial ages with estimated recruitments
   }
-  else
-  {
+  else {
     if (recdev_do_early > 0 && recdev_options(2) >= 0) //  do logic on basis of recdev_options(2), which is read, not recdev_PH which can be reset to a neg. value
     {
-      for (i = recdev_early_start; i <= recdev_early_end; i++)
-      {
+      for (i = recdev_early_start; i <= recdev_early_end; i++) {
         if (i >= styr - nages)
           biasadj(i) = biasadj_full(i);
       }
     }
-    if (do_recdev > 0 && recdev_PH_rd >= 0)
-    {
-      for (i = recdev_start; i <= recdev_end; i++)
-      {
+    if (do_recdev > 0 && recdev_PH_rd >= 0) {
+      for (i = recdev_start; i <= recdev_end; i++) {
         if (i >= styr - nages)
           biasadj(i) = biasadj_full(i);
       }
     }
-    if (Do_Forecast > 0 && recdev_options(3) >= 0)
-    {
-      for (i = recdev_end + 1; i <= YrMax; i++)
-      {
+    if (Do_Forecast > 0 && recdev_options(3) >= 0) {
+      for (i = recdev_end + 1; i <= YrMax; i++) {
         biasadj(i) = biasadj_full(i);
       }
     }
-    if (recdev_read > 0)
-    {
-      for (j = 1; j <= recdev_read; j++)
-      {
+    if (recdev_read > 0) {
+      for (j = 1; j <= recdev_read; j++) {
         y = recdev_input(j, 1);
         if (y >= recdev_first && y <= YrMax)
           biasadj(y) = biasadj_full(y);
@@ -61,24 +51,21 @@ FUNCTION void setup_recdevs()
   }
   sd_offset_rec = sum(biasadj) * sd_offset;
   //  SS_Label_Info_7.2 #Copy recdev parm vectors into full time series vector
-  if (recdev_do_early > 0)
-  {
+  if (recdev_do_early > 0) {
     recdev(recdev_early_start, recdev_early_end) = recdev_early(recdev_early_start, recdev_early_end);
   }
-  if (do_recdev == 1)
-  {
+  if (do_recdev == 1) {
     recdev(recdev_start, recdev_end) = recdev1(recdev_start, recdev_end);
   }
-  else if (do_recdev >= 2)
-  {
+  else if (do_recdev >= 2) {
     recdev(recdev_start, recdev_end) = recdev2(recdev_start, recdev_end);
   }
   if (Do_Forecast > 0 && do_recdev > 0)
     recdev(recdev_end + 1, YrMax) = Fcast_recruitments(recdev_end + 1, YrMax); // only needed here for reporting
-  } //  end setup for recdevs
+} //  end setup for recdevs
 
 FUNCTION void get_initial_conditions()
-  {
+{
   //*********************************************************************
   /*  SS_Label_Function_23 #get_initial_conditions */
   natage.initialize();
@@ -86,7 +73,7 @@ FUNCTION void get_initial_conditions()
   annual_catch.initialize();
   annual_F.initialize();
   Recr.initialize();
-  save_gparm = 0;  //  index for saving time-varying changes to biology quantities
+  save_gparm = 0; //  index for saving time-varying changes to biology quantities
 
   if (SzFreq_Nmeth > 0)
     SzFreq_exp.initialize();
@@ -102,27 +89,24 @@ FUNCTION void get_initial_conditions()
   //  following call is to routine that does this for all timevary parameters
   //  that are then copied over to replace the base parameter for MG, SRR, Q, Selex, or Tag as needed
   make_timevaryparm(); //  this fills array parm_timevary for all years;   densitydependence must be done year-by-year later
-  if (MG_active(0) > 0 || save_for_report > 0)
-  {
+  if (MG_active(0) > 0 || save_for_report > 0) {
     get_MGsetup(y);
   }
-  #ifdef DO_ONCE
+#ifdef DO_ONCE
   if (do_once == 1)
     echoinput << " MGsetup OK " << endl;
-  #endif
+#endif
   if (MG_active(2) > 0)
     get_growth1(); // seasonal effects and CV
-  #ifdef DO_ONCE
+#ifdef DO_ONCE
   if (do_once == 1)
     echoinput << " growth1 OK" << endl;
-  #endif
-  if (MG_active(2) > 0 || do_once == 1)
-  {
+#endif
+  if (MG_active(2) > 0 || do_once == 1) {
     ALK_subseas_update = 1; //  to indicate that all ALKs need calculation
     get_growth2(y);
     t = styr - 1;
-    for (s = 1; s <= nseas; s++)
-    {
+    for (s = 1; s <= nseas; s++) {
       t++;
       for (subseas = 1; subseas <= N_subseas; subseas++) //  do all subseasons in first year
       {
@@ -133,17 +117,14 @@ FUNCTION void get_initial_conditions()
 
     //  SS_Label_Info_16.2.4.3  #propagate Ave_Size from early years forward until first year that has time-vary growth
     k = styr + 1;
-    do
-    {
-      for (s = 1; s <= nseas; s++)
-      {
+    do {
+      for (s = 1; s <= nseas; s++) {
         t = styr + (k - styr) * nseas + s - 1;
         Ave_Size(t, 1) = Ave_Size(t - nseas, 1);
       } // end season loop
       k++;
     } while (timevary_MG(k, 2) == 0 && k <= YrMax);
-    if (k <= YrMax)
-    {
+    if (k <= YrMax) {
       t = styr + (k - styr) * nseas;
       Ave_Size(t, 1) = Ave_Size(t - nseas, 1); // prep for time-vary next yr
     }
@@ -154,30 +135,26 @@ FUNCTION void get_initial_conditions()
   if (Hermaphro_Option != 0)
     get_Hermaphro();
 
-  if (do_once>0 || MG_active(1) > 0)
-  {
-    get_natmort();  // gets base M (e.g. M1) by season and stores it in natM(t,0).  Later, pred_M2 is added by area
-    for (s = 1; s <= nseas; s++)
-    {
-      natM(t_base - 2 * nseas + s) = natM(t_base + s);  //  copy to virgin
-      natM(t_base - nseas + s) = natM(t_base + s);   //  then to init_conditions year
+  if (do_once > 0 || MG_active(1) > 0) {
+    get_natmort(); // gets base M (e.g. M1) by season and stores it in natM(t,0).  Later, pred_M2 is added by area
+    for (s = 1; s <= nseas; s++) {
+      natM(t_base - 2 * nseas + s) = natM(t_base + s); //  copy to virgin
+      natM(t_base - nseas + s) = natM(t_base + s); //  then to init_conditions year
     }
   }
 
-  #ifdef DO_ONCE
+#ifdef DO_ONCE
   if (do_once == 1)
     echoinput << "natmort OK" << endl;
-  #endif
+#endif
 
   if (MG_active(4) > 0)
     get_recr_distribution();
-  if (y >= Bmark_Yr(7) && y <= Bmark_Yr(8))
-  {
+  if (y >= Bmark_Yr(7) && y <= Bmark_Yr(8)) {
     for (gp = 1; gp <= N_GP; gp++)
       for (p = 1; p <= pop; p++)
         for (settle = 1; settle <= N_settle_timings; settle++)
-          if (recr_dist_pattern(gp, settle, p) > 0)
-          {
+          if (recr_dist_pattern(gp, settle, p) > 0) {
             recr_dist_unf(gp, settle, p) += recr_dist(y, gp, settle, p);
             if (gender == 2)
               recr_dist_unf(gp + N_GP, settle, p) += recr_dist(y, gp + N_GP, settle, p);
@@ -186,79 +163,66 @@ FUNCTION void get_initial_conditions()
 
   if (MG_active(5) > 0)
     get_migration();
-  #ifdef DO_ONCE
-  if (do_once == 1)
-  {
+#ifdef DO_ONCE
+  if (do_once == 1) {
     echoinput << "migr OK" << endl;
   }
-  #endif
-  if (MG_active(7) > 0)
-  {
+#endif
+  if (MG_active(7) > 0) {
     get_catch_mult(y, catch_mult_pointer);
-    for (j = styr + 1; j <= YrMax; j++)
-    {
+    for (j = styr + 1; j <= YrMax; j++) {
       catch_mult(j) = catch_mult(y);
     }
   }
 
-  if (Use_AgeKeyZero > 0)
-  {
+  if (Use_AgeKeyZero > 0) {
     if (MG_active(6) > 0)
       get_age_age(Use_AgeKeyZero, AgeKey_StartAge, AgeKey_Linear1, AgeKey_Linear2); //  call function to get the age_age key
-    if (save_for_report == 1 && store_agekey_add > 0)
-    {
+    if (save_for_report == 1 && store_agekey_add > 0) {
       save_agekey_count = N_ageerr + 1; //  first blank key after the used keys
       age_age(save_agekey_count) = age_age(Use_AgeKeyZero);
       age_err(save_agekey_count) = age_err(Use_AgeKeyZero);
     }
-  #ifdef DO_ONCE
-    if (do_once == 1)
-    {
+#ifdef DO_ONCE
+    if (do_once == 1) {
       echoinput << "age_err key recalc in " << y << endl;
     }
-  #endif
+#endif
   }
 
-  if (save_for_report > 0)
-  {
+  if (save_for_report > 0) {
     get_saveGparm();
   }
 
   //  SS_Label_Info_23.2 #Calculate selectivity in the initial year
   get_selectivity();
-  #ifdef DO_ONCE
-  if (do_once == 1)
-  {
+#ifdef DO_ONCE
+  if (do_once == 1) {
     echoinput << "selectivity OK" << endl;
     echoinput << "Calculate ALK" << endl;
   }
-  #endif
+#endif
 
   //  SS_Label_Info_23.3 #Loop seasons and subseasons
   t = styr - 1;
-  for (s = 1; s <= nseas; s++)
-  {
+  for (s = 1; s <= nseas; s++) {
     t++;
 
-    if (WTage_rd > 0)
-    {
+    if (WTage_rd > 0) {
       for (g = 1; g <= gmorph; g++)
-        if (use_morph(g) > 0)
-        {
+        if (use_morph(g) > 0) {
           Wt_Age_beg(s, g) = Wt_Age_t(t, 0, g);
           Wt_Age_mid(s, g) = Wt_Age_t(t, -1, g);
           if (s == spawn_seas)
             fec(g) = Wt_Age_t(t, -2, g);
         }
     }
-    else if (MG_active(2) > 0 || MG_active(3) > 0 || save_for_report > 0 || do_once == 1)
-    {
+    else if (MG_active(2) > 0 || MG_active(3) > 0 || save_for_report > 0 || do_once == 1) {
       //       Make_Fecundity();
       if (s == spawn_seas && spawn_seas == 1)
         get_mat_fec();
       for (g = 1; g <= gmorph; g++)
-        if (use_morph(g) > 0)
-        {
+        if (use_morph(g) > 0) {
           subseas = 1;
           ALK_idx = (s - 1) * N_subseas + subseas;
           Wt_Age_beg(s, g) = (ALK(ALK_idx, g) * wt_len(s, GP(g))); // wt-at-age at beginning of period
@@ -271,66 +235,59 @@ FUNCTION void get_initial_conditions()
     Wt_Age_t(t, 0) = Wt_Age_beg(s);
 
     for (g = 1; g <= gmorph; g++)
-      if (use_morph(g) > 0)
-      {
+      if (use_morph(g) > 0) {
         //  SS_Label_Info_23.3.3 #for each platoon, combine size_at_age distribution with length selectivity and weight-at-length to get combined selectivity vectors
         Make_FishSelex();
       }
 
     //  SS_Label_Info_23.3.4 #add predator M2 to M1 to update seasonal, areal natM in styr and calc surv for use in Pope's
 
-      if(N_pred>0)
-      {
-//  rebase natM to M1, which is stored in the p=0 section of array
-        for(p = 1; p <= pop; p++)
-        {
-          natM(t, p) = natM(t,0);
-        }
-//  calc M2
-        for (f1 = 1; f1 <= N_pred; f1++)
-        {
-          f = predator(f1);
-          pred_M2(f1, t) = mgp_adj(predparm_pointer(f1)); //  base with no seasonal effect
-          if (nseas > 1)
-            pred_M2(f1, t) *= mgp_adj(predparm_pointer(f1) + s);
-          pred_M2(f1, t-nseas) = pred_M2(f1, t);
-          pred_M2(f1, t-nseas-nseas) = pred_M2(f1, t);
-          p = fleet_area(f);  //  area this predator occurs in
-
-  //  a new array for indexing g and gpi could simplify below
-  //        for (gp = 1; gp <= N_GP * gender * N_settle_timings; gp++)
-  //  add each M2 to get total M
-          for (gp = 1; gp <= N_GP * gender; gp++)
-          {
-            g = g_Start(gp); //  base platoon
-            for (settle = 1; settle <= N_settle_timings; settle++)
-            {
-              g += N_platoon;
-              int gpi = GP3(g); // GP*gender*settlement
-              natM(t, p,gpi) += pred_M2(f1, t) * sel_num(s, f, g);
-              if (do_once == 1 && p == 1)
-                echoinput << "init " << y << " s " << s << " t " << t << " area " << 0 << " gp " << gpi << "  M1: " << natM(t,0, gpi) << endl;
-              if (do_once == 1)
-                echoinput << "init " << y << " s " << s << " t " << t << " area " << p << " gp " << gpi << "  M1+M2: " << natM(t, p, gpi) << endl;
-            }
+    if (N_pred > 0) {
+      //  rebase natM to M1, which is stored in the p=0 section of array
+      for (p = 1; p <= pop; p++) {
+        natM(t, p) = natM(t, 0);
+      }
+      //  calc M2
+      for (f1 = 1; f1 <= N_pred; f1++) {
+        f = predator(f1);
+        pred_M2(f1, t) = mgp_adj(predparm_pointer(f1)); //  base with no seasonal effect
+        if (nseas > 1)
+          pred_M2(f1, t) *= mgp_adj(predparm_pointer(f1) + s);
+        pred_M2(f1, t - nseas) = pred_M2(f1, t);
+        pred_M2(f1, t - nseas - nseas) = pred_M2(f1, t);
+        p = fleet_area(f); //  area this predator occurs in
+
+        //  a new array for indexing g and gpi could simplify below
+        //        for (gp = 1; gp <= N_GP * gender * N_settle_timings; gp++)
+        //  add each M2 to get total M
+        for (gp = 1; gp <= N_GP * gender; gp++) {
+          g = g_Start(gp); //  base platoon
+          for (settle = 1; settle <= N_settle_timings; settle++) {
+            g += N_platoon;
+            int gpi = GP3(g); // GP*gender*settlement
+            natM(t, p, gpi) += pred_M2(f1, t) * sel_num(s, f, g);
+            if (do_once == 1 && p == 1)
+              echoinput << "init " << y << " s " << s << " t " << t << " area " << 0 << " gp " << gpi << "  M1: " << natM(t, 0, gpi) << endl;
+            if (do_once == 1)
+              echoinput << "init " << y << " s " << s << " t " << t << " area " << p << " gp " << gpi << "  M1+M2: " << natM(t, p, gpi) << endl;
           }
         }
-        natM(t-nseas) = natM(t);  //for initial equilibrium
-        natM(t-nseas-nseas) = natM(t);  //  for virgin
       }
+      natM(t - nseas) = natM(t); // for initial equilibrium
+      natM(t - nseas - nseas) = natM(t); //  for virgin
+    }
 
-      for(p = 1; p <= pop; p++)
-      {
-        int s1 = (p - 1) * nseas + s;
-        surv1(s1) = mfexp( - natM(t,p) * seasdur_half(s));
-        surv2(s1) = square(surv1(s1));
-      }
+    for (p = 1; p <= pop; p++) {
+      int s1 = (p - 1) * nseas + s;
+      surv1(s1) = mfexp(-natM(t, p) * seasdur_half(s));
+      surv2(s1) = square(surv1(s1));
+    }
   } // end season (s) loop in biology, mortality and selectivity calcs in initial year
 
-  #ifdef DO_ONCE
+#ifdef DO_ONCE
   if (do_once == 1)
     echoinput << "Begin calculating virgin age struc " << endl;
-  #endif
+#endif
   //  SS_Label_Info_23.4 #calculate unfished (virgin) numbers-at-age
   eq_yr = styr - 2;
   bio_yr = styr;
@@ -344,35 +301,34 @@ FUNCTION void get_initial_conditions()
     equ_Recr = 1.0;
     Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation.  Returns SPR because R = 1.0
     SSBpR_virgin = SSB_equil; //  spawners per recruit.  Needed for Sr_fxn = 10
-    SSBpR_virgin_adj = SSB_equil;  //  also needed for Sr_fxn 10.  Will get revised in benchmark to use averaged biology if requested.
-    if(SR_fxn == 10)  // B-H with a,b
+    SSBpR_virgin_adj = SSB_equil; //  also needed for Sr_fxn 10.  Will get revised in benchmark to use averaged biology if requested.
+    if (SR_fxn == 10) // B-H with a,b
     {
-  //  WHAM based on R = A*S/(1+B*S)
-  //  log_SR_a = log(4 * SR_h/(exp(log_SPR0)*(1 - SR_h)));
-  //  log_SR_b = log((5*SR_h - 1)/((1-SR_h)*SR_R0*exp(log_SPR0)));
-  //  h = a * SPR0 / (4. + a * SPR0)
-  //  R0 = 1/b * (a-1/SPR0)
+      //  WHAM based on R = A*S/(1+B*S)
+      //  log_SR_a = log(4 * SR_h/(exp(log_SPR0)*(1 - SR_h)));
+      //  log_SR_b = log((5*SR_h - 1)/((1-SR_h)*SR_R0*exp(log_SPR0)));
+      //  h = a * SPR0 / (4. + a * SPR0)
+      //  R0 = 1/b * (a-1/SPR0)
 
       alpha = mfexp(SR_parm(3));
       beta = mfexp(SR_parm(4));
       steepness = alpha * SSBpR_virgin_adj / (4. + alpha * SSBpR_virgin_adj);
       Recr_virgin = 1. / beta * (alpha - (1. / SSBpR_virgin_adj));
-//      warning << " before AB_calcs " << "parm " << SR_parm(1) << " calc " << log(Recr_virgin) << endl;
+      //      warning << " before AB_calcs " << "parm " << SR_parm(1) << " calc " << log(Recr_virgin) << endl;
       SR_parm(1) = log(Recr_virgin);
       SR_parm(2) = steepness;
     }
     else {
       Recr_virgin = mfexp(SR_parm(1));
     }
-  
-  for (int i = 1; i <= N_SRparm2; i++)
-  {
-    SR_parm_byyr(eq_yr, i) = SR_parm(i);
-    SR_parm_virg(i) = SR_parm(i);
-    SR_parm_work(i) = SR_parm(i);
-  }
-//  if (SR_fxn == 3) warning << "tester_A: " << SR_parm_work(1) << " base: " << SR_parm(1) << endl;
-//  if (SR_fxn == 10) warning << "tester_A: " << SR_parm_work(4) << " base: " << SR_parm(4) << endl;
+
+    for (int i = 1; i <= N_SRparm2; i++) {
+      SR_parm_byyr(eq_yr, i) = SR_parm(i);
+      SR_parm_virg(i) = SR_parm(i);
+      SR_parm_work(i) = SR_parm(i);
+    }
+    //  if (SR_fxn == 3) warning << "tester_A: " << SR_parm_work(1) << " base: " << SR_parm(1) << endl;
+    //  if (SR_fxn == 10) warning << "tester_A: " << SR_parm_work(4) << " base: " << SR_parm(4) << endl;
     equ_Recr = Recr_virgin;
     exp_rec(eq_yr, 1) = Recr_virgin; //  expected Recr from s-r parms
     exp_rec(eq_yr, 2) = Recr_virgin;
@@ -380,14 +336,14 @@ FUNCTION void get_initial_conditions()
     exp_rec(eq_yr, 4) = Recr_virgin;
     Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation
     SSB_virgin = SSB_equil;
-//    SSBpR_virgin = SSB_equil / Recr_virgin; //  spawners per recruit already calculated
-    if(Do_Benchmark==0)  // assign values that would be created in benchmark section
+    //    SSBpR_virgin = SSB_equil / Recr_virgin; //  spawners per recruit already calculated
+    if (Do_Benchmark == 0) // assign values that would be created in benchmark section
     {
-      Mgmt_quant(1) = SSB_virgin;
+      Mgmt_quant(1) = SSB_virgin; //  can be overwritten in benchmark by updated SSB_unf
       SSB_unf = SSB_virgin;
       Recr_unf = Recr_virgin;
-      Mgmt_quant(2) = totbio;  //  from equil calcs
-      Mgmt_quant(3) = smrybio;  //  from equil calcs
+      Mgmt_quant(2) = totbio; //  from equil calcs
+      Mgmt_quant(3) = smrybio; //  from equil calcs
       Mgmt_quant(4) = Recr_virgin;
     }
     Smry_Table(styr - 2, 1) = totbio; //  from equil calcs
@@ -395,55 +351,45 @@ FUNCTION void get_initial_conditions()
     Smry_Table(styr - 2, 3) = smrynum; //  from equil calcs
     SSB_pop_gp(eq_yr) = SSB_equil_pop_gp; // dimensions of pop x N_GP
     if (Hermaphro_Option != 0)
-      MaleSPB(eq_yr) = MaleSSB_equil_pop_gp;
+      MaleSSB(eq_yr) = MaleSSB_equil_pop_gp;
     SSB_yr(eq_yr) = SSB_equil;
     SR_parm_byyr(eq_yr, N_SRparm2 + 1) = SSB_equil;
     SR_parm_virg(N_SRparm2 + 1) = SSB_equil;
     SR_parm_work(N_SRparm2 + 1) = SSB_equil;
     t = styr - 2 * nseas - 1;
     for (s = 1; s <= nseas; s++)
-      for (p = 1; p <= pop; p++)
-      {
-        for (g = 1; g <= gmorph; g++)
-        {
-          if (use_morph(g) > 0)
-          {
+      for (p = 1; p <= pop; p++) {
+        for (g = 1; g <= gmorph; g++) {
+          if (use_morph(g) > 0) {
             natage(t + s, p, g)(0, nages) = equ_numbers(s, p, g)(0, nages);
             Z_rate(t + s, p, g)(0, nages) = equ_Z(s, p, g)(0, nages);
           }
         }
       }
-    if (save_for_report > 0)
-    {
+    if (save_for_report > 0) {
       SSB_B_yr(eq_yr).initialize();
       SSB_N_yr(eq_yr).initialize();
-      for (s = 1; s <= nseas; s++)
-        {
-          for (p = 1; p <= pop; p++)
-            for (g = 1; g <= gmorph; g++)
-              if (use_morph(g) > 0)
-              {
-                if (s == spawn_seas && sx(g) == 1)
-                {
-                  SSB_B_yr(eq_yr) += make_mature_bio(GP4(g)) * natage(t + s, p, g);
-                  SSB_N_yr(eq_yr) += make_mature_numbers(GP4(g)) * natage(t + s, p, g);
-                }
-                Save_PopAge(t + s, p, g) = natage(t + s, p, g);
-                Save_PopAge(t + s, p + pop, g) = elem_prod(natage(t + s, p, g), mfexp(-Z_rate(t + s, p, g) * 0.5 * seasdur(s)));
-                if (Settle_seas(settle_g(g)) == s)
-                  Recr(p, t + 1 + Settle_seas_offset(settle_g(g))) += equ_Recr * recr_dist(y, GP(g), settle_g(g), p) * platoon_distr(GP2(g));
-                Save_PopBio(t + s, p, g) = elem_prod(natage(t + s, p, g), Wt_Age_beg(s, g));
-                Save_PopBio(t + s, p + pop, g) = elem_prod(Save_PopAge(t + s, p + pop, g), Wt_Age_mid(s, g));
+      for (s = 1; s <= nseas; s++) {
+        for (p = 1; p <= pop; p++)
+          for (g = 1; g <= gmorph; g++)
+            if (use_morph(g) > 0) {
+              if (s == spawn_seas && sx(g) == 1) {
+                SSB_B_yr(eq_yr) += make_mature_bio(GP4(g)) * natage(t + s, p, g);
+                SSB_N_yr(eq_yr) += make_mature_numbers(GP4(g)) * natage(t + s, p, g);
               }
-        for (int ff = 1; ff <= N_pred; ff++)
-        {
+              Save_PopAge(t + s, p, g) = natage(t + s, p, g);
+              Save_PopAge(t + s, p + pop, g) = elem_prod(natage(t + s, p, g), mfexp(-Z_rate(t + s, p, g) * 0.5 * seasdur(s)));
+              if (Settle_seas(settle_g(g)) == s)
+                Recr(p, t + 1 + Settle_seas_offset(settle_g(g))) += equ_Recr * recr_dist(y, GP(g), settle_g(g), p) * platoon_distr(GP2(g));
+              Save_PopBio(t + s, p, g) = elem_prod(natage(t + s, p, g), Wt_Age_beg(s, g));
+              Save_PopBio(t + s, p + pop, g) = elem_prod(Save_PopAge(t + s, p + pop, g), Wt_Age_mid(s, g));
+            }
+        for (int ff = 1; ff <= N_pred; ff++) {
           f = predator(ff);
-          for (g = 1; g <= 6; g++)
-          {
+          for (g = 1; g <= 6; g++) {
             catch_fleet(t + s, f, g) = equ_catch_fleet(g, s, f);
           }
-          for (g = 1; g <= gmorph; g++)
-          {
+          for (g = 1; g <= gmorph; g++) {
             catage(t + s, f, g) = equ_catage(s, f, g);
           }
         }
@@ -454,45 +400,36 @@ FUNCTION void get_initial_conditions()
   {
   }
 
-//  SS_Label_Info_23.5  #Calculate equilibrium using initial F
-  #ifdef DO_ONCE
+  //  SS_Label_Info_23.5  #Calculate equilibrium using initial F
+#ifdef DO_ONCE
   if (do_once == 1)
     echoinput << "Begin calculating initial age structure" << endl;
-  #endif
+#endif
   eq_yr = styr - 1;
   bio_yr = styr;
-  if (fishery_on_off == 1)
-  {
+  if (fishery_on_off == 1) {
     Fishon = 1;
   }
-  else
-  {
+  else {
     Fishon = 0;
   }
 
-  for (f = 1; f <= N_SRparm2; f++)
-  {
-    if (SR_parm_timevary(f) == 0)
-    {
+  for (f = 1; f <= N_SRparm2; f++) {
+    if (SR_parm_timevary(f) == 0) {
       //  no change to SR_parm_work
     }
-    else
-    {
+    else {
       SR_parm_work(f) = parm_timevary(SR_parm_timevary(f), eq_yr);
-//      warning << "tester_B: " << SR_parm_work(f) << " timevary " << " base " << SR_parm(f) <<endl;
-//      warning << parm_timevary(2) << endl;
-
+      //      warning << "tester_B: " << SR_parm_work(f) << " timevary " << " base " << SR_parm(f) <<endl;
+      //      warning << parm_timevary(2) << endl;
     }
     SR_parm_byyr(eq_yr, f) = SR_parm_work(f);
   }
-  for (s = 1; s <= nseas; s++)
-  {
+  for (s = 1; s <= nseas; s++) {
     t = styr - nseas - 1 + s;
-    for (int ff = 1; ff <= N_catchfleets(0); ff++)
-    {
+    for (int ff = 1; ff <= N_catchfleets(0); ff++) {
       f = fish_fleet_area(0, ff);
-      if (init_F_loc(s, f) > 0)
-      {
+      if (init_F_loc(s, f) > 0) {
         Hrate(f, t) = init_F(init_F_loc(s, f));
       }
     }
@@ -522,12 +459,11 @@ FUNCTION void get_initial_conditions()
     Do_Equil_Calc(equ_Recr);
     CrashPen += Equ_penalty;
   }
-  else
-  {
+  else {
     //  SS_Label_Info_23.5.1.2  #Adjustments  include spawner-recruitment function
     //  do initial equilibrium with R1 based on offset from spawner-recruitment curve, using same approach as the benchmark calculations
     //  first get SPR for this init_F
-    //  SPAWN-RECR:   calc initial equilibrium pop, SPB, Recruitment
+    //  SPAWN-RECR:   calc initial equilibrium pop, SSB, Recruitment
     //    equ_Recr=Recr_virgin;
     equ_Recr = R1_exp * regime_change;
 
@@ -554,7 +490,7 @@ FUNCTION void get_initial_conditions()
 
   SSB_pop_gp(eq_yr) = SSB_equil_pop_gp; // dimensions of pop x N_GP
   if (Hermaphro_Option != 0)
-    MaleSPB(eq_yr) = MaleSSB_equil_pop_gp;
+    MaleSSB(eq_yr) = MaleSSB_equil_pop_gp;
   SSB_yr(eq_yr) = SSB_equil;
   SR_parm_byyr(eq_yr, N_SRparm2 + 1) = SSB_equil;
   SR_parm_work(N_SRparm2 + 1) = SSB_equil;
@@ -580,68 +516,55 @@ FUNCTION void get_initial_conditions()
       }
     }
   */
-//  if (save_for_report > 0)
+  //  if (save_for_report > 0)
   {
-    for (s = 1; s <= nseas; s++)
-    {
+    for (s = 1; s <= nseas; s++) {
       t = styr - nseas - 1 + s;
-      for (int ff = 1; ff <= N_catchfleets(0); ff++)
-      {
+      for (int ff = 1; ff <= N_catchfleets(0); ff++) {
         f = fish_fleet_area(0, ff);
-        for (g = 1; g <= 6; g++)
-        {
+        for (g = 1; g <= 6; g++) {
           catch_fleet(t, f, g) = equ_catch_fleet(g, s, f);
           annual_catch(styr - 1, g) += equ_catch_fleet(g, s, f);
         }
-        for (g = 1; g <= gmorph; g++)
-        {
+        for (g = 1; g <= gmorph; g++) {
           catage(t, f, g) = equ_catage(s, f, g);
         }
       }
-      for (int ff = 1; ff <= N_pred; ff++)
-      {
+      for (int ff = 1; ff <= N_pred; ff++) {
         f = predator(ff);
-        for (g = 1; g <= 6; g++)
-        {
+        for (g = 1; g <= 6; g++) {
           catch_fleet(t, f, g) = equ_catch_fleet(g, s, f);
         }
-        for (g = 1; g <= gmorph; g++)
-        {
+        for (g = 1; g <= gmorph; g++) {
           catage(t, f, g) = equ_catage(s, f, g);
         }
       }
     }
-    for (k = 1; k <= 3; k++)
-    {
+    for (k = 1; k <= 3; k++) {
       Smry_Table(styr - 1, k + 3) = annual_catch(styr - 1, k);
     }
   }
 
-  for (s = 1; s <= nseas; s++)
-  {
+  for (s = 1; s <= nseas; s++) {
     t = styr - nseas - 1 + s;
     a = styr - 1 + s;
     for (p = 1; p <= pop; p++)
-      for (g = 1; g <= gmorph; g++)
-      {
+      for (g = 1; g <= gmorph; g++) {
         natage(t, p, g)(0, nages) = equ_numbers(s, p, g)(0, nages);
         natage(a, p, g)(0, nages) = equ_numbers(s, p, g)(0, nages);
         Z_rate(t, p, g) = equ_Z(s, p, g);
       }
   }
 
-  if (save_for_report > 0)
-  {
+  if (save_for_report > 0) {
     t = styr - nseas - 1;
     SSB_B_yr(eq_yr).initialize();
     SSB_N_yr(eq_yr).initialize();
     for (s = 1; s <= nseas; s++)
       for (p = 1; p <= pop; p++)
         for (g = 1; g <= gmorph; g++)
-          if (use_morph(g) > 0)
-          {
-            if (s == spawn_seas && sx(g) == 1)
-            {
+          if (use_morph(g) > 0) {
+            if (s == spawn_seas && sx(g) == 1) {
               SSB_B_yr(eq_yr) += make_mature_bio(GP4(g)) * natage(t + s, p, g);
               SSB_N_yr(eq_yr) += make_mature_numbers(GP4(g)) * natage(t + s, p, g);
             }
@@ -661,24 +584,19 @@ FUNCTION void get_initial_conditions()
 
   // if recrdevs start before styr, then use them to adjust the initial agecomp
   //  apply a fraction of the bias adjustment, so bias adjustment gets less linearly as proceed back in time
-  if (recdev_first < styr)
-  {
-    if (do_recdev <= 2 && SR_fxn != 4)
-    {
+  if (recdev_first < styr) {
+    if (do_recdev <= 2 && SR_fxn != 4) {
       for (p = 1; p <= pop; p++)
         for (g = 1; g <= gmorph; g++)
-          for (a = styr - recdev_first; a >= 1; a--)
-          {
+          for (a = styr - recdev_first; a >= 1; a--) {
             j = styr - a;
             natage(styr, p, g, a) *= mfexp(recdev(j) - biasadj(j) * half_sigmaRsq);
           }
     }
-    else
-    {
+    else {
       for (p = 1; p <= pop; p++)
         for (g = 1; g <= gmorph; g++)
-          for (a = styr - recdev_first; a >= 1; a--)
-          {
+          for (a = styr - recdev_first; a >= 1; a--) {
             j = styr - a;
             natage(styr, p, g, a) *= mfexp(recdev(j));
           }
@@ -687,82 +605,69 @@ FUNCTION void get_initial_conditions()
   SSB_pop_gp(styr) = SSB_pop_gp(styr - 1); //  placeholder in case not calculated early in styr
 
   //  note:  the above keeps SSB_pop_gp(styr) = SSB_equil.  It does not adjust for initial agecomp, but probably should
-  } //  end initial_conditions
+} //  end initial_conditions
 
 //*********************************************************************
 FUNCTION void get_time_series()
-  {
+{
   /*  SS_Label_Function_24 get_time_series */
   dvariable crashtemp;
   dvariable crashtemp1;
   dvariable interim_tot_catch;
   dvariable Z_adjuster;
-  dvariable R0_use;  // annually updated variable if SR_update_SSBpR0_timeseries == 1; gets passed to Spawn_Recr() function
-  dvariable SSB_use;
 
   if (Do_Morphcomp > 0)
     Morphcomp_exp.initialize();
 
   //  SS_Label_Info_24.0 #Retrieve spawning biomass and recruitment from the initial equilibrium
-  //  SPAWN-RECR:   begin of time series, retrieve last spbio and recruitment
+  //  SPAWN-RECR:   begin of time series, retrieve last SSBio and recruitment
   SSB_current = SSB_yr(styr); //  need these initial assignments in case recruitment distribution occurs before spawnbio&recruits
-  if (recdev_doit(styr - 1) > 0)
-  {
+  if (recdev_doit(styr - 1) > 0) {
     Recruits = R1 * mfexp(recdev(styr - 1) - biasadj(styr - 1) * half_sigmaRsq);
   }
-  else
-  {
+  else {
     Recruits = R1;
   }
 
   //  SS_Label_Info_24.1 #Loop the years
-  for (y = styr; y <= endyr; y++)
-  {
+  for (y = styr; y <= endyr; y++) {
     yz = y;
     if (STD_Yr_Reverse_F(y) > 0)
       F_std(STD_Yr_Reverse_F(y)) = 0.0;
     t_base = styr + (y - styr) * nseas - 1;
 
-    for (f = 1; f <= N_SRparm2; f++)
-    {
-      if (SR_parm_timevary(f) == 0)
-      {
+    for (f = 1; f <= N_SRparm2; f++) {
+      if (SR_parm_timevary(f) == 0) {
         //  no change to SR_parm_work
       }
-      else
-      {
+      else {
         SR_parm_work(f) = parm_timevary(SR_parm_timevary(f), y);
-//        warning << "tester_C: " << SR_parm_work(f) << " timevary_year " << endl;
+        //        warning << "tester_C: " << SR_parm_work(f) << " timevary_year " << endl;
       }
       SR_parm_byyr(y, f) = SR_parm_work(f);
     }
 
-      //  SS_Label_Info_24.1.1 #store begin of year quantities for use in density-dependent processes
+    //  SS_Label_Info_24.1.1 #store begin of year quantities for use in density-dependent processes
     {
       env_data(y, -1) = log(SSB_current / SSB_yr(styr - 1));
-      if (recdev_doit(y) > 0)
-      {
+      if (recdev_doit(y) > 0) {
         env_data(y, -2) = recdev(y);
       } //  store so can do density-dependence
-      else
-      { //  should be 0.0
+      else { //  should be 0.0
       }
       t = t_base + 1; // first season
       s = 1;
-      if (WTage_rd > 0)
-      {
+      if (WTage_rd > 0) {
         Wt_Age_beg(s) = Wt_Age_t(t, 0);
         Wt_Age_mid(s) = Wt_Age_t(t, -1);
       }
-      else if (timevary_MG(y, 2) > 0 || timevary_MG(y, 3) > 0 || save_for_report == 1)
-      {
+      else if (timevary_MG(y, 2) > 0 || timevary_MG(y, 3) > 0 || save_for_report == 1) {
         get_growth3(y, t, 1, 1); //  before season loop, used for summary biomass
         ALK_subseas_update(1) = 1; // do 1st subseas of 1st season;  ADD THIS LINE for 3.30.17
         Make_AgeLength_Key(s, 1); //  this will give wt_age_beg before any time-varying parameter changes for this year
         ALK_idx = (s - 1) * N_subseas + 1;
         for (g = 1; g <= gmorph; g++)
-          if (use_morph(g) > 0)
-          {
+          if (use_morph(g) > 0) {
             Wt_Age_beg(s, g) = (ALK(ALK_idx, g) * wt_len(s, GP(g))); // wt-at-age at beginning of period
           }
       }
@@ -770,12 +675,10 @@ FUNCTION void get_time_series()
       smrynum = 0.0;
       //  do not do totbio here because new recruits have not yet occurred
       for (g = 1; g <= gmorph; g++)
-        if (use_morph(g) > 0)
-        {
-          for (p = 1; p <= pop; p++)
-          {
+        if (use_morph(g) > 0) {
+          for (p = 1; p <= pop; p++) {
             smrybio += natage(t, p, g)(Smry_Age, nages) * Wt_Age_beg(1, g)(Smry_Age, nages); // calc before recruitment and time-vary biology applied
-            smrynum += sum(natage(t, p, g)(Smry_Age, nages)); //sums to accumulate across platoons and settlements
+            smrynum += sum(natage(t, p, g)(Smry_Age, nages)); // sums to accumulate across platoons and settlements
           }
         }
       env_data(y, -3) = log(smrybio / Smry_Table(styr - 1, 2));
@@ -785,37 +688,31 @@ FUNCTION void get_time_series()
       Smry_Table(y, 3) = smrynum;
     }
 
-      //  SS_Label_Info_24.1.1 #skip biology updating if y=styr because already done
-    if (y > styr)
-    {
+    //  SS_Label_Info_24.1.1 #skip biology updating if y=styr because already done
+    if (y > styr) {
       if (do_densitydependent == 1)
         make_densitydependent_parm(y); //  call to adjust for density dependence
 
       //  SS_Label_Info_24.1.1 #Update the time varying biology factors if necessary
       if (timevary_MG(y, 0) > 0 || save_for_report > 0)
         get_MGsetup(y);
-      if (timevary_MG(y, 2) > 0)
-      {
+      if (timevary_MG(y, 2) > 0) {
         ALK_subseas_update = 1; // indicate that all ALKs will need re-estimation
         get_growth2(y); //  propagates growth to each season this year and to begin next year
         get_growth3(y, t, 1, 1); //  cleans up the linear growth range for begin of this year
       }
-      if (timevary_MG(y, 3) > 0)
-      {
+      if (timevary_MG(y, 3) > 0) {
         get_wtlen(); //  stores values for all seasons
         //  note that get_mat_fec() will get called in the season loop because it may need the ALK for a later season
         // but Maunder's M in get_natmort() may use the fecundity vector, so would be using the most recently calculated  Problem??
         if (Hermaphro_Option != 0)
           get_Hermaphro();
       }
-      if (timevary_MG(y, 1) > 0)
-      {
+      if (timevary_MG(y, 1) > 0) {
         get_natmort();
       }
-      else
-      {
-        for (s = 1; s <= nseas; s++)
-        {
+      else {
+        for (s = 1; s <= nseas; s++) {
           natM(t_base + s) = natM(t_base - nseas + s);
         } // set M equal to last year's;
           // does all areas (p), but if there are predators, then add of pred_M2 occurs in season loop below
@@ -823,13 +720,11 @@ FUNCTION void get_time_series()
 
       if (timevary_MG(y, 4) > 0)
         get_recr_distribution();
-      if (y >= Bmark_Yr(7) && y <= Bmark_Yr(8))
-      {
+      if (y >= Bmark_Yr(7) && y <= Bmark_Yr(8)) {
         for (gp = 1; gp <= N_GP; gp++)
           for (p = 1; p <= pop; p++)
             for (settle = 1; settle <= N_settle_timings; settle++)
-              if (recr_dist_pattern(gp, settle, p) > 0)
-              {
+              if (recr_dist_pattern(gp, settle, p) > 0) {
                 recr_dist_unf(gp, settle, p) += recr_dist(y, gp, settle, p);
                 if (gender == 2)
                   recr_dist_unf(gp + N_GP, settle, p) += recr_dist(y, gp + N_GP, settle, p);
@@ -837,42 +732,35 @@ FUNCTION void get_time_series()
       }
       if (timevary_MG(y, 5) > 0)
         get_migration();
-      if (timevary_MG(y, 7) > 0)
-      {
+      if (timevary_MG(y, 7) > 0) {
         get_catch_mult(y, catch_mult_pointer);
       }
 
-      if (Use_AgeKeyZero > 0)
-      {
-        if (timevary_MG(y, 6) > 0)
-        {
+      if (Use_AgeKeyZero > 0) {
+        if (timevary_MG(y, 6) > 0) {
           get_age_age(Use_AgeKeyZero, AgeKey_StartAge, AgeKey_Linear1, AgeKey_Linear2); //  call function to get the age_age key
-          if (save_for_report == 1 && store_agekey_add > 0)
-          {
+          if (save_for_report == 1 && store_agekey_add > 0) {
             save_agekey_count++; //  next blank key after the used keys
             age_age(save_agekey_count) = age_age(Use_AgeKeyZero);
             age_err(save_agekey_count) = age_err(Use_AgeKeyZero);
           }
 
-  #ifdef DO_ONCE
+#ifdef DO_ONCE
           if (do_once == 1)
             echoinput << " ageerr_key recalc in " << y << endl;
-  #endif
+#endif
         }
       }
 
-      if (save_for_report > 0)
-      {
-        if (timevary_MG(y, 1) > 0 || timevary_MG(y, 2) > 0 || timevary_MG(y, 3) > 0)
-        {
+      if (save_for_report > 0) {
+        if (timevary_MG(y, 1) > 0 || timevary_MG(y, 2) > 0 || timevary_MG(y, 3) > 0) {
           get_saveGparm();
         }
       }
     }
 
     //  SS_Label_Info_24.2  #Loop the seasons
-    for (s = 1; s <= nseas; s++)
-    {
+    for (s = 1; s <= nseas; s++) {
       if (docheckup == 1)
         echoinput << endl
                   << "************************************" << endl
@@ -886,43 +774,36 @@ FUNCTION void get_time_series()
       //  SS_Label_Info_24.2.1 #Update the age-length key and the fishery selectivity for this season
 
       //      if(timevary_MG(y,2)>0 || timevary_MG(y,3)>0 || save_for_report==1 || WTage_rd>0)
-      if (timevary_MG(y, 2) > 0 || save_for_report == 1)
-      {
+      if (timevary_MG(y, 2) > 0 || save_for_report == 1) {
         get_growth3(y, t, s, 1); // first subseas of season=s
         Make_AgeLength_Key(s, 1);
 
         get_growth3(y, t, s, mid_subseas); //  for midseason
         Make_AgeLength_Key(s, mid_subseas);
         //  SPAWN-RECR:   call Make_Fecundity in time series
-        if (s == spawn_seas)
-        {
-          if (spawn_subseas != 1 && spawn_subseas != mid_subseas)
-          {
+        if (s == spawn_seas) {
+          if (spawn_subseas != 1 && spawn_subseas != mid_subseas) {
             subseas = spawn_subseas;
             get_growth3(y, t, s, subseas);
             Make_AgeLength_Key(s, subseas); //  spawn subseas
           }
         }
       }
-      if (WTage_rd > 0)
-      {
+      if (WTage_rd > 0) {
         Wt_Age_beg(s) = Wt_Age_t(t, 0);
         Wt_Age_mid(s) = Wt_Age_t(t, -1);
-        if (s == spawn_seas)
-        {
+        if (s == spawn_seas) {
           fec = Wt_Age_t(t, -2);
         }
       }
-      else if (timevary_MG(y, 2) > 0 || timevary_MG(y, 3) > 0 || save_for_report > 0 || do_once == 1)
-      {
+      else if (timevary_MG(y, 2) > 0 || timevary_MG(y, 3) > 0 || save_for_report > 0 || do_once == 1) {
         if (s == spawn_seas)
           get_mat_fec();
         //         Make_Fecundity();
         ALK_idx = (s - 1) * N_subseas + 1; //  subseas=1
         int ALK_idx2 = (s - 1) * N_subseas + mid_subseas;
         for (g = 1; g <= gmorph; g++)
-          if (use_morph(g) > 0)
-          {
+          if (use_morph(g) > 0) {
             Wt_Age_beg(s, g) = (ALK(ALK_idx, g) * wt_len(s, GP(g))); // wt-at-age at beginning of period
             Wt_Age_mid(s, g) = ALK(ALK_idx2, g) * wt_len(s, GP(g)); // use for fisheries with no size selectivity
           }
@@ -933,72 +814,64 @@ FUNCTION void get_time_series()
       if (y > styr) // because styr is done as part of initial conditions
       {
         for (g = 1; g <= gmorph; g++)
-          if (use_morph(g) > 0)
-          {
+          if (use_morph(g) > 0) {
             Make_FishSelex();
           }
 
-//  rebase natM to M1
-        for(p = 1; p <= pop; p++)
-        {
-          natM(t, p) = natM(t,0);
+        //  rebase natM to M1
+        for (p = 1; p <= pop; p++) {
+          natM(t, p) = natM(t, 0);
         }
         // SS_Label_Info_24.x.x #add predator M2 inside the yr,seas loop
-        if(N_pred>0)
-        {
-    //  add pred_M2 by area
-          for (f1 = 1; f1 <= N_pred; f1++)
-          {
+        if (N_pred > 0) {
+          //  add pred_M2 by area
+          for (f1 = 1; f1 <= N_pred; f1++) {
             f = predator(f1);
             pred_M2(f1, t) = mgp_adj(predparm_pointer(f1)); //  base with no seasonal effect
             if (nseas > 1)
               pred_M2(f1, t) *= mgp_adj(predparm_pointer(f1) + s);
-            p = fleet_area(f);  //  area this predator occurs in
+            p = fleet_area(f); //  area this predator occurs in
 
-    //  a new array for indexing g and gpi could simplify below
-    //        for (gp = 1; gp <= N_GP * gender * N_settle_timings; gp++)
+            //  a new array for indexing g and gpi could simplify below
+            //        for (gp = 1; gp <= N_GP * gender * N_settle_timings; gp++)
 
-            for (gp = 1; gp <= N_GP * gender; gp++)
-            {
+            for (gp = 1; gp <= N_GP * gender; gp++) {
               g = g_Start(gp); //  base platoon
-              for (settle = 1; settle <= N_settle_timings; settle++)
-              {
+              for (settle = 1; settle <= N_settle_timings; settle++) {
                 g += N_platoon;
                 int gpi = GP3(g); // GP*gender*settlement
-                natM(t, p,gpi) += pred_M2(f1, t) * sel_num(s, f, g);
-                 if (do_once == 1 && p == 1)
-                    echoinput << y << " s " << s << " t " << t << " area " << 0 << " gp " << gpi << "  M1: " << natM(t,0, gpi) << endl;
-                  if (do_once == 1)
-                    echoinput << y << " s " << s << " t " << t << " area " << p << " gp " << gpi << "  M1+M2: " << natM(t, p, gpi) << endl;
+                natM(t, p, gpi) += pred_M2(f1, t) * sel_num(s, f, g);
+                if (do_once == 1 && p == 1)
+                  echoinput << y << " s " << s << " t " << t << " area " << 0 << " gp " << gpi << "  M1: " << natM(t, 0, gpi) << endl;
+                if (do_once == 1)
+                  echoinput << y << " s " << s << " t " << t << " area " << p << " gp " << gpi << "  M1+M2: " << natM(t, p, gpi) << endl;
               }
             }
           }
         }
 
-        for(p = 1; p <= pop; p++)
-        {
+        for (p = 1; p <= pop; p++) {
           int s1 = (p - 1) * nseas + s;
-          surv1(s1) = mfexp(-natM(t,p) * seasdur_half(s));
+          surv1(s1) = mfexp(-natM(t, p) * seasdur_half(s));
           surv2(s1) = square(surv1(s1));
         }
       }
       //  SS_Label_Info_24.2.2 #Compute spawning biomass if this is spawning season so recruits could occur later this season
-      //  SPAWN-RECR:   calc SPB in time series if spawning is at beginning of the season
+      //  SPAWN-RECR:   calc SSB in time series if spawning is at beginning of the season
       if (s == spawn_seas && spawn_time_seas < 0.0001) //  compute spawning biomass if spawning at beginning of season so recruits could occur later this season
       {
         SSB_pop_gp(y).initialize();
         SSB_B_yr(y).initialize();
         SSB_N_yr(y).initialize();
         Smry_Table(y, 15) = 0.0;
-        for (p = 1; p <= pop; p++)
-        {
+        for (p = 1; p <= pop; p++) {
           for (g = 1; g <= gmorph; g++)
             if (sx(g) == 1 && use_morph(g) > 0) //  female
             {
               SSB_pop_gp(y, p, GP4(g)) += fracfemale_mult * fec(g) * natage(t, p, g); // accumulates SSB by area and by growthpattern
               SSB_B_yr(y) += fracfemale_mult * make_mature_bio(GP4(g)) * natage(t, p, g);
               SSB_N_yr(y) += fracfemale_mult * make_mature_numbers(GP4(g)) * natage(t, p, g);
-              Smry_Table(y, 15) += fracfemale_mult * natage(t, p, g) * elem_prod(fec(g), r_ages);  //  for mean age of female spawners = GenTime
+              Smry_Table(y, 15) += fracfemale_mult * natage(t, p, g) * elem_prod(fec(g), r_ages); //  for mean age of female spawners = GenTime
               //            SSB_pop_gp(y,p,GP4(g)) += fec(g)*natage(t,p,g);   // accumulates SSB by area and by growthpattern
               //            SSB_B_yr(y) += make_mature_bio(GP4(g))*natage(t,p,g);
               //            SSB_N_yr(y) += make_mature_numbers(GP4(g))*natage(t,p,g);
@@ -1009,18 +882,17 @@ FUNCTION void get_time_series()
 
         if (Hermaphro_Option != 0) // get male biomass
         {
-          MaleSPB(y).initialize();
-          for (p = 1; p <= pop; p++)
-          {
+          MaleSSB(y).initialize();
+          for (p = 1; p <= pop; p++) {
             for (g = 1; g <= gmorph; g++)
               if (sx(g) == 2 && use_morph(g) > 0) //  male; all assumed to be mature
               {
-                MaleSPB(y, p, GP4(g)) += Wt_Age_t(t, 0, g) * natage(t, p, g); // accumulates SSB by area and by growthpattern
+                MaleSSB(y, p, GP4(g)) += Wt_Age_t(t, 0, g) * natage(t, p, g); // accumulates SSB by area and by growthpattern
               }
           }
-          if (Hermaphro_maleSPB > 0.0) // add MaleSPB to female SSB
+          if (Hermaphro_maleSSB > 0.0) // add MaleSSB to female SSB
           {
-            SSB_current += Hermaphro_maleSPB * sum(MaleSPB(y));
+            SSB_current += Hermaphro_maleSSB * sum(MaleSSB(y));
             SSB_yr(y) = SSB_current;
           }
         }
@@ -1033,8 +905,7 @@ FUNCTION void get_time_series()
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
         }
-        else
-        {
+        else {
           R0_use = mfexp(SR_parm_work(1));
           equ_Recr = R0_use;
           Fishon = 0;
@@ -1042,18 +913,17 @@ FUNCTION void get_time_series()
           bio_yr = y;
           Do_Equil_Calc(R0_use); //  call function to do equilibrium calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
-          SSBpR_virgin_adj = SSB_use / R0_use;  //  update 
-          if (fishery_on_off == 1)
-          {
+          SSBpR_virgin_adj = SSB_use / R0_use; //  update
+          if (fishery_on_off == 1) {
             Fishon = 1;
           }
-          else
-          {
+          else {
             Fishon = 0;
           }
         }
         Recruits = Spawn_Recr(SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr using either virgin or adjusted R0 and SSB0
-        if (SR_fxn != 7) apply_recdev(Recruits, R0_use); //  apply recruitment deviation
+        if (SR_fxn != 7)
+          apply_recdev(Recruits, R0_use); //  apply recruitment deviation
         // distribute Recruitment of age 0 fish among the current and future settlements; and among areas and morphs
         //  use t offset for each birth event:  Settlement_offset(settle)
         //  so the total number of Recruits will be relative to their numbers at the time of the set of settlement_events.
@@ -1069,26 +939,23 @@ FUNCTION void get_time_series()
         //  NOTE:  the distributed recruits are added into natage because more than one settlement can occur in same season
         //  but each settlement has a unique "g", so maybe additive is not necessary
         for (g = 1; g <= gmorph; g++)
-          if (use_morph(g) > 0)
-          {
+          if (use_morph(g) > 0) {
             settle = settle_g(g);
-            for (p = 1; p <= pop; p++)
-            {
+            for (p = 1; p <= pop; p++) {
               if (y == styr)
                 natage(t + Settle_seas_offset(settle), p, g, Settle_age(settle)) = 0.0; //  to negate the additive code
               natage(t + Settle_seas_offset(settle), p, g, Settle_age(settle)) +=
                   Recruits * recr_dist(y, GP(g), settle, p) * platoon_distr(GP2(g)) *
                   mfexp(natM(t, p, GP3(g), Settle_age(settle)) * Settle_timing_seas(settle));
-                Recr(p, t + Settle_seas_offset(settle)) += Recruits * recr_dist(y, GP(g), settle, p) * platoon_distr(GP2(g));
+              Recr(p, t + Settle_seas_offset(settle)) += Recruits * recr_dist(y, GP(g), settle, p) * platoon_distr(GP2(g));
               //  the adjustment for mortality increases recruit value for elapsed time since begin of season because M will then be applied from beginning of season
               if (docheckup == 1)
-                echoinput << y << " Recruits, dist, surv, result  " << Recruits << " " << recr_dist(y, GP(g), settle, p) << " " << mfexp(natM(t, p, GP3(g), Settle_age(settle)) * Settle_timing_seas(settle)) << " " << natage(t + Settle_seas_offset(settle), p, g, Settle_age(settle)) << " M "<<natM(t, p, GP3(g), Settle_age(settle)) * Settle_timing_seas(settle)<<endl;
+                echoinput << y << " Recruits, dist, surv, result  " << Recruits << " " << recr_dist(y, GP(g), settle, p) << " " << mfexp(natM(t, p, GP3(g), Settle_age(settle)) * Settle_timing_seas(settle)) << " " << natage(t + Settle_seas_offset(settle), p, g, Settle_age(settle)) << " M " << natM(t, p, GP3(g), Settle_age(settle)) * Settle_timing_seas(settle) << endl;
             }
           }
       }
 
-      else
-      {
+      else {
         //  spawning biomass and total recruits will be calculated later so they can use Z
       }
 
@@ -1096,11 +963,9 @@ FUNCTION void get_time_series()
       totbio = 0.;
       smrybio = 0.; //  reset to zero happens every season, but accumulation and storage only in season=1; after area loop
       smrynum = 0.;
-      for (p = 1; p <= pop; p++)
-      {
+      for (p = 1; p <= pop; p++) {
         for (g = 1; g <= gmorph; g++)
-          if (use_morph(g) > 0)
-          {
+          if (use_morph(g) > 0) {
             //  SS_Label_Info_24.3.1 #Get middle of season numbers-at-age from M only;
             int s1 = (p - 1) * nseas + s;
             Nmid(g) = elem_prod(natage(t, p, g), surv1(s1, GP3(g))); //  get numbers-at-age(g,a) surviving to middle of time period
@@ -1108,8 +973,7 @@ FUNCTION void get_time_series()
               echoinput << p << " " << g << " " << GP3(g) << " area & morph " << endl
                         << "N-at-age " << natage(t, p, g)(0, min(6, nages)) << endl
                         << "survival " << surv1(s, GP3(g))(0, min(6, nages)) << endl;
-            if (save_for_report == 1)
-            {
+            if (save_for_report == 1) {
               //  SS_Label_Info_24.3.2 #Store some beginning of season quantities
               Save_PopLen(t, p, g) = 0.0;
               Save_PopLen(t, p + pop, g) = 0.0; // later put midseason here
@@ -1120,18 +984,16 @@ FUNCTION void get_time_series()
               Save_PopBio(t, p, g) = 0.0;
               Save_PopBio(t, p + pop, g) = 0.0; // later put midseason here
               ALK_idx = (s - 1) * N_subseas + 1;
-              for (a = 0; a <= nages; a++)
-              {
+              for (a = 0; a <= nages; a++) {
                 Save_PopLen(t, p, g) += value(natage(t, p, g, a)) * value(ALK(ALK_idx, g, a));
                 Save_PopWt(t, p, g) += value(natage(t, p, g, a)) * value(elem_prod(ALK(ALK_idx, g, a), wt_len(s, GP(g))));
                 Save_PopAge(t, p, g, a) = value(natage(t, p, g, a));
                 Save_PopBio(t, p, g, a) = value(natage(t, p, g, a)) * value(Wt_Age_beg(s, g, a));
               } // close age loop
-              if (s == 1)
-              {
+              if (s == 1) {
                 totbio += natage(t, p, g)(0, nages) * Wt_Age_beg(s, g)(0, nages);
                 smrybio += natage(t, p, g)(Smry_Age, nages) * Wt_Age_beg(s, g)(Smry_Age, nages);
-                smrynum += sum(natage(t, p, g)(Smry_Age, nages)); //sums to accumulate across platoons and settlements
+                smrynum += sum(natage(t, p, g)(Smry_Age, nages)); // sums to accumulate across platoons and settlements
               }
             }
           }
@@ -1139,8 +1001,7 @@ FUNCTION void get_time_series()
         //  SS_Label_Info_24.3.3 #Do fishing mortality
         catage_tot.initialize();
 
-        if ((catch_seas_area(t, p, 0) == 1 && fishery_on_off == 1))
-        {
+        if ((catch_seas_area(t, p, 0) == 1 && fishery_on_off == 1)) {
           if (F_Method > 1) //  not Pope's
           {
             //  SS_Label_Info_24.3.3.3 #use the hybrid F method by selected fleets
@@ -1149,24 +1010,21 @@ FUNCTION void get_time_series()
             if (k < F_PH_time(0, t)) //  some fleet needs hybrid this phase
             {
               //  SS_Label_Info_24.3.3.3.1 #Start by doing a Pope's approximation
-              for (int ff = 1; ff <= N_catchfleets(p); ff++)  // loop fleets in this area (p)
+              for (int ff = 1; ff <= N_catchfleets(p); ff++) // loop fleets in this area (p)
               {
                 f = fish_fleet_area(p, ff);
                 if (k < F_PH_time(f, t)) // do hybrid F for this fleet
                 {
                   vbio.initialize();
                   for (g = 1; g <= gmorph; g++)
-                    if (use_morph(g) > 0)
-                    {
-                      if (catchunits(f) == 1)
-                      {
+                    if (use_morph(g) > 0) {
+                      if (catchunits(f) == 1) {
                         vbio += Nmid(g) * sel_ret_bio(s, f, g);
                       } // retained catch bio
-                      else
-                      {
+                      else {
                         vbio += Nmid(g) * sel_ret_num(s, f, g);
                       } // retained catch numbers
-                    } //close gmorph loop
+                    } // close gmorph loop
                   //  SS_Label_Info_24.3.3.3.2 #Apply constraint so that no fleet's initial calculation of harvest rate would exceed 95%
                   temp = catch_ret_obs(f, t) / (vbio + 0.1 * catch_ret_obs(f, t)); //  Pope's rate  robust
                   join1 = 1. / (1. + mfexp(30. * (temp - 0.95))); // steep logistic joiner at harvest rate of 0.95
@@ -1177,15 +1035,12 @@ FUNCTION void get_time_series()
               }
 
               //  SS_Label_Info_24.3.3.3.4 #Do a specified number of loops to tune up these F values to more closely match the observed catch
-              for (int tune_F = 1; tune_F <= F_Tune - 1; tune_F++)
-              {
+              for (int tune_F = 1; tune_F <= F_Tune - 1; tune_F++) {
                 //  SS_Label_Info_24.3.3.3.5 #add F+M to get Z
                 for (g = 1; g <= gmorph; g++)
-                  if (use_morph(g) > 0)
-                  {
-                    Z_rate(t, p, g) = natM(t, p, GP3(g));  //  already includes predators
-                    for (int ff = 1; ff <= N_catchfleets(p); ff++)
-                    {
+                  if (use_morph(g) > 0) {
+                    Z_rate(t, p, g) = natM(t, p, GP3(g)); //  already includes predators
+                    for (int ff = 1; ff <= N_catchfleets(p); ff++) {
                       f = fish_fleet_area(p, ff);
                       Z_rate(t, p, g) += sel_dead_num(s, f, g) * Hrate(f, t);
                     }
@@ -1198,39 +1053,34 @@ FUNCTION void get_time_series()
                   interim_tot_catch = 0.0; // this is the expected total catch that would occur with the current Hrates and Z
                   // totcatch_byarea(t,p) is now recalculated here just for the fleets doing hybrid in this phase
                   double target_catch = 0.0;
-                  for (int ff = 1; ff <= N_catchfleets(p); ff++)
-                  {
+                  for (int ff = 1; ff <= N_catchfleets(p); ff++) {
                     f = fish_fleet_area(p, ff);
-                    
+
                     if (current_phase() < F_PH_time(f, t)) // so still doing hybrid; skips bycatch fleets
                     {
                       for (g = 1; g <= gmorph; g++)
-                        if (use_morph(g) > 0)
-                        {
-                          if (catchunits(f) == 1)
-                          {
+                        if (use_morph(g) > 0) {
+                          if (catchunits(f) == 1) {
                             interim_tot_catch += catch_mult(y, f) * Hrate(f, t) * elem_prod(natage(t, p, g), sel_ret_bio(s, f, g)) * Zrate2(p, g); // biomass basis
                           }
-                          else
-                          {
+                          else {
                             interim_tot_catch += catch_mult(y, f) * Hrate(f, t) * elem_prod(natage(t, p, g), sel_ret_num(s, f, g)) * Zrate2(p, g); //  numbers basis
                           }
-                        } //close gmorph loop
+                        } // close gmorph loop
                       target_catch += catch_ret_obs(f, t);
                     }
                   } // close fishery
                   Z_adjuster = target_catch / (interim_tot_catch + 0.0001);
                   for (g = 1; g <= gmorph; g++)
-                    if (use_morph(g) > 0)
-                    {
+                    if (use_morph(g) > 0) {
                       Z_rate(t, p, g) = natM(t, p, GP3(g)) + Z_adjuster * (Z_rate(t, p, g) - natM(t, p, GP3(g))); // find adjusted Z
                       Zrate2(p, g) = elem_div((1. - mfexp(-seasdur(s) * Z_rate(t, p, g))), Z_rate(t, p, g));
                     }
 
-                  for (int ff = 1; ff <= N_catchfleets(p); ff++) //loop over fishing  fleets with input catch
+                  for (int ff = 1; ff <= N_catchfleets(p); ff++) // loop over fishing  fleets with input catch
                   {
                     f = fish_fleet_area(p, ff);
-//                    if (fleet_type(f) == 1)
+                    //                    if (fleet_type(f) == 1)
                     {
                       if (current_phase() < F_PH_time(f, t)) //  skips bycatch fleets and fixed F values
                       {
@@ -1238,17 +1088,14 @@ FUNCTION void get_time_series()
                         //  since catch = N * F*sel * (1-e(-Z))/Z
                         //  so F = catch / (N*sel * (1-e(-Z)) /Z )
                         for (g = 1; g <= gmorph; g++)
-                          if (use_morph(g) > 0)
-                          {
-                            if (catchunits(f) == 1)
-                            {
+                          if (use_morph(g) > 0) {
+                            if (catchunits(f) == 1) {
                               vbio += elem_prod(natage(t, p, g), sel_ret_bio(s, f, g)) * Zrate2(p, g);
                             }
-                            else
-                            {
+                            else {
                               vbio += elem_prod(natage(t, p, g), sel_ret_num(s, f, g)) * Zrate2(p, g);
                             }
-                          } //close gmorph loop
+                          } // close gmorph loop
                         temp = catch_ret_obs(f, t) / (catch_mult(y, f) * vbio + 0.0001); //  prototype new F
                         join1 = 1. / (1. + mfexp(30. * (temp - 0.95 * max_harvest_rate)));
                         Hrate(f, t) = join1 * temp + (1. - join1) * max_harvest_rate; //  new F value for this fleet
@@ -1264,15 +1111,12 @@ FUNCTION void get_time_series()
             {
               //  SS_Label_Info_24.3.3.2.1 #For each platoon, loop fleets to calculate Z = M+sum(F)
               for (g = 1; g <= gmorph; g++)
-                if (use_morph(g) > 0)
-                {
-                  Z_rate(t, p, g) = natM(t, p, GP3(g));  //  already includes predators M2
+                if (use_morph(g) > 0) {
+                  Z_rate(t, p, g) = natM(t, p, GP3(g)); //  already includes predators M2
 
-                  for (int ff = 1; ff <= N_catchfleets(p); ff++)
-                  {
+                  for (int ff = 1; ff <= N_catchfleets(p); ff++) {
                     f = fish_fleet_area(p, ff);
-                    if (catch_seas_area(t, p, f) == 1)
-                    {
+                    if (catch_seas_area(t, p, f) == 1) {
                       Z_rate(t, p, g) += sel_dead_num(s, f, g) * Hrate(f, t);
                     }
                   }
@@ -1280,14 +1124,11 @@ FUNCTION void get_time_series()
                 }
 
               //  SS_Label_Info_24.3.3.2.2 #For each fleet, loop platoons and accumulate catch
-              for (int ff = 1; ff <= N_catchfleets(0); ff++)
-              {
+              for (int ff = 1; ff <= N_catchfleets(0); ff++) {
                 f = fish_fleet_area(0, ff);
-                if (catch_seas_area(t, p, f) == 1)
-                {
+                if (catch_seas_area(t, p, f) == 1) {
                   for (g = 1; g <= gmorph; g++)
-                    if (use_morph(g) > 0)
-                    {
+                    if (use_morph(g) > 0) {
                       catch_fleet(t, f, 1) += Hrate(f, t) * elem_prod(natage(t, p, g), sel_bio(s, f, g)) * Zrate2(p, g);
                       catch_fleet(t, f, 2) += Hrate(f, t) * elem_prod(natage(t, p, g), sel_dead_bio(s, f, g)) * Zrate2(p, g);
                       catch_fleet(t, f, 3) += Hrate(f, t) * elem_prod(natage(t, p, g), sel_ret_bio(s, f, g)) * Zrate2(p, g); // retained bio
@@ -1295,47 +1136,41 @@ FUNCTION void get_time_series()
                       catch_fleet(t, f, 5) += Hrate(f, t) * elem_prod(natage(t, p, g), sel_dead_num(s, f, g)) * Zrate2(p, g);
                       catch_fleet(t, f, 6) += Hrate(f, t) * elem_prod(natage(t, p, g), sel_ret_num(s, f, g)) * Zrate2(p, g); // retained numbers
                       catage(t, f, g) = Hrate(f, t) * elem_prod(elem_prod(natage(t, p, g), sel_dead_num(s, f, g)), Zrate2(p, g));
-                      if (Do_Retain(f) > 0)
-                      {
+                      if (Do_Retain(f) > 0) {
                         disc_age(t, disc_fleet_list(f), g) = Hrate(f, t) * elem_prod(elem_prod(natage(t, p, g), sel_num(s, f, g)), Zrate2(p, g)); //  selected numbers
                         disc_age(t, disc_fleet_list(f) + N_retain_fleets, g) = Hrate(f, t) * elem_prod(elem_prod(natage(t, p, g), sel_ret_num(s, f, g)), Zrate2(p, g)); //  selected numbers
                       }
-                    } //close gmorph loop
+                    } // close gmorph loop
                 }
               } // close fishery
             } //  end continuous F method
           }
-          else  //  doing F with Pope's approximation.  Predators cannot be used
+          else //  doing F with Pope's approximation.  Predators cannot be used
           {
             //  SS_Label_Info_24.3.3.1 #Use F_Method=1 for Pope's approximation
             //  SS_Label_Info_24.3.3.1.1 #note that pred_M2 not implemented for Pope's
-            for (int ff = 1; ff <= N_catchfleets(p); ff++)
-            {
+            for (int ff = 1; ff <= N_catchfleets(p); ff++) {
               f = fish_fleet_area(p, ff);
-              if (catch_seas_area(t, p, f) == 1)
-              {
+              if (catch_seas_area(t, p, f) == 1) {
                 dvar_matrix catage_w = catage(t, f); // do shallow copy
 
                 //  SS_Label_Info_24.3.3.1.2 #loop over platoons and calculate the vulnerable biomass for each fleet
                 vbio.initialize();
                 for (g = 1; g <= gmorph; g++)
-                  if (use_morph(g) > 0)
-                  {
+                  if (use_morph(g) > 0) {
                     // use sel_l to get total catch and use sel_l_r to get retained vbio
                     // note that vbio in numbers can be used for both survey abund and fishery available "biomass"
                     // vbio is for retained catch only;  harvest rate = retainedcatch/vbio;
                     // then harvestrate*catage_w = total kill by this fishery for this morph
 
-                    if (catchunits(f) == 1)
-                    {
+                    if (catchunits(f) == 1) {
                       vbio += Nmid(g) * sel_ret_bio(s, f, g);
                     } // retained catch bio
-                    else
-                    {
+                    else {
                       vbio += Nmid(g) * sel_ret_num(s, f, g);
                     } // retained catch numbers
 
-                  } //close gmorph loop
+                  } // close gmorph loop
                 if (docheckup == 1)
                   echoinput << "fleet vbio obs_catch catch_mult vbio*catchmult" << f << " " << vbio << " " << catch_ret_obs(f, t) << " " << catch_mult(y, f) << " " << catch_mult(y, f) * vbio << endl;
                 //  SS_Label_Info_24.3.3.1.3 #Calculate harvest rate for each fleet from catch/vulnerable biomass
@@ -1343,20 +1178,18 @@ FUNCTION void get_time_series()
                 crashtemp = max_harvest_rate - catch_ret_obs(f, t) / (catch_mult(y, f) * vbio + NilNumbers);
                 crashtemp1 = posfun(crashtemp, 0.000001, CrashPen);
                 harvest_rate = max_harvest_rate - crashtemp1;
-                if (crashtemp < 0. && rundetail >= 2)
-                {
+                if (crashtemp < 0. && rundetail >= 2) {
                   cout << y << " " << f << " crash vbio*catchmult " << catch_ret_obs(f, t) / (catch_mult(y, f) * (vbio + NilNumbers)) << " " << crashtemp << " " << crashtemp1 << " " << CrashPen << " " << harvest_rate << endl;
                 }
                 Hrate(f, t) = harvest_rate;
 
                 //  SS_Label_Info_24.3.3.1.4 #Store various catch quantities in catch_fleet
                 for (g = 1; g <= gmorph; g++)
-                  if (use_morph(g) > 0)
-                  {
+                  if (use_morph(g) > 0) {
                     catage_w(g) = harvest_rate * elem_prod(Nmid(g), sel_dead_num(s, f, g)); // total kill numbers at age
                     if (docheckup == 1)
                       echoinput << "killrate " << sel_dead_num(s, f, g)(0, min(6, nages)) << endl;
-                    catage_tot(g) += catage_w(g); //catch at age for all fleets
+                    catage_tot(g) += catage_w(g); // catch at age for all fleets
                     catch_fleet(t, f, 2) += Hrate(f, t) * Nmid(g) * sel_dead_bio(s, f, g); // total fishery kill in biomass
                     catch_fleet(t, f, 5) += Hrate(f, t) * Nmid(g) * sel_dead_num(s, f, g); // total fishery kill in numbers
                     catch_fleet(t, f, 1) += Hrate(f, t) * Nmid(g) * sel_bio(s, f, g); //  total fishery encounter in biomass
@@ -1369,20 +1202,16 @@ FUNCTION void get_time_series()
 
             //  SS_Label_Info_24.3.3.1.5 #Check for catch_total across fleets being greater than population numbers
             for (g = 1; g <= gmorph; g++)
-              if (use_morph(g) > 0)
-              {
+              if (use_morph(g) > 0) {
                 for (a = 0; a <= nages; a++) //  check for negative abundance, starting at age 1
                 {
-                  if (natage(t, p, g, a) > 0.0)
-                  {
+                  if (natage(t, p, g, a) > 0.0) {
                     crashtemp = max_harvest_rate - catage_tot(g, a) / (Nmid(g, a) + 0.0000001);
                     crashtemp1 = posfun(crashtemp, 0.000001, CrashPen);
-                    if (crashtemp < 0. && rundetail >= 2)
-                    {
+                    if (crashtemp < 0. && rundetail >= 2) {
                       cout << " crash age " << catage_tot(g, a) / (Nmid(g, a) + 0.0000001) << " " << crashtemp << " " << crashtemp1 << " " << CrashPen << " " << (max_harvest_rate - crashtemp1) * Nmid(g, a) << endl;
                     }
-                    if (crashtemp < 0. && docheckup == 1)
-                    {
+                    if (crashtemp < 0. && docheckup == 1) {
                       echoinput << " crash age " << catage_tot(g, a) / (Nmid(g, a) + 0.0000001) << " " << crashtemp << " " << crashtemp1 << " " << CrashPen << " " << (max_harvest_rate - crashtemp1) * Nmid(g, a) << endl;
                     }
                     catage_tot(g, a) = (max_harvest_rate - crashtemp1) * Nmid(g, a);
@@ -1390,8 +1219,7 @@ FUNCTION void get_time_series()
                     temp = natage(t, p, g, a) * surv2(s, GP3(g), a) - catage_tot(g, a) * surv1(s, GP3(g), a);
                     Z_rate(t, p, g, a) = -log(temp / natage(t, p, g, a)) / seasdur(s);
                   }
-                  else
-                  {
+                  else {
                     Z_rate(t, p, g, a) = -log(surv2(s, GP3(g), a)) / seasdur(s);
                   }
                 }
@@ -1400,38 +1228,31 @@ FUNCTION void get_time_series()
               }
           } //  end Pope's approx
         } //  end have some catch in this seas x area
-        else
-        {
+        else {
           //  SS_Label_Info_24.3.3.4 #No catch or fishery turned off, so set Z=M
           for (g = 1; g <= gmorph; g++)
-            if (use_morph(g) > 0)
-            {
-              Z_rate(t, p, g) = natM(t, p, GP3(g));  //  includes predators
+            if (use_morph(g) > 0) {
+              Z_rate(t, p, g) = natM(t, p, GP3(g)); //  includes predators
               Zrate2(p, g) = elem_div((1. - mfexp(-seasdur(s) * Z_rate(t, p, g))), Z_rate(t, p, g));
             }
         }
 
-      //  SS_Label_Info_24.3.3.4 #save vulnerable biomass and numbers.  Use middle of season
-        if (bigsaver == 1)
-        {
+        //  SS_Label_Info_24.3.3.4 #save vulnerable biomass and numbers.  Use middle of season
+        if (bigsaver == 1) {
           vuln_bio(t) = 0.0;
           vuln_num(t) = 0.0;
           for (g = 1; g <= gmorph; g++)
-          if (use_morph(g) > 0)
-          {
-            for (f = 1; f<= Nfleet; f++)
-            {
-              vuln_bio(t, f) += sel_bio(s, f, g) * elem_prod(natage(t, p, g), mfexp(-Z_rate(t, p, g) * 0.5 * seasdur(s)));
-              vuln_num(t, f) += sel_num(s, f, g) * elem_prod(natage(t, p, g), mfexp(-Z_rate(t, p, g) * 0.5 * seasdur(s)));
+            if (use_morph(g) > 0) {
+              for (f = 1; f <= Nfleet; f++) {
+                vuln_bio(t, f) += sel_bio(s, f, g) * elem_prod(natage(t, p, g), mfexp(-Z_rate(t, p, g) * 0.5 * seasdur(s)));
+                vuln_num(t, f) += sel_num(s, f, g) * elem_prod(natage(t, p, g), mfexp(-Z_rate(t, p, g) * 0.5 * seasdur(s)));
+              }
             }
-          }
         }
-        for (f1 = 1; f1 <= N_pred; f1++)
-        {
+        for (f1 = 1; f1 <= N_pred; f1++) {
           f = predator(f1);
           for (g = 1; g <= gmorph; g++)
-            if (use_morph(g) > 0)
-            {
+            if (use_morph(g) > 0) {
               catch_fleet(t, f, 1) += pred_M2(f1, t) * elem_prod(natage(t, p, g), sel_bio(s, f, g)) * Zrate2(p, g);
               catch_fleet(t, f, 2) += pred_M2(f1, t) * elem_prod(natage(t, p, g), sel_dead_bio(s, f, g)) * Zrate2(p, g);
               catch_fleet(t, f, 3) += pred_M2(f1, t) * elem_prod(natage(t, p, g), sel_ret_bio(s, f, g)) * Zrate2(p, g); // retained bio
@@ -1439,11 +1260,10 @@ FUNCTION void get_time_series()
               catch_fleet(t, f, 5) += pred_M2(f1, t) * elem_prod(natage(t, p, g), sel_dead_num(s, f, g)) * Zrate2(p, g);
               catch_fleet(t, f, 6) += pred_M2(f1, t) * elem_prod(natage(t, p, g), sel_ret_num(s, f, g)) * Zrate2(p, g); // retained numbers
               catage(t, f, g) = pred_M2(f1, t) * elem_prod(elem_prod(natage(t, p, g), sel_dead_num(s, f, g)), Zrate2(p, g));
-            } //close gmorph loop
+            } // close gmorph loop
         }
-      } //close area loop
-      if (s == 1 && save_for_report == 1)
-      {
+      } // close area loop
+      if (s == 1 && save_for_report == 1) {
         Smry_Table(y, 1) = totbio;
         Smry_Table(y, 2) = smrybio;
         Smry_Table(y, 3) = smrynum;
@@ -1456,33 +1276,31 @@ FUNCTION void get_time_series()
         SSB_B_yr(y).initialize();
         SSB_N_yr(y).initialize();
         Smry_Table(y, 15) = 0.0;
-        for (p = 1; p <= pop; p++)
-        {
+        for (p = 1; p <= pop; p++) {
           for (g = 1; g <= gmorph; g++)
             if (sx(g) == 1 && use_morph(g) > 0) //  female
             {
               SSB_pop_gp(y, p, GP4(g)) += fracfemale_mult * fec(g) * elem_prod(natage(t, p, g), mfexp(-Z_rate(t, p, g) * spawn_time_seas)); // accumulates SSB by area and by growthpattern
               SSB_B_yr(y) += fracfemale_mult * make_mature_bio(GP4(g)) * elem_prod(natage(t, p, g), mfexp(-Z_rate(t, p, g) * spawn_time_seas));
               SSB_N_yr(y) += fracfemale_mult * make_mature_numbers(GP4(g)) * elem_prod(natage(t, p, g), mfexp(-Z_rate(t, p, g) * spawn_time_seas));
-              Smry_Table(y, 15) += fracfemale_mult * elem_prod(natage(t, p, g), mfexp(-Z_rate(t, p, g) * spawn_time_seas)) * elem_prod(fec(g), r_ages);  //  for mean age of female spawners = GenTime
+              Smry_Table(y, 15) += fracfemale_mult * elem_prod(natage(t, p, g), mfexp(-Z_rate(t, p, g) * spawn_time_seas)) * elem_prod(fec(g), r_ages); //  for mean age of female spawners = GenTime
             }
         }
         SSB_current = sum(SSB_pop_gp(y));
         SSB_yr(y) = SSB_current;
         if (Hermaphro_Option != 0) // get male biomass
         {
-          MaleSPB(y).initialize();
-          for (p = 1; p <= pop; p++)
-          {
+          MaleSSB(y).initialize();
+          for (p = 1; p <= pop; p++) {
             for (g = 1; g <= gmorph; g++)
               if (sx(g) == 2 && use_morph(g) > 0) //  male; all assumed to be mature
               {
-                MaleSPB(y, p, GP4(g)) += Wt_Age_t(t, 0, g) * elem_prod(natage(t, p, g), mfexp(-Z_rate(t, p, g) * spawn_time_seas)); // accumulates SSB by area and by growthpattern
+                MaleSSB(y, p, GP4(g)) += Wt_Age_t(t, 0, g) * elem_prod(natage(t, p, g), mfexp(-Z_rate(t, p, g) * spawn_time_seas)); // accumulates SSB by area and by growthpattern
               }
           }
-          if (Hermaphro_maleSPB > 0.0) // add MaleSPB to female SSB
+          if (Hermaphro_maleSSB > 0.0) // add MaleSSB to female SSB
           {
-            SSB_current += Hermaphro_maleSPB * sum(MaleSPB(y));
+            SSB_current += Hermaphro_maleSSB * sum(MaleSSB(y));
             SSB_yr(y) = SSB_current;
           }
         }
@@ -1494,43 +1312,40 @@ FUNCTION void get_time_series()
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
         }
-        else  //  update SSB_use and R0_use where will update SSBpR0 inside the Spawn_recr fxn
+        else //  update SSB_use and R0_use where will update SSBpR0 inside the Spawn_recr fxn
         {
-          R0_use = mfexp(SR_parm_work(1));  //  check to be sure this works when R0 is derived from B-H with alpha, beta parameters
+          R0_use = mfexp(SR_parm_work(1)); //  check to be sure this works when R0 is derived from B-H with alpha, beta parameters
           Fishon = 0;
           eq_yr = y;
           bio_yr = y;
           Do_Equil_Calc(R0_use); //  call function to do equilibrium calculation
           SSB_use = SSB_equil;
-          SSBpR_virgin_adj = SSB_use / R0_use;  //  update 
-          if (fishery_on_off == 1)
-          {
+          SSBpR_virgin_adj = SSB_use / R0_use; //  update
+          if (fishery_on_off == 1) {
             Fishon = 1;
           }
-          else
-          {
+          else {
             Fishon = 0;
           }
         }
 
         Recruits = Spawn_Recr(SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr
-        if (SR_fxn != 7) apply_recdev(Recruits, R0_use); //  apply recruitment deviation
+        if (SR_fxn != 7)
+          apply_recdev(Recruits, R0_use); //  apply recruitment deviation
 
         // distribute Recruitment among settlements, areas and morphs
         //  note that because SSB_current is calculated at end of season to take into account Z,
         //  this means that recruitment cannot occur until a subsequent season
         for (g = 1; g <= gmorph; g++)
-          if (use_morph(g) > 0)
-          {
+          if (use_morph(g) > 0) {
             settle = settle_g(g);
-            for (p = 1; p <= pop; p++)
-            {
+            for (p = 1; p <= pop; p++) {
               if (y == styr)
                 natage(t + Settle_seas_offset(settle), p, g, Settle_age(settle)) = 0.0; //  to negate the additive code
 
               natage(t + Settle_seas_offset(settle), p, g, Settle_age(settle)) += Recruits * recr_dist(y, GP(g), settle, p) * platoon_distr(GP2(g)) *
                   mfexp(natM(t, p, GP3(g), Settle_age(settle)) * Settle_timing_seas(settle));
-                Recr(p, t + Settle_seas_offset(settle)) += Recruits * recr_dist(y, GP(g), settle, p) * platoon_distr(GP2(g));
+              Recr(p, t + Settle_seas_offset(settle)) += Recruits * recr_dist(y, GP(g), settle, p) * platoon_distr(GP2(g));
               if (docheckup == 1)
                 echoinput << y << " Recruits, dist, surv, result" << Recruits << " " << recr_dist(y, GP(g), settle, p) << " " << mfexp(natM(t, p, GP3(g), Settle_age(settle)) * Settle_timing_seas(settle)) << " " << natage(t + Settle_seas_offset(settle), p, g, Settle_age(settle)) << endl;
             }
@@ -1538,40 +1353,32 @@ FUNCTION void get_time_series()
       }
 
       //  SS_Label_Info_24.6 #Survival to next season and saving midseason numbers and biomass
-      for (p = 1; p <= pop; p++)
-      {
-        if (s == nseas)
-        {
+      for (p = 1; p <= pop; p++) {
+        if (s == nseas) {
           k = 1;
         }
-        else
-        {
+        else {
           k = 0;
         } //      advance age or not
         for (g = 1; g <= gmorph; g++)
-          if (use_morph(g) > 0)
-          {
+          if (use_morph(g) > 0) {
             settle = settle_g(g);
 
             {
               j = Settle_age(settle);
-              if (s < nseas && Settle_seas(settle) <= s)
-              {
+              if (s < nseas && Settle_seas(settle) <= s) {
                 natage(t + 1, p, g, j) = natage(t, p, g, j) * mfexp(-Z_rate(t, p, g, j) * seasdur(s)); // advance new recruits within year
               }
-              for (a = j + 1; a < nages; a++)
-              {
+              for (a = j + 1; a < nages; a++) {
                 natage(t + 1, p, g, a) = natage(t, p, g, a - k) * mfexp(-Z_rate(t, p, g, a - k) * seasdur(s));
               }
               natage(t + 1, p, g, nages) = natage(t, p, g, nages) * mfexp(-Z_rate(t, p, g, nages) * seasdur(s)); // plus group
               if (s == nseas)
                 natage(t + 1, p, g, nages) += natage(t, p, g, nages - 1) * mfexp(-Z_rate(t, p, g, nages - 1) * seasdur(s));
-              if (save_for_report == 1)
-              {
+              if (save_for_report == 1) {
                 j = p + pop;
                 ALK_idx = (s - 1) * N_subseas + mid_subseas;
-                for (a = 0; a <= nages; a++)
-                {
+                for (a = 0; a <= nages; a++) {
                   Save_PopLen(t, j, g) += value(natage(t, p, g, a) * mfexp(-Z_rate(t, p, g, a) * 0.5 * seasdur(s))) * value(ALK(ALK_idx, g, a));
                   Save_PopWt(t, j, g) += value(natage(t, p, g, a) * mfexp(-Z_rate(t, p, g, a) * 0.5 * seasdur(s))) * value(elem_prod(ALK(ALK_idx, g, a), wt_len(s, GP(g))));
                   Save_PopAge(t, j, g, a) = value(natage(t, p, g, a) * mfexp(-Z_rate(t, p, g, a) * 0.5 * seasdur(s)));
@@ -1579,8 +1386,7 @@ FUNCTION void get_time_series()
                 } // close age loop
               }
             }
-            if (docheckup == 1)
-            {
+            if (docheckup == 1) {
               echoinput << g << " natM:   " << natM(t, p, GP3(g))(0, min(6, nages)) << endl;
               echoinput << g << " Z:      " << Z_rate(t, p, g)(0, min(6, nages)) << endl;
               echoinput << g << " N_surv: " << natage(t + 1, p, g)(0, min(6, nages)) << endl;
@@ -1591,27 +1397,20 @@ FUNCTION void get_time_series()
       //  SS_Label_Info_24.7  #call to Get_expected_values
       Get_expected_values(y, t);
       //  SS_Label_Info_24.8  #hermaphroditism
-      if (Hermaphro_Option != 0)
-      {
-        if (Hermaphro_seas == -1 || Hermaphro_seas == s)
-        {
+      if (Hermaphro_Option != 0) {
+        if (Hermaphro_seas == -1 || Hermaphro_seas == s) {
           k = gmorph / 2; //  because first half of the "g" are females
           for (p = 1; p <= pop; p++) //   area
             for (g = 1; g <= k; g++) //  loop females
-              if (use_morph(g) > 0)
-              {
-                if (Hermaphro_Option == 1)
-                {
-                  for (a = 1; a < nages; a++)
-                  {
+              if (use_morph(g) > 0) {
+                if (Hermaphro_Option == 1) {
+                  for (a = 1; a < nages; a++) {
                     natage(t + 1, p, g + k, a) += natage(t + 1, p, g, a) * Hermaphro_val(GP4(g), a - 1); // increment males with females
                     natage(t + 1, p, g, a) *= (1. - Hermaphro_val(GP4(g), a - 1)); // decrement females
                   }
                 }
-                else if (Hermaphro_Option == -1)
-                {
-                  for (a = 1; a < nages; a++)
-                  {
+                else if (Hermaphro_Option == -1) {
+                  for (a = 1; a < nages; a++) {
                     natage(t + 1, p, g, a) += natage(t + 1, p, g + k, a) * Hermaphro_val(GP4(g + k), a - 1); // increment females with males
                     natage(t + 1, p, g + k, a) *= (1. - Hermaphro_val(GP4(g + k), a - 1)); // decrement males
                   }
@@ -1621,7 +1420,7 @@ FUNCTION void get_time_series()
       }
 
       //  SS_Label_Info_24.9  #migration
-      //do migration between populations, for each gmorph and age  PROBLEM  need new container so future recruits not wiped out!
+      // do migration between populations, for each gmorph and age  PROBLEM  need new container so future recruits not wiped out!
       if (do_migration > 0) // movement between areas in time series
       {
         natage_temp = natage(t + 1);
@@ -1629,8 +1428,7 @@ FUNCTION void get_time_series()
         for (p = 1; p <= pop; p++) //   source population
           for (p2 = 1; p2 <= pop; p2++) //  destination population
             for (g = 1; g <= gmorph; g++)
-              if (use_morph(g) > 0)
-              {
+              if (use_morph(g) > 0) {
                 k = move_pattern(s, GP4(g), p, p2);
                 if (k > 0)
                   natage(t + 1, p2, g) += elem_prod(natage_temp(p, g), migrrate(y, k));
@@ -1638,11 +1436,9 @@ FUNCTION void get_time_series()
       } //  end migration
 
       //  SS_Label_Info_24.10  #save selectivity*Hrate for tag-recapture
-      if (Do_TG > 0 && t >= TG_timestart)
-      {
+      if (Do_TG > 0 && t >= TG_timestart) {
         for (g = 1; g <= gmorph; g++)
-          for (f = 1; f <= Nfleet; f++)
-          {
+          for (f = 1; f <= Nfleet; f++) {
             Sel_for_tag(t, f, g) = sel_ret_num(s, f, g) * Hrate(f, t);
           }
       }
@@ -1652,36 +1448,29 @@ FUNCTION void get_time_series()
       dvariable tempbase;
       dvariable tempM;
       dvariable tempZ;
-      if (fishery_on_off == 1 && (bigsaver == 1 || (F_ballpark_yr >= styr)))
-      {
-        for (int ff = 1; ff <= N_catchfleets(0); ff++)
-        {
+      if (fishery_on_off == 1 && (bigsaver == 1 || (F_ballpark_yr >= styr))) {
+        for (int ff = 1; ff <= N_catchfleets(0); ff++) {
           f = fish_fleet_area(0, ff);
-          for (k = 1; k <= 6; k++)
-          {
+          for (k = 1; k <= 6; k++) {
             annual_catch(y, k) += catch_fleet(t, f, k);
             if (k <= 3)
               Smry_Table(y, k + 3) = annual_catch(y, k);
           }
-          if (F_Method == 1)
-          {
+          if (F_Method == 1) {
             annual_F(y, 1) += Hrate(f, t);
           }
-          else
-          {
+          else {
             annual_F(y, 1) += Hrate(f, t) * seasdur(s);
           }
         }
 
-        if (s == nseas)
-        {
+        if (s == nseas) {
           //  sum across p and g the number of survivors to end of the year
           //  also project from the initial numbers and M, the number of survivors without F
           //  then F = ln(n+1/n)(M+F) - ln(n+1/n)(M only), but ln(n) cancels out, so only need the ln of the ratio of the two ending quantities
 
           // calculated average F weighted by numbers (option 5 is unweighted)
-          if (F_reporting != 5)
-          {
+          if (F_reporting != 5) {
             tempbase = 0.0;
             tempM = 0.0;
             tempZ = 0.0;
@@ -1691,15 +1480,12 @@ FUNCTION void get_time_series()
             for (a = F_reporting_ages(1); a <= F_reporting_ages(2); a++) //  should not let a go higher than nages-2 because of accumulator
             {
               for (g = 1; g <= gmorph; g++)
-                if (use_morph(g) > 0)
-                {
-                  for (p = 1; p <= pop; p++)
-                  {
+                if (use_morph(g) > 0) {
+                  for (p = 1; p <= pop; p++) {
                     tempbase += natage(t - nseas + 1, p, g, a); // sum of numbers at beginning of year
                     tempZ += natage(t + 1, p, g, a + 1); // numbers at beginning of next year
                     temp3 = natage(t - nseas + 1, p, g, a); //  numbers at begin of year
-                    for (j = 1; j <= nseas; j++)
-                    {
+                    for (j = 1; j <= nseas; j++) {
                       temp3 *= mfexp(-seasdur(j) * natM(t - nseas + j, p, GP3(g), a));
                     }
                     tempM += temp3; //  survivors if just M operating
@@ -1710,8 +1496,7 @@ FUNCTION void get_time_series()
             annual_F(y, 3) = log(tempbase) - log(tempM); // M
           } // end if F_reporting!=5
 
-          else
-          { // F_reporting==5 (ICES-style arithmetic mean across ages)
+          else { // F_reporting==5 (ICES-style arithmetic mean across ages)
             //  like option 4 above, but F is calculated 1 age at a time to get a
             //  unweighted average across ages within each year
             countN = 0.0; // used for count of Fs included in average
@@ -1722,15 +1507,12 @@ FUNCTION void get_time_series()
               tempZ = 0.0;
               //  accumulate numbers across all morphs, sexes, and areas
               for (g = 1; g <= gmorph; g++)
-                if (use_morph(g) > 0)
-                {
-                  for (p = 1; p <= pop; p++)
-                  {
+                if (use_morph(g) > 0) {
+                  for (p = 1; p <= pop; p++) {
                     tempbase += natage(t - nseas + 1, p, g, a); // sum of numbers at beginning of year
                     tempZ += natage(t + 1, p, g, a + 1); // numbers at beginning of next year
                     temp3 = natage(t - nseas + 1, p, g, a); //  numbers at begin of year
-                    for (j = 1; j <= nseas; j++)
-                    {
+                    for (j = 1; j <= nseas; j++) {
                       temp3 *= mfexp(-seasdur(j) * natM(t - nseas + j, p, GP3(g), a));
                     }
                     tempM += temp3; //  survivors if just M operating
@@ -1747,34 +1529,27 @@ FUNCTION void get_time_series()
 
           if (STD_Yr_Reverse_F(y) > 0) //  save selected std quantity
           {
-            if (F_reporting <= 1)
-            {
+            if (F_reporting <= 1) {
               F_std(STD_Yr_Reverse_F(y)) = annual_catch(y, 2) / Smry_Table(y, 2); // dead catch biomass/summary biomass
               //  does not exactly correspond to F, which is for total catch
             }
-            else if (F_reporting == 2)
-            {
+            else if (F_reporting == 2) {
               F_std(STD_Yr_Reverse_F(y)) = annual_catch(y, 5) / Smry_Table(y, 3); // dead catch numbers/summary numbers
             }
-            else if (F_reporting == 3)
-            {
+            else if (F_reporting == 3) {
               F_std(STD_Yr_Reverse_F(y)) = annual_F(y, 1);
             }
-            else if (F_reporting == 4 || F_reporting == 5)
-            {
+            else if (F_reporting == 4 || F_reporting == 5) {
               F_std(STD_Yr_Reverse_F(y)) = annual_F(y, 2);
             }
           }
         } //  end s==nseas
       }
-      if (write_bodywt > 0)
-      {
-        for (g = 1; g <= gmorph; g++)
-        {
+      if (write_bodywt > 0) {
+        for (g = 1; g <= gmorph; g++) {
           gg = sx(g);
 
-          if (ishadow(GP2(g)) == 0)
-          {
+          if (ishadow(GP2(g)) == 0) {
             if (s == spawn_seas)
               bodywtout << y << " " << s << " " << gg << " " << GP4(g) << " " << Bseas(g) << " " << -2 << " " << fec(g) << " #fecundity " << endl;
             bodywtout << y << " " << s << " " << gg << " " << GP4(g) << " " << Bseas(g) << " " << 0 << " " << Wt_Age_beg(s, g) << " #popwt_beg " << endl;
@@ -1782,13 +1557,12 @@ FUNCTION void get_time_series()
           }
         }
       }
-    } //close season loop
+    } // close season loop
     //  SS_Label_Info_24.12 #End loop of seasons
 
     //  SS_Label_Info_24.13 #Use current F intensity to calculate the equilibrium SPR for this year
     //    if( (save_for_report>0) || ((sd_phase() || mceval_phase()) && (initial_params::mc_phase==0)) )
-    if (bigsaver == 1)
-    {
+    if (bigsaver == 1) {
       eq_yr = y;
       equ_Recr = Recr_virgin;
       bio_yr = y;
@@ -1796,18 +1570,16 @@ FUNCTION void get_time_series()
       Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation with current year's biology
       Smry_Table(y, 11) = SSB_equil;
       Smry_Table(y, 13) = GenTime;
-      if( SR_fxn == 10 )
-      {
-        temp = SSB_equil / Recr_virgin;  //  current year's SPB/R with current biology at age
+      if (SR_fxn == 10) {
+        temp = SSB_equil / Recr_virgin; //  current year's SSB/R with current biology at age
         alpha = mfexp(SR_parm_work(3));
         beta = mfexp(SR_parm_work(4));
-        SR_parm_byyr(y, 2) =  alpha * temp / (4. + alpha * temp);  //  implied steepness
-        SR_parm_byyr(y, 1) = log( 1. / beta * (alpha - (1. / temp)));  //  implied ln_R0
+        SR_parm_byyr(y, 2) = alpha * temp / (4. + alpha * temp); //  implied steepness
+        SR_parm_byyr(y, 1) = log(1. / beta * (alpha - (1. / temp))); //  implied ln_R0
       }
       Fishon = 1;
       Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation with current year's biology and F
-      if (STD_Yr_Reverse_Ofish(y) > 0)
-      {
+      if (STD_Yr_Reverse_Ofish(y) > 0) {
         SPR_std(STD_Yr_Reverse_Ofish(y)) = SSB_equil / Smry_Table(y, 11);
       }
       Smry_Table(y, 9) = (totbio);
@@ -1815,29 +1587,28 @@ FUNCTION void get_time_series()
       Smry_Table(y, 12) = (SSB_equil);
       Smry_Table(y, 14) = (YPR_dead);
     }
-  } //close year loop
+  } // close year loop
 
   //  average quantities accumulated during the time series
-  if (Do_Benchmark > 0)
-  {
+  if (Do_Benchmark > 0) {
     recr_dist(styr - 3) = recr_dist_unf / float(Bmark_Yr(8) - Bmark_Yr(7) + 1);
   }
 
   if (Do_TG > 0)
     Tag_Recapture();
 
-  } //  end time_series
-  #ifdef DO_ONCE
-  if (do_once == 1)
+} //  end time_series
+#ifdef DO_ONCE
+if (do_once == 1)
   echoinput << " finished time series " << endl;
-  #endif
+#endif
 
 //  SS_Label_Info_24.16  # end of time series function
 
 //********************************************************************
- /*  SS_Label_FUNCTION 30 Do_Equil_Calc */
+/*  SS_Label_FUNCTION 30 Do_Equil_Calc */
 FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
-  {
+{
   int t_base;
   int t;
   int s;
@@ -1870,14 +1641,11 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
   GenTime = 0.0;
 
   // first seed the recruits; seems redundant
-  for (g = 1; g <= gmorph; g++)
-  {
-    if (use_morph(g) > 0)
-    {
+  for (g = 1; g <= gmorph; g++) {
+    if (use_morph(g) > 0) {
       settle = settle_g(g);
 
-      for (p = 1; p <= pop; p++)
-      {
+      for (p = 1; p <= pop; p++) {
         equ_numbers(Settle_seas(settle), p, g, Settle_age(settle)) = equ_Recr * recr_dist(y, GP(g), settle, p) * platoon_distr(GP2(g)) *
             mfexp(natM(t_base + Settle_seas(settle), p, GP3(g), Settle_age(settle)) * Settle_timing_seas(settle));
       }
@@ -1886,29 +1654,23 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
 
   for (a = 0; a <= 3 * nages; a++) // go to 3x nages to approximate the infinite tail, then add the infinite tail
   {
-    if (a <= nages)
-    {
+    if (a <= nages) {
       a1 = a;
     }
-    else
-    {
+    else {
       a1 = nages;
     } // because selex and biology max out at nages
 
-    for (s = 1; s <= nseas; s++)
-    {
+    for (s = 1; s <= nseas; s++) {
       t = t_base + s;
 
       for (g = 1; g <= gmorph; g++) //  need to loop g inside of a because of hermaphroditism
-        if (use_morph(g) > 0)
-        {
+        if (use_morph(g) > 0) {
           gg = sx(g); // gender
           settle = settle_g(g);
 
-          for (p = 1; p <= pop; p++)
-          {
-            if (s == Settle_seas(settle) && a == Settle_age(settle))
-            {
+          for (p = 1; p <= pop; p++) {
+            if (s == Settle_seas(settle) && a == Settle_age(settle)) {
               equ_numbers(Settle_seas(settle), p, g, Settle_age(settle)) = equ_Recr * recr_dist(y, GP(g), settle, p) * platoon_distr(GP2(g)) *
                   mfexp(natM(t_base + Settle_seas(settle), p, GP3(g), Settle_age(settle)) * Settle_timing_seas(settle));
             }
@@ -1920,13 +1682,11 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
               {
                 N_mid = N_beg * surv1(s, GP3(g), a1); // numbers at middle of season
                 Nsurvive = N_mid; // initial number of fishery survivors
-                if (Fishon == 1)
-                { //  remove catch this round
+                if (Fishon == 1) { //  remove catch this round
                   // check to see if total harves would exceed max_harvest_rate
                   crashtemp = 0.;
                   harvest_rate = 1.0;
-                  for (int ff = 1; ff <= N_catchfleets(p); ff++)
-                  {
+                  for (int ff = 1; ff <= N_catchfleets(p); ff++) {
                     f = fish_fleet_area(p, ff);
                     crashtemp += Hrate(f, t) * sel_dead_num(s, f, g, a1);
                   }
@@ -1938,8 +1698,7 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
                     harvest_rate = join1 + (1. - join1) * upselex / (crashtemp); // ratio by which all Hrates will be adjusted
                   }
 
-                  for (int ff = 1; ff <= N_catchfleets(p); ff++)
-                  {
+                  for (int ff = 1; ff <= N_catchfleets(p); ff++) {
                     f = fish_fleet_area(p, ff);
                     temp = N_mid * Hrate(f, t) * harvest_rate; // numbers that would be caught if fully selected
                     Nsurvive -= temp * sel_dead_num(s, f, g, a1); //  survival from fishery kill
@@ -1956,8 +1715,7 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
 
                 Nsurvive *= surv1(s, GP3(g), a1); // decay to end of season
 
-                if (a <= a1)
-                {
+                if (a <= a1) {
                   equ_Z(s, p, g, a1) = -(log((Nsurvive + 1.0e-13) / (N_beg + 1.0e-10))) / seasdur(s);
                   Fishery_Survival = equ_Z(s, p, g, a1) - natM(t, p, GP3(g), a1);
                 }
@@ -1967,12 +1725,9 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
               else // Continuous F for method 2 or 3
               {
                 equ_Z(s, p, g, a1) = natM(t, p, GP3(g), a1);
-                if (Fishon == 1)
-                {
-                  if (a1 <= nages)
-                  {
-                    for (int ff = 1; ff <= N_catchfleets(p); ff++)
-                    {
+                if (Fishon == 1) {
+                  if (a1 <= nages) {
+                    for (int ff = 1; ff <= N_catchfleets(p); ff++) {
                       f = fish_fleet_area(p, ff);
                       equ_Z(s, p, g, a1) += sel_dead_num(s, f, g, a1) * Hrate(f, t);
                     }
@@ -1982,30 +1737,23 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
               } //  end F method
               Survivors(p, g) = Nsurvive;
             }
-            else
-            {
+            else {
               equ_Z(s, p, g, a1) = natM(t, p, GP3(g), a1);
             }
           } // end pop
         } // end morph
 
-      if (Hermaphro_Option != 0)
-      {
-        if (Hermaphro_seas == -1 || Hermaphro_seas == s)
-        {
-          for (p = 1; p <= pop; p++)
-          {
+      if (Hermaphro_Option != 0) {
+        if (Hermaphro_seas == -1 || Hermaphro_seas == s) {
+          for (p = 1; p <= pop; p++) {
             k = gmorph / 2;
             for (g = 1; g <= k; g++)
-              if (use_morph(g) > 0)
-              {
-                if (Hermaphro_Option == 1)
-                {
+              if (use_morph(g) > 0) {
+                if (Hermaphro_Option == 1) {
                   Survivors(p, g + k) += Survivors(p, g) * Hermaphro_val(GP4(g), a1); // increment males with females
                   Survivors(p, g) *= (1. - Hermaphro_val(GP4(g), a1)); // decrement females
                 }
-                else if (Hermaphro_Option == -1)
-                {
+                else if (Hermaphro_Option == -1) {
                   Survivors(p, g) += Survivors(p, g + k) * Hermaphro_val(GP4(g + k), a1); // increment females with males
                   Survivors(p, g + k) *= (1. - Hermaphro_val(GP4(g + k), a1)); // decrement males
                 }
@@ -2017,11 +1765,9 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
       {
         Survivors2.initialize();
         for (g = 1; g <= gmorph; g++)
-          if (use_morph(g) > 0)
-          {
+          if (use_morph(g) > 0) {
             for (p = 1; p <= pop; p++)
-              for (p2 = 1; p2 <= pop; p2++)
-              {
+              for (p2 = 1; p2 <= pop; p2++) {
                 k = move_pattern(s, GP4(g), p, p2);
                 if (k > 0)
                   Survivors2(p2, g) += Survivors(p, g) * migrrate(bio_yr, k, a1);
@@ -2031,34 +1777,27 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
       } // end do migration
 
       for (g = 1; g <= gmorph; g++)
-        if (use_morph(g) > 0)
-        {
-          for (p = 1; p <= pop; p++)
-          {
+        if (use_morph(g) > 0) {
+          for (p = 1; p <= pop; p++) {
             if (s == nseas) // into next age at season 1
             {
-              if (a == 3 * nages)
-              {
+              if (a == 3 * nages) {
                 // end of the cohort
               }
               else if (a == (3 * nages - 1)) // do infinite tail; note that it uses Z from nseas as if it applies annually
               {
-                if (F_Method == 1)
-                {
+                if (F_Method == 1) {
                   equ_numbers(1, p, g, a + 1) = Survivors(p, g) / (1. - exp(-equ_Z(nseas, p, g, nages)));
                 }
-                else
-                {
+                else {
                   equ_numbers(1, p, g, a + 1) = Survivors(p, g) / (1. - exp(-equ_Z(nseas, p, g, nages)));
                 }
               }
-              else
-              {
+              else {
                 equ_numbers(1, p, g, a + 1) = Survivors(p, g);
               }
             }
-            else
-            {
+            else {
               equ_numbers(s + 1, p, g, a) = Survivors(p, g); // same age, next season
             }
           }
@@ -2068,23 +1807,18 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
 
   // now calc contribution to catch and ssb
   for (g = 1; g <= gmorph; g++)
-    if (use_morph(g) > 0)
-    {
+    if (use_morph(g) > 0) {
       gg = sx(g);
       for (s = 1; s <= nseas; s++)
-        for (p = 1; p <= pop; p++)
-        {
+        for (p = 1; p <= pop; p++) {
           t = t_base + s;
           Zrate2(p, g) = elem_div((1. - mfexp(-seasdur(s) * equ_Z(s, p, g))), equ_Z(s, p, g));
           equ_numbers(s, p, g, nages) += sum(equ_numbers(s, p, g)(nages + 1, 3 * nages));
-          if (Fishon == 1)
-          {
-            if (F_Method >= 2)
-            {
+          if (Fishon == 1) {
+            if (F_Method >= 2) {
               if (s < Bseas(g))
                 Zrate2(p, g, 0) = 0.0;
-              for (int ff = 1; ff <= N_catchfleets(p); ff++)
-              {
+              for (int ff = 1; ff <= N_catchfleets(p); ff++) {
                 f = fish_fleet_area(p, ff);
                 equ_catch_fleet(2, s, f) += Hrate(f, t) * elem_prod(equ_numbers(s, p, g)(0, nages), sel_dead_bio(s, f, g)) * Zrate2(p, g); // dead catch bio
                 equ_catch_fleet(5, s, f) += Hrate(f, t) * elem_prod(equ_numbers(s, p, g)(0, nages), sel_dead_num(s, f, g)) * Zrate2(p, g); // deadfish catch numbers
@@ -2100,9 +1834,8 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
               // already done in the age loop
             }
           }
-          
-          for (f1 = 1; f1 <= N_pred; f1++)
-          {
+
+          for (f1 = 1; f1 <= N_pred; f1++) {
             f = predator(f1);
             equ_catch_fleet(2, s, f) += pred_M2(f1, t) * elem_prod(equ_numbers(s, p, g)(0, nages), sel_dead_bio(s, f, g)) * Zrate2(p, g); // dead catch bio
             equ_catch_fleet(5, s, f) += pred_M2(f1, t) * elem_prod(equ_numbers(s, p, g)(0, nages), sel_dead_num(s, f, g)) * Zrate2(p, g); // deadfish catch numbers
@@ -2113,16 +1846,14 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
             equ_catage(s, f, g) = pred_M2(f1, t) * elem_prod(elem_prod(equ_numbers(s, p, g)(0, nages), sel_dead_num(s, f, g)), Zrate2(p, g));
           }
 
-          if (s == 1)
-          {
+          if (s == 1) {
             totbio += equ_numbers(s, p, g)(0, nages) * Wt_Age_beg(s, g)(0, nages);
             smrybio += equ_numbers(s, p, g)(Smry_Age, nages) * Wt_Age_beg(s, g)(Smry_Age, nages);
             smrynum += sum(equ_numbers(s, p, g)(Smry_Age, nages));
             smryage += equ_numbers(s, p, g)(Smry_Age, nages) * r_ages(Smry_Age, nages);
           }
           //  SPAWN-RECR:   calc generation time, etc.
-          if (s == spawn_seas)
-          {
+          if (s == spawn_seas) {
             if (gg == 1) // compute equilibrium spawning biomass for females
             {
               tempvec_a = elem_prod(equ_numbers(s, p, g)(0, nages), mfexp(-spawn_time_seas * equ_Z(s, p, g)(0, nages)));
@@ -2135,8 +1866,7 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
               //               equ_mat_num+=elem_prod(equ_numbers(s,p,g)(0,nages),mfexp(-spawn_time_seas*equ_Z(s,p,g)(0,nages)))*make_mature_numbers(GP4(g));
               //               GenTime+=tempvec_a*elem_prod(fec(g),r_ages);
             }
-            else if (Hermaphro_Option != 0 && gg == 2)
-            {
+            else if (Hermaphro_Option != 0 && gg == 2) {
               tempvec_a = elem_prod(equ_numbers(s, p, g)(0, nages), mfexp(-spawn_time_seas * equ_Z(s, p, g)(0, nages)));
               MaleSSB_equil_pop_gp(p, GP4(g)) += tempvec_a * Wt_Age_beg(s, g)(0, nages);
             }
@@ -2149,63 +1879,50 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
   YPR_N_dead = sum(equ_catch_fleet(5)); // dead numbers per recruit
   YPR_enc = sum(equ_catch_fleet(1)); //  encountered biomass per recruit
   YPR_ret = sum(equ_catch_fleet(3)); // retained biomass per recruit
-  YPR_opt = 0.0; //dead biomass per recruit except excludes non-optimized bycatch
+  YPR_opt = 0.0; // dead biomass per recruit except excludes non-optimized bycatch
   // YPR_opt used in F0.1 and in biomass based MSY searches
   YPR_val_vec.initialize(); // retained biomass per recruit as vector, should be same as YPR_ret
 
-  for (int ff = 1; ff <= N_catchfleets(0); ff++)
-  {
+  for (int ff = 1; ff <= N_catchfleets(0); ff++) {
     f = fish_fleet_area(0, ff);
-    for (s = 1; s <= nseas; s++)
-    {
+    for (s = 1; s <= nseas; s++) {
       YPR_opt += equ_catch_fleet(2, s, f) * YPR_mask(f); //  using dead catch excluding non-optimized bycatch fleets
       YPR_val_vec(f) += equ_catch_fleet(3, s, f) * YPR_mask(f); //  using retained catch so YPR_mask should be redundant
     }
   }
 
-  if (Fishon == 1)
-  {
-  //  shortcut.  equ_M_std using M for area 1, gp 1 only
-    if (F_reporting <= 1)
-    {
+  if (Fishon == 1) {
+    //  shortcut.  equ_M_std using M for area 1, gp 1 only
+    if (F_reporting <= 1) {
       equ_F_std = YPR_dead / smrybio;
       equ_M_std = natM(t_base + 1, 1, 1, int(nages / 2));
     }
-    else if (F_reporting == 2)
-    {
+    else if (F_reporting == 2) {
       equ_F_std = YPR_N_dead / smrynum;
       equ_M_std = natM(t_base + 1, 1, 1, int(nages / 2));
     }
-    else if (F_reporting == 3)
-    {
+    else if (F_reporting == 3) {
       equ_M_std = natM(t_base + 1, 1, 1, int(nages / 2));
-      if (F_Method == 1)
-      {
-        for (s = 1; s <= nseas; s++)
-        {
+      if (F_Method == 1) {
+        for (s = 1; s <= nseas; s++) {
           t = t_base + s;
-          for (int ff = 1; ff <= N_catchfleets(0); ff++)
-          {
+          for (int ff = 1; ff <= N_catchfleets(0); ff++) {
             f = fish_fleet_area(0, ff);
             equ_F_std += Hrate(f, t);
           }
         }
       }
-      else
-      {
-        for (s = 1; s <= nseas; s++)
-        {
+      else {
+        for (s = 1; s <= nseas; s++) {
           t = t_base + s;
-          for (int ff = 1; ff <= N_catchfleets(0); ff++)
-          {
+          for (int ff = 1; ff <= N_catchfleets(0); ff++) {
             f = fish_fleet_area(0, ff);
             equ_F_std += Hrate(f, t) * seasdur(s);
           }
         }
       }
     }
-    else if (F_reporting == 4)
-    {
+    else if (F_reporting == 4) {
       tempbase = 0.0;
       tempM = 0.0;
       tempZ = 0.0;
@@ -2213,16 +1930,13 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
       for (a = F_reporting_ages(1); a <= F_reporting_ages(2); a++) //  should not let a go higher than nages-2 because of accumulator
       {
         for (g = 1; g <= gmorph; g++)
-          if (use_morph(g) > 0)
-          {
-            for (p = 1; p <= pop; p++)
-            {
+          if (use_morph(g) > 0) {
+            for (p = 1; p <= pop; p++) {
               tempbase += equ_numbers(1, p, g, a); // sum of numbers at beginning of year
               tempZ += equ_numbers(1, p, g, a + 1); // numbers at beginning of next year
               temp3 = equ_numbers(1, p, g, a); //  numbers at begin of year
-              for (int kkk = 1; kkk <= nseas; kkk++)
-              {
-                temp3 *= mfexp(-seasdur(kkk) * natM(t_base+kkk, p, GP3(g), a));
+              for (int kkk = 1; kkk <= nseas; kkk++) {
+                temp3 *= mfexp(-seasdur(kkk) * natM(t_base + kkk, p, GP3(g), a));
               }
               tempM += temp3; //  survivors if just M operating
             }
@@ -2231,8 +1945,7 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
       equ_F_std = log(tempM) - log(tempZ); // F=Z-M
       equ_M_std = log(tempbase) - log(tempM); // M
     }
-    else if (F_reporting == 5)
-    {
+    else if (F_reporting == 5) {
       //  F_reporting==5 (ICES-style arithmetic mean across ages)
       //  like option 4 above, but F is calculated 1 age at a time to get a
       //  unweighted average across ages within each year
@@ -2245,16 +1958,13 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
         tempZ = 0.0;
         //  accumulate numbers across all morphs, sexes, and areas
         for (g = 1; g <= gmorph; g++)
-          if (use_morph(g) > 0)
-          {
-            for (p = 1; p <= pop; p++)
-            {
+          if (use_morph(g) > 0) {
+            for (p = 1; p <= pop; p++) {
               tempbase += equ_numbers(1, p, g, a); // sum of numbers at beginning of year
               tempZ += equ_numbers(1, p, g, a + 1); // numbers at beginning of next year
               temp3 = equ_numbers(1, p, g, a); //  numbers at begin of year
-              for (int kkk = 1; kkk <= nseas; kkk++)
-              {
-                temp3 *= mfexp(-seasdur(kkk) * natM(t_base+kkk, p, GP3(g), a));
+              for (int kkk = 1; kkk <= nseas; kkk++) {
+                temp3 *= mfexp(-seasdur(kkk) * natM(t_base + kkk, p, GP3(g), a));
               }
               tempM += temp3; //  survivors if just M operating
             }
@@ -2270,12 +1980,9 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
   }
 
   Cost = 0;
-  for (f = 1; f <= Nfleet; f++)
-  {
-    if (YPR_mask(f) == 1)
-    {
-      for (s = 1; s <= nseas; s++)
-      {
+  for (f = 1; f <= Nfleet; f++) {
+    if (YPR_mask(f) == 1) {
+      for (s = 1; s <= nseas; s++) {
         Cost += CostPerF(f) * Hrate(f, t_base + s);
       }
     }
@@ -2284,9 +1991,9 @@ FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
   SSB_equil = sum(SSB_equil_pop_gp);
   GenTime /= SSB_equil;
   smryage /= smrynum;
-  if (Hermaphro_maleSPB > 0.0) // add MaleSPB to female SSB
+  cumF /= (r_ages(nages) - r_ages(Smry_Age) + 1.);
+  if (Hermaphro_maleSSB > 0.0) // add MaleSSB to female SSB
   {
-    SSB_equil += Hermaphro_maleSPB * sum(MaleSSB_equil_pop_gp);
+    SSB_equil += Hermaphro_maleSSB * sum(MaleSSB_equil_pop_gp);
   }
-  } //  end equil calcs
-
+} //  end equil calcs
diff --git a/SS_proced.tpl b/SS_proced.tpl
index 534adf53..3e545ba7 100644
--- a/SS_proced.tpl
+++ b/SS_proced.tpl
@@ -206,15 +206,15 @@ PROCEDURE_SECTION
       temp = sqrt((temp + 0.0000001) / (double(recdev_end - recdev_start + 1)));
       if (mcmc_counter == 0 && mceval_counter == 0)
       {
-        cout << current_phase() << " " << niter << " -log(L): " << obj_fun << "  Spbio: " << value(SSB_yr(styr)) << " " << value(SSB_yr(endyr));
+        cout << current_phase() << " " << niter << " -log(L): " << obj_fun << "  SSBio: " << value(SSB_yr(styr)) << " " << value(SSB_yr(endyr));
       }
       else if (mcmc_counter > 0)
       {
-        cout << " MCMC: " << mcmc_counter << " -log(L): " << obj_fun << "  Spbio: " << value(SSB_yr(styr)) << " " << value(SSB_yr(endyr));
+        cout << " MCMC: " << mcmc_counter << " -log(L): " << obj_fun << "  SSBio: " << value(SSB_yr(styr)) << " " << value(SSB_yr(endyr));
       }
       else if (mceval_counter > 0)
       {
-        cout << " MCeval: " << mceval_counter << " -log(L): " << obj_fun << "  Spbio: " << value(SSB_yr(styr)) << " " << value(SSB_yr(endyr));
+        cout << " MCeval: " << mceval_counter << " -log(L): " << obj_fun << "  SSBio: " << value(SSB_yr(styr)) << " " << value(SSB_yr(endyr));
       }
       if (F_Method > 1 && sum(catch_like) > 0.01)
       {
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 2299f346..b54f0bd6 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1148,11 +1148,11 @@
   int Hermaphro_seas;
   int Hermaphro_firstage;
   number Hermaphro_seas_rd;
-  number Hermaphro_maleSPB;
+  number Hermaphro_maleSSB;
  LOCAL_CALCS
   // clang-format on
   Hermaphro_seas = 0;
-  Hermaphro_maleSPB = 0.0;
+  Hermaphro_maleSSB = 0.0;
   Hermaphro_firstage = 0;
   MGparm_Hermaphro = 0;
   
@@ -1175,8 +1175,8 @@
     //  so  2.3 will do switch in season 2 beginning with age 3.
     echoinput << Hermaphro_seas << "  Hermaphro_season (-1 means all seasons)" << endl;
     echoinput << Hermaphro_firstage << "  Hermaphro_firstage (from decimal part of seas input; note that firstage can only be a single digit, so 9 is max" << endl;
-    *(ad_comm::global_datafile) >> Hermaphro_maleSPB; // read as a fraction (0.0 to 1.0) of the male SSB added into the total SSB
-    echoinput << Hermaphro_maleSPB << "  Hermaphro_maleSPB " << endl;
+    *(ad_comm::global_datafile) >> Hermaphro_maleSSB; // read as a fraction (0.0 to 1.0) of the male SSB added into the total SSB
+    echoinput << Hermaphro_maleSSB << "  Hermaphro_maleSSB " << endl;
   }
   // clang-format off
  END_CALCS
@@ -2183,6 +2183,7 @@
     SR_update_SSBpR0_timeseries = 0;
     break;
   }
+  echoinput << "SRupdate " << SR_update_parm << " use " << SR_update_SSBpR0_bmark << " rd " << SR_update_SSBpR0_rd<< endl;
   echoinput << "SR_Npar and N_SRparm2 and N_SRparm3:  " << N_SRparm(SR_fxn) << " " << N_SRparm2 << " " << N_SRparm3 << endl;
   // clang-format off
  END_CALCS
@@ -5815,7 +5816,7 @@
     Extra_Std_N += YrMax - (styr - 2) + 1;
     if (More_Std_Input(12) == 2) Extra_Std_N += YrMax - (styr - 2) + 1; //  for recruitment
   }
-  // add 3 values for ln(Spbio)
+  // add 3 values for ln(SSBio)
   // (years are automatically generated as startyr, mid-point, and endyr)
   Do_se_LnSSB = Extra_Std_N + 1;
   Extra_Std_N += 3;
@@ -6869,23 +6870,23 @@
     }
   }
   
-  //  output ln(SPB) std for selected years
-  echoinput << " do ln(SPB) std labels for 3 years" << endl;
+  //  output ln(SSB) std for selected years
+  echoinput << " do ln(SSB) std labels for 3 years" << endl;
   CoVar_Count++;
   j++;
   active_parm(CoVar_Count) = j;
   sprintf(onenum, "%d", styr);
-  ParmLabel += "ln(SPB)_" + onenum + CRLF(1);
+  ParmLabel += "ln(SSB)_" + onenum + CRLF(1);
   CoVar_Count++;
   j++;
   active_parm(CoVar_Count) = j;
   sprintf(onenum, "%d", int((endyr + styr) / 2));
-  ParmLabel += "ln(SPB)_" + onenum + CRLF(1);
+  ParmLabel += "ln(SSB)_" + onenum + CRLF(1);
   CoVar_Count++;
   j++;
   active_parm(CoVar_Count) = j;
   sprintf(onenum, "%d", endyr);
-  ParmLabel += "ln(SPB)_" + onenum + CRLF(1);
+  ParmLabel += "ln(SSB)_" + onenum + CRLF(1);
   
   if (Do_se_smrybio > 0)
   {
diff --git a/SS_readdata_330.tpl b/SS_readdata_330.tpl
index d212bcde..56277cb9 100644
--- a/SS_readdata_330.tpl
+++ b/SS_readdata_330.tpl
@@ -5035,10 +5035,10 @@
     if (STD_Yr_Reverse(y) > 0)
     {
       j++;
-      STD_Yr_Reverse(y) = j; // use for SPB and recruitment
+      STD_Yr_Reverse(y) = j; // use for SSB and recruitment
       if (y >= styr)
       {
-        // depletion must start in year AFTER first catch.  It could vary earlier if recdevs happened enough earlier to change spbio, but this is not included
+        // depletion must start in year AFTER first catch.  It could vary earlier if recdevs happened enough earlier to change SSBio, but this is not included
         if ((depletion_basis > 0 && y > first_catch_yr) || y == endyr)
         {
           N_STD_Yr_Dep++;
diff --git a/SS_write.tpl b/SS_write.tpl
index 96d516b3..a3664db4 100644
--- a/SS_write.tpl
+++ b/SS_write.tpl
@@ -1011,7 +1011,7 @@ FUNCTION void write_rebuilder_output()
       rebuild_dat << exp_rec(y, 4) << " ";
     }
     rebuild_dat << " #recruits; first value is R0 (virgin)" << endl;
-    rebuild_dat << SSB_yr(styr - 2) << " " << SSB_yr(styr, k) << " #spbio; first value is SSB_virgin (virgin)" << endl;
+    rebuild_dat << SSB_yr(styr - 2) << " " << SSB_yr(styr, k) << " #SSBio; first value is SSB_virgin (virgin)" << endl;
     rebuild_dat << 1 << " ";
     for (y = styr; y <= k; y++)
       rebuild_dat << 0 << " ";
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index a6accdd4..82794514 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -1516,8 +1516,8 @@ FUNCTION void write_bigoutput()
           if (s == spawn_seas)
           {
             temp = sum(SSB_pop_gp(y, p));
-            if (Hermaphro_maleSPB > 0)
-              temp += Hermaphro_maleSPB * sum(MaleSPB(y, p));
+            if (Hermaphro_maleSSB > 0)
+              temp += Hermaphro_maleSSB * sum(MaleSSB(y, p));
             SS2out << temp;
           }
           else
@@ -1529,7 +1529,7 @@ FUNCTION void write_bigoutput()
           {
             SS2out << SSB_pop_gp(y, p);
             if (Hermaphro_Option != 0)
-              SS2out << MaleSPB(y, p);
+              SS2out << MaleSSB(y, p);
           }
           else
           {
@@ -1710,7 +1710,7 @@ FUNCTION void write_bigoutput()
   if (k < 4)
     k = 4;
   // quantities to store summary statistics
-  dvector rmse(1, k); //  used in the SpBio, Index, Lencomp and Agecomp reports
+  dvector rmse(1, k); //  used in the SSBio, Index, Lencomp and Agecomp reports
   dvector Hrmse(1, k);
   dvector Rrmse(1, k);
   dvector n_rmse(1, k);
@@ -4733,33 +4733,11 @@ FUNCTION void SPR_profile()
   for (s = 1; s <= nseas; s++)
   {
     t = styr - 3 * nseas + s - 1;
-
-    if (MG_active(2) > 0 || MG_active(3) > 0 || save_for_report > 0 || WTage_rd > 0)
-    {
-      subseas = 1;
-      ALK_idx = (s - 1) * N_subseas + subseas; //  for midseason
-      Make_AgeLength_Key(s, subseas); //  for begin season
-      subseas = mid_subseas;
-      ALK_idx = (s - 1) * N_subseas + subseas; //  for midseason
-      Make_AgeLength_Key(s, subseas); //  for midseason
-      if (s == spawn_seas)
-      {
-        subseas = spawn_subseas;
-        if (spawn_subseas != 1 && spawn_subseas != mid_subseas)
-        {
-          //don't call get_growth3(subseas) because using an average ave_size
-          Make_AgeLength_Key(s, subseas); //  spawn subseas
-        }
-        get_mat_fec();
-      }
-    }
-
-    for (g = 1; g <= gmorph; g++)
-      if (use_morph(g) > 0)
-      {
-        ALK_idx = (s - 1) * N_subseas + mid_subseas; //  for midseason
-        Make_FishSelex();
-      }
+    Wt_Age_beg(s) = Wt_Age_t(t, 0); //  used for smrybio
+    Wt_Age_mid(s) = Wt_Age_t(t, -1);
+    if (s == spawn_seas)
+      fec = Wt_Age_t(t, -2);
+    report5 << 0 << " y: " << y << " updated_Repro_output spr/ypr: " << fec(1) << endl;
   }
 
   SS2out << "SPRloop Iter Bycatch Fmult F_std SPR YPR_dead YPR_dead*Recr YPR_ret*Recr Revenue Cost Profit SSB Recruits SSB/Bzero Tot_Catch ";
@@ -5013,7 +4991,7 @@ FUNCTION void Global_MSY()
   //  GLOBAL_MSY with knife-edge age selection, then slot-age selection
   SS2out << endl
          << pick_report_name(55) << endl;
-  y = styr - 3; //  stores the averaged
+  y = styr - 3; //  stores the averaged biology and selectivity, etc. from benchmark
   yz = y;
   bio_yr = y;
   eq_yr = y;
@@ -5092,7 +5070,9 @@ FUNCTION void Global_MSY()
       SS2out << "Actual ";
       show_MSY = 2; //  invokes just brief output in benchmark
       did_MSY = 0;
+    report5 << 0 << " y: " << y << " updated_Repro_output global_1: " << fec(1) << endl;
       Get_Benchmarks(show_MSY);
+    report5 << 0 << " y: " << y << " updated_Repro_output global_2: " << fec(1) << endl;
       did_MSY = 0;
     }
   }
diff --git a/SS_write_ssnew.tpl b/SS_write_ssnew.tpl
index fdd984be..85aaccb6 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -4,9 +4,9 @@
 // SS_Label_file  #
 
 //********************************************************************
- /*  SS_Label_FUNCTION 38 write_nudata */
+/*  SS_Label_FUNCTION 38 write_nudata */
 FUNCTION void write_nudata()
-  {
+{
   //  code for multinomial distribution developed by Ian Stewart, Oct 2005
 
   dvector temp_mult(1, 50000);
@@ -23,24 +23,20 @@ FUNCTION void write_nudata()
     irand_seed = long(time(&start));
 
   random_number_generator radm(irand_seed);
-  for (i = 1; i <= 1234; i++)
-  {
+  for (i = 1; i <= 1234; i++) {
     temp = randn(radm);
   }
 
-  for (Nudat = 1; Nudat <= N_nudata; Nudat++)
-  {
-    if (Nudat == 1)
-    {
+  for (Nudat = 1; Nudat <= N_nudata; Nudat++) {
+    if (Nudat == 1) {
       echoinput << "Begin writing data_echo.ss_new file" << endl;
       newdatfilename = "data_echo.ss_new";
-	    datinfostring = "echo_input_data";
+      datinfostring = "echo_input_data";
     }
-    else if (Nudat == 2)
-    {
+    else if (Nudat == 2) {
       echoinput << "Begin writing data_expval.ss file" << endl;
       newdatfilename = "data_expval.ss";
-	    datinfostring = "expected_values";
+      datinfostring = "expected_values";
     }
     else // data_boot files
     {
@@ -48,19 +44,17 @@ FUNCTION void write_nudata()
       Nubootdat = Nudat - 2;
       anystring2 = "     ";
       sprintf(anystring2, "%d", Nubootdat);
-      if (Nubootdat < 10)
-      {
+      if (Nubootdat < 10) {
         newdatfilename = "data_boot_00" + anystring2 + ".ss";
       }
-      else if (Nubootdat < 100)
-      {
+      else if (Nubootdat < 100) {
         newdatfilename = "data_boot_0" + anystring2 + ".ss";
       }
       else // Nubootdat > 99
       {
         newdatfilename = "data_boot_" + anystring2 + ".ss";
       }
-	    datinfostring = "bootstrap";
+      datinfostring = "bootstrap";
     }
     anystring = ssnew_pathname + newdatfilename;
     report1.open(anystring);
@@ -69,8 +63,8 @@ FUNCTION void write_nudata()
             << "#_Start_time: " << ctime(&start);
     report1 << "#_" << datinfostring << endl;
     report1 << Data_Comments << endl;
-	if (Nudat > 2)
-	  report1 << "#_bootstrap file: " << Nubootdat << "  irand_seed: " << irand_seed << " first rand#: " << randn(radm) << endl;
+    if (Nudat > 2)
+      report1 << "#_bootstrap file: " << Nubootdat << "  irand_seed: " << irand_seed << " first rand#: " << randn(radm) << endl;
 
     report1 << version_info(1) << version_info(2) << version_info(3) << endl;
     report1 << styr << " #_StartYr" << endl;
@@ -90,8 +84,7 @@ FUNCTION void write_nudata()
     report1 << "#_catch_mult: 0=no; 1=yes" << endl;
     report1 << "#_rows are fleets" << endl
             << "#_fleet_type fishery_timing area catch_units need_catch_mult fleetname" << endl;
-    for (f = 1; f <= Nfleet; f++)
-    {
+    for (f = 1; f <= Nfleet; f++) {
       report1 << fleet_setup(f) << " " << fleetname(f) << "  # " << f << endl;
     }
     report1 << "#Bycatch_fleet_input_goes_next" << endl;
@@ -102,8 +95,7 @@ FUNCTION void write_nudata()
     report1 << "#e:  last year of range" << endl;
     report1 << "#f:  not used" << endl;
     report1 << "# a   b   c   d   e   f " << endl;
-    for (f = 1; f <= Nfleet; f++)
-    {
+    for (f = 1; f <= Nfleet; f++) {
       if (fleet_type(f) == 2)
         report1 << bycatch_setup(f) << "  # " << fleetname(f) << endl;
     }
@@ -115,22 +107,16 @@ FUNCTION void write_nudata()
       report1 << "#_catch_se:  standard error of log(catch)" << endl;
       report1 << "#_NOTE:  catch data is ignored for survey fleets" << endl;
       k = 0;
-      for (f = 1; f <= Nfleet; f++)
-      {
-        if (fleet_type(f) <= 2)
-        {
-          for (y = styr - 1; y <= endyr; y++)
-          {
-            for (s = 1; s <= nseas; s++)
-            {
+      for (f = 1; f <= Nfleet; f++) {
+        if (fleet_type(f) <= 2) {
+          for (y = styr - 1; y <= endyr; y++) {
+            for (s = 1; s <= nseas; s++) {
               k++;
               t = styr + (y - styr) * nseas + s - 1;
-              if (y == styr - 1)
-              {
+              if (y == styr - 1) {
                 g = -999;
               }
-              else
-              {
+              else {
                 g = y;
               }
               report1 << g << " " << s << " " << f << " " << catch_ret_obs(f, t) << " " << catch_se(t, f) << endl;
@@ -146,7 +132,7 @@ FUNCTION void write_nudata()
       report1 << "#_errtype:  -1=normal; 0=lognormal; 1=lognormal with bias correction; >1=df for T-dist" << endl;
       report1 << "#_SD_report: 0=not; 1=include survey expected value with se" << endl;
       report1 << "#_note that link functions are specified in Q_setup section of control file" << endl;
-      report1 << "#_dataunits = 36 and 35 should use Q_type 5 to provide offset parameter" <<endl;
+      report1 << "#_dataunits = 36 and 35 should use Q_type 5 to provide offset parameter" << endl;
       report1 << "#_fleet units errtype SD_report" << endl;
       for (f = 1; f <= Nfleet; f++)
         report1 << f << " " << Svy_units(f) << " " << Svy_errtype(f) << " " << Svy_sdreport(f) << " # " << fleetname(f) << endl;
@@ -154,8 +140,7 @@ FUNCTION void write_nudata()
 
       if (Svy_N > 0)
         for (f = 1; f <= Nfleet; f++)
-          for (i = 1; i <= Svy_N_fleet(f); i++)
-          {
+          for (i = 1; i <= Svy_N_fleet(f); i++) {
             t = Svy_time_t(f, i);
             ALK_time = Svy_ALK_time(f, i);
             report1 << Show_Time(t, 1) << " " << Svy_super(f, i) * data_time(ALK_time, f, 1) << " " << f * Svy_use(f, i) << " ";
@@ -170,22 +155,19 @@ FUNCTION void write_nudata()
       report1 << "# note: only enter units and errtype for fleets with discard " << endl;
       report1 << "# note: discard data is the total for an entire season, so input of month here must be to a month in that season" << endl;
       report1 << "#_fleet units errtype" << endl;
-      if (Ndisc_fleets > 0)
-      {
+      if (Ndisc_fleets > 0) {
         for (f = 1; f <= Nfleet; f++)
           if (disc_units(f) > 0)
             report1 << f << " " << disc_units(f) << " " << disc_errtype(f) << " # " << fleetname(f) << endl;
         report1 << "#_year month fleet obs stderr" << endl;
         for (f = 1; f <= Nfleet; f++)
-          for (i = 1; i <= disc_N_fleet(f); i++)
-          {
+          for (i = 1; i <= disc_N_fleet(f); i++) {
             ALK_time = disc_time_ALK(f, i);
             report1 << Show_Time(disc_time_t(f, i), 1) << " " << yr_disc_super(f, i) * data_time(ALK_time, f, 1) << " " << f * yr_disc_use(f, i) << " ";
             report1 << obs_disc(f, i) << " " << cv_disc(f, i) << " #_ " << fleetname(f) << endl;
           }
       }
-      else
-      {
+      else {
         report1 << "# ";
       }
       report1 << "-9999 0 0 0.0 0.0 # terminator for discard data " << endl;
@@ -197,10 +179,8 @@ FUNCTION void write_nudata()
       report1 << DF_bodywt << " #_DF_for_meanbodysize_T-distribution_like" << endl;
       report1 << "# note:  type=1 for mean length; type=2 for mean body weight " << endl;
       report1 << "#_year month fleet part type obs stderr" << endl;
-      if (nobs_mnwt > 0)
-      {
-        for (i = 1; i <= nobs_mnwt; i++)
-        {
+      if (nobs_mnwt > 0) {
+        for (i = 1; i <= nobs_mnwt; i++) {
           f = abs(mnwtdata(3, i));
           report1 << Show_Time(mnwtdata(1, i), 1) << " " << mnwtdata(2, i) << " " << mnwtdata(3, i) << " " << mnwtdata(4, i) << " " << mnwtdata(5, i) << " " << mnwtdata(6, i) << " " << mnwtdata(7, i) - var_adjust(3, f) << " #_ " << fleetname(f) << endl;
         }
@@ -212,27 +192,23 @@ FUNCTION void write_nudata()
       report1 << "#" << endl
               << "# set up population length bin structure (note - irrelevant if not using size data and using empirical wtatage" << endl;
       report1 << LenBin_option << " # length bin method: 1=use databins; 2=generate from binwidth,min,max below; 3=read vector" << endl;
-      if (LenBin_option == 1)
-      {
+      if (LenBin_option == 1) {
         report1 << "# no additional input for option 1" << endl;
         report1 << "# read binwidth, minsize, lastbin size for option 2" << endl;
         report1 << "# read N poplen bins, then vector of bin lower boundaries, for option 3" << endl;
       }
-      else if (LenBin_option == 2)
-      {
+      else if (LenBin_option == 2) {
         report1 << binwidth2 << " # binwidth for population size comp " << endl;
         report1 << minLread << " # minimum size in the population (lower edge of first bin and size at age 0.00) " << endl;
         report1 << maxLread << " # maximum size in the population (lower edge of last bin) " << endl;
       }
-      else
-      {
+      else {
         report1 << nlength << " # number of population size bins " << endl;
         report1 << len_bins << endl;
       }
 
       report1 << use_length_data << " # use length composition data (0/1/2) where 2 invokes new comp_control format" << endl;
-      if (use_length_data > 0)
-      {
+      if (use_length_data > 0) {
         report1 << "#_mintailcomp: upper and lower distribution for females and males separately are accumulated until exceeding this level." << endl;
         report1 << "#_addtocomp:  after accumulation of tails; this value added to all bins" << endl;
         report1 << "#_combM+F: males and females treated as combined sex below this bin number " << endl;
@@ -241,17 +217,14 @@ FUNCTION void write_nudata()
         report1 << "#_ParmSelect:  consecutive index for dirichlet or MV_Tweedie" << endl;
         report1 << "#_minsamplesize: minimum sample size; set to 1 to match 3.24, minimum value is 0.001" << endl;
         report1 << "#" << endl;
-        if(use_length_data == 1)
-        {
+        if (use_length_data == 1) {
           report1 << "#_Using old format for composition controls" << endl;
-        report1 << "#_mintailcomp addtocomp combM+F CompressBins CompError ParmSelect minsamplesize" << endl;
-        for (f = 1; f <= Nfleet; f++)
-        {
-          report1 << min_tail_L(0, f) << " " << min_comp_L(0, f) << " " << CombGender_L(0, f) << " " << AccumBin_L(0, f) << " " << Comp_Err_L(0, f) << " " << Comp_Err_L2(0, f) << " " << min_sample_size_L(0, f) << " #_fleet:" << f << "_" << fleetname(f) << endl;
-        }
+          report1 << "#_mintailcomp addtocomp combM+F CompressBins CompError ParmSelect minsamplesize" << endl;
+          for (f = 1; f <= Nfleet; f++) {
+            report1 << min_tail_L(0, f) << " " << min_comp_L(0, f) << " " << CombGender_L(0, f) << " " << AccumBin_L(0, f) << " " << Comp_Err_L(0, f) << " " << Comp_Err_L2(0, f) << " " << min_sample_size_L(0, f) << " #_fleet:" << f << "_" << fleetname(f) << endl;
+          }
         }
-        else if (use_length_data == 2)
-        {
+        else if (use_length_data == 2) {
           report1 << "#_Using new list format for composition controls" << endl;
           report1 << "#_use negative fleet value to fill for all higher numbered fleets (recommended!)" << endl;
           report1 << "#_must enter in fleet, partition order; but only need to enter for used combos" << endl;
@@ -267,10 +240,8 @@ FUNCTION void write_nudata()
                 << len_bins_dat << endl;
         //  report1<<nobsl_rd<<" #_N_Length_obs"<<endl;
         report1 << "#_year month fleet sex part Nsamp datavector(female-male)" << endl;
-        if (nobsl_rd > 0)
-        {
-          for (i = 0; i <= nobsl_rd - 1; i++)
-          {
+        if (nobsl_rd > 0) {
+          for (i = 0; i <= nobsl_rd - 1; i++) {
             report1 << lendata[i] << endl;
           }
         }
@@ -279,19 +250,16 @@ FUNCTION void write_nudata()
           report1 << "0 ";
         report1 << endl;
       }
-      else
-      {
+      else {
         report1 << "# see manual for format of length composition data " << endl;
       }
 
       report1 << "#" << endl
               << n_abins << " #_N_age_bins" << endl;
-      if (n_abins > 0)
-      {
+      if (n_abins > 0) {
         report1 << age_bins1 << endl;
       }
-      else
-      {
+      else {
         report1 << "# ";
       }
       report1 << N_ageerr << " #_N_ageerror_definitions" << endl;
@@ -307,8 +275,7 @@ FUNCTION void write_nudata()
       report1 << "#_minsamplesize: minimum sample size; set to 1 to match 3.24, minimum value is 0.001" << endl;
       report1 << "#" << endl;
       report1 << "#_mintailcomp addtocomp combM+F CompressBins CompError ParmSelect minsamplesize" << endl;
-      for (f = 1; f <= Nfleet; f++)
-      {
+      for (f = 1; f <= Nfleet; f++) {
         if (n_abins <= 0)
           report1 << "# ";
         report1 << min_tail_A(f) << " " << min_comp_A(f) << " " << CombGender_A(f) << " " << AccumBin_A(f) << " " << Comp_Err_A(f) << " " << Comp_Err_A2(f) << " " << min_sample_size_A(f) << " #_fleet:" << f << "_" << fleetname(f) << endl;
@@ -320,10 +287,8 @@ FUNCTION void write_nudata()
       report1 << "# sex codes:  0=combined; 1=use female only; 2=use male only; 3=use both as joint sex*length distribution" << endl;
       report1 << "# partition codes:  (0=combined; 1=discard; 2=retained" << endl;
       report1 << "#_year month fleet sex part ageerr Lbin_lo Lbin_hi Nsamp datavector(female-male)" << endl;
-      if (nobsa_rd > 0)
-      {
-        for (i = 0; i <= nobsa_rd - 1; i++)
-        {
+      if (nobsa_rd > 0) {
+        for (i = 0; i <= nobsa_rd - 1; i++) {
           report1 << Age_Data[i] << endl;
         }
       }
@@ -337,26 +302,20 @@ FUNCTION void write_nudata()
 
       report1 << "#" << endl
               << use_meansizedata << " #_Use_MeanSize-at-Age_obs (0/1)" << endl;
-      if (use_meansizedata > 0)
-      {
+      if (use_meansizedata > 0) {
         report1 << "# sex codes:  0=combined; 1=use female only; 2=use male only; 3=use both as joint sex*length distribution" << endl;
         report1 << "# partition codes:  0=combined; 1=discard; 2=retained" << endl;
         report1 << "# ageerr codes:  positive means mean length-at-age; negative means mean bodywt_at_age" << endl;
         report1 << "#_year month fleet sex part ageerr ignore datavector(female-male)" << endl;
         report1 << "#                                          samplesize(female-male)" << endl;
-        if (nobs_ms_rd > 0)
-        {
-          if (finish_starter == 999)
-          {
-            for (i = 1; i <= nobs_ms_rd; i++)
-            {
+        if (nobs_ms_rd > 0) {
+          if (finish_starter == 999) {
+            for (i = 1; i <= nobs_ms_rd; i++) {
               report1 << sizeAge_Data[i] << endl;
             }
           }
-          else
-          {
-            for (i = 0; i <= nobs_ms_rd - 1; i++)
-            {
+          else {
+            for (i = 0; i <= nobs_ms_rd - 1; i++) {
               report1 << sizeAge_Data[i] << endl;
             }
           }
@@ -371,24 +330,24 @@ FUNCTION void write_nudata()
               << N_envvar << " #_N_environ_variables" << endl;
       report1 << "# -2 in year will subtract mean for that env_var; -1 will subtract mean and divide by stddev (e.g. Z-score)" << endl;
       report1 << "#_year variable value" << endl;
-      if (N_envvar > 0)
-      {
+      if (N_envvar > 0) {
         for (i = 0; i <= N_envdata - 1; i++)
           report1 << env_temp[i] << endl;
         report1 << "-9999 0 0" << endl;
       }
 
-      report1 << "#" << endl << "# Sizefreq data. Defined by method because a fleet can use multiple methods" << endl;
+      report1 << "#" << endl
+              << "# Sizefreq data. Defined by method because a fleet can use multiple methods" << endl;
       report1 << SzFreq_Nmeth_rd << " # N sizefreq methods to read (or -1 for expanded options)" << endl;
       if (SzFreq_Nmeth_rd < 0) {
         report1 << SzFreq_Nmeth << " # N sizefreq methods to read" << endl;
       }
-      if (SzFreq_Nmeth != 0)
-      {
+      if (SzFreq_Nmeth != 0) {
         report1 << "# each row below has entry for each sizefreq method " << endl;
         report1 << "#_ ";
-        for (int j = 1; j <= SzFreq_Nmeth; j++ )
-          { report1 << j << " ";}
+        for (int j = 1; j <= SzFreq_Nmeth; j++) {
+          report1 << j << " ";
+        }
         report1 << " # Method" << endl;
         report1 << SzFreq_Nbins << " #_Sizefreq N bins" << endl;
         report1 << SzFreq_units << " #_Sizefreq units(1=bio/2=num)" << endl;
@@ -396,32 +355,31 @@ FUNCTION void write_nudata()
         report1 << SzFreq_mincomp << " #_Sizefreq:  small constant to add to comps" << endl;
         report1 << SzFreq_nobs << " #_Sizefreq number of obs per method" << endl;
         if (SzFreq_Nmeth_rd < 0) {
-          report1 << Comp_Err_Sz <<  " #_Comp_Error:  0=multinomial, 1=dirichlet using Theta*n, 2=dirichlet using beta, 3=MV_Tweedie" << endl;
+          report1 << Comp_Err_Sz << " #_Comp_Error:  0=multinomial, 1=dirichlet using Theta*n, 2=dirichlet using beta, 3=MV_Tweedie" << endl;
           report1 << Comp_Err_Sz2 << " #_ParmSelect: consecutive index for dirichlet or MV_Tweedie comp_error" << endl;
         }
         report1 << "#_Sizefreq bins. one row for each method" << endl
                 << "#Note: negative value for first bin makes it accumulate all smaller fish vs. truncate small fish" << endl;
-        for (i = 1; i <= SzFreq_Nmeth; i++)
-        { report1 << SzFreq_Omit_Small(i) * SzFreq_bins1(i, 1) << SzFreq_bins1(i)(2, SzFreq_Nbins(i)) << endl; }
-        report1 << "#_method year month fleet sex part Nsamp <data> " << endl << SzFreq_obs1 << endl;
+        for (i = 1; i <= SzFreq_Nmeth; i++) {
+          report1 << SzFreq_Omit_Small(i) * SzFreq_bins1(i, 1) << SzFreq_bins1(i)(2, SzFreq_Nbins(i)) << endl;
+        }
+        report1 << "#_method year month fleet sex part Nsamp <data> " << endl
+                << SzFreq_obs1 << endl;
       }
 
       // begin tagging data section #1 (observed data)
       report1 << "# " << endl
               << Do_TG_rd << " # do tags (0/1/2); where 2 allows entry of TG_min_recap" << endl;
-      if (Do_TG_rd > 0)
-      {
+      if (Do_TG_rd > 0) {
         // info on dimensions of tagging data
         report1 << N_TG << " # N tag groups" << endl;
         report1 << N_TG_recap << " # N recap events" << endl;
         report1 << TG_mixperiod << " # TG_mixperiod ## (latency) is the first period in which logL is calculated for this tag group (0 = release period)" << endl;
         report1 << TG_maxperiods << " # max periods ##  to track recaptures (units=seasons), after which tags are still read into this accumulator period" << endl;
-        if (Do_TG_rd == 2)
-        {
+        if (Do_TG_rd == 2) {
           report1 << TG_min_recap << " # TG_min_recap ## tag group's N recaps >=mixperiod must be >= min_recap to include tag group in logL)" << endl;
         }
-        else
-        {
+        else {
           report1 << "# COND:  TG_min_recap ##  use Do_TG=2 to invoke reading TG_min_recap after TG_maxperiods" << endl;
         }
 
@@ -432,8 +390,7 @@ FUNCTION void write_nudata()
 
         // tag recaptures
         report1 << "#_TG year seas fleet Nrecap" << endl;
-        for (j = 1; j <= N_TG_recap; j++)
-        {
+        for (j = 1; j <= N_TG_recap; j++) {
           // fill in first 4 columns:
           for (k = 1; k <= 5; k++)
             report1 << TG_recap_data(j, k) << " ";
@@ -444,19 +401,16 @@ FUNCTION void write_nudata()
 
       report1 << "#" << endl
               << Do_Morphcomp << " #    morphcomp data(0/1) " << endl;
-      if (Do_Morphcomp > 0)
-      {
+      if (Do_Morphcomp > 0) {
         report1 << Morphcomp_nobs_rd << "  #  Nobs" << endl;
         report1 << Morphcomp_nmorph << " # Nmorphs" << endl;
         report1 << Morphcomp_mincomp << " # add_to_comp" << endl;
         report1 << "#_year, month, fleet, null, Nsamp, datavector_by_Nmorphs" << endl;
-        for (i = 1; i <= Morphcomp_nobs_rd; i++)
-        {
+        for (i = 1; i <= Morphcomp_nobs_rd; i++) {
           report1 << Morphcomp_obs_rd << endl;
         }
       }
-      else
-      {
+      else {
         report1 << "#  Nobs, Nmorphs, mincomp" << endl;
         report1 << "#_year, seas, type, partition, Nsamp, datavector_by_Nmorphs" << endl;
       }
@@ -478,33 +432,28 @@ FUNCTION void write_nudata()
       report1 << "#_catch_se:  standard error of log(catch)" << endl;
       report1 << "#_NOTE:  catch data is ignored for survey fleets" << endl;
       k = 0;
-      for (f = 1; f <= Nfleet; f++)
-      {
-        if (fleet_type(f) <= 2)
-        {
-          for (y = styr - 1; y <= endyr; y++)
-          {
-            for (s = 1; s <= nseas; s++)
-            {
+      for (f = 1; f <= Nfleet; f++) {
+        if (fleet_type(f) <= 2) {
+          for (y = styr - 1; y <= endyr; y++) {
+            for (s = 1; s <= nseas; s++) {
               k++;
               t = styr + (y - styr) * nseas + s - 1;
-              if (y == styr - 1)
-              { report1 << -999 << " "; }
-              else
-              { report1 << y << " "; }
+              if (y == styr - 1) {
+                report1 << -999 << " ";
+              }
+              else {
+                report1 << y << " ";
+              }
               report1 << s << " " << f << " ";
-                if (fleet_type(f) == 2 && catch_ret_obs(f, t) > 0.0)
-                {
-                  report1 << 0.1 << " " << catch_se(t, f) << endl; //  for bycatch only fleet
-                }
-                else if (catchunits(f) == 1)
-                {
-                  report1 << catch_fleet(t, f, 3) << " " << catch_se(t, f) << endl;
-                }
-                else
-                {
-                  report1 << catch_fleet(t, f, 6) << " " << catch_se(t, f) << endl;
-                }
+              if (fleet_type(f) == 2 && catch_ret_obs(f, t) > 0.0) {
+                report1 << 0.1 << " " << catch_se(t, f) << endl; //  for bycatch only fleet
+              }
+              else if (catchunits(f) == 1) {
+                report1 << catch_fleet(t, f, 3) << " " << catch_se(t, f) << endl;
+              }
+              else {
+                report1 << catch_fleet(t, f, 6) << " " << catch_se(t, f) << endl;
+              }
             }
           }
         }
@@ -517,15 +466,14 @@ FUNCTION void write_nudata()
       report1 << "#_errtype:  -1=normal; 0=lognormal; 1=lognormal with bias correction; >1=df for T-dist" << endl;
       report1 << "#_SD_report: 0=not; 1=include survey expected value with se" << endl;
       report1 << "#_note that link functions are specified in Q_setup section of control file" << endl;
-      report1 << "#_dataunits = 36 and 35 should use Q_type 5 to provide offset parameter" <<endl;
+      report1 << "#_dataunits = 36 and 35 should use Q_type 5 to provide offset parameter" << endl;
       report1 << "#_fleet units errtype SD_report" << endl;
       for (f = 1; f <= Nfleet; f++)
         report1 << f << " " << Svy_units(f) << " " << Svy_errtype(f) << " " << Svy_sdreport(f) << " # " << fleetname(f) << endl;
       report1 << "#_year month index obs err" << endl;
       if (Svy_N > 0)
         for (f = 1; f <= Nfleet; f++)
-          for (i = 1; i <= Svy_N_fleet(f); i++)
-          {
+          for (i = 1; i <= Svy_N_fleet(f); i++) {
             t = Svy_time_t(f, i);
             ALK_time = Svy_ALK_time(f, i);
             report1 << Show_Time(t, 1) << " " << Svy_super(f, i) * data_time(ALK_time, f, 1) << " " << f * Svy_use(f, i) << " ";
@@ -533,14 +481,13 @@ FUNCTION void write_nudata()
             {
               report1 << Svy_est(f, i);
             }
-            else if (Svy_errtype(f) == -2) // gamma 
+            else if (Svy_errtype(f) == -2) // gamma
             {
               //  need gamma here
             }
-            else
-            {
-              report1 << mfexp(Svy_est(f, i));  //  lognormal or T-dist or lognormal w/bias
-            } 
+            else {
+              report1 << mfexp(Svy_est(f, i)); //  lognormal or T-dist or lognormal w/bias
+            }
             report1 << " " << Svy_se_rd(f, i) << " #_orig_obs: " << Svy_obs(f, i) << " " << fleetname(f) << endl;
           }
       report1 << "-9999 1 1 1 1 # terminator for survey observations " << endl;
@@ -552,16 +499,14 @@ FUNCTION void write_nudata()
       report1 << "# note: only enter units and errtype for fleets with discard " << endl;
       report1 << "# note: discard data is the total for an entire season, so input of month here must be to a month in that season" << endl;
       report1 << "#_fleet units errtype" << endl;
-      if (Ndisc_fleets > 0)
-      {
+      if (Ndisc_fleets > 0) {
         for (f = 1; f <= Nfleet; f++)
           if (disc_units(f) > 0)
             report1 << f << " " << disc_units(f) << " " << disc_errtype(f) << " # " << fleetname(f) << endl;
         report1 << "#_year month fleet obs stderr" << endl;
         for (f = 1; f <= Nfleet; f++)
           if (disc_N_fleet(f) > 0)
-            for (i = 1; i <= disc_N_fleet(f); i++)
-            {
+            for (i = 1; i <= disc_N_fleet(f); i++) {
               ALK_time = disc_time_ALK(f, i);
               report1 << Show_Time(disc_time_t(f, i), 1) << " " << yr_disc_super(f, i) * data_time(ALK_time, f, 1) << " " << f * yr_disc_use(f, i) << " ";
               {
@@ -570,8 +515,7 @@ FUNCTION void write_nudata()
               report1 << " " << cv_disc(f, i) << " #_orig_obs: " << obs_disc(f, i) << " #_ " << fleetname(f) << endl;
             }
       }
-      else
-      {
+      else {
         report1 << "# ";
       }
       report1 << "-9999 0 0 0.0 0.0 # terminator for discard data " << endl;
@@ -584,10 +528,8 @@ FUNCTION void write_nudata()
       report1 << DF_bodywt << " #_DF_for_meanbodysize_T-distribution_like" << endl;
       report1 << "# note:  type=1 for mean length; type=2 for mean body weight " << endl;
       report1 << "#_year month fleet part type obs stderr" << endl;
-      if (nobs_mnwt > 0)
-      {
-        for (i = 1; i <= nobs_mnwt; i++)
-        {
+      if (nobs_mnwt > 0) {
+        for (i = 1; i <= nobs_mnwt; i++) {
           f = abs(mnwtdata(3, i));
           report1 << Show_Time(mnwtdata(1, i), 1) << " " << mnwtdata(2, i) << " " << mnwtdata(3, i) << " " << mnwtdata(4, i) << " " << mnwtdata(5, i) << " " << exp_mnwt(i) << " " << mnwtdata(7, i) - var_adjust(3, f) << " #_orig_obs: " << mnwtdata(6, i) << "  #_ " << fleetname(f) << endl;
         }
@@ -599,27 +541,23 @@ FUNCTION void write_nudata()
       report1 << "#" << endl
               << "# set up population length bin structure (note - irrelevant if not using size data and using empirical wtatage" << endl;
       report1 << LenBin_option << " # length bin method: 1=use databins; 2=generate from binwidth,min,max below; 3=read vector" << endl;
-      if (LenBin_option == 1)
-      {
+      if (LenBin_option == 1) {
         report1 << "# no additional input for option 1" << endl;
         report1 << "# read binwidth, minsize, lastbin size for option 2" << endl;
         report1 << "# read N poplen bins, then vector of bin lower boundaries, for option 3" << endl;
       }
-      else if (LenBin_option == 2)
-      {
+      else if (LenBin_option == 2) {
         report1 << binwidth2 << " # binwidth for population size comp " << endl;
         report1 << minLread << " # minimum size in the population (lower edge of first bin and size at age 0.00) " << endl;
         report1 << maxLread << " # maximum size in the population (lower edge of last bin) " << endl;
       }
-      else
-      {
+      else {
         report1 << nlength << " # number of population size bins " << endl;
         report1 << len_bins << endl;
       }
 
       report1 << use_length_data << " # use length composition data (0/1/2) where 2 invokes new comp_comtrol format" << endl;
-      if (use_length_data > 0)
-      {
+      if (use_length_data > 0) {
         report1 << "#_mintailcomp: upper and lower distribution for females and males separately are accumulated until exceeding this level." << endl;
         report1 << "#_addtocomp:  after accumulation of tails; this value added to all bins" << endl;
         report1 << "#_combM+F: males and females treated as combined sex below this bin number " << endl;
@@ -628,17 +566,14 @@ FUNCTION void write_nudata()
         report1 << "#_ParmSelect:  consecutive index for dirichlet or MV_Tweedie" << endl;
         report1 << "#_minsamplesize: minimum sample size; set to 1 to match 3.24, minimum value is 0.001" << endl;
         report1 << "#" << endl;
-        if(use_length_data == 1)
-        {
+        if (use_length_data == 1) {
           report1 << "#_Using old format for composition controls" << endl;
-        report1 << "#_mintailcomp addtocomp combM+F CompressBins CompError ParmSelect minsamplesize" << endl;
-        for (f = 1; f <= Nfleet; f++)
-        {
-          report1 << min_tail_L(0, f) << " " << min_comp_L(0, f) << " " << CombGender_L(0, f) << " " << AccumBin_L(0, f) << " " << Comp_Err_L(0, f) << " " << Comp_Err_L2(0, f) << " " << min_sample_size_L(0, f) << " #_fleet:" << f << "_" << fleetname(f) << endl;
-        }
+          report1 << "#_mintailcomp addtocomp combM+F CompressBins CompError ParmSelect minsamplesize" << endl;
+          for (f = 1; f <= Nfleet; f++) {
+            report1 << min_tail_L(0, f) << " " << min_comp_L(0, f) << " " << CombGender_L(0, f) << " " << AccumBin_L(0, f) << " " << Comp_Err_L(0, f) << " " << Comp_Err_L2(0, f) << " " << min_sample_size_L(0, f) << " #_fleet:" << f << "_" << fleetname(f) << endl;
+          }
         }
-        else if (use_length_data == 2)
-        {
+        else if (use_length_data == 2) {
           report1 << "#_Using new list format for composition controls" << endl;
           report1 << "#_use negative fleet value to fill for all higher numbered fleets (recommended!)" << endl;
           report1 << "#_must enter in fleet, partition order; but only need to enter for used combos" << endl;
@@ -654,12 +589,9 @@ FUNCTION void write_nudata()
                 << len_bins_dat << endl;
         //  report1<<sum(Nobs_l)<<" #_N_Length_obs"<<endl;
         report1 << "#_year month fleet sex part Nsamp datavector(female-male)" << endl;
-        for (f = 1; f <= Nfleet; f++)
-        {
-          if (Nobs_l(f) > 0)
-          {
-            for (i = 1; i <= Nobs_l(f); i++)
-            {
+        for (f = 1; f <= Nfleet; f++) {
+          if (Nobs_l(f) > 0) {
+            for (i = 1; i <= Nobs_l(f); i++) {
               k = 1000;
               if (nsamp_l(f, i) < k)
                 k = nsamp_l(f, i);
@@ -673,19 +605,16 @@ FUNCTION void write_nudata()
           report1 << "0 ";
         report1 << endl;
       }
-      else
-      {
+      else {
         report1 << "# see manual for format of length composition data " << endl;
       }
 
       report1 << "#" << endl
               << n_abins << " #_N_age_bins" << endl;
-      if (n_abins > 0)
-      {
+      if (n_abins > 0) {
         report1 << age_bins1 << endl;
       }
-      else
-      {
+      else {
         report1 << "# ";
       }
       report1 << N_ageerr << " #_N_ageerror_definitions" << endl;
@@ -701,8 +630,7 @@ FUNCTION void write_nudata()
       report1 << "#_minsamplesize: minimum sample size; set to 1 to match 3.24, minimum value is 0.001" << endl;
       report1 << "#" << endl;
       report1 << "#_mintailcomp addtocomp combM+F CompressBins CompError ParmSelect minsamplesize" << endl;
-      for (f = 1; f <= Nfleet; f++)
-      {
+      for (f = 1; f <= Nfleet; f++) {
         if (n_abins <= 0)
           report1 << "# ";
         report1 << min_tail_A(f) << " " << min_comp_A(f) << " " << CombGender_A(f) << " " << AccumBin_A(f) << " " << Comp_Err_A(f) << " " << Comp_Err_A2(f) << " " << min_sample_size_A(f) << " #_fleet:" << f << "_" << fleetname(f) << endl;
@@ -715,12 +643,9 @@ FUNCTION void write_nudata()
       report1 << "# partition codes:  (0=combined; 1=discard; 2=retained" << endl;
       report1 << "#_year month fleet sex part ageerr Lbin_lo Lbin_hi Nsamp datavector(female-male)" << endl;
       if (Nobs_a_tot > 0)
-        for (f = 1; f <= Nfleet; f++)
-        {
-          if (Nobs_a(f) >= 1)
-          {
-            for (i = 1; i <= Nobs_a(f); i++)
-            {
+        for (f = 1; f <= Nfleet; f++) {
+          if (Nobs_a(f) >= 1) {
+            for (i = 1; i <= Nobs_a(f); i++) {
               k = 1000;
               if (nsamp_a(f, i) < k)
                 k = nsamp_a(f, i); // note that nsamp is adjusted by var_adjust, so var_adjust
@@ -740,26 +665,20 @@ FUNCTION void write_nudata()
 
       report1 << "#" << endl
               << use_meansizedata << " #_Use_MeanSize-at-Age_obs (0/1)" << endl;
-      if (use_meansizedata > 0)
-      {
+      if (use_meansizedata > 0) {
         report1 << "# sex codes:  0=combined; 1=use female only; 2=use male only; 3=use both as joint sex*length distribution" << endl;
         report1 << "# partition codes:  0=combined; 1=discard; 2=retained" << endl;
         report1 << "# ageerr codes:  positive means mean length-at-age; negative means mean bodywt_at_age" << endl;
         report1 << "#_year month fleet sex part ageerr ignore datavector(female-male)" << endl;
         report1 << "#                                          samplesize(female-male)" << endl;
-        for (f = 1; f <= Nfleet; f++)
-        {
-          if (Nobs_ms(f) > 0)
-          {
-            for (i = 1; i <= Nobs_ms(f); i++)
-            {
+        for (f = 1; f <= Nfleet; f++) {
+          if (Nobs_ms(f) > 0) {
+            for (i = 1; i <= Nobs_ms(f); i++) {
               report1 << header_ms(f, i)(1) << " " << header_ms_rd(f, i)(2, 3) << " " << header_ms(f, i)(4, 7);
-              for (a = 1; a <= n_abins2; a++)
-              {
+              for (a = 1; a <= n_abins2; a++) {
                 report1 << " ";
                 temp = exp_ms(f, i, a);
-                if (temp <= 0.)
-                {
+                if (temp <= 0.) {
                   temp = 0.0001;
                 }
                 report1 << temp;
@@ -782,24 +701,24 @@ FUNCTION void write_nudata()
               << N_envvar << " #_N_environ_variables" << endl;
       report1 << "# -2 in year will subtract mean for that env_var; -1 will subtract mean and divide by stddev (e.g. Z-score)" << endl;
       report1 << "#_year variable value" << endl;
-      if (N_envvar > 0)
-      {
+      if (N_envvar > 0) {
         for (i = 0; i <= N_envdata - 1; i++)
           report1 << env_temp[i] << endl;
         report1 << "-9999 0 0" << endl;
       }
 
-      report1 << "#" << endl << "# Sizefreq data. Defined by method because a fleet can use multiple methods" << endl;
+      report1 << "#" << endl
+              << "# Sizefreq data. Defined by method because a fleet can use multiple methods" << endl;
       report1 << SzFreq_Nmeth_rd << " # N sizefreq methods to read (or -1 for expanded options)" << endl;
       if (SzFreq_Nmeth_rd < 0) {
         report1 << SzFreq_Nmeth << " # N sizefreq methods to read" << endl;
       }
-     if (SzFreq_Nmeth != 0)
-      {
+      if (SzFreq_Nmeth != 0) {
         report1 << "# each row below has entry for each sizefreq method " << endl;
         report1 << "#_ ";
-        for (int j = 1; j <= SzFreq_Nmeth; j++ )
-          { report1 << j << " ";}
+        for (int j = 1; j <= SzFreq_Nmeth; j++) {
+          report1 << j << " ";
+        }
         report1 << " # Method" << endl;
         report1 << SzFreq_Nbins << " #_Sizefreq N bins" << endl;
         report1 << SzFreq_units << " #_Sizefreq units(1=bio/2=num)" << endl;
@@ -807,13 +726,14 @@ FUNCTION void write_nudata()
         report1 << SzFreq_mincomp << " #_Sizefreq:  small constant to add to comps" << endl;
         report1 << SzFreq_nobs << " #_Sizefreq number of obs per method" << endl;
         if (SzFreq_Nmeth_rd < 0) {
-          report1 << Comp_Err_Sz <<  " #_Comp_Error:  0=multinomial, 1=dirichlet using Theta*n, 2=dirichlet using beta, 3=MV_Tweedie" << endl;
+          report1 << Comp_Err_Sz << " #_Comp_Error:  0=multinomial, 1=dirichlet using Theta*n, 2=dirichlet using beta, 3=MV_Tweedie" << endl;
           report1 << Comp_Err_Sz2 << " #_ParmSelect: consecutive index for dirichlet or MV_Tweedie comp_error" << endl;
         }
         report1 << "#_Sizefreq bins. one row for each method" << endl
                 << "#Note: negative value for first bin makes it accumulate all smaller fish vs. truncate small fish" << endl;
-        for (i = 1; i <= SzFreq_Nmeth; i++)
-        { report1 << SzFreq_Omit_Small(i) * SzFreq_bins1(i, 1) << SzFreq_bins1(i)(2, SzFreq_Nbins(i)) << endl; }
+        for (i = 1; i <= SzFreq_Nmeth; i++) {
+          report1 << SzFreq_Omit_Small(i) * SzFreq_bins1(i, 1) << SzFreq_bins1(i)(2, SzFreq_Nbins(i)) << endl;
+        }
         report1 << "#_method year month fleet sex part Nsamp <data> " << endl;
         for (iobs = 1; iobs <= SzFreq_totobs; iobs++) {
           report1 << SzFreq_obs1(iobs)(1, 7) << " " << SzFreq_exp(iobs) << endl;
@@ -823,8 +743,7 @@ FUNCTION void write_nudata()
       // begin tagging data section #2 (expected values)
       report1 << "#" << endl
               << Do_TG << " # do tags (0/1)" << endl;
-      if (Do_TG > 0)
-      {
+      if (Do_TG > 0) {
         // info on dimensions of tagging data
         report1 << N_TG << " # N tag groups" << endl;
         report1 << N_TG_recap << " # N recap events" << endl;
@@ -840,8 +759,7 @@ FUNCTION void write_nudata()
         report1 << "#_Note: Expected values for tag recaptures are reported only for the same combinations of" << endl;
         report1 << "#       group, year, area, and fleet that had observed recaptures. " << endl;
         report1 << "#_TG year seas fleet Nrecap" << endl;
-        for (j = 1; j <= N_TG_recap; j++)
-        {
+        for (j = 1; j <= N_TG_recap; j++) {
           // fill in first 4 columns:
           for (k = 1; k <= 4; k++)
             report1 << TG_recap_data(j, k) << " ";
@@ -858,20 +776,17 @@ FUNCTION void write_nudata()
 
       report1 << "#" << endl
               << Do_Morphcomp << " #    morphcomp data(0/1) " << endl;
-      if (Do_Morphcomp > 0)
-      {
+      if (Do_Morphcomp > 0) {
         report1 << "# note that raw data, not bootstrap are reported here " << endl;
         report1 << Morphcomp_nobs << "  #  Nobs" << endl;
         report1 << Morphcomp_nmorph << " # Nmorphs" << endl;
         report1 << Morphcomp_mincomp << " # add_to_comp" << endl;
         report1 << "#_year, month, fleet, null, Nsamp, datavector_by_Nmorphs" << endl;
-        for (i = 1; i <= Morphcomp_nobs; i++)
-        {
+        for (i = 1; i <= Morphcomp_nobs; i++) {
           report1 << Morphcomp_obs(i)(1, 5) << " " << Morphcomp_exp(i) << endl;
         }
       }
-      else
-      {
+      else {
         report1 << "#  Nobs, Nmorphs, mincomp" << endl;
         report1 << "#_year, seas, type, partition, Nsamp, datavector_by_Nmorphs" << endl;
       }
@@ -893,32 +808,27 @@ FUNCTION void write_nudata()
       report1 << "#_catch_se:  standard error of log(catch)" << endl;
       report1 << "#_NOTE:  catch data is ignored for survey fleets" << endl;
       k = 0;
-      for (f = 1; f <= Nfleet; f++)
-      {
-        if (fleet_type(f) <= 2)
-        {
-          for (y = styr - 1; y <= endyr; y++)
-          {
-            for (s = 1; s <= nseas; s++)
-            {
+      for (f = 1; f <= Nfleet; f++) {
+        if (fleet_type(f) <= 2) {
+          for (y = styr - 1; y <= endyr; y++) {
+            for (s = 1; s <= nseas; s++) {
               k++;
               t = styr + (y - styr) * nseas + s - 1;
-              if (y == styr - 1)
-              { report1 << -999 << " "; }
-              else
-              { report1 << y << " "; }
+              if (y == styr - 1) {
+                report1 << -999 << " ";
+              }
+              else {
+                report1 << y << " ";
+              }
               report1 << s << " " << f << " ";
-              if (fleet_type(f) == 2 && catch_ret_obs(f, t) > 0.0)
-              {
+              if (fleet_type(f) == 2 && catch_ret_obs(f, t) > 0.0) {
                 report1 << 0.1 << " " << catch_se(t, f) << endl; //  for bycatch only fleet
               }
-              else if (catchunits(f) == 1)
-              {
+              else if (catchunits(f) == 1) {
                 report1 << catch_fleet(t, f, 3) * mfexp(randn(radm) * catch_se(t, f) - 0.5 * catch_se(t, f) * catch_se(t, f))
                         << " " << catch_se(t, f) << endl;
               }
-              else
-              {
+              else {
                 report1 << catch_fleet(t, f, 6) * mfexp(randn(radm) * catch_se(t, f) - 0.5 * catch_se(t, f) * catch_se(t, f))
                         << " " << catch_se(t, f) << endl;
               }
@@ -934,15 +844,14 @@ FUNCTION void write_nudata()
       report1 << "#_errtype:  -1=normal; 0=lognormal; 1=lognormal with bias correction; >1=df for T-dist" << endl;
       report1 << "#_SD_report: 0=not; 1=include survey expected value with se" << endl;
       report1 << "#_note that link functions are specified in Q_setup section of control file" << endl;
-      report1 << "#_dataunits = 36 and 35 should use Q_type 5 to provide offset parameter" <<endl;
+      report1 << "#_dataunits = 36 and 35 should use Q_type 5 to provide offset parameter" << endl;
       report1 << "#_fleet units errtype SD_report" << endl;
       for (f = 1; f <= Nfleet; f++)
         report1 << f << " " << Svy_units(f) << " " << Svy_errtype(f) << " " << Svy_sdreport(f) << " # " << fleetname(f) << endl;
       report1 << "#_year month index obs err" << endl;
       if (Svy_N > 0)
         for (f = 1; f <= Nfleet; f++)
-          for (i = 1; i <= Svy_N_fleet(f); i++)
-          {
+          for (i = 1; i <= Svy_N_fleet(f); i++) {
             t = Svy_time_t(f, i);
             ALK_time = Svy_ALK_time(f, i);
             double newobs = 0.0;
@@ -961,7 +870,7 @@ FUNCTION void write_nudata()
               temp = sqrt((df + 1.) / df);
               newobs = value(mfexp(Svy_est(f, i) + randn(radm) * Svy_se_use(f, i) * temp)); //  adjusts the sd by the df sample size
             }
-            if (Svy_minval(f) >= 0.0 && Svy_errtype(f) != 0)  // this logic may need adjustment
+            if (Svy_minval(f) >= 0.0 && Svy_errtype(f) != 0) // this logic may need adjustment
               newobs = max(newobs, 0.5 * Svy_minval(f));
             report1 << newobs << " " << Svy_se_rd(f, i) << " #_orig_obs: " << Svy_obs(f, i) << " " << fleetname(f) << endl;
           }
@@ -974,41 +883,34 @@ FUNCTION void write_nudata()
       report1 << "# note: only enter units and errtype for fleets with discard " << endl;
       report1 << "# note: discard data is the total for an entire season, so input of month here must be to a month in that season" << endl;
       report1 << "#_Fleet units errtype" << endl;
-      if (Ndisc_fleets > 0)
-      {
+      if (Ndisc_fleets > 0) {
         for (f = 1; f <= Nfleet; f++)
           if (disc_units(f) > 0)
             report1 << f << " " << disc_units(f) << " " << disc_errtype(f) << " # " << fleetname(f) << endl;
         report1 << "#_year month fleet obs stderr" << endl;
         for (f = 1; f <= Nfleet; f++)
-          for (i = 1; i <= disc_N_fleet(f); i++)
-          {
+          for (i = 1; i <= disc_N_fleet(f); i++) {
             ALK_time = disc_time_ALK(f, i);
             report1 << Show_Time(disc_time_t(f, i), 1) << " " << yr_disc_super(f, i) * data_time(ALK_time, f, 1) << " " << f * yr_disc_use(f, i) << " ";
-            if (disc_errtype(f) >= 1)
-            {
+            if (disc_errtype(f) >= 1) {
               temp = exp_disc(f, i) + randn(radm) * sd_disc(f, i) * sqrt((disc_errtype(f) + 1.) / disc_errtype(f)) * exp_disc(f, i);
               if (temp < 0.001)
                 temp = 0.001;
             }
-            else if (disc_errtype(f) == 0)
-            {
+            else if (disc_errtype(f) == 0) {
               temp = exp_disc(f, i) + randn(radm) * sd_disc(f, i);
               if (temp < 0.001)
                 temp = 0.001;
             }
-            else if (disc_errtype(f) == -1)
-            {
+            else if (disc_errtype(f) == -1) {
               temp = exp_disc(f, i) + randn(radm) * sd_disc(f, i);
               if (temp < 0.001)
                 temp = 0.001;
             }
-            else if (disc_errtype(f) == -2)
-            {
+            else if (disc_errtype(f) == -2) {
               temp = exp_disc(f, i) * mfexp(randn(radm) * sd_disc(f, i));
             }
-            else if (disc_errtype(f) == -3)
-            {
+            else if (disc_errtype(f) == -3) {
               temp = exp_disc(f, i) + randn(radm) * (sd_disc(f, i) / sqrt(cumd_norm((1 - exp_disc(f, i)) / sd_disc(f, i)) - cumd_norm((0 - exp_disc(f, i)) / sd_disc(f, i))));
               if (temp < 0.001)
                 temp = 0.001;
@@ -1019,8 +921,7 @@ FUNCTION void write_nudata()
             report1 << " " << temp << " " << cv_disc(f, i) << " #_orig_obs: " << obs_disc(f, i) << " #_ " << fleetname(f) << endl;
           }
       }
-      else
-      {
+      else {
         report1 << "# ";
       }
       report1 << "-9999 0 0 0.0 0.0 # terminator for discard data " << endl;
@@ -1035,13 +936,10 @@ FUNCTION void write_nudata()
 
       // NOTE, the se stored in mnwtdata(7,i) was adjusted in prelim calc to include the input var_adjustment
       //  so var_adjust is subtracted here when the observation is written
-      if (nobs_mnwt > 0)
-      {
-        for (i = 1; i <= nobs_mnwt; i++)
-        {
+      if (nobs_mnwt > 0) {
+        for (i = 1; i <= nobs_mnwt; i++) {
           temp = exp_mnwt(i) + randn(radm) * mnwtdata(7, i) * sqrt((DF_bodywt + 1.) / DF_bodywt) * exp_mnwt(i);
-          if (temp <= 0.0)
-          {
+          if (temp <= 0.0) {
             temp = 0.0001;
           }
           f = abs(mnwtdata(3, i));
@@ -1055,27 +953,23 @@ FUNCTION void write_nudata()
       report1 << "#" << endl
               << "# set up population length bin structure (note - irrelevant if not using size data and using empirical wtatage" << endl;
       report1 << LenBin_option << " # length bin method: 1=use databins; 2=generate from binwidth,min,max below; 3=read vector" << endl;
-      if (LenBin_option == 1)
-      {
+      if (LenBin_option == 1) {
         report1 << "# no additional input for option 1" << endl;
         report1 << "# read binwidth, minsize, lastbin size for option 2" << endl;
         report1 << "# read N poplen bins, then vector of bin lower boundaries, for option 3" << endl;
       }
-      else if (LenBin_option == 2)
-      {
+      else if (LenBin_option == 2) {
         report1 << binwidth2 << " # binwidth for population size comp " << endl;
         report1 << minLread << " # minimum size in the population (lower edge of first bin and size at age 0.00) " << endl;
         report1 << maxLread << " # maximum size in the population (lower edge of last bin) " << endl;
       }
-      else
-      {
+      else {
         report1 << nlength << " # number of population size bins " << endl;
         report1 << len_bins << endl;
       }
 
       report1 << use_length_data << " # use length composition data (0/1/2) where 2 invokes new comp_comtrol format" << endl;
-      if (use_length_data > 0)
-      {
+      if (use_length_data > 0) {
         report1 << "#_mintailcomp: upper and lower distribution for females and males separately are accumulated until exceeding this level." << endl;
         report1 << "#_addtocomp:  after accumulation of tails; this value added to all bins" << endl;
         report1 << "#_combM+F: males and females treated as combined sex below this bin number " << endl;
@@ -1084,17 +978,14 @@ FUNCTION void write_nudata()
         report1 << "#_ParmSelect:  consecutive index for dirichlet or MV_Tweedie" << endl;
         report1 << "#_minsamplesize: minimum sample size; set to 1 to match 3.24, minimum value is 0.001" << endl;
         report1 << "#" << endl;
-        if(use_length_data == 1)
-        {
+        if (use_length_data == 1) {
           report1 << "#_Using old format for composition controls" << endl;
-        report1 << "#_mintailcomp addtocomp combM+F CompressBins CompError ParmSelect minsamplesize" << endl;
-        for (f = 1; f <= Nfleet; f++)
-        {
-          report1 << min_tail_L(0, f) << " " << min_comp_L(0, f) << " " << CombGender_L(0, f) << " " << AccumBin_L(0, f) << " " << Comp_Err_L(0, f) << " " << Comp_Err_L2(0, f) << " " << min_sample_size_L(0, f) << " #_fleet:" << f << "_" << fleetname(f) << endl;
-        }
+          report1 << "#_mintailcomp addtocomp combM+F CompressBins CompError ParmSelect minsamplesize" << endl;
+          for (f = 1; f <= Nfleet; f++) {
+            report1 << min_tail_L(0, f) << " " << min_comp_L(0, f) << " " << CombGender_L(0, f) << " " << AccumBin_L(0, f) << " " << Comp_Err_L(0, f) << " " << Comp_Err_L2(0, f) << " " << min_sample_size_L(0, f) << " #_fleet:" << f << "_" << fleetname(f) << endl;
+          }
         }
-        else if (use_length_data == 2)
-        {
+        else if (use_length_data == 2) {
           report1 << "#_Using new list format for composition controls" << endl;
           report1 << "#_use negative fleet value to fill for all higher numbered fleets (recommended!)" << endl;
           report1 << "#_must enter in fleet, partition order; but only need to enter for used combos" << endl;
@@ -1109,17 +1000,12 @@ FUNCTION void write_nudata()
         report1 << nlen_bin << " #_N_LengthBins" << endl
                 << len_bins_dat << endl;
         report1 << "#_year month fleet sex part Nsamp datavector(female-male)" << endl;
-        for (f = 1; f <= Nfleet; f++)
-        {
-          if (Nobs_l(f) > 0)
-          {
-            for (i = 1; i <= Nobs_l(f); i++)
-            {
+        for (f = 1; f <= Nfleet; f++) {
+          if (Nobs_l(f) > 0) {
+            for (i = 1; i <= Nobs_l(f); i++) {
               int parti = mkt_l(f, i);
-              switch (Comp_Err_L(parti, f))
-              {
-                case 0:
-                {
+              switch (Comp_Err_L(parti, f)) {
+                case 0: {
                   Nsamp_DM = nsamp_l(f, i);
                   break;
                 }
@@ -1130,9 +1016,9 @@ FUNCTION void write_nudata()
                   Nsamp_DM = value(1. / (1. + dirichlet_Parm) + nsamp_l(f, i) * dirichlet_Parm / (1. + dirichlet_Parm));
                   break;
                 }
-                case 2:  //  Dirichlet #2
+                case 2: //  Dirichlet #2
                 {
-                  dirichlet_Parm = mfexp(selparm(Comp_Err_parmloc(Comp_Err_L2(parti,f), 1))); //  Thorson's beta from eq 12
+                  dirichlet_Parm = mfexp(selparm(Comp_Err_parmloc(Comp_Err_L2(parti, f), 1))); //  Thorson's beta from eq 12
                   // effN_DM = (n+n*beta)/(n+beta)
                   Nsamp_DM = value((nsamp_l(f, i) + dirichlet_Parm * nsamp_l(f, i)) / (dirichlet_Parm + nsamp_l(f, i)));
                   break;
@@ -1154,7 +1040,7 @@ FUNCTION void write_nudata()
               }
 
               report1 << header_l_rd(f, i)(1, 5) << " " << Nsamp_DM << " " << exp_l_temp_dat << endl;
-//              report1 << header_l_rd(f, i)(1, 3) << " " << gen_l(f, i) << " " << header_l_rd(f, i)(5) << " " << Nsamp_DM << " " << exp_l_temp_dat << endl;
+              //              report1 << header_l_rd(f, i)(1, 3) << " " << gen_l(f, i) << " " << header_l_rd(f, i)(5) << " " << Nsamp_DM << " " << exp_l_temp_dat << endl;
             }
           }
         }
@@ -1163,19 +1049,16 @@ FUNCTION void write_nudata()
           report1 << "0 ";
         report1 << endl;
       }
-      else
-      {
+      else {
         report1 << "# see manual for format of length composition data " << endl;
       }
 
       report1 << "#" << endl
               << n_abins << " #_N_age_bins" << endl;
-      if (n_abins > 0)
-      {
+      if (n_abins > 0) {
         report1 << age_bins1 << endl;
       }
-      else
-      {
+      else {
         report1 << "# ";
       }
       report1 << N_ageerr << " #_N_ageerror_definitions" << endl;
@@ -1187,12 +1070,11 @@ FUNCTION void write_nudata()
       report1 << "#_combM+F: males and females treated as combined sex below this bin number " << endl;
       report1 << "#_compressbins: accumulate upper tail by this number of bins; acts simultaneous with mintailcomp; set=0 for no forced accumulation" << endl;
       report1 << "#_Comp_Error:  0=multinomial, 1=dirichlet using Theta*n, 2=dirichlet using beta, 3=MV_Tweedie" << endl;
-        report1 << "#_ParmSelect:  consecutive index for dirichlet or MV_Tweedie" << endl;
+      report1 << "#_ParmSelect:  consecutive index for dirichlet or MV_Tweedie" << endl;
       report1 << "#_minsamplesize: minimum sample size; set to 1 to match 3.24, minimum value is 0.001" << endl;
       report1 << "#" << endl;
       report1 << "#_mintailcomp addtocomp combM+F CompressBins CompError ParmSelect minsamplesize" << endl;
-      for (f = 1; f <= Nfleet; f++)
-      {
+      for (f = 1; f <= Nfleet; f++) {
         if (n_abins <= 0)
           report1 << "# ";
         report1 << min_tail_A(f) << " " << min_comp_A(f) << " " << CombGender_A(f) << " " << AccumBin_A(f) << " " << Comp_Err_A(f) << " " << Comp_Err_A2(f) << " " << min_sample_size_A(f) << " #_fleet:" << f << "_" << fleetname(f) << endl;
@@ -1206,29 +1088,24 @@ FUNCTION void write_nudata()
 
       report1 << "#_year month fleet sex part ageerr Lbin_lo Lbin_hi Nsamp datavector(female-male)" << endl;
       if (Nobs_a_tot > 0)
-        for (f = 1; f <= Nfleet; f++)
-        {
-          if (Nobs_a(f) > 0)
-          {
-            for (i = 1; i <= Nobs_a(f); i++)
-            {
-              switch (Comp_Err_A(f))
-              {
-                case 0:
-                {
+        for (f = 1; f <= Nfleet; f++) {
+          if (Nobs_a(f) > 0) {
+            for (i = 1; i <= Nobs_a(f); i++) {
+              switch (Comp_Err_A(f)) {
+                case 0: {
                   Nsamp_DM = nsamp_a(f, i);
                   break;
                 }
                 case 1: //  Dirichlet #1
                 {
-                  dirichlet_Parm = mfexp(selparm(Comp_Err_parmloc(Comp_Err_A2(f),1))); //  Thorson's theta from eq 10
+                  dirichlet_Parm = mfexp(selparm(Comp_Err_parmloc(Comp_Err_A2(f), 1))); //  Thorson's theta from eq 10
                   // effN_DM = 1/(1+theta) + n*theta/(1+theta)
                   Nsamp_DM = value(1. / (1. + dirichlet_Parm) + nsamp_a(f, i) * dirichlet_Parm / (1. + dirichlet_Parm));
                   break;
                 }
-                case 2:  //  Dirichlet #2
+                case 2: //  Dirichlet #2
                 {
-                  dirichlet_Parm = mfexp(selparm(Comp_Err_parmloc(Comp_Err_A2(f),1))); //  Thorson's beta from eq 12
+                  dirichlet_Parm = mfexp(selparm(Comp_Err_parmloc(Comp_Err_A2(f), 1))); //  Thorson's beta from eq 12
                   // effN_DM = (n+n*beta)/(n+beta)      computed in Fit_LenComp
                   Nsamp_DM = value((nsamp_a(f, i) + dirichlet_Parm * nsamp_a(f, i)) / (dirichlet_Parm + nsamp_a(f, i)));
                   break;
@@ -1263,26 +1140,20 @@ FUNCTION void write_nudata()
 
       report1 << "#" << endl
               << use_meansizedata << " #_Use_MeanSize-at-Age_obs (0/1)" << endl;
-      if (use_meansizedata > 0)
-      {
+      if (use_meansizedata > 0) {
         report1 << "# sex codes:  0=combined; 1=use female only; 2=use male only; 3=use both as joint sex*length distribution" << endl;
         report1 << "# partition codes:  0=combined; 1=discard; 2=retained" << endl;
         report1 << "# ageerr codes:  positive means mean length-at-age; negative means mean bodywt_at_age" << endl;
         report1 << "#_year month fleet sex part ageerr ignore datavector(female-male)" << endl;
         report1 << "#                                          samplesize(female-male)" << endl;
-        for (f = 1; f <= Nfleet; f++)
-        {
-          if (Nobs_ms(f) > 0)
-          {
-            for (i = 1; i <= Nobs_ms(f); i++)
-            {
+        for (f = 1; f <= Nfleet; f++) {
+          if (Nobs_ms(f) > 0) {
+            for (i = 1; i <= Nobs_ms(f); i++) {
               report1 << header_ms(f, i)(1) << " " << header_ms_rd(f, i)(2, 3) << " " << header_ms(f, i)(4, 7);
-              for (a = 1; a <= n_abins2; a++)
-              {
+              for (a = 1; a <= n_abins2; a++) {
                 report1 << " ";
                 temp = exp_ms(f, i, a) + randn(radm) * exp_ms_sq(f, i, a) / obs_ms_n(f, i, a);
-                if (temp <= 0.)
-                {
+                if (temp <= 0.) {
                   temp = 0.0001;
                 }
                 report1 << temp;
@@ -1305,24 +1176,24 @@ FUNCTION void write_nudata()
               << N_envvar << " #_N_environ_variables" << endl;
       report1 << "# -2 in year will subtract mean for that env_var; -1 will subtract mean and divide by stddev (e.g. Z-score)" << endl;
       report1 << "#_year variable value" << endl;
-      if (N_envvar > 0)
-      {
+      if (N_envvar > 0) {
         for (i = 0; i <= N_envdata - 1; i++)
           report1 << env_temp[i] << endl;
         report1 << "-9999 0 0" << endl;
       }
 
-      report1 << "#" << endl << "# Sizefreq data. Defined by method because a fleet can use multiple methods" << endl;
+      report1 << "#" << endl
+              << "# Sizefreq data. Defined by method because a fleet can use multiple methods" << endl;
       report1 << SzFreq_Nmeth_rd << " # N sizefreq methods to read (or -1 for expanded options)" << endl;
       if (SzFreq_Nmeth_rd < 0) {
         report1 << SzFreq_Nmeth << " # N sizefreq methods to read" << endl;
       }
-      if (SzFreq_Nmeth != 0)
-      {
+      if (SzFreq_Nmeth != 0) {
         report1 << "# each row below has entry for each sizefreq method " << endl;
         report1 << "#_ ";
-        for (int j = 1; j <= SzFreq_Nmeth; j++ )
-          { report1 << j << " ";}
+        for (int j = 1; j <= SzFreq_Nmeth; j++) {
+          report1 << j << " ";
+        }
         report1 << " # Method" << endl;
         report1 << SzFreq_Nbins << " #_Sizefreq N bins" << endl;
         report1 << SzFreq_units << " #_Sizefreq units(1=bio/2=num)" << endl;
@@ -1330,52 +1201,50 @@ FUNCTION void write_nudata()
         report1 << SzFreq_mincomp << " #_Sizefreq:  small constant to add to comps" << endl;
         report1 << SzFreq_nobs << " #_Sizefreq number of obs per method" << endl;
         if (SzFreq_Nmeth_rd < 0) {
-          report1 << Comp_Err_Sz <<  " #_Comp_Error:  0=multinomial, 1=dirichlet using Theta*n, 2=dirichlet using beta, 3=MV_Tweedie" << endl;
+          report1 << Comp_Err_Sz << " #_Comp_Error:  0=multinomial, 1=dirichlet using Theta*n, 2=dirichlet using beta, 3=MV_Tweedie" << endl;
           report1 << Comp_Err_Sz2 << " #_ParmSelect: consecutive index for dirichlet or MV_Tweedie comp_error" << endl;
         }
         report1 << "#_Sizefreq bins. one row for each method" << endl
                 << "#Note: negative value for first bin makes it accumulate all smaller fish vs. truncate small fish" << endl;
-        for (i = 1; i <= SzFreq_Nmeth; i++)
-        { report1 << SzFreq_Omit_Small(i) * SzFreq_bins1(i, 1) << SzFreq_bins1(i)(2, SzFreq_Nbins(i)) << endl; }
+        for (i = 1; i <= SzFreq_Nmeth; i++) {
+          report1 << SzFreq_Omit_Small(i) * SzFreq_bins1(i, 1) << SzFreq_bins1(i)(2, SzFreq_Nbins(i)) << endl;
+        }
         report1 << "#_method year month fleet sex part Nsamp <data> " << endl;
         j = 2 * max(SzFreq_Nbins);
         dvector temp_probs3(1, j);
         dvector SzFreq_newdat(1, j);
-        for (iobs = 1; iobs <= SzFreq_totobs; iobs++)
-        {
-          f = SzFreq_obs1(iobs, 1);  //  sizefreq method
+        for (iobs = 1; iobs <= SzFreq_totobs; iobs++) {
+          f = SzFreq_obs1(iobs, 1); //  sizefreq method
           double Nsamp_dat = 50000;
           if (SzFreq_obs1(iobs, 7) < Nsamp_dat)
-          Nsamp_dat = SzFreq_obs1(iobs, 7);
+            Nsamp_dat = SzFreq_obs1(iobs, 7);
           SzFreq_newdat.initialize();
 
-              switch (Comp_Err_Sz(f))
-              {
-                case 0:
-                {
-                  Nsamp_DM = Nsamp_dat;
-                  break;
-                }
-                case 1: //  Dirichlet #1
-                {
-                  dirichlet_Parm = mfexp(selparm(Comp_Err_parmloc(Comp_Err_Sz2(f),1))); //  Thorson's theta from eq 10
-                  // effN_DM = 1/(1+theta) + n*theta/(1+theta)
-                  Nsamp_DM = value(1. / (1. + dirichlet_Parm) + Nsamp_dat * dirichlet_Parm / (1. + dirichlet_Parm));
-                  break;
-                }
-                case 2:  //  Dirichlet #2
-                {
-                  dirichlet_Parm = mfexp(selparm(Comp_Err_parmloc(Comp_Err_Sz2(f),1)));  //  Thorson's beta from eq 12
-                  // effN_DM = (n+n*beta)/(n+beta)      computed in Fit_LenComp
-                  Nsamp_DM = value((nsamp_l(f, i) + dirichlet_Parm * nsamp_l(f, i)) / (dirichlet_Parm + Nsamp_dat));
-                  break;
-                }
-                case 3: //  MV_Tweedie
-                {
-                  //  need MV_tweedie
-                  break;
-                }
-              }
+          switch (Comp_Err_Sz(f)) {
+            case 0: {
+              Nsamp_DM = Nsamp_dat;
+              break;
+            }
+            case 1: //  Dirichlet #1
+            {
+              dirichlet_Parm = mfexp(selparm(Comp_Err_parmloc(Comp_Err_Sz2(f), 1))); //  Thorson's theta from eq 10
+              // effN_DM = 1/(1+theta) + n*theta/(1+theta)
+              Nsamp_DM = value(1. / (1. + dirichlet_Parm) + Nsamp_dat * dirichlet_Parm / (1. + dirichlet_Parm));
+              break;
+            }
+            case 2: //  Dirichlet #2
+            {
+              dirichlet_Parm = mfexp(selparm(Comp_Err_parmloc(Comp_Err_Sz2(f), 1))); //  Thorson's beta from eq 12
+              // effN_DM = (n+n*beta)/(n+beta)      computed in Fit_LenComp
+              Nsamp_DM = value((nsamp_l(f, i) + dirichlet_Parm * nsamp_l(f, i)) / (dirichlet_Parm + Nsamp_dat));
+              break;
+            }
+            case 3: //  MV_Tweedie
+            {
+              //  need MV_tweedie
+              break;
+            }
+          }
 
           temp_probs3(1, SzFreq_Setup2(iobs)) = value(SzFreq_exp(iobs));
           temp_mult.fill_multinomial(radm, temp_probs3(1, SzFreq_Setup2(iobs))); // create multinomial draws with prob = expected values
@@ -1385,35 +1254,30 @@ FUNCTION void write_nudata()
           }
 
           report1 << SzFreq_obs1(iobs)(1, 7) << " " << SzFreq_newdat(1, SzFreq_Setup2(iobs)) << endl;
-        }        
+        }
       }
 
       // begin tagging data section #3 (bootstrap data)
       report1 << "#" << endl
               << Do_TG << " # do tags (0/1)" << endl;
-      if (Do_TG > 0)
-      {
+      if (Do_TG > 0) {
         dvector temp_negbin(1, 50000);
 
         // changes authored by Gavin Fay in June 2016 in SS3 3.24Y
         TG_recap_gen.initialize();
         int N_TG_recap_gen = 0;
-        for (TG = 1; TG <= N_TG; TG++)
-        {
+        for (TG = 1; TG <= N_TG; TG++) {
           overdisp = TG_parm(2 * N_TG + TG);
 
           dvector TG_fleet_probs(1, Nfleet);
           dvector temp_tags(1, Nfleet);
           //  problem:  TG_recap_exp only dimensioned to TG_endtime
-          for (t = 0; t <= min(TG_maxperiods, TG_endtime(TG)); t++)
-          {
-            if (value(TG_recap_exp(TG, t, 0)) > 0)
-            {
+          for (t = 0; t <= min(TG_maxperiods, TG_endtime(TG)); t++) {
+            if (value(TG_recap_exp(TG, t, 0)) > 0) {
               temp_negbin.initialize();
               temp_negbin.fill_randnegbinomial(value(TG_recap_exp(TG, t, 0)), value(overdisp), radm);
-              //cout << TG << " " << t << " " << temp_negbin <<  " " << TG_recap_exp(TG,t,0) << " " << value(overdisp) << endl;
-              if (temp_negbin(1) > 0)
-              {
+              // cout << TG << " " << t << " " << temp_negbin <<  " " << TG_recap_exp(TG,t,0) << " " << value(overdisp) << endl;
+              if (temp_negbin(1) > 0) {
                 TG_fleet_probs = value(TG_recap_exp(TG, t)(1, Nfleet)) / temp_negbin(1);
                 temp_tags = 0.0;
                 temp_mult.fill_multinomial(radm, TG_fleet_probs);
@@ -1421,10 +1285,8 @@ FUNCTION void write_nudata()
                 {
                   temp_tags(temp_mult(compindex)) += 1.0;
                 }
-                for (f = 1; f <= Nfleet; f++)
-                {
-                  if (temp_tags(f) > 0)
-                  {
+                for (f = 1; f <= Nfleet; f++) {
+                  if (temp_tags(f) > 0) {
                     N_TG_recap_gen += 1;
                     TG_recap_gen(N_TG_recap_gen, 1) = TG;
                     TG_recap_gen(N_TG_recap_gen, 2) = TG_release(TG, 3) + int((t + TG_release(TG, 4) - 1) / nseas);
@@ -1455,8 +1317,7 @@ FUNCTION void write_nudata()
         report1 << "#_Note: Bootstrap values for tag recaptures are produced only for the same combinations of" << endl;
         report1 << "#       group, year, area, and fleet that had observed recaptures. " << endl;
         report1 << "#_TG year seas fleet Nrecap" << endl;
-        for (j = 1; j <= N_TG_recap_gen; j++)
-        {
+        for (j = 1; j <= N_TG_recap_gen; j++) {
           report1 << TG_recap_gen(j) << endl;
         }
       }
@@ -1464,20 +1325,17 @@ FUNCTION void write_nudata()
 
       report1 << "#" << endl
               << Do_Morphcomp << " #    morphcomp data(0/1) " << endl;
-      if (Do_Morphcomp > 0)
-      {
+      if (Do_Morphcomp > 0) {
         report1 << "# note that raw data, not bootstrap are reported here " << endl;
         report1 << Morphcomp_nobs << "  #  Nobs" << endl;
         report1 << Morphcomp_nmorph << " # Nmorphs" << endl;
         report1 << Morphcomp_mincomp << " # add_to_comp" << endl;
         report1 << "#_year, month, fleet, null, Nsamp, datavector_by_Nmorphs (no error added!!!)" << endl;
-        for (i = 1; i <= Morphcomp_nobs; i++)
-        {
+        for (i = 1; i <= Morphcomp_nobs; i++) {
           report1 << Morphcomp_obs(i)(1, 5) << " " << Morphcomp_exp(i) << endl;
         }
       }
-      else
-      {
+      else {
         report1 << "#  Nobs, Nmorphs, mincomp" << endl;
         report1 << "#_year, seas, type, partition, Nsamp, datavector_by_Nmorphs" << endl;
       }
@@ -1496,12 +1354,12 @@ FUNCTION void write_nudata()
 
   //  report1 << "ENDDATA" << endl;
   return;
-  } //  end of write data
+} //  end of write data
 
 //********************************************************************
- /*  SS_Label_FUNCTION 39 write_nucontrol  write new control file and starter file */
+/*  SS_Label_FUNCTION 39 write_nucontrol  write new control file and starter file */
 FUNCTION void write_nucontrol()
-  {
+{
   echoinput << "Write starter.ss_new file " << endl;
   anystring = ssnew_pathname + "starter.ss_new";
   ofstream NuStart(anystring);
@@ -1514,16 +1372,13 @@ FUNCTION void write_nucontrol()
   NuStart << readparfile << " # 0=use init values in control file; 1=use ss.par" << endl;
   NuStart << rundetail << " # run display detail (0 = minimal; 1=one line per iter; 2=each logL)" << endl;
   NuStart << reportdetail << " # detailed output (0=minimal for data-limited, 1=high (w/ wtatage.ss_new), 2=brief, 3=custom) " << endl;
-  if (reportdetail == 3)
-  {
+  if (reportdetail == 3) {
     NuStart << "# custom report options: -100 to start with minimal; -101 to start with all; -number to remove, +number to add, -999 to end" << endl;
-    for (unsigned j = 0; j <= reportdetail_list.size() - 1; j++)
-    {
+    for (unsigned j = 0; j <= reportdetail_list.size() - 1; j++) {
       NuStart << reportdetail_list[j](1) << endl;
     }
   }
-  else
-  {
+  else {
     NuStart << "#COND: custom report options: -100 to start with minimal; -101 to start with all; -number to remove, +number to add, -999 to end" << endl;
   }
 
@@ -1548,16 +1403,14 @@ FUNCTION void write_nucontrol()
   NuStart << final_conv << " # final convergence criteria (e.g. 1.0e-04) " << endl;
   NuStart << retro_yr - endyr << " # retrospective year relative to end year (e.g. -4)" << endl;
   NuStart << Smry_Age << " # min age for calc of summary biomass" << endl;
-  NuStart << depletion_basis_rd << " # Depletion basis:  denom is: 0=skip; 1=X*SPBvirgin; 2=X*SPBmsy; 3=X*SPB_styr; 4=X*SPB_endyr; 5=X*dyn_Bzero;  values>=11 invoke N multiyr with 10s & 100s digit; append .1 to invoke log(ratio); e.g. 122.1 produces log(12 year trailing average of B/Bmsy)" << endl;
+  NuStart << depletion_basis_rd << " # Depletion basis:  denom is: 0=skip; 1=X*SSBvirgin; 2=X*SSBmsy; 3=X*SSB_styr; 4=X*SSB_endyr; 5=X*dyn_Bzero;  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)" << endl;
   NuStart << depletion_level << " # Fraction (X) for Depletion denominator (e.g. 0.4)" << endl;
   NuStart << SPR_reporting << " # SPR_report_basis:  0=skip; 1=(1-SPR)/(1-SPR_tgt); 2=(1-SPR)/(1-SPR_MSY); 3=(1-SPR)/(1-SPR_Btarget); 4=rawSPR" << endl;
   NuStart << F_reporting << " # F_std_reporting_units: 0=skip; 1=exploitation(Bio); 2=exploitation(Num); 3=sum(Apical_F's); 4=mean F for range of ages (numbers weighted); 5=unweighted mean F for range of ages" << endl;
-  if (F_reporting == 4 || F_reporting == 5)
-  {
+  if (F_reporting == 4 || F_reporting == 5) {
     NuStart << F_reporting_ages << " # min and max age over which mean F will be calculated, with F=Z-M" << endl;
   }
-  else
-  {
+  else {
     NuStart << "#COND 10 15 #_min and max age over which mean F will be calculated with F_reporting=4 or 5" << endl;
   }
   NuStart << F_std_basis_rd << " # F_std_scaling: 0=no scaling; 1=F/Fspr; 2=F/Fmsy; 3=F/Fbtgt; where F means annual F_std, Fmsy means F_std@msy; values >=11 invoke N multiyr using 10s and 100s digit; append .1 to invoke log(ratio)" << endl;
@@ -1577,13 +1430,11 @@ FUNCTION void write_nucontrol()
   NuFore << Do_Benchmark << " # Benchmarks: 0=skip; 1=calc F_spr,F_btgt,F_msy; 2=calc F_spr,F0.1,F_msy; 3=add F_Blimit; " << endl;
   NuFore << Do_MSY << " # Do_MSY: 1= set to F(SPR); 2=calc F(MSY); 3=set to F(Btgt) or F0.1; 4=set to F(endyr); 5=calc F(MEY) with MSY_unit options" << endl;
   NuFore << "# if Do_MSY=5, enter MSY_Units; then list fleet_ID, cost/F, price/mt, include_in_Fmey_scaling; # -fleet_ID to fill; -9999 to terminate" << endl;
-  if (Do_MSY == 5)
-  {
+  if (Do_MSY == 5) {
     NuFore << MSY_units << " # MSY_units: 1=dead biomass, 2=dead biomass w/o excluded bycatch fleet, 3=retained biomass; 4=profits using price and costs" << endl;
     NuFore << "# Note: if a fleet's catch is excluded from the Fmey search, its catch or profits are still included in the MSY value using historical F levels from Bmark_years" << endl;
     NuFore << "# Fleet Cost_per_F Price_per_F include_in_Fmey_search" << endl;
-    for (f = 1; f <= Nfleet; f++)
-    {
+    for (f = 1; f <= Nfleet; f++) {
       if (YPR_mask(f) > 0.0)
         NuFore << f << " " << CostPerF(f) << " " << PricePerF(f) << " " << AdjustBenchF(f) << endl;
     }
@@ -1605,38 +1456,38 @@ FUNCTION void write_nucontrol()
   NuFore << N_Fcast_Yrs << " # N forecast years " << endl;
   NuFore << Fcast_Flevel << " # Fmult (only used for Do_Forecast==5) such that apical_F(f)=Fmult*relF(f)" << endl;
   anystring = "";
-  if(Fcast_yr_rd(1) != -12345)
-  {   //  write in old format
+  if (Fcast_yr_rd(1) != -12345) { //  write in old format
     NuFore << "#_Fcast_years for averaging:  beg_selex, end_selex, beg_relF, end_relF, beg_mean recruits, end_recruits  (enter actual year, or values of 0 or -integer to be rel. endyr)" << endl
-         << Fcast_yr_rd << endl
-         << "# " << Fcast_yr << endl;
+           << Fcast_yr_rd << endl
+           << "# " << Fcast_yr << endl;
     NuFore << Fcast_timevary_Selex_rd << " # Forecast selectivity (0=fcast selex is mean from year range; 1=fcast selectivity from time-vary parms). NOTE: logic reverses in new format" << endl;
-    //  
+    //
     NuFore << "# A revised protocol for the Fcast_yr specification is available and recommended. Template is below." << endl;
-          warnstream << "A revised protocol for the Fcast_yr specification is available and recommended.";
-          write_message (NOTE, 1);
+    warnstream << "A revised protocol for the Fcast_yr specification is available and recommended.";
+    write_message(NOTE, 1);
     anystring = "#";
   }
-//  else
-  {  //  new list based format for Fcast years
-  NuFore << anystring << endl << anystring << "-12345  # code to invoke new format for expanded fcast year controls" << endl
-         << "# biology and selectivity vectors are updated annually in the forecast according to timevary parameters, so check end year of blocks and dev vectors" << endl
-         << "# input in this section directs creation of means over historical years to override any time_vary changes" << endl
-				 << "# Factors implemented so far: 1=M, 4=recr_dist, 5=migration, 10=selectivity, 11=rel_F, 12=recruitment" << endl
-         << "# rel_F and Recruitment also have additional controls later in forecast.ss" << endl
-         << "# input as list: Factor, method (0, 1), st_yr, end_yr" << endl
-         << "# Terminate with -9999 for Factor" << endl
-         << "# st_yr and end_yr input can be actual year; <=0 sets rel. to timeseries endyr; Except -999 for st_yr sets to first year if time series" << endl
-//				 << "#_Factor: 1=M, 2=growth, 3=wtlen, 4=recr_dist&femfrac, 5=migration, 6=ageerror, 7=catchmult, 8=hermaphroditism" << endl
-         << "# Method = 0 (or omitted) continue using time_vary parms; 1  use mean of derived factor over specified year range"<<endl;
+  //  else
+  { //  new list based format for Fcast years
+    NuFore << anystring << endl
+           << anystring << "-12345  # code to invoke new format for expanded fcast year controls" << endl
+           << "# biology and selectivity vectors are updated annually in the forecast according to timevary parameters, so check end year of blocks and dev vectors" << endl
+           << "# input in this section directs creation of means over historical years to override any time_vary changes" << endl
+           << "# Factors implemented so far: 1=M, 4=recr_dist, 5=migration, 10=selectivity, 11=rel_F, 12=recruitment" << endl
+           << "# rel_F and Recruitment also have additional controls later in forecast.ss" << endl
+           << "# input as list: Factor, method (0, 1), st_yr, end_yr" << endl
+           << "# Terminate with -9999 for Factor" << endl
+           << "# st_yr and end_yr input can be actual year; <=0 sets rel. to timeseries endyr; Except -999 for st_yr sets to first year if time series" << endl
+           //				 << "#_Factor: 1=M, 2=growth, 3=wtlen, 4=recr_dist&femfrac, 5=migration, 6=ageerror, 7=catchmult, 8=hermaphroditism" << endl
+           << "# Method = 0 (or omitted) continue using time_vary parms; 1  use mean of derived factor over specified year range" << endl;
     NuFore << "# Factor method st_yr end_yr " << endl;
     for (int i = 1; i <= 12; i++)
-    if (Fcast_MGparm_ave_rd(i, 1) > 0)
-	  {
-      NuFore << anystring << Fcast_MGparm_ave_rd(i) << " # " << MGtype_Lbl(i) << "; use: "  << Fcast_MGparm_ave(i) << endl;
-    }
+      if (Fcast_MGparm_ave_rd(i, 1) > 0) {
+        NuFore << anystring << Fcast_MGparm_ave_rd(i) << " # " << MGtype_Lbl(i) << "; use: " << Fcast_MGparm_ave(i) << endl;
+      }
 
-    NuFore << anystring << "-9999 0 0 0" << endl << "#" <<endl;
+    NuFore << anystring << "-9999 0 0 0" << endl
+           << "#" << endl;
   }
 
   NuFore << HarvestPolicy << " # 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) " << endl;
@@ -1644,28 +1495,26 @@ FUNCTION void write_nucontrol()
   NuFore << H4010_top_rd << " # 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 " << endl;
   NuFore << H4010_bot << " # Control rule cutoff for no F (as frac of Bzero, e.g. 0.10) " << endl;
   NuFore << H4010_scale_rd << " # 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 " << endl;
-  if (H4010_scale_rd < 0)
-  {
+  if (H4010_scale_rd < 0) {
     j = H4010_scale_vec_rd.size() - 1;
-    for (int s = 0; s <= j; s++)
-    {
+    for (int s = 0; s <= j; s++) {
       NuFore << H4010_scale_vec_rd[s] << endl;
     }
   }
 
-  NuFore << "#" << endl << Fcast_Loop_Control(1) << " #_N forecast loops (1=OFL only; 2=ABC; 3=get F from forecast ABC catch with allocations applied)" << endl;
+  NuFore << "#" << endl
+         << Fcast_Loop_Control(1) << " #_N forecast loops (1=OFL only; 2=ABC; 3=get F from forecast ABC catch with allocations applied)" << endl;
   NuFore << Fcast_Loop_Control(2) << " # First forecast loop with stochastic recruitment" << endl;
   NuFore << Fcast_Loop_Control(3) << " # Forecast base recruitment:  0= spawn_recr; 1=mult*spawn_recr_fxn; 2=mult*VirginRecr; 3=deprecated; 4=mult*mean_over_yr_range" << endl;
   NuFore << "# for option 4, set phase for fore_recr_devs to -1 in control to get constant mean in MCMC, else devs will be applied" << endl;
-  if (Fcast_Loop_Control(3) == 0)
-  {
+  if (Fcast_Loop_Control(3) == 0) {
     NuFore << 1.0 << " # Value multiplier is ignored" << endl;
   }
-  else
-  {
+  else {
     NuFore << Fcast_Loop_Control(4) << " # multiplier on base recruitment " << endl;
   }
-  NuFore << Fcast_Loop_Control(5) << " # not used" << endl << "#" << endl;
+  NuFore << Fcast_Loop_Control(5) << " # not used" << endl
+         << "#" << endl;
 
   NuFore << Fcast_Cap_FirstYear << "  # FirstYear for caps and allocations (should be after years with fixed inputs) " << endl;
 
@@ -1684,10 +1533,8 @@ FUNCTION void write_nucontrol()
   NuFore << "# enter list of:  season, fleet, relF; if used, terminate with season=-9999" << endl;
   {
     for (s = 1; s <= nseas; s++)
-      for (f = 1; f <= Nfleet; f++)
-      {
-        if (Fcast_RelF_Use(s, f) > 0.0)
-        {
+      for (f = 1; f <= Nfleet; f++) {
+        if (Fcast_RelF_Use(s, f) > 0.0) {
           if (Fcast_RelF_Basis == 1)
             NuFore << "# ";
           NuFore << s << " " << f << " " << Fcast_RelF_Use(s, f) << endl;
@@ -1699,24 +1546,21 @@ FUNCTION void write_nucontrol()
   }
 
   NuFore << "# enter list of: fleet number, max annual catch for fleets with a max; terminate with fleet=-9999" << endl;
-  for (f = 1; f <= Nfleet; f++)
-  {
+  for (f = 1; f <= Nfleet; f++) {
     if (Fcast_MaxFleetCatch(f) > -1 && fleet_type(f) == 1)
       NuFore << f << " " << Fcast_MaxFleetCatch(f) << endl;
   }
   NuFore << "-9999 -1" << endl;
 
   NuFore << "# enter list of area ID and max annual catch; terminate with area=-9999" << endl;
-  for (p = 1; p <= pop; p++)
-  {
+  for (p = 1; p <= pop; p++) {
     if (Fcast_MaxAreaCatch(p) > -1)
       NuFore << p << " " << Fcast_MaxAreaCatch(p) << endl;
   }
   NuFore << "-9999 -1" << endl;
 
   NuFore << "# enter list of fleet number and allocation group assignment, if any; terminate with fleet=-9999" << endl;
-  for (f = 1; f <= Nfleet; f++)
-  {
+  for (f = 1; f <= Nfleet; f++) {
     if (Allocation_Fleet_Assignments(f) > 0)
       NuFore << f << " " << Allocation_Fleet_Assignments(f) << endl;
   }
@@ -1726,27 +1570,22 @@ FUNCTION void write_nucontrol()
   NuFore << "# list sequentially because read values fill to end of N forecast" << endl;
   NuFore << "# terminate with -9999 in year field " << endl;
 
-  if (Fcast_Catch_Allocation_Groups > 0)
-  {
-    if (finish_starter == 999)
-    {
+  if (Fcast_Catch_Allocation_Groups > 0) {
+    if (finish_starter == 999) {
       NuFore << endyr + 1 << " " << Fcast_Catch_Allocation(1) << endl;
     }
-    else
-    {
+    else {
       j = Fcast_Catch_Allocation_list.size() - 1;
       for (k = 0; k <= j - 1; k++)
         NuFore << Fcast_Catch_Allocation_list[k] << endl;
     }
     NuFore << " -9999 ";
-    for (j = 1; j <= Fcast_Catch_Allocation_Groups; j++)
-    {
+    for (j = 1; j <= Fcast_Catch_Allocation_Groups; j++) {
       NuFore << " 1 ";
     }
     NuFore << endl;
   }
-  else
-  {
+  else {
     NuFore << "# no allocation groups" << endl;
   }
 
@@ -1758,8 +1597,7 @@ FUNCTION void write_nucontrol()
   if (Fcast_InputCatch_Basis == -1)
     NuFore << " Basis ";
   NuFore << endl;
-  for (j = 1; j <= N_Fcast_Input_Catches; j++)
-  {
+  for (j = 1; j <= N_Fcast_Input_Catches; j++) {
     NuFore << Fcast_InputCatch_rd(j) << endl;
   }
   NuFore << "-9999 1 1 0 ";
@@ -1785,19 +1623,17 @@ FUNCTION void write_nucontrol()
   if (N_platoon == 1)
     report4 << "#_Cond ";
   else
-    sd_ratio_rd = (sd_ratio_rd < 0)? -platoon_sd_ratio: platoon_sd_ratio;
+    sd_ratio_rd = (sd_ratio_rd < 0) ? -platoon_sd_ratio : platoon_sd_ratio;
   report4 << sd_ratio_rd << " #_Platoon_within/between_stdev_ratio (no read if N_platoons=1)" << endl;
   report4 << "#_Cond sd_ratio_rd < 0: platoon_sd_ratio parameter required after movement params." << endl;
   if (N_platoon == 1)
     report4 << "#_Cond ";
   report4 << platoon_distr(1, N_platoon) << " #vector_platoon_dist_(-1_in_first_val_gives_normal_approx)" << endl;
   report4 << "#" << endl;
-  if (finish_starter == 999)
-  {
+  if (finish_starter == 999) {
     report4 << 2 << " # recr_dist_method for parameters:  2=main effects for GP, Settle timing, Area; 3=each Settle entity; 4=none, only when N_GP*Nsettle*pop==1" << endl;
   }
-  else
-  {
+  else {
     report4 << recr_dist_method << " # recr_dist_method for parameters:  2=main effects for GP, Area, Settle timing; 3=each Settle entity; 4=none (only when N_GP*Nsettle*pop==1)" << endl;
   }
   report4 << recr_dist_area << " # not yet implemented; Future usage: Spawner-Recruitment: 1=global; 2=by area" << endl;
@@ -1806,37 +1642,31 @@ FUNCTION void write_nucontrol()
   report4 << "#GPattern month  area  age (for each settlement assignment)" << endl
           << settlement_pattern_rd << endl
           << "#" << endl;
-  if (pop == 1)
-  {
+  if (pop == 1) {
     report4 << "#_Cond 0 # N_movement_definitions goes here if Nareas > 1" << endl
             << "#_Cond 1.0 # first age that moves (real age at begin of season, not integer) also cond on do_migration>0" << endl
             << "#_Cond 1 1 1 2 4 10 # example move definition for seas=1, morph=1, source=1 dest=2, age1=4, age2=10" << endl;
   }
-  else
-  {
+  else {
     report4 << do_migration << " #_N_movement_definitions" << endl;
-    if (do_migration > 0)
-    {
+    if (do_migration > 0) {
       report4 << migr_firstage << " # first age that moves (real age at begin of season, not integer)" << endl
               << "# seas,GP,source_area,dest_area,minage,maxage" << endl
               << move_def << endl;
     }
-    else
-    {
+    else {
       report4 << "#_Cond 1.0 # first age that moves (real age at begin of season, not integer) if do_migration>0" << endl
               << "#_Cond 1 1 1 2 4 10 # example move definition for seas=1, GP=1, source=1 dest=2, age1=4, age2=10" << endl;
     }
   }
   report4 << "#" << endl;
   report4 << N_Block_Designs << " #_Nblock_Patterns" << endl;
-  if (N_Block_Designs > 0)
-  {
+  if (N_Block_Designs > 0) {
     report4 << Nblk << " #_blocks_per_pattern " << endl
             << "# begin and end years of blocks" << endl
             << Block_Design << endl;
   }
-  else
-  {
+  else {
     report4 << "#_Cond " << 0 << " #_blocks_per_pattern " << endl
             << "# begin and end years of blocks" << endl;
   }
@@ -1862,50 +1692,41 @@ FUNCTION void write_nucontrol()
           << "# setup for M, growth, wt-len, maturity, fecundity, (hermaphro), recr_distr, cohort_grow, (movement), (age error), (catch_mult), sex ratio " << endl;
   report4 << "#_NATMORT" << endl
           << natM_type << " #_natM_type:_0=1Parm; 1=N_breakpoints;_2=Lorenzen;_3=agespecific;_4=agespec_withseasinterpolate;_5=BETA:_Maunder_link_to_maturity;_6=Lorenzen_range" << endl;
-  if (natM_type == 0)
-  {
+  if (natM_type == 0) {
     report4 << "  #_no additional input for selected M option; read 1P per morph" << endl;
   }
-  else if (natM_type == 1)
-  {
+  else if (natM_type == 1) {
     report4 << N_natMparms << " #_N_breakpoints" << endl
             << NatM_break << " # age(real) at M breakpoints" << endl;
   }
-  else if (natM_type == 2)
-  {
+  else if (natM_type == 2) {
     report4 << natM_amin << " #_reference age for Lorenzen M; read 1P per morph" << endl;
   }
-  else if (natM_type == 6)
-  {
+  else if (natM_type == 6) {
     report4 << natM_amin << " #_minimum age for Lorenzen" << endl
             << natM_amax << " #_maximum age for Lorenzen; read 1P per morph" << endl;
   }
-  else if (natM_type >= 3 && natM_type < 5)
-  {
+  else if (natM_type >= 3 && natM_type < 5) {
     report4 << " #_Age_natmort_by sex x growthpattern (nest GP in sex)" << endl
             << Age_NatMort << endl;
   }
-  else
-  {
+  else {
     report4 << natM_5_opt << "  #_Maunder_M suboptions: 1 (4 parm per sex*GP, using age_maturity), 2 (4 parm, same), 3 (6 parm)" << endl;
     report4 << "#_Note:_parm2(young_fish_power)_has_neg_value_(plaus._range:~-3_to_0.0);linear_@_-1.0; const_@_0.0" << endl;
   }
   report4 << "#" << endl;
   report4 << Grow_type << " # GrowthModel: 1=vonBert with L1&L2; 2=Richards with L1&L2; 3=age_specific_K_incr; 4=age_specific_K_decr; 5=age_specific_K_each; 6=NA; 7=NA; 8=growth cessation" << endl;
-  if (Grow_type <= 5 || Grow_type == 8)
-  {
+  if (Grow_type <= 5 || Grow_type == 8) {
     report4 << AFIX << " #_Age(post-settlement) for L1 (aka Amin); first growth parameter is size at this age; linear growth below this" << endl
             << AFIX2 << " #_Age(post-settlement) for L2 (aka Amax); 999 to treat as Linf" << endl
             << Linf_decay << " #_exponential decay for growth above maxage (value should approx initial Z; -999 replicates 3.24; -998 to not allow growth above maxage)" << endl;
     report4 << "0  #_placeholder for future growth feature" << endl;
-    if (Grow_type >= 3 && Grow_type <= 5)
-    {
+    if (Grow_type >= 3 && Grow_type <= 5) {
       report4 << Age_K_count << " # number of K multipliers to read" << endl
               << Age_K_points << " # ages for K multiplier" << endl;
     }
   }
-  else
-  {
+  else {
     report4 << " #_growth type not implemented" << endl;
   }
   report4 << "#" << endl;
@@ -1913,22 +1734,18 @@ FUNCTION void write_nucontrol()
   report4 << CV_depvar << " #_CV_Growth_Pattern:  0 CV=f(LAA); 1 CV=F(A); 2 SD=F(LAA); 3 SD=F(A); 4 logSD=F(A)" << endl;
   report4 << "#" << endl;
   report4 << Maturity_Option << " #_maturity_option:  1=length logistic; 2=age logistic; 3=read age-maturity matrix by growth_pattern; 4=read age-fecundity; 5=disabled; 6=read length-maturity" << endl;
-  if (Maturity_Option == 3)
-  {
+  if (Maturity_Option == 3) {
     report4 << "#_Age_Maturity by growth pattern" << endl
             << Age_Maturity << endl;
   }
-  else if (Maturity_Option == 4)
-  {
+  else if (Maturity_Option == 4) {
     report4 << "#_Age_Fecundity by growth pattern" << endl
             << Age_Maturity << endl;
   }
-  else if (Maturity_Option == 5)
-  {
+  else if (Maturity_Option == 5) {
     report4 << "#_Age_Fecundity by growth pattern from wt-at-age.ss now invoked by read bodywt flag" << endl;
   }
-  else if (Maturity_Option == 6)
-  {
+  else if (Maturity_Option == 6) {
     report4 << "#_Length_Maturity by growth pattern" << endl
             << Length_Maturity << endl;
   }
@@ -1938,10 +1755,9 @@ FUNCTION void write_nucontrol()
   }
   report4 << Fecund_Option << " #_fecundity_at_length option:(1)eggs=Wt*(a+b*Wt);(2)eggs=a*L^b;(3)eggs=a*Wt^b; (4)eggs=a+b*L; (5)eggs=a+b*W" << endl;
   report4 << Hermaphro_Option << " #_hermaphroditism option:  0=none; 1=female-to-male age-specific fxn; -1=male-to-female age-specific fxn" << endl;
-  if (Hermaphro_Option != 0)
-  {
+  if (Hermaphro_Option != 0) {
     report4 << Hermaphro_seas_rd << " # Hermaphro_season.first_age (seas=-1 means all seasons; first_age must be 0 to 9)" << endl
-            << Hermaphro_maleSPB << " # fraction_of_maleSSB_added_to_total_SSB " << endl;
+            << Hermaphro_maleSSB << " # fraction_of_maleSSB_added_to_total_SSB " << endl;
   }
 
   report4 << MGparm_def << " #_parameter_offset_approach for M, G, CV_G:  1- direct, no offset**; 2- male=fem_parm*exp(male_parm); 3: male=female*exp(parm) then old=young*exp(parm)" << endl;
@@ -1953,36 +1769,29 @@ FUNCTION void write_nucontrol()
   report4 << endl;
   report4 << "#_ LO HI INIT PRIOR PR_SD PR_type PHASE env_var&link dev_link dev_minyr dev_maxyr dev_PH Block Block_Fxn" << endl;
   NP = 0;
-  for (gg = 1; gg <= gender; gg++)
-  {
-    for (gp = 1; gp <= N_GP; gp++)
-    {
+  for (gg = 1; gg <= gender; gg++) {
+    for (gp = 1; gp <= N_GP; gp++) {
       report4 << "# Sex: " << gg << "  BioPattern: " << gp << "  NatMort" << endl;
-      for (k = 1; k <= N_natMparms; k++)
-      {
+      for (k = 1; k <= N_natMparms; k++) {
         NP++;
         MGparm_1(NP, 3) = value(MGparm(NP));
         report4 << MGparm_1(NP) << " # " << ParmLabel(NP) << endl;
       }
       report4 << "# Sex: " << gg << "  BioPattern: " << gp << "  Growth" << endl;
-      for (k = 1; k <= N_growparms; k++)
-      {
+      for (k = 1; k <= N_growparms; k++) {
         NP++;
         MGparm_1(NP, 3) = value(MGparm(NP));
         report4 << MGparm_1(NP) << " # " << ParmLabel(NP) << endl;
       }
       report4 << "# Sex: " << gg << "  BioPattern: " << gp << "  WtLen" << endl;
-      for (k = 1; k <= 2; k++)
-      {
+      for (k = 1; k <= 2; k++) {
         NP++;
         MGparm_1(NP, 3) = value(MGparm(NP));
         report4 << MGparm_1(NP) << " # " << ParmLabel(NP) << endl;
       }
-      if (gg == 1)
-      {
+      if (gg == 1) {
         report4 << "# Sex: " << gg << "  BioPattern: " << gp << "  Maturity&Fecundity" << endl;
-        for (k = 1; k <= 4; k++)
-        {
+        for (k = 1; k <= 4; k++) {
           NP++;
           MGparm_1(NP, 3) = value(MGparm(NP));
           report4 << MGparm_1(NP) << " # " << ParmLabel(NP) << endl;
@@ -1991,10 +1800,8 @@ FUNCTION void write_nucontrol()
     }
   }
   report4 << "# Hermaphroditism" << endl;
-  if (Hermaphro_Option != 0)
-  {
-    for (k = 1; k <= 3; k++)
-    {
+  if (Hermaphro_Option != 0) {
+    for (k = 1; k <= 3; k++) {
       NP++;
       MGparm_1(NP, 3) = value(MGparm(NP));
       report4 << MGparm_1(NP) << " # " << ParmLabel(NP) << endl;
@@ -2003,10 +1810,8 @@ FUNCTION void write_nucontrol()
 
   report4 << "#  Recruitment Distribution " << endl;
   j = NP + 1;
-  if (MGP_CGD > j)
-  {
-    for (k = j; k <= MGP_CGD - 1; k++)
-    {
+  if (MGP_CGD > j) {
+    for (k = j; k <= MGP_CGD - 1; k++) {
       NP++;
       MGparm_1(NP, 3) = value(MGparm(NP));
       report4 << MGparm_1(NP) << " # " << ParmLabel(NP) << endl;
@@ -2019,10 +1824,8 @@ FUNCTION void write_nucontrol()
   report4 << MGparm_1(NP) << " # " << ParmLabel(NP) << endl;
 
   report4 << "#  Movement" << endl;
-  if (do_migration > 0)
-  {
-    for (k = 1; k <= 2 * do_migration; k++)
-    {
+  if (do_migration > 0) {
+    for (k = 1; k <= 2 * do_migration; k++) {
       NP++;
       MGparm_1(NP, 3) = value(MGparm(NP));
       report4 << MGparm_1(NP) << " # " << ParmLabel(NP) << endl;
@@ -2030,18 +1833,15 @@ FUNCTION void write_nucontrol()
   }
 
   report4 << "#  Platoon StDev Ratio " << endl;
-  if (N_platoon > 1 && sd_ratio_rd < 0)
-  {
+  if (N_platoon > 1 && sd_ratio_rd < 0) {
     NP++;
     MGparm_1(NP, 3) = value(MGparm(NP));
     report4 << MGparm_1(NP) << " # " << ParmLabel(NP) << endl;
   }
-  
+
   report4 << "#  Age Error from parameters" << endl;
-  if (Use_AgeKeyZero > 0)
-  {
-    for (k = 1; k <= 7; k++)
-    {
+  if (Use_AgeKeyZero > 0) {
+    for (k = 1; k <= 7; k++) {
       NP++;
       MGparm_1(NP, 3) = value(MGparm(NP));
       report4 << MGparm_1(NP) << " # " << ParmLabel(NP) << endl;
@@ -2049,11 +1849,9 @@ FUNCTION void write_nucontrol()
   }
 
   report4 << "#  catch multiplier" << endl;
-  if (catch_mult_pointer > 0)
-  {
+  if (catch_mult_pointer > 0) {
     for (k = 1; k <= Nfleet; k++)
-      if (need_catch_mult(k) == 1)
-      {
+      if (need_catch_mult(k) == 1) {
         NP++;
         MGparm_1(NP, 3) = value(MGparm(NP));
         report4 << MGparm_1(NP) << " # " << ParmLabel(NP) << endl;
@@ -2071,16 +1869,13 @@ FUNCTION void write_nucontrol()
   if (frac_female_pointer == -1) //  3.24 format
   {
     // placeholders to change fracfemale (3.24) to MGparm (3.30)
-    for (gp = 1; gp <= N_GP; gp++)
-    {
+    for (gp = 1; gp <= N_GP; gp++) {
       report4 << " 0.000001 0.999999 " << femfrac(gp) << " 0.5  0.5 0 -99 0 0 0 0 0 0 0 "
               << "# FracFemale_GP_" << gp << endl;
     }
   }
-  else
-  {
-    for (gp = 1; gp <= N_GP; gp++)
-    {
+  else {
+    for (gp = 1; gp <= N_GP; gp++) {
       NP++;
       MGparm_1(NP, 3) = value(MGparm(NP));
       report4 << MGparm_1(NP) << " # " << ParmLabel(NP) << endl;
@@ -2088,8 +1883,7 @@ FUNCTION void write_nucontrol()
   }
 
   report4 << "#  M2 parameter for each predator fleet" << endl;
-  for (int gp = 1; gp <= N_predparms; gp++)
-  {
+  for (int gp = 1; gp <= N_predparms; gp++) {
     NP++;
     MGparm_1(NP, 3) = value(MGparm(NP));
     report4 << MGparm_1(NP) << " # " << ParmLabel(NP) << endl;
@@ -2097,20 +1891,17 @@ FUNCTION void write_nucontrol()
 
   report4 << "#" << endl;
   j = N_MGparm;
-  if (timevary_parm_cnt_MG > 0)
-  {
+  if (timevary_parm_cnt_MG > 0) {
     report4 << "# timevary MG parameters " << endl
             << "#_ LO HI INIT PRIOR PR_SD PR_type  PHASE" << endl;
-    for (f = 1; f <= timevary_parm_cnt_MG; f++)
-    {
+    for (f = 1; f <= timevary_parm_cnt_MG; f++) {
       NP++;
       timevary_parm_rd[f](3) = value(timevary_parm(f));
       report4 << timevary_parm_rd[f] << " # " << ParmLabel(NP) << endl;
     }
     report4 << "# info on dev vectors created for MGparms are reported with other devs after tag parameter section " << endl;
   }
-  else
-  {
+  else {
     report4 << "#_no timevary MG parameters" << endl;
   }
 
@@ -2118,34 +1909,31 @@ FUNCTION void write_nucontrol()
   report4 << "#_seasonal_effects_on_biology_parms" << endl
           << MGparm_seas_effects << " #_femwtlen1,femwtlen2,mat1,mat2,fec1,fec2,Malewtlen1,malewtlen2,L1,K" << endl;
   report4 << "#_ LO HI INIT PRIOR PR_SD PR_type PHASE" << endl;
-  if (MGparm_doseas > 0)
-  {
-    for (f = 1; f <= N_MGparm_seas; f++)
-    {
+  if (MGparm_doseas > 0) {
+    for (f = 1; f <= N_MGparm_seas; f++) {
       NP++;
       j++;
       MGparm_seas_1(f, 3) = value(MGparm(j));
       report4 << MGparm_seas_1(f) << " # " << ParmLabel(NP) << endl;
     }
   }
-  else
-  {
+  else {
     report4 << "#_Cond -2 2 0 0 -1 99 -2 #_placeholder when no seasonal MG parameters" << endl;
   }
 
   report4 << "#" << endl;
   report4 << SR_fxn << " #_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" << endl;
   report4 << init_equ_steepness << "  # 0/1 to use steepness in initial equ recruitment calculation" << endl;
-  report4 << SR_update_SSBpR0_rd <<  "#  SR_update_SSBpR0" << endl <<
-  "#  0 - OK, but only if no timevary biology or SR parm" << endl <<
-  "#  1 - best: update SSBpR0 for benchmark and for time series only if SRparm R0 or h (not regime) is set to have time-varying property" << endl <<
-  "#  2 - incorrect (old, incorrect SS3 approach):  always update SSBpR0 for benchmark's use of spawner-recruitment, but only for the time series if there is a timevary SR parm" << endl <<
-  "#  3 - option:  do not update SSBpR0 (do keep start year SSBpR0), even if R0 or h is set to have time-varying property" << endl << "#" << endl;
+  report4 << SR_update_SSBpR0_rd << "  #  SR_update_SSBpR0" << endl
+          << "#  0 - OK, but only if no timevary biology or SR parm" << endl
+          << "#  1 - best: update SSBpR0 for benchmark and for time series only if SRparm R0 or h (not regime) is set to have time-varying property" << endl
+          << "#  2 - incorrect (old, incorrect SS3 approach):  always update SSBpR0 for benchmark's use of spawner-recruitment, but only for the time series if there is a timevary SR parm" << endl
+          << "#  3 - option:  do not update SSBpR0 (do keep start year SSBpR0), even if R0 or h is set to have time-varying property" << endl
+          << "#" << endl;
   report4 << "#_          LO            HI          INIT         PRIOR         PR_SD       PR_type      PHASE    env-var    use_dev   dev_mnyr   dev_mxyr     dev_PH      Block    Blk_Fxn #  parm_name" << endl;
   report4.unsetf(std::ios_base::fixed);
   report4.unsetf(std::ios_base::floatfield);
-  for (f = 1; f <= N_SRparm2; f++)
-  {
+  for (f = 1; f <= N_SRparm2; f++) {
     NP++;
     SR_parm_1(f, 3) = value(SR_parm(f));
     for (j = 1; j <= 6; j++)
@@ -2156,11 +1944,9 @@ FUNCTION void write_nucontrol()
   }
   report4.unsetf(std::ios_base::fixed);
   report4.unsetf(std::ios_base::floatfield);
-  if (N_SRparm3 > N_SRparm2)
-  {
+  if (N_SRparm3 > N_SRparm2) {
     report4 << "# timevary SR parameters" << endl;
-    for (f = timevary_parm_start_SR; f <= timevary_parm_cnt_SR; f++)
-    {
+    for (f = timevary_parm_start_SR; f <= timevary_parm_cnt_SR; f++) {
       NP++;
       timevary_parm_rd[f](3) = value(timevary_parm(f));
       report4 << timevary_parm_rd[f] << " # " << ParmLabel(NP) << endl;
@@ -2169,8 +1955,7 @@ FUNCTION void write_nucontrol()
     report4.unsetf(std::ios_base::fixed);
     report4.unsetf(std::ios_base::floatfield);
   }
-  else
-  {
+  else {
     report4 << "#_no timevary SR parameters" << endl;
   }
 
@@ -2179,12 +1964,10 @@ FUNCTION void write_nucontrol()
   report4 << recdev_end << " # last year of main recr_devs; forecast devs start in following year" << endl;
   report4 << recdev_PH_rd << " #_recdev phase " << endl;
   report4 << recdev_adv << " # (0/1) to read 13 advanced options" << endl;
-  if (recdev_adv == 0)
-  {
+  if (recdev_adv == 0) {
     onenum = "#_Cond ";
   }
-  else
-  {
+  else {
     onenum = " ";
   }
   report4 << onenum << recdev_early_start_rd << " #_recdev_early_start (0=none; neg value makes relative to recdev_start)" << endl;
@@ -2202,99 +1985,77 @@ FUNCTION void write_nucontrol()
   report4 << onenum << recdev_read << " #_read_recdevs" << endl;
   report4 << "#_end of advanced SR options" << endl;
   report4 << "#" << endl;
-  if (recdev_cycle > 0)
-  {
-    for (y = 1; y <= recdev_cycle; y++)
-    {
+  if (recdev_cycle > 0) {
+    for (y = 1; y <= recdev_cycle; y++) {
       NP++;
       recdev_cycle_parm_RD(y, 3) = value(recdev_cycle_parm(y));
       report4 << recdev_cycle_parm_RD(y) << " # " << ParmLabel(NP) << endl;
     }
   }
-  else
-  {
+  else {
     report4 << "#_placeholder for full parameter lines for recruitment cycles" << endl;
   }
-  if (recdev_read > 0)
-  {
+  if (recdev_read > 0) {
     report4 << "# Specified recr devs to read" << endl;
     report4 << "#_year Input_value # Final_value" << endl;
-    for (j = 1; j <= recdev_read; j++)
-    {
+    for (j = 1; j <= recdev_read; j++) {
       y = recdev_input(j, 1);
       report4 << recdev_input(j) << " # ";
-      if (y >= recdev_first)
-      {
+      if (y >= recdev_first) {
         report4 << recdev(y) << endl;
       }
-      else
-      {
+      else {
         report4 << " not used " << endl;
       }
     }
   }
-  else
-  {
+  else {
     report4 << "# read specified recr devs" << endl;
     report4 << "#_year Input_value" << endl;
   }
   report4 << "#" << endl;
   report4 << "# all recruitment deviations" << endl
           << "# ";
-  if (recdev_do_early > 0)
-  {
-    for (y = recdev_early_start; y <= recdev_early_end; y++)
-    {
+  if (recdev_do_early > 0) {
+    for (y = recdev_early_start; y <= recdev_early_end; y++) {
       report4 << " " << y << "E";
     }
   }
-  if (do_recdev > 0)
-  {
-    for (y = recdev_start; y <= recdev_end; y++)
-    {
+  if (do_recdev > 0) {
+    for (y = recdev_start; y <= recdev_end; y++) {
       report4 << " " << y << "R";
     }
   }
-  if (Do_Forecast > 0)
-  {
-    for (y = recdev_end + 1; y <= YrMax; y++)
-    {
+  if (Do_Forecast > 0) {
+    for (y = recdev_end + 1; y <= YrMax; y++) {
       report4 << " " << y << "F";
     }
   }
   report4 << endl
           << "# ";
-  if (recdev_do_early > 0)
-  {
-    for (y = recdev_early_start; y <= recdev_early_end; y++)
-    {
+  if (recdev_do_early > 0) {
+    for (y = recdev_early_start; y <= recdev_early_end; y++) {
       NP++;
       report4 << " " << recdev(y);
     }
   }
 
-  if (do_recdev > 0)
-  {
-    for (y = recdev_start; y <= recdev_end; y++)
-    {
+  if (do_recdev > 0) {
+    for (y = recdev_start; y <= recdev_end; y++) {
       NP++;
       report4 << " " << recdev(y);
     }
   }
 
-  if (Do_Forecast > 0 && do_recdev > 0)
-  {
-    for (y = recdev_end + 1; y <= YrMax; y++)
-    {
+  if (Do_Forecast > 0 && do_recdev > 0) {
+    for (y = recdev_end + 1; y <= YrMax; y++) {
       NP++;
       report4 << " " << recdev(y);
     }
     report4 << endl;
-    if (Do_Impl_Error > 0)
-    {
+    if (Do_Impl_Error > 0) {
       report4 << "# implementation error by year in forecast: ";
-      for (y = endyr + 1; y <= YrMax; y++)
-      {
+      for (y = endyr + 1; y <= YrMax; y++) {
         NP++;
         report4 << " " << Fcast_impl_error(y);
       }
@@ -2308,12 +2069,10 @@ FUNCTION void write_nucontrol()
 
   report4 << F_Method << " # 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)" << endl;
   report4 << max_harvest_rate << " # max F (methods 2-4) or harvest fraction (method 1)" << endl;
-  if (F_Method == 1)
-  {
+  if (F_Method == 1) {
     report4 << "# F_Method 1:  no additional input needed" << endl;
   }
-  else if (F_Method == 2)
-  {
+  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;
@@ -2322,29 +2081,28 @@ FUNCTION void write_nucontrol()
     if (F_detail > 0)
       report4 << F_setup2 << endl;
   }
-  else if (F_Method == 3)
-  {
+  else if (F_Method == 3) {
     report4 << F_Tune << "  # N iterations for tuning in hybrid mode; recommend 3 (faster) to 5 (more precise if many fleets)" << endl;
   }
-  else if (F_Method == 4)
-  {
+  else if (F_Method == 4) {
     report4 << "# 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" << endl;
-    report4 << "# (A) fleet;" << endl <<"# (B) F_starting_value (ignored if start_PH=1 or reading from ss3.par);" <<
-    endl << "# (C) start_PH for fleet's Fparms (99 to stay in hybrid, <0 to stay at starting value)" << endl << 
-    "# Terminate list with -9999 for fleet (use -9998 to read fleet-time specific F values after reading N hybrid tune loops)" << endl;
+    report4 << "# (A) fleet;" << endl
+            << "# (B) F_starting_value (ignored if start_PH=1 or reading from ss3.par);" << endl
+            << "# (C) start_PH for fleet's Fparms (99 to stay in hybrid, <0 to stay at starting value)" << endl
+            << "# Terminate list with -9999 for fleet (use -9998 to read fleet-time specific F values after reading N hybrid tune loops)" << endl;
     report4 << "# (A) (B) (C)" << endl;
-    for (unsigned j = 1; j <= F_Method_4_input.size() - 2; j++)
-    {
+    for (unsigned j = 1; j <= F_Method_4_input.size() - 2; j++) {
       report4 << F_Method_4_input[j] << " # " << fleetname(F_Method_4_input[j](1)) << endl;
     }
-    if (F_detail <=0 )
-    {report4 << -9999 << " 1 1 # end of list" << endl <<
-       "#F_detail template: fleet year seas F_value catch_se phase" << endl; }
-    else
-    {report4 << -9998 << " 1 1 # end of list, trigger reading F_detail" << endl; }
+    if (F_detail <= 0) {
+      report4 << -9999 << " 1 1 # end of list" << endl
+              << "#F_detail template: fleet year seas F_value catch_se phase" << endl;
+    }
+    else {
+      report4 << -9998 << " 1 1 # end of list, trigger reading F_detail" << endl;
+    }
     report4 << F_Tune << " #_number of loops for hybrid tuning; 4 precise; 3 faster; 2 enough if switching to parms is enabled" << endl;
-    if (F_detail > 0)
-    {
+    if (F_detail > 0) {
       report4 << " # 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" << endl;
       report4 << "#fleet year seas F_value catch_se phase" << endl;
       report4 << F_setup2 << endl;
@@ -2356,22 +2114,18 @@ FUNCTION void write_nucontrol()
   report4 << "#_initial_F_parms; for each fleet x season that has init_catch; nest season in fleet; count = " << N_init_F2 << endl;
   report4 << "#_for unconstrained init_F, use an arbitrary initial catch and set lambda=0 for its logL" << endl;
   report4 << "#_ LO HI INIT PRIOR PR_SD  PR_type  PHASE" << endl;
-  if (finish_starter == 999)
-  {
-    for (f = 1; f <= Nfleet1; f++)
-    {
+  if (finish_starter == 999) {
+    for (f = 1; f <= Nfleet1; f++) {
       NP++;
-  init_F_parm_1(f, 3) = value(init_F(f));
+      init_F_parm_1(f, 3) = value(init_F(f));
       if (obs_equ_catch(1, f) != 0.)
         report4 << init_F_parm_1(f) << " # " << ParmLabel(NP) << endl;
     }
   }
-  else if (N_init_F2 > 0)
-  {
-    for (f = 1; f <= N_init_F2; f++)
-    {
+  else if (N_init_F2 > 0) {
+    for (f = 1; f <= N_init_F2; f++) {
       NP++;
-  init_F_parm_1(f, 3) = value(init_F(f));
+      init_F_parm_1(f, 3) = value(init_F(f));
       report4 << init_F_parm_1(f) << " # " << ParmLabel(NP) << endl;
     }
   }
@@ -2380,22 +2134,19 @@ FUNCTION void write_nucontrol()
           << "# F rates by fleet x season" << endl;
   report4 << "#_year: ";
   for (y = styr; y <= YrMax; y++)
-    for (s = 1; s <= nseas; s++)
-    {
+    for (s = 1; s <= nseas; s++) {
       report4 << " " << y;
     }
   report4 << endl
           << "# seas: ";
   for (y = styr; y <= YrMax; y++)
-    for (s = 1; s <= nseas; s++)
-    {
+    for (s = 1; s <= nseas; s++) {
       report4 << " " << s;
     }
   report4 << endl;
   j = styr + (YrMax - styr) * nseas + nseas - 1;
   for (f = 1; f <= Nfleet; f++)
-    if (fleet_type(f) <= 2)
-    {
+    if (fleet_type(f) <= 2) {
       report4 << "# " << fleetname(f) << Hrate(f)(styr, j) << endl;
     }
   NP += N_Fparm;
@@ -2422,10 +2173,8 @@ FUNCTION void write_nucontrol()
   }
 
   report4 << "#_   fleet      link link_info  extra_se   biasadj     float  #  fleetname" << endl;
-  for (f = 1; f <= Nfleet; f++)
-  {
-    if (Svy_N_fleet(f) > 0)
-    {
+  for (f = 1; f <= Nfleet; f++) {
+    if (Svy_N_fleet(f) > 0) {
       report4 << " " << setw(9) << f;
       for (j = 1; j <= 5; j++)
         report4 << setw(10) << Q_setup(f, j);
@@ -2436,13 +2185,11 @@ FUNCTION void write_nucontrol()
           << "#" << endl;
 
   report4 << "#_Q_parameters" << endl;
-  if (Q_Npar > 0)
-  {
+  if (Q_Npar > 0) {
     report4 << "#_          LO            HI          INIT         PRIOR         PR_SD       PR_type      PHASE    env-var    use_dev   dev_mnyr   dev_mxyr     dev_PH      Block    Blk_Fxn  #  parm_name" << endl;
     report4.unsetf(std::ios_base::fixed);
     report4.unsetf(std::ios_base::floatfield);
-    for (f = 1; f <= Q_Npar; f++)
-    {
+    for (f = 1; f <= Q_Npar; f++) {
       NP++;
       Q_parm_1(f, 3) = value(Q_parm(f));
       for (j = 1; j <= 6; j++)
@@ -2454,12 +2201,10 @@ FUNCTION void write_nucontrol()
     report4.unsetf(std::ios_base::fixed);
     report4.unsetf(std::ios_base::floatfield);
 
-    if (timevary_parm_start_Q > 0)
-    {
+    if (timevary_parm_start_Q > 0) {
       report4 << "# timevary Q parameters " << endl;
       report4 << "#_          LO            HI          INIT         PRIOR         PR_SD       PR_type     PHASE  #  parm_name" << endl;
-      for (f = timevary_parm_start_Q; f <= timevary_parm_cnt_Q; f++)
-      {
+      for (f = timevary_parm_start_Q; f <= timevary_parm_cnt_Q; f++) {
         NP++;
         timevary_parm_rd[f](3) = value(timevary_parm(f));
         for (j = 1; j <= 6; j++)
@@ -2468,8 +2213,7 @@ FUNCTION void write_nucontrol()
       }
       report4 << "# info on dev vectors created for Q parms are reported with other devs after tag parameter section " << endl;
     }
-    else
-    {
+    else {
       report4 << "#_no timevary Q parameters" << endl;
     }
     report4.unsetf(std::ios_base::fixed);
@@ -2533,21 +2277,17 @@ FUNCTION void write_nucontrol()
 
   {
     k = 0;
-    for (f = 1; f <= 2 * Nfleet; f++)
-    {
-      if (f > Nfleet)
-      {
+    for (f = 1; f <= 2 * Nfleet; f++) {
+      if (f > Nfleet) {
         f1 = f - Nfleet;
         anystring = "AgeSelex";
       }
-      else
-      {
+      else {
         f1 = f;
         anystring = "LenSelex";
       }
       report4 << "# " << f1 << "   " << fleetname(f1) << " " << anystring << endl;
-      for (j = 1; j <= N_selparmvec(f); j++)
-      {
+      for (j = 1; j <= N_selparmvec(f); j++) {
         NP++;
         k++;
         selparm_1(k)(3) = value(selparm(k));
@@ -2558,13 +2298,11 @@ FUNCTION void write_nucontrol()
         report4 << "  #  " << ParmLabel(NP) << endl;
       }
     }
-    if (Comp_Err_ParmCount > 0)
-    {
+    if (Comp_Err_ParmCount > 0) {
       report4 << "#_Dirichlet and/or MV Tweedie parameters for composition error" << endl;
       report4 << "#_multiple_fleets_can_refer_to_same_parm;_but_list_cannot_have_gaps" << endl;
       k = Comp_Err_Parm_Start;
-      for (f = 1; f <= Comp_Err_ParmCount; f++)
-      {
+      for (f = 1; f <= Comp_Err_ParmCount; f++) {
         k++;
         NP++;
         selparm_1(k)(3) = value(selparm(k));
@@ -2575,18 +2313,15 @@ FUNCTION void write_nucontrol()
         report4 << "  #  " << ParmLabel(NP) << endl;
       }
     }
-    else
-    {
+    else {
       report4 << "#_No_Dirichlet parameters" << endl;
     }
 
-    if (N_selparm3 > N_selparm)
-    {
+    if (N_selparm3 > N_selparm) {
       report4 << "# timevary selex parameters " << endl;
       report4 << "#_          LO            HI          INIT         PRIOR         PR_SD       PR_type    PHASE  #  parm_name" << endl;
       //    for (f=timevary_parm_start_sel;f<=timevary_parm_cnt_sel;f++)
-      for (int f = timevary_parm_start_sel; f <= timevary_parm_start_sel + N_selparm3 - N_selparm - 1; f++)
-      {
+      for (int f = timevary_parm_start_sel; f <= timevary_parm_start_sel + N_selparm3 - N_selparm - 1; f++) {
         NP++;
         timevary_parm_rd[f](3) = value(timevary_parm(f));
         for (j = 1; j <= 6; j++)
@@ -2595,31 +2330,26 @@ FUNCTION void write_nucontrol()
       }
       report4 << "# info on dev vectors created for selex parms are reported with other devs after tag parameter section " << endl;
     }
-    else
-    {
+    else {
       report4 << "#_no timevary selex parameters" << endl;
     }
 
     report4 << "#" << endl
             << TwoD_AR_do << "   #  use 2D_AR1 selectivity? (0/1)" << endl;
-    if (TwoD_AR_do > 0)
-    {
+    if (TwoD_AR_do > 0) {
       k = timevary_parm_start_sel + N_selparm3 - N_selparm - 1; //  starting point in timevary_parm_rd
       report4 << "#_specifications for 2D_AR1 and associated parameters" << endl;
       report4 << "#_specs:  fleet, ymin, ymax, amin, amax, sigma_amax, use_rho, len1/age2, devphase, before_range, after_range" << endl;
       report4 << "#_sigma_amax>amin means create sigma parm for each bin from min to sigma_amax; sigma_amax<0 means just one sigma parm is read and used for all bins" << endl;
-      for (j = 1; j <= TwoD_AR_cnt; j++)
-      {
+      for (j = 1; j <= TwoD_AR_cnt; j++) {
         ivector tempvec(1, 13); //  fleet, ymin, ymax, amin, amax, sigma_amax, use_rho, len1/age2, devphase
         tempvec(1, 13) = TwoD_AR_def[j](1, 13);
         tempvec(6) = TwoD_AR_def_rd[j](6); //  restore the read value in case it got changed
-        int isigmasel = TwoD_AR_def[j](13);  //  index of first sigmasel parm in selparm
-        if (tempvec(8) == 1)
-        {
+        int isigmasel = TwoD_AR_def[j](13); //  index of first sigmasel parm in selparm
+        if (tempvec(8) == 1) {
           anystring = "LEN";
         }
-        else
-        {
+        else {
           anystring = "AGE";
         }
 
@@ -2627,16 +2357,14 @@ FUNCTION void write_nucontrol()
         int sigma_amax = tempvec(6);
         int use_rho = tempvec(7);
         int amin = tempvec(4);
-        for (a = amin; a <= sigma_amax; a++)
-        {
+        for (a = amin; a <= sigma_amax; a++) {
           dvector dtempvec(1, 7); //  Lo, Hi, init, prior, prior_sd, prior_type, phase;
           k++;
           dtempvec = timevary_parm_rd[k](1, 7);
-          dtempvec(3) = value ( selparm(isigmasel + a - amin) );
-          report4 << dtempvec << "  # sigma_sel for fleet:_" << tempvec(1) << "; " << anystring << "_" << a <<endl;
+          dtempvec(3) = value(selparm(isigmasel + a - amin));
+          report4 << dtempvec << "  # sigma_sel for fleet:_" << tempvec(1) << "; " << anystring << "_" << a << endl;
         }
-        if (use_rho == 1)
-        {
+        if (use_rho == 1) {
           dvector dtempvec(1, 7); //  Lo, Hi, init, prior, prior_sd, prior_type, phase;
           k++;
           dtempvec = timevary_parm_rd[k](1, 7);
@@ -2648,12 +2376,11 @@ FUNCTION void write_nucontrol()
       }
       report4 << "-9999  0 0 0 0 0 0 0 0 0 0 # terminator" << endl;
     }
-    else
-    {
+    else {
       report4 << "#_no 2D_AR1 selex offset used" << endl;
       report4 << "#_specs:  fleet, ymin, ymax, amin, amax, sigma_amax, use_rho, len1/age2, devphase, before_range, after_range" << endl;
       report4 << "#_sigma_amax>amin means create sigma parm for each bin from min to sigma_amax; sigma_amax<0 means just one sigma parm is read and used for all bins" << endl;
-      report4 << "#_needed parameters follow each fleet's specifications"<<endl;
+      report4 << "#_needed parameters follow each fleet's specifications" << endl;
       report4 << "# -9999  0 0 0 0 0 0 0 0 0 0 # terminator" << endl;
     }
 
@@ -2665,37 +2392,31 @@ FUNCTION void write_nucontrol()
 
   report4 << "#" << endl
           << "# Tag loss and Tag reporting parameters go next" << endl;
-  if (Do_TG > 0)
-  {
+  if (Do_TG > 0) {
     report4 << 1 << " # TG_custom:  0=no read and autogen if tag data exist; 1=read" << endl;
     report4 << "#_Note -  tag parameters cannot be time-varying" << endl;
     report4 << "#_Note -  phase=-1000 sets parm value to previous parm; phase=-100X sets to parm(X) value" << endl;
-    for (f = 1; f <= 3 * N_TG + 2 * Nfleet1; f++)
-    {
+    for (f = 1; f <= 3 * N_TG + 2 * Nfleet1; f++) {
       NP++;
       report4 << TG_parm2(f)(1, 2) << " " << TG_parm(f) << " " << TG_parm2(f)(4, 14) << " # " << ParmLabel(NP) << endl;
     }
   }
-  else
-  {
+  else {
     report4 << "0  # TG_custom:  0=no read and autogen if tag data exist; 1=read" << endl
             << "#_Cond -6 6 1 1 2 0.01 -4 0 0 0 0 0 0 0  #_placeholder if no parameters" << endl;
     ;
   }
   report4 << "#" << endl;
-  if (timevary_cnt == 0)
-  {
+  if (timevary_cnt == 0) {
     report4 << "# no timevary parameters" << endl
             << "#" << endl;
   }
-  else
-  {
+  else {
     report4 << "# deviation vectors for timevary parameters" << endl
             << "#  base   base first block   block  env  env   dev   dev   dev   dev   dev" << endl
             << "#  type  index  parm trend pattern link  var  vectr link _mnyr  mxyr phase  dev_vector" << endl;
 
-    for (j = 1; j <= timevary_cnt; j++)
-    {
+    for (j = 1; j <= timevary_cnt; j++) {
       //        report4.precision(6);
       //        report4.unsetf(std::ios_base::fixed);
       //        report4.unsetf(std::ios_base::floatfield);
@@ -2745,36 +2466,30 @@ FUNCTION void write_nucontrol()
 
   report4 << "#" << endl
           << "# lambdas (for info only; columns are phases)" << endl;
-  if (Svy_N > 0)
-  {
+  if (Svy_N > 0) {
     for (f = 1; f <= Nfleet; f++)
       report4 << "# " << surv_lambda(f) << " #_CPUE/survey:_" << f << endl;
   }
-  if (nobs_disc > 0)
-  {
+  if (nobs_disc > 0) {
     for (f = 1; f <= Nfleet; f++)
       report4 << "# " << disc_lambda(f) << " #_discard:_" << f << endl;
   }
-  if (nobs_mnwt > 0)
-  {
+  if (nobs_mnwt > 0) {
     for (f = 1; f <= Nfleet; f++)
       report4 << "# " << mnwt_lambda(f) << " #_meanbodywt:" << f << endl;
   }
-  if (Nobs_l_tot > 0)
-  {
+  if (Nobs_l_tot > 0) {
     for (f = 1; f <= Nfleet; f++)
       report4 << "# " << length_lambda(f) << " #_lencomp:_" << f << endl;
   }
-  if (Nobs_a_tot > 0)
-  {
+  if (Nobs_a_tot > 0) {
     for (f = 1; f <= Nfleet; f++)
       report4 << "# " << age_lambda(f) << " #_agecomp:_" << f << endl;
   }
   if (SzFreq_Nmeth > 0)
     for (f = 1; f <= SzFreq_N_Like; f++)
       report4 << "# " << SzFreq_lambda(f) << " #_sizefreq:_" << f << endl;
-  if (nobs_ms_tot > 0)
-  {
+  if (nobs_ms_tot > 0) {
     for (f = 1; f <= Nfleet; f++)
       report4 << "# " << sizeage_lambda(f) << " #_size-age:_" << f << endl;
   }
@@ -2783,8 +2498,7 @@ FUNCTION void write_nucontrol()
   report4 << "# " << recrdev_lambda << " #_recruitments" << endl;
   report4 << "# " << parm_prior_lambda << " #_parameter-priors" << endl;
   report4 << "# " << parm_dev_lambda << " #_parameter-dev-vectors" << endl;
-  if (Do_TG > 0)
-  {
+  if (Do_TG > 0) {
     for (TG = 1; TG <= N_TG; TG++)
       report4 << "# " << TG_lambda1(TG) << " #_TG-comp_group:_" << TG << endl;
     for (TG = 1; TG <= N_TG; TG++)
@@ -2797,15 +2511,15 @@ FUNCTION void write_nucontrol()
 
   report4 << Do_More_Std << " # (0/1/2) read specs for more stddev reporting: 0 = skip, 1 = read specs for reporting stdev for selectivity, size, and numbers, 2 = add options for M,Dyn. Bzero, SmryBio" << endl;
 
-  //3868      Do_Selex_Std=More_Std_Input(1);
-  //3869      Selex_Std_AL=More_Std_Input(2);
-  //3870      Selex_Std_Year=More_Std_Input(3);
-  //3872      Selex_Std_Cnt=More_Std_Input(4);
-  //3873      Do_Growth_Std=More_Std_Input(5);
-  //3875      Growth_Std_Cnt=More_Std_Input(6);
-  //3876      Do_NatAge_Std=More_Std_Input(7);
-  //3877      NatAge_Std_Year=More_Std_Input(8);
-  //3879      NatAge_Std_Cnt=More_Std_Input(9);
+  // 3868      Do_Selex_Std=More_Std_Input(1);
+  // 3869      Selex_Std_AL=More_Std_Input(2);
+  // 3870      Selex_Std_Year=More_Std_Input(3);
+  // 3872      Selex_Std_Cnt=More_Std_Input(4);
+  // 3873      Do_Growth_Std=More_Std_Input(5);
+  // 3875      Growth_Std_Cnt=More_Std_Input(6);
+  // 3876      Do_NatAge_Std=More_Std_Input(7);
+  // 3877      NatAge_Std_Year=More_Std_Input(8);
+  // 3879      NatAge_Std_Cnt=More_Std_Input(9);
 
   if (Do_More_Std == 0) // empty/dummy values when extra stddev reporting not used
   {
@@ -2831,39 +2545,31 @@ FUNCTION void write_nucontrol()
   }
   if (Do_More_Std > 0) // vectors associated with options 1 and 2
   {
-    if (Do_Selex_Std > 0)
-    {
+    if (Do_Selex_Std > 0) {
       report4 << Selex_Std_Pick << " # vector with selex std bins (-1 in first bin to self-generate)" << endl;
     }
-    else
-    {
+    else {
       report4 << " # -1 # list of bin #'s for selex std (-1 in first bin to self-generate)" << endl;
     }
     //    if(Do_Growth_Std>0){
-    if (More_Std_Input(5) > 0)
-    {
+    if (More_Std_Input(5) > 0) {
       report4 << Growth_Std_Pick << " # vector with growth std ages picks (-1 in first bin to self-generate)" << endl;
     }
-    else
-    {
+    else {
       report4 << " # -1 # list of ages for growth std (-1 in first bin to self-generate)" << endl;
     }
-    if (Do_NatAge_Std != 0)
-    {
+    if (Do_NatAge_Std != 0) {
       report4 << NatAge_Std_Pick << " # vector with NatAge std ages (-1 in first bin to self-generate)" << endl;
     }
-    else
-    {
+    else {
       report4 << " # -1 # list of ages for NatAge std (-1 in first bin to self-generate)" << endl;
     }
     if (Do_More_Std == 2) // additional output when option 2 is selected
     {
-      if (Do_NatM_Std > 0)
-      {
+      if (Do_NatM_Std > 0) {
         report4 << NatM_Std_Pick << " # vector with NatM std ages picks (-1 in first bin to self-generate)" << endl;
       }
-      else
-      {
+      else {
         report4 << " # -1 # list of ages for NatM std (-1 in first bin to self-generate)" << endl;
       }
     }
@@ -2871,5 +2577,4 @@ FUNCTION void write_nucontrol()
   report4 << fim << endl
           << endl; // end of file indicator
   return;
-  } //  end of write nucontrol
-
+} //  end of write nucontrol

From 33738c4e54c360417276ae1cfdd2c416011cad2f Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Fri, 4 Oct 2024 16:23:39 -0700
Subject: [PATCH 19/22] add HCR_anchor in forecast.ss

---
 SS_benchfore.tpl    | 37 ++++++++++++++++++++-----------------
 SS_param.tpl        |  1 +
 SS_readdata_330.tpl |  4 ++--
 SS_write_report.tpl |  6 +++---
 SS_write_ssnew.tpl  |  3 ++-
 5 files changed, 28 insertions(+), 23 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 9bcb1edb..001ab198 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -776,8 +776,6 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_unf); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
       report5 << " Benchmark SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << SSBpR_unf << " equil: " << Equ_SpawnRecr_Result << endl;
     }
-    report5 << 0 << " y: " << y << " Repro_output_by_age_for_morph_1 bench " << fec(1) << endl;
-//    report5 << "Repro_output_by_age_for_morph_1: " << fec(1) << endl;
 
   }
   SR_parm_work(N_SRparm2 + 1) = SSB_unf;
@@ -2211,6 +2209,11 @@ FUNCTION void Get_Forecast()
         break;
       }
     }
+    if (Fcast_Loop_Control(5) <= 1)
+    {HCR_anchor = SSB_unf;}
+    else if (Fcast_Loop_Control(5) ==2)
+    {HCR_anchor = SSB_virgin;}
+    report5 << "Control_rule_anchor_approach: " << Fcast_Loop_Control(5) << " HCR_anchor: " << HCR_anchor << endl;
     report5 << "#" << endl;
   }
 
@@ -2227,7 +2230,7 @@ FUNCTION void Get_Forecast()
 
   for (int Fcast_Loop1 = 1; Fcast_Loop1 <= jloop; Fcast_Loop1++) //   for different forecast conditions
   {
-    report5 << Fcast_Loop1 << " y: " << 0 << " Repro_output_by_age_for_morph_1 top_forecast: " << fec(1) << endl;
+//    report5 << Fcast_Loop1 << " y: " << 0 << " Repro_output_by_age_for_morph_1 top_forecast: " << fec(1) << endl;
 
     switch (Fcast_Loop1) //  select which ABC_loops to use
     {
@@ -2315,7 +2318,7 @@ FUNCTION void Get_Forecast()
         }
       }
     }
-    report5 << Fcast_Loop1 << " y: " << y << " updated_Repro_output_by_age_for_morph_1 endyr: " << fec(1) << endl;
+//    report5 << Fcast_Loop1 << " y: " << y << " updated_Repro_output_by_age_for_morph_1 endyr: " << fec(1) << endl;
     for (y = endyr + 1; y <= YrMax; y++)
     {
       t_base = styr + (y - styr) * nseas - 1;
@@ -2505,7 +2508,7 @@ FUNCTION void Get_Forecast()
                   Wt_Age_mid(s, g) = ALK(ALK_idx, g) * wt_len(s, GP(g)); // use for fisheries with no size selectivity
                 }
             }
-    report5 << Fcast_Loop1 << " y: " << y << " updated_Repro_output_by_age_for_morph_1 annual: " << fec(1) << endl;
+//    report5 << Fcast_Loop1 << " y: " << y << " updated_Repro_output_by_age_for_morph_1 annual: " << fec(1) << endl;
             Wt_Age_t(t, 0) = Wt_Age_beg(s);
             for (g = 1; g <= gmorph; g++)
               if (use_morph(g) > 0)
@@ -2661,9 +2664,9 @@ FUNCTION void Get_Forecast()
           }
           else if (ABC_Loop == 2 && s == 1) // Calc the buffer in season 1, will use last year's spawnbio if multiseas and spawnseas !=1
           {
-            temp = SSB_unf;
-            join1 = 1. / (1. + mfexp(10. * (SSB_current - H4010_bot * temp)));
-            join2 = 1. / (1. + mfexp(10. * (SSB_current - H4010_top * temp)));
+
+            join1 = 1. / (1. + mfexp(10. * (SSB_current - H4010_bot * HCR_anchor)));
+            join2 = 1. / (1. + mfexp(10. * (SSB_current - H4010_top * HCR_anchor)));
 
             switch (HarvestPolicy)
             {
@@ -2676,8 +2679,8 @@ FUNCTION void Get_Forecast()
                 // ramp scales catch as f(B) and buffer (H4010_scale) applied to F
                 {
                   ABC_buffer(y) = H4010_scale_vec(y) *
-                          ((0.0001 * SSB_current / (H4010_bot * temp)) * (join1) // low
-                                      + (0.0001 + (1.0 - 0.0001) * (H4010_top * temp / SSB_current) * (SSB_current - H4010_bot * temp) / (H4010_top * temp - H4010_bot * temp)) * (1.0 - join1) // curve
+                          ((0.0001 * SSB_current / (H4010_bot * HCR_anchor)) * (join1) // low
+                                      + (0.0001 + (1.0 - 0.0001) * (H4010_top * HCR_anchor / SSB_current) * (SSB_current - H4010_bot * HCR_anchor) / (H4010_top * HCR_anchor - H4010_bot * HCR_anchor)) * (1.0 - join1) // curve
                                       ) *
                           (join2) // scale combo
                       +
@@ -2688,8 +2691,8 @@ FUNCTION void Get_Forecast()
                 // ramp scales F as f(B) and buffer (H4010_scale) applied to F
                 {
                   ABC_buffer(y) = H4010_scale_vec(y) *
-                          ((0.0001 * SSB_current / (H4010_bot * temp)) * (join1) // low
-                                      + (0.0001 + (1.0 - 0.0001) * (SSB_current - H4010_bot * temp) / (H4010_top * temp - H4010_bot * temp)) * (1.0 - join1) // curve
+                          ((0.0001 * SSB_current / (H4010_bot * HCR_anchor)) * (join1) // low
+                                      + (0.0001 + (1.0 - 0.0001) * (SSB_current - H4010_bot * HCR_anchor) / (H4010_top * HCR_anchor - H4010_bot * HCR_anchor)) * (1.0 - join1) // curve
                                       ) *
                           (join2) // scale combo
                       +
@@ -2700,8 +2703,8 @@ FUNCTION void Get_Forecast()
                 // ramp scales catch as f(B) and buffer (H4010_scale) applied to catch
                 {
                   ABC_buffer(y) = 1.0 *
-                          ((0.0001 * SSB_current / (H4010_bot * temp)) * (join1) // low
-                                      + (0.0001 + (1.0 - 0.0001) * (H4010_top * temp / SSB_current) * (SSB_current - H4010_bot * temp) / (H4010_top * temp - H4010_bot * temp)) * (1.0 - join1) // curve
+                          ((0.0001 * SSB_current / (H4010_bot * HCR_anchor)) * (join1) // low
+                                      + (0.0001 + (1.0 - 0.0001) * (H4010_top * HCR_anchor / SSB_current) * (SSB_current - H4010_bot * HCR_anchor) / (H4010_top * HCR_anchor - H4010_bot * HCR_anchor)) * (1.0 - join1) // curve
                                       ) *
                           (join2) // scale combo
                       +
@@ -2712,8 +2715,8 @@ FUNCTION void Get_Forecast()
                 // ramp scales F as f(B) and buffer (H4010_scale) applied to catch
                 {
                   ABC_buffer(y) = 1.0 *
-                          ((0.0001 * SSB_current / (H4010_bot * temp)) * (join1) // low
-                                      + (0.0001 + (1.0 - 0.0001) * (SSB_current - H4010_bot * temp) / (H4010_top * temp - H4010_bot * temp)) * (1.0 - join1) // curve
+                          ((0.0001 * SSB_current / (H4010_bot * HCR_anchor)) * (join1) // low
+                                      + (0.0001 + (1.0 - 0.0001) * (SSB_current - H4010_bot * HCR_anchor) / (H4010_top * HCR_anchor - H4010_bot * HCR_anchor)) * (1.0 - join1) // curve
                                       ) *
                           (join2) // scale combo
                       +
@@ -3518,7 +3521,7 @@ FUNCTION void Get_Forecast()
             f = fish_fleet_area(0, ff);
             if (fleet_type(f) == 1)
             {
-              if (ABC_Loop == 2 && HarvestPolicy >= 3)
+              if (ABC_Loop == 2 && HarvestPolicy >= 3)  //  alternative ABC_buffer approach
               {
                 catch_fleet(t, f) *= H4010_scale_vec(y);
               }
diff --git a/SS_param.tpl b/SS_param.tpl
index ed5e5a29..7a9cd6f7 100644
--- a/SS_param.tpl
+++ b/SS_param.tpl
@@ -229,6 +229,7 @@ else {
   init_bounded_vector Fcast_recruitments(recdev_end+1,s,recdev_LO,recdev_HI,Fcast_recr_PH2)
   init_bounded_vector Fcast_impl_error(endyr+1,j,-1,1,k)
   vector ABC_buffer(endyr+1,YrMax);
+  number HCR_anchor  //  basis (denominator) bor inflection in control rule
 
 //  SPAWN-RECR:   define some spawning biomass and recruitment entities
   number SSB_virgin
diff --git a/SS_readdata_330.tpl b/SS_readdata_330.tpl
index 56277cb9..96658403 100644
--- a/SS_readdata_330.tpl
+++ b/SS_readdata_330.tpl
@@ -4345,8 +4345,8 @@
       "even when the base is set to the mean of earlier recruitments" << endl;
     }
 
-    echoinput << Fcast_Loop_Control(5) << " #echo: loop control 5 not used" << endl;
-
+    echoinput << Fcast_Loop_Control(5) << " #control rule anchor: 1=unfished_benchmark_SSB(old_approach), 2=virgin_SSB " << endl;
+    
     echoinput << "#next enter year in which Fcast loop 3 caps and allocations begin to be applied" << endl;
     *(ad_comm::global_datafile) >> Fcast_Cap_FirstYear;
     echoinput << Fcast_Cap_FirstYear << " # echoed value" << endl;
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 82794514..aa5c234e 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -4737,7 +4737,7 @@ FUNCTION void SPR_profile()
     Wt_Age_mid(s) = Wt_Age_t(t, -1);
     if (s == spawn_seas)
       fec = Wt_Age_t(t, -2);
-    report5 << 0 << " y: " << y << " updated_Repro_output spr/ypr: " << fec(1) << endl;
+//    report5 << 0 << " y: " << y << " updated_Repro_output spr/ypr: " << fec(1) << endl;
   }
 
   SS2out << "SPRloop Iter Bycatch Fmult F_std SPR YPR_dead YPR_dead*Recr YPR_ret*Recr Revenue Cost Profit SSB Recruits SSB/Bzero Tot_Catch ";
@@ -5070,9 +5070,9 @@ FUNCTION void Global_MSY()
       SS2out << "Actual ";
       show_MSY = 2; //  invokes just brief output in benchmark
       did_MSY = 0;
-    report5 << 0 << " y: " << y << " updated_Repro_output global_1: " << fec(1) << endl;
+//    report5 << 0 << " y: " << y << " updated_Repro_output global_1: " << fec(1) << endl;
       Get_Benchmarks(show_MSY);
-    report5 << 0 << " y: " << y << " updated_Repro_output global_2: " << fec(1) << endl;
+//    report5 << 0 << " y: " << y << " updated_Repro_output global_2: " << fec(1) << endl;
       did_MSY = 0;
     }
   }
diff --git a/SS_write_ssnew.tpl b/SS_write_ssnew.tpl
index 85aaccb6..03eb531c 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -1493,6 +1493,7 @@ FUNCTION void write_nucontrol()
   NuFore << HarvestPolicy << " # 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) " << endl;
   NuFore << "# values for top, bottom and buffer exist, but not used when Policy=0" << endl;
   NuFore << H4010_top_rd << " # 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 " << endl;
+  NuFore << "# Also see HCR_anchor below" << endl;
   NuFore << H4010_bot << " # Control rule cutoff for no F (as frac of Bzero, e.g. 0.10) " << endl;
   NuFore << H4010_scale_rd << " # 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 " << endl;
   if (H4010_scale_rd < 0) {
@@ -1513,7 +1514,7 @@ FUNCTION void write_nucontrol()
   else {
     NuFore << Fcast_Loop_Control(4) << " # multiplier on base recruitment " << endl;
   }
-  NuFore << Fcast_Loop_Control(5) << " # not used" << endl
+  NuFore << Fcast_Loop_Control(5) << " # HCR_anchor: 0 or 1 uses unfished benchmark SSB (old hardwired approach), 2 = virgin SSB" << endl
          << "#" << endl;
 
   NuFore << Fcast_Cap_FirstYear << "  # FirstYear for caps and allocations (should be after years with fixed inputs) " << endl;

From 424f3c66b39e343a2dd3533a6f6deb12c496f097 Mon Sep 17 00:00:00 2001
From: Ian Taylor <ian.taylor@noaa.gov>
Date: Fri, 18 Oct 2024 09:43:01 -0700
Subject: [PATCH 20/22] revert change in capitalization of Recr_Virgin

---
 SS_readcontrol_330.tpl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index b54f0bd6..054f7c74 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -6515,7 +6515,7 @@
       active_parm(CoVar_Count) = j;
       if (y == styr - 2)
       {
-        ParmLabel += "Recr_virgin";
+        ParmLabel += "Recr_Virgin";
       }
       else if (y == styr - 1)
       {

From 27d40957dff93e112515b47e7745601442145dae Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Thu, 17 Oct 2024 16:07:03 -0700
Subject: [PATCH 21/22] latest update

---
 SS_benchfore.tpl   | 25 +++++++++++++------------
 SS_param.tpl       |  2 +-
 SS_write_ssnew.tpl |  2 +-
 3 files changed, 15 insertions(+), 14 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 001ab198..74e2f7e2 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -767,7 +767,8 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   if (show_MSY == 1)
   {
     report5 << "SR_parms for benchmark: " << SR_parm_work << endl
-            << "Benchmark biology averaged over years: " << Bmark_Yr(1) << " " << Bmark_Yr(2) << " flag for updating SSBpR0 = " << SR_update_SSBpR0_bmark << endl;
+            << "Benchmark biology averaged over years: " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl << 
+            "input.SR_update_SSBpR0_rd: " << SR_update_SSBpR0_rd << "flag for updating SSBpR0_Bmark: " << SR_update_SSBpR0_bmark << endl;
     Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SSBpR_virgin); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
     report5 << " Virgin SSB, R0, SPR0: " << SSB_virgin << " " << Recr_virgin << " "  << SSBpR_virgin << " equil: " << Equ_SpawnRecr_Result << endl;
     if ( SR_update_SSBpR0_bmark == 1)
@@ -2176,10 +2177,16 @@ FUNCTION void Get_Forecast()
       {
         H4010_top = H4010_top_rd;
       }
+    if (Fcast_Loop_Control(5) <= 1)
+    {HCR_anchor = SSB_unf;}
+    else if (Fcast_Loop_Control(5) ==2)
+    {HCR_anchor = SSB_virgin;}
     report5 << "#" << endl;
     report5 << "N_forecast_yrs: " << N_Fcast_Yrs << endl;
-    report5 << "OY_Control_Rule "
-            << " Inflection: " << H4010_top << " Intercept: " << H4010_bot << " Scale: " << H4010_scale_vec(endyr + 1) << "; ";
+    report5 << "OY_Control_Rule:  Inflection: " << H4010_top << " Intercept: " << H4010_bot << " Scale: " << H4010_scale_vec(endyr + 1) << endl
+            << "Control_rule_anchor_approach: " << Fcast_Loop_Control(5) << " HCR_anchor: " << HCR_anchor << endl;
+    report5 << "#" << endl;
+
     switch (HarvestPolicy)
     {
       case 0: // none
@@ -2209,13 +2216,7 @@ FUNCTION void Get_Forecast()
         break;
       }
     }
-    if (Fcast_Loop_Control(5) <= 1)
-    {HCR_anchor = SSB_unf;}
-    else if (Fcast_Loop_Control(5) ==2)
-    {HCR_anchor = SSB_virgin;}
-    report5 << "Control_rule_anchor_approach: " << Fcast_Loop_Control(5) << " HCR_anchor: " << HCR_anchor << endl;
-    report5 << "#" << endl;
-  }
+    }
 
   int jloop;
   if (fishery_on_off == 1 || Do_Dyn_Bzero > 0)
@@ -2264,7 +2265,7 @@ FUNCTION void Get_Forecast()
       if (HarvestPolicy == 0)
         report5 << "pop year ABC_Loop season No_buffer bio-all bio-Smry SpawnBio Depletion recruit-0 ";
       if (HarvestPolicy <= 2)
-        report5 << "pop year ABC_Loop season Ramp&Buffer bio-all bio-Smry SpawnBio Depletion recruit-0 ";
+        report5 << "pop year ABC_Loop season Ramp&Buffer Buffer2 bio-all bio-Smry SpawnBio Depletion recruit-0 ";
       if (HarvestPolicy >= 3)
         report5 << "pop year ABC_Loop season Ramp bio-all bio-Smry SpawnBio Depletion recruit-0 ";
       for (int ff = 1; ff <= N_catchfleets(0); ff++)
@@ -3136,7 +3137,7 @@ FUNCTION void Get_Forecast()
             }
             if (show_MSY == 1)
             {
-              report5 << p << " " << y << " " << ABC_Loop << " " << s << " " << ABC_buffer(y) << " " << totbio << " " << smrybio << " ";
+              report5 << p << " " << y << " " << ABC_Loop << " " << s << " " << ABC_buffer(y) << " " << H4010_scale_vec(y) << " " << totbio << " " << smrybio << " ";
               if (s == spawn_seas)
               {
                 report5 << SSB_current << " ";
diff --git a/SS_param.tpl b/SS_param.tpl
index 7a9cd6f7..b49727bb 100644
--- a/SS_param.tpl
+++ b/SS_param.tpl
@@ -229,7 +229,7 @@ else {
   init_bounded_vector Fcast_recruitments(recdev_end+1,s,recdev_LO,recdev_HI,Fcast_recr_PH2)
   init_bounded_vector Fcast_impl_error(endyr+1,j,-1,1,k)
   vector ABC_buffer(endyr+1,YrMax);
-  number HCR_anchor  //  basis (denominator) bor inflection in control rule
+  number HCR_anchor  //  basis (denominator) for inflection in control rule.  Select virgin SSB or benchmark SSB
 
 //  SPAWN-RECR:   define some spawning biomass and recruitment entities
   number SSB_virgin
diff --git a/SS_write_ssnew.tpl b/SS_write_ssnew.tpl
index 03eb531c..f5416543 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -1493,9 +1493,9 @@ FUNCTION void write_nucontrol()
   NuFore << HarvestPolicy << " # 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) " << endl;
   NuFore << "# values for top, bottom and buffer exist, but not used when Policy=0" << endl;
   NuFore << H4010_top_rd << " # 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 " << endl;
-  NuFore << "# Also see HCR_anchor below" << endl;
   NuFore << H4010_bot << " # Control rule cutoff for no F (as frac of Bzero, e.g. 0.10) " << endl;
   NuFore << H4010_scale_rd << " # 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 " << endl;
+  NuFore << "# Also see HCR_anchor below" << endl;
   if (H4010_scale_rd < 0) {
     j = H4010_scale_vec_rd.size() - 1;
     for (int s = 0; s <= j; s++) {

From f0bfa6f0ccdf93aefe7e54f2645b9c8401154e0f Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Thu, 31 Oct 2024 17:00:23 -0400
Subject: [PATCH 22/22] go back to g++12.a

---
 Compile/Make_SS_warn.bat | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Compile/Make_SS_warn.bat b/Compile/Make_SS_warn.bat
index af9b1430..f53510ee 100644
--- a/Compile/Make_SS_warn.bat
+++ b/Compile/Make_SS_warn.bat
@@ -28,6 +28,6 @@ tpl2cpp ss3
 
 g++ -c -std=c++17 -O2 -D_FILE_OFFSET_BITS=64  -DUSE_ADMB_CONTRIBS -D_USE_MATH_DEFINES -I. -I"C:\ADMB-13.2\include" -I"C:\ADMB-13.2\include\contrib" -Wall -Wextra -o ss3.obj ss3.cpp
 
-g++ -static -o ss3.exe ss3.obj "C:\ADMB-13.2\lib\libadmb-contrib-mingw64-g++13.a"
+g++ -static -o ss3.exe ss3.obj "C:\ADMB-13.2\lib\libadmb-contrib-mingw64-g++12.a"
 
 dir *.exe