From c48e891bdbcc8eeb92d9ef488b7b6ea4dcc1b91d Mon Sep 17 00:00:00 2001
From: RickMethot <richard.methot@noaa.gov>
Date: Wed, 8 Feb 2023 16:24:40 -0800
Subject: [PATCH 01/58] 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 cc9b6f97..290028fd 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 bc42d9b5..696da19a 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1944,13 +1944,13 @@
 !!//  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;
@@ -2033,6 +2033,13 @@
       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 f51aa464..07528817 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;
@@ -4796,7 +4800,7 @@ 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 fdfdf82f8f05605bad84a1d74fc0da56a0742198 Mon Sep 17 00:00:00 2001
From: RickMethot <richard.methot@noaa.gov>
Date: Mon, 13 Feb 2023 17:36:35 -0800
Subject: [PATCH 02/58] 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 290028fd..512803fe 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 07528817..e3e46dbd 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 9119b3df213b129cad4f0733e390af0443c19dd1 Mon Sep 17 00:00:00 2001
From: RickMethot <richard.methot@noaa.gov>
Date: Mon, 13 Feb 2023 17:43:58 -0800
Subject: [PATCH 03/58] 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 d6aa468c7236bf4c27fc9f4b26ca3e9a01198f45 Mon Sep 17 00:00:00 2001
From: RickMethot <richard.methot@noaa.gov>
Date: Fri, 19 May 2023 11:14:13 -0700
Subject: [PATCH 04/58] 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 696da19a..30a5f22c 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1979,7 +1979,7 @@
   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 e3e46dbd..0c4dcdaf 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 f8533caab5db4d5320d97ce9d227eb2fa08e2061 Mon Sep 17 00:00:00 2001
From: RickMethot <richard.methot@noaa.gov>
Date: Fri, 19 May 2023 17:06:15 -0700
Subject: [PATCH 05/58] 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 512803fe..5bd02654 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -3652,6 +3652,14 @@ 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 0c4dcdaf..0eb617ff 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 a1722ebb063e58b12c982bb748cb2ab8ba0430f9 Mon Sep 17 00:00:00 2001
From: RickMethot <richard.methot@noaa.gov>
Date: Wed, 31 May 2023 09:40:07 -0700
Subject: [PATCH 06/58] 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 5bd02654..657cc7ee 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 ab567cf06be155e83c310d293aa425c6e1445f50 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 07/58] 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 0eb617ff..ebe62f95 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 83d5b71f336ea6331f932a867c6dac45df2df853 Mon Sep 17 00:00:00 2001
From: "Richard.Methot" <1365818351113302@mil>
Date: Tue, 28 May 2024 14:39:34 -0700
Subject: [PATCH 08/58] 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 4f96850a4e0d2bde613f98c25249601180adef8f 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 09/58] 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 657cc7ee..9f6577d6 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;
   }
@@ -2580,6 +2580,7 @@ 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;
@@ -3218,7 +3219,8 @@ 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 30a5f22c..58f24521 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1663,6 +1663,7 @@
 
 !!//  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;
 
@@ -1711,6 +1712,7 @@
   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();
@@ -1811,6 +1813,7 @@
       {
         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
@@ -1968,6 +1971,7 @@
   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
@@ -1979,6 +1983,8 @@
   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)
@@ -2125,6 +2131,9 @@
         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 ebe62f95..61ce49f8 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 707aa32d73b66a2fd61cab99bdfa47287895480d 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 10/58] 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 9f6577d6..30802ac0 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 61ce49f8..0f0d10e9 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 1034c6e65d48f8897791516b1d925913d1912d86 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 11/58] 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 58f24521..0a66f8e0 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1986,7 +1986,11 @@
   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 0f0d10e9..70b49ad7 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 edc7ca9a9d7da342521ec924dc644d49edb5ec87 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 12/58] 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 d11c35ff570f503e8597dbdc6793437ca9174b05 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 13/58] 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 30802ac0..66259197 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);
@@ -2581,7 +2597,7 @@ 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;
@@ -3221,7 +3237,7 @@ 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 70b49ad7..71d0ea45 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 545bb59385c0f3ab74b8c4b8e69de7419abfaab8 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 14/58] 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 66259197..67a06898 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 2bd30c2da1fe3cb542ad3dfa6f015e2475ee0d10 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 15/58] 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 67a06898..0ddc922e 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 0a66f8e0..c4cd8a2a 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -6485,7 +6485,7 @@
       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 55216152d989d5d527e8c4524432f2332defd2df 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 16/58] 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 0ddc922e..fa527705 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 71d0ea45..0fe3f0c0 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;
 
@@ -4915,8 +4915,8 @@ 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 c04d9b4612223bc42d1ffceec15309293469fbb5 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 17/58] 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 fa527705..484d010c 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);
@@ -2596,7 +2596,7 @@ 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;
@@ -3236,7 +3236,7 @@ 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 c4cd8a2a..bec821cd 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1950,8 +1950,21 @@
 !!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
@@ -1971,7 +1984,7 @@
   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
@@ -1983,7 +1996,7 @@
   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)
@@ -2136,8 +2149,8 @@
           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;
@@ -2149,6 +2162,34 @@
     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 04c450d2..590c76df 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 1d2e75a6f91ad0cf4a8b87c62bea341fc51f8a77 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 18/58] too many changes

---
 SS_benchfore.tpl       | 82 +++++++++++++++++++++++-------------------
 SS_global.tpl          |  4 +--
 SS_param.tpl           |  9 +++--
 SS_popdyn.tpl          | 36 +++++++++----------
 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     |  6 ++--
 10 files changed, 103 insertions(+), 111 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 484d010c..58e85267 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)
@@ -2578,19 +2588,19 @@ 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
                   {
                     natage(t, p, g, 0) = 0.0; // these fish do not yet exist
-                    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;
               }
             }
@@ -2619,7 +2629,6 @@ 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
@@ -3218,18 +3227,18 @@ 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;
               }
             }
@@ -3668,7 +3677,7 @@ 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
 
@@ -3676,7 +3685,7 @@ 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
@@ -3684,6 +3693,7 @@ 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..110bce12 100644
--- a/SS_param.tpl
+++ b/SS_param.tpl
@@ -159,7 +159,7 @@ 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;
@@ -241,9 +241,12 @@ 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 +325,7 @@ 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);
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 79b1d59f..6b51ce91 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -383,7 +383,7 @@ FUNCTION void get_initial_conditions()
 //    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
@@ -395,7 +395,7 @@ 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;
@@ -527,7 +527,7 @@ FUNCTION void get_initial_conditions()
     //  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 +554,7 @@ 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;
@@ -697,14 +697,12 @@ FUNCTION void get_time_series()
   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)
   {
@@ -983,7 +981,7 @@ FUNCTION void get_time_series()
         }
       }
       //  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();
@@ -1009,18 +1007,18 @@ FUNCTION void get_time_series()
 
         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;
           }
         }
@@ -1471,18 +1469,18 @@ FUNCTION void get_time_series()
         SSB_yr(y) = SSB_current;
         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;
           }
         }
@@ -1798,7 +1796,7 @@ FUNCTION void get_time_series()
       Smry_Table(y, 13) = GenTime;
       if( SR_fxn == 10 )
       {
-        temp = SSB_equil / Recr_virgin;  //  current year's SPB/R with current biology at age
+        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
@@ -2284,9 +2282,9 @@ 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
+  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
 
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 bec821cd..a2e2057c 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1155,11 +1155,11 @@
   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;
   
@@ -1182,8 +1182,8 @@
     //  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
@@ -2190,6 +2190,7 @@
     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
@@ -5827,7 +5828,7 @@
     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;
@@ -6881,23 +6882,23 @@
     }
   }
   
-  //  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 0fe3f0c0..571e2e4c 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);
@@ -4738,33 +4738,11 @@ 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 ";
@@ -5016,7 +4994,7 @@ 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;
@@ -5095,7 +5073,9 @@ 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 590c76df..7c037fe3 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -1548,7 +1548,7 @@ 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;
@@ -1941,7 +1941,7 @@ FUNCTION void write_nucontrol()
   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;
@@ -2136,7 +2136,7 @@ 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 << SR_update_SSBpR0_rd <<  "#  SR_update_SSBpR0" << 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 <<

From 72bac37779aefe74611ae32bc0f22785c0adc14d 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 19/58] 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 58e85267..f7a3a3b1 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)
@@ -2663,9 +2666,9 @@ 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)
             {
@@ -2678,8 +2681,8 @@ 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
                       +
@@ -2690,8 +2693,8 @@ 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
                       +
@@ -2702,8 +2705,8 @@ 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
                       +
@@ -2714,8 +2717,8 @@ 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
                       +
@@ -3520,7 +3523,7 @@ 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 110bce12..b077172f 100644
--- a/SS_param.tpl
+++ b/SS_param.tpl
@@ -235,6 +235,7 @@ PARAMETER_SECTION
   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 571e2e4c..72b5d79d 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -4742,7 +4742,7 @@ 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 ";
@@ -5073,9 +5073,9 @@ 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 7c037fe3..44188a2c 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -1642,6 +1642,7 @@ 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)
@@ -1665,7 +1666,7 @@ FUNCTION void write_nucontrol()
   {
     NuFore << Fcast_Loop_Control(4) << " # multiplier on base recruitment " << endl;
   }
-  NuFore << Fcast_Loop_Control(5) << " # not used" << endl << "#" << 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 1712c7c5254d7a4c9c7332ff39d868d23827d2a4 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 20/58] 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 a2e2057c..6df633b6 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -6527,7 +6527,7 @@
       active_parm(CoVar_Count) = j;
       if (y == styr - 2)
       {
-        ParmLabel += "Recr_virgin";
+        ParmLabel += "Recr_Virgin";
       }
       else if (y == styr - 1)
       {

From 7ffbff5c9a034a44bc0ec500c9cb5e3fb7bcebe7 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 21/58] 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 f7a3a3b1..ce9ded30 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++)
@@ -3138,7 +3139,7 @@ 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 b077172f..b6f9341b 100644
--- a/SS_param.tpl
+++ b/SS_param.tpl
@@ -235,7 +235,7 @@ PARAMETER_SECTION
   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 44188a2c..30a11a62 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -1642,9 +1642,9 @@ 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;

From 7f14cd6f0a1a7d6ef89a7c600598893ca35339c7 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Thu, 23 Jan 2025 14:33:17 -0800
Subject: [PATCH 22/58] add 3 lines to mgmt_quant

---
 SS_benchfore.tpl       | 52 ++++++++++++++++++++++++------------------
 SS_popdyn.tpl          |  2 +-
 SS_readcontrol_330.tpl | 20 +++++++++++++++-
 SS_recruit.tpl         |  2 +-
 SS_write_report.tpl    | 18 +++++++++++----
 5 files changed, 64 insertions(+), 30 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index ce9ded30..234b2c08 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -9,9 +9,9 @@
 // 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
+// SSBpR_virgin is calculated in popdyn using the start year biology
+// SSBpR_virgin_adj  used in equil_spawn_recr.  _adj means could be updated if SR_update_SSBpR0_timeseries == 1.
+// Also used to get alpha in equil_spawn_recr B-H
 
 FUNCTION void setup_Benchmark()  // and forecast
   {
@@ -754,12 +754,13 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
      Recr_unf = Recr_virgin;
      SSB_unf = SSB_virgin;
      SSBpR_unf = SSB_unf / Recr_unf;
+    SSBpR_virgin_adj = SSB_unf / Recr_unf;  //  so same as SSBpR_virgin, but is the version that will be used in equil_spawn_recr()
   }
   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);
+    Do_Equil_Calc(Recr_unf);  // this calcs SSB using benchmark biology
     SSB_unf = SSB_equil;  // equilibrium unfished SSB using the benchmark averaged Recr_unf and benchmark averaged biology
     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 
@@ -767,17 +768,21 @@ 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 << 
-            "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;
+            << "Benchmark biology averaged over years: " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl << 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, 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 << " " << SSB_virgin/Recr_virgin << " equil: " << Equ_SpawnRecr_Result << endl;
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin, SSBpR_virgin); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    report5 << " Benchmark SSB, R0, virgin_SPR0: " << SSB_unf << " " << Recr_unf << " "  << SSBpR_virgin << " equil: " << Equ_SpawnRecr_Result << 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;
+      Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_adj, SSBpR_virgin_adj); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+      report5 << " Benchmark SSB, R0, bench_SPR0: " << SSB_unf << " " << Recr_unf << " "  << SSBpR_virgin_adj << " equil: " << Equ_SpawnRecr_Result << endl;
     }
-
+    Mgmt_quant(19) = Recr_unf;
+    Mgmt_quant(20) = SSB_unf;
+    Mgmt_quant(21) = SSB_unf;  //  placeholder to be replaced by SSB_HCR_infl
   }
   SR_parm_work(N_SRparm2 + 1) = SSB_unf;
   Mgmt_quant(1) = SSB_unf;
@@ -928,7 +933,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
 
     //  SPAWN-RECR:   calc equil spawn-recr in YPR; need to make this area-specific
     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
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_adj, 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);
@@ -1043,7 +1048,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     if (rundetail > 0 && mceval_counter == 0 && show_MSY == 1)
       echoinput << "Calculated F0.1: " << Btgt_Fmult << endl;
     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
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_adj, 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
@@ -1139,7 +1144,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         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
-        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
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_adj, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         yld1(ii) = Equ_SpawnRecr_Result(1);
       }
 
@@ -1360,7 +1365,7 @@ 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 / 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
+      Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_adj, 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;
@@ -1387,12 +1392,13 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         report5 << endl;
       }
 
-      Mgmt_quant(15) = yld1(1);
       Mgmt_quant(12) = Bmsy;
       Mgmt_quant(13) = MSY_SPR;
       Mgmt_quant(14) = equ_F_std;
+      Mgmt_quant(15) = yld1(1);
       Mgmt_quant(16) = YPR_ret * Recr_msy;
       Mgmt_quant(17) = Bmsy / SSB_unf;
+      Mgmt_quant(18) = Recr_msy;
       Vbio1_MSY = smrybio;
       Vbio_MSY = totbio;
     }
@@ -1453,7 +1459,7 @@ 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 / 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
+          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_adj, 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;
@@ -1525,12 +1531,14 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       YPR_msy_profit = YPR_msy_revenue - Cost;
       MSY = yld1(1);
       MSY_Fmult = Fmult;
-      Mgmt_quant(15) = yld1(1);
       Mgmt_quant(12) = Bmsy;
       Mgmt_quant(13) = MSY_SPR;
       Mgmt_quant(14) = equ_F_std;
+      Mgmt_quant(15) = yld1(1);
       Mgmt_quant(16) = YPR_ret * Recr_msy;
       Mgmt_quant(17) = Bmsy / SSB_unf;
+      Mgmt_quant(18) = Recr_msy;
+
       Vbio1_MSY = smrybio;
       Vbio_MSY = totbio;
 
@@ -1747,7 +1755,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         SPR_Btgt2 = SSB_equil / SSBpR_unf;
         //  SPAWN-RECR:   calc equil spawn-recr for Btarget calcs;  need to make area-specific
         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
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_adj, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         yld1(ii) = Equ_SpawnRecr_Result(1);
       }
 
@@ -1816,9 +1824,9 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     Btgt_Fmult2 = Fmult;
     if (rundetail > 0 && mceval_counter == 0 && show_MSY == 1)
       echoinput << "Calculated F_Blimit " << Btgt_Fmult2 << " " << Btgt2 / Blim_report << endl;
-    Mgmt_quant(18) = Btgt2;
-    Mgmt_quant(19) = equ_F_std;
-    Mgmt_quant(20) = sum(equ_catch_fleet(2)) * Equ_SpawnRecr_Result(2);
+    Mgmt_quant(22) = Btgt2;
+    Mgmt_quant(23) = equ_F_std;
+    Mgmt_quant(24) = sum(equ_catch_fleet(2)) * Equ_SpawnRecr_Result(2);
   } //  end finding F for Blimit
 
   if (rundetail > 0 && mceval_counter == 0 && show_MSY == 1)
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 6b51ce91..efedf516 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -536,7 +536,7 @@ FUNCTION void get_initial_conditions()
     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, SSBpR_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_virgin_adj, 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;
 
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 6df633b6..42e07f53 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -5871,7 +5871,7 @@
       // clang-format on
       if (Do_Benchmark > 0)
   {
-    N_STD_Mgmt_Quant = 17;
+    N_STD_Mgmt_Quant = 21;
     if (Do_Benchmark == 3) N_STD_Mgmt_Quant += 3; //  for Blimit
   }
   else
@@ -6678,6 +6678,24 @@
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
+// add quantities needed when time-vary life history is used; but report here for all cases; elements 18-21 of mgmt_quant
+    ParmLabel += "Recr_MSY_bmarkbio" + CRLF(1);
+    CoVar_Count++;
+    j++;
+    active_parm(CoVar_Count) = j;
+    ParmLabel += "Recr_unfished_bmarkbio" + CRLF(1);
+    CoVar_Count++;
+    j++;
+    active_parm(CoVar_Count) = j;
+    ParmLabel += "SSB_unfished_bmarkbio" + CRLF(1);
+    CoVar_Count++;
+    j++;
+    active_parm(CoVar_Count) = j;
+    ParmLabel += "SSB_HCR_infl" + CRLF(1);
+    CoVar_Count++;
+    j++;
+    active_parm(CoVar_Count) = j;
+
     if (Do_Benchmark == 3)
     {
       ParmLabel += "SSB_Blim" + CRLF(1);
diff --git a/SS_recruit.tpl b/SS_recruit.tpl
index 645dbcf3..88815fa9 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& SSBpR_current)
+    const prevariable& SSB_virgin_use, const prevariable& Recr_virgin_use, const prevariable& SSBpR_virgin_adj, 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
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 72b5d79d..558aad3f 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -4742,10 +4742,10 @@ 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 << " repro_output for 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 ";
+  SS2out << "SPRloop Iter Bycatch Fmult F_std SSBpR YpR_dead YpR_dead*Recr YpR_ret*Recr Revenue Cost Profit SSB Recruits SSB/Bzero Tot_Catch ";
   for (f = 1; f <= Nfleet; f++)
   {
     if (fleet_type(f) <= 2)
@@ -4789,20 +4789,28 @@ FUNCTION void SPR_profile()
     k = 1;
   }
   for (int with_BYC = 0; with_BYC <= k; with_BYC++)
-    for (int SPRloop1 = 0; SPRloop1 <= SPRloop1_end; SPRloop1++)
+    for (int SPRloop1 = -1; SPRloop1 <= SPRloop1_end; SPRloop1++)
     {
       Fmultchanger1 = value(pow(0.0001 / Fcrash, 0.025));
       Fmultchanger2 = value(Fcrash / 39.);
       SPRloops = 40;
       switch (SPRloop1)
       {
+        case -1:
+        {
+          SPRloops = 1;
+          Fmult2 = 0.0;
+          break;
+        }
         case 0:
         {
+          SPRloops = 40;
           Fmult2 = maxpossF;
           break;
         }
         case 1:
         {
+          SPRloops = 40;
           Fmult2 = Fcrash;
           break;
         }
@@ -4894,7 +4902,7 @@ FUNCTION void SPR_profile()
         Do_Equil_Calc(equ_Recr);
         //  SPAWN-RECR:   calc equil spawn-recr in the SPR loop
         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
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_adj, 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)
@@ -4954,7 +4962,7 @@ FUNCTION void SPR_profile()
           {
             SS2out << " " << SSB_equil_pop_gp(p, gp) * Btgt_prof_rec;
           }
-        SS2out << endl;
+        SS2out << " R " << equ_Recr << "  SSB " << SSB_equil << endl;
         if (SPRloop1 == 0)
         {
           Fmult2 -= Fmultchanger0;

From cec04047f0fa418422ab18519ab28c818f53ecba Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Thu, 20 Feb 2025 08:49:35 -0800
Subject: [PATCH 23/58] add 4 lines to mgmt_quant to display more benchmark
 quantities

---
 SS_benchfore.tpl       | 36 ++++++++++++++++++++----------------
 SS_popdyn.tpl          |  2 +-
 SS_readcontrol_330.tpl |  6 +++++-
 SS_write_ssnew.tpl     |  2 +-
 4 files changed, 27 insertions(+), 19 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 234b2c08..a63857c6 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -783,6 +783,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     Mgmt_quant(19) = Recr_unf;
     Mgmt_quant(20) = SSB_unf;
     Mgmt_quant(21) = SSB_unf;  //  placeholder to be replaced by SSB_HCR_infl
+    Mgmt_quant(22) = SSB_virgin;
   }
   SR_parm_work(N_SRparm2 + 1) = SSB_unf;
   Mgmt_quant(1) = SSB_unf;
@@ -1824,9 +1825,9 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     Btgt_Fmult2 = Fmult;
     if (rundetail > 0 && mceval_counter == 0 && show_MSY == 1)
       echoinput << "Calculated F_Blimit " << Btgt_Fmult2 << " " << Btgt2 / Blim_report << endl;
-    Mgmt_quant(22) = Btgt2;
-    Mgmt_quant(23) = equ_F_std;
-    Mgmt_quant(24) = sum(equ_catch_fleet(2)) * Equ_SpawnRecr_Result(2);
+    Mgmt_quant(N_STD_Mgmt_Quant - 2) = Btgt2;
+    Mgmt_quant(N_STD_Mgmt_Quant - 1) = equ_F_std;
+    Mgmt_quant(N_STD_Mgmt_Quant) = sum(equ_catch_fleet(2)) * Equ_SpawnRecr_Result(2);
   } //  end finding F for Blimit
 
   if (rundetail > 0 && mceval_counter == 0 && show_MSY == 1)
@@ -2172,23 +2173,26 @@ FUNCTION void Get_Forecast()
       }
     }
 
-    if (H4010_top_rd < 0.0)
-      {
-        H4010_top = Bmsy / SSB_unf;
-        if (H4010_bot > 0.25)
-        {
-          warnstream << "control rule cutoff is large (" << H4010_bot << "); so may not be < calculated Bmsy/SSB_unf (" << H4010_top << ")";
-          write_message (WARN, 0);
-        }
-      }
-      else
-      {
-        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;}
+
+    if (H4010_top_rd < 0.0)
+    {
+      H4010_top = Bmsy / HCR_anchor;  // convert to fraction
+      if (H4010_bot > 0.25)
+      {
+        warnstream << "control rule cutoff is large (" << H4010_bot << "); so may not be < calculated Bmsy/SSB_unf (" << H4010_top << ")";
+        write_message (WARN, 0);
+      }
+    }
+    else
+    {
+      H4010_top = H4010_top_rd;
+    }
+
+    Mgmt_quant(21) = H4010_top * HCR_anchor;
     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) << endl
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index efedf516..adc7e1d9 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -383,8 +383,8 @@ FUNCTION void get_initial_conditions()
 //    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;  //  can be overwritten in benchmark by updated SSB_unf
       SSB_unf = SSB_virgin;
+      Mgmt_quant(1) = SSB_unf;  //  can be overwritten in benchmark by updated SSB_unf
       Recr_unf = Recr_virgin;
       Mgmt_quant(2) = totbio;  //  from equil calcs
       Mgmt_quant(3) = smrybio;  //  from equil calcs
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 42e07f53..a4a8bbb5 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -5871,7 +5871,7 @@
       // clang-format on
       if (Do_Benchmark > 0)
   {
-    N_STD_Mgmt_Quant = 21;
+    N_STD_Mgmt_Quant = 22;
     if (Do_Benchmark == 3) N_STD_Mgmt_Quant += 3; //  for Blimit
   }
   else
@@ -6695,6 +6695,10 @@
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
+    ParmLabel += "SSB_virgin_again" + CRLF(1);
+    CoVar_Count++;
+    j++;
+    active_parm(CoVar_Count) = j;
 
     if (Do_Benchmark == 3)
     {
diff --git a/SS_write_ssnew.tpl b/SS_write_ssnew.tpl
index 30a11a62..0d4ad371 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -1641,7 +1641,7 @@ 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 << 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 as the inflection " << 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;

From f232d531f82da34f5ac89638ab2fc5ae575461c1 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Fri, 21 Feb 2025 16:40:31 -0800
Subject: [PATCH 24/58] assure align of SRR curve and SPR/YPR profile

---
 SS_benchfore.tpl    | 45 ++++++++++++++++++++++-----------------------
 SS_param.tpl        |  2 +-
 SS_popdyn.tpl       | 12 ++++++------
 SS_recruit.tpl      |  4 ++--
 SS_write_report.tpl | 12 +++++++-----
 5 files changed, 38 insertions(+), 37 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index a63857c6..4f86b30a 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -10,7 +10,7 @@
 // SPR refers to spawner potential ratio which is the ratio of SSBpR at some level of F to SSBpR with F = 0
 
 // SSBpR_virgin is calculated in popdyn using the start year biology
-// SSBpR_virgin_adj  used in equil_spawn_recr.  _adj means could be updated if SR_update_SSBpR0_timeseries == 1.
+// SSBpR_virgin_4SRR  is passed to equil_spawn_recr.  _adj means could be updated if SR_update_SSBpR0_timeseries == 1.
 // Also used to get alpha in equil_spawn_recr B-H
 
 FUNCTION void setup_Benchmark()  // and forecast
@@ -749,12 +749,19 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       SR_parm_work(j) = temp / (Bmark_Yr(10) - Bmark_Yr(9) + 1.);
     }
   }
+  Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SSBpR_virgin_4SRR, SSBpR_virgin); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+  report5 << endl << " virgin - SSB, R0, SPR0: " << SSB_virgin << " " << Recr_virgin << " "  << SSBpR_virgin << " " << SSBpR_virgin << " equil: " << Equ_SpawnRecr_Result << endl<<endl;
   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;
-     SSBpR_unf = SSB_unf / Recr_unf;
-    SSBpR_virgin_adj = SSB_unf / Recr_unf;  //  so same as SSBpR_virgin, but is the version that will be used in equil_spawn_recr()
+    Recr_unf = Recr_virgin;
+    SSB_unf = SSB_virgin;
+    Fishon = 0;
+    Recr_unf = Recr_virgin;
+    Do_Equil_Calc(Recr_unf);  // this calcs SSB using benchmark biology
+    temp1 = SSB_equil;  // equilibrium unfished SSB using the benchmark averaged Recr_unf and benchmark averaged biology
+    temp2 = temp1 / Recr_unf;
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SSBpR_virgin_4SRR, temp2); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    report5 << " virgSRR_&_bmarkbio - SSB, R0, SPR0: " << SSB_virgin << " " << Recr_virgin << " "  << SSBpR_virgin << " " << SSBpR_virgin_4SRR << " equil: " << Equ_SpawnRecr_Result << endl<<endl;
   }
   else  // use benchmark biology in the spawner-recruitment R0,h calculations
   {
@@ -763,23 +770,15 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     Do_Equil_Calc(Recr_unf);  // this calcs SSB using benchmark biology
     SSB_unf = SSB_equil;  // equilibrium unfished SSB using the benchmark averaged Recr_unf and benchmark averaged biology
     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 
+    SSBpR_virgin_4SRR = SSB_unf / Recr_unf;  //  update 
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_4SRR, SSBpR_unf); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    report5 << " bmarkSRR_&_bmarkbio - SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << SSBpR_unf << " " << SSBpR_virgin_4SRR << " equil: " << Equ_SpawnRecr_Result << endl<<endl;
   }
   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 << 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, 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 << " " << SSB_virgin/Recr_virgin << " equil: " << Equ_SpawnRecr_Result << endl;
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin, SSBpR_virgin); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    report5 << " Benchmark SSB, R0, virgin_SPR0: " << SSB_unf << " " << Recr_unf << " "  << SSBpR_virgin << " equil: " << Equ_SpawnRecr_Result << 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_virgin_adj, SSBpR_virgin_adj); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-      report5 << " Benchmark SSB, R0, bench_SPR0: " << SSB_unf << " " << Recr_unf << " "  << SSBpR_virgin_adj << " equil: " << Equ_SpawnRecr_Result << endl;
-    }
     Mgmt_quant(19) = Recr_unf;
     Mgmt_quant(20) = SSB_unf;
     Mgmt_quant(21) = SSB_unf;  //  placeholder to be replaced by SSB_HCR_infl
@@ -934,7 +933,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
 
     //  SPAWN-RECR:   calc equil spawn-recr in YPR; need to make this area-specific
     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_virgin_adj, SSBpR_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, SSBpR_virgin_4SRR, 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);
@@ -1049,7 +1048,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     if (rundetail > 0 && mceval_counter == 0 && show_MSY == 1)
       echoinput << "Calculated F0.1: " << Btgt_Fmult << endl;
     SSBpR_temp = SSB_equil;
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_adj, SSBpR_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, SSBpR_virgin_4SRR, 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
@@ -1145,7 +1144,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         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
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_adj, SSBpR_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, SSBpR_virgin_4SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         yld1(ii) = Equ_SpawnRecr_Result(1);
       }
 
@@ -1185,7 +1184,7 @@ 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;
+//        " SSB_unf " << SSB_unf << " recr " <<Recr_unf<< " SSB_equil " << SSB_equil << " ssbpr_virginadj: " << SSBpR_virgin_4SRR << " Btgt " << Btgt << endl;
       }
     } // end search loop
 
@@ -1366,7 +1365,7 @@ 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 / SSBpR_unf;
       SSBpR_temp = SSB_equil;
-      Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_adj, SSBpR_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, SSBpR_virgin_4SRR, 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;
@@ -1460,7 +1459,7 @@ 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 / SSBpR_unf;
           SSBpR_temp = SSB_equil;
-          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_adj, SSBpR_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, SSBpR_virgin_4SRR, 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;
@@ -1756,7 +1755,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         SPR_Btgt2 = SSB_equil / SSBpR_unf;
         //  SPAWN-RECR:   calc equil spawn-recr for Btarget calcs;  need to make area-specific
         SSBpR_temp = SSB_equil;
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_adj, SSBpR_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, SSBpR_virgin_4SRR, 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 b6f9341b..4af7af91 100644
--- a/SS_param.tpl
+++ b/SS_param.tpl
@@ -166,7 +166,7 @@ PARAMETER_SECTION
   number half_sigmaRsq;
   number sigmaR;
   number SSBpR_virgin;
-  number SSBpR_virgin_adj;
+  number SSBpR_virgin_4SRR;
   number regime_change;
   number rho;
   number dirichlet_Parm;
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index adc7e1d9..fd3f7347 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
     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.
+    SSBpR_virgin_4SRR = 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 * SSBpR_virgin_adj / (4. + alpha * SSBpR_virgin_adj);
-      Recr_virgin = 1. / beta * (alpha - (1. / SSBpR_virgin_adj));
+      steepness = alpha * SSBpR_virgin_4SRR / (4. + alpha * SSBpR_virgin_4SRR);
+      Recr_virgin = 1. / beta * (alpha - (1. / SSBpR_virgin_4SRR));
 //      warning << " before AB_calcs " << "parm " << SR_parm(1) << " calc " << log(Recr_virgin) << endl;
       SR_parm(1) = log(Recr_virgin);
       SR_parm(2) = steepness;
@@ -536,7 +536,7 @@ FUNCTION void get_initial_conditions()
     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, SSBpR_virgin_adj, SSBpR_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_virgin_4SRR, 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;
 
@@ -1040,7 +1040,7 @@ 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 
+          SSBpR_virgin_4SRR = SSB_use / R0_use;  //  update 
           if (fishery_on_off == 1)
           {
             Fishon = 1;
@@ -1500,7 +1500,7 @@ 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 
+          SSBpR_virgin_4SRR = SSB_use / R0_use;  //  update 
           if (fishery_on_off == 1)
           {
             Fishon = 1;
diff --git a/SS_recruit.tpl b/SS_recruit.tpl
index 88815fa9..474e30ed 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& SSBpR_virgin_adj, const prevariable& SSBpR_current)
+    const prevariable& SSB_virgin_use, const prevariable& Recr_virgin_use, const prevariable& SSBpR_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
@@ -316,7 +316,7 @@ 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
-      alpha = 4.0 * steepness / (SSBpR_virgin_adj * (1. - steepness));
+      alpha = 4.0 * steepness / (SSBpR_virgin_use * (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;
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 558aad3f..605facfe 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 / (SSBpR_virgin_adj * (1. - steepness));
+      alpha = 4.0 * steepness / (SSBpR_virgin_4SRR * (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. / SSBpR_virgin_adj))) << endl;  //  virgin R0
-      SS2out << "steepness_derived: " << alpha * SSBpR_virgin_adj / (4. + alpha * SSBpR_virgin_adj) << endl;  // steepness virgin
+      SS2out << "ln(R0)_derived: " << log( 1. / beta * (alpha - (1. / SSBpR_virgin_4SRR))) << endl;  //  virgin R0
+      SS2out << "steepness_derived: " << alpha * SSBpR_virgin_4SRR / (4. + alpha * SSBpR_virgin_4SRR) << endl;  // steepness virgin
       break;
     }
     case 8:
@@ -4741,10 +4741,12 @@ FUNCTION void SPR_profile()
     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 << " repro_output for spr/ypr: " << fec(1) << endl;
+      SS2out << " repro_output for spr/ypr: " << fec(1) << endl;}
   }
 
+  SS2out << "unfished values for SRR: SSB " << SSB_unf << " R " << Recr_unf << " SSBpR " << SSBpR_virgin_4SRR << endl;
   SS2out << "SPRloop Iter Bycatch Fmult F_std SSBpR YpR_dead YpR_dead*Recr YpR_ret*Recr Revenue Cost Profit SSB Recruits SSB/Bzero Tot_Catch ";
   for (f = 1; f <= Nfleet; f++)
   {
@@ -4902,7 +4904,7 @@ FUNCTION void SPR_profile()
         Do_Equil_Calc(equ_Recr);
         //  SPAWN-RECR:   calc equil spawn-recr in the SPR loop
         SSBpR_temp = SSB_equil;
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_adj, SSBpR_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, SSBpR_virgin_4SRR, 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 e69f40e879772145c6f22436f78d2291754367ae Mon Sep 17 00:00:00 2001
From: Rick-Methot-NOAA <richard.methot@noaa.gov>
Date: Tue, 25 Feb 2025 15:54:07 -0800
Subject: [PATCH 25/58] adjust SPR in profile to match old approach

---
 SS_write_report.tpl | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 605facfe..51a21d98 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -4746,6 +4746,29 @@ FUNCTION void SPR_profile()
       SS2out << " repro_output for spr/ypr: " << fec(1) << endl;}
   }
 
+  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;
+    Fishon = 0;
+    Recr_unf = Recr_virgin;
+    Do_Equil_Calc(Recr_unf);  // this calcs SSB using benchmark biology
+    temp1 = SSB_equil;  // equilibrium unfished SSB using the benchmark averaged Recr_unf and benchmark averaged biology
+    temp2 = temp1 / Recr_unf;
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SSBpR_virgin_4SRR, temp2); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    SS2out << " virgSRR_&_bmarkbio - SSB, R0, SPR0: " << SSB_virgin << " " << Recr_virgin << " "  << SSBpR_virgin << " " << SSBpR_virgin_4SRR << " equil: " << Equ_SpawnRecr_Result << endl<<endl;
+  }
+  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);  // this calcs SSB using benchmark biology
+    SSB_unf = SSB_equil;  // equilibrium unfished SSB using the benchmark averaged Recr_unf and benchmark averaged biology
+    temp2 = SSB_unf / Recr_unf; //  this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
+    SSBpR_virgin_4SRR = SSB_unf / Recr_unf;  //  update 
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_4SRR, temp2); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    SS2out << " bmarkSRR_&_bmarkbio - SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << temp2 << " " << SSBpR_virgin_4SRR << " equil: " << Equ_SpawnRecr_Result << endl<<endl;
+  }
   SS2out << "unfished values for SRR: SSB " << SSB_unf << " R " << Recr_unf << " SSBpR " << SSBpR_virgin_4SRR << endl;
   SS2out << "SPRloop Iter Bycatch Fmult F_std SSBpR YpR_dead YpR_dead*Recr YpR_ret*Recr Revenue Cost Profit SSB Recruits SSB/Bzero Tot_Catch ";
   for (f = 1; f <= Nfleet; f++)

From 806611fbc4d6278c240525dd79fbd5a9b566ab15 Mon Sep 17 00:00:00 2001
From: Rick-Methot-NOAA <richard.methot@noaa.gov>
Date: Tue, 11 Mar 2025 10:35:36 -0700
Subject: [PATCH 26/58] WIP

---
 SS_benchfore.tpl | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 4f86b30a..6ac46694 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -754,12 +754,11 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   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;
     Fishon = 0;
-    Recr_unf = Recr_virgin;
-    Do_Equil_Calc(Recr_unf);  // this calcs SSB using benchmark biology
-    temp1 = SSB_equil;  // equilibrium unfished SSB using the benchmark averaged Recr_unf and benchmark averaged biology
-    temp2 = temp1 / Recr_unf;
+//    Recr_unf = Recr_virgin;
+    Do_Equil_Calc(Recr_virgin);  // this calcs SSB
+    SSB_unf = SSB_equil;  // equilibrium unfished SSB using the benchmark averaged Recr_unf and benchmark averaged biology
+    temp2 = SSB_unf / Recr_virgin;
     Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SSBpR_virgin_4SRR, temp2); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
     report5 << " virgSRR_&_bmarkbio - SSB, R0, SPR0: " << SSB_virgin << " " << Recr_virgin << " "  << SSBpR_virgin << " " << SSBpR_virgin_4SRR << " equil: " << Equ_SpawnRecr_Result << endl<<endl;
   }
@@ -779,9 +778,12 @@ 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 << endl <<
             "input_SR_update_SSBpR0_rd: " << SR_update_SSBpR0_rd << ";  flag for updating SSBpR0_Bmark: " << SR_update_SSBpR0_bmark << endl;
-    Mgmt_quant(19) = Recr_unf;
-    Mgmt_quant(20) = SSB_unf;
-    Mgmt_quant(21) = SSB_unf;  //  placeholder to be replaced by SSB_HCR_infl
+    SSB_equil = Equ_SpawnRecr_Result(1);
+    dvariable R_equil = Equ_SpawnRecr_Result(2);
+    Mgmt_quant(19) = R_equil;
+    Do_Equil_Calc(R_equil);  // this calcs SSB using benchmark biology
+    Mgmt_quant(20) = SSB_equil;
+    Mgmt_quant(21) = SSB_equil;  //  placeholder to be replaced by SSB_HCR_infl
     Mgmt_quant(22) = SSB_virgin;
   }
   SR_parm_work(N_SRparm2 + 1) = SSB_unf;

From 8676e7ab4f077eed5c3c1fc4ce6e3f9950b58d93 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Thu, 13 Mar 2025 15:25:07 -0700
Subject: [PATCH 27/58] still a WIP

---
 SS_benchfore.tpl       | 129 +++++++++++++++++++++++------------------
 SS_param.tpl           |   4 +-
 SS_popdyn.tpl          |  23 ++++----
 SS_readcontrol_330.tpl |   5 ++
 SS_recruit.tpl         |   4 +-
 SS_write_report.tpl    |  22 +++----
 6 files changed, 103 insertions(+), 84 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 6ac46694..9e33d32c 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -10,8 +10,7 @@
 // SPR refers to spawner potential ratio which is the ratio of SSBpR at some level of F to SSBpR with F = 0
 
 // SSBpR_virgin is calculated in popdyn using the start year biology
-// SSBpR_virgin_4SRR  is passed to equil_spawn_recr.  _adj means could be updated if SR_update_SSBpR0_timeseries == 1.
-// Also used to get alpha in equil_spawn_recr B-H
+// SSBpR_virgin_4_SRR  used to get alpha in equil_spawn_recr B-H
 
 FUNCTION void setup_Benchmark()  // and forecast
   {
@@ -749,48 +748,58 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       SR_parm_work(j) = temp / (Bmark_Yr(10) - Bmark_Yr(9) + 1.);
     }
   }
-  Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SSBpR_virgin_4SRR, SSBpR_virgin); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-  report5 << endl << " virgin - SSB, R0, SPR0: " << SSB_virgin << " " << Recr_virgin << " "  << SSBpR_virgin << " " << SSBpR_virgin << " equil: " << Equ_SpawnRecr_Result << endl<<endl;
-  if (SR_update_SSBpR0_bmark == 0)  //  use virgin biology for the spawner-recruitment R0,h calculations in bmark
+
+  Recr_unf = mfexp(SR_parm_work(1));
+  Fishon = 0;
+  Do_Equil_Calc(Recr_unf);  // this calcs SSB as SSB_equil using benchmark biology
+  dvariable SPR_bench = SSB_equil / Recr_unf;  // SSBpR using bench biology
+
+  //  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
+//  if(bench_update_equil == 0) // legacy approach that omits recalc of equilibrium R,SSB
   {
-    Recr_unf = Recr_virgin;
-    Fishon = 0;
-//    Recr_unf = Recr_virgin;
-    Do_Equil_Calc(Recr_virgin);  // this calcs SSB
-    SSB_unf = SSB_equil;  // equilibrium unfished SSB using the benchmark averaged Recr_unf and benchmark averaged biology
-    temp2 = SSB_unf / Recr_virgin;
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SSBpR_virgin_4SRR, temp2); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    report5 << " virgSRR_&_bmarkbio - SSB, R0, SPR0: " << SSB_virgin << " " << Recr_virgin << " "  << SSBpR_virgin << " " << SSBpR_virgin_4SRR << " equil: " << Equ_SpawnRecr_Result << endl<<endl;
+    SSB_unf = SSB_equil;
+    SSB0_4_SRR = SSB_equil;
+    R0_4_SRR = Recr_unf;
+    report5 << " only SPR:  " << SSB_equil << " Recr: " << Recr_unf << " SPR: " << SSB0_4_SRR / R0_4_SRR << " bench SPR: " << SPR_bench << endl;
+   }
+//  else if (SR_update_SSBpR0_bmark == 0)  //  retain virgin SSBpR0 for SRR
+  {
+    // this is the correct approach.  It uses the same SRR as the time series and calculates an new equilibrium point using benchmark SPR
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SPR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    R0_4_SRR = Equ_SpawnRecr_Result(2);
+    SSB0_4_SRR = Equ_SpawnRecr_Result(1);
+    Do_Equil_Calc(R0_4_SRR);  // this calcs SSB as SSB_equil using benchmark biology
+    report5 << " use virgin SPR in SRR - SSB: " << SSB_virgin << " Recr: " << Recr_virgin << " SPR: " << SSB_virgin / Recr_virgin << " bench SPR: " << SPR_bench << " new equil: " << Equ_SpawnRecr_Result << " per_R_calc: " << SSB_equil << endl;
   }
-  else  // use benchmark biology in the spawner-recruitment R0,h calculations
+//  else  // use benchmark biology (aka _unf) for SSBpR0 calcs [incorrect approach, unless there are time-varying R0 or h parameters]
   {
-    Fishon = 0;
-    Recr_unf = mfexp(SR_parm_work(1));
-    Do_Equil_Calc(Recr_unf);  // this calcs SSB using benchmark biology
-    SSB_unf = SSB_equil;  // equilibrium unfished SSB using the benchmark averaged Recr_unf and benchmark averaged biology
-    SSBpR_unf = SSB_unf / Recr_unf; //  this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
-    SSBpR_virgin_4SRR = SSB_unf / Recr_unf;  //  update 
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_4SRR, SSBpR_unf); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    report5 << " bmarkSRR_&_bmarkbio - SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << SSBpR_unf << " " << SSBpR_virgin_4SRR << " equil: " << Equ_SpawnRecr_Result << endl<<endl;
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_equil, Recr_unf, SPR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    R0_4_SRR = Equ_SpawnRecr_Result(2);
+    SSB0_4_SRR = Equ_SpawnRecr_Result(1);
+    Do_Equil_Calc(R0_4_SRR);  // this calcs SSB as SSB_equil using benchmark biology
+    report5 << " use bench SPR in SRR - SSB:  " << SSB_equil << " Recr: " << Recr_unf << " SPR: " << SSB0_4_SRR / R0_4_SRR << " bench SPR: " << SPR_bench << " new equil: " << Equ_SpawnRecr_Result << " per_R_calc: " << SSB_equil << endl;
   }
+
   if (show_MSY == 1)
   {
+    SR_parm_work(N_SRparm2 + 1) = SSB0_4_SRR;
+    Mgmt_quant(1) = SSB_equil;
+    Mgmt_quant(2) = totbio;  // this is calculated in Do_Equil_Calc
+    Mgmt_quant(3) = smrybio;
+    Mgmt_quant(4) = Recr_unf;
     report5 << "SR_parms for benchmark: " << SR_parm_work << endl
             << "Benchmark biology averaged over years: " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl << endl <<
             "input_SR_update_SSBpR0_rd: " << SR_update_SSBpR0_rd << ";  flag for updating SSBpR0_Bmark: " << SR_update_SSBpR0_bmark << endl;
     SSB_equil = Equ_SpawnRecr_Result(1);
-    dvariable R_equil = Equ_SpawnRecr_Result(2);
-    Mgmt_quant(19) = R_equil;
-    Do_Equil_Calc(R_equil);  // this calcs SSB using benchmark biology
+    Mgmt_quant(19) = Equ_SpawnRecr_Result(2); // recruitment
     Mgmt_quant(20) = SSB_equil;
     Mgmt_quant(21) = SSB_equil;  //  placeholder to be replaced by SSB_HCR_infl
     Mgmt_quant(22) = SSB_virgin;
   }
-  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)
@@ -813,13 +822,13 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     last_calc = 0.;
     Fchange = -4.0;
 
-    equ_Recr = 1.0;
+    equ_Recr = 1.0;  // so calls to Do_Equil_Calc will return values of SSBpR
     Fishon = 0;
     dvariable SPR_target100;
     SPR_target100 = SPR_target * 100.;
 
-    Do_Equil_Calc(equ_Recr);
-    SSBpR_unf = SSB_unf / Recr_unf; //  this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
+    Do_Equil_Calc(equ_Recr);  //  where equ_Recr has been set to 1.0
+    SSBpR_unf = SSB_equil / equ_Recr; //  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)
     {
@@ -935,7 +944,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
 
     //  SPAWN-RECR:   calc equil spawn-recr in YPR; need to make this area-specific
     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_virgin_4SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, 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);
@@ -1050,7 +1059,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     if (rundetail > 0 && mceval_counter == 0 && show_MSY == 1)
       echoinput << "Calculated F0.1: " << Btgt_Fmult << endl;
     SSBpR_temp = SSB_equil;
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_4SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, 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
@@ -1074,20 +1083,26 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   else //  find F giving Btarget      SS_Label_720
   {
     // ******************************************************
+
+    if (SR_update_SSBpR0_bmark == 0)  //  use virgin biology for the spawner-recruitment R0,h calculations
+    {Btgttgt = BTGT_target * SSB_virgin;}
+    else
+    {Btgttgt = BTGT_target * SSB_unf;}
     if (show_MSY == 1)
     {
-      report5 << "#" << endl;
-  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;}
-  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++)
-        {
-          report5 << " SSB_Area:" << p << "_GP:" << gp;
-        }
-      report5 << endl;
+     report5 << "#" << endl;
+     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_virgin << " where SSBpR_unf = " << SSBpR_virgin << endl;}
+     else
+     {report5 << "Find_target_SSB/Bzero; where Bzero is for Bmark biology and updated SPR0: " << SSB_unf << " where SSBpR_unf = " << SSBpR_virgin_4_SRR << 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++)
+      {
+        report5 << " SSB_Area:" << p << "_GP:" << gp;
+      }
+    report5 << endl;
     }
 
     F1(1) = log(1.0e-3);
@@ -1107,8 +1122,6 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       Nloops = 28;
     }
 
-    Btgttgt = BTGT_target * SSB_unf;
-
     for (j = 0; j <= Nloops; j++) // loop find Btarget
     {
       if (fabs(Fchange) <= Closer2)
@@ -1146,7 +1159,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         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
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_4SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         yld1(ii) = Equ_SpawnRecr_Result(1);
       }
 
@@ -1186,7 +1199,7 @@ 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_4SRR << " Btgt " << Btgt << endl;
+//        " SSB_unf " << SSB_unf << " recr " <<Recr_unf<< " SSB_equil " << SSB_equil << " ssbpr_virginadj: " << SSBpR_virgin_4_SRR << " Btgt " << Btgt << endl;
       }
     } // end search loop
 
@@ -1367,7 +1380,7 @@ 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 / SSBpR_unf;
       SSBpR_temp = SSB_equil;
-      Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_4SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+      Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, 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;
@@ -1461,7 +1474,7 @@ 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 / SSBpR_unf;
           SSBpR_temp = SSB_equil;
-          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_4SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, 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;
@@ -1757,7 +1770,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         SPR_Btgt2 = SSB_equil / SSBpR_unf;
         //  SPAWN-RECR:   calc equil spawn-recr for Btarget calcs;  need to make area-specific
         SSBpR_temp = SSB_equil;
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_4SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         yld1(ii) = Equ_SpawnRecr_Result(1);
       }
 
@@ -2635,7 +2648,7 @@ FUNCTION void Get_Forecast()
               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 per recruit calculation
               if (fishery_on_off == 1)
               {
                 Fishon = 1;
@@ -3274,7 +3287,7 @@ FUNCTION void Get_Forecast()
               Fishon = 0;
               eq_yr = y;
               bio_yr = y;
-              Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation
+              Do_Equil_Calc(equ_Recr); //  call function to do per recruit calculation
               if (fishery_on_off == 1)
               {
                 Fishon = 1;
@@ -3696,7 +3709,7 @@ FUNCTION void Get_Forecast()
         equ_Recr = Recr_unf;
         bio_yr = y;
         Fishon = 0;
-        Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation
+        Do_Equil_Calc(equ_Recr); //  call function to do per recruit calculation
 
         Smry_Table(y, 11) = SSB_equil;
         Smry_Table(y, 13) = GenTime;
@@ -3709,7 +3722,7 @@ FUNCTION void Get_Forecast()
           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
+        Do_Equil_Calc(equ_Recr); //  call function to do per recruit 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);
diff --git a/SS_param.tpl b/SS_param.tpl
index 4af7af91..d174efc7 100644
--- a/SS_param.tpl
+++ b/SS_param.tpl
@@ -166,7 +166,9 @@ PARAMETER_SECTION
   number half_sigmaRsq;
   number sigmaR;
   number SSBpR_virgin;
-  number SSBpR_virgin_4SRR;
+  number SSB0_4_SRR;
+  number R0_4_SRR;
+  number SSBpR_virgin_4_SRR;  // value of SSB/R used in SRR
   number regime_change;
   number rho;
   number dirichlet_Parm;
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index fd3f7347..752cc348 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -342,9 +342,8 @@ FUNCTION void get_initial_conditions()
   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
+    Do_Equil_Calc(equ_Recr); //  call function to do per recruit calculation.  Returns SPR because R = 1.0
     SSBpR_virgin = SSB_equil; //  spawners per recruit.  Needed for Sr_fxn = 10
-    SSBpR_virgin_4SRR = 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 +354,8 @@ FUNCTION void get_initial_conditions()
 
       alpha = mfexp(SR_parm(3));
       beta = mfexp(SR_parm(4));
-      steepness = alpha * SSBpR_virgin_4SRR / (4. + alpha * SSBpR_virgin_4SRR);
-      Recr_virgin = 1. / beta * (alpha - (1. / SSBpR_virgin_4SRR));
+      steepness = alpha * SSBpR_virgin / (4. + alpha * SSBpR_virgin);
+      Recr_virgin = 1. / beta * (alpha - (1. / SSBpR_virgin));
 //      warning << " before AB_calcs " << "parm " << SR_parm(1) << " calc " << log(Recr_virgin) << endl;
       SR_parm(1) = log(Recr_virgin);
       SR_parm(2) = steepness;
@@ -378,9 +377,8 @@ FUNCTION void get_initial_conditions()
     exp_rec(eq_yr, 2) = Recr_virgin;
     exp_rec(eq_yr, 3) = Recr_virgin;
     exp_rec(eq_yr, 4) = Recr_virgin;
-    Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation
+    Do_Equil_Calc(equ_Recr); //  call function to do per recruit 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
     {
       SSB_unf = SSB_virgin;
@@ -536,7 +534,7 @@ FUNCTION void get_initial_conditions()
     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, SSBpR_virgin_4SRR, SSBpR_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;
 
@@ -1038,9 +1036,8 @@ FUNCTION void get_time_series()
           Fishon = 0;
           eq_yr = y;
           bio_yr = y;
-          Do_Equil_Calc(R0_use); //  call function to do equilibrium calculation with current year's biology and adjusted R0
+          Do_Equil_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
-          SSBpR_virgin_4SRR = SSB_use / R0_use;  //  update 
           if (fishery_on_off == 1)
           {
             Fishon = 1;
@@ -1498,9 +1495,8 @@ 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 per recruit calculation
           SSB_use = SSB_equil;
-          SSBpR_virgin_4SRR = SSB_use / R0_use;  //  update 
           if (fishery_on_off == 1)
           {
             Fishon = 1;
@@ -1791,7 +1787,7 @@ FUNCTION void get_time_series()
       equ_Recr = Recr_virgin;
       bio_yr = y;
       Fishon = 0;
-      Do_Equil_Calc(equ_Recr); //  call function to do equilibrium calculation with current year's biology
+      Do_Equil_Calc(equ_Recr); //  call function to do per recruit calculation with current year's biology
       Smry_Table(y, 11) = SSB_equil;
       Smry_Table(y, 13) = GenTime;
       if( SR_fxn == 10 )
@@ -1803,7 +1799,7 @@ FUNCTION void get_time_series()
         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
+      Do_Equil_Calc(equ_Recr); //  call function to do per recruit calculation with current year's biology and F
       if (STD_Yr_Reverse_Ofish(y) > 0)
       {
         SPR_std(STD_Yr_Reverse_Ofish(y)) = SSB_equil / Smry_Table(y, 11);
@@ -1834,6 +1830,7 @@ FUNCTION void get_time_series()
 
 //********************************************************************
  /*  SS_Label_FUNCTION 30 Do_Equil_Calc */
+ // This function does per recruit calculations, so produces an age composition that is in equilibrium with M+F
 FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
   {
   int t_base;
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index a4a8bbb5..8b1aea35 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1957,9 +1957,11 @@
 //  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
+  int bench_update_equil
  LOCAL_CALCS
   SR_update_SSBpR0_bmark = 0;
   SR_update_SSBpR0_timeseries = 0;
+  bench_update_equil = 0;
   echoinput<<SR_update_SSBpR0_rd<<"  #  controls effect of time-varying biology on spawner-recruitment updating" << endl;
  END_CALCS
 
@@ -2180,14 +2182,17 @@
   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;
+    bench_update_equil = 1;
     break;
   case 2:
     SR_update_SSBpR0_bmark = 1;
     SR_update_SSBpR0_timeseries = 0;
+    bench_update_equil = 0;
     break;
   case 3:
     SR_update_SSBpR0_bmark = 0;
     SR_update_SSBpR0_timeseries = 0;
+    bench_update_equil = 1;
     break;
   }
   echoinput << "SRupdate " << SR_update_parm << " use " << SR_update_SSBpR0_bmark << " rd " << SR_update_SSBpR0_rd<< endl;
diff --git a/SS_recruit.tpl b/SS_recruit.tpl
index 474e30ed..cd938550 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& SSBpR_virgin_use, const prevariable& SSBpR_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
@@ -282,7 +282,9 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
   dvariable SRZ_0;
   dvariable srz_min;
   dvariable SRZ_surv;
+  dvariable SSBpR_virgin_use;
 
+  SSBpR_virgin_use = SSB_virgin_use / Recr_virgin_use;  //  local instance of SSBpR_virgin_4_SRR
   steepness = SRparm(2); //  common usage but some different
   //  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)
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 51a21d98..2eae335a 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 / (SSBpR_virgin_4SRR * (1. - steepness));
+      alpha = 4.0 * steepness / (SSBpR_virgin_4_SRR * (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. / SSBpR_virgin_4SRR))) << endl;  //  virgin R0
-      SS2out << "steepness_derived: " << alpha * SSBpR_virgin_4SRR / (4. + alpha * SSBpR_virgin_4SRR) << endl;  // steepness virgin
+      SS2out << "ln(R0)_derived: " << log( 1. / beta * (alpha - (1. / SSBpR_virgin_4_SRR))) << endl;  //  virgin R0
+      SS2out << "steepness_derived: " << alpha * SSBpR_virgin_4_SRR / (4. + alpha * SSBpR_virgin_4_SRR) << endl;  // steepness virgin
       break;
     }
     case 8:
@@ -4733,7 +4733,6 @@ FUNCTION void SPR_profile()
   bio_t_base = styr + (bio_yr - styr) * nseas - 1;
 
   //  SPAWN-RECR:  call make_fecundity for benchmark bio for SPR loop
-  //  this code section that creates fecundity and selectivity seems antiquated; why is it different from the averages used for benchmark?
 
   for (s = 1; s <= nseas; s++)
   {
@@ -4745,7 +4744,9 @@ FUNCTION void SPR_profile()
       fec = Wt_Age_t(t, -2);
       SS2out << " repro_output for spr/ypr: " << fec(1) << endl;}
   }
+  SS2out << " stored - SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << SSBpR_virgin << " " << SSBpR_virgin_4_SRR<<endl;
 
+//  do not recalculate here so force using values from benchmark
   if (SR_update_SSBpR0_bmark == 0)  //  use virgin biology for the spawner-recruitment R0,h calculations in bmark
   {
     Recr_unf = Recr_virgin;
@@ -4755,8 +4756,8 @@ FUNCTION void SPR_profile()
     Do_Equil_Calc(Recr_unf);  // this calcs SSB using benchmark biology
     temp1 = SSB_equil;  // equilibrium unfished SSB using the benchmark averaged Recr_unf and benchmark averaged biology
     temp2 = temp1 / Recr_unf;
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SSBpR_virgin_4SRR, temp2); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    SS2out << " virgSRR_&_bmarkbio - SSB, R0, SPR0: " << SSB_virgin << " " << Recr_virgin << " "  << SSBpR_virgin << " " << SSBpR_virgin_4SRR << " equil: " << Equ_SpawnRecr_Result << endl<<endl;
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, temp2); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    SS2out << " virgSRR_&_bmarkbio - SSB, R0, SPR0: " << SSB_virgin << " " << Recr_virgin << " "  << SSBpR_virgin << " " << SSBpR_virgin_4_SRR << " equil: " << Equ_SpawnRecr_Result << endl<<endl;
   }
   else  // use benchmark biology in the spawner-recruitment R0,h calculations
   {
@@ -4765,11 +4766,10 @@ FUNCTION void SPR_profile()
     Do_Equil_Calc(Recr_unf);  // this calcs SSB using benchmark biology
     SSB_unf = SSB_equil;  // equilibrium unfished SSB using the benchmark averaged Recr_unf and benchmark averaged biology
     temp2 = SSB_unf / Recr_unf; //  this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
-    SSBpR_virgin_4SRR = SSB_unf / Recr_unf;  //  update 
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_4SRR, temp2); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    SS2out << " bmarkSRR_&_bmarkbio - SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << temp2 << " " << SSBpR_virgin_4SRR << " equil: " << Equ_SpawnRecr_Result << endl<<endl;
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, temp2); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    SS2out << " bmarkSRR_&_bmarkbio - SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << temp2 << " " << SSBpR_virgin_4_SRR << " equil: " << Equ_SpawnRecr_Result << endl<<endl;
   }
-  SS2out << "unfished values for SRR: SSB " << SSB_unf << " R " << Recr_unf << " SSBpR " << SSBpR_virgin_4SRR << endl;
+  SS2out << "unfished values for SRR: SSB " << SSB_unf << " R " << Recr_unf << " SSBpR " << SSBpR_virgin_4_SRR << endl;
   SS2out << "SPRloop Iter Bycatch Fmult F_std SSBpR YpR_dead YpR_dead*Recr YpR_ret*Recr Revenue Cost Profit SSB Recruits SSB/Bzero Tot_Catch ";
   for (f = 1; f <= Nfleet; f++)
   {
@@ -4927,7 +4927,7 @@ FUNCTION void SPR_profile()
         Do_Equil_Calc(equ_Recr);
         //  SPAWN-RECR:   calc equil spawn-recr in the SPR loop
         SSBpR_temp = SSB_equil;
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_unf, Recr_unf, SSBpR_virgin_4SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, 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 e8953f8e771f62baa42a6a3da108912f4e784635 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Fri, 14 Mar 2025 11:42:52 -0700
Subject: [PATCH 28/58] add backward compat flag to starter

---
 SS_readstarter.tpl | 16 ++++++++++++++++
 SS_write_ssnew.tpl |  1 +
 2 files changed, 17 insertions(+)

diff --git a/SS_readstarter.tpl b/SS_readstarter.tpl
index c9b7724e..7406f6b8 100644
--- a/SS_readstarter.tpl
+++ b/SS_readstarter.tpl
@@ -705,6 +705,7 @@
   int ender;
   int irand_seed;
   int irand_seed_rd;
+  int TV_bio_compat;  // flag in 3.30.24 for impact of timevary biology on benchmark SRR calculations
   int F_std_multi; // for multi-year averaging of F_std
   int F_std_log; // for log(ratio) of F_std
   int F_std_basis;
@@ -806,6 +807,21 @@
           echoinput << "random number seed:  " << irand_seed << endl;
           tempin = 0;
         }
+
+        echoinput << "now read flag for dealing with impact of time-varying biology on benchmark SRR calculations" << endl;
+        *(ad_comm::global_datafile) >> tempin;
+        if (tempin == 3.30)  // old format file that does not provide input
+        {
+          ender = 1;
+          TV_bio_compat = 0;
+        }
+        else  // new input beginning 3.30.24
+        {
+          TV_bio_compat = int(tempin);
+          echoinput << "Compatibility flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs:  " << TV_bio_compat << endl;
+          tempin = 0;
+        }
+
         if (ender == 0)
         {
           *(ad_comm::global_datafile) >> tempin;
diff --git a/SS_write_ssnew.tpl b/SS_write_ssnew.tpl
index 0d4ad371..5e79c37a 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -1564,6 +1564,7 @@ FUNCTION void write_nucontrol()
   NuStart << double(mcmc_output_detail) + MCMC_bump << " # MCMC output detail: integer part (0=default; 1=adds obj func components; 2= +write_report_for_each_mceval); and decimal part (added to SR_LN(R0) on first call to mcmc)" << endl;
   NuStart << ALK_tolerance << " # ALK tolerance ***disabled in code" << endl;
   NuStart << irand_seed_rd << " # random number seed for bootstrap data (-1 to use long(time) as seed): # " << irand_seed << endl;
+  NuStart << TV_bio_compat << " # Compatibility flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs >=3.30.24" << endl;
   NuStart << "3.30 # check value for end of file and for version control" << endl;
   NuStart.close();
 

From 5bcfa050b63fc76d398230b9ed1bec1d69447b34 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Thu, 20 Mar 2025 15:56:14 -0700
Subject: [PATCH 29/58] WIP - new approach not showing difference

---
 SS_benchfore.tpl       | 146 ++++++++++++++++++++++++++++-------------
 SS_param.tpl           |   2 +-
 SS_popdyn.tpl          |  14 ++--
 SS_readcontrol_330.tpl |  55 +---------------
 SS_readstarter.tpl     |   8 +--
 SS_write_report.tpl    |   7 +-
 SS_write_ssnew.tpl     |   8 +--
 7 files changed, 124 insertions(+), 116 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 9e33d32c..81a2a327 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -646,7 +646,6 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
 
       //  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)
       {
         {
@@ -749,54 +748,107 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     }
   }
 
-  Recr_unf = mfexp(SR_parm_work(1));
+ /*  
+ Early thoughts: 
+ 1 #  SR_update_SSBpR0
+  #  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 (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
+
+ Flags:
+  timevary_MG_firstyr == YrMax  // means that no biology is time-varying
+  timevary_parm_start_SR > 0 //  means that R0 or h (i.e. any except regime, sigmaR, autocorr) is time-varying, so SSBpR0 gets updated for time series and for bench
+  timevary_bio_4SRR is new user selected flag:  0 for legacy, vs 1 for improved use of timevary biology in SRR calcs
+
+ Legacy approach:
+ SSBpR0 set at start year using start year biology
+ SSBpR0 updated during time series if there is time-varying R0, but does not call equil_spawn_recr_calc
+ SSBpR with benchmark biology used in benchmark calculations 
+ SSBpR0 for benchmark always uses bench biology, which is incorrect
+ SSB_bench (aka SSB_unf) does not call equil_spawn_recr_calc, it is just R * SSBpR, so is incomplete accounting for effect of timevary bio
+ Btgttgt is a fraction of SSB_bench (no options)
+ Btgttgt2 can be fraction of SSB_MSY or fraction of SSB_virgin, but not SSB_bench
+ HCR inflection is a fraction of SSB_bench (no options)
+ depletion basis is user-selected as SSB_virgin or SSB_msy
+ SSB_msy uses equil_spawn_recr_calc in its creation, but SSB_bench does not.  So they are inconsistent
+ none of the above is an issue if there is no timevarying biology
+ -------
+ Improved approach
+ SSBpR0 set at start year using start year biology
+ SSBpR0 updated during time series if there is time-varying R0; PLUS NEW: equil_spawn_recr_calc called to get new equilibrium R0, SSB0
+ SSBpR0 for benchmark stays at virgin unless timevary_bio_4SRR == 0, or if timevary_parm_start_SR > 0
+ Btgttgt can now use either frac*SSB_bench or frac*SSB_virgin  
+ Btgttgt2 can be fraction of SSB_MSY, of SSB_virgin, or of SSB_bench
+ HCR inflection adds option to use SSB_virgin or SSB_bench
+ depletion adds option to use SSB_bench
+ */
+  Recr_unf = mfexp(SR_parm_work(1));  // R0 to be used
   Fishon = 0;
-  Do_Equil_Calc(Recr_unf);  // this calcs SSB as SSB_equil using benchmark biology
-  dvariable SPR_bench = SSB_equil / Recr_unf;  // SSBpR using bench biology
-
-  //  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
-//  if(bench_update_equil == 0) // legacy approach that omits recalc of equilibrium R,SSB
-  {
-    SSB_unf = SSB_equil;
-    SSB0_4_SRR = SSB_equil;
-    R0_4_SRR = Recr_unf;
-    report5 << " only SPR:  " << SSB_equil << " Recr: " << Recr_unf << " SPR: " << SSB0_4_SRR / R0_4_SRR << " bench SPR: " << SPR_bench << endl;
-   }
-//  else if (SR_update_SSBpR0_bmark == 0)  //  retain virgin SSBpR0 for SRR
+  Do_Equil_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
+  dvariable SSBpR_bench = SSB_equil / Recr_unf;
+
+  if( timevary_MG_firstyr == YrMax && WTage_rd == 0)  // no time-varying biology
   {
-    // this is the correct approach.  It uses the same SRR as the time series and calculates an new equilibrium point using benchmark SPR
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SPR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    R0_4_SRR = Equ_SpawnRecr_Result(2);
-    SSB0_4_SRR = Equ_SpawnRecr_Result(1);
-    Do_Equil_Calc(R0_4_SRR);  // this calcs SSB as SSB_equil using benchmark biology
-    report5 << " use virgin SPR in SRR - SSB: " << SSB_virgin << " Recr: " << Recr_virgin << " SPR: " << SSB_virgin / Recr_virgin << " bench SPR: " << SPR_bench << " new equil: " << Equ_SpawnRecr_Result << " per_R_calc: " << SSB_equil << endl;
+    SSB0_4_SRR = SSB_virgin;
+    R0_4_SRR = Recr_virgin;
+    SSB_unf = SSB_equil;  //  should this also depend on timevary_parm_start_SR > 0???
   }
-//  else  // use benchmark biology (aka _unf) for SSBpR0 calcs [incorrect approach, unless there are time-varying R0 or h parameters]
+  else  //  there is some timevary biology, with any WTage_rd == 1 qualifying as timevarying without actually chacking for different values in diff years
   {
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_equil, Recr_unf, SPR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    R0_4_SRR = Equ_SpawnRecr_Result(2);
-    SSB0_4_SRR = Equ_SpawnRecr_Result(1);
-    Do_Equil_Calc(R0_4_SRR);  // this calcs SSB as SSB_equil using benchmark biology
-    report5 << " use bench SPR in SRR - SSB:  " << SSB_equil << " Recr: " << Recr_unf << " SPR: " << SSB0_4_SRR / R0_4_SRR << " bench SPR: " << SPR_bench << " new equil: " << Equ_SpawnRecr_Result << " per_R_calc: " << SSB_equil << endl;
+    if( timevary_bio_4SRR == 0)  // legacy approach;  this switch is read from starter.ss
+    {
+      warnstream << "There is timevary biology and the legacy approach to benchmark calculations is being used; user should be aware";
+      write_message (WARN, 0);
+      if(timevary_parm_start_SR == 0)  // no timevary SRR parms
+      {
+        SSB_unf = SSB_equil;
+        R0_4_SRR = Recr_unf;
+        SSB0_4_SRR = SSB_equil;  // this is legacy, but incorrect, as it moves equil off the SRR, rather than along the SRR
+        //  Equil_Spawn_Recr_Fxn will be called in more complete approach to use SSBpR_bench to move along the SRR
+      }
+      else // there are timevary SRR parms.  Legacy code is same
+      {
+        SSB_unf = SSB_equil;
+        R0_4_SRR = Recr_unf;
+        SSB0_4_SRR = SSB_equil;  // this is legacy, but incorrect, as it moves equil off the SRR, rather than along the SRR
+        SSBpR_bench = SSB0_4_SRR / R0_4_SRR;
+      }
+      report5 << " legacy: Recr: " << R0_4_SRR << " SSB: " << SSB0_4_SRR << " bench SPR: " << SSBpR_bench << endl;
+    }
+
+    else  // more complete approach to time vary biology will be used (introduced in 3.30.24)
+    {
+      if(timevary_parm_start_SR == 0)  // no timevary SRR parms, so use SSB_virgin, Recr_virgin which will create virgin SSBpR0 
+      {
+        SSB0_4_SRR = SSB_virgin;
+        R0_4_SRR = Recr_virgin;
+        //  get new equilibrium point using original SRR and SSBpR_bench
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        SSB_unf = Equ_SpawnRecr_Result(1);
+        Recr_unf = Equ_SpawnRecr_Result(2);
+        report5 << " use virgin SSBpR0 in SRR - SSB: " << SSB_virgin << " Recr: " << Recr_virgin << " SPR: " << SSB_virgin / Recr_virgin << " bench SPR: " << SSBpR_bench << " new equil: " << Equ_SpawnRecr_Result << endl;
+      }
+      else  //  use benchmark quantities for SRR
+      {
+        //  Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_equil, Recr_unf, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+      }
+      Do_Equil_Calc(R0_4_SRR);  // this calcs SSBpR and returns it as SSB_equil using benchmark biology
+      SSB_unf = SSB_equil;
+      report5 << " CHECK! - SSB_unf and updated equilibrium SSB0_4_SRR: " << SSB_unf << " " << SSB0_4_SRR << endl;
+    }
   }
 
   if (show_MSY == 1)
   {
     SR_parm_work(N_SRparm2 + 1) = SSB0_4_SRR;
-    Mgmt_quant(1) = SSB_equil;
+    Mgmt_quant(1) = SSB_unf;
     Mgmt_quant(2) = totbio;  // this is calculated in Do_Equil_Calc
     Mgmt_quant(3) = smrybio;
     Mgmt_quant(4) = Recr_unf;
     report5 << "SR_parms for benchmark: " << SR_parm_work << endl
-            << "Benchmark biology averaged over years: " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl << endl <<
-            "input_SR_update_SSBpR0_rd: " << SR_update_SSBpR0_rd << ";  flag for updating SSBpR0_Bmark: " << SR_update_SSBpR0_bmark << endl;
-    SSB_equil = Equ_SpawnRecr_Result(1);
-    Mgmt_quant(19) = Equ_SpawnRecr_Result(2); // recruitment
-    Mgmt_quant(20) = SSB_equil;
-    Mgmt_quant(21) = SSB_equil;  //  placeholder to be replaced by SSB_HCR_infl
+            << "Benchmark biology averaged over years: " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl << endl;
+    Mgmt_quant(19) = R0_4_SRR; // recruitment
+    Mgmt_quant(20) = SSB_unf;
+    Mgmt_quant(21) = SSB_unf;  //  placeholder to be replaced by SSB_HCR_infl
     Mgmt_quant(22) = SSB_virgin;
   }
 
@@ -1084,14 +1136,14 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   {
     // ******************************************************
 
-    if (SR_update_SSBpR0_bmark == 0)  //  use virgin biology for the spawner-recruitment R0,h calculations
-    {Btgttgt = BTGT_target * SSB_virgin;}
+    if (timevary_bio_4SRR == 0)
+    {Btgttgt = BTGT_target * SSB_unf;}  //  current SS3 approach
     else
     {Btgttgt = BTGT_target * SSB_unf;}
     if (show_MSY == 1)
     {
      report5 << "#" << endl;
-     if (SR_update_SSBpR0_bmark == 0)  //  use virgin biology for the spawner-recruitment R0,h calculations
+     if (timevary_bio_4SRR == 0)  //  use virgin biology for the spawner-recruitment R0,h calculations
      {report5 << "Find_target_SSB/Bzero; where Bzero is Virgin SSB:" << SSB_virgin << " where SSBpR_unf = " << SSBpR_virgin << endl;}
      else
      {report5 << "Find_target_SSB/Bzero; where Bzero is for Bmark biology and updated SPR0: " << SSB_unf << " where SSBpR_unf = " << SSBpR_virgin_4_SRR << endl;}
@@ -1852,8 +1904,9 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   {
     report5 << "#" << endl
             << "Management_report" << endl;
-    report5 << "Steepness_Recr_SSB_virgin(R0) " << SR_parm(2) << " " << Recr_virgin << " " << SSB_virgin << endl;
-    report5 << "Steepness_Recr_SSB_benchmark " << SR_parm_work(2) << " " << Recr_unf << " " << SSB_unf << endl;
+    report5 << "Virgin: Steepness_Recr_SSB " << SR_parm(2) << " " << Recr_virgin << " " << SSB_virgin << endl;
+    report5 << "Bench:  Steepness_Recr_SSB " << SR_parm_work(2) << " " << R0_4_SRR << " " << SSB0_4_SRR << endl;
+    report5 << "unf  :  Steepness_Recr_SSB " << SR_parm_work(2) << " " << Recr_unf << " " << SSB_unf << endl;
     report5 << "#" << endl
             << "Summary_age: " << Smry_Age << endl;
     report5 << "#_Bmark_years: beg_bio, end_bio, beg_selex, end_selex, beg_relF, end_relF, beg_recr_dist, end_recr_dist, beg_SRparm, end_SRparm" << endl
@@ -2636,7 +2689,7 @@ FUNCTION void Get_Forecast()
             }
             //  SPAWN-RECR:   get recruitment in forecast;  needs to be area-specific
             // SR_fxn
-            if (SR_update_SSBpR0_timeseries == 0) //  R0 is not time-varying
+            if (timevary_parm_start_SR == 0) //  R0 is not time-varying
             {
               R0_use = Recr_virgin;
               SSB_use = SSB_virgin;
@@ -2649,7 +2702,8 @@ FUNCTION void Get_Forecast()
               eq_yr = y;
               bio_yr = y;
               Do_Equil_Calc(R0_use); //  call function to do per recruit calculation
-              if (fishery_on_off == 1)
+          //  should call equil_spawn_recr_fxn here to get updated equilibrium with the new SSB/R
+          if (fishery_on_off == 1)
               {
                 Fishon = 1;
               }
@@ -2660,6 +2714,7 @@ FUNCTION void Get_Forecast()
               SSB_use = SSB_equil;
             }
             Recruits = Spawn_Recr(SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr
+            warning << y << " SSB0: " << SSB_use << " R0: " << R0_use << " SSB_curr: " << SSB_current << " R: " << Recruits << endl;
             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
             {
@@ -3275,7 +3330,7 @@ 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_SSBpR0_timeseries == 0) //  R0 is not time-varying
+            if (timevary_parm_start_SR == 0) //  R0 is not time-varying
             {
               R0_use = Recr_virgin;
               SSB_use = SSB_virgin;
@@ -3288,7 +3343,8 @@ FUNCTION void Get_Forecast()
               eq_yr = y;
               bio_yr = y;
               Do_Equil_Calc(equ_Recr); //  call function to do per recruit calculation
-              if (fishery_on_off == 1)
+          //  should call equil_spawn_recr_fxn here to get updated equilibrium with the new SSB/R
+          if (fishery_on_off == 1)
               {
                 Fishon = 1;
               }
diff --git a/SS_param.tpl b/SS_param.tpl
index d174efc7..e8d532c5 100644
--- a/SS_param.tpl
+++ b/SS_param.tpl
@@ -247,7 +247,7 @@ PARAMETER_SECTION
   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 R0_use
 
   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
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 752cc348..e58d4627 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -382,10 +382,10 @@ FUNCTION void get_initial_conditions()
     if(Do_Benchmark==0)  // assign values that would be created in benchmark section
     {
       SSB_unf = SSB_virgin;
-      Mgmt_quant(1) = SSB_unf;  //  can be overwritten in benchmark by updated SSB_unf
-      Recr_unf = Recr_virgin;
-      Mgmt_quant(2) = totbio;  //  from equil calcs
-      Mgmt_quant(3) = smrybio;  //  from equil calcs
+      Mgmt_quant(1) = SSB_unf; //  will be overwritten in benchmark
+      Recr_unf = Recr_virgin;  //  will be overwritten in benchmark
+      Mgmt_quant(2) = totbio;  //  from Do_Equil_Calc
+      Mgmt_quant(3) = smrybio;  //  from Do_Equil_Calc
       Mgmt_quant(4) = Recr_virgin;
     }
     Smry_Table(styr - 2, 1) = totbio; //  from equil calcs
@@ -1024,7 +1024,7 @@ 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_SSBpR0_timeseries == 0) //  SRparm are not time-varying
+        if (timevary_parm_start_SR == 0) //  SRparm are not time-varying
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
@@ -1038,6 +1038,7 @@ FUNCTION void get_time_series()
           bio_yr = y;
           Do_Equil_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
+          //  should call equil_spawn_recr_fxn here to get updated equilibrium with the new SSB/R
           if (fishery_on_off == 1)
           {
             Fishon = 1;
@@ -1484,7 +1485,7 @@ 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_SSBpR0_timeseries == 0) //  SR parms are not time-varying
+        if (timevary_parm_start_SR == 0) //  SR parms are not time-varying
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
@@ -1497,6 +1498,7 @@ FUNCTION void get_time_series()
           bio_yr = y;
           Do_Equil_Calc(R0_use); //  call function to do per recruit calculation
           SSB_use = SSB_equil;
+          //  should call equil_spawn_recr_fxn here to get updated equilibrium with the new SSB/R
           if (fishery_on_off == 1)
           {
             Fishon = 1;
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 8b1aea35..f49d1c2c 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1950,20 +1950,7 @@
 !!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 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
-  int bench_update_equil
- LOCAL_CALCS
-  SR_update_SSBpR0_bmark = 0;
-  SR_update_SSBpR0_timeseries = 0;
-  bench_update_equil = 0;
-  echoinput<<SR_update_SSBpR0_rd<<"  #  controls effect of time-varying biology on spawner-recruitment updating" << endl;
- END_CALCS
+  init_int itemp;
 
 //   echoinput<<sigmaR_dendep<<"  #  future feature:  0/1 to make realized sigmaR a function of SR curvature"<<endl;
 
@@ -1981,12 +1968,11 @@
   int SR_env_target
   int SR_autocorr;  // will be calculated later
 
-  int timevary_parm_start_SR;
+  int timevary_parm_start_SR;  //   == 0 means that no relevant parms are timevarying
   int firstSRparm;
   int timevary_parm_cnt_SR;
   ivector timevary_SRparm(styr-3,YrMax+1);
   ivector SR_parm_timevary(1,N_SRparm2);
-  int SR_update_parm  // 0/1 flag to control updating of SPR0 for timevary biology 
 
  LOCAL_CALCS
   // clang-format on
@@ -1998,7 +1984,6 @@
   SR_parm_timevary.initialize();
   SR_env_link = 0;
   SR_env_target = 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)
@@ -2150,11 +2135,9 @@
         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_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;
   if (timevary_parm_start_SR > 0)
   {
@@ -2164,38 +2147,6 @@
     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;
-    bench_update_equil = 1;
-    break;
-  case 2:
-    SR_update_SSBpR0_bmark = 1;
-    SR_update_SSBpR0_timeseries = 0;
-    bench_update_equil = 0;
-    break;
-  case 3:
-    SR_update_SSBpR0_bmark = 0;
-    SR_update_SSBpR0_timeseries = 0;
-    bench_update_equil = 1;
-    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
diff --git a/SS_readstarter.tpl b/SS_readstarter.tpl
index 7406f6b8..eb978211 100644
--- a/SS_readstarter.tpl
+++ b/SS_readstarter.tpl
@@ -705,7 +705,7 @@
   int ender;
   int irand_seed;
   int irand_seed_rd;
-  int TV_bio_compat;  // flag in 3.30.24 for impact of timevary biology on benchmark SRR calculations
+  int timevary_bio_4SRR;  // flag in 3.30.24 for impact of timevary biology on benchmark SRR calculations
   int F_std_multi; // for multi-year averaging of F_std
   int F_std_log; // for log(ratio) of F_std
   int F_std_basis;
@@ -813,12 +813,12 @@
         if (tempin == 3.30)  // old format file that does not provide input
         {
           ender = 1;
-          TV_bio_compat = 0;
+          timevary_bio_4SRR = 0;
         }
         else  // new input beginning 3.30.24
         {
-          TV_bio_compat = int(tempin);
-          echoinput << "Compatibility flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs:  " << TV_bio_compat << endl;
+          timevary_bio_4SRR = int(tempin);
+          echoinput << "Compatibility flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs:  " << timevary_bio_4SRR << endl;
           tempin = 0;
         }
 
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 2eae335a..a30f85ca 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -4747,7 +4747,8 @@ FUNCTION void SPR_profile()
   SS2out << " stored - SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << SSBpR_virgin << " " << SSBpR_virgin_4_SRR<<endl;
 
 //  do not recalculate here so force using values from benchmark
-  if (SR_update_SSBpR0_bmark == 0)  //  use virgin biology for the spawner-recruitment R0,h calculations in bmark
+ /*
+  if (timevary_bio_4SRR == 0)  //  use virgin biology for the spawner-recruitment R0,h calculations in bmark
   {
     Recr_unf = Recr_virgin;
     SSB_unf = SSB_virgin;
@@ -4769,7 +4770,9 @@ FUNCTION void SPR_profile()
     Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, temp2); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
     SS2out << " bmarkSRR_&_bmarkbio - SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << temp2 << " " << SSBpR_virgin_4_SRR << " equil: " << Equ_SpawnRecr_Result << endl<<endl;
   }
-  SS2out << "unfished values for SRR: SSB " << SSB_unf << " R " << Recr_unf << " SSBpR " << SSBpR_virgin_4_SRR << endl;
+ */
+  // Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); 
+  SS2out << "unfished values for SRR: SSB " << SSB0_4_SRR << " R " << R0_4_SRR << " SSBpR " << "  SSBpR: " << SSB0_4_SRR / R0_4_SRR << endl;
   SS2out << "SPRloop Iter Bycatch Fmult F_std SSBpR YpR_dead YpR_dead*Recr YpR_ret*Recr Revenue Cost Profit SSB Recruits SSB/Bzero Tot_Catch ";
   for (f = 1; f <= Nfleet; f++)
   {
diff --git a/SS_write_ssnew.tpl b/SS_write_ssnew.tpl
index 5e79c37a..b9e19cb1 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -1564,7 +1564,7 @@ FUNCTION void write_nucontrol()
   NuStart << double(mcmc_output_detail) + MCMC_bump << " # MCMC output detail: integer part (0=default; 1=adds obj func components; 2= +write_report_for_each_mceval); and decimal part (added to SR_LN(R0) on first call to mcmc)" << endl;
   NuStart << ALK_tolerance << " # ALK tolerance ***disabled in code" << endl;
   NuStart << irand_seed_rd << " # random number seed for bootstrap data (-1 to use long(time) as seed): # " << irand_seed << endl;
-  NuStart << TV_bio_compat << " # Compatibility flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs >=3.30.24" << endl;
+  NuStart << timevary_bio_4SRR << " # Compatibility flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs >=3.30.24" << endl;
   NuStart << "3.30 # check value for end of file and for version control" << endl;
   NuStart.close();
 
@@ -2138,11 +2138,7 @@ 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 << 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 << " 0 #  not_used" << 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 013a176bbe246c43cef0d12d1bfa1a641bea11cb Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Fri, 21 Mar 2025 16:03:00 -0700
Subject: [PATCH 30/58] by jove, I think he did it

---
 SS_benchfore.tpl       | 17 ++++++++---------
 SS_objfunc.tpl         | 11 +++++++++++
 SS_readcontrol_330.tpl |  8 ++++----
 SS_write_report.tpl    | 25 -------------------------
 4 files changed, 23 insertions(+), 38 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 81a2a327..3a61921d 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -801,8 +801,9 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       if(timevary_parm_start_SR == 0)  // no timevary SRR parms
       {
         SSB_unf = SSB_equil;
-        R0_4_SRR = Recr_unf;
+        R0_4_SRR = Recr_unf;  // same as Recr_virgin because no timevary SRparms
         SSB0_4_SRR = SSB_equil;  // this is legacy, but incorrect, as it moves equil off the SRR, rather than along the SRR
+        SSBpR_bench = SSB0_4_SRR / R0_4_SRR;
         //  Equil_Spawn_Recr_Fxn will be called in more complete approach to use SSBpR_bench to move along the SRR
       }
       else // there are timevary SRR parms.  Legacy code is same
@@ -831,7 +832,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       {
         //  Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_equil, Recr_unf, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
       }
-      Do_Equil_Calc(R0_4_SRR);  // this calcs SSBpR and returns it as SSB_equil using benchmark biology
+      Do_Equil_Calc(Recr_unf);  // this calcs SSBpR and returns it as SSB_equil using benchmark biology and the updated equil Recr
       SSB_unf = SSB_equil;
       report5 << " CHECK! - SSB_unf and updated equilibrium SSB0_4_SRR: " << SSB_unf << " " << SSB0_4_SRR << endl;
     }
@@ -846,9 +847,9 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     Mgmt_quant(4) = Recr_unf;
     report5 << "SR_parms for benchmark: " << SR_parm_work << endl
             << "Benchmark biology averaged over years: " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl << endl;
-    Mgmt_quant(19) = R0_4_SRR; // recruitment
-    Mgmt_quant(20) = SSB_unf;
-    Mgmt_quant(21) = SSB_unf;  //  placeholder to be replaced by SSB_HCR_infl
+    Mgmt_quant(19) = SSB_unf;  // placeholder for depletion denominator
+    Mgmt_quant(20) = SSB_unf;  //  placeholder to be replaced by SSB_HCR_infl
+    Mgmt_quant(21) = SSB_unf;
     Mgmt_quant(22) = SSB_virgin;
   }
 
@@ -2259,7 +2260,7 @@ FUNCTION void Get_Forecast()
       H4010_top = H4010_top_rd;
     }
 
-    Mgmt_quant(21) = H4010_top * HCR_anchor;
+    Mgmt_quant(20) = HCR_anchor;
     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) << endl
@@ -2714,7 +2715,6 @@ FUNCTION void Get_Forecast()
               SSB_use = SSB_equil;
             }
             Recruits = Spawn_Recr(SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr
-            warning << y << " SSB0: " << SSB_use << " R0: " << R0_use << " SSB_curr: " << SSB_current << " R: " << Recruits << endl;
             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
             {
@@ -3779,9 +3779,8 @@ FUNCTION void Get_Forecast()
         }
         Fishon = 1;
         Do_Equil_Calc(equ_Recr); //  call function to do per recruit 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);
+          {SPR_std(STD_Yr_Reverse_Ofish(y)) = SSB_equil / Smry_Table(y, 11);}
         Smry_Table(y, 9) = totbio;
         Smry_Table(y, 10) = smrybio;
         Smry_Table(y, 12) = SSB_equil;
diff --git a/SS_objfunc.tpl b/SS_objfunc.tpl
index 82b91498..474153ee 100644
--- a/SS_objfunc.tpl
+++ b/SS_objfunc.tpl
@@ -1187,21 +1187,25 @@ FUNCTION void Process_STDquant()
     case 1:
     {
       depletion /= (depletion_level * SSB_virgin);
+      Mgmt_quant(19) = SSB_virgin;
       break;
     }
     case 2:
     {
       depletion /= (depletion_level * Bmsy);
+      Mgmt_quant(19) = Bmsy;
       break;
     }
     case 3:
     {
       depletion /= (depletion_level * SSB_yr(styr));
+      Mgmt_quant(19) = SSB_yr(styr);
       break;
     }
     case 4:
     {
       depletion /= (depletion_level * SSB_yr(endyr));
+      Mgmt_quant(19) = SSB_yr(endyr);
       break;
     }
     case 5:  //  dynamic Bzero
@@ -1213,6 +1217,13 @@ FUNCTION void Process_STDquant()
         depletion(STD_Yr_Reverse_Dep(y)) /= ( depletion_level * Extra_Std(Do_Dyn_Bzero + y - (styr - 2)));
 //        warning<<depletion(STD_Yr_Reverse_Dep(y))<<endl;
       }
+      Mgmt_quant(19) = 1.;
+      break;
+    }
+    case 6:  // depletion based on benchmark unfished SSB
+    {
+      depletion /= (depletion_level * SSB0_4_SRR);
+      Mgmt_quant(19) = SSB0_4_SRR;
       break;
     }
   }
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index f49d1c2c..ced24029 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -6635,19 +6635,19 @@
     j++;
     active_parm(CoVar_Count) = j;
 // add quantities needed when time-vary life history is used; but report here for all cases; elements 18-21 of mgmt_quant
-    ParmLabel += "Recr_MSY_bmarkbio" + CRLF(1);
+    ParmLabel += "18.Recr_MSY_bmarkbio" + CRLF(1);
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
-    ParmLabel += "Recr_unfished_bmarkbio" + CRLF(1);
+    ParmLabel += "19.Depletion_denom" + CRLF(1);
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
-    ParmLabel += "SSB_unfished_bmarkbio" + CRLF(1);
+    ParmLabel += "20.HCR_anchor" + CRLF(1);
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
-    ParmLabel += "SSB_HCR_infl" + CRLF(1);
+    ParmLabel += "ignore" + CRLF(1);
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index a30f85ca..212f5ed1 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -4747,31 +4747,6 @@ FUNCTION void SPR_profile()
   SS2out << " stored - SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << SSBpR_virgin << " " << SSBpR_virgin_4_SRR<<endl;
 
 //  do not recalculate here so force using values from benchmark
- /*
-  if (timevary_bio_4SRR == 0)  //  use virgin biology for the spawner-recruitment R0,h calculations in bmark
-  {
-    Recr_unf = Recr_virgin;
-    SSB_unf = SSB_virgin;
-    Fishon = 0;
-    Recr_unf = Recr_virgin;
-    Do_Equil_Calc(Recr_unf);  // this calcs SSB using benchmark biology
-    temp1 = SSB_equil;  // equilibrium unfished SSB using the benchmark averaged Recr_unf and benchmark averaged biology
-    temp2 = temp1 / Recr_unf;
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, temp2); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    SS2out << " virgSRR_&_bmarkbio - SSB, R0, SPR0: " << SSB_virgin << " " << Recr_virgin << " "  << SSBpR_virgin << " " << SSBpR_virgin_4_SRR << " equil: " << Equ_SpawnRecr_Result << endl<<endl;
-  }
-  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);  // this calcs SSB using benchmark biology
-    SSB_unf = SSB_equil;  // equilibrium unfished SSB using the benchmark averaged Recr_unf and benchmark averaged biology
-    temp2 = SSB_unf / Recr_unf; //  this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, temp2); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    SS2out << " bmarkSRR_&_bmarkbio - SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << temp2 << " " << SSBpR_virgin_4_SRR << " equil: " << Equ_SpawnRecr_Result << endl<<endl;
-  }
- */
-  // Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); 
   SS2out << "unfished values for SRR: SSB " << SSB0_4_SRR << " R " << R0_4_SRR << " SSBpR " << "  SSBpR: " << SSB0_4_SRR / R0_4_SRR << endl;
   SS2out << "SPRloop Iter Bycatch Fmult F_std SSBpR YpR_dead YpR_dead*Recr YpR_ret*Recr Revenue Cost Profit SSB Recruits SSB/Bzero Tot_Catch ";
   for (f = 1; f <= Nfleet; f++)

From 0bc8855a6c54efae9d36279f44fe1d5cf0c054a9 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Wed, 26 Mar 2025 16:25:56 -0700
Subject: [PATCH 31/58] align depletion_basis and Btarget and HCR anchor

---
 SS_benchfore.tpl       | 60 +++++++++++++++++++++++++++---------------
 SS_param.tpl           |  1 -
 SS_popdyn.tpl          |  4 +--
 SS_readcontrol_330.tpl |  5 ++++
 SS_readdata_330.tpl    | 20 +++++++++++---
 SS_readstarter.tpl     |  2 +-
 SS_recruit.tpl         |  2 +-
 SS_write_report.tpl    | 14 +++++-----
 SS_write_ssnew.tpl     |  9 ++++---
 9 files changed, 76 insertions(+), 41 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 3a61921d..a851db30 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -10,7 +10,7 @@
 // SPR refers to spawner potential ratio which is the ratio of SSBpR at some level of F to SSBpR with F = 0
 
 // SSBpR_virgin is calculated in popdyn using the start year biology
-// SSBpR_virgin_4_SRR  used to get alpha in equil_spawn_recr B-H
+// SSBpR_virgin  used to get alpha in equil_spawn_recr B-H
 
 FUNCTION void setup_Benchmark()  // and forecast
   {
@@ -776,7 +776,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
  SSBpR0 set at start year using start year biology
  SSBpR0 updated during time series if there is time-varying R0; PLUS NEW: equil_spawn_recr_calc called to get new equilibrium R0, SSB0
  SSBpR0 for benchmark stays at virgin unless timevary_bio_4SRR == 0, or if timevary_parm_start_SR > 0
- Btgttgt can now use either frac*SSB_bench or frac*SSB_virgin  
+ Btgttgt can now use either frac*SSB_bench or frac*SSB_virgin by using the existing flag for depletion basis
  Btgttgt2 can be fraction of SSB_MSY, of SSB_virgin, or of SSB_bench
  HCR inflection adds option to use SSB_virgin or SSB_bench
  depletion adds option to use SSB_bench
@@ -792,7 +792,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     R0_4_SRR = Recr_virgin;
     SSB_unf = SSB_equil;  //  should this also depend on timevary_parm_start_SR > 0???
   }
-  else  //  there is some timevary biology, with any WTage_rd == 1 qualifying as timevarying without actually chacking for different values in diff years
+  else  //  there is some timevary biology (with any WTage_rd == 1 qualifying as timevarying without actually chacking for different values in diff years)
   {
     if( timevary_bio_4SRR == 0)  // legacy approach;  this switch is read from starter.ss
     {
@@ -806,8 +806,11 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         SSBpR_bench = SSB0_4_SRR / R0_4_SRR;
         //  Equil_Spawn_Recr_Fxn will be called in more complete approach to use SSBpR_bench to move along the SRR
       }
-      else // there are timevary SRR parms.  Legacy code is same
+      else // there are timevary SRR parms, so use benchmark biology to create a whole new SRR
       {
+        Recr_unf = mfexp(SR_parm_work(1));  // R0 to be used
+        // steepness and other SR parms will also come from SR_parm_work
+        Do_Equil_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
         SSB_unf = SSB_equil;
         R0_4_SRR = Recr_unf;
         SSB0_4_SRR = SSB_equil;  // this is legacy, but incorrect, as it moves equil off the SRR, rather than along the SRR
@@ -818,7 +821,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
 
     else  // more complete approach to time vary biology will be used (introduced in 3.30.24)
     {
-      if(timevary_parm_start_SR == 0)  // no timevary SRR parms, so use SSB_virgin, Recr_virgin which will create virgin SSBpR0 
+      if(timevary_parm_start_SR == 0)  // no timevary SRR parms, so SRR will use SSB_virgin, Recr_virgin to internally create virgin SSBpR0 
       {
         SSB0_4_SRR = SSB_virgin;
         R0_4_SRR = Recr_virgin;
@@ -826,15 +829,25 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         SSB_unf = Equ_SpawnRecr_Result(1);
         Recr_unf = Equ_SpawnRecr_Result(2);
-        report5 << " use virgin SSBpR0 in SRR - SSB: " << SSB_virgin << " Recr: " << Recr_virgin << " SPR: " << SSB_virgin / Recr_virgin << " bench SPR: " << SSBpR_bench << " new equil: " << Equ_SpawnRecr_Result << endl;
+        if (show_MSY == 1) report5 << " use virgin SSBpR0 in SRR - SSB: " << SSB_virgin << " Recr: " << Recr_virgin << " SPR: " << SSB_virgin / Recr_virgin << " bench SPR: " << SSBpR_bench << " new equil: " << Equ_SpawnRecr_Result << endl;
       }
-      else  //  use benchmark quantities for SRR
+      else  //  use benchmark quantities for SRR, so everything can change
       {
-        //  Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_equil, Recr_unf, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        //  get new equilibrium point for the benchmark SRR
+        Recr_unf = mfexp(SR_parm_work(1));  // R0 to be used
+        Fishon = 0;
+        Do_Equil_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
+        SSBpR_bench = SSB_equil / Recr_unf;
+        SSB0_4_SRR = SSB_equil;
+        SSB_unf = SSB_equil;
+        R0_4_SRR = Recr_unf;
+        // verify
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_equil, Recr_unf, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        if (show_MSY == 1) report5 << " use bench SSBpR0 in SRR - SSB: " << SSB_unf << " Recr: " << Recr_unf << " SPR: " << SSBpR_bench << " new equil: " << Equ_SpawnRecr_Result << endl;
       }
       Do_Equil_Calc(Recr_unf);  // this calcs SSBpR and returns it as SSB_equil using benchmark biology and the updated equil Recr
       SSB_unf = SSB_equil;
-      report5 << " CHECK! - SSB_unf and updated equilibrium SSB0_4_SRR: " << SSB_unf << " " << SSB0_4_SRR << endl;
+      if (show_MSY == 1) report5 << " CHECK! - SSB_unf based on updated SRR (if any): " << SSB_unf << endl;
     }
   }
 
@@ -1137,17 +1150,18 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   {
     // ******************************************************
 
-    if (timevary_bio_4SRR == 0)
-    {Btgttgt = BTGT_target * SSB_unf;}  //  current SS3 approach
+    if (depletion_basis == 1) 
+      {Btgttgt = BTGT_target * SSB_virgin;}
     else
-    {Btgttgt = BTGT_target * SSB_unf;}
-    if (show_MSY == 1)
+      {Btgttgt = BTGT_target * SSB_unf;}  //  current SS3 approach uses benchmark biology
+
+      if (show_MSY == 1)
     {
      report5 << "#" << endl;
-     if (timevary_bio_4SRR == 0)  //  use virgin biology for the spawner-recruitment R0,h calculations
-     {report5 << "Find_target_SSB/Bzero; where Bzero is Virgin SSB:" << SSB_virgin << " where SSBpR_unf = " << SSBpR_virgin << endl;}
+     if (depletion_basis == 1)
+     {report5 << "Find_target_SSB as fraction: " << BTGT_target << " of Virgin SSB:" << SSB_virgin << endl;}
      else
-     {report5 << "Find_target_SSB/Bzero; where Bzero is for Bmark biology and updated SPR0: " << SSB_unf << " where SSBpR_unf = " << SSBpR_virgin_4_SRR << endl;}
+     {report5 << "Find_target_SSB as fraction: " << BTGT_target << " of SSB_unf: "<< SSB_unf << endl;}
      report5  << "Iter Fmult ann_F SPR Catch SSB Recruits SSB/Bzero Tot_catch";
 
     for (p = 1; p <= pop; p++)
@@ -1252,7 +1266,6 @@ 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_4_SRR << " Btgt " << Btgt << endl;
       }
     } // end search loop
 
@@ -1780,6 +1793,11 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       Btgttgt2 = Blim_frac * Bmsy;
       Blim_report = value(Bmsy);
     }
+    else if (depletion_basis == 1)
+    {
+      Btgttgt2 = -Blim_frac * SSB_virgin;
+      Blim_report = value(SSB_virgin);
+    }
     else
     {
       Btgttgt2 = -Blim_frac * SSB_virgin;
@@ -2241,14 +2259,14 @@ FUNCTION void Get_Forecast()
       }
     }
 
-    if (Fcast_Loop_Control(5) <= 1)
-    {HCR_anchor = SSB_unf;}
-    else if (Fcast_Loop_Control(5) ==2)
+    if (Fcast_Loop_Control(5) == 1)
     {HCR_anchor = SSB_virgin;}
+    else if (Fcast_Loop_Control(5) == 2)
+    {HCR_anchor = SSB_unf;}
 
     if (H4010_top_rd < 0.0)
     {
-      H4010_top = Bmsy / HCR_anchor;  // convert to fraction
+      H4010_top = Bmsy / HCR_anchor;  // convert to fraction of anchor
       if (H4010_bot > 0.25)
       {
         warnstream << "control rule cutoff is large (" << H4010_bot << "); so may not be < calculated Bmsy/SSB_unf (" << H4010_top << ")";
diff --git a/SS_param.tpl b/SS_param.tpl
index e8d532c5..3f850ebf 100644
--- a/SS_param.tpl
+++ b/SS_param.tpl
@@ -168,7 +168,6 @@ PARAMETER_SECTION
   number SSBpR_virgin;
   number SSB0_4_SRR;
   number R0_4_SRR;
-  number SSBpR_virgin_4_SRR;  // value of SSB/R used in SRR
   number regime_change;
   number rho;
   number dirichlet_Parm;
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index e58d4627..d27225db 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -356,11 +356,11 @@ FUNCTION void get_initial_conditions()
       beta = mfexp(SR_parm(4));
       steepness = alpha * SSBpR_virgin / (4. + alpha * SSBpR_virgin);
       Recr_virgin = 1. / beta * (alpha - (1. / SSBpR_virgin));
-//      warning << " before AB_calcs " << "parm " << SR_parm(1) << " calc " << log(Recr_virgin) << endl;
       SR_parm(1) = log(Recr_virgin);
       SR_parm(2) = steepness;
     }
-    else {
+    else
+    {
       Recr_virgin = mfexp(SR_parm(1));
     }
   
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index ced24029..26936674 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -6955,6 +6955,11 @@
       depletion_basis_label += " " + onenum + "%*Dyn_Bzero";
       break;
     }
+    case 6:
+    {
+      depletion_basis_label += " " + onenum + "%*Bmark_Biomass";
+      break;
+    }
   }
   if (depletion_log == 1) depletion_basis_label += ";log";
   if (depletion_multi > 1)
diff --git a/SS_readdata_330.tpl b/SS_readdata_330.tpl
index 96658403..901d92d6 100644
--- a/SS_readdata_330.tpl
+++ b/SS_readdata_330.tpl
@@ -4345,7 +4345,19 @@
       "even when the base is set to the mean of earlier recruitments" << endl;
     }
 
-    echoinput << Fcast_Loop_Control(5) << " #control rule anchor: 1=unfished_benchmark_SSB(old_approach), 2=virgin_SSB " << endl;
+    if (Fcast_Loop_Control(5) == 0)  //  default before 3.30.24
+    {
+      echoinput << "basis for HCR anchor was not set; setting to 2 to match default before 3.30.24" << endl;
+      warnstream << "basis for HCR anchor was not set; setting to 2 to match default before 3.30.24";
+      write_message(ADJUST, 0);
+      Fcast_Loop_Control(5) = 2;
+    }
+    echoinput << Fcast_Loop_Control(5) << " #control rule anchor: 1=virgin_SSB; 2=unfished_benchmark_SSB(old_approach)" << endl;
+    if (depletion_basis == 1 && Fcast_Loop_Control(5) == 2)
+    {
+      warnstream << "depletion_basis is using virgin but HCR anchor is using SSB_unf from benchmark. Are you sure?";
+      write_message(WARN, 0);
+    }
     
     echoinput << "#next enter year in which Fcast loop 3 caps and allocations begin to be applied" << endl;
     *(ad_comm::global_datafile) >> Fcast_Cap_FirstYear;
@@ -4814,16 +4826,16 @@
       warnstream << "Set F_std_basis=0 because no benchmark or forecast";
       write_message(WARN, 0);
     }
-    if (depletion_basis == 2)
+    if (depletion_basis == 2 || depletion_basis == 6 )
     {
       depletion_basis = 1;
-      warnstream << "Change depletion basis to 1 because benchmarks are off";
+      warnstream << "Change depletion basis to 1 because benchmarks were not requested";
       write_message(WARN, 0);
     }
     if (SPR_reporting >= 1 && SPR_reporting <= 3)
     {
       SPR_reporting = 4;
-      warnstream << "Change SPR_reporting to 4 because benchmarks are off";
+      warnstream << "Change SPR_reporting to 4 because benchmarks were not requested";
       write_message(WARN, 0);
     }
   }
diff --git a/SS_readstarter.tpl b/SS_readstarter.tpl
index eb978211..e2ab712f 100644
--- a/SS_readstarter.tpl
+++ b/SS_readstarter.tpl
@@ -643,7 +643,7 @@
   int depletion_basis;
   int depletion_multi;
   int depletion_log;
-  init_number depletion_basis_rd; // 0=skip; 1=B0; 2=Bmsy; 3=B_styr; 4=B_endyr; 5=dynamic_Bzero; values >=11 invoke multiyr with 10's digit; append .1 to invoke log(ratio) with hundreds digit
+  init_number depletion_basis_rd; // 0=skip; 1=B0; 2=Bmsy; 3=B_styr; 4=B_endyr; 5=dynamic_Bzero; 6=Bmark_SSB_unf;  values >=11 invoke multiyr with 10's digit; append .1 to invoke log(ratio) with hundreds digit
  LOCAL_CALCS
   // clang-format on
   echoinput << depletion_basis_rd << "  depletion_basis as read; this is also known as Bratio and is a std quantity; has multi-yr and log(ratio) options" << endl;
diff --git a/SS_recruit.tpl b/SS_recruit.tpl
index cd938550..2fb0b3c4 100644
--- a/SS_recruit.tpl
+++ b/SS_recruit.tpl
@@ -284,7 +284,7 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
   dvariable SRZ_surv;
   dvariable SSBpR_virgin_use;
 
-  SSBpR_virgin_use = SSB_virgin_use / Recr_virgin_use;  //  local instance of SSBpR_virgin_4_SRR
+  SSBpR_virgin_use = SSB_virgin_use / Recr_virgin_use;
   steepness = SRparm(2); //  common usage but some different
   //  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)
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 212f5ed1..7a9688e5 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -1845,8 +1845,8 @@ FUNCTION void write_bigoutput()
       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 << " #_Regime_parameter_used_to_offset_from_SRR";}
+      if (j == (N_SRparm2 - 1) && SR_parm_timevary(j) > 0) //  timevary regime exists
+      {SS2out << " #_Regime_parameter_used_to_offset_from_SRR";}
       SS2out << endl;
     }
 
@@ -1858,7 +1858,7 @@ FUNCTION void write_bigoutput()
     {
       case 3: // Beverton-Holt with steepness
     {
-      alpha = 4.0 * steepness / (SSBpR_virgin_4_SRR * (1. - steepness));
+      alpha = 4.0 * steepness / (SSBpR_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;
@@ -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. / SSBpR_virgin_4_SRR))) << endl;  //  virgin R0
-      SS2out << "steepness_derived: " << alpha * SSBpR_virgin_4_SRR / (4. + alpha * SSBpR_virgin_4_SRR) << endl;  // steepness virgin
+      SS2out << "ln(R0)_derived: " << log( 1. / beta * (alpha - (1. / SSBpR_virgin))) << endl;  //  virgin R0
+      SS2out << "steepness_derived: " << alpha * SSBpR_virgin / (4. + alpha * SSBpR_virgin) << endl;  // steepness virgin
       break;
     }
     case 8:
@@ -4744,7 +4744,7 @@ FUNCTION void SPR_profile()
       fec = Wt_Age_t(t, -2);
       SS2out << " repro_output for spr/ypr: " << fec(1) << endl;}
   }
-  SS2out << " stored - SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << SSBpR_virgin << " " << SSBpR_virgin_4_SRR<<endl;
+  SS2out << " stored - SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << SSBpR_virgin << " " << SSBpR_virgin<<endl;
 
 //  do not recalculate here so force using values from benchmark
   SS2out << "unfished values for SRR: SSB " << SSB0_4_SRR << " R " << R0_4_SRR << " SSBpR " << "  SSBpR: " << SSB0_4_SRR / R0_4_SRR << endl;
@@ -4965,7 +4965,7 @@ FUNCTION void SPR_profile()
           {
             SS2out << " " << SSB_equil_pop_gp(p, gp) * Btgt_prof_rec;
           }
-        SS2out << " R " << equ_Recr << "  SSB " << SSB_equil << endl;
+        SS2out << endl;
         if (SPRloop1 == 0)
         {
           Fmult2 -= Fmultchanger0;
diff --git a/SS_write_ssnew.tpl b/SS_write_ssnew.tpl
index b9e19cb1..1a134ca6 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -1548,7 +1548,8 @@ 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*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_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;  6=X*Bmark_SSB_unf; 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 << "# If value = 1, then Btarget in benchmark will be a fraction of SSB_virgin, else will be a fraction of SSB_benchmark" << 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;
@@ -1592,7 +1593,7 @@ FUNCTION void write_nucontrol()
   }
 
   NuFore << SPR_target << " # SPR target (e.g. 0.40)" << endl;
-  NuFore << BTGT_target << " # Biomass target (e.g. 0.40)" << endl;
+  NuFore << BTGT_target << " # Biomass target (e.g. 0.40) as fraction of SSB_virgin if depletion basis = 1, else as fraction of SSB_unfished in benchmark" << endl;
   if (Do_Benchmark == 3)
     NuFore << Blim_frac << " # COND: Do_Benchmark==3;  Blimit as fraction of Bmsy (neg value to use as frac of Bzero) (e.g. 0.50)" << endl;
   NuFore << "#_Bmark_years: beg_bio, end_bio, beg_selex, end_selex, beg_relF, end_relF, beg_recr_dist, end_recr_dist, beg_SRparm, end_SRparm (enter actual year, or values of 0 or -integer to be rel. endyr)" << endl
@@ -1645,7 +1646,7 @@ 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 as the inflection " << 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;
+  NuFore << "# Also see HCR_anchor below to use virgin vs benchmark SSB as basis" << endl;
   if (H4010_scale_rd < 0)
   {
     j = H4010_scale_vec_rd.size() - 1;
@@ -1667,7 +1668,7 @@ FUNCTION void write_nucontrol()
   {
     NuFore << Fcast_Loop_Control(4) << " # multiplier on base recruitment " << 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_Loop_Control(5) << " # HCR_anchor: 0 or 2 uses unfished benchmark SSB (old hardwired approach); 1 = virgin SSB" << endl << "#" << endl;
 
   NuFore << Fcast_Cap_FirstYear << "  # FirstYear for caps and allocations (should be after years with fixed inputs) " << endl;
 

From 1b251cded4675baf6c42f6f7c72967e2a00083c6 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Thu, 27 Mar 2025 11:42:31 -0700
Subject: [PATCH 32/58] rename Do_Equil_Calc; remove erroneous application of
 regime in initial_equil

---
 SS_benchfore.tpl    | 34 +++++++++++++++++-----------------
 SS_popdyn.tpl       | 30 +++++++++++++++---------------
 SS_write_report.tpl |  6 +++---
 3 files changed, 35 insertions(+), 35 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index a851db30..933beacd 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -783,7 +783,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
  */
   Recr_unf = mfexp(SR_parm_work(1));  // R0 to be used
   Fishon = 0;
-  Do_Equil_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
+  SSBpR_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
   dvariable SSBpR_bench = SSB_equil / Recr_unf;
 
   if( timevary_MG_firstyr == YrMax && WTage_rd == 0)  // no time-varying biology
@@ -810,7 +810,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       {
         Recr_unf = mfexp(SR_parm_work(1));  // R0 to be used
         // steepness and other SR parms will also come from SR_parm_work
-        Do_Equil_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
+        SSBpR_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
         SSB_unf = SSB_equil;
         R0_4_SRR = Recr_unf;
         SSB0_4_SRR = SSB_equil;  // this is legacy, but incorrect, as it moves equil off the SRR, rather than along the SRR
@@ -836,7 +836,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         //  get new equilibrium point for the benchmark SRR
         Recr_unf = mfexp(SR_parm_work(1));  // R0 to be used
         Fishon = 0;
-        Do_Equil_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
+        SSBpR_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
         SSBpR_bench = SSB_equil / Recr_unf;
         SSB0_4_SRR = SSB_equil;
         SSB_unf = SSB_equil;
@@ -845,7 +845,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_equil, Recr_unf, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         if (show_MSY == 1) report5 << " use bench SSBpR0 in SRR - SSB: " << SSB_unf << " Recr: " << Recr_unf << " SPR: " << SSBpR_bench << " new equil: " << Equ_SpawnRecr_Result << endl;
       }
-      Do_Equil_Calc(Recr_unf);  // this calcs SSBpR and returns it as SSB_equil using benchmark biology and the updated equil Recr
+      SSBpR_Calc(Recr_unf);  // this calcs SSBpR and returns it as SSB_equil using benchmark biology and the updated equil Recr
       SSB_unf = SSB_equil;
       if (show_MSY == 1) report5 << " CHECK! - SSB_unf based on updated SRR (if any): " << SSB_unf << endl;
     }
@@ -893,7 +893,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     dvariable SPR_target100;
     SPR_target100 = SPR_target * 100.;
 
-    Do_Equil_Calc(equ_Recr);  //  where equ_Recr has been set to 1.0
+    SSBpR_Calc(equ_Recr);  //  where equ_Recr has been set to 1.0
     SSBpR_unf = SSB_equil / equ_Recr; //  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)
@@ -939,7 +939,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         }
 
         Fishon = 1;
-        Do_Equil_Calc(equ_Recr);
+        SSBpR_Calc(equ_Recr);
         yld1(ii) = 100. * SSB_equil / SSBpR_unf; //  spawning potential ratio
       }
       SPR_actual = yld1(1); //  spawning potential ratio
@@ -1051,7 +1051,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       }
       //  else  Hrate for bycatch fleets already set
     }
-    Do_Equil_Calc(equ_Recr);
+    SSBpR_Calc(equ_Recr);
     F01_origin = YPR_opt / Fmult;
 
     BTGT_target = 0.1; //  now relative to Bmark
@@ -1083,7 +1083,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
             }
           } //  else  Hrate for bycatch fleets set above
         }
-        Do_Equil_Calc(equ_Recr);
+        SSBpR_Calc(equ_Recr);
         yld1(ii) = YPR_opt;
       }
 
@@ -1222,7 +1222,7 @@ 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 in units of SSB/R,
+        SSBpR_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
@@ -1442,7 +1442,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         //  else  Hrate for bycatch fleets already set
       }
 
-      Do_Equil_Calc(equ_Recr);
+      SSBpR_Calc(equ_Recr);
       //  SPAWN-RECR:   calc spawn-recr for MSY calcs;  need to make area-specific
       MSY_SPR = SSB_equil / SSBpR_unf;
       SSBpR_temp = SSB_equil;
@@ -1536,7 +1536,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
               }
             } //  else  Hrate for bycatch fleets set above
           }
-          Do_Equil_Calc(equ_Recr);
+          SSBpR_Calc(equ_Recr);
           //  SPAWN-RECR:   calc spawn-recr for MSY calcs;  need to make area-specific
           MSY_SPR = SSB_equil / SSBpR_unf;
           SSBpR_temp = SSB_equil;
@@ -1687,7 +1687,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
           }
 
         Fishon = 0;
-        Do_Equil_Calc(equ_Recr);
+        SSBpR_Calc(equ_Recr);
         report5 << "Equil_N_at_age_M_only_Recr_MSY" << endl
                 << "Seas Area GP Sex subM" << age_vector << endl;
         for (s = 1; s <= nseas; s++)
@@ -1837,7 +1837,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
           }
           //  else  Hrate for bycatch fleets already set
         }
-        Do_Equil_Calc(equ_Recr);
+        SSBpR_Calc(equ_Recr);
         SPR_Btgt2 = SSB_equil / SSBpR_unf;
         //  SPAWN-RECR:   calc equil spawn-recr for Btarget calcs;  need to make area-specific
         SSBpR_temp = SSB_equil;
@@ -2720,7 +2720,7 @@ FUNCTION void Get_Forecast()
               Fishon = 0;
               eq_yr = y;
               bio_yr = y;
-              Do_Equil_Calc(R0_use); //  call function to do per recruit calculation
+              SSBpR_Calc(R0_use); //  call function to do per recruit calculation
           //  should call equil_spawn_recr_fxn here to get updated equilibrium with the new SSB/R
           if (fishery_on_off == 1)
               {
@@ -3360,7 +3360,7 @@ FUNCTION void Get_Forecast()
               Fishon = 0;
               eq_yr = y;
               bio_yr = y;
-              Do_Equil_Calc(equ_Recr); //  call function to do per recruit calculation
+              SSBpR_Calc(equ_Recr); //  call function to do per recruit calculation
           //  should call equil_spawn_recr_fxn here to get updated equilibrium with the new SSB/R
           if (fishery_on_off == 1)
               {
@@ -3783,7 +3783,7 @@ FUNCTION void Get_Forecast()
         equ_Recr = Recr_unf;
         bio_yr = y;
         Fishon = 0;
-        Do_Equil_Calc(equ_Recr); //  call function to do per recruit calculation
+        SSBpR_Calc(equ_Recr); //  call function to do per recruit calculation
 
         Smry_Table(y, 11) = SSB_equil;
         Smry_Table(y, 13) = GenTime;
@@ -3796,7 +3796,7 @@ FUNCTION void Get_Forecast()
           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 per recruit calculation
+        SSBpR_Calc(equ_Recr); //  call function to do per recruit calculation
         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_popdyn.tpl b/SS_popdyn.tpl
index d27225db..de8fc784 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -1,8 +1,8 @@
 // SS_Label_file  #12. **SS_popdyn.tpl**
 // SS_Label_file  # * <u>setup_recdevs()</u>
-// SS_Label_file  # * <u>get_initial_conditions()</u> // does virgin and initial year by calling <u>Do_Equil_Calc()</u> with F=0, then F=init_F
+// SS_Label_file  # * <u>get_initial_conditions()</u> // does virgin and initial year by calling <u>SSBpR_Calc()</u> with F=0, then F=init_F
 // SS_Label_file  # * <u>get_time_series()</u>  //  loops the years, calling biology, selectivity and spawn-recr functions as needed
-// SS_Label_file  # * <u>Do_Equil_Calc()</u>  // does per-recruit calculations and returns SSB/R and Y/R
+// SS_Label_file  # * <u>SSBpR_Calc()</u>  // does per-recruit calculations and returns SSB/R and Y/R
 // SS_Label_file  #
 
 FUNCTION void setup_recdevs()
@@ -342,7 +342,7 @@ FUNCTION void get_initial_conditions()
   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 per recruit calculation.  Returns SPR because R = 1.0
+    SSBpR_Calc(equ_Recr); //  call function to do per recruit calculation.  Returns SPR because R = 1.0
     SSBpR_virgin = SSB_equil; //  spawners per recruit.  Needed for Sr_fxn = 10
     if(SR_fxn == 10)  // B-H with a,b
     {
@@ -377,7 +377,7 @@ FUNCTION void get_initial_conditions()
     exp_rec(eq_yr, 2) = Recr_virgin;
     exp_rec(eq_yr, 3) = Recr_virgin;
     exp_rec(eq_yr, 4) = Recr_virgin;
-    Do_Equil_Calc(equ_Recr); //  call function to do per recruit calculation
+    SSBpR_Calc(equ_Recr); //  call function to do per recruit calculation
     SSB_virgin = SSB_equil;
     if(Do_Benchmark==0)  // assign values that would be created in benchmark section
     {
@@ -516,8 +516,8 @@ FUNCTION void get_initial_conditions()
     exp_rec(eq_yr, 2) = R1;
     exp_rec(eq_yr, 3) = R1;
     exp_rec(eq_yr, 4) = R1;
-    equ_Recr = R1; //  equ_Recr is used inside of Do_Equil_Calc
-    Do_Equil_Calc(equ_Recr);
+    equ_Recr = R1; //  equ_Recr is used inside of SSBpR_Calc
+    SSBpR_Calc(equ_Recr);
     CrashPen += Equ_penalty;
   }
   else
@@ -527,9 +527,9 @@ FUNCTION void get_initial_conditions()
     //  first get SPR for this init_F
     //  SPAWN-RECR:   calc initial equilibrium pop, SSB, Recruitment
     //    equ_Recr=Recr_virgin;
-    equ_Recr = R1_exp * regime_change;
-
-    Do_Equil_Calc(equ_Recr);
+//    equ_Recr = R1_exp * regime_change;  //  NOTE:  seems wrong to apply regime here
+    equ_Recr = R1_exp;
+    SSBpR_Calc(equ_Recr);
     CrashPen += Equ_penalty;
     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
@@ -543,7 +543,7 @@ FUNCTION void get_initial_conditions()
     exp_rec(eq_yr, 3) = equ_Recr;
     exp_rec(eq_yr, 4) = equ_Recr;
     R1 = equ_Recr;
-    Do_Equil_Calc(equ_Recr); // calculated SSB_equil
+    SSBpR_Calc(equ_Recr); // calculated SSB_equil
     CrashPen += Equ_penalty;
   }
   Smry_Table(styr - 1, 1) = totbio; //  from equil calcs
@@ -1036,7 +1036,7 @@ FUNCTION void get_time_series()
           Fishon = 0;
           eq_yr = y;
           bio_yr = y;
-          Do_Equil_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
+          SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
           //  should call equil_spawn_recr_fxn here to get updated equilibrium with the new SSB/R
           if (fishery_on_off == 1)
@@ -1496,7 +1496,7 @@ FUNCTION void get_time_series()
           Fishon = 0;
           eq_yr = y;
           bio_yr = y;
-          Do_Equil_Calc(R0_use); //  call function to do per recruit calculation
+          SSBpR_Calc(R0_use); //  call function to do per recruit calculation
           SSB_use = SSB_equil;
           //  should call equil_spawn_recr_fxn here to get updated equilibrium with the new SSB/R
           if (fishery_on_off == 1)
@@ -1789,7 +1789,7 @@ FUNCTION void get_time_series()
       equ_Recr = Recr_virgin;
       bio_yr = y;
       Fishon = 0;
-      Do_Equil_Calc(equ_Recr); //  call function to do per recruit calculation with current year's biology
+      SSBpR_Calc(equ_Recr); //  call function to do per recruit calculation with current year's biology
       Smry_Table(y, 11) = SSB_equil;
       Smry_Table(y, 13) = GenTime;
       if( SR_fxn == 10 )
@@ -1801,7 +1801,7 @@ FUNCTION void get_time_series()
         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 per recruit calculation with current year's biology and F
+      SSBpR_Calc(equ_Recr); //  call function to do per recruit calculation with current year's biology and F
       if (STD_Yr_Reverse_Ofish(y) > 0)
       {
         SPR_std(STD_Yr_Reverse_Ofish(y)) = SSB_equil / Smry_Table(y, 11);
@@ -1833,7 +1833,7 @@ FUNCTION void get_time_series()
 //********************************************************************
  /*  SS_Label_FUNCTION 30 Do_Equil_Calc */
  // This function does per recruit calculations, so produces an age composition that is in equilibrium with M+F
-FUNCTION void Do_Equil_Calc(const prevariable& equ_Recr)
+FUNCTION void SSBpR_Calc(const prevariable& equ_Recr)
   {
   int t_base;
   int t;
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 7a9688e5..655a4ca2 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -1,6 +1,6 @@
 // SS_Label_file  #19. **SS_write_report.tpl**
 // SS_Label_file  # * <u>write_bigoutput()</u>  // produces *report.sso* and *compreport.sso*
-// SS_Label_file  # * <u>SPR_profile()</u>  //  calls Do_Equil_Calc() and Equil_Spawn_Recr_Fxn() over a range of F to get SPR, YPR, and SSB and catch curves
+// SS_Label_file  # * <u>SPR_profile()</u>  //  calls SSBpR_Calc() and Equil_Spawn_Recr_Fxn() over a range of F to get SPR, YPR, and SSB and catch curves
 // SS_Label_file  # * <u>global_MSY()</u>  // similar to SPR_profile but first changes all selectivities to knife edge and profiles on age-at-entry
 // SS_Label_file  #
 
@@ -4782,7 +4782,7 @@ FUNCTION void SPR_profile()
     SPRloop1_end = 7;
   }
   int SPRloops;
-  Do_Equil_Calc(equ_Recr);
+  SSBpR_Calc(equ_Recr);
   if (N_bycatch == 0)
   {
     k = 0;
@@ -4902,7 +4902,7 @@ FUNCTION void SPR_profile()
           }
         Fishon = 1;
 
-        Do_Equil_Calc(equ_Recr);
+        SSBpR_Calc(equ_Recr);
         //  SPAWN-RECR:   calc equil spawn-recr in the SPR loop
         SSBpR_temp = SSB_equil;
         Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR

From 0ad975fe1f73cdf83ed03b1f42686f51e7e26bc6 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Fri, 28 Mar 2025 16:20:07 -0700
Subject: [PATCH 33/58] revise SRparm timevary to track R0 h

---
 SS_popdyn.tpl          | 15 +++++++++++----
 SS_readcontrol_330.tpl | 15 +++++++++------
 2 files changed, 20 insertions(+), 10 deletions(-)

diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index de8fc784..c4e55ffc 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -1024,21 +1024,27 @@ 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 (timevary_parm_start_SR == 0) //  SRparm are not time-varying
+        if (timevary_parm_start_SR == 0 || timevary_SRparm (y) == 0) //  SRparm are not time-varying (but regime still could be)
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
+          warning << y << " virgin "<<SSB_use<<" "<<R0_use <<"  steep " << SR_parm_work(2);
         }
-        else
+        else  //  timevary 
         {
           R0_use = mfexp(SR_parm_work(1));
+          //  timevary steepness is in SR_parm_work(2) and will be applied inside of Equil_Spawn_Recr_Fxn
           equ_Recr = R0_use;
           Fishon = 0;
           eq_yr = y;
           bio_yr = y;
           SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
-          //  should call equil_spawn_recr_fxn here to get updated equilibrium with the new SSB/R
+          SSBpR_temp = SSB_use / R0_use;  // get unfished SSBpR
+          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_use, R0_use, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+          warning << y << " pR only "<<SSB_use<<" "<<R0_use<<"  steep " << SR_parm_work(2)<< " equil: "<<Equ_SpawnRecr_Result;
+          R0_use = Equ_SpawnRecr_Result(2);
+          SSB_use = Equ_SpawnRecr_Result(1);
           if (fishery_on_off == 1)
           {
             Fishon = 1;
@@ -1049,6 +1055,7 @@ FUNCTION void get_time_series()
           }
         }
         Recruits = Spawn_Recr(SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr using either virgin or adjusted R0 and SSB0
+        warning <<"   SSB_current: " << SSB_current << "  recruits: "<<Recruits<< endl;
         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)
@@ -1490,7 +1497,7 @@ 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 if (timevary_SRparm (y) > 0)
         {
           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 26936674..eaed1c0f 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -2068,9 +2068,11 @@
   }
   // flag for recruitment autocorrelation
   echoinput << " Do recruitment_autocorr: " << SR_autocorr << endl;
+
+  // note that the regime parameter seems to bypass use of timevary_SRparm, but timevary_SRparm is used for R0, h beginning 3.30.24
   timevary_used = 0;
-  for (j = 1; j <= N_SRparm(SR_fxn) + 2; j++)
-    if (j != N_SRparm(SR_fxn) + 1) //  because sigmaR and autocorr cannot be time-varying
+  for (j = 1; j <= N_SRparm2 - 1; j++)  // so omits autocorr
+    if (j != N_SRparm2 - 2) //  because sigmaR cannot be time-varying
     {
       if (SR_parm_1(j, 13) == 0 && SR_parm_1(j, 8) == 0 && SR_parm_1(j, 9) == 0)
       {
@@ -2097,7 +2099,7 @@
         timevary_setup(2) = j; //  index of base parm within that type of parameter
         timevary_setup(13) = firstSRparm + j; //  index of base parm relative to ParCount which is continuous across all types of parameters
         timevary_setup(3) = timevary_parm_cnt + 1; //  first parameter within total list of all timevary parms
-        timevary_pass = 1; // placeholder; not used for SR parms
+        timevary_pass = 0; // placeholder; not used for SR parms
         //  set up env link info
         echoinput << " check for env " << SR_parm_1(j, 8) << endl;
         k = int(abs(SR_parm_1(j, 8)) / 100); //  find the env link code
@@ -2132,9 +2134,10 @@
           create_timevary(SR_parm_1(j), timevary_setup, timevary_pass, autogen_timevary(timevary_setup(1)), f, block_design_null, env_data_pass, N_parm_dev, finish_starter);
         }
         timevary_def.push_back(timevary_setup(1, 14));
-        for (y = styr - 3; y <= YrMax + 1; y++) {
-          timevary_SRparm(y) = timevary_pass(y);
-        } // year vector for this category og MGparm
+        for (y = styr - 3; y <= YrMax + 1; y++)
+        {
+          if (timevary_pass(y) > 0 && j != N_SRparm2 - 1) timevary_SRparm(y , YrMax) = timevary_pass(y);  //  set timevary flag, except for regime parameter
+        }
       }
     }
   

From d1343125650b9d0a313307692c0f6b3414154750 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Mon, 31 Mar 2025 15:39:44 -0700
Subject: [PATCH 34/58] refactor variable names and continue testing

---
 SS_benchfore.tpl       |  88 ++++++++++++++--------------
 SS_objfunc.tpl         |  18 +++---
 SS_param.tpl           |  14 ++---
 SS_popdyn.tpl          |  84 +++++++++++++--------------
 SS_prelim.tpl          |  12 ++--
 SS_proced.tpl          |  12 ++--
 SS_readcontrol_330.tpl | 126 ++++++++++++++++++++---------------------
 SS_recruit.tpl         |  40 ++++++-------
 SS_timevaryparm.tpl    |  10 ++--
 SS_write.tpl           |  16 +++---
 SS_write_report.tpl    |  38 ++++++-------
 SS_write_ssnew.tpl     |   8 +--
 12 files changed, 233 insertions(+), 233 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 933beacd..d2f202c8 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -415,7 +415,7 @@ FUNCTION void setup_Benchmark()  // and forecast
         }
         // recr_dist_unf is accumulated while doing the time_series
         // then its mean is calculated in Get_Benchmarks and assigned to recr_dist
-        //  the SR_parm_bench is calculated from Bmark_yrs 9-10 in benchmark code using values stored in SR_parm_byyr
+        //  the SRparm_bench is calculated from Bmark_yrs 9-10 in benchmark code using values stored in SRparm_byyr
       }
 
       //  calc average selectivity to use in equil; store in styr-3
@@ -733,18 +733,18 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
 
   for (j = 1; j <= N_SRparm2; j++)
   {
-    if (SR_parm_timevary(j) == 0)
+    if (SRparm_timevary(j) == 0)
     {
-      SR_parm_work(j) = SR_parm(j);
+      SRparm_work(j) = SRparm(j);
     }
     else
     {
       temp = 0.;
       for (int y = Bmark_Yr(9); y <= Bmark_Yr(10); y++)
       {
-        temp += SR_parm_byyr(y, j);
+        temp += SRparm_byyr(y, j);
       }
-      SR_parm_work(j) = temp / (Bmark_Yr(10) - Bmark_Yr(9) + 1.);
+      SRparm_work(j) = temp / (Bmark_Yr(10) - Bmark_Yr(9) + 1.);
     }
   }
 
@@ -756,7 +756,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
 
  Flags:
   timevary_MG_firstyr == YrMax  // means that no biology is time-varying
-  timevary_parm_start_SR > 0 //  means that R0 or h (i.e. any except regime, sigmaR, autocorr) is time-varying, so SSBpR0 gets updated for time series and for bench
+  timevary_parm_SR_first > 0 //  means that R0 or h (i.e. any except regime, sigmaR, autocorr) is time-varying, so SSBpR0 gets updated for time series and for bench
   timevary_bio_4SRR is new user selected flag:  0 for legacy, vs 1 for improved use of timevary biology in SRR calcs
 
  Legacy approach:
@@ -775,22 +775,24 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
  Improved approach
  SSBpR0 set at start year using start year biology
  SSBpR0 updated during time series if there is time-varying R0; PLUS NEW: equil_spawn_recr_calc called to get new equilibrium R0, SSB0
- SSBpR0 for benchmark stays at virgin unless timevary_bio_4SRR == 0, or if timevary_parm_start_SR > 0
+ SSBpR0 for benchmark stays at virgin unless timevary_bio_4SRR == 0, or if timevary_parm_SR_first > 0
  Btgttgt can now use either frac*SSB_bench or frac*SSB_virgin by using the existing flag for depletion basis
  Btgttgt2 can be fraction of SSB_MSY, of SSB_virgin, or of SSB_bench
  HCR inflection adds option to use SSB_virgin or SSB_bench
  depletion adds option to use SSB_bench
  */
-  Recr_unf = mfexp(SR_parm_work(1));  // R0 to be used
+  Recr_unf = mfexp(SRparm_work(1));  // R0 to be used
   Fishon = 0;
   SSBpR_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
   dvariable SSBpR_bench = SSB_equil / Recr_unf;
 
+  report5 << "virgin: " << Recr_virgin << " " << SSB_virgin << endl;
+  report5 << "bench: " << Recr_unf << " " << SSB_equil << endl;
   if( timevary_MG_firstyr == YrMax && WTage_rd == 0)  // no time-varying biology
   {
     SSB0_4_SRR = SSB_virgin;
     R0_4_SRR = Recr_virgin;
-    SSB_unf = SSB_equil;  //  should this also depend on timevary_parm_start_SR > 0???
+    SSB_unf = SSB_equil;  //  should this also depend on timevary_parm_SR_first > 0???
   }
   else  //  there is some timevary biology (with any WTage_rd == 1 qualifying as timevarying without actually chacking for different values in diff years)
   {
@@ -798,18 +800,17 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     {
       warnstream << "There is timevary biology and the legacy approach to benchmark calculations is being used; user should be aware";
       write_message (WARN, 0);
-      if(timevary_parm_start_SR == 0)  // no timevary SRR parms
+      if(timevary_parm_SR_first == 0)  // no timevary SRR parms
       {
         SSB_unf = SSB_equil;
         R0_4_SRR = Recr_unf;  // same as Recr_virgin because no timevary SRparms
         SSB0_4_SRR = SSB_equil;  // this is legacy, but incorrect, as it moves equil off the SRR, rather than along the SRR
         SSBpR_bench = SSB0_4_SRR / R0_4_SRR;
-        //  Equil_Spawn_Recr_Fxn will be called in more complete approach to use SSBpR_bench to move along the SRR
       }
-      else // there are timevary SRR parms, so use benchmark biology to create a whole new SRR
+      else // there are timevary SRR parms
       {
-        Recr_unf = mfexp(SR_parm_work(1));  // R0 to be used
-        // steepness and other SR parms will also come from SR_parm_work
+        Recr_unf = mfexp(SRparm_work(1));  // R0 to be used
+        // steepness and other SR parms will also come from SRparm_work
         SSBpR_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
         SSB_unf = SSB_equil;
         R0_4_SRR = Recr_unf;
@@ -821,20 +822,20 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
 
     else  // more complete approach to time vary biology will be used (introduced in 3.30.24)
     {
-      if(timevary_parm_start_SR == 0)  // no timevary SRR parms, so SRR will use SSB_virgin, Recr_virgin to internally create virgin SSBpR0 
+      if(timevary_parm_SR_first == 0)  // no timevary SRR parms, so SRR will use SSB_virgin, Recr_virgin to internally create virgin SSBpR0 
       {
         SSB0_4_SRR = SSB_virgin;
         R0_4_SRR = Recr_virgin;
         //  get new equilibrium point using original SRR and SSBpR_bench
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_virgin, Recr_virgin, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB_virgin, Recr_virgin, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         SSB_unf = Equ_SpawnRecr_Result(1);
         Recr_unf = Equ_SpawnRecr_Result(2);
         if (show_MSY == 1) report5 << " use virgin SSBpR0 in SRR - SSB: " << SSB_virgin << " Recr: " << Recr_virgin << " SPR: " << SSB_virgin / Recr_virgin << " bench SPR: " << SSBpR_bench << " new equil: " << Equ_SpawnRecr_Result << endl;
       }
-      else  //  use benchmark quantities for SRR, so everything can change
+      else  //  use updated SRparms and benchmark biology
       {
         //  get new equilibrium point for the benchmark SRR
-        Recr_unf = mfexp(SR_parm_work(1));  // R0 to be used
+        Recr_unf = mfexp(SRparm_work(1));  // R0 to be used
         Fishon = 0;
         SSBpR_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
         SSBpR_bench = SSB_equil / Recr_unf;
@@ -842,23 +843,22 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         SSB_unf = SSB_equil;
         R0_4_SRR = Recr_unf;
         // verify
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_equil, Recr_unf, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB_equil, Recr_unf, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         if (show_MSY == 1) report5 << " use bench SSBpR0 in SRR - SSB: " << SSB_unf << " Recr: " << Recr_unf << " SPR: " << SSBpR_bench << " new equil: " << Equ_SpawnRecr_Result << endl;
       }
       SSBpR_Calc(Recr_unf);  // this calcs SSBpR and returns it as SSB_equil using benchmark biology and the updated equil Recr
       SSB_unf = SSB_equil;
-      if (show_MSY == 1) report5 << " CHECK! - SSB_unf based on updated SRR (if any): " << SSB_unf << endl;
     }
   }
 
   if (show_MSY == 1)
   {
-    SR_parm_work(N_SRparm2 + 1) = SSB0_4_SRR;
+    SRparm_work(N_SRparm2 + 1) = SSB0_4_SRR;
     Mgmt_quant(1) = SSB_unf;
     Mgmt_quant(2) = totbio;  // this is calculated in Do_Equil_Calc
     Mgmt_quant(3) = smrybio;
     Mgmt_quant(4) = Recr_unf;
-    report5 << "SR_parms for benchmark: " << SR_parm_work << endl
+    report5 << "SRparms for benchmark: " << SRparm_work << endl
             << "Benchmark biology averaged over years: " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl << endl;
     Mgmt_quant(19) = SSB_unf;  // placeholder for depletion denominator
     Mgmt_quant(20) = SSB_unf;  //  placeholder to be replaced by SSB_HCR_infl
@@ -1010,7 +1010,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
 
     //  SPAWN-RECR:   calc equil spawn-recr in YPR; need to make this area-specific
     SSBpR_temp = SSB_equil;  //  based on most recent call to Do_Equil_Calc
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB0_4_SRR, R0_4_SRR, 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);
@@ -1125,7 +1125,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     if (rundetail > 0 && mceval_counter == 0 && show_MSY == 1)
       echoinput << "Calculated F0.1: " << Btgt_Fmult << endl;
     SSBpR_temp = SSB_equil;
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB0_4_SRR, R0_4_SRR, 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
@@ -1226,7 +1226,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         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
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         yld1(ii) = Equ_SpawnRecr_Result(1);
       }
 
@@ -1402,7 +1402,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         }
         if (F_Method == 1)
         {
-          Fmax = (Btgt_Fmult + SPR_Fmult) * 0.5 * SR_parm_work(2) / 0.05;
+          Fmax = (Btgt_Fmult + SPR_Fmult) * 0.5 * SRparm_work(2) / 0.05;
         } //  previously /0.18
         F1(1) = -log(Fmax / Btgt_Fmult - 1.);
         F2(1) = -log(Fmax / Btgt_Fmult - 1.);
@@ -1446,7 +1446,7 @@ 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 / SSBpR_unf;
       SSBpR_temp = SSB_equil;
-      Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+      Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB0_4_SRR, R0_4_SRR, 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;
@@ -1540,7 +1540,7 @@ 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 / SSBpR_unf;
           SSBpR_temp = SSB_equil;
-          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB0_4_SRR, R0_4_SRR, 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;
@@ -1841,7 +1841,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         SPR_Btgt2 = SSB_equil / SSBpR_unf;
         //  SPAWN-RECR:   calc equil spawn-recr for Btarget calcs;  need to make area-specific
         SSBpR_temp = SSB_equil;
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         yld1(ii) = Equ_SpawnRecr_Result(1);
       }
 
@@ -1923,9 +1923,9 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   {
     report5 << "#" << endl
             << "Management_report" << endl;
-    report5 << "Virgin: Steepness_Recr_SSB " << SR_parm(2) << " " << Recr_virgin << " " << SSB_virgin << endl;
-    report5 << "Bench:  Steepness_Recr_SSB " << SR_parm_work(2) << " " << R0_4_SRR << " " << SSB0_4_SRR << endl;
-    report5 << "unf  :  Steepness_Recr_SSB " << SR_parm_work(2) << " " << Recr_unf << " " << SSB_unf << endl;
+    report5 << "Virgin: Steepness_Recr_SSB " << SRparm(2) << " " << Recr_virgin << " " << SSB_virgin << endl;
+    report5 << "Bench:  Steepness_Recr_SSB " << SRparm_work(2) << " " << R0_4_SRR << " " << SSB0_4_SRR << endl;
+    report5 << "unf  :  Steepness_Recr_SSB " << SRparm_work(2) << " " << Recr_unf << " " << SSB_unf << endl;
     report5 << "#" << endl
             << "Summary_age: " << Smry_Age << endl;
     report5 << "#_Bmark_years: beg_bio, end_bio, beg_selex, end_selex, beg_relF, end_relF, beg_recr_dist, end_recr_dist, beg_SRparm, end_SRparm" << endl
@@ -2423,15 +2423,15 @@ FUNCTION void Get_Forecast()
       t_base = styr + (y - styr) * nseas - 1;
       for (f = 1; f <= N_SRparm2; f++)
       {
-        if (SR_parm_timevary(f) == 0)
+        if (SRparm_timevary(f) == 0)
         {
-          //  no change to SR_parm_work
+          //  no change to SRparm_work
         }
         else
         {
-          SR_parm_work(f) = parm_timevary(SR_parm_timevary(f), y);
+          SRparm_work(f) = parm_timevary(SRparm_timevary(f), y);
         }
-        SR_parm_byyr(y, f) = SR_parm_work(f);
+        SRparm_byyr(y, f) = SRparm_work(f);
       }
       env_data(y, -1) = log(SSB_current / SSB_yr(styr - 1)); //  store most recent value for density-dependent effects, NOTE - off by a year if recalc'ed at beginning of season 1
       env_data(y, -2) = recdev(y); //  store for density-dependent effects
@@ -2708,14 +2708,14 @@ FUNCTION void Get_Forecast()
             }
             //  SPAWN-RECR:   get recruitment in forecast;  needs to be area-specific
             // SR_fxn
-            if (timevary_parm_start_SR == 0) //  R0 is not time-varying
+            if (timevary_parm_SR_first == 0) //  R0 is not time-varying
             {
               R0_use = Recr_virgin;
               SSB_use = SSB_virgin;
             }
             else
             {
-              R0_use = mfexp(SR_parm_work(1));
+              R0_use = mfexp(SRparm_work(1));
               equ_Recr = R0_use;
               Fishon = 0;
               eq_yr = y;
@@ -3348,14 +3348,14 @@ 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 (timevary_parm_start_SR == 0) //  R0 is not time-varying
+            if (timevary_parm_SR_first == 0) //  R0 is not time-varying
             {
               R0_use = Recr_virgin;
               SSB_use = SSB_virgin;
             }
             else
             {
-              R0_use = mfexp(SR_parm_work(1));
+              R0_use = mfexp(SRparm_work(1));
               equ_Recr = R0_use;
               Fishon = 0;
               eq_yr = y;
@@ -3790,10 +3790,10 @@ FUNCTION void Get_Forecast()
         if( SR_fxn == 10 )
         {
           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
-          SR_parm_byyr(y, 1) = log( 1. / beta * (alpha - (1. / temp)));  //  implied ln_R0
+          alpha = mfexp(SRparm_work(3));
+          beta = mfexp(SRparm_work(4));
+          SRparm_byyr(y, 2) =  alpha * temp / (4. + alpha * temp);  //  implied steepness
+          SRparm_byyr(y, 1) = log( 1. / beta * (alpha - (1. / temp)));  //  implied ln_R0
         }
         Fishon = 1;
         SSBpR_Calc(equ_Recr); //  call function to do per recruit calculation
diff --git a/SS_objfunc.tpl b/SS_objfunc.tpl
index 474153ee..c4655bac 100644
--- a/SS_objfunc.tpl
+++ b/SS_objfunc.tpl
@@ -745,8 +745,8 @@ FUNCTION void evaluate_the_objective_function()
   //The recruitment prior is assumed to be a lognormal pdf with expected
   // value equal to the deterministic stock-recruitment curve          // SS_Label_260
   //  R1 deviation is weighted by ave_age because R1 represents a time series of recruitments
-  //  SR_parm(N_SRparm+1) is sigmaR
-  //  SR_parm(N_SRparm+4) is rho, the autocorrelation coefficient
+  //  SRparm(N_SRparm+1) is sigmaR
+  //  SRparm(N_SRparm+4) is rho, the autocorrelation coefficient
   //  POP code from Ianelli
   //  if (rho>0)
   //    for (i=styr_rec+1;i<=endyr;i++)
@@ -767,7 +767,7 @@ FUNCTION void evaluate_the_objective_function()
       }
       else
       {
-        rho = SR_parm(N_SRparm2);
+        rho = SRparm(N_SRparm2);
         recr_like += square(recdev(recdev_first)) / two_sigmaRsq;
         for (y = recdev_first + 1; y <= recdev_end; y++)
         {
@@ -778,7 +778,7 @@ FUNCTION void evaluate_the_objective_function()
     }
     else
     {
-      rho = SR_parm(N_SRparm2);
+      rho = SRparm(N_SRparm2);
       dvariable dev;
       dvariable dev_last;
       if (recdev_first >= styr)
@@ -884,10 +884,10 @@ FUNCTION void evaluate_the_objective_function()
     }
 
     for (i = 1; i <= N_SRparm3; i++)
-      if (SR_parm_PRtype(i) > 0 && (active(SR_parm(i)) || Do_all_priors > 0))
+      if (SRparm_PRtype(i) > 0 && (active(SRparm(i)) || Do_all_priors > 0))
       {
-        SR_parm_Like(i) = Get_Prior(SR_parm_PRtype(i), SR_parm_LO(i), SR_parm_HI(i), SR_parm_PR(i), SR_parm_CV(i), SR_parm(i));
-        parm_like += SR_parm_Like(i);
+        SRparm_Like(i) = Get_Prior(SRparm_PRtype(i), SRparm_LO(i), SRparm_HI(i), SRparm_PR(i), SRparm_CV(i), SRparm(i));
+        parm_like += SRparm_Like(i);
       }
     //  SS_Label_Info_25.14 #logL for recdev_cycle
     if (recdev_cycle > 0)
@@ -1847,8 +1847,8 @@ FUNCTION void get_posteriors()
   }
   for (i = 1; i <= N_SRparm3; i++)
   {
-    if (active(SR_parm(i)))
-      posts << SR_parm(i) << " ";
+    if (active(SRparm(i)))
+      posts << SRparm(i) << " ";
   }
 
   if (recdev_cycle > 0)
diff --git a/SS_param.tpl b/SS_param.tpl
index 3f850ebf..ed0dc25f 100644
--- a/SS_param.tpl
+++ b/SS_param.tpl
@@ -157,11 +157,11 @@ PARAMETER_SECTION
   4darray recr_dist(styr-3,YrMax,1,N_GP*gender,1,N_settle_timings,1,pop);
   3darray recr_dist_unf(1,N_GP*gender,1,N_settle_timings,1,pop);
   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, SSB   Time_vary implementation of spawner-recruitment
-  vector SR_parm_virg(1,N_SRparm2+1)
-  vector SR_parm_work(1,N_SRparm2+1)
+!!//  SS_Label_Info_5.1.2 #Create SRparm vector, recruitment vectors
+  init_bounded_number_vector SRparm(1,N_SRparm3,SRparm_LO,SRparm_HI,SRparm_PH)
+  matrix SRparm_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 SRparm_virg(1,N_SRparm2+1)
+  vector SRparm_work(1,N_SRparm2+1)
   number two_sigmaRsq;
   number half_sigmaRsq;
   number sigmaR;
@@ -174,7 +174,7 @@ PARAMETER_SECTION
  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(SRparm(N_SRparm2)!=0.0 || SRparm_PH(N_SRparm2)>0) {SR_autocorr=1;} else {SR_autocorr=0;}  // flag for recruitment autocorrelation
   if (do_recdev == 1)
   {
     k = recdev_start;
@@ -632,7 +632,7 @@ PARAMETER_SECTION
   vector init_F_Like(1,N_init_F)
   vector Q_parm_Like(1,Q_Npar2)
   vector selparm_Like(1,N_selparm2)
-  vector SR_parm_Like(1,N_SRparm3)
+  vector SRparm_Like(1,N_SRparm3)
   vector recdev_cycle_Like(1,recdev_cycle)
 !! k=Do_TG*(3*N_TG+2*Nfleet1);
   vector TG_parm_Like(1,k);
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index c4e55ffc..35a426ef 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -8,7 +8,7 @@
 FUNCTION void setup_recdevs()
   {
   //  SS_Label_Info_7.1 #Set up recruitment bias_adjustment vector
-  sigmaR = SR_parm(N_SRparm(SR_fxn) + 1);
+  sigmaR = SRparm(N_SRparm(SR_fxn) + 1);
   two_sigmaRsq = 2.0 * sigmaR * sigmaR;
   half_sigmaRsq = 0.5 * sigmaR * sigmaR;
 
@@ -352,26 +352,26 @@ FUNCTION void get_initial_conditions()
   //  h = a * SPR0 / (4. + a * SPR0)
   //  R0 = 1/b * (a-1/SPR0)
 
-      alpha = mfexp(SR_parm(3));
-      beta = mfexp(SR_parm(4));
+      alpha = mfexp(SRparm(3));
+      beta = mfexp(SRparm(4));
       steepness = alpha * SSBpR_virgin / (4. + alpha * SSBpR_virgin);
       Recr_virgin = 1. / beta * (alpha - (1. / SSBpR_virgin));
-      SR_parm(1) = log(Recr_virgin);
-      SR_parm(2) = steepness;
+      SRparm(1) = log(Recr_virgin);
+      SRparm(2) = steepness;
     }
     else
     {
-      Recr_virgin = mfexp(SR_parm(1));
+      Recr_virgin = mfexp(SRparm(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);
+    SRparm_byyr(eq_yr, i) = SRparm(i);
+    SRparm_virg(i) = SRparm(i);
+    SRparm_work(i) = SRparm(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;
+//  if (SR_fxn == 3) warning << "tester_A: " << SRparm_work(1) << " base: " << SRparm(1) << endl;
+//  if (SR_fxn == 10) warning << "tester_A: " << SRparm_work(4) << " base: " << SRparm(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;
@@ -395,9 +395,9 @@ FUNCTION void get_initial_conditions()
     if (Hermaphro_Option != 0)
       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;
+    SRparm_byyr(eq_yr, N_SRparm2 + 1) = SSB_equil;
+    SRparm_virg(N_SRparm2 + 1) = SSB_equil;
+    SRparm_work(N_SRparm2 + 1) = SSB_equil;
     t = styr - 2 * nseas - 1;
     for (s = 1; s <= nseas; s++)
       for (p = 1; p <= pop; p++)
@@ -470,18 +470,18 @@ FUNCTION void get_initial_conditions()
 
   for (f = 1; f <= N_SRparm2; f++)
   {
-    if (SR_parm_timevary(f) == 0)
+    if (SRparm_timevary(f) == 0)
     {
-      //  no change to SR_parm_work
+      //  no change to SRparm_work
     }
     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;
+      SRparm_work(f) = parm_timevary(SRparm_timevary(f), eq_yr);
+//      warning << "tester_B: " << SRparm_work(f) << " timevary " << " base " << SRparm(f) <<endl;
 //      warning << parm_timevary(2) << endl;
 
     }
-    SR_parm_byyr(eq_yr, f) = SR_parm_work(f);
+    SRparm_byyr(eq_yr, f) = SRparm_work(f);
   }
   for (s = 1; s <= nseas; s++)
   {
@@ -499,14 +499,14 @@ FUNCTION void get_initial_conditions()
   //  change with 3.30.12 to allow R0 to change according to a timevary effect
   //  exp_rec(eq_yr,1)=Recr_virgin;
   //  R1_exp=Recr_virgin;
-  R1_exp = mfexp(SR_parm_work(1));
+  R1_exp = mfexp(SRparm_work(1));
   exp_rec(eq_yr, 1) = R1_exp;
   //  SS_Label_Info_23.5.1  #Apply adjustments to the recruitment level
   //  SPAWN-RECR:   adjust recruitment for the initial equilibrium
   regime_change = 1.0;
-  if (SR_parm_timevary(N_SRparm2 - 1) > 0) //  timevary regime exists
+  if (SRparm_timevary(N_SRparm2 - 1) > 0) //  timevary regime exists
   {
-    regime_change = mfexp(SR_parm_work(N_SRparm2 - 1));
+    regime_change = mfexp(SRparm_work(N_SRparm2 - 1));
   }
 
   if (init_equ_steepness == 0) // Adjustments do not include spawner-recruitment steepness
@@ -534,7 +534,7 @@ FUNCTION void get_initial_conditions()
     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, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_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;
 
@@ -554,8 +554,8 @@ FUNCTION void get_initial_conditions()
   if (Hermaphro_Option != 0)
     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;
+  SRparm_byyr(eq_yr, N_SRparm2 + 1) = SSB_equil;
+  SRparm_work(N_SRparm2 + 1) = SSB_equil;
   SSB_yr(styr) = SSB_equil;
   env_data(styr - 1, -1) = 0.0;
   env_data(styr - 1, -2) = 0.0;
@@ -721,16 +721,16 @@ FUNCTION void get_time_series()
 
     for (f = 1; f <= N_SRparm2; f++)
     {
-      if (SR_parm_timevary(f) == 0)
+      if (SRparm_timevary(f) == 0)
       {
-        //  no change to SR_parm_work
+        //  no change to SRparm_work
       }
       else
       {
-        SR_parm_work(f) = parm_timevary(SR_parm_timevary(f), y);
-//        warning << "tester_C: " << SR_parm_work(f) << " timevary_year " << endl;
+        SRparm_work(f) = parm_timevary(SRparm_timevary(f), y);
+//        warning << "tester_C: " << SRparm_work(f) << " timevary_year " << endl;
       }
-      SR_parm_byyr(y, f) = SR_parm_work(f);
+      SRparm_byyr(y, f) = SRparm_work(f);
     }
 
       //  SS_Label_Info_24.1.1 #store begin of year quantities for use in density-dependent processes
@@ -1024,16 +1024,16 @@ 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 (timevary_parm_start_SR == 0 || timevary_SRparm (y) == 0) //  SRparm are not time-varying (but regime still could be)
+        if (timevary_parm_SR_first == 0 || timevary_SRparm(y) == 0) //  SRparm are not time-varying (but regime still could be)
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
-          warning << y << " virgin "<<SSB_use<<" "<<R0_use <<"  steep " << SR_parm_work(2);
+          warning << y << " virgin "<<SSB_use<<" "<<R0_use <<"  steep " << SRparm_work(2);
         }
         else  //  timevary 
         {
-          R0_use = mfexp(SR_parm_work(1));
-          //  timevary steepness is in SR_parm_work(2) and will be applied inside of Equil_Spawn_Recr_Fxn
+          R0_use = mfexp(SRparm_work(1));
+          //  timevary steepness is in SRparm_work(2) and will be applied inside of Equil_Spawn_Recr_Fxn
           equ_Recr = R0_use;
           Fishon = 0;
           eq_yr = y;
@@ -1041,8 +1041,8 @@ FUNCTION void get_time_series()
           SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
           SSBpR_temp = SSB_use / R0_use;  // get unfished SSBpR
-          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB_use, R0_use, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-          warning << y << " pR only "<<SSB_use<<" "<<R0_use<<"  steep " << SR_parm_work(2)<< " equil: "<<Equ_SpawnRecr_Result;
+          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB_use, R0_use, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+          warning << y << " pR only "<<SSB_use<<" "<<R0_use<<"  steep " << SRparm_work(2)<< " equil: "<<Equ_SpawnRecr_Result;
           R0_use = Equ_SpawnRecr_Result(2);
           SSB_use = Equ_SpawnRecr_Result(1);
           if (fishery_on_off == 1)
@@ -1492,14 +1492,14 @@ 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 (timevary_parm_start_SR == 0) //  SR parms are not time-varying
+        if (timevary_parm_SR_first == 0) //  SR parms are not time-varying
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
         }
         else if (timevary_SRparm (y) > 0)
         {
-          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(SRparm_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;
@@ -1802,10 +1802,10 @@ FUNCTION void get_time_series()
       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
+        alpha = mfexp(SRparm_work(3));
+        beta = mfexp(SRparm_work(4));
+        SRparm_byyr(y, 2) =  alpha * temp / (4. + alpha * temp);  //  implied steepness
+        SRparm_byyr(y, 1) = log( 1. / beta * (alpha - (1. / temp)));  //  implied ln_R0
       }
       Fishon = 1;
       SSBpR_Calc(equ_Recr); //  call function to do per recruit calculation with current year's biology and F
diff --git a/SS_prelim.tpl b/SS_prelim.tpl
index b23dff21..b58f1a05 100644
--- a/SS_prelim.tpl
+++ b/SS_prelim.tpl
@@ -689,9 +689,9 @@
 
     for (i = 1; i <= N_SRparm3; i++)
     {
-      SR_parm(i) = SR_parm_RD(i);
+      SRparm(i) = SRparm_RD(i);
     }
-    echoinput << " SRR_parms read from ctl " << SR_parm << endl;
+    echoinput << " SRR_parms read from ctl " << SRparm << endl;
 
     if (recdev_cycle > 0)
     {
@@ -863,13 +863,13 @@
   MGparm_use = value(MGparm);
 
   echoinput << endl
-            << " now check SR_parm bounds and priors and do jitter if requested " << endl;
+            << " now check SRparm bounds and priors and do jitter if requested " << endl;
   for (i = 1; i <= N_SRparm3; i++)
   {
-    SR_parm(i) = Check_Parm(i, SR_parm_PH(i), SR_parm_LO(i), SR_parm_HI(i), SR_parm_PRtype(i), SR_parm_PR(i), SR_parm_CV(i), jitter, SR_parm(i));
+    SRparm(i) = Check_Parm(i, SRparm_PH(i), SRparm_LO(i), SRparm_HI(i), SRparm_PRtype(i), SRparm_PR(i), SRparm_CV(i), jitter, SRparm(i));
   }
-  echoinput << " SRR_parms after check " << SR_parm << endl;
-  SR_parm_use = value(SR_parm);
+  echoinput << " SRR_parms after check " << SRparm << endl;
+  SRparm_use = value(SRparm);
 
   recdev_use.initialize();
   if (recdev_cycle > 0)
diff --git a/SS_proced.tpl b/SS_proced.tpl
index 3e545ba7..8d4896aa 100644
--- a/SS_proced.tpl
+++ b/SS_proced.tpl
@@ -24,8 +24,8 @@ PROCEDURE_SECTION
   {
     if (mcmc_counter == 0)
     {
-      SR_parm(1) += MCMC_bump;
-      cout << mcmc_counter << "   adjusted SR_parm in first mcmc call " << SR_parm(1) << "  by  " << MCMC_bump << endl;
+      SRparm(1) += MCMC_bump;
+      cout << mcmc_counter << "   adjusted SRparm in first mcmc call " << SRparm(1) << "  by  " << MCMC_bump << endl;
     }
 
     mcmc_counter++;
@@ -255,11 +255,11 @@ PROCEDURE_SECTION
           ParmTrace << " " << MGparm(j);
         }
       }
-      for (j = 1; j <= SR_parm_PH.indexmax(); j++)
+      for (j = 1; j <= SRparm_PH.indexmax(); j++)
       {
-        if (SR_parm_PH(j) >= 0)
+        if (SRparm_PH(j) >= 0)
         {
-          ParmTrace << " " << SR_parm(j);
+          ParmTrace << " " << SRparm(j);
         }
       }
       if (recdev_cycle > 0)
@@ -384,7 +384,7 @@ PROCEDURE_SECTION
       ParmTrace << current_phase() << " " << niter << " " << obj_fun << " " << obj_fun - last_objfun
                 << " " << value(SSB_yr(styr)) << " " << value(SSB_yr(endyr)) << " " << biasadj(styr) << " " << max(biasadj) << " " << biasadj(endyr);
       ParmTrace << " " << MGparm << " ";
-      ParmTrace << SR_parm << " ";
+      ParmTrace << SRparm << " ";
       if (recdev_cycle > 0)
         ParmTrace << recdev_cycle_parm;
       if (recdev_do_early > 0)
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index eaed1c0f..7a28a785 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1959,8 +1959,8 @@
   int N_SRparm2
   int N_SRparm3  //  with timevary links included
 !!N_SRparm2=N_SRparm(SR_fxn)+3;
-  init_matrix SR_parm_1(1,N_SRparm2,1,14)
-!!echoinput<<" SR parms "<<endl<<SR_parm_1<<endl;
+  init_matrix SRparm_1(1,N_SRparm2,1,14)
+!!echoinput<<" SR parms "<<endl<<SRparm_1<<endl;
    int SR_env_link
 //  !!echoinput<<SR_env_link<<" SR_env_link "<<endl;
     int SR_env_target_RD   // 0=none; 1=devs; 2=R0; 3=steepness
@@ -1968,20 +1968,20 @@
   int SR_env_target
   int SR_autocorr;  // will be calculated later
 
-  int timevary_parm_start_SR;  //   == 0 means that no relevant parms are timevarying
+  int timevary_parm_SR_first;  //   == 0 means that no relevant parms are timevarying
   int firstSRparm;
-  int timevary_parm_cnt_SR;
+  int timevary_parm_SR_last;
   ivector timevary_SRparm(styr-3,YrMax+1);
-  ivector SR_parm_timevary(1,N_SRparm2);
+  ivector SRparm_timevary(1,N_SRparm2);
 
  LOCAL_CALCS
   // clang-format on
   //  SS_Label_Info_4.6.1 #Create S-R parameter labels
   firstSRparm = ParCount;
-  timevary_parm_cnt_SR = 0;
-  timevary_parm_start_SR = 0;
+  timevary_parm_SR_last = 0;
+  timevary_parm_SR_first = 0;
   timevary_SRparm.initialize();
-  SR_parm_timevary.initialize();
+  SRparm_timevary.initialize();
   SR_env_link = 0;
   SR_env_target = 0;
 
@@ -2056,9 +2056,9 @@
   ParmLabel += "SR_autocorr";
   ParCount += N_SRparm2;
   
-  if (SR_parm_1(N_SRparm2 - 2, 7) > 0) varparm_estimated(2) = 1; //  sigmaR is estimated so need sd_offset=1
+  if (SRparm_1(N_SRparm2 - 2, 7) > 0) varparm_estimated(2) = 1; //  sigmaR is estimated so need sd_offset=1
   
-  if (SR_parm_1(N_SRparm2, 3) != 0.0 || SR_parm_1(N_SRparm2, 7) > 0)
+  if (SRparm_1(N_SRparm2, 3) != 0.0 || SRparm_1(N_SRparm2, 7) > 0)
   {
     SR_autocorr = 1;
   }
@@ -2074,19 +2074,19 @@
   for (j = 1; j <= N_SRparm2 - 1; j++)  // so omits autocorr
     if (j != N_SRparm2 - 2) //  because sigmaR cannot be time-varying
     {
-      if (SR_parm_1(j, 13) == 0 && SR_parm_1(j, 8) == 0 && SR_parm_1(j, 9) == 0)
+      if (SRparm_1(j, 13) == 0 && SRparm_1(j, 8) == 0 && SRparm_1(j, 9) == 0)
       {
         //  no time-vary parameter effects
       }
       else //  set up a timevary parameter definition
       {
+        timevary_used = 1;
         ivector timevary_setup(1, 14); //  temporary vector for timevary specs
         timevary_setup.initialize();
-        if (timevary_parm_start_SR == 0) timevary_parm_start_SR = timevary_parm_cnt + 1;
+        if (timevary_parm_SR_first == 0) timevary_parm_SR_first = timevary_parm_cnt + 1;  // cumulative index for first timevary SRparm
         echoinput << " timevary for SR parm: " << j << endl;
-        timevary_used = 1;
         timevary_cnt++; //  count parameters with time-vary effect
-        SR_parm_timevary(j) = timevary_cnt; //  base SR parameter will use this timevary specification
+        SRparm_timevary(j) = timevary_cnt; //  base SR parameter will use this timevary specification
         timevary_setup(1) = 2; //  indicates a SR parm
         if (autogen_timevary(2) == 0)
         {
@@ -2101,37 +2101,37 @@
         timevary_setup(3) = timevary_parm_cnt + 1; //  first parameter within total list of all timevary parms
         timevary_pass = 0; // placeholder; not used for SR parms
         //  set up env link info
-        echoinput << " check for env " << SR_parm_1(j, 8) << endl;
-        k = int(abs(SR_parm_1(j, 8)) / 100); //  find the env link code
+        echoinput << " check for env " << SRparm_1(j, 8) << endl;
+        k = int(abs(SRparm_1(j, 8)) / 100); //  find the env link code
         timevary_setup(6) = k; //  link code for env
-        if (SR_parm_1(j, 8) > 0) //  env variable used
+        if (SRparm_1(j, 8) > 0) //  env variable used
         {
-          timevary_setup(7) = int(abs(SR_parm_1(j, 8))) - k * 100;
+          timevary_setup(7) = int(abs(SRparm_1(j, 8))) - k * 100;
           k = timevary_setup(7);
           //         for(y=styr-1;y<=YrMax;y++) env_data_pass(y)=env_data_RD(y,k);
           env_data_pass(1) = env_data_minyr(k);
           env_data_pass(2) = env_data_maxyr(k);
         }
-        else if (abs(SR_parm_1(j, 8) > 0)) //  density-dependence
+        else if (abs(SRparm_1(j, 8) > 0)) //  density-dependence
         {
-          timevary_setup(7) = -int(abs(SR_parm_1(j, 8)) - k * 100);
+          timevary_setup(7) = -int(abs(SRparm_1(j, 8)) - k * 100);
           do_densitydependent = 1;
           k = 0;
           env_data_pass.initialize();
         }
   
-        if (SR_parm_1(j, 13) > 0) //  doing blocks
+        if (SRparm_1(j, 13) > 0) //  doing blocks
         {
-          if (SR_parm_1(j, 13) > N_Block_Designs)
+          if (SRparm_1(j, 13) > N_Block_Designs)
           {
             warnstream << "SR block request exceeds N_block patterns";
             write_message (FATAL, 0); // EXIT!
           }
-          create_timevary(SR_parm_1(j), timevary_setup, timevary_pass, autogen_timevary(timevary_setup(1)), f, Block_Design(SR_parm_1(j, 13)), env_data_pass, N_parm_dev, finish_starter);
+          create_timevary(SRparm_1(j), timevary_setup, timevary_pass, autogen_timevary(timevary_setup(1)), f, Block_Design(SRparm_1(j, 13)), env_data_pass, N_parm_dev, finish_starter);
         }
         else
         {
-          create_timevary(SR_parm_1(j), timevary_setup, timevary_pass, autogen_timevary(timevary_setup(1)), f, block_design_null, env_data_pass, N_parm_dev, finish_starter);
+          create_timevary(SRparm_1(j), timevary_setup, timevary_pass, autogen_timevary(timevary_setup(1)), f, block_design_null, env_data_pass, N_parm_dev, finish_starter);
         }
         timevary_def.push_back(timevary_setup(1, 14));
         for (y = styr - 3; y <= YrMax + 1; y++)
@@ -2142,55 +2142,55 @@
     }
   
   N_SRparm3 = N_SRparm2;
-  if (timevary_parm_start_SR > 0)
+  if (timevary_parm_SR_first > 0)
   {
-    timevary_parm_cnt_SR = timevary_parm_cnt;
+    timevary_parm_SR_last = timevary_parm_cnt;
     if (timevary_used == 1) autogen_timevary(2) = 1; //  indicate that some parameter is time-varying
-    N_SRparm3 += (timevary_parm_cnt_SR - timevary_parm_start_SR + 1);
-    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;
+    N_SRparm3 += (timevary_parm_SR_last - timevary_parm_SR_first + 1);
+    echoinput << " SR timevary_parm_cnt start and end " << timevary_parm_SR_first << " " << timevary_parm_SR_last << endl;
+    echoinput << "link to timevary parms:  " << SRparm_timevary << endl;
   }
   echoinput << "SR_Npar and N_SRparm2 and N_SRparm3:  " << N_SRparm(SR_fxn) << " " << N_SRparm2 << " " << N_SRparm3 << endl;
   // clang-format off
  END_CALCS
 
-  vector SR_parm_LO(1,N_SRparm3)
-  vector SR_parm_HI(1,N_SRparm3)
-  vector SR_parm_RD(1,N_SRparm3)
-  vector SR_parm_PR(1,N_SRparm3)
-  ivector SR_parm_PRtype(1,N_SRparm3)
-  vector SR_parm_CV(1,N_SRparm3)
-  ivector SR_parm_PH(1,N_SRparm3)
+  vector SRparm_LO(1,N_SRparm3)
+  vector SRparm_HI(1,N_SRparm3)
+  vector SRparm_RD(1,N_SRparm3)
+  vector SRparm_PR(1,N_SRparm3)
+  ivector SRparm_PRtype(1,N_SRparm3)
+  vector SRparm_CV(1,N_SRparm3)
+  ivector SRparm_PH(1,N_SRparm3)
 
  LOCAL_CALCS
       // clang-format on
       for (i = 1; i <= N_SRparm2; i++)
   {
-    SR_parm_LO(i) = SR_parm_1(i, 1);
-    SR_parm_HI(i) = SR_parm_1(i, 2);
-    SR_parm_RD(i) = SR_parm_1(i, 3);
-    SR_parm_PR(i) = SR_parm_1(i, 4);
-    SR_parm_CV(i) = SR_parm_1(i, 5);
-    SR_parm_PRtype(i) = SR_parm_1(i, 6);
-    SR_parm_PH(i) = SR_parm_1(i, 7);
+    SRparm_LO(i) = SRparm_1(i, 1);
+    SRparm_HI(i) = SRparm_1(i, 2);
+    SRparm_RD(i) = SRparm_1(i, 3);
+    SRparm_PR(i) = SRparm_1(i, 4);
+    SRparm_CV(i) = SRparm_1(i, 5);
+    SRparm_PRtype(i) = SRparm_1(i, 6);
+    SRparm_PH(i) = SRparm_1(i, 7);
   }
-  if (timevary_parm_start_SR > 0)
+  if (timevary_parm_SR_first > 0)
   {
     j = N_SRparm2;
-    for (f = timevary_parm_start_SR; f <= timevary_parm_cnt_SR; f++)
+    for (f = timevary_parm_SR_first; f <= timevary_parm_SR_last; f++)
     {
       j++;
       echoinput << f << " " << j << " " << timevary_parm_rd[f] << endl;
-      SR_parm_LO(j) = timevary_parm_rd[f](1);
-      SR_parm_HI(j) = timevary_parm_rd[f](2);
-      SR_parm_RD(j) = timevary_parm_rd[f](3);
-      SR_parm_PR(j) = timevary_parm_rd[f](4);
-      SR_parm_PRtype(j) = timevary_parm_rd[f](6);
-      SR_parm_CV(j) = timevary_parm_rd[f](5);
-      SR_parm_PH(j) = timevary_parm_rd[f](7);
+      SRparm_LO(j) = timevary_parm_rd[f](1);
+      SRparm_HI(j) = timevary_parm_rd[f](2);
+      SRparm_RD(j) = timevary_parm_rd[f](3);
+      SRparm_PR(j) = timevary_parm_rd[f](4);
+      SRparm_PRtype(j) = timevary_parm_rd[f](6);
+      SRparm_CV(j) = timevary_parm_rd[f](5);
+      SRparm_PH(j) = timevary_parm_rd[f](7);
     }
   }
-  echoinput << "SR_parm_RD: " << SR_parm_RD << endl;
+  echoinput << "SRparm_RD: " << SRparm_RD << endl;
   // clang-format off
  END_CALCS
 
@@ -5902,19 +5902,19 @@
     }
   }
   
-  for (j = 1; j <= SR_parm_PH.indexmax(); j++)
+  for (j = 1; j <= SRparm_PH.indexmax(); j++)
   {
     ParCount++;
-    if (SR_parm_PH(j) == -9999) {
-      SR_parm_1(j, 3) = prof_var(prof_var_cnt);
-      SR_parm_RD(j, 3) = SR_parm_1(j, 3);
+    if (SRparm_PH(j) == -9999) {
+      SRparm_1(j, 3) = prof_var(prof_var_cnt);
+      SRparm_RD(j, 3) = SRparm_1(j, 3);
       prof_var_cnt += 1;
     }
-    if (depletion_fleet > 0 && depletion_type < 2 && SR_parm_PH(j) > 0) SR_parm_PH(j)++; //  add 1 to phase if using depletion fleet
-    if (depletion_fleet > 0 && depletion_type < 2 && j == 1) SR_parm_PH(1) = 1; //  R0 active in phase 1, unless type==2
-    if (SR_parm_PH(j) > Turn_off_phase2) SR_parm_PH(j) = -1;
-    if (SR_parm_PH(j) > max_phase) max_phase = SR_parm_PH(j);
-    if (SR_parm_PH(j) >= 0)
+    if (depletion_fleet > 0 && depletion_type < 2 && SRparm_PH(j) > 0) SRparm_PH(j)++; //  add 1 to phase if using depletion fleet
+    if (depletion_fleet > 0 && depletion_type < 2 && j == 1) SRparm_PH(1) = 1; //  R0 active in phase 1, unless type==2
+    if (SRparm_PH(j) > Turn_off_phase2) SRparm_PH(j) = -1;
+    if (SRparm_PH(j) > max_phase) max_phase = SRparm_PH(j);
+    if (SRparm_PH(j) >= 0)
     {
       active_count++;
       active_parm(active_count) = ParCount;
@@ -7082,7 +7082,7 @@
 
 //  containers for parameter values after jitter
     vector MGparm_use(1,N_MGparm2)
-    vector SR_parm_use(1,N_SRparm3);
+    vector SRparm_use(1,N_SRparm3);
     vector recdev_cycle_use(1,recdev_cycle);
     vector recdev_use(recdev_first,YrMax);
     vector recdev_RD(recdev_first,YrMax);
diff --git a/SS_recruit.tpl b/SS_recruit.tpl
index 2fb0b3c4..93263b20 100644
--- a/SS_recruit.tpl
+++ b/SS_recruit.tpl
@@ -27,7 +27,7 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_use, const prevariab
   //  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
 
-  regime_change = SR_parm_work(N_SRparm2 - 1); //  this is a persistent deviation off the S/R curve
+  regime_change = SRparm_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_use,SSB_virgin_use which could have been adjusted adjusted above from R0,SSB_virgin
@@ -42,14 +42,14 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_use, const prevariab
     //  SS_Label_43.3.2  Ricker
     case 2: // ricker
     {
-      steepness = SR_parm_work(2);
+      steepness = SRparm_work(2);
       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);
+      steepness = SRparm_work(2);
       NewRecruits = (4. * steepness * Recr_virgin_use * SSB_curr_adj) /
           (SSB_virgin_use * (1. - steepness) + (5. * steepness - 1.) * SSB_curr_adj);
       break;
@@ -57,8 +57,8 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_use, const prevariab
 
       case 10: // Beverton-Holt with alpha beta  per WHAM:  R = A*S/(1+B*S)
       {
-        dvariable alpha = mfexp(SR_parm_work(3));
-        dvariable beta = mfexp(SR_parm_work(4));
+        dvariable alpha = mfexp(SRparm_work(3));
+        dvariable beta = mfexp(SRparm_work(4));
         NewRecruits =  (alpha * SSB_curr_adj) / (1.0 + beta * SSB_curr_adj);
         break;
       }
@@ -73,8 +73,8 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_use, const prevariab
     case 5: // hockey stick  where "steepness" is now the fraction of B0 below which recruitment declines linearly
       //  the 3rd parameter allows for a minimum recruitment level
       {
-        steepness = SR_parm_work(2);
-        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
+        steepness = SRparm_work(2);
+        temp = SRparm_work(3) * Recr_virgin_use + SSB_curr_adj / (steepness * SSB_virgin_use) * (Recr_virgin_use - SRparm_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;
       }
@@ -82,7 +82,7 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_use, const prevariab
     //  SS_Label_43.3.6  Beverton-Holt, with constraint to have constant R about Bzero
     case 6: //Beverton-Holt constrained
     {
-      steepness = SR_parm_work(2);
+      steepness = SRparm_work(2);
 //      dvariable SPR = SSB_virgin_use / Recr_virgin;
 //      alpha = ((4.0 * steepness) / (1. - steepness)) / SPR ;
 //      beta = (1.0 / Recr_virgin) * (alpha - (1.0 / SPR));
@@ -104,15 +104,15 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_use, const prevariab
       // 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_use;  //  total population fecundity is the number of pups produced
-      // Sfrac=SR_parm(2);
+      // Sfrac=SRparm(2);
       SRZ_0 = log(1.0 / (SSB_virgin_use / Recr_virgin_use));
-      steepness = SR_parm_work(2);
+      steepness = SRparm_work(2);
       srz_min = SRZ_0 * (1.0 - steepness);
-      SRZ_surv = mfexp((1. - pow((SSB_curr_adj / SSB_virgin_use), SR_parm_work(3))) * (srz_min - SRZ_0) + SRZ_0); //  survival
+      SRZ_surv = mfexp((1. - pow((SSB_curr_adj / SSB_virgin_use), SRparm_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
-      //        if(SR_env_target==1) SRZ_surv*=mfexp(SR_parm(N_SRparm2-2)* env_data(y,SR_env_link));   // environ effect on survival
+      //        if(SR_env_target==1) SRZ_surv*=mfexp(SRparm(N_SRparm2-2)* env_data(y,SR_env_link));   // environ effect on survival
       if (recdev_cycle > 0)
       {
         gg = y - (styr + (int((y - styr) / recdev_cycle)) * recdev_cycle) + 1;
@@ -141,10 +141,10 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_use, const prevariab
     //  SS_Label_43.3.8  Shepherd
     case 8: // Shepherd 3-parameter SRR. per Punt & Cope 2017
     {
-      Shepherd_c = SR_parm_work(3);
-      Shepherd_c2 = pow(0.2, SR_parm_work(3));
+      Shepherd_c = SRparm_work(3);
+      Shepherd_c2 = pow(0.2, SRparm_work(3));
       Hupper = 1.0 / (5.0 * Shepherd_c2);
-      steepness = 0.2 + (SR_parm_work(2) - 0.2) / (0.8) * (Hupper - 0.2);
+      steepness = 0.2 + (SRparm_work(2) - 0.2) / (0.8) * (Hupper - 0.2);
       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));
@@ -154,8 +154,8 @@ FUNCTION dvariable Spawn_Recr(const prevariable& SSB_virgin_use, const prevariab
     //  SS_Label_43.3.8  Ricker-power
     case 9: // Ricker power 3-parameter SRR.  per Punt & Cope 2017
     {
-      steepness = SR_parm_work(2);
-      dvariable RkrPower = SR_parm_work(3);
+      steepness = SRparm_work(2);
+      dvariable RkrPower = SRparm_work(3);
       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
@@ -177,7 +177,7 @@ FUNCTION void apply_recdev(prevariable& NewRecruits, const prevariable& Recr_vir
   //    exp_rec(y,2) is with regime shift or other env effect;
   //    exp_rec(y,3) is with bias adjustment
   //    exp_rec(y,4) is with dev
-  regime_change = SR_parm_work(N_SRparm2 - 1); //  this is a persistent deviation off the S/R curve
+  regime_change = SRparm_work(N_SRparm2 - 1); //  this is a persistent deviation off the S/R curve
 
   if (recdev_cycle > 0)
   {
@@ -446,8 +446,8 @@ FUNCTION dvar_vector Equil_Spawn_Recr_Fxn(const dvar_vector& SRparm,
 //   Recs = (SPRF0/SPR) * (1.0 - pow(Top,1.0/Power));
 //   Recs = posfun(Recs,0.0001,Penal);
 //   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));
+        steepness = 0.2 + (10.0 - 0.2)/(1+exp(-SRparm_work(2)));
+        dvariable RkrPower=exp(SRparm_work(3));
         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);
diff --git a/SS_timevaryparm.tpl b/SS_timevaryparm.tpl
index 3c721455..b4f6b1d1 100644
--- a/SS_timevaryparm.tpl
+++ b/SS_timevaryparm.tpl
@@ -52,15 +52,15 @@ FUNCTION void make_timevaryparm()
       }
       case 2: // SR
       {
-        baseparm = SR_parm(timevary_setup(2)); //  index of base parm
-        baseparm_min(tvary) = SR_parm_LO(timevary_setup(2));
-        baseparm_max(tvary) = SR_parm_HI(timevary_setup(2));
+        baseparm = SRparm(timevary_setup(2)); //  index of base parm
+        baseparm_min(tvary) = SRparm_LO(timevary_setup(2));
+        baseparm_max(tvary) = SRparm_HI(timevary_setup(2));
         if (do_once == 1)
-          echoinput << "base SR_parm " << baseparm << endl;
+          echoinput << "base SRparm " << baseparm << endl;
         for (j = timevary_setup(3); j < timevary_def[tvary + 1](3); j++)
         {
           timevary_parm_cnt_all++;
-          timevary_parm(timevary_parm_cnt_all) = SR_parm(N_SRparm(SR_fxn) + 3 + j - timevary_parm_start_SR + 1);
+          timevary_parm(timevary_parm_cnt_all) = SRparm(N_SRparm(SR_fxn) + 3 + j - timevary_parm_SR_first + 1);
           if (do_once == 1)
             echoinput << j << " timevary_parm: " << timevary_parm(timevary_parm_cnt_all) << endl;
         }
diff --git a/SS_write.tpl b/SS_write.tpl
index a3664db4..1ec1a4b6 100644
--- a/SS_write.tpl
+++ b/SS_write.tpl
@@ -125,7 +125,7 @@ FUNCTION void write_summaryoutput()
     for (j = 1; j <= N_parm_dev; j++)
       report2 << parm_dev(j) << " ";
   }
-  report2 << SR_parm << " ";
+  report2 << SRparm << " ";
   if (recdev_cycle > 0)
     report2 << recdev_cycle_parm << " ";
   if (recdev_do_early > 0)
@@ -180,14 +180,14 @@ FUNCTION void write_summaryoutput()
     }
   }
 
-  report2 << runnumber << " SR_parm ";
+  report2 << runnumber << " SRparm ";
   for (i = 1; i <= N_SRparm3 + recdev_cycle; i++)
   {
     NP++;
     report2 << " " << ParmLabel(NP);
   }
   report2 << endl
-          << runnumber << " SR_parm " << SR_parm << " ";
+          << runnumber << " SRparm " << SRparm << " ";
   if (recdev_cycle > 0)
     report2 << recdev_cycle_parm;
   report2 << endl;
@@ -453,8 +453,8 @@ FUNCTION void write_SS_summary()
   for (j = 1; j <= N_SRparm3; j++)
   {
     NP++;
-    SS_smry << ParmLabel(NP) << " " << SR_parm(j) << " ";
-    if (active(SR_parm(j)))
+    SS_smry << ParmLabel(NP) << " " << SRparm(j) << " ";
+    if (active(SRparm(j)))
     {
       active_count++;
       SS_smry << CoVar(active_count, 1) << " Act ";
@@ -463,7 +463,7 @@ FUNCTION void write_SS_summary()
     {
       SS_smry << 0.0 << " Fix ";
     }
-    SS_smry << (SR_parm(j) - SR_parm_LO(j)) / (SR_parm_HI(j) - SR_parm_LO(j) + 1.0e-6) << endl;
+    SS_smry << (SRparm(j) - SRparm_LO(j)) / (SRparm_HI(j) - SRparm_LO(j) + 1.0e-6) << endl;
   }
 
   if (recdev_cycle > 0)
@@ -989,7 +989,7 @@ FUNCTION void write_rebuilder_output()
   rebuilder << SSB_yr(styr - 2) << " " << SSB_yr(styr, k) << " #SpawnBio" << endl;
 
   //i. steepness; SigmaR; rho
-  rebuilder << SR_parm(2) << " " << sigmaR << " " << SR_parm(N_SRparm2) << " # spawn-recr steepness, sigmaR, autocorr" << endl;
+  rebuilder << SRparm(2) << " " << sigmaR << " " << SRparm(N_SRparm2) << " # spawn-recr steepness, sigmaR, autocorr" << endl;
 
   if (mceval_counter == 0)
   {
@@ -1042,7 +1042,7 @@ FUNCTION void write_rebuilder_output()
     rebuild_dat << "# Which probability to product detailed results for (1=0.5; 2=0.6; etc.)" << endl
                 << 3 << endl;
     rebuild_dat << "# Steepness sigma-R Auto-correlation" << endl
-                << SR_parm(2) << " " << sigmaR << " " << 0 << endl;
+                << SRparm(2) << " " << sigmaR << " " << 0 << endl;
     rebuild_dat << "# Target SPR rate (FMSY Proxy); manually change to SPR_MSY if not using SPR_target" << endl
                 << SPR_target << endl;
     rebuild_dat << "# Discount rate (for cumulative catch)" << endl
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 655a4ca2..b5eba96f 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -647,12 +647,12 @@ FUNCTION void write_bigoutput()
     {
       NP++;
       Activ = 0;
-      if (active(SR_parm(j)))
+      if (active(SRparm(j)))
       {
         active_count++;
         Activ = 1;
       }
-      Report_Parm(NP, active_count, Activ, SR_parm(j), SR_parm_LO(j), SR_parm_HI(j), SR_parm_RD(j), SR_parm_use(j), SR_parm_PR(j), SR_parm_CV(j), SR_parm_PRtype(j), SR_parm_PH(j), SR_parm_Like(j));
+      Report_Parm(NP, active_count, Activ, SRparm(j), SRparm_LO(j), SRparm_HI(j), SRparm_RD(j), SRparm_use(j), SRparm_PR(j), SRparm_CV(j), SRparm_PRtype(j), SRparm_PH(j), SRparm_Like(j));
     }
 
     if (recdev_cycle > 0)
@@ -1778,12 +1778,12 @@ FUNCTION void write_bigoutput()
     Durbin /= (var + 1.0e-09);
     var /= (n_rmse(1) + 1.0e-09);
 
-    dvariable steepness = SR_parm(2);
+    dvariable steepness = SRparm(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
+           << SRparm(1) << " Ln(R0) " << mfexp(SRparm(1)) << endl
            << steepness << " steepness" << endl
            << Bmsy / SSB_virgin << " Bmsy/Bzero ";
     if (SR_fxn == 8)
@@ -1791,22 +1791,22 @@ FUNCTION void write_bigoutput()
       dvariable Shepherd_c;
       dvariable Shepherd_c2;
       dvariable Hupper;
-      Shepherd_c = SR_parm(3);
+      Shepherd_c = SRparm(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);
+      temp = 0.2 + (SRparm(2) - 0.2) / (0.8) * (Hupper - 0.2);
       SS2out << " Shepherd_c: " << Shepherd_c << " steepness_limit: " << Hupper << " Adjusted_steepness: " << temp;
     }
     else if (SR_fxn == 9)
     {
-      SS2out << " Ricker_Power: " << SR_parm(3);
+      SS2out << " Ricker_Power: " << SRparm(3);
     }
 
     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
+    SS2out << SRparm(N_SRparm2 - 1) << " init_eq:  see below" << endl
            << recdev_start << " " << recdev_end << " main_recdev:start_end" << endl
            << recdev_adj(1) << " " << recdev_adj(2, 5) << " breakpoints_for_bias_adjustment_ramp " << endl;
 
@@ -1842,10 +1842,10 @@ FUNCTION void write_bigoutput()
     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 << j << " " << ParmLabel(firstSRparm + j) << " " << SRparm(j) << " " << SRparm_PH(j);
+      if (SRparm_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
+      if (j == (N_SRparm2 - 1) && SRparm_timevary(j) > 0) //  timevary regime exists
       {SS2out << " #_Regime_parameter_used_to_offset_from_SRR";}
       SS2out << endl;
     }
@@ -1860,7 +1860,7 @@ FUNCTION void write_bigoutput()
     {
       alpha = 4.0 * steepness / (SSBpR_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 << "Ln(R0): " << SRparm(1) << endl << "R0: " << mfexp(SRparm(1)) << endl;
       SS2out << "steepness: " << steepness << endl;
       SS2out << "Ln(alpha)_derived: " << log(alpha) << " alpha " << alpha << endl;
       SS2out << "Ln(beta)_derived: " << log(beta) << " beta " << beta;
@@ -1868,8 +1868,8 @@ FUNCTION void write_bigoutput()
     }
       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 << "Ln(alpha): " << SRparm(3) << " alpha " << mfexp(SRparm(3)) << endl;
+      SS2out << "Ln(beta): " << SRparm(4) << " beta " << mfexp(SRparm(4)) << endl;
       SS2out << "ln(R0)_derived: " << log( 1. / beta * (alpha - (1. / SSBpR_virgin))) << endl;  //  virgin R0
       SS2out << "steepness_derived: " << alpha * SSBpR_virgin / (4. + alpha * SSBpR_virgin) << endl;  // steepness virgin
       break;
@@ -1879,10 +1879,10 @@ FUNCTION void write_bigoutput()
       dvariable Shepherd_c;
       dvariable Shepherd_c2;
       dvariable Hupper;
-      Shepherd_c = SR_parm(3);
+      Shepherd_c = SRparm(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);
+      temp = 0.2 + (SRparm(2) - 0.2) / (0.8) * (Hupper - 0.2);
       SS2out << "Shepherd_c: " << Shepherd_c << endl << "Shepard_steepness_limit: " << Hupper << endl << "Shepard_adjusted_steepness: " << temp << endl;
       break;
     }
@@ -2006,7 +2006,7 @@ FUNCTION void write_bigoutput()
       }
       else
       {SS2out << " - - ";}
-      SS2out << SR_parm_byyr(y)(1,N_SRparm2) << endl;
+      SS2out << SRparm_byyr(y)(1,N_SRparm2) << endl;
     }
 
     // REPORT_KEYWORD SPAWN_RECR_CURVE
@@ -2017,7 +2017,7 @@ FUNCTION void write_bigoutput()
                << pick_report_name(20) << endl;
         SS2out << "SSB/SSB_virgin    SSB    Recruitment" << endl;
         y = styr;
-        SR_parm_work = SR_parm_byyr(styr);
+        SRparm_work = SRparm_byyr(styr);
         for (f = 1; f <= 120; f++)
         {
           SSB_current = double(f) / 100. * SSB_virgin;
@@ -4905,7 +4905,7 @@ FUNCTION void SPR_profile()
         SSBpR_Calc(equ_Recr);
         //  SPAWN-RECR:   calc equil spawn-recr in the SPR loop
         SSBpR_temp = SSB_equil;
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB0_4_SRR, R0_4_SRR, 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)
diff --git a/SS_write_ssnew.tpl b/SS_write_ssnew.tpl
index 1a134ca6..0dd77741 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -2146,11 +2146,11 @@ FUNCTION void write_nucontrol()
   for (f = 1; f <= N_SRparm2; f++)
   {
     NP++;
-    SR_parm_1(f, 3) = value(SR_parm(f));
+    SRparm_1(f, 3) = value(SRparm(f));
     for (j = 1; j <= 6; j++)
-      report4 << setw(14) << SR_parm_1(f, j);
+      report4 << setw(14) << SRparm_1(f, j);
     for (j = 7; j <= 14; j++)
-      report4 << setw(11) << SR_parm_1(f, j);
+      report4 << setw(11) << SRparm_1(f, j);
     report4 << " # " << ParmLabel(NP) << endl;
   }
   report4.unsetf(std::ios_base::fixed);
@@ -2158,7 +2158,7 @@ FUNCTION void write_nucontrol()
   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_SR_first; f <= timevary_parm_SR_last; f++)
     {
       NP++;
       timevary_parm_rd[f](3) = value(timevary_parm(f));

From a101320bf26511b74ccbe9ea82d3673178821c54 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Thu, 3 Apr 2025 15:46:19 -0700
Subject: [PATCH 35/58] timevary_SRparm_controls_working

---
 SS_benchfore.tpl       | 103 ++++++++++++++++++++++++++---------------
 SS_param.tpl           |   1 +
 SS_popdyn.tpl          |  59 +++++++++++++++--------
 SS_readcontrol_330.tpl |  12 ++++-
 4 files changed, 117 insertions(+), 58 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index d2f202c8..957081c0 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -747,6 +747,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       SRparm_work(j) = temp / (Bmark_Yr(10) - Bmark_Yr(9) + 1.);
     }
   }
+  SRparm_bench = SRparm_work;
 
  /*  
  Early thoughts: 
@@ -2706,33 +2707,47 @@ FUNCTION void Get_Forecast()
                 SSB_yr(y) = SSB_current;
               }
             }
-            //  SPAWN-RECR:   get recruitment in forecast;  needs to be area-specific
-            // SR_fxn
-            if (timevary_parm_SR_first == 0) //  R0 is not time-varying
-            {
-              R0_use = Recr_virgin;
-              SSB_use = SSB_virgin;
-            }
-            else
-            {
-              R0_use = mfexp(SRparm_work(1));
-              equ_Recr = R0_use;
-              Fishon = 0;
-              eq_yr = y;
-              bio_yr = y;
-              SSBpR_Calc(R0_use); //  call function to do per recruit calculation
-          //  should call equil_spawn_recr_fxn here to get updated equilibrium with the new SSB/R
+            //  SPAWN-RECR:   get recruitment in at beginning of a season in forecast;
+        if (timevary_SRparm(y) == 0) //  SRparm use virgin values (but regime still could be)
+        {
+          R0_use = Recr_virgin;
+          SSB_use = SSB_virgin;
+          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+        }
+        else if (timevary_SRparm(y) == 1)  //  update R0_use and SSB_use in this year
+                                           //  values will carry forward into subsequent years
+        {
+          R0_use = mfexp(SRparm_work(1));
+          //  timevary steepness is in SRparm_work(2) and will be applied inside of Equil_Spawn_Recr_Fxn() and Spawn_Recr()
+          equ_Recr = R0_use;
+          Fishon = 0;
+          eq_yr = y;
+          bio_yr = y;
+          SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
+          SSB_use = SSB_equil;
+          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+
+          // test that this stays on equilibrium.  It does.
+//          SSBpR_temp = SSB_use / R0_use;  // get unfished SSBpR
+//          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB_use, R0_use, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+//          warning << y << " pR only "<<SSB_use<<" "<<R0_use<<"  steep " << SRparm_work(2)<< " equil: "<<Equ_SpawnRecr_Result;
+//          R0_use = Equ_SpawnRecr_Result(2);
+//          SSB_use = Equ_SpawnRecr_Result(1);
           if (fishery_on_off == 1)
-              {
-                Fishon = 1;
-              }
-              else
-              {
-                Fishon = 0;
-              }
-              SSB_use = SSB_equil;
-            }
-            Recruits = Spawn_Recr(SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr
+          {
+            Fishon = 1;
+          }
+          else
+          {
+            Fishon = 0;
+          }
+        }
+        else  //  flag is 2
+        {
+          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+        }
+        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 (Fcast_Loop1 < Fcast_Loop_Control(2)) //  use expected recruitment  this should include environ effect - CHECK THIS
             {
@@ -3345,24 +3360,34 @@ FUNCTION void Get_Forecast()
                 SSB_yr(y) = SSB_current;
               }
             }
-            //  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 (timevary_parm_SR_first == 0) //  R0 is not time-varying
+            //  SS_Label_Info_24.3.4.1 #Get recruitment from this spawning biomass after start of the season
+            //  SPAWN-RECR
+            if (timevary_SRparm(y) == 0) //  SRparm use virgin values (but regime still could be)
             {
               R0_use = Recr_virgin;
               SSB_use = SSB_virgin;
+              warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
             }
-            else
+            else if (timevary_SRparm(y) == 1)  //  update R0_use and SSB_use in this year
+                                               //  values will carry forward into subsequent years
             {
               R0_use = mfexp(SRparm_work(1));
+              //  timevary steepness is in SRparm_work(2) and will be applied inside of Equil_Spawn_Recr_Fxn() and Spawn_Recr()
               equ_Recr = R0_use;
               Fishon = 0;
               eq_yr = y;
               bio_yr = y;
-              SSBpR_Calc(equ_Recr); //  call function to do per recruit calculation
-          //  should call equil_spawn_recr_fxn here to get updated equilibrium with the new SSB/R
-          if (fishery_on_off == 1)
+              SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
+              SSB_use = SSB_equil;
+              warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+    
+              // test that this stays on equilibrium.  It does.
+    //          SSBpR_temp = SSB_use / R0_use;  // get unfished SSBpR
+    //          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB_use, R0_use, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    //          warning << y << " pR only "<<SSB_use<<" "<<R0_use<<"  steep " << SRparm_work(2)<< " equil: "<<Equ_SpawnRecr_Result;
+    //          R0_use = Equ_SpawnRecr_Result(2);
+    //          SSB_use = Equ_SpawnRecr_Result(1);
+              if (fishery_on_off == 1)
               {
                 Fishon = 1;
               }
@@ -3370,11 +3395,13 @@ FUNCTION void Get_Forecast()
               {
                 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
+            else  //  flag is 2
+            {
+              warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+            }
+            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  among the settlements, areas and morphs
             for (g = 1; g <= gmorph; g++)
               if (use_morph(g) > 0)
diff --git a/SS_param.tpl b/SS_param.tpl
index ed0dc25f..2409c944 100644
--- a/SS_param.tpl
+++ b/SS_param.tpl
@@ -162,6 +162,7 @@ PARAMETER_SECTION
   matrix SRparm_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 SRparm_virg(1,N_SRparm2+1)
   vector SRparm_work(1,N_SRparm2+1)
+  vector SRparm_bench(1,N_SRparm2+1)
   number two_sigmaRsq;
   number half_sigmaRsq;
   number sigmaR;
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 35a426ef..25f67d93 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -1022,29 +1022,32 @@ 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 (timevary_parm_SR_first == 0 || timevary_SRparm(y) == 0) //  SRparm are not time-varying (but regime still could be)
+        //  SPAWN-RECR:   calc recruitment in time series
+        if (timevary_SRparm(y) == 0) //  SRparm use virgin values (but regime still could be)
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
-          warning << y << " virgin "<<SSB_use<<" "<<R0_use <<"  steep " << SRparm_work(2);
+          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
-        else  //  timevary 
+        else if (timevary_SRparm(y) == 1)  //  update R0_use and SSB_use in this year
+                                           //  values will carry forward into subsequent years
         {
           R0_use = mfexp(SRparm_work(1));
-          //  timevary steepness is in SRparm_work(2) and will be applied inside of Equil_Spawn_Recr_Fxn
+          //  timevary steepness is in SRparm_work(2) and will be applied inside of Equil_Spawn_Recr_Fxn() and Spawn_Recr()
           equ_Recr = R0_use;
           Fishon = 0;
           eq_yr = y;
           bio_yr = y;
           SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
-          SSBpR_temp = SSB_use / R0_use;  // get unfished SSBpR
-          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB_use, R0_use, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-          warning << y << " pR only "<<SSB_use<<" "<<R0_use<<"  steep " << SRparm_work(2)<< " equil: "<<Equ_SpawnRecr_Result;
-          R0_use = Equ_SpawnRecr_Result(2);
-          SSB_use = Equ_SpawnRecr_Result(1);
+          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+
+          // test that this stays on equilibrium.  It does.
+//          SSBpR_temp = SSB_use / R0_use;  // get unfished SSBpR
+//          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB_use, R0_use, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+//          warning << y << " pR only "<<SSB_use<<" "<<R0_use<<"  steep " << SRparm_work(2)<< " equil: "<<Equ_SpawnRecr_Result;
+//          R0_use = Equ_SpawnRecr_Result(2);
+//          SSB_use = Equ_SpawnRecr_Result(1);
           if (fishery_on_off == 1)
           {
             Fishon = 1;
@@ -1054,8 +1057,12 @@ FUNCTION void get_time_series()
             Fishon = 0;
           }
         }
+        else  //  flag is 2
+        {
+          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+        }
         Recruits = Spawn_Recr(SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr using either virgin or adjusted R0 and SSB0
-        warning <<"   SSB_current: " << SSB_current << "  recruits: "<<Recruits<< endl;
+//        warning <<"  SSB: " << SSB_current << "  R: " << Recruits << endl;
         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)
@@ -1492,20 +1499,31 @@ 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 (timevary_parm_SR_first == 0) //  SR parms are not time-varying
+        if (timevary_SRparm(y) == 0) //  SRparm use virgin values (but regime still could be)
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
+          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
-        else if (timevary_SRparm (y) > 0)
+        else if (timevary_SRparm(y) == 1)  //  update R0_use and SSB_use in this year
+                                           //  values will carry forward into subsequent years
         {
-          R0_use = mfexp(SRparm_work(1));  //  check to be sure this works when R0 is derived from B-H with alpha, beta parameters
+          R0_use = mfexp(SRparm_work(1));
+          //  timevary steepness is in SRparm_work(2) and will be applied inside of Equil_Spawn_Recr_Fxn() and Spawn_Recr()
+          equ_Recr = R0_use;
           Fishon = 0;
           eq_yr = y;
           bio_yr = y;
-          SSBpR_Calc(R0_use); //  call function to do per recruit calculation
+          SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
-          //  should call equil_spawn_recr_fxn here to get updated equilibrium with the new SSB/R
+          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+
+          // test that this stays on equilibrium.  It does.
+//          SSBpR_temp = SSB_use / R0_use;  // get unfished SSBpR
+//          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB_use, R0_use, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+//          warning << y << " pR only "<<SSB_use<<" "<<R0_use<<"  steep " << SRparm_work(2)<< " equil: "<<Equ_SpawnRecr_Result;
+//          R0_use = Equ_SpawnRecr_Result(2);
+//          SSB_use = Equ_SpawnRecr_Result(1);
           if (fishery_on_off == 1)
           {
             Fishon = 1;
@@ -1515,8 +1533,11 @@ FUNCTION void get_time_series()
             Fishon = 0;
           }
         }
-
-        Recruits = Spawn_Recr(SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr
+        else  //  flag is 2
+        {
+          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+        }
+        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 among settlements, areas and morphs
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 7a28a785..fb2d948a 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -2134,9 +2134,19 @@
           create_timevary(SRparm_1(j), timevary_setup, timevary_pass, autogen_timevary(timevary_setup(1)), f, block_design_null, env_data_pass, N_parm_dev, finish_starter);
         }
         timevary_def.push_back(timevary_setup(1, 14));
+        int SRflag;
+        SRflag = 0;
         for (y = styr - 3; y <= YrMax + 1; y++)
         {
-          if (timevary_pass(y) > 0 && j != N_SRparm2 - 1) timevary_SRparm(y , YrMax) = timevary_pass(y);  //  set timevary flag, except for regime parameter
+          if (timevary_pass(y) > 0 && j != N_SRparm2 - 1)
+          {
+            timevary_SRparm(y) = timevary_pass(y);  //  set timevary flag, except for regime parameter
+            SRflag = 1; //  first change point
+          }
+          else if(SRflag == 1)
+          {
+            timevary_SRparm(y) = 2;  //  flag to carry forward current SRR info
+          }
         }
       }
     }

From bf0931bc87faa4597bf39a86e56cf891149c30b8 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Fri, 4 Apr 2025 15:36:51 -0700
Subject: [PATCH 36/58] start cleanup reporting to Spawn_Recr table

---
 SS_benchfore.tpl       |  62 +++++++++++------------
 SS_popdyn.tpl          |  16 +-----
 SS_prelim.tpl          |   9 ++--
 SS_readcontrol_330.tpl |  17 ++++---
 SS_recruit.tpl         |   2 +-
 SS_timevaryparm.tpl    |   2 +-
 SS_write_report.tpl    | 110 ++++++++++++++++++++++++++++++++---------
 SS_write_ssnew.tpl     |   2 +-
 8 files changed, 132 insertions(+), 88 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 957081c0..84b7c961 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -735,7 +735,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   {
     if (SRparm_timevary(j) == 0)
     {
-      SRparm_work(j) = SRparm(j);
+      SRparm_bench(j) = SRparm(j);
     }
     else
     {
@@ -744,7 +744,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       {
         temp += SRparm_byyr(y, j);
       }
-      SRparm_work(j) = temp / (Bmark_Yr(10) - Bmark_Yr(9) + 1.);
+      SRparm_bench(j) = temp / (Bmark_Yr(10) - Bmark_Yr(9) + 1.);
     }
   }
   SRparm_bench = SRparm_work;
@@ -757,7 +757,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
 
  Flags:
   timevary_MG_firstyr == YrMax  // means that no biology is time-varying
-  timevary_parm_SR_first > 0 //  means that R0 or h (i.e. any except regime, sigmaR, autocorr) is time-varying, so SSBpR0 gets updated for time series and for bench
+  timevary_SRparm_first > 0 //  means that R0 or h (i.e. any except regime, sigmaR, autocorr) is time-varying, so SSBpR0 gets updated for time series and for bench
   timevary_bio_4SRR is new user selected flag:  0 for legacy, vs 1 for improved use of timevary biology in SRR calcs
 
  Legacy approach:
@@ -776,13 +776,13 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
  Improved approach
  SSBpR0 set at start year using start year biology
  SSBpR0 updated during time series if there is time-varying R0; PLUS NEW: equil_spawn_recr_calc called to get new equilibrium R0, SSB0
- SSBpR0 for benchmark stays at virgin unless timevary_bio_4SRR == 0, or if timevary_parm_SR_first > 0
+ SSBpR0 for benchmark stays at virgin unless timevary_bio_4SRR == 0, or if timevary_SRparm_first > 0
  Btgttgt can now use either frac*SSB_bench or frac*SSB_virgin by using the existing flag for depletion basis
  Btgttgt2 can be fraction of SSB_MSY, of SSB_virgin, or of SSB_bench
  HCR inflection adds option to use SSB_virgin or SSB_bench
  depletion adds option to use SSB_bench
  */
-  Recr_unf = mfexp(SRparm_work(1));  // R0 to be used
+  Recr_unf = mfexp(SRparm_bench(1));  // R0 to be used
   Fishon = 0;
   SSBpR_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
   dvariable SSBpR_bench = SSB_equil / Recr_unf;
@@ -793,7 +793,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   {
     SSB0_4_SRR = SSB_virgin;
     R0_4_SRR = Recr_virgin;
-    SSB_unf = SSB_equil;  //  should this also depend on timevary_parm_SR_first > 0???
+    SSB_unf = SSB_equil;  //  should this also depend on timevary_SRparm_first > 0???
   }
   else  //  there is some timevary biology (with any WTage_rd == 1 qualifying as timevarying without actually chacking for different values in diff years)
   {
@@ -801,7 +801,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     {
       warnstream << "There is timevary biology and the legacy approach to benchmark calculations is being used; user should be aware";
       write_message (WARN, 0);
-      if(timevary_parm_SR_first == 0)  // no timevary SRR parms
+      if(timevary_SRparm_first == 0)  // no timevary SRR parms
       {
         SSB_unf = SSB_equil;
         R0_4_SRR = Recr_unf;  // same as Recr_virgin because no timevary SRparms
@@ -810,25 +810,25 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       }
       else // there are timevary SRR parms
       {
-        Recr_unf = mfexp(SRparm_work(1));  // R0 to be used
-        // steepness and other SR parms will also come from SRparm_work
+        Recr_unf = mfexp(SRparm_bench(1));  // R0 to be used
+        // steepness and other SR parms will also come from SRparm_bench
         SSBpR_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
         SSB_unf = SSB_equil;
         R0_4_SRR = Recr_unf;
         SSB0_4_SRR = SSB_equil;  // this is legacy, but incorrect, as it moves equil off the SRR, rather than along the SRR
         SSBpR_bench = SSB0_4_SRR / R0_4_SRR;
       }
-      report5 << " legacy: Recr: " << R0_4_SRR << " SSB: " << SSB0_4_SRR << " bench SPR: " << SSBpR_bench << endl;
+      if (show_MSY == 1) report5 << " legacy: Recr: " << R0_4_SRR << " SSB: " << SSB0_4_SRR << " bench SPR: " << SSBpR_bench << endl;
     }
 
     else  // more complete approach to time vary biology will be used (introduced in 3.30.24)
     {
-      if(timevary_parm_SR_first == 0)  // no timevary SRR parms, so SRR will use SSB_virgin, Recr_virgin to internally create virgin SSBpR0 
+      if(timevary_SRparm_first == 0)  // no timevary SRR parms, so SRR will use SSB_virgin, Recr_virgin to internally create virgin SSBpR0 
       {
         SSB0_4_SRR = SSB_virgin;
         R0_4_SRR = Recr_virgin;
         //  get new equilibrium point using original SRR and SSBpR_bench
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB_virgin, Recr_virgin, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_bench, SSB_virgin, Recr_virgin, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         SSB_unf = Equ_SpawnRecr_Result(1);
         Recr_unf = Equ_SpawnRecr_Result(2);
         if (show_MSY == 1) report5 << " use virgin SSBpR0 in SRR - SSB: " << SSB_virgin << " Recr: " << Recr_virgin << " SPR: " << SSB_virgin / Recr_virgin << " bench SPR: " << SSBpR_bench << " new equil: " << Equ_SpawnRecr_Result << endl;
@@ -836,7 +836,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       else  //  use updated SRparms and benchmark biology
       {
         //  get new equilibrium point for the benchmark SRR
-        Recr_unf = mfexp(SRparm_work(1));  // R0 to be used
+        Recr_unf = mfexp(SRparm_bench(1));  // R0 to be used
         Fishon = 0;
         SSBpR_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
         SSBpR_bench = SSB_equil / Recr_unf;
@@ -844,7 +844,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         SSB_unf = SSB_equil;
         R0_4_SRR = Recr_unf;
         // verify
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB_equil, Recr_unf, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_bench, SSB_equil, Recr_unf, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         if (show_MSY == 1) report5 << " use bench SSBpR0 in SRR - SSB: " << SSB_unf << " Recr: " << Recr_unf << " SPR: " << SSBpR_bench << " new equil: " << Equ_SpawnRecr_Result << endl;
       }
       SSBpR_Calc(Recr_unf);  // this calcs SSBpR and returns it as SSB_equil using benchmark biology and the updated equil Recr
@@ -854,12 +854,12 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
 
   if (show_MSY == 1)
   {
-    SRparm_work(N_SRparm2 + 1) = SSB0_4_SRR;
+    SRparm_bench(N_SRparm2 + 1) = SSB0_4_SRR;
     Mgmt_quant(1) = SSB_unf;
     Mgmt_quant(2) = totbio;  // this is calculated in Do_Equil_Calc
     Mgmt_quant(3) = smrybio;
     Mgmt_quant(4) = Recr_unf;
-    report5 << "SRparms for benchmark: " << SRparm_work << endl
+    report5 << "SRparms for benchmark: " << SRparm_bench << endl
             << "Benchmark biology averaged over years: " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl << endl;
     Mgmt_quant(19) = SSB_unf;  // placeholder for depletion denominator
     Mgmt_quant(20) = SSB_unf;  //  placeholder to be replaced by SSB_HCR_infl
@@ -1011,7 +1011,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
 
     //  SPAWN-RECR:   calc equil spawn-recr in YPR; need to make this area-specific
     SSBpR_temp = SSB_equil;  //  based on most recent call to Do_Equil_Calc
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_bench, SSB0_4_SRR, R0_4_SRR, 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);
@@ -1126,7 +1126,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     if (rundetail > 0 && mceval_counter == 0 && show_MSY == 1)
       echoinput << "Calculated F0.1: " << Btgt_Fmult << endl;
     SSBpR_temp = SSB_equil;
-    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+    Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_bench, SSB0_4_SRR, R0_4_SRR, 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
@@ -1227,7 +1227,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         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
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_bench, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         yld1(ii) = Equ_SpawnRecr_Result(1);
       }
 
@@ -1403,7 +1403,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         }
         if (F_Method == 1)
         {
-          Fmax = (Btgt_Fmult + SPR_Fmult) * 0.5 * SRparm_work(2) / 0.05;
+          Fmax = (Btgt_Fmult + SPR_Fmult) * 0.5 * SRparm_bench(2) / 0.05;
         } //  previously /0.18
         F1(1) = -log(Fmax / Btgt_Fmult - 1.);
         F2(1) = -log(Fmax / Btgt_Fmult - 1.);
@@ -1447,7 +1447,7 @@ 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 / SSBpR_unf;
       SSBpR_temp = SSB_equil;
-      Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+      Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_bench, SSB0_4_SRR, R0_4_SRR, 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;
@@ -1541,7 +1541,7 @@ 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 / SSBpR_unf;
           SSBpR_temp = SSB_equil;
-          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_bench, SSB0_4_SRR, R0_4_SRR, 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;
@@ -1842,7 +1842,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         SPR_Btgt2 = SSB_equil / SSBpR_unf;
         //  SPAWN-RECR:   calc equil spawn-recr for Btarget calcs;  need to make area-specific
         SSBpR_temp = SSB_equil;
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_bench, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         yld1(ii) = Equ_SpawnRecr_Result(1);
       }
 
@@ -1925,8 +1925,8 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     report5 << "#" << endl
             << "Management_report" << endl;
     report5 << "Virgin: Steepness_Recr_SSB " << SRparm(2) << " " << Recr_virgin << " " << SSB_virgin << endl;
-    report5 << "Bench:  Steepness_Recr_SSB " << SRparm_work(2) << " " << R0_4_SRR << " " << SSB0_4_SRR << endl;
-    report5 << "unf  :  Steepness_Recr_SSB " << SRparm_work(2) << " " << Recr_unf << " " << SSB_unf << endl;
+    report5 << "Bench:  Steepness_Recr_SSB " << SRparm_bench(2) << " " << R0_4_SRR << " " << SSB0_4_SRR << endl;
+    report5 << "unf  :  Steepness_Recr_SSB " << SRparm_bench(2) << " " << Recr_unf << " " << SSB_unf << endl;
     report5 << "#" << endl
             << "Summary_age: " << Smry_Age << endl;
     report5 << "#_Bmark_years: beg_bio, end_bio, beg_selex, end_selex, beg_relF, end_relF, beg_recr_dist, end_recr_dist, beg_SRparm, end_SRparm" << endl
@@ -2746,7 +2746,7 @@ FUNCTION void Get_Forecast()
         {
           warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
-        Recruits = Spawn_Recr(SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr using either virgin or adjusted R0 and SSB0
+        Recruits = Spawn_Recr(SRparm_work, 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 (Fcast_Loop1 < Fcast_Loop_Control(2)) //  use expected recruitment  this should include environ effect - CHECK THIS
@@ -3380,13 +3380,7 @@ FUNCTION void Get_Forecast()
               SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
               SSB_use = SSB_equil;
               warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
-    
-              // test that this stays on equilibrium.  It does.
-    //          SSBpR_temp = SSB_use / R0_use;  // get unfished SSBpR
-    //          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB_use, R0_use, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-    //          warning << y << " pR only "<<SSB_use<<" "<<R0_use<<"  steep " << SRparm_work(2)<< " equil: "<<Equ_SpawnRecr_Result;
-    //          R0_use = Equ_SpawnRecr_Result(2);
-    //          SSB_use = Equ_SpawnRecr_Result(1);
+
               if (fishery_on_off == 1)
               {
                 Fishon = 1;
@@ -3400,7 +3394,7 @@ FUNCTION void Get_Forecast()
             {
               warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
             }
-            Recruits = Spawn_Recr(SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr using either virgin or adjusted R0 and SSB0
+            Recruits = Spawn_Recr(SRparm_work, 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  among the settlements, areas and morphs
             for (g = 1; g <= gmorph; g++)
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 25f67d93..7a00757d 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -1042,12 +1042,6 @@ FUNCTION void get_time_series()
           SSB_use = SSB_equil;
           warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
 
-          // test that this stays on equilibrium.  It does.
-//          SSBpR_temp = SSB_use / R0_use;  // get unfished SSBpR
-//          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB_use, R0_use, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-//          warning << y << " pR only "<<SSB_use<<" "<<R0_use<<"  steep " << SRparm_work(2)<< " equil: "<<Equ_SpawnRecr_Result;
-//          R0_use = Equ_SpawnRecr_Result(2);
-//          SSB_use = Equ_SpawnRecr_Result(1);
           if (fishery_on_off == 1)
           {
             Fishon = 1;
@@ -1061,7 +1055,7 @@ FUNCTION void get_time_series()
         {
           warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
-        Recruits = Spawn_Recr(SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr using either virgin or adjusted R0 and SSB0
+        Recruits = Spawn_Recr(SRparm_work, SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr using either virgin or adjusted R0 and SSB0
 //        warning <<"  SSB: " << SSB_current << "  R: " << Recruits << endl;
         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
@@ -1518,12 +1512,6 @@ FUNCTION void get_time_series()
           SSB_use = SSB_equil;
           warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
 
-          // test that this stays on equilibrium.  It does.
-//          SSBpR_temp = SSB_use / R0_use;  // get unfished SSBpR
-//          Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB_use, R0_use, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-//          warning << y << " pR only "<<SSB_use<<" "<<R0_use<<"  steep " << SRparm_work(2)<< " equil: "<<Equ_SpawnRecr_Result;
-//          R0_use = Equ_SpawnRecr_Result(2);
-//          SSB_use = Equ_SpawnRecr_Result(1);
           if (fishery_on_off == 1)
           {
             Fishon = 1;
@@ -1537,7 +1525,7 @@ FUNCTION void get_time_series()
         {
           warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
-        Recruits = Spawn_Recr(SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr using either virgin or adjusted R0 and SSB0
+        Recruits = Spawn_Recr(SRparm_work, 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 among settlements, areas and morphs
diff --git a/SS_prelim.tpl b/SS_prelim.tpl
index b58f1a05..c37b8fc0 100644
--- a/SS_prelim.tpl
+++ b/SS_prelim.tpl
@@ -701,12 +701,9 @@
       }
     }
 
-    if (recdev_do_early > 0)
-      recdev_early.initialize();
-    if (Do_Forecast > 0 && do_recdev != 0)
-      Fcast_recruitments.initialize();
-    if (Do_Impl_Error > 0)
-      Fcast_impl_error.initialize();
+    if (recdev_do_early > 0) recdev_early.initialize();
+    if (Do_Forecast > 0 && do_recdev != 0) Fcast_recruitments.initialize();
+    if (Do_Impl_Error > 0) Fcast_impl_error.initialize();
 
     if (do_recdev == 1)
     {
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index fb2d948a..19c5c5be 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -52,6 +52,7 @@
   init_int WTage_rd  // 0 means do not read wtatage.ss; 1 means read and use wtatage.ss and also read and use growth parameters
                      //  future option 2 will suppress reading and use of growth
 !!echoinput<<WTage_rd<<" wtatage switch "<<endl;
+!!if (WTage_rd > 0) timevary_MG_firstyr = styr;
   init_int N_GP  // number of growth patterns (morphs)
 !!echoinput<<N_GP<<" N growth patterns "<<endl;
   init_int N_platoon  //  number of platoons  1, 3, 5 are best values to use
@@ -1968,7 +1969,7 @@
   int SR_env_target
   int SR_autocorr;  // will be calculated later
 
-  int timevary_parm_SR_first;  //   == 0 means that no relevant parms are timevarying
+  int timevary_SRparm_first;  //   == 0 means that no relevant parms are timevarying
   int firstSRparm;
   int timevary_parm_SR_last;
   ivector timevary_SRparm(styr-3,YrMax+1);
@@ -1979,7 +1980,7 @@
   //  SS_Label_Info_4.6.1 #Create S-R parameter labels
   firstSRparm = ParCount;
   timevary_parm_SR_last = 0;
-  timevary_parm_SR_first = 0;
+  timevary_SRparm_first = 0;
   timevary_SRparm.initialize();
   SRparm_timevary.initialize();
   SR_env_link = 0;
@@ -2083,7 +2084,7 @@
         timevary_used = 1;
         ivector timevary_setup(1, 14); //  temporary vector for timevary specs
         timevary_setup.initialize();
-        if (timevary_parm_SR_first == 0) timevary_parm_SR_first = timevary_parm_cnt + 1;  // cumulative index for first timevary SRparm
+        if (timevary_SRparm_first == 0) timevary_SRparm_first = timevary_parm_cnt + 1;  // cumulative index for first timevary SRparm
         echoinput << " timevary for SR parm: " << j << endl;
         timevary_cnt++; //  count parameters with time-vary effect
         SRparm_timevary(j) = timevary_cnt; //  base SR parameter will use this timevary specification
@@ -2152,12 +2153,12 @@
     }
   
   N_SRparm3 = N_SRparm2;
-  if (timevary_parm_SR_first > 0)
+  if (timevary_SRparm_first > 0)
   {
     timevary_parm_SR_last = timevary_parm_cnt;
     if (timevary_used == 1) autogen_timevary(2) = 1; //  indicate that some parameter is time-varying
-    N_SRparm3 += (timevary_parm_SR_last - timevary_parm_SR_first + 1);
-    echoinput << " SR timevary_parm_cnt start and end " << timevary_parm_SR_first << " " << timevary_parm_SR_last << endl;
+    N_SRparm3 += (timevary_parm_SR_last - timevary_SRparm_first + 1);
+    echoinput << " SR timevary_parm_cnt start and end " << timevary_SRparm_first << " " << timevary_parm_SR_last << endl;
     echoinput << "link to timevary parms:  " << SRparm_timevary << endl;
   }
   echoinput << "SR_Npar and N_SRparm2 and N_SRparm3:  " << N_SRparm(SR_fxn) << " " << N_SRparm2 << " " << N_SRparm3 << endl;
@@ -2184,10 +2185,10 @@
     SRparm_PRtype(i) = SRparm_1(i, 6);
     SRparm_PH(i) = SRparm_1(i, 7);
   }
-  if (timevary_parm_SR_first > 0)
+  if (timevary_SRparm_first > 0)
   {
     j = N_SRparm2;
-    for (f = timevary_parm_SR_first; f <= timevary_parm_SR_last; f++)
+    for (f = timevary_SRparm_first; f <= timevary_parm_SR_last; f++)
     {
       j++;
       echoinput << f << " " << j << " " << timevary_parm_rd[f] << endl;
diff --git a/SS_recruit.tpl b/SS_recruit.tpl
index 93263b20..eaf4c980 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_use, const prevariable& Recr_virgin_use, const prevariable& SSB_current)
+FUNCTION dvariable Spawn_Recr(const dvar_vector& SRparm_work, const prevariable& SSB_virgin_use, const prevariable& Recr_virgin_use, const prevariable& SSB_current)
   {
   RETURN_ARRAYS_INCREMENT();
   dvariable NewRecruits;
diff --git a/SS_timevaryparm.tpl b/SS_timevaryparm.tpl
index b4f6b1d1..86259979 100644
--- a/SS_timevaryparm.tpl
+++ b/SS_timevaryparm.tpl
@@ -60,7 +60,7 @@ FUNCTION void make_timevaryparm()
         for (j = timevary_setup(3); j < timevary_def[tvary + 1](3); j++)
         {
           timevary_parm_cnt_all++;
-          timevary_parm(timevary_parm_cnt_all) = SRparm(N_SRparm(SR_fxn) + 3 + j - timevary_parm_SR_first + 1);
+          timevary_parm(timevary_parm_cnt_all) = SRparm(N_SRparm(SR_fxn) + 3 + j - timevary_SRparm_first + 1);
           if (do_once == 1)
             echoinput << j << " timevary_parm: " << timevary_parm(timevary_parm_cnt_all) << endl;
         }
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index b5eba96f..8b5d9e2b 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -1779,7 +1779,6 @@ FUNCTION void write_bigoutput()
     var /= (n_rmse(1) + 1.0e-09);
 
     dvariable steepness = SRparm(2);
-
     SS2out << endl
            << pick_report_name(19);
     SS2out << "  Function: " << SR_fxn << "  RecDev_method: " << do_recdev << "   sum_recdev: " << sum_recdev << endl
@@ -1836,23 +1835,99 @@ 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 << "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;
+    y = styr - 1;
+    SS2out << "Init " << SSB_yr(y) << " " << exp_rec(y) << " - " << 0.0 << " Init " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " " << 0.0 << endl;
+
+    if (recdev_first < styr)
+    {
+      for (y = recdev_first; y <= styr - 1; y++)
+      {
+        SS2out << y << " " << SSB_yr(styr - 1) << " " << exp_rec(styr - 1, 1) << " " << exp_rec(styr - 1, 2) << " " << exp_rec(styr - 1, 3) * mfexp(-biasadj(y) * half_sigmaRsq) << " " << exp_rec(styr - 1, 3) * mfexp(recdev(y) - biasadj(y) * half_sigmaRsq) << " "
+               << recdev(y) << " " << biasadj(y) << " Init_age " << SSB_B_yr(styr - 1) << " " << SSB_N_yr(styr - 1) << " " << recdev(y) << endl; // newdev approach uses devs for initial agecomp directly
+      }
+    }
+    for (y = styr; y <= YrMax; y++)
+    {
+      SS2out << y << " " << SSB_yr(y) << " " << exp_rec(y) << " ";
+      if (recdev_do_early > 0 && y >= recdev_early_start && y <= recdev_early_end)
+      {
+        SS2out << log(exp_rec(y, 4) / exp_rec(y, 3)) << " " << biasadj(y) << " Early " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " " << recdev(y);
+      }
+      else if (y >= recdev_start && y <= recdev_end)
+      {
+        SS2out << log(exp_rec(y, 4) / exp_rec(y, 3)) << " " << biasadj(y) << " Main " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " " << recdev(y);
+      }
+      else if (Do_Forecast > 0 && y > recdev_end)
+      {
+        SS2out << log(exp_rec(y, 4) / exp_rec(y, 3)) << " " << biasadj(y);
+        if (y <= endyr)
+        {
+          SS2out << " Late ";
+        }
+        else
+        {
+          SS2out << " Fore ";
+        }
+        SS2out << SSB_B_yr(y) << " " << SSB_N_yr(y) << " ";
+        if (do_recdev > 0)
+        {
+          SS2out << Fcast_recruitments(y);
+        }
+        else
+        {
+          SS2out << " 0.0";
+        }
+      }
+      else
+      {
+        SS2out << " _ _ Fixed";
+      }
+      SS2out << endl;
+    }
+
     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;
+    SS2out << SR_fxn << " # SR_Function" << endl;
+    SS2out << N_SRparm2 << " # N_SRparms" << endl;
+
+    SS2out << "# " <<endl << "Flags_for_timevary_biology_and_SR" << endl;
+    SS2out << timevary_bio_4SRR << " # timevary_bio_4SRR  #_Compatibility_flag_for_legacy_(0)_vs_improved_(1)_impact_of_timevary_biology_on_benchmark_SRR_calcs" << endl;
+    SS2out << timevary_MG_firstyr << " # timevary_MG_firstyr ";
+    if( timevary_MG_firstyr == YrMax)
+    { SS2out << " #_No_timevary_MGparm " << endl; }
+    else
+    { SS2out << " #_some_timevary_MGparm_or_EWAA: " << timevary_MG_firstyr << endl; }
+
+    SS2out << "#" << endl << "#_SRparm  parm_label value phase" << endl;
     for (int j = 1; j <=N_SRparm2; j++)
     {
-      SS2out << j << " " << ParmLabel(firstSRparm + j) << " " << SRparm(j) << " " << SRparm_PH(j);
+      SS2out << "# " << j << " " << ParmLabel(firstSRparm + j) << " " << SRparm(j) << " " << SRparm_PH(j);
       if (SRparm_timevary(j) > 0 && j <= 4 ) //  timevary SRparm exists
-      {SS2out << " #_is_time_vary,_so_SRR_updates_base_SPR_annually";} 
+      {SS2out << " #_TV";} 
       if (j == (N_SRparm2 - 1) && SRparm_timevary(j) > 0) //  timevary regime exists
-      {SS2out << " #_Regime_parameter_used_to_offset_from_SRR";}
+      {SS2out << " #_Regime_used_to_offset_from_SRR";}
       SS2out << endl;
     }
 
-    SS2out << "# " <<endl;
-    SS2out << "sigmaR: "<< sigmaR  << endl;
-    SS2out << "SPR0_(virgin): " << SSBpR_virgin << " #_uses_biology_from_start_year: " << styr <<endl;
+    if( timevary_SRparm_first == 0)
+    { SS2out << "0  #_No_timevary_SRparms,_other_than_regime " << endl; }
+    else
+    {
+      for (y = styr; y <= YrMax; y++) if (timevary_SRparm(y) == 1) SS2out << y;
+      SS2out << "  # timevary_SRparm_begin_year" << endl;
+    }
+
+    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;
+    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 << "SSBpR0_(virgin): " << SSBpR_virgin << " #_uses_biology_from_start_year: " << styr <<endl;
+    SS2out << "SSBpR_unfished_benchmark: " << Mgmt_quant(1) / Mgmt_quant(4) << "  #_based_on_averaging_biology_over_benchmark_year_range " << endl;
 
     switch (SR_fxn)
     {
@@ -1893,17 +1968,6 @@ FUNCTION void write_bigoutput()
     }
     }
 
-    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 << "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;
 
@@ -2021,7 +2085,7 @@ FUNCTION void write_bigoutput()
         for (f = 1; f <= 120; f++)
         {
           SSB_current = double(f) / 100. * SSB_virgin;
-          temp = Spawn_Recr(SSB_virgin, Recr_virgin, SSB_current);
+          temp = Spawn_Recr(SRparm_work, SSB_virgin, Recr_virgin, SSB_current);
           SS2out << SSB_current / SSB_virgin << " " << SSB_current << " " << temp << endl;
         }
       }
@@ -4905,7 +4969,7 @@ FUNCTION void SPR_profile()
         SSBpR_Calc(equ_Recr);
         //  SPAWN-RECR:   calc equil spawn-recr in the SPR loop
         SSBpR_temp = SSB_equil;
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_work, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_bench , SSB0_4_SRR, R0_4_SRR, 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)
diff --git a/SS_write_ssnew.tpl b/SS_write_ssnew.tpl
index 0dd77741..147cf597 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -2158,7 +2158,7 @@ FUNCTION void write_nucontrol()
   if (N_SRparm3 > N_SRparm2)
   {
     report4 << "# timevary SR parameters" << endl;
-    for (f = timevary_parm_SR_first; f <= timevary_parm_SR_last; f++)
+    for (f = timevary_SRparm_first; f <= timevary_parm_SR_last; f++)
     {
       NP++;
       timevary_parm_rd[f](3) = value(timevary_parm(f));

From aa4eab0ca02a58744bf37f43b12ca59b67e00e19 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Fri, 25 Apr 2025 11:54:40 -0700
Subject: [PATCH 37/58] add SPR_reporting option 5

updates the descriptions of SPR_reporting and adds option to report raw SPR
---
 SS_objfunc.tpl         | 8 ++++++--
 SS_readcontrol_330.tpl | 7 ++++++-
 SS_readdata_330.tpl    | 4 ++--
 SS_readstarter.tpl     | 2 +-
 SS_write_ssnew.tpl     | 2 +-
 5 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/SS_objfunc.tpl b/SS_objfunc.tpl
index c4655bac..7d6315e3 100644
--- a/SS_objfunc.tpl
+++ b/SS_objfunc.tpl
@@ -1150,7 +1150,7 @@ FUNCTION void Process_STDquant()
 
   switch (SPR_reporting)
   {
-    case 0: // keep as raw value
+    case 0: // no scaling.  this option skips SPR_reporting
     {
       break;
     }
@@ -1170,11 +1170,15 @@ FUNCTION void Process_STDquant()
       SPR_std = (1. - SPR_std) / (1. - SPR_Btgt);
       break;
     }
-    case 4:
+    case 4:  //  1-%SPR
     {
       SPR_std = 1. - SPR_std;
       break;
     }
+    case 5:  //  raw %SPR
+    {
+      break;
+    }
   }
 
   switch (depletion_basis)
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 19c5c5be..ba7f2694 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -6984,7 +6984,12 @@
   
   switch (SPR_reporting)
   {
-    case 0: // keep as raw value
+    case 0: // skip SPR reporting
+    {
+      SPR_report_label += " raw_SPR";
+      break;
+    }
+    case 5: // keep as raw %SPR value
     {
       SPR_report_label += " raw_SPR";
       break;
diff --git a/SS_readdata_330.tpl b/SS_readdata_330.tpl
index 901d92d6..ad64c3b7 100644
--- a/SS_readdata_330.tpl
+++ b/SS_readdata_330.tpl
@@ -4834,8 +4834,8 @@
     }
     if (SPR_reporting >= 1 && SPR_reporting <= 3)
     {
-      SPR_reporting = 4;
-      warnstream << "Change SPR_reporting to 4 because benchmarks were not requested";
+      SPR_reporting = 5;
+      warnstream << "Change SPR_reporting to 5 (raw %SPR) because benchmarks were not requested";
       write_message(WARN, 0);
     }
   }
diff --git a/SS_readstarter.tpl b/SS_readstarter.tpl
index e2ab712f..8143e984 100644
--- a/SS_readstarter.tpl
+++ b/SS_readstarter.tpl
@@ -669,7 +669,7 @@
 
   init_number depletion_level;
 !!echoinput << depletion_level << "  depletion_level" << endl;
-  init_int SPR_reporting; // 0=skip; 1=SPR; 2=SPR_MSY; 3=SPR_Btarget; 4=(1-SPR)
+  init_int SPR_reporting; // 0=skip; 1=SPR; 2=SPR_MSY; 3=SPR_Btarget; 4=(1-SPR); 5=SPR
 !!echoinput << SPR_reporting << "  SPR_reporting" << endl;
   init_int F_reporting; // 0=skip; 1=exploit(Bio); 2=exploit(Num); 3=sum(frates); 4=true F for range of ages; 5=unweighted avg F for range of ages
  LOCAL_CALCS
diff --git a/SS_write_ssnew.tpl b/SS_write_ssnew.tpl
index 147cf597..e1741e0f 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -1551,7 +1551,7 @@ FUNCTION void write_nucontrol()
   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;  6=X*Bmark_SSB_unf; 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 << "# If value = 1, then Btarget in benchmark will be a fraction of SSB_virgin, else will be a fraction of SSB_benchmark" << 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 << 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=1-SPR; 5=SPR" << 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)
   {

From 2beff82ceb38825c51dd875a888219ee37f53ec7 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Fri, 16 May 2025 16:05:51 -0700
Subject: [PATCH 38/58] clean up ss_new and spawn_recr output

---
 SS_benchfore.tpl    |  4 +--
 SS_write_report.tpl | 38 ++++++----------------
 SS_write_ssnew.tpl  | 77 +++++++++++++++++++++++----------------------
 3 files changed, 50 insertions(+), 69 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 84b7c961..9737e283 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -1801,8 +1801,8 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     }
     else
     {
-      Btgttgt2 = -Blim_frac * SSB_virgin;
-      Blim_report = value(SSB_virgin);
+      Btgttgt2 = -Blim_frac * SSB_unf;
+      Blim_report = value(SSB_unf);
     }
 
     for (j = 0; j <= Nloops; j++) // loop find Btarget
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 8b5d9e2b..faf51371 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -1891,8 +1891,6 @@ FUNCTION void write_bigoutput()
 
     SS2out << endl << "#New_Expanded_Spawn_Recr_report" << endl << pick_report_name(19) << endl;
     SS2out << SR_fxn << " # SR_Function" << endl;
-    SS2out << N_SRparm2 << " # N_SRparms" << endl;
-
     SS2out << "# " <<endl << "Flags_for_timevary_biology_and_SR" << endl;
     SS2out << timevary_bio_4SRR << " # timevary_bio_4SRR  #_Compatibility_flag_for_legacy_(0)_vs_improved_(1)_impact_of_timevary_biology_on_benchmark_SRR_calcs" << endl;
     SS2out << timevary_MG_firstyr << " # timevary_MG_firstyr ";
@@ -1901,6 +1899,7 @@ FUNCTION void write_bigoutput()
     else
     { SS2out << " #_some_timevary_MGparm_or_EWAA: " << timevary_MG_firstyr << endl; }
 
+    SS2out << N_SRparm2 << " # N_SRparms" << endl;
     SS2out << "#" << endl << "#_SRparm  parm_label value phase" << endl;
     for (int j = 1; j <=N_SRparm2; j++)
     {
@@ -1920,7 +1919,7 @@ FUNCTION void write_bigoutput()
       SS2out << "  # timevary_SRparm_begin_year" << endl;
     }
 
-    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 << "#" << 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;
     for ( int k = 1; k <=9; k+=2) 
     { if (Bmark_Yr(k+1) > Bmark_Yr(k))
@@ -1938,7 +1937,7 @@ FUNCTION void write_bigoutput()
       SS2out << "Ln(R0): " << SRparm(1) << endl << "R0: " << mfexp(SRparm(1)) << endl;
       SS2out << "steepness: " << steepness << endl;
       SS2out << "Ln(alpha)_derived: " << log(alpha) << " alpha " << alpha << endl;
-      SS2out << "Ln(beta)_derived: " << log(beta) << " beta " << beta;
+      SS2out << "Ln(beta)_derived: " << log(beta) << " beta " << beta << endl;
       break;
     }
       case 10: // Beverton-Holt with alpha, beta
@@ -2000,22 +1999,12 @@ 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;
-    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;
+    SS2out << "Yr SpawnBio exp_recr with_regime bias_adjusted pred_recr dev biasadjuster era mature_bio mature_num raw_dev SPR0_curr " << 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;
+    SS2out << "Virg " << SSB_yr(y) << " " << exp_rec(y) << " - " << 0.0 << " Virg " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " 0.0 " << " " << SSBpR_virgin << endl;
     y = styr - 1;
-    SS2out << "Init " << SSB_yr(y) << " " << exp_rec(y) << " - " << 0.0 << " Init " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " " << 0.0 << endl;
+    SS2out << "Init " << SSB_yr(y) << " " << exp_rec(y) << " - " << 0.0 << " Init " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " " << 0.0  << " " << SSBpR_virgin << endl;
 
     if (recdev_first < styr)
     {
@@ -2059,18 +2048,9 @@ FUNCTION void write_bigoutput()
       }
       else
       {
-        SS2out << " _ _ Fixed";
-      }
-      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 << " _ _ Fixed  " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " _ ";
       }
-      else
-      {SS2out << " - - ";}
-      SS2out << SRparm_byyr(y)(1,N_SRparm2) << endl;
+      SS2out << " " << Smry_Table(y, 11) / Recr_virgin << endl;
     }
 
     // REPORT_KEYWORD SPAWN_RECR_CURVE
diff --git a/SS_write_ssnew.tpl b/SS_write_ssnew.tpl
index e1741e0f..9b6948f0 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -1509,11 +1509,11 @@ FUNCTION void write_nucontrol()
           << version_info2 << endl;
   if (N_SC > 0)
     NuStart << Starter_Comments << endl;
-  NuStart << datfilename << endl
-          << ctlfilename << endl;
-  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;
+  NuStart << datfilename << " #_datfile" << endl
+          << ctlfilename << " #_ctlfile" << endl;
+  NuStart << readparfile << " #_init_values_src:  0 (use init values in control file); 1 (use ss3.par)" << endl;
+  NuStart << rundetail << " #_screen_display:  0 (minimal); 1 (one line per iter); 2 (each logL)" << endl;
+  NuStart << reportdetail << " #_report_table_selection:  0 (minimal; no wtatage.ss_new); 1 (all tables); 2 (brief), 3 (custom, read list) " << endl;
   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;
@@ -1524,35 +1524,36 @@ FUNCTION void write_nucontrol()
   }
   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;
+    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;
   }
 
-  NuStart << docheckup << " # write 1st iteration details to echoinput.sso file (0,1) " << endl;
-  NuStart << Do_ParmTrace << " # write parm values to ParmTrace.sso (0=no,1=good,active; 2=good,all; 3=every_iter,all_parms; 4=every,active)" << endl;
-  NuStart << Do_CumReport << " # write to cumreport.sso (0=no,1=like&timeseries; 2=add survey fits)" << endl;
-  NuStart << Do_all_priors << " # Include prior_like for non-estimated parameters (0,1) " << endl;
-  NuStart << SoftBound << " # Use Soft Boundaries to aid convergence (0,1) (recommended)" << endl;
+  NuStart << docheckup << " #_checkup:  write more 1st iteration age-specific details to echoinput.sso file (0,1) " << endl;
+  NuStart << Do_ParmTrace << " #_parmtrace:  write parm values to ParmTrace.sso:  0 (no); 1 (good_iter,active_parms); 2 (good,all); 3 (every,all); 4 (every,active)" << endl;
+  NuStart << Do_CumReport << " #_cumreport:  write to cumreport.sso: 0 (no); 1 (like&timeseries); 2 (add survey fits)" << endl;
+  NuStart << Do_all_priors << " #_prior_like:  include prior_like for non-estimated parameters (0,1) " << endl;
+  NuStart << SoftBound << " #_soft_bounds:  Use Soft Boundaries to aid convergence (0,1) (recommended)" << endl;
   NuStart << "#" << endl
-          << N_nudata_read << " # Number of datafiles to produce:  0 turns off all *.ss_new; 1st is data_echo.ss_new, 2nd is data_expval.ss, 3rd and higher are data_boot_**N.ss," << endl;
-  NuStart << Turn_off_phase_rd << " # Turn off estimation for parameters entering after this phase" << endl;
+          << N_nudata_read << " #_N_bootstraps:  Number of datafiles to produce:  0 turns off all *.ss_new; 1st is data_echo.ss_new, 2nd is data_expval.ss, 3rd and higher are data_boot_**N.ss," << endl;
+  NuStart << Turn_off_phase_rd << " #_last_estimation_phase:  turn off estimation for parameters entering after this phase" << endl;
   NuStart << "#" << endl
-          << burn_intvl << " # MCeval burn interval" << endl;
-  NuStart << thin_intvl << " # MCeval thin interval" << endl;
-  NuStart << jitter << " # jitter initial parm value by this fraction" << endl;
-  NuStart << STD_Yr_min_rd << " # min year for sdreport outputs (-1 for styr); #_" << STD_Yr_min << endl;
-  NuStart << STD_Yr_max_rd << " # max year for sdreport outputs (-1 for endyr+1; -2 for endyr+Nforecastyrs); #_" << STD_Yr_max << endl;
-  NuStart << N_STD_Yr_RD << " # N individual STD years " << endl;
+          << burn_intvl << " #_MCMCburn" << endl;
+  NuStart << thin_intvl << " #_MCMCthin" << endl;
+  NuStart << jitter << " # jitter_fraction:  jitter within parameter bounds" << endl;
+
+  NuStart << STD_Yr_min_rd << " #_minyr_sdreport:  min year for sdreport outputs (-1 for styr); #_" << STD_Yr_min << endl;
+  NuStart << STD_Yr_max_rd << " #_maxyr_sdreport:  max year for sdreport outputs (-1 for endyr+1; -2 for endyr+Nforecastyrs); #_" << STD_Yr_max << endl;
+  NuStart << N_STD_Yr_RD << " #_N_STD_yrs:  N individual STD years " << endl;
   NuStart << "#COND: vector of year values if N>0" << endl
           << STD_Yr_RD << endl;
 
-  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*SSBvirgin; 2=X*SSBmsy; 3=X*SSB_styr; 4=X*SSB_endyr; 5=X*dyn_Bzero;  6=X*Bmark_SSB_unf; 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 << final_conv << " #_converge_criterion: (e.g. 1.0e-04) " << endl;
+  NuStart << retro_yr - endyr << " #_retro_yr:  retrospective year relative to end year (e.g. -4)" << endl;
+  NuStart << Smry_Age << " #_min_age_summary_bio" << endl;
+  NuStart << depletion_basis_rd << " #_depl_basis:  Depletion denom is: 0=skip; 1=X*SSB_virgin; 2=X*SSB_msy; 3=X*SSB_styr; 4=X*SSB_endyr; 5=X*dyn_Bzero; 6=X*SSB_unf_bmark; values>=11 invoke N multiyr with 10s & 100s digit; append .1 to invoke log(ratio); e.g. 122.1 produces log(12 yr trailing average of B/Bmsy)" << endl;
   NuStart << "# If value = 1, then Btarget in benchmark will be a fraction of SSB_virgin, else will be a fraction of SSB_benchmark" << 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=1-SPR; 5=SPR" << 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;
+  NuStart << depletion_level << " #_depl_denom_frac:  fraction (X) for Depletion denominator (e.g. 0.4)" << endl;
+  NuStart << SPR_reporting << " #_SPR_basis:  0 (skip); 1 (1-SPR)/(1-SPR_tgt); 2 (1-SPR)/(1-SPR_MSY); 3 (1-SPR)/(1-SPR_Btarget); 4 (1-SPR); 5 (SPR)" << endl;
+  NuStart << F_reporting << " # F_std_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)
   {
     NuStart << F_reporting_ages << " # min and max age over which mean F will be calculated, with F=Z-M" << endl;
@@ -1561,12 +1562,12 @@ FUNCTION void write_nucontrol()
   {
     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;
-  NuStart << double(mcmc_output_detail) + MCMC_bump << " # MCMC output detail: integer part (0=default; 1=adds obj func components; 2= +write_report_for_each_mceval); and decimal part (added to SR_LN(R0) on first call to mcmc)" << endl;
-  NuStart << ALK_tolerance << " # ALK tolerance ***disabled in code" << endl;
-  NuStart << irand_seed_rd << " # random number seed for bootstrap data (-1 to use long(time) as seed): # " << irand_seed << endl;
-  NuStart << timevary_bio_4SRR << " # Compatibility flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs >=3.30.24" << endl;
-  NuStart << "3.30 # check value for end of file and for version control" << endl;
+  NuStart << F_std_basis_rd << " # F_std_basis: 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;
+  NuStart << double(mcmc_output_detail) + MCMC_bump << " #_MCMC_output_detail: integer part (0=default; 1=adds obj func components; 2= +write_report_for_each_mceval); and decimal part (added to SR_LN(R0) on first call to mcmc)" << endl;
+  NuStart << ALK_tolerance << " #_deprecated:  ALK tolerance ***disabled in code" << endl;
+  NuStart << irand_seed_rd << " #_seed:  random number seed for bootstrap data (-1 to use long(time) as seed): # " << irand_seed << endl;
+  NuStart << timevary_bio_4SRR << " #_Compatibility:  flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs >=3.30.24" << endl;
+  NuStart << "3.30 #_final:  check value for end of file and for version control" << endl;
   NuStart.close();
 
   echoinput << "Write forecast.ss_new file " << endl;
@@ -1576,7 +1577,7 @@ FUNCTION void write_nucontrol()
   if (N_FC > 0)
     NuFore << Forecast_Comments << endl;
   NuFore << "# for all year entries except rebuilder; enter either: actual year, -999 for styr, 0 for endyr, neg number for rel. endyr" << endl;
-  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_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)
@@ -1594,13 +1595,13 @@ FUNCTION void write_nucontrol()
 
   NuFore << SPR_target << " # SPR target (e.g. 0.40)" << endl;
   NuFore << BTGT_target << " # Biomass target (e.g. 0.40) as fraction of SSB_virgin if depletion basis = 1, else as fraction of SSB_unfished in benchmark" << endl;
-  if (Do_Benchmark == 3)
-    NuFore << Blim_frac << " # COND: Do_Benchmark==3;  Blimit as fraction of Bmsy (neg value to use as frac of Bzero) (e.g. 0.50)" << endl;
-  NuFore << "#_Bmark_years: beg_bio, end_bio, beg_selex, end_selex, beg_relF, end_relF, beg_recr_dist, end_recr_dist, beg_SRparm, end_SRparm (enter actual year, or values of 0 or -integer to be rel. endyr)" << endl
+  if (Do_Benchmark != 3) NuFore << "#";
+  NuFore << Blim_frac << " # COND: Do_Benchmark==3;  Blimit as fraction of Bmsy (neg value to use as frac of SSB_virgin or SSB_unfished) (e.g. 0.50)";
+  NuFore << "#" << endl << "# Bmark_years: beg_bio, end_bio, beg_selex, end_selex, beg_relF, end_relF, beg_recr_dist, end_recr_dist, beg_SRparm, end_SRparm (enter actual year, or values of 0 or -integer to be rel. endyr)" << endl
          << Bmark_Yr_rd << endl
          << "# " << Bmark_Yr << endl;
   NuFore << "# value <0 convert to endyr-value; except -999 converts to start_yr; must be >=start_yr and <=endyr" << endl;
-  NuFore << Bmark_RelF_Basis << " #Bmark_relF_Basis: 1 = use year range; 2 = set relF same as forecast below" << endl;
+  NuFore << Bmark_RelF_Basis << " # Bmark_relF_Basis: 1 = use year range; 2 = set relF same as forecast below" << endl;
   NuFore << "#" << endl
          << Do_Forecast_rd << " # Forecast: -1=none; 0=simple_1yr; 1=F(SPR); 2=F(MSY) 3=F(Btgt) or F0.1; 4=Ave F (uses first-last relF yrs); 5=input annual F scalar" << endl;
   NuFore << "# where none and simple require no input after this line; simple sets forecast F same as end year F" << endl;
@@ -1621,7 +1622,7 @@ FUNCTION void write_nucontrol()
   }
 //  else
   {  //  new list based format for Fcast years
-  NuFore << anystring << endl << anystring << "-12345  # code to invoke new format for expanded fcast year controls" << endl
+  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

From 0a5451d3b163e1a9a3398b689af4b6fd2b76132b Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Thu, 22 May 2025 12:14:09 -0700
Subject: [PATCH 39/58] Change approach for invoking Bmsy as the HCR_inflection

---
 SS_benchfore.tpl       | 27 +++++++++++++++++----------
 SS_popdyn.tpl          | 12 ++++++------
 SS_readcontrol_330.tpl |  2 +-
 SS_readdata_330.tpl    | 11 ++++++++---
 SS_write_ssnew.tpl     | 12 ++++++------
 5 files changed, 38 insertions(+), 26 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 9737e283..e156cb78 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -2264,8 +2264,10 @@ FUNCTION void Get_Forecast()
     {HCR_anchor = SSB_virgin;}
     else if (Fcast_Loop_Control(5) == 2)
     {HCR_anchor = SSB_unf;}
+    else if (Fcast_Loop_Control(5) == 3)
+    {HCR_anchor = Bmsy;}  // so H4010_top_rd should be 1.0;
 
-    if (H4010_top_rd < 0.0)
+    if (H4010_top_rd < 0.0)  // legacy approach.  This has already been converted to new approach in readdata
     {
       H4010_top = Bmsy / HCR_anchor;  // convert to fraction of anchor
       if (H4010_bot > 0.25)
@@ -2278,13 +2280,20 @@ FUNCTION void Get_Forecast()
     {
       H4010_top = H4010_top_rd;
     }
+    if (Fcast_Loop_Control(5) == 3 && H4010_top_rd != 1.0)
+    {  
+      warnstream << "HCR_anchor is BMSY; so H4010_top normally is 1.0; are you sure you want:  " << H4010_top;
+      write_message (WARN, 0);
+    }
 
-    Mgmt_quant(20) = HCR_anchor;
+    Mgmt_quant(20) = H4010_top * HCR_anchor;
     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) << endl
-            << "Control_rule_anchor_approach: " << Fcast_Loop_Control(5) << " HCR_anchor: " << HCR_anchor << endl;
-    report5 << "#" << endl;
+            << "Control_rule_anchor_approach: " << Fcast_Loop_Control(5) << " HCR_anchor: " << HCR_anchor << endl
+            << "intercept(SSB): " << H4010_bot * HCR_anchor << endl
+            << "Inflection(SSB): " << H4010_top * HCR_anchor << endl
+            << "#" << endl;
 
     switch (HarvestPolicy)
     {
@@ -2712,7 +2721,6 @@ FUNCTION void Get_Forecast()
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
-          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         else if (timevary_SRparm(y) == 1)  //  update R0_use and SSB_use in this year
                                            //  values will carry forward into subsequent years
@@ -2725,7 +2733,7 @@ FUNCTION void Get_Forecast()
           bio_yr = y;
           SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
-          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
 
           // test that this stays on equilibrium.  It does.
 //          SSBpR_temp = SSB_use / R0_use;  // get unfished SSBpR
@@ -2744,7 +2752,7 @@ FUNCTION void Get_Forecast()
         }
         else  //  flag is 2
         {
-          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         Recruits = Spawn_Recr(SRparm_work, SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr using either virgin or adjusted R0 and SSB0
 
@@ -3366,7 +3374,6 @@ FUNCTION void Get_Forecast()
             {
               R0_use = Recr_virgin;
               SSB_use = SSB_virgin;
-              warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
             }
             else if (timevary_SRparm(y) == 1)  //  update R0_use and SSB_use in this year
                                                //  values will carry forward into subsequent years
@@ -3379,7 +3386,7 @@ FUNCTION void Get_Forecast()
               bio_yr = y;
               SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
               SSB_use = SSB_equil;
-              warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//              warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
 
               if (fishery_on_off == 1)
               {
@@ -3392,7 +3399,7 @@ FUNCTION void Get_Forecast()
             }
             else  //  flag is 2
             {
-              warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//              warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
             }
             Recruits = Spawn_Recr(SRparm_work, 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
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 7a00757d..2acdfb82 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -1027,7 +1027,7 @@ FUNCTION void get_time_series()
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
-          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         else if (timevary_SRparm(y) == 1)  //  update R0_use and SSB_use in this year
                                            //  values will carry forward into subsequent years
@@ -1040,7 +1040,7 @@ FUNCTION void get_time_series()
           bio_yr = y;
           SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
-          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
 
           if (fishery_on_off == 1)
           {
@@ -1053,7 +1053,7 @@ FUNCTION void get_time_series()
         }
         else  //  flag is 2
         {
-          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         Recruits = Spawn_Recr(SRparm_work, SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr using either virgin or adjusted R0 and SSB0
 //        warning <<"  SSB: " << SSB_current << "  R: " << Recruits << endl;
@@ -1497,7 +1497,7 @@ FUNCTION void get_time_series()
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
-          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         else if (timevary_SRparm(y) == 1)  //  update R0_use and SSB_use in this year
                                            //  values will carry forward into subsequent years
@@ -1510,7 +1510,7 @@ FUNCTION void get_time_series()
           bio_yr = y;
           SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
-          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
 
           if (fishery_on_off == 1)
           {
@@ -1523,7 +1523,7 @@ FUNCTION void get_time_series()
         }
         else  //  flag is 2
         {
-          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         Recruits = Spawn_Recr(SRparm_work, 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
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index ba7f2694..30ce918f 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -6657,7 +6657,7 @@
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
-    ParmLabel += "20.HCR_anchor" + CRLF(1);
+    ParmLabel += "20.HCR_inflect" + CRLF(1);
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
diff --git a/SS_readdata_330.tpl b/SS_readdata_330.tpl
index ad64c3b7..33d383e0 100644
--- a/SS_readdata_330.tpl
+++ b/SS_readdata_330.tpl
@@ -4281,8 +4281,8 @@
       echoinput << "HarvestPolicy=0, so values for top, bottom, buffer will be ignored" << endl;
 
     echoinput << HarvestPolicy << "  # echoed HarvestPolicy " << endl;
-    *(ad_comm::global_datafile) >> H4010_top_rd; //  use -1 to set H4010_top to Bmsy/SSB_unf
-    echoinput << H4010_top_rd << "   # echoed control rule inflection (-1 to set to Bmsy/SSB_unf)" << endl;
+    *(ad_comm::global_datafile) >> H4010_top_rd; //  as fraction of HCR_anchor; use -1 as legacy approach to set H4010_top to Bmsy/SSB_unf
+    echoinput << H4010_top_rd << "   # echoed control rule inflection" << endl;
     *(ad_comm::global_datafile) >> H4010_bot;
     echoinput << H4010_bot << "   # echoed control rule cutoff " << endl;
     *(ad_comm::global_datafile) >> H4010_scale_rd;
@@ -4352,7 +4352,12 @@
       write_message(ADJUST, 0);
       Fcast_Loop_Control(5) = 2;
     }
-    echoinput << Fcast_Loop_Control(5) << " #control rule anchor: 1=virgin_SSB; 2=unfished_benchmark_SSB(old_approach)" << endl;
+    if (H4010_top_rd < 0)  // convert old legacy approach to new approach for using Bmsy
+    {
+      Fcast_Loop_Control(5) = 3;
+      H4010_top_rd = 1.0;
+    }
+    echoinput << Fcast_Loop_Control(5) << " #control rule anchor: 1=virgin_SSB; 2=unfished_benchmark_SSB(old_approach); 3=Bmsy" << endl;
     if (depletion_basis == 1 && Fcast_Loop_Control(5) == 2)
     {
       warnstream << "depletion_basis is using virgin but HCR anchor is using SSB_unf from benchmark. Are you sure?";
diff --git a/SS_write_ssnew.tpl b/SS_write_ssnew.tpl
index 9b6948f0..98b0b162 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -1643,11 +1643,11 @@ 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 as the inflection " << 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 to use virgin vs benchmark SSB as basis" << endl;
+  NuFore << "# values for top, bottom and buffer required, but not used when Policy=0" << endl;
+  NuFore << H4010_top_rd << " # Control rule inflection for constant F (as frac of HCR_anchor, see below); must be > control rule cutoff" << endl;
+  NuFore << H4010_bot << " # Control rule cutoff for no F (as frac of HCR_anchor, 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]. -year fills from year to YrMax " << endl;
+  NuFore << "# Also see HCR_anchor below to use virgin vs benchmark SSB or Bmsy as basis for inflection and cutoff" << endl;
   if (H4010_scale_rd < 0)
   {
     j = H4010_scale_vec_rd.size() - 1;
@@ -1669,7 +1669,7 @@ FUNCTION void write_nucontrol()
   {
     NuFore << Fcast_Loop_Control(4) << " # multiplier on base recruitment " << endl;
   }
-  NuFore << Fcast_Loop_Control(5) << " # HCR_anchor: 0 or 2 uses unfished benchmark SSB (old hardwired approach); 1 = virgin SSB" << endl << "#" << endl;
+  NuFore << Fcast_Loop_Control(5) << " # HCR_anchor: 0 or 2 uses unfished benchmark SSB (old hardwired approach); 1 = virgin SSB; 3 = BMSY" << endl << "#" << endl;
 
   NuFore << Fcast_Cap_FirstYear << "  # FirstYear for caps and allocations (should be after years with fixed inputs) " << endl;
 

From 9d8330074c6de5aa043c48386c2f351a4d5ecfde Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Tue, 3 Jun 2025 10:28:31 -0700
Subject: [PATCH 40/58] git stash pop

---
 SS_benchfore.tpl       | 27 ++++++++++-----------------
 SS_popdyn.tpl          | 12 ++++++------
 SS_readcontrol_330.tpl |  2 +-
 SS_readdata_330.tpl    | 11 +++--------
 SS_write_ssnew.tpl     | 12 ++++++------
 5 files changed, 26 insertions(+), 38 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index e156cb78..9737e283 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -2264,10 +2264,8 @@ FUNCTION void Get_Forecast()
     {HCR_anchor = SSB_virgin;}
     else if (Fcast_Loop_Control(5) == 2)
     {HCR_anchor = SSB_unf;}
-    else if (Fcast_Loop_Control(5) == 3)
-    {HCR_anchor = Bmsy;}  // so H4010_top_rd should be 1.0;
 
-    if (H4010_top_rd < 0.0)  // legacy approach.  This has already been converted to new approach in readdata
+    if (H4010_top_rd < 0.0)
     {
       H4010_top = Bmsy / HCR_anchor;  // convert to fraction of anchor
       if (H4010_bot > 0.25)
@@ -2280,20 +2278,13 @@ FUNCTION void Get_Forecast()
     {
       H4010_top = H4010_top_rd;
     }
-    if (Fcast_Loop_Control(5) == 3 && H4010_top_rd != 1.0)
-    {  
-      warnstream << "HCR_anchor is BMSY; so H4010_top normally is 1.0; are you sure you want:  " << H4010_top;
-      write_message (WARN, 0);
-    }
 
-    Mgmt_quant(20) = H4010_top * HCR_anchor;
+    Mgmt_quant(20) = HCR_anchor;
     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) << endl
-            << "Control_rule_anchor_approach: " << Fcast_Loop_Control(5) << " HCR_anchor: " << HCR_anchor << endl
-            << "intercept(SSB): " << H4010_bot * HCR_anchor << endl
-            << "Inflection(SSB): " << H4010_top * HCR_anchor << endl
-            << "#" << endl;
+            << "Control_rule_anchor_approach: " << Fcast_Loop_Control(5) << " HCR_anchor: " << HCR_anchor << endl;
+    report5 << "#" << endl;
 
     switch (HarvestPolicy)
     {
@@ -2721,6 +2712,7 @@ FUNCTION void Get_Forecast()
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
+          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         else if (timevary_SRparm(y) == 1)  //  update R0_use and SSB_use in this year
                                            //  values will carry forward into subsequent years
@@ -2733,7 +2725,7 @@ FUNCTION void Get_Forecast()
           bio_yr = y;
           SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
-//          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
 
           // test that this stays on equilibrium.  It does.
 //          SSBpR_temp = SSB_use / R0_use;  // get unfished SSBpR
@@ -2752,7 +2744,7 @@ FUNCTION void Get_Forecast()
         }
         else  //  flag is 2
         {
-//          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         Recruits = Spawn_Recr(SRparm_work, SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr using either virgin or adjusted R0 and SSB0
 
@@ -3374,6 +3366,7 @@ FUNCTION void Get_Forecast()
             {
               R0_use = Recr_virgin;
               SSB_use = SSB_virgin;
+              warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
             }
             else if (timevary_SRparm(y) == 1)  //  update R0_use and SSB_use in this year
                                                //  values will carry forward into subsequent years
@@ -3386,7 +3379,7 @@ FUNCTION void Get_Forecast()
               bio_yr = y;
               SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
               SSB_use = SSB_equil;
-//              warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+              warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
 
               if (fishery_on_off == 1)
               {
@@ -3399,7 +3392,7 @@ FUNCTION void Get_Forecast()
             }
             else  //  flag is 2
             {
-//              warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+              warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
             }
             Recruits = Spawn_Recr(SRparm_work, 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
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 2acdfb82..7a00757d 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -1027,7 +1027,7 @@ FUNCTION void get_time_series()
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
-//          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         else if (timevary_SRparm(y) == 1)  //  update R0_use and SSB_use in this year
                                            //  values will carry forward into subsequent years
@@ -1040,7 +1040,7 @@ FUNCTION void get_time_series()
           bio_yr = y;
           SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
-//          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
 
           if (fishery_on_off == 1)
           {
@@ -1053,7 +1053,7 @@ FUNCTION void get_time_series()
         }
         else  //  flag is 2
         {
-//          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         Recruits = Spawn_Recr(SRparm_work, SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr using either virgin or adjusted R0 and SSB0
 //        warning <<"  SSB: " << SSB_current << "  R: " << Recruits << endl;
@@ -1497,7 +1497,7 @@ FUNCTION void get_time_series()
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
-//          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         else if (timevary_SRparm(y) == 1)  //  update R0_use and SSB_use in this year
                                            //  values will carry forward into subsequent years
@@ -1510,7 +1510,7 @@ FUNCTION void get_time_series()
           bio_yr = y;
           SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
-//          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
 
           if (fishery_on_off == 1)
           {
@@ -1523,7 +1523,7 @@ FUNCTION void get_time_series()
         }
         else  //  flag is 2
         {
-//          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         Recruits = Spawn_Recr(SRparm_work, 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
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 30ce918f..ba7f2694 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -6657,7 +6657,7 @@
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
-    ParmLabel += "20.HCR_inflect" + CRLF(1);
+    ParmLabel += "20.HCR_anchor" + CRLF(1);
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
diff --git a/SS_readdata_330.tpl b/SS_readdata_330.tpl
index 33d383e0..ad64c3b7 100644
--- a/SS_readdata_330.tpl
+++ b/SS_readdata_330.tpl
@@ -4281,8 +4281,8 @@
       echoinput << "HarvestPolicy=0, so values for top, bottom, buffer will be ignored" << endl;
 
     echoinput << HarvestPolicy << "  # echoed HarvestPolicy " << endl;
-    *(ad_comm::global_datafile) >> H4010_top_rd; //  as fraction of HCR_anchor; use -1 as legacy approach to set H4010_top to Bmsy/SSB_unf
-    echoinput << H4010_top_rd << "   # echoed control rule inflection" << endl;
+    *(ad_comm::global_datafile) >> H4010_top_rd; //  use -1 to set H4010_top to Bmsy/SSB_unf
+    echoinput << H4010_top_rd << "   # echoed control rule inflection (-1 to set to Bmsy/SSB_unf)" << endl;
     *(ad_comm::global_datafile) >> H4010_bot;
     echoinput << H4010_bot << "   # echoed control rule cutoff " << endl;
     *(ad_comm::global_datafile) >> H4010_scale_rd;
@@ -4352,12 +4352,7 @@
       write_message(ADJUST, 0);
       Fcast_Loop_Control(5) = 2;
     }
-    if (H4010_top_rd < 0)  // convert old legacy approach to new approach for using Bmsy
-    {
-      Fcast_Loop_Control(5) = 3;
-      H4010_top_rd = 1.0;
-    }
-    echoinput << Fcast_Loop_Control(5) << " #control rule anchor: 1=virgin_SSB; 2=unfished_benchmark_SSB(old_approach); 3=Bmsy" << endl;
+    echoinput << Fcast_Loop_Control(5) << " #control rule anchor: 1=virgin_SSB; 2=unfished_benchmark_SSB(old_approach)" << endl;
     if (depletion_basis == 1 && Fcast_Loop_Control(5) == 2)
     {
       warnstream << "depletion_basis is using virgin but HCR anchor is using SSB_unf from benchmark. Are you sure?";
diff --git a/SS_write_ssnew.tpl b/SS_write_ssnew.tpl
index 98b0b162..9b6948f0 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -1643,11 +1643,11 @@ 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 required, but not used when Policy=0" << endl;
-  NuFore << H4010_top_rd << " # Control rule inflection for constant F (as frac of HCR_anchor, see below); must be > control rule cutoff" << endl;
-  NuFore << H4010_bot << " # Control rule cutoff for no F (as frac of HCR_anchor, 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]. -year fills from year to YrMax " << endl;
-  NuFore << "# Also see HCR_anchor below to use virgin vs benchmark SSB or Bmsy as basis for inflection and cutoff" << 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 as the inflection " << 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 to use virgin vs benchmark SSB as basis" << endl;
   if (H4010_scale_rd < 0)
   {
     j = H4010_scale_vec_rd.size() - 1;
@@ -1669,7 +1669,7 @@ FUNCTION void write_nucontrol()
   {
     NuFore << Fcast_Loop_Control(4) << " # multiplier on base recruitment " << endl;
   }
-  NuFore << Fcast_Loop_Control(5) << " # HCR_anchor: 0 or 2 uses unfished benchmark SSB (old hardwired approach); 1 = virgin SSB; 3 = BMSY" << endl << "#" << endl;
+  NuFore << Fcast_Loop_Control(5) << " # HCR_anchor: 0 or 2 uses unfished benchmark SSB (old hardwired approach); 1 = virgin SSB" << endl << "#" << endl;
 
   NuFore << Fcast_Cap_FirstYear << "  # FirstYear for caps and allocations (should be after years with fixed inputs) " << endl;
 

From eaba2636e3d5827888804e27be02001b1fea411e Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Tue, 3 Jun 2025 11:46:29 -0700
Subject: [PATCH 41/58] redo code for Bmsy as HCR inflection

---
 SS_benchfore.tpl       | 26 +++++++++++++++++---------
 SS_popdyn.tpl          | 12 ++++++------
 SS_readcontrol_330.tpl |  2 +-
 SS_readdata_330.tpl    | 11 ++++++++---
 SS_write_ssnew.tpl     | 12 ++++++------
 5 files changed, 38 insertions(+), 25 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 9737e283..4a0f762a 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -2264,8 +2264,10 @@ FUNCTION void Get_Forecast()
     {HCR_anchor = SSB_virgin;}
     else if (Fcast_Loop_Control(5) == 2)
     {HCR_anchor = SSB_unf;}
+    else if (Fcast_Loop_Control(5) == 3)
+    {HCR_anchor = Bmsy;}  // so H4010_top_rd should be 1.0;
 
-    if (H4010_top_rd < 0.0)
+    if (H4010_top_rd < 0.0)  // legacy approach.  This has already been converted to new approach in readdata
     {
       H4010_top = Bmsy / HCR_anchor;  // convert to fraction of anchor
       if (H4010_bot > 0.25)
@@ -2278,13 +2280,20 @@ FUNCTION void Get_Forecast()
     {
       H4010_top = H4010_top_rd;
     }
+    if (Fcast_Loop_Control(5) == 3 && H4010_top_rd != 1.0)
+    {  
+      warnstream << "HCR_anchor is BMSY; so H4010_top normally is 1.0; are you sure you want:  " << H4010_top;
+      write_message (WARN, 0);
+    }
 
-    Mgmt_quant(20) = HCR_anchor;
+    Mgmt_quant(20) = H4010_top * HCR_anchor;
     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) << endl
-            << "Control_rule_anchor_approach: " << Fcast_Loop_Control(5) << " HCR_anchor: " << HCR_anchor << endl;
-    report5 << "#" << endl;
+            << "Control_rule_anchor_approach: " << Fcast_Loop_Control(5) << " HCR_anchor: " << HCR_anchor << endl
+            << "intercept(SSB): " << H4010_bot * HCR_anchor << endl
+            << "Inflection(SSB): " << H4010_top * HCR_anchor << endl
+            << "#" << endl;
 
     switch (HarvestPolicy)
     {
@@ -2725,7 +2734,7 @@ FUNCTION void Get_Forecast()
           bio_yr = y;
           SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
-          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
 
           // test that this stays on equilibrium.  It does.
 //          SSBpR_temp = SSB_use / R0_use;  // get unfished SSBpR
@@ -2744,7 +2753,7 @@ FUNCTION void Get_Forecast()
         }
         else  //  flag is 2
         {
-          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         Recruits = Spawn_Recr(SRparm_work, SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr using either virgin or adjusted R0 and SSB0
 
@@ -3366,7 +3375,6 @@ FUNCTION void Get_Forecast()
             {
               R0_use = Recr_virgin;
               SSB_use = SSB_virgin;
-              warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
             }
             else if (timevary_SRparm(y) == 1)  //  update R0_use and SSB_use in this year
                                                //  values will carry forward into subsequent years
@@ -3379,7 +3387,7 @@ FUNCTION void Get_Forecast()
               bio_yr = y;
               SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
               SSB_use = SSB_equil;
-              warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//              warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
 
               if (fishery_on_off == 1)
               {
@@ -3392,7 +3400,7 @@ FUNCTION void Get_Forecast()
             }
             else  //  flag is 2
             {
-              warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//              warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
             }
             Recruits = Spawn_Recr(SRparm_work, 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
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 7a00757d..2acdfb82 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -1027,7 +1027,7 @@ FUNCTION void get_time_series()
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
-          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         else if (timevary_SRparm(y) == 1)  //  update R0_use and SSB_use in this year
                                            //  values will carry forward into subsequent years
@@ -1040,7 +1040,7 @@ FUNCTION void get_time_series()
           bio_yr = y;
           SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
-          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
 
           if (fishery_on_off == 1)
           {
@@ -1053,7 +1053,7 @@ FUNCTION void get_time_series()
         }
         else  //  flag is 2
         {
-          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         Recruits = Spawn_Recr(SRparm_work, SSB_use, R0_use, SSB_current); // calls to function Spawn_Recr using either virgin or adjusted R0 and SSB0
 //        warning <<"  SSB: " << SSB_current << "  R: " << Recruits << endl;
@@ -1497,7 +1497,7 @@ FUNCTION void get_time_series()
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
-          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         else if (timevary_SRparm(y) == 1)  //  update R0_use and SSB_use in this year
                                            //  values will carry forward into subsequent years
@@ -1510,7 +1510,7 @@ FUNCTION void get_time_series()
           bio_yr = y;
           SSBpR_Calc(R0_use); //  call function to do per recruit calculation with current year's biology and adjusted R0
           SSB_use = SSB_equil;
-          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//          warning << y << " update_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
 
           if (fishery_on_off == 1)
           {
@@ -1523,7 +1523,7 @@ FUNCTION void get_time_series()
         }
         else  //  flag is 2
         {
-          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//          warning << y << " carry_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         Recruits = Spawn_Recr(SRparm_work, 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
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index ba7f2694..30ce918f 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -6657,7 +6657,7 @@
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
-    ParmLabel += "20.HCR_anchor" + CRLF(1);
+    ParmLabel += "20.HCR_inflect" + CRLF(1);
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
diff --git a/SS_readdata_330.tpl b/SS_readdata_330.tpl
index ad64c3b7..33d383e0 100644
--- a/SS_readdata_330.tpl
+++ b/SS_readdata_330.tpl
@@ -4281,8 +4281,8 @@
       echoinput << "HarvestPolicy=0, so values for top, bottom, buffer will be ignored" << endl;
 
     echoinput << HarvestPolicy << "  # echoed HarvestPolicy " << endl;
-    *(ad_comm::global_datafile) >> H4010_top_rd; //  use -1 to set H4010_top to Bmsy/SSB_unf
-    echoinput << H4010_top_rd << "   # echoed control rule inflection (-1 to set to Bmsy/SSB_unf)" << endl;
+    *(ad_comm::global_datafile) >> H4010_top_rd; //  as fraction of HCR_anchor; use -1 as legacy approach to set H4010_top to Bmsy/SSB_unf
+    echoinput << H4010_top_rd << "   # echoed control rule inflection" << endl;
     *(ad_comm::global_datafile) >> H4010_bot;
     echoinput << H4010_bot << "   # echoed control rule cutoff " << endl;
     *(ad_comm::global_datafile) >> H4010_scale_rd;
@@ -4352,7 +4352,12 @@
       write_message(ADJUST, 0);
       Fcast_Loop_Control(5) = 2;
     }
-    echoinput << Fcast_Loop_Control(5) << " #control rule anchor: 1=virgin_SSB; 2=unfished_benchmark_SSB(old_approach)" << endl;
+    if (H4010_top_rd < 0)  // convert old legacy approach to new approach for using Bmsy
+    {
+      Fcast_Loop_Control(5) = 3;
+      H4010_top_rd = 1.0;
+    }
+    echoinput << Fcast_Loop_Control(5) << " #control rule anchor: 1=virgin_SSB; 2=unfished_benchmark_SSB(old_approach); 3=Bmsy" << endl;
     if (depletion_basis == 1 && Fcast_Loop_Control(5) == 2)
     {
       warnstream << "depletion_basis is using virgin but HCR anchor is using SSB_unf from benchmark. Are you sure?";
diff --git a/SS_write_ssnew.tpl b/SS_write_ssnew.tpl
index 9b6948f0..98b0b162 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -1643,11 +1643,11 @@ 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 as the inflection " << 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 to use virgin vs benchmark SSB as basis" << endl;
+  NuFore << "# values for top, bottom and buffer required, but not used when Policy=0" << endl;
+  NuFore << H4010_top_rd << " # Control rule inflection for constant F (as frac of HCR_anchor, see below); must be > control rule cutoff" << endl;
+  NuFore << H4010_bot << " # Control rule cutoff for no F (as frac of HCR_anchor, 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]. -year fills from year to YrMax " << endl;
+  NuFore << "# Also see HCR_anchor below to use virgin vs benchmark SSB or Bmsy as basis for inflection and cutoff" << endl;
   if (H4010_scale_rd < 0)
   {
     j = H4010_scale_vec_rd.size() - 1;
@@ -1669,7 +1669,7 @@ FUNCTION void write_nucontrol()
   {
     NuFore << Fcast_Loop_Control(4) << " # multiplier on base recruitment " << endl;
   }
-  NuFore << Fcast_Loop_Control(5) << " # HCR_anchor: 0 or 2 uses unfished benchmark SSB (old hardwired approach); 1 = virgin SSB" << endl << "#" << endl;
+  NuFore << Fcast_Loop_Control(5) << " # HCR_anchor: 0 or 2 uses unfished benchmark SSB (old hardwired approach); 1 = virgin SSB; 3 = BMSY" << endl << "#" << endl;
 
   NuFore << Fcast_Cap_FirstYear << "  # FirstYear for caps and allocations (should be after years with fixed inputs) " << endl;
 

From 37db2c929955e84d1920cc3eb81cd37dee75df8f Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Tue, 3 Jun 2025 15:16:19 -0700
Subject: [PATCH 42/58] add bench SR_curve; cleanup spawn_recr report

---
 SS_benchfore.tpl       |  6 ++--
 SS_param.tpl           |  1 +
 SS_readcontrol_330.tpl |  3 ++
 SS_write_report.tpl    | 71 ++++++++++++++++++++++--------------------
 SS_write_ssnew.tpl     |  2 +-
 5 files changed, 46 insertions(+), 37 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 4a0f762a..fa585379 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -785,7 +785,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   Recr_unf = mfexp(SRparm_bench(1));  // R0 to be used
   Fishon = 0;
   SSBpR_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
-  dvariable SSBpR_bench = SSB_equil / Recr_unf;
+  SSBpR_bench = SSB_equil / Recr_unf;
 
   report5 << "virgin: " << Recr_virgin << " " << SSB_virgin << endl;
   report5 << "bench: " << Recr_unf << " " << SSB_equil << endl;
@@ -855,10 +855,10 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   if (show_MSY == 1)
   {
     SRparm_bench(N_SRparm2 + 1) = SSB0_4_SRR;
-    Mgmt_quant(1) = SSB_unf;
+    Mgmt_quant(1) = SSB0_4_SRR;
     Mgmt_quant(2) = totbio;  // this is calculated in Do_Equil_Calc
     Mgmt_quant(3) = smrybio;
-    Mgmt_quant(4) = Recr_unf;
+    Mgmt_quant(4) = R0_4_SRR;
     report5 << "SRparms for benchmark: " << SRparm_bench << endl
             << "Benchmark biology averaged over years: " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl << endl;
     Mgmt_quant(19) = SSB_unf;  // placeholder for depletion denominator
diff --git a/SS_param.tpl b/SS_param.tpl
index 2409c944..d8ff05f9 100644
--- a/SS_param.tpl
+++ b/SS_param.tpl
@@ -167,6 +167,7 @@ PARAMETER_SECTION
   number half_sigmaRsq;
   number sigmaR;
   number SSBpR_virgin;
+  number SSBpR_bench;
   number SSB0_4_SRR;
   number R0_4_SRR;
   number regime_change;
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 30ce918f..bc8999fa 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1971,6 +1971,7 @@
 
   int timevary_SRparm_first;  //   == 0 means that no relevant parms are timevarying
   int firstSRparm;
+  int timevary_SRparm_first_yr;  //   year
   int timevary_parm_SR_last;
   ivector timevary_SRparm(styr-3,YrMax+1);
   ivector SRparm_timevary(1,N_SRparm2);
@@ -1981,6 +1982,7 @@
   firstSRparm = ParCount;
   timevary_parm_SR_last = 0;
   timevary_SRparm_first = 0;
+  timevary_SRparm_first_yr = 0;
   timevary_SRparm.initialize();
   SRparm_timevary.initialize();
   SR_env_link = 0;
@@ -2142,6 +2144,7 @@
           if (timevary_pass(y) > 0 && j != N_SRparm2 - 1)
           {
             timevary_SRparm(y) = timevary_pass(y);  //  set timevary flag, except for regime parameter
+            timevary_SRparm_first_yr = y;
             SRflag = 1; //  first change point
           }
           else if(SRflag == 1)
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index faf51371..29e259b7 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -77,7 +77,9 @@ FUNCTION void write_bigoutput()
   SS2out << "Data_File: " << datfilename << endl;
   SS2out << "Control_File: " << ctlfilename << endl;
   if (readparfile >= 1)
-    SS2out << "Start_parm_values_from_SS.PAR" << endl;
+    {SS2out << "Start_parm_values_from_SS.PAR" << endl;}
+    else
+    {SS2out << "Start_parm_values_from_control_file" << endl;}
   SS2out << endl
          << "Convergence_Level: " << objective_function_value::pobjfun->gmax << " is_final_gradient" << endl;
   temp = get_ln_det_value();
@@ -1889,44 +1891,36 @@ FUNCTION void write_bigoutput()
       SS2out << endl;
     }
 
-    SS2out << endl << "#New_Expanded_Spawn_Recr_report" << endl << pick_report_name(19) << endl;
+    SS2out << endl << "#Expanded_Spawn_Recr_report" << endl << pick_report_name(19) << endl;
     SS2out << SR_fxn << " # SR_Function" << endl;
-    SS2out << "# " <<endl << "Flags_for_timevary_biology_and_SR" << endl;
-    SS2out << timevary_bio_4SRR << " # timevary_bio_4SRR  #_Compatibility_flag_for_legacy_(0)_vs_improved_(1)_impact_of_timevary_biology_on_benchmark_SRR_calcs" << endl;
-    SS2out << timevary_MG_firstyr << " # timevary_MG_firstyr ";
-    if( timevary_MG_firstyr == YrMax)
-    { SS2out << " #_No_timevary_MGparm " << endl; }
-    else
-    { SS2out << " #_some_timevary_MGparm_or_EWAA: " << timevary_MG_firstyr << endl; }
-
     SS2out << N_SRparm2 << " # N_SRparms" << endl;
-    SS2out << "#" << endl << "#_SRparm  parm_label value phase" << endl;
+    SS2out << "#" << endl << "#_SRparm  parm_label value phase TV_year" << endl;
     for (int j = 1; j <=N_SRparm2; j++)
     {
       SS2out << "# " << j << " " << ParmLabel(firstSRparm + j) << " " << SRparm(j) << " " << SRparm_PH(j);
       if (SRparm_timevary(j) > 0 && j <= 4 ) //  timevary SRparm exists
-      {SS2out << " #_TV";} 
-      if (j == (N_SRparm2 - 1) && SRparm_timevary(j) > 0) //  timevary regime exists
-      {SS2out << " #_Regime_used_to_offset_from_SRR";}
-      SS2out << endl;
+      {SS2out << " " << timevary_SRparm_first_yr;} else {SS2out << " -";}
+       SS2out << endl;
     }
-
-    if( timevary_SRparm_first == 0)
-    { SS2out << "0  #_No_timevary_SRparms,_other_than_regime " << endl; }
+    SS2out << "#" << endl;
+    if (SRparm_timevary(N_SRparm2 - 1) > 0) //  timevary regime exists
+      {SS2out << " #_Regime_used_to_offset_from_SRR";}
+    SS2out << timevary_bio_4SRR << " # timevary_bio_4SRR  #_Compatibility_flag_for_legacy_(0)_vs_improved_(1)_impact_of_timevary_biology_on_benchmark_SRR_calcs" << endl;
+    if( timevary_MG_firstyr == YrMax)
+    { SS2out << " #_No_timevary_MGparm" << endl; }
     else
-    {
-      for (y = styr; y <= YrMax; y++) if (timevary_SRparm(y) == 1) SS2out << y;
-      SS2out << "  # timevary_SRparm_begin_year" << endl;
-    }
+    { SS2out << timevary_MG_firstyr << " #_first year_timevary_MGparm_(or_any_year_EWAA) " << endl; }
 
-    SS2out << "#" << 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;
+    SS2out << "#" << endl << "Quantities for MSY and other benchmark calculations " << endl
+      << "Benchmark_index: 1 2 3 4 5 6 7 8 9 10" << endl
+      << "Benchmark_label: beg_bio end_bio beg_selex end_selex beg_relF end_relF beg_recr_dist end_recr_dist beg_SRparm end_SRparm" << endl
+      << "Benchmark_years: " << Bmark_Yr << 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 << "#_NOTE:_using_range_of_years_can_reduce_standard_error_of_result;_do_this_only_when_timevarying_makes_necessary:  " << k << " " << Bmark_Yr(k) << " " << Bmark_Yr(k+1) << endl;}
     }
-    SS2out << "SSBpR0_(virgin): " << SSBpR_virgin << " #_uses_biology_from_start_year: " << styr <<endl;
-    SS2out << "SSBpR_unfished_benchmark: " << Mgmt_quant(1) / Mgmt_quant(4) << "  #_based_on_averaging_biology_over_benchmark_year_range " << endl;
+    SS2out << "SSBpR0_virgin: " << SSBpR_virgin << " #_uses_biology_from_start_year: " << styr <<endl;
+    SS2out << "SSBpR_unfished_benchmark: " << SSBpR_bench << "  #_uses_biology_over_benchmark_year_range " << endl;
 
     switch (SR_fxn)
     {
@@ -1998,13 +1992,13 @@ FUNCTION void write_bigoutput()
         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 " << endl;
+    SS2out << endl  << "#" << endl << init_equ_steepness << "  # Initial_equilibrium:_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 SSBpR(yr) " << 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 " << " " << SSBpR_virgin << endl;
+    SS2out << "Virg " << SSB_yr(y) << " " << exp_rec(y) << " _ " << 0.0 << " Virg " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " _ " << SSBpR_virgin << endl;
     y = styr - 1;
-    SS2out << "Init " << SSB_yr(y) << " " << exp_rec(y) << " - " << 0.0 << " Init " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " " << 0.0  << " " << SSBpR_virgin << endl;
+    SS2out << "Init " << SSB_yr(y) << " " << exp_rec(y) << " _ " << 0.0 << " Init " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " _ " << SSBpR_virgin << endl;
 
     if (recdev_first < styr)
     {
@@ -2058,9 +2052,9 @@ FUNCTION void write_bigoutput()
     {
       {
         SS2out << endl
-               << pick_report_name(20) << endl;
+               << pick_report_name(20) << endl
+               << "# using_virgin_SR_parameters:  " << SRparm_work << endl;
         SS2out << "SSB/SSB_virgin    SSB    Recruitment" << endl;
-        y = styr;
         SRparm_work = SRparm_byyr(styr);
         for (f = 1; f <= 120; f++)
         {
@@ -2068,6 +2062,17 @@ FUNCTION void write_bigoutput()
           temp = Spawn_Recr(SRparm_work, SSB_virgin, Recr_virgin, SSB_current);
           SS2out << SSB_current / SSB_virgin << " " << SSB_current << " " << temp << endl;
         }
+        SS2out << endl
+               << "SPAWN_RECR_CURVE report:20 Benchmark" << endl  //  revise this name per r4ss needs
+               << "# using_benchmark_SR_parameters:  " << SRparm_bench << endl;
+        SS2out << "SSB/SSB_benchmark    SSB    Recruitment" << endl;
+        for (f = 1; f <= 120; f++)
+        {
+          SSB_current = double(f) / 100. * SSB0_4_SRR;
+          temp = Spawn_Recr(SRparm_bench, SSB0_4_SRR, R0_4_SRR, SSB_current);
+          SS2out << SSB_current / SSB0_4_SRR << " " << SSB_current << " " << temp << endl;
+        }
+
       }
     }
 
diff --git a/SS_write_ssnew.tpl b/SS_write_ssnew.tpl
index 98b0b162..99ff2299 100644
--- a/SS_write_ssnew.tpl
+++ b/SS_write_ssnew.tpl
@@ -2138,7 +2138,7 @@ 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 << 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; 10=B-H_ab" << endl;
   report4 << init_equ_steepness << "  # 0/1 to use steepness in initial equ recruitment calculation" << endl;
   report4 << " 0 #  not_used" << 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;

From 7ea4fdeb976b98ad8b2bf0f1424605e9b0c85242 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Thu, 5 Jun 2025 17:14:25 -0700
Subject: [PATCH 43/58] easy fix for spiny dogfish using SRR 7

---
 SS_benchfore.tpl    | 2 +-
 SS_write_report.tpl | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index fa585379..8a6db2c6 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -2721,7 +2721,7 @@ FUNCTION void Get_Forecast()
         {
           R0_use = Recr_virgin;
           SSB_use = SSB_virgin;
-          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
+//          warning << y << " virgin_SRR; SSB_use: "<<SSB_use<<"  R0_use: "<<R0_use <<"  steep: " << SRparm_work(2) << endl;
         }
         else if (timevary_SRparm(y) == 1)  //  update R0_use and SSB_use in this year
                                            //  values will carry forward into subsequent years
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 29e259b7..8e4e6a45 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -2051,11 +2051,12 @@ FUNCTION void write_bigoutput()
     if (pick_report_use(20) == "Y")
     {
       {
-        SS2out << endl
+      SRparm_work = SRparm_byyr(styr);
+      y = styr;
+      SS2out << endl
                << pick_report_name(20) << endl
                << "# using_virgin_SR_parameters:  " << SRparm_work << endl;
         SS2out << "SSB/SSB_virgin    SSB    Recruitment" << endl;
-        SRparm_work = SRparm_byyr(styr);
         for (f = 1; f <= 120; f++)
         {
           SSB_current = double(f) / 100. * SSB_virgin;

From 2e35ec3a5430755d24df5f2d6a1e722f1a3ba97e Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Wed, 11 Jun 2025 10:09:22 -0700
Subject: [PATCH 44/58] repair legacy HCR_anchor; cleanup warnings

---
 SS_benchfore.tpl       |  6 ++----
 SS_readcontrol_330.tpl | 10 ++++++++++
 SS_readdata_330.tpl    |  2 +-
 3 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 8a6db2c6..b58f1629 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -787,8 +787,8 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   SSBpR_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
   SSBpR_bench = SSB_equil / Recr_unf;
 
-  report5 << "virgin: " << Recr_virgin << " " << SSB_virgin << endl;
-  report5 << "bench: " << Recr_unf << " " << SSB_equil << endl;
+//  report5 << "virgin: " << Recr_virgin << " " << SSB_virgin << endl;
+//  report5 << "bench: " << Recr_unf << " " << SSB_equil << endl;
   if( timevary_MG_firstyr == YrMax && WTage_rd == 0)  // no time-varying biology
   {
     SSB0_4_SRR = SSB_virgin;
@@ -799,8 +799,6 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   {
     if( timevary_bio_4SRR == 0)  // legacy approach;  this switch is read from starter.ss
     {
-      warnstream << "There is timevary biology and the legacy approach to benchmark calculations is being used; user should be aware";
-      write_message (WARN, 0);
       if(timevary_SRparm_first == 0)  // no timevary SRR parms
       {
         SSB_unf = SSB_equil;
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index bc8999fa..375d34ce 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1817,12 +1817,22 @@
         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
     if ((timevary_MG(y, 2) > 0 || timevary_MG(y, 3) > 0) && natM_type == 5 && natM_5_opt < 3) timevary_MG(y, 1) = 1;
   
     echoinput << y << " timevary_MG: " << timevary_MG(y) << endl;
   }
 
+  if( timevary_MG_firstyr == YrMax && WTage_rd == 0)  // no time-varying biology
+  {
+    if( timevary_bio_4SRR == 0)  // legacy approach;  this switch is read from starter.ss
+    {
+      warnstream << "There is timevary biology and the legacy approach to benchmark calculations is being used; user should be aware";
+      write_message(WARN, 0);
+    }
+  }
+
   for (y = endyr + 1; y <= YrMax; y++)
   {
     for (f = 1; f <= 7; f++)
diff --git a/SS_readdata_330.tpl b/SS_readdata_330.tpl
index 33d383e0..0ba0045d 100644
--- a/SS_readdata_330.tpl
+++ b/SS_readdata_330.tpl
@@ -4345,7 +4345,7 @@
       "even when the base is set to the mean of earlier recruitments" << endl;
     }
 
-    if (Fcast_Loop_Control(5) == 0)  //  default before 3.30.24
+    if (Fcast_Loop_Control(5) <= 0)  //  default before 3.30.24
     {
       echoinput << "basis for HCR anchor was not set; setting to 2 to match default before 3.30.24" << endl;
       warnstream << "basis for HCR anchor was not set; setting to 2 to match default before 3.30.24";

From c5381f41c5698d3922eac37f75c085d35d35c357 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Wed, 11 Jun 2025 10:28:23 -0700
Subject: [PATCH 45/58] restore global_msy to report.sso

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

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index b58f1629..eadc9e65 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -2021,20 +2021,19 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   }
   else if (show_MSY == 2) //  do brief output
   {
-    report5 << SPR_actual / 100. << " " << SPR_Fmult << " " << Mgmt_quant(10) << " " << YPR_spr_dead / Vbio1_spr << " " << Bspr_rec << " "
+    SS2out << 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 << " # ";
 
-    report5 << SPR_Btgt << " " << Btgt / SSB_unf << " " << Btgt_Fmult << " " << Mgmt_quant(7) << " " << YPR_Btgt_dead / Vbio1_Btgt << " " << Btgt_Rec << " "
+    SS2out << 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 << " # ";
 
-    report5 << MSY_SPR << " " << Bmsy / SSB_unf << " " << MSY_Fmult << " " << Mgmt_quant(14) << " " << MSY / (Vbio1_MSY * Recr_msy) << " " << Recr_msy << " "
+    SS2out << 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;
   }
   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
 

From 03df832e9863e51a3d34bb949585a4ed275b5263 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Wed, 11 Jun 2025 21:05:10 +0000
Subject: [PATCH 46/58] fix par file line in starter to match new text

---
 .github/workflows/run-ss3-no-est.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/run-ss3-no-est.yml b/.github/workflows/run-ss3-no-est.yml
index c77bf619..d2f438d2 100644
--- a/.github/workflows/run-ss3-no-est.yml
+++ b/.github/workflows/run-ss3-no-est.yml
@@ -116,7 +116,7 @@ jobs:
             file.rename(file.path(dir, "forecast.ss_new"), file.path(dir,"forecast.ss"))
             # rename control and data files to standardized names (from the starter files)
             start <- readLines(file.path(dir, "starter.ss"))
-            first_val_line <- grep("0=use init values in control file", start, fixed = TRUE)
+            first_val_line <- grep("read from .par file", start, fixed = TRUE)
             datname <- start[first_val_line-2]
             ctlname <- start[first_val_line-1]
             print(datname)

From 28c2df84ad6799170dafc7f4294bec1fca9dea55 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Wed, 11 Jun 2025 21:25:10 +0000
Subject: [PATCH 47/58] fix forecast file removal line

---
 .github/workflows/run-ss3-no-est.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/run-ss3-no-est.yml b/.github/workflows/run-ss3-no-est.yml
index d2f438d2..399fb650 100644
--- a/.github/workflows/run-ss3-no-est.yml
+++ b/.github/workflows/run-ss3-no-est.yml
@@ -111,7 +111,7 @@ jobs:
             on.exit(system(paste0("cd ", wd)))
             # delete old starter files, rename forecast.ss_new and starter.ss_new files
             file.remove(file.path(dir, "starter.ss"))
-            file.remove(file.path("forecast.ss"))
+            file.remove(file.path(dir, "forecast.ss"))
             file.rename(file.path(dir, "starter.ss_new"), file.path(dir,"starter.ss"))
             file.rename(file.path(dir, "forecast.ss_new"), file.path(dir,"forecast.ss"))
             # rename control and data files to standardized names (from the starter files)

From 8ab82444720246da3f34bda98a842af75724d964 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Thu, 12 Jun 2025 13:19:51 +0000
Subject: [PATCH 48/58] try different fix to starter file lines

---
 .github/workflows/run-ss3-no-est.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/run-ss3-no-est.yml b/.github/workflows/run-ss3-no-est.yml
index 399fb650..ccd0e537 100644
--- a/.github/workflows/run-ss3-no-est.yml
+++ b/.github/workflows/run-ss3-no-est.yml
@@ -116,9 +116,10 @@ jobs:
             file.rename(file.path(dir, "forecast.ss_new"), file.path(dir,"forecast.ss"))
             # rename control and data files to standardized names (from the starter files)
             start <- readLines(file.path(dir, "starter.ss"))
-            first_val_line <- grep("read from .par file", start, fixed = TRUE)
-            datname <- start[first_val_line-2]
-            ctlname <- start[first_val_line-1]
+            datname <- start[grep("#_datfile", start, fixed = TRUE)]
+            datname <- gsub(" #_datfile", "", datname)
+            ctlname <- start[grep("#_ctlfile", start, fixed = TRUE)]
+            ctlname <- gsub(" #_ctlfile", "", ctlname)
             print(datname)
             print(ctlname)
             file.remove(file.path(dir, datname))

From c744d30a4adaa2bea1858f261b5c95d2e072eb42 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Mon, 16 Jun 2025 13:44:26 -0700
Subject: [PATCH 49/58] fix logic for reading of timevary_bio_4SRR

---
 SS_readcontrol_330.tpl | 10 ++++++++--
 SS_readstarter.tpl     |  8 ++++++--
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 375d34ce..81004344 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1824,12 +1824,18 @@
     echoinput << y << " timevary_MG: " << timevary_MG(y) << endl;
   }
 
-  if( timevary_MG_firstyr == YrMax && WTage_rd == 0)  // no time-varying biology
+  if( timevary_MG_firstyr < YrMax || WTage_rd == 1)  //  time-varying biology
   {
     if( timevary_bio_4SRR == 0)  // legacy approach;  this switch is read from starter.ss
     {
-      warnstream << "There is timevary biology and the legacy approach to benchmark calculations is being used; user should be aware";
+      warnstream << "There is timevary biology and the legacy approach to benchmark calculations is being used; user should be aware of possible impacts to benchmark results";
       write_message(WARN, 0);
+        if( timevary_bio_4SRR_rd == -1)  // older starter file did not contain necessary flag
+        {
+          warnstream << "There is timevary biology, so the flag for timevary_bio_4SRR must be set to 0 (old default) or 1 (new improved) in starter.ss";
+// make this a WARN while testing, then change to FATAL for operational code
+          write_message(WARN, 0);
+        }
     }
   }
 
diff --git a/SS_readstarter.tpl b/SS_readstarter.tpl
index 8143e984..348b4a70 100644
--- a/SS_readstarter.tpl
+++ b/SS_readstarter.tpl
@@ -706,6 +706,7 @@
   int irand_seed;
   int irand_seed_rd;
   int timevary_bio_4SRR;  // flag in 3.30.24 for impact of timevary biology on benchmark SRR calculations
+  int timevary_bio_4SRR_rd;  // flag in 3.30.24 for impact of timevary biology on benchmark SRR calculations
   int F_std_multi; // for multi-year averaging of F_std
   int F_std_log; // for log(ratio) of F_std
   int F_std_basis;
@@ -809,15 +810,18 @@
         }
 
         echoinput << "now read flag for dealing with impact of time-varying biology on benchmark SRR calculations" << endl;
+        timevary_bio_4SRR = 0;
+        timevary_bio_4SRR_rd = -1;
         *(ad_comm::global_datafile) >> tempin;
-        if (tempin == 3.30)  // old format file that does not provide input
+        if (tempin == 3.30)  // starter file does not contain the new line for timevary_bio_4SRR, so assign default
         {
           ender = 1;
           timevary_bio_4SRR = 0;
         }
-        else  // new input beginning 3.30.24
+        else  // new input line beginning 3.30.24
         {
           timevary_bio_4SRR = int(tempin);
+          timevary_bio_4SRR_rd = 0;  //  indicates that line was read
           echoinput << "Compatibility flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs:  " << timevary_bio_4SRR << endl;
           tempin = 0;
         }

From cf6b0c580d6c11e1c9adb9b54aeb05ce90b72dc3 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Thu, 26 Jun 2025 09:44:20 -0400
Subject: [PATCH 50/58] Update run-ss3-no-est.yml with updated t-v models test
 models branch

---
 .github/workflows/run-ss3-no-est.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/run-ss3-no-est.yml b/.github/workflows/run-ss3-no-est.yml
index ccd0e537..066b05b4 100644
--- a/.github/workflows/run-ss3-no-est.yml
+++ b/.github/workflows/run-ss3-no-est.yml
@@ -38,6 +38,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: 'nmfs-ost/ss3-test-models'
+          ref: t-v-models-update
           path: test-models-repo
 
       - name: Update Ubuntu packages

From abeda199d3986d278219677815b402f2dea3497e Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Thu, 26 Jun 2025 15:38:40 -0400
Subject: [PATCH 51/58] Update run-ss3-with-est.yml

---
 .github/workflows/run-ss3-with-est.yml | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/run-ss3-with-est.yml b/.github/workflows/run-ss3-with-est.yml
index cee49885..89ac2dba 100644
--- a/.github/workflows/run-ss3-with-est.yml
+++ b/.github/workflows/run-ss3-with-est.yml
@@ -1,5 +1,4 @@
 # Build SS3 and run test models with estimation and hessian
-# Only runs manual run or if run-ss3-no-est.yml runs successfully
 name: run-ss3-with-est
 on:
   workflow_dispatch:
@@ -8,16 +7,16 @@ on:
   #     - '**.tpl'
   #   branches:
   #     - main
-  workflow_run:
-    workflows: ["run-ss3-no-est"]
-    types:
-      - completed
-  # pull_request:
-  #   types: ['opened', 'edited', 'reopened', 'synchronize', 'ready_for_review']
-  #   paths:
-  #     - '**.tpl'
-  #   branches:
-  #     - main
+  # workflow_run:
+  #   workflows: ["run-ss3-no-est"]
+  #   types:
+  #     - completed
+  pull_request:
+    types: ['opened', 'edited', 'reopened', 'synchronize', 'ready_for_review']
+    paths:
+      - '**.tpl'
+    branches:
+      - main
 
 # Run fast running SS3 test models with estimation
 jobs:
@@ -36,6 +35,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: 'nmfs-ost/ss3-test-models'
+          ref: t-v-models-update
           path: test-models-repo
 
       - name: Update Ubuntu packages

From 92319350c33de60f2277f7e143b69d73c161a872 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Thu, 26 Jun 2025 15:40:43 -0400
Subject: [PATCH 52/58] Update run-ss3-with-est.yml with simple PR trigger

---
 .github/workflows/run-ss3-with-est.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/run-ss3-with-est.yml b/.github/workflows/run-ss3-with-est.yml
index 89ac2dba..25d7f1c8 100644
--- a/.github/workflows/run-ss3-with-est.yml
+++ b/.github/workflows/run-ss3-with-est.yml
@@ -12,7 +12,6 @@ on:
   #   types:
   #     - completed
   pull_request:
-    types: ['opened', 'edited', 'reopened', 'synchronize', 'ready_for_review']
     paths:
       - '**.tpl'
     branches:

From 7d972b3c983e71ded7ccdd9af2cc8687aeab4a76 Mon Sep 17 00:00:00 2001
From: iantaylor-NOAA <ian.taylor@noaa.gov>
Date: Thu, 26 Jun 2025 14:38:05 -0700
Subject: [PATCH 53/58] minor changes to capitalization

- useful element of defunct PR discussed in: https://github.com/nmfs-ost/ss3-source-code/pull/683#pullrequestreview-2963734396
---
 SS_write_report.tpl | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 8e4e6a45..7b6979cc 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -4792,9 +4792,8 @@ FUNCTION void SPR_profile()
     if (s == spawn_seas)
     {
       fec = Wt_Age_t(t, -2);
-      SS2out << " repro_output for spr/ypr: " << fec(1) << endl;}
+      SS2out << " repro_output for SPR/YPR: " << fec(1) << endl;}
   }
-  SS2out << " stored - SSB, R0, SPR0: " << SSB_unf << " " << Recr_unf << " "  << SSBpR_virgin << " " << SSBpR_virgin<<endl;
 
 //  do not recalculate here so force using values from benchmark
   SS2out << "unfished values for SRR: SSB " << SSB0_4_SRR << " R " << R0_4_SRR << " SSBpR " << "  SSBpR: " << SSB0_4_SRR / R0_4_SRR << endl;

From 3e749c01594dc76e4da1c763d8b633a6fbea47ee Mon Sep 17 00:00:00 2001
From: iantaylor-NOAA <ian.taylor@noaa.gov>
Date: Thu, 26 Jun 2025 15:59:37 -0700
Subject: [PATCH 54/58] temporarily changing the r4ss install in test to use
 branch

---
 .github/workflows/test-r4ss-with-ss3.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-r4ss-with-ss3.yml b/.github/workflows/test-r4ss-with-ss3.yml
index e1d9e618..fcf49d09 100644
--- a/.github/workflows/test-r4ss-with-ss3.yml
+++ b/.github/workflows/test-r4ss-with-ss3.yml
@@ -52,7 +52,7 @@ jobs:
         run: Rscript -e 'install.packages(c("remotes","parallely", "furrr", "future"))'
 
       - name: Install r4ss
-        run: Rscript -e 'remotes::install_github("r4ss/r4ss")'
+        run: Rscript -e 'remotes::install_github("r4ss/r4ss@expanded_SR")'
 
       # - name: Get admb and put in path, linux
       #   run: |

From ec03c54d9a6a5cced7c5018fc67e40457ea9a48e Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 30 Jun 2025 11:04:13 -0400
Subject: [PATCH 55/58] Update run-ss3-with-est.yml

---
 .github/workflows/run-ss3-with-est.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/run-ss3-with-est.yml b/.github/workflows/run-ss3-with-est.yml
index 25d7f1c8..462ac398 100644
--- a/.github/workflows/run-ss3-with-est.yml
+++ b/.github/workflows/run-ss3-with-est.yml
@@ -20,7 +20,7 @@ on:
 # Run fast running SS3 test models with estimation
 jobs:
   run-ss3-with-est:
-    if: ${{ github.event_name == 'workflow_dispatch' || (github.event.pull_request.draft == 'false' && github.event.workflow_run.conclusion == 'success') }}
+    # if: ${{ github.event_name == 'workflow_dispatch' || (github.event.pull_request.draft == 'false'}}
     runs-on: ubuntu-latest
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

From 37650520d55c1476fe54f3fbcfb9c3980e3b7c5c Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Mon, 30 Jun 2025 14:22:27 -0700
Subject: [PATCH 56/58] revise mgmt_quant labels; fix wt_age_mid for global

---
 SS_popdyn.tpl          | 2 ++
 SS_readcontrol_330.tpl | 8 ++++----
 SS_write_report.tpl    | 3 +--
 3 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 2acdfb82..90e8cf2e 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -269,6 +269,7 @@ FUNCTION void get_initial_conditions()
     }
 
     Wt_Age_t(t, 0) = Wt_Age_beg(s);
+    Wt_Age_t(t, -1) = Wt_Age_mid(s);
 
     for (g = 1; g <= gmorph; g++)
       if (use_morph(g) > 0)
@@ -925,6 +926,7 @@ FUNCTION void get_time_series()
       }
 
       Wt_Age_t(t, 0) = Wt_Age_beg(s);
+      Wt_Age_t(t, -1) = Wt_Age_mid(s);
 
       if (y > styr) // because styr is done as part of initial conditions
       {
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 81004344..306b37b0 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -6668,19 +6668,19 @@
     j++;
     active_parm(CoVar_Count) = j;
 // add quantities needed when time-vary life history is used; but report here for all cases; elements 18-21 of mgmt_quant
-    ParmLabel += "18.Recr_MSY_bmarkbio" + CRLF(1);
+    ParmLabel += "Recr_MSY_bmarkbio" + CRLF(1);
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
-    ParmLabel += "19.Depletion_denom" + CRLF(1);
+    ParmLabel += "Depletion_denom" + CRLF(1);
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
-    ParmLabel += "20.HCR_inflect" + CRLF(1);
+    ParmLabel += "HCR_inflect" + CRLF(1);
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
-    ParmLabel += "ignore" + CRLF(1);
+    ParmLabel += "SSB_unfished_again" + CRLF(1);
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 7b6979cc..0817971b 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -4788,13 +4788,12 @@ FUNCTION void SPR_profile()
   {
     t = styr - 3 * nseas + s - 1;
     Wt_Age_beg(s) = Wt_Age_t(t, 0); //  used for smrybio
-    Wt_Age_mid(s) = Wt_Age_t(t, -1);
+    Wt_Age_mid(s) = Wt_Age_t(t, -1);  //  used in global MSY
     if (s == spawn_seas)
     {
       fec = Wt_Age_t(t, -2);
       SS2out << " repro_output for SPR/YPR: " << fec(1) << endl;}
   }
-
 //  do not recalculate here so force using values from benchmark
   SS2out << "unfished values for SRR: SSB " << SSB0_4_SRR << " R " << R0_4_SRR << " SSBpR " << "  SSBpR: " << SSB0_4_SRR / R0_4_SRR << endl;
   SS2out << "SPRloop Iter Bycatch Fmult F_std SSBpR YpR_dead YpR_dead*Recr YpR_ret*Recr Revenue Cost Profit SSB Recruits SSB/Bzero Tot_Catch ";

From fe43c461f77a955cac7d738d14e1f314918daff9 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Thu, 3 Jul 2025 14:14:45 -0700
Subject: [PATCH 57/58] rework logic in bench; revise the extra mgmt_quant

---
 SS_benchfore.tpl       | 107 ++++++++++++++++++-----------------------
 SS_readcontrol_330.tpl |   4 +-
 SS_write_report.tpl    |   4 +-
 3 files changed, 52 insertions(+), 63 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index eadc9e65..87683d9d 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -750,11 +750,6 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   SRparm_bench = SRparm_work;
 
  /*  
- Early thoughts: 
- 1 #  SR_update_SSBpR0
-  #  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 (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
-
  Flags:
   timevary_MG_firstyr == YrMax  // means that no biology is time-varying
   timevary_SRparm_first > 0 //  means that R0 or h (i.e. any except regime, sigmaR, autocorr) is time-varying, so SSBpR0 gets updated for time series and for bench
@@ -762,6 +757,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
 
  Legacy approach:
  SSBpR0 set at start year using start year biology
+ SSBpR0 is not itself saved; instead R0_4_SRR and SSB0_4_SRR are saved and passed to the spawn_recruit functions
  SSBpR0 updated during time series if there is time-varying R0, but does not call equil_spawn_recr_calc
  SSBpR with benchmark biology used in benchmark calculations 
  SSBpR0 for benchmark always uses bench biology, which is incorrect
@@ -782,87 +778,80 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
  HCR inflection adds option to use SSB_virgin or SSB_bench
  depletion adds option to use SSB_bench
  */
-  Recr_unf = mfexp(SRparm_bench(1));  // R0 to be used
+  Recr_unf = Recr_virgin;  // default
+  SSB0_4_SRR = SSB_virgin;  // default
+  R0_4_SRR = Recr_virgin;
   Fishon = 0;
   SSBpR_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
+  // provides basis for values needed below
+  SSB_unf = SSB_equil;
   SSBpR_bench = SSB_equil / Recr_unf;
 
-//  report5 << "virgin: " << Recr_virgin << " " << SSB_virgin << endl;
-//  report5 << "bench: " << Recr_unf << " " << SSB_equil << endl;
-  if( timevary_MG_firstyr == YrMax && WTage_rd == 0)  // no time-varying biology
-  {
-    SSB0_4_SRR = SSB_virgin;
-    R0_4_SRR = Recr_virgin;
-    SSB_unf = SSB_equil;  //  should this also depend on timevary_SRparm_first > 0???
-  }
-  else  //  there is some timevary biology (with any WTage_rd == 1 qualifying as timevarying without actually chacking for different values in diff years)
+  if(timevary_SRparm_first == 0)  // no timevary SRR parms
   {
-    if( timevary_bio_4SRR == 0)  // legacy approach;  this switch is read from starter.ss
+    if( timevary_MG_firstyr == YrMax && WTage_rd == 0)  // no time-varying biology
     {
-      if(timevary_SRparm_first == 0)  // no timevary SRR parms
-      {
-        SSB_unf = SSB_equil;
-        R0_4_SRR = Recr_unf;  // same as Recr_virgin because no timevary SRparms
-        SSB0_4_SRR = SSB_equil;  // this is legacy, but incorrect, as it moves equil off the SRR, rather than along the SRR
-        SSBpR_bench = SSB0_4_SRR / R0_4_SRR;
-      }
-      else // there are timevary SRR parms
+      R0_4_SRR = Recr_virgin;
+      SSB0_4_SRR = SSB_virgin;
+      SSB_unf = SSB_virgin;
+    }
+    else // there is time-varying biology
+    {
+      R0_4_SRR = Recr_virgin;  // same as Recr_virgin because no timevary SRparms
+      if( timevary_bio_4SRR == 0)  // legacy approach;  this switch is read from starter.ss
       {
-        Recr_unf = mfexp(SRparm_bench(1));  // R0 to be used
-        // steepness and other SR parms will also come from SRparm_bench
-        SSBpR_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
         SSB_unf = SSB_equil;
-        R0_4_SRR = Recr_unf;
-        SSB0_4_SRR = SSB_equil;  // this is legacy, but incorrect, as it moves equil off the SRR, rather than along the SRR
-        SSBpR_bench = SSB0_4_SRR / R0_4_SRR;
+        SSB0_4_SRR = SSB_equil;  // this is inaccurate legacy, as it moves equil off the SRR, rather than along the SRR
       }
-      if (show_MSY == 1) report5 << " legacy: Recr: " << R0_4_SRR << " SSB: " << SSB0_4_SRR << " bench SPR: " << SSBpR_bench << endl;
-    }
-
-    else  // more complete approach to time vary biology will be used (introduced in 3.30.24)
-    {
-      if(timevary_SRparm_first == 0)  // no timevary SRR parms, so SRR will use SSB_virgin, Recr_virgin to internally create virgin SSBpR0 
+      else
       {
-        SSB0_4_SRR = SSB_virgin;
-        R0_4_SRR = Recr_virgin;
         //  get new equilibrium point using original SRR and SSBpR_bench
         Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_bench, SSB_virgin, Recr_virgin, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
         SSB_unf = Equ_SpawnRecr_Result(1);
         Recr_unf = Equ_SpawnRecr_Result(2);
         if (show_MSY == 1) report5 << " use virgin SSBpR0 in SRR - SSB: " << SSB_virgin << " Recr: " << Recr_virgin << " SPR: " << SSB_virgin / Recr_virgin << " bench SPR: " << SSBpR_bench << " new equil: " << Equ_SpawnRecr_Result << endl;
       }
-      else  //  use updated SRparms and benchmark biology
-      {
-        //  get new equilibrium point for the benchmark SRR
-        Recr_unf = mfexp(SRparm_bench(1));  // R0 to be used
-        Fishon = 0;
-        SSBpR_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
-        SSBpR_bench = SSB_equil / Recr_unf;
-        SSB0_4_SRR = SSB_equil;
-        SSB_unf = SSB_equil;
-        R0_4_SRR = Recr_unf;
-        // verify
-        Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_bench, SSB_equil, Recr_unf, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
-        if (show_MSY == 1) report5 << " use bench SSBpR0 in SRR - SSB: " << SSB_unf << " Recr: " << Recr_unf << " SPR: " << SSBpR_bench << " new equil: " << Equ_SpawnRecr_Result << endl;
-      }
-      SSBpR_Calc(Recr_unf);  // this calcs SSBpR and returns it as SSB_equil using benchmark biology and the updated equil Recr
-      SSB_unf = SSB_equil;
+      SSBpR_bench = SSB_unf / Recr_unf;
+    }
+  }
+  else // there are timevary SRR parms; use same code regardless of timevary biology.  Legacy approach does not include new equilibrium
+  {
+    Recr_unf = mfexp(SRparm_bench(1));  // R0 to be used
+    // note that steepness will get updated when SRparm_bench is used in Equ_SpawnRecr_Result
+    SSBpR_Calc(Recr_unf);  // this returns SSB_equil using benchmark biology
+    SSB_unf = SSB_equil;
+    SSBpR_bench = SSB_equil / Recr_unf;
+    if( timevary_bio_4SRR == 0)  // legacy approach;  this switch is read from starter.ss
+    {
+      R0_4_SRR = Recr_unf;
+      SSB0_4_SRR = SSB_equil;  // this is legacy, but incorrect, as it moves equil off the SRR, rather than along the SRR
+    }
+    else  // use improved approach with updated SRparms and benchmark biology
+    {
+      //  get new equilibrium point for the benchmark SRR
+      Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_bench, SSB_equil, Recr_unf, SSBpR_bench); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+      SSB_unf = Equ_SpawnRecr_Result(1);
+      SSB0_4_SRR = Equ_SpawnRecr_Result(1);
+      Recr_unf = Equ_SpawnRecr_Result(2);
+      R0_4_SRR = Equ_SpawnRecr_Result(2);
+
+      if (show_MSY == 1) report5 << " use bench SSBpR0 in SRR - SSB: " << SSB_unf << " Recr: " << Recr_unf << " SPR: " << SSBpR_bench << " new equil: " << Equ_SpawnRecr_Result << endl;
     }
   }
 
   if (show_MSY == 1)
   {
-    SRparm_bench(N_SRparm2 + 1) = SSB0_4_SRR;
-    Mgmt_quant(1) = SSB0_4_SRR;
+    SRparm_bench(N_SRparm2 + 1) = SSB_unf;
+    Mgmt_quant(1) = SSB_unf;
     Mgmt_quant(2) = totbio;  // this is calculated in Do_Equil_Calc
     Mgmt_quant(3) = smrybio;
-    Mgmt_quant(4) = R0_4_SRR;
+    Mgmt_quant(4) = Recr_unf;
     report5 << "SRparms for benchmark: " << SRparm_bench << endl
             << "Benchmark biology averaged over years: " << Bmark_Yr(1) << " " << Bmark_Yr(2) << endl << endl;
     Mgmt_quant(19) = SSB_unf;  // placeholder for depletion denominator
     Mgmt_quant(20) = SSB_unf;  //  placeholder to be replaced by SSB_HCR_infl
-    Mgmt_quant(21) = SSB_unf;
-    Mgmt_quant(22) = SSB_virgin;
+    Mgmt_quant(21) = R0_4_SRR;
+    Mgmt_quant(22) = SSB0_4_SRR;
   }
 
   // find Fspr             SS_Label_710
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 306b37b0..88992625 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -6680,11 +6680,11 @@
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
-    ParmLabel += "SSB_unfished_again" + CRLF(1);
+    ParmLabel += "R0_for_SRR_bench" + CRLF(1);
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
-    ParmLabel += "SSB_virgin_again" + CRLF(1);
+    ParmLabel += "SSB_for_SRR_bench" + CRLF(1);
     CoVar_Count++;
     j++;
     active_parm(CoVar_Count) = j;
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 0817971b..5f6fa39b 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -4963,9 +4963,9 @@ FUNCTION void SPR_profile()
           if (SPRloop1 == 0)
             Fcrash = Fmult2;
         }
-        SS2out << SPRloop1 << " " << SPRloop << " " << with_BYC << " " << Fmult2 << " " << equ_F_std << " " << SSB_equil / (SSB_unf / Recr_unf) << " " << YPR_dead << " "
+        SS2out << SPRloop1 << " " << SPRloop << " " << with_BYC << " " << Fmult2 << " " << equ_F_std << " " << SSB_equil / (SSB0_4_SRR / R0_4_SRR) << " " << YPR_dead << " "
                << YPR_dead * Btgt_prof_rec << " " << YPR_ret * Btgt_prof_rec << " " << (PricePerF * YPR_val_vec) * Btgt_prof_rec
-               << " " << Cost << " " << (PricePerF * YPR_val_vec) * Btgt_prof_rec - Cost << " " << Btgt_prof << " " << Btgt_prof_rec << " " << Btgt_prof / SSB_unf
+               << " " << Cost << " " << (PricePerF * YPR_val_vec) * Btgt_prof_rec - Cost << " " << Btgt_prof << " " << Btgt_prof_rec << " " << Btgt_prof / SSB0_4_SRR
                << " " << value(sum(equ_catch_fleet(2)) * Btgt_prof_rec);
         for (f = 1; f <= Nfleet; f++)
           if (fleet_type(f) <= 2)

From 53a6c3e80cc6a02644da19405fd4d627ebade0db Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Tue, 8 Jul 2025 10:33:10 -0400
Subject: [PATCH 58/58] return to using main test branch repo for ghas

---
 .github/workflows/run-ss3-no-est.yml   | 1 -
 .github/workflows/run-ss3-with-est.yml | 1 -
 2 files changed, 2 deletions(-)

diff --git a/.github/workflows/run-ss3-no-est.yml b/.github/workflows/run-ss3-no-est.yml
index 066b05b4..ccd0e537 100644
--- a/.github/workflows/run-ss3-no-est.yml
+++ b/.github/workflows/run-ss3-no-est.yml
@@ -38,7 +38,6 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: 'nmfs-ost/ss3-test-models'
-          ref: t-v-models-update
           path: test-models-repo
 
       - name: Update Ubuntu packages
diff --git a/.github/workflows/run-ss3-with-est.yml b/.github/workflows/run-ss3-with-est.yml
index 462ac398..2225df50 100644
--- a/.github/workflows/run-ss3-with-est.yml
+++ b/.github/workflows/run-ss3-with-est.yml
@@ -34,7 +34,6 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: 'nmfs-ost/ss3-test-models'
-          ref: t-v-models-update
           path: test-models-repo
 
       - name: Update Ubuntu packages