From d99136cf5599f0743762ed7d8f416f454398e43c Mon Sep 17 00:00:00 2001
From: "kathryn.doering" <kathryn.doering@noaa.gov>
Date: Thu, 16 Sep 2021 13:01:52 -0400
Subject: [PATCH 1/3] Fix: increment warning where forgotten

---
 SS_benchfore.tpl | 8 ++++----
 SS_expval.tpl    | 2 +-
 SS_objfunc.tpl   | 2 +-
 SS_popdyn.tpl    | 8 ++++----
 SS_selex.tpl     | 2 +-
 5 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index a55ee2b7..22d7af1d 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -128,7 +128,7 @@ FUNCTION void setup_Benchmark()
         for (s=1;s<=nseas;s++)
         {
           if(Fcast_RelF_Use(s,f)==0. && bycatch_setup(f,3)>0) 
-            {Fcast_RelF_Use(s,f)=1.0e-6;  warning<<N_warn<<" setting positive forecast relF for bycatch fleet: "<<f<<endl;}
+            {Fcast_RelF_Use(s,f)=1.0e-6;  N_warn++; warning<<N_warn<<" setting positive forecast relF for bycatch fleet: "<<f<<endl;}
         }
       }
       if(N_Fcast_Input_Catches>0)
@@ -137,7 +137,7 @@ FUNCTION void setup_Benchmark()
         for (s=1;s<=nseas;s++)
         {
           if(Fcast_RelF_special(s,f)==1 && Fcast_RelF_Use(s,f)==0.0) 
-            {Fcast_RelF_Use(s,f)=1.0e-6;  warning<<N_warn<<" setting positive forecast relF for forecast only fleet: "<<f<<endl;}
+            {Fcast_RelF_Use(s,f)=1.0e-6;  N_warn++; warning<<N_warn<<" setting positive forecast relF for forecast only fleet: "<<f<<endl;}
         }
       }
     }  //  end getting quantities for forecasts
@@ -2087,7 +2087,7 @@ FUNCTION void Get_Forecast()
                       }
                       join1=1./(1.+mfexp(30.*(temp-0.95*max_harvest_rate)));
                       Hrate(f,t)=join1*temp + (1.-join1)*max_harvest_rate; // new F value for this fleet, constrained by max_harvest_rate
-//                      if(f==1)  warning<<N_warn<<" "<<y<<" "<<Tune_F<<" stored old F "<<H_temp(f)<<" catch "<<C_temp(f)<<" tempF "<<temp<<" join "<<join1<<" new F "<<Hrate(f,t)<<endl;
+//                      if(f==1)  N_warn++; warning<<N_warn<<" "<<y<<" "<<Tune_F<<" stored old F "<<H_temp(f)<<" catch "<<C_temp(f)<<" tempF "<<temp<<" join "<<join1<<" new F "<<Hrate(f,t)<<endl;
                       C_old(f)=C_temp(f);
                       H_old(f)=H_temp(f);
                     }
@@ -2377,7 +2377,7 @@ FUNCTION void Get_Forecast()
                  countN += 1; // increment count of values included in average
                  annual_F(y,2) += log(tempM)-log(tempZ);  // F=Z-M
                  annual_F(y,3) += log(tempbase)-log(tempM);  // M
-//              if(save_for_report==1)  warning<<N_warn<<" "<<y<<"  age: "<<a<<" count: "<<countN<<" Z: "<<log(tempbase)-log(tempZ)<<" M: "<<log(tempbase)-log(tempM)<<" F: "<<log(tempM)-log(tempZ)<<" "<<annual_F(y)(2,3)<<endl;
+//              if(save_for_report==1)  N_warn++; warning<<N_warn<<" "<<y<<"  age: "<<a<<" count: "<<countN<<" Z: "<<log(tempbase)-log(tempZ)<<" M: "<<log(tempbase)-log(tempM)<<" F: "<<log(tempM)-log(tempZ)<<" "<<annual_F(y)(2,3)<<endl;
             }
             annual_F(y,3) /= countN;  // M
             annual_F(y,2) /= countN;   // F
diff --git a/SS_expval.tpl b/SS_expval.tpl
index 6bdce6ce..58d7d2cc 100644
--- a/SS_expval.tpl
+++ b/SS_expval.tpl
@@ -468,7 +468,7 @@ FUNCTION void Get_expected_values(const int y,const int t);
                   exp_disc(f,j)=catch_fleet(t,f,4)-catch_fleet(t,f,6);   // discard in numbers
                   if(disc_units(f)==2) exp_disc(f,j) /= (catch_fleet(t,f,4) + 0.0000001);
                 }
-                if(exp_disc(f,j)<0.0)  warning<<N_warn<<" "<<f<<" "<<j<<" "<<exp_disc(f,j)<<" catches "<<catch_fleet(t,f)<<endl;
+                if(exp_disc(f,j)<0.0)  N_warn++; warning<<N_warn<<" "<<f<<" "<<j<<" "<<exp_disc(f,j)<<" catches "<<catch_fleet(t,f)<<endl;
               }
               else
               {
diff --git a/SS_objfunc.tpl b/SS_objfunc.tpl
index 137bf750..b06e0084 100644
--- a/SS_objfunc.tpl
+++ b/SS_objfunc.tpl
@@ -1302,7 +1302,7 @@ FUNCTION dvariable Get_Prior(const int T, const double& Pmin, const double& Pmax
         mu=(Pr-Pmin) / (Pmax-Pmin);  // CASAL's v
         tau=(Pr-Pmin)*(Pmax-Pr)/square(Psd)-1.0;
         Bprior=tau*mu;  Aprior=tau*(1.0-mu);  // CASAL's m and n
-        if(Bprior<=1.0 || Aprior <=1.0) { warning<<N_warn<<" "<<" bad Beta prior "<<Pval<<" "<<Pr<<endl;N_warn++;}
+        if(Bprior<=1.0 || Aprior <=1.0) { N_warn++; warning<<N_warn<<" "<<" bad Beta prior "<<Pval<<" "<<Pr<<endl;}
         Prior_Like =  (1.0-Bprior)*log(Pconst+Pval-Pmin) + (1.0-Aprior)*log(Pconst+Pmax-Pval)
               -(1.0-Bprior)*log(Pconst+Pr-Pmin) - (1.0-Aprior)*log(Pconst+Pmax-Pr);
         break;
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 8b6ae387..3bcac580 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -57,7 +57,7 @@ FUNCTION void setup_recdevs()
     else if(do_recdev>=2)
       {recdev(recdev_start,recdev_end)=recdev2(recdev_start,recdev_end);}
     if(Do_Forecast>0 && do_recdev>0) recdev(recdev_end+1,YrMax)=Fcast_recruitments(recdev_end+1,YrMax);  // only needed here for reporting
-//      if(mcmc_counter>0)  warning<<N_warn<<" "<<mcmc_counter<<" MGparm "<<MGparm<<" SRparm "<<SR_parm<<" recdev "<<recdev2<<" fore_rec "<<Fcast_recruitments<<" selparm "<<selparm<<" q: "<<Q_parm<<endl;
+//      if(mcmc_counter>0)  N_warn++; warning<<N_warn<<" "<<mcmc_counter<<" MGparm "<<MGparm<<" SRparm "<<SR_parm<<" recdev "<<recdev2<<" fore_rec "<<Fcast_recruitments<<" selparm "<<selparm<<" q: "<<Q_parm<<endl;
   }  //  end setup for recdevs
 
 FUNCTION void get_initial_conditions()
@@ -487,7 +487,7 @@ FUNCTION void get_initial_conditions()
         Save_PopBio(t+s,p,g)=elem_prod(natage(t+s,p,g),Wt_Age_beg(s,g));
         Save_PopBio(t+s,p+pop,g)=elem_prod(Save_PopAge(t+s,p+pop,g),Wt_Age_mid(s,g));
 
-//         warning<<N_warn<<" "<<s<<" init  "<<t+Settle_seas_offset(settle_g(g))<<endl;
+//         N_warn++; warning<<N_warn<<" "<<s<<" init  "<<t+Settle_seas_offset(settle_g(g))<<endl;
         Recr(p,t+1+Settle_seas_offset(settle_g(g)))+=equ_Recr*recr_dist(y,GP(g),settle_g(g),p)*platoon_distr(GP2(g));
       }
     }
@@ -574,7 +574,7 @@ FUNCTION void get_time_series()
           else
           {  //  should be 0.0
           }
-//           warning<<N_warn<<" "<<y<<" "<<SSB_current<<" "<<SSB_yr(styr-1)<<" "<<recdev(y)<<" env: "<<env_data(y)<<endl;
+//           N_warn++; warning<<N_warn<<" "<<y<<" "<<SSB_current<<" "<<SSB_yr(styr-1)<<" "<<recdev(y)<<" env: "<<env_data(y)<<endl;
         t=t_base+1;  // first season
         s=1;
       if(WTage_rd>0)
@@ -1403,7 +1403,7 @@ FUNCTION void get_time_series()
               countN += 1; // increment count of values included in average
               annual_F(y,2) += log(tempM)-log(tempZ);  // F=Z-M
               annual_F(y,3) += log(tempbase)-log(tempM);  // M
-//              if(save_for_report==1)  warning<<N_warn<<" "<<y<<"  age: "<<a<<" count: "<<countN<<" Z: "<<log(tempbase)-log(tempZ)<<" M: "<<log(tempbase)-log(tempM)<<" F: "<<log(tempM)-log(tempZ)<<" "<<annual_F(y)(2,3)<<endl;
+//              if(save_for_report==1)  N_warn++; warning<<N_warn<<" "<<y<<"  age: "<<a<<" count: "<<countN<<" Z: "<<log(tempbase)-log(tempZ)<<" M: "<<log(tempbase)-log(tempM)<<" F: "<<log(tempM)-log(tempZ)<<" "<<annual_F(y)(2,3)<<endl;
             }
             annual_F(y,3) /= countN;  // M
             annual_F(y,2) /= countN;   // F
diff --git a/SS_selex.tpl b/SS_selex.tpl
index 99d05197..26eed10e 100644
--- a/SS_selex.tpl
+++ b/SS_selex.tpl
@@ -1133,7 +1133,7 @@ FUNCTION void get_selectivity()
                   {tempvec_a(a)=sp(j-seltype(f,4));}  //  use female parameter for males
                 else  //  so value is -999 so set to next younger age
                 {tempvec_a(a) = tempvec_a(a-1);}
-          //     warning<<N_warn<<" "<<" sex "<<gg<<" a "<<a<<"  j "<<j<<"  sp "<<sp(j)<<" use "<<tempvec_a(a)<<endl;
+          //     N_warn++; warning<<N_warn<<" "<<" sex "<<gg<<" a "<<a<<"  j "<<j<<"  sp "<<sp(j)<<" use "<<tempvec_a(a)<<endl;
               }
               int low_bin  = int(value(sp(2)));
               int high_bin = int(value(sp(3)));

From 3fb1a0f69222fd18fb19a69f45211fe07e26959f Mon Sep 17 00:00:00 2001
From: "kathryn.doering" <kathryn.doering@noaa.gov>
Date: Thu, 16 Sep 2021 13:57:16 -0400
Subject: [PATCH 2/3] fix: wrap if statement

---
 SS_expval.tpl | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/SS_expval.tpl b/SS_expval.tpl
index 58d7d2cc..a78b117d 100644
--- a/SS_expval.tpl
+++ b/SS_expval.tpl
@@ -468,8 +468,11 @@ FUNCTION void Get_expected_values(const int y,const int t);
                   exp_disc(f,j)=catch_fleet(t,f,4)-catch_fleet(t,f,6);   // discard in numbers
                   if(disc_units(f)==2) exp_disc(f,j) /= (catch_fleet(t,f,4) + 0.0000001);
                 }
-                if(exp_disc(f,j)<0.0)  N_warn++; warning<<N_warn<<" "<<f<<" "<<j<<" "<<exp_disc(f,j)<<" catches "<<catch_fleet(t,f)<<endl;
-              }
+                if(exp_disc(f,j)<0.0) {
+			      N_warn++;
+				  warning<<N_warn<<" "<<f<<" "<<j<<" "<<exp_disc(f,j)<<" catches "<<catch_fleet(t,f)<<endl;
+                }  
+			  }
               else
               {
                 exp_disc(f,j)=-1.;

From b2a8bae8120596e8e33c8d1c59ff141c75615eef Mon Sep 17 00:00:00 2001
From: "kathryn.doering" <kathryn.doering@noaa.gov>
Date: Thu, 16 Sep 2021 14:05:44 -0400
Subject: [PATCH 3/3] warnings: rm commented out warnings

---
 SS_benchfore.tpl       | 2 --
 SS_global.tpl          | 2 --
 SS_popdyn.tpl          | 5 -----
 SS_readcontrol_330.tpl | 1 -
 SS_readdata_330.tpl    | 1 -
 SS_selex.tpl           | 1 -
 6 files changed, 12 deletions(-)

diff --git a/SS_benchfore.tpl b/SS_benchfore.tpl
index 22d7af1d..982910ba 100644
--- a/SS_benchfore.tpl
+++ b/SS_benchfore.tpl
@@ -2087,7 +2087,6 @@ FUNCTION void Get_Forecast()
                       }
                       join1=1./(1.+mfexp(30.*(temp-0.95*max_harvest_rate)));
                       Hrate(f,t)=join1*temp + (1.-join1)*max_harvest_rate; // new F value for this fleet, constrained by max_harvest_rate
-//                      if(f==1)  N_warn++; warning<<N_warn<<" "<<y<<" "<<Tune_F<<" stored old F "<<H_temp(f)<<" catch "<<C_temp(f)<<" tempF "<<temp<<" join "<<join1<<" new F "<<Hrate(f,t)<<endl;
                       C_old(f)=C_temp(f);
                       H_old(f)=H_temp(f);
                     }
@@ -2377,7 +2376,6 @@ FUNCTION void Get_Forecast()
                  countN += 1; // increment count of values included in average
                  annual_F(y,2) += log(tempM)-log(tempZ);  // F=Z-M
                  annual_F(y,3) += log(tempbase)-log(tempM);  // M
-//              if(save_for_report==1)  N_warn++; warning<<N_warn<<" "<<y<<"  age: "<<a<<" count: "<<countN<<" Z: "<<log(tempbase)-log(tempZ)<<" M: "<<log(tempbase)-log(tempM)<<" F: "<<log(tempM)-log(tempZ)<<" "<<annual_F(y)(2,3)<<endl;
             }
             annual_F(y,3) /= countN;  // M
             annual_F(y,2) /= countN;   // F
diff --git a/SS_global.tpl b/SS_global.tpl
index e6da27a5..42e41534 100644
--- a/SS_global.tpl
+++ b/SS_global.tpl
@@ -279,7 +279,6 @@ GLOBALS_SECTION
       if (z>0)  //  blocks with z as the block pattern
       {
         Nblocks=0.5*(block_design_pass.size());
-//        if(z>N_Block_Designs) {N_warn++;  warning<<N_warn<<" "<<"parm: "<<j<<" ERROR, Block > N Blocks "<<z<<" "<<N_Block_Designs<<endl; exit(1);}
         k=int(baseparm_list(14));  //  block method
         echoinput<<"block pattern: "<<z<<" method "<<k<<" Nblocks: "<<Nblocks<<endl;
 
@@ -595,7 +594,6 @@ GLOBALS_SECTION
        }
 //       timevary_setup(12)=-5;  //  set reasonable phase for devs;
 //       baseparm_list(12)=-5;
-//       N_warn++;  warning<<N_warn<<" "<<"A parameter dev vector has been created with phase set to negative.  Edit phase as needed "<<endl;
       }
       timevary_parm_rd.push_back (dvector(tempvec(1,7)));
 
diff --git a/SS_popdyn.tpl b/SS_popdyn.tpl
index 3bcac580..f2ee4bb3 100644
--- a/SS_popdyn.tpl
+++ b/SS_popdyn.tpl
@@ -57,7 +57,6 @@ FUNCTION void setup_recdevs()
     else if(do_recdev>=2)
       {recdev(recdev_start,recdev_end)=recdev2(recdev_start,recdev_end);}
     if(Do_Forecast>0 && do_recdev>0) recdev(recdev_end+1,YrMax)=Fcast_recruitments(recdev_end+1,YrMax);  // only needed here for reporting
-//      if(mcmc_counter>0)  N_warn++; warning<<N_warn<<" "<<mcmc_counter<<" MGparm "<<MGparm<<" SRparm "<<SR_parm<<" recdev "<<recdev2<<" fore_rec "<<Fcast_recruitments<<" selparm "<<selparm<<" q: "<<Q_parm<<endl;
   }  //  end setup for recdevs
 
 FUNCTION void get_initial_conditions()
@@ -486,8 +485,6 @@ FUNCTION void get_initial_conditions()
         Save_PopAge(t+s,p+pop,g)=elem_prod(natage(t+s,p,g),mfexp(-Z_rate(t+s,p,g)*0.5*seasdur(s)));
         Save_PopBio(t+s,p,g)=elem_prod(natage(t+s,p,g),Wt_Age_beg(s,g));
         Save_PopBio(t+s,p+pop,g)=elem_prod(Save_PopAge(t+s,p+pop,g),Wt_Age_mid(s,g));
-
-//         N_warn++; warning<<N_warn<<" "<<s<<" init  "<<t+Settle_seas_offset(settle_g(g))<<endl;
         Recr(p,t+1+Settle_seas_offset(settle_g(g)))+=equ_Recr*recr_dist(y,GP(g),settle_g(g),p)*platoon_distr(GP2(g));
       }
     }
@@ -574,7 +571,6 @@ FUNCTION void get_time_series()
           else
           {  //  should be 0.0
           }
-//           N_warn++; warning<<N_warn<<" "<<y<<" "<<SSB_current<<" "<<SSB_yr(styr-1)<<" "<<recdev(y)<<" env: "<<env_data(y)<<endl;
         t=t_base+1;  // first season
         s=1;
       if(WTage_rd>0)
@@ -1403,7 +1399,6 @@ FUNCTION void get_time_series()
               countN += 1; // increment count of values included in average
               annual_F(y,2) += log(tempM)-log(tempZ);  // F=Z-M
               annual_F(y,3) += log(tempbase)-log(tempM);  // M
-//              if(save_for_report==1)  N_warn++; warning<<N_warn<<" "<<y<<"  age: "<<a<<" count: "<<countN<<" Z: "<<log(tempbase)-log(tempZ)<<" M: "<<log(tempbase)-log(tempM)<<" F: "<<log(tempM)-log(tempZ)<<" "<<annual_F(y)(2,3)<<endl;
             }
             annual_F(y,3) /= countN;  // M
             annual_F(y,2) /= countN;   // F
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index d8326c95..45f507de 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -3359,7 +3359,6 @@
           selparm_1(k,2)=new_upper_bound;
 
            warning<<N_warn<<" "<<"new min, max, init, prior: "<<selparm_1(k)(1,4)<<endl;
-//          if (selparm_1(k,8) !=0 || selparm_1(k,9)!=0 || selparm_1(k,13)!=0)  warning<<N_warn<<" "<<"Timevarying, so you must do timevary parm conversion manually"<<endl;
         }
     }
     parmcount+=N_selparmvec(f);
diff --git a/SS_readdata_330.tpl b/SS_readdata_330.tpl
index f7982805..9a913110 100644
--- a/SS_readdata_330.tpl
+++ b/SS_readdata_330.tpl
@@ -2165,7 +2165,6 @@
                obs_a_all(1,f,a)+=obs_a(f,j,n_abins+a);  //  males
              }
            }
-//            warning<<N_warn<<" "<<obs_a(f,j)(1,6)<<endl;
          }
        }
      }
diff --git a/SS_selex.tpl b/SS_selex.tpl
index 26eed10e..8d04dbc1 100644
--- a/SS_selex.tpl
+++ b/SS_selex.tpl
@@ -1133,7 +1133,6 @@ FUNCTION void get_selectivity()
                   {tempvec_a(a)=sp(j-seltype(f,4));}  //  use female parameter for males
                 else  //  so value is -999 so set to next younger age
                 {tempvec_a(a) = tempvec_a(a-1);}
-          //     N_warn++; warning<<N_warn<<" "<<" sex "<<gg<<" a "<<a<<"  j "<<j<<"  sp "<<sp(j)<<" use "<<tempvec_a(a)<<endl;
               }
               int low_bin  = int(value(sp(2)));
               int high_bin = int(value(sp(3)));