Merge pull request #474 from nmfs-stock-synthesis/466-allow-late-recd…

…evs-to-be-expected-value-for-an-index implement changes and warnings for recr surveys
nmfs-ost · Jul 17, 2023 · 98229c8 · 98229c8
2 parents a9ce5a7 + 2a42a9d
commit 98229c8
Show file tree

Hide file tree

Showing 3 changed files with 20 additions and 67 deletions.
diff --git a/SS_expval.tpl b/SS_expval.tpl
@@ -334,38 +334,17 @@ FUNCTION void Get_expected_values(const int y, const int t);
                   }
                   case 31: // exp(recruitment deviation)  #31
                   {
-                    if (y >= recdev_start && y <= recdev_end)
-                    {
-                      vbio = mfexp(recdev(y));
-                    }
-                    else
-                    {
-                      vbio = 1.0;
-                    }
+                    vbio = mfexp(recdev(y));
                     break;
                   }
                   case 36: // recruitment deviation  #36
                   {
-                    if (y >= recdev_start && y <= recdev_end)
-                    {
-                      vbio = recdev(y);
-                    }
-                    else
-                    {
-                      vbio = 0.0;
-                    }
+                    vbio = recdev(y);
                     break;
                   }
                   case 32: // recruitment without density-dependence (for pre-recruit survey) #32
                   {
-                    if (y >= recdev_start && y <= recdev_end)
-                    {
-                      vbio = SSB_current * mfexp(recdev(y));
-                    }
-                    else
-                    {
-                      vbio = SSB_current;
-                    }
+                    vbio = SSB_current * mfexp(recdev(y));
                     break;
                   }
                   case 33: // recruitment  #33
@@ -439,49 +418,6 @@ FUNCTION void Get_expected_values(const int y, const int t);
                 }
 
                 // SS_Label_Info_46.1.1 #note order of operations,  vbio raised to a power, then constant is added, then later multiplied by Q.  Needs work
-                /*
-   //  old code here
-               switch (Q_setup(f,1))  //  switch is based on the link type: (1=simple q; 2=mirror; 3=q and power; 4=mirror with offset in q)
-               {
-                 case 2:
-                 {
-                   //  no break, so do same as case 1
-                 }
-                 case 4:
-                 {
-                   //  no break, so do same as case 1
-                 }
-                 case 1:
-                 {
-                   if(Q_setup(f,5)==1 && y<=endyr)  // float Q will be calculated and applied in objfun section, so temporarily store vbio in svy_est.
-                   	                                // note that if y is in forecast, then Q has already been calculated so can be applied in the else clause here
-                   {
-                     if(Svy_errtype(f)>=0)  //  lognormal or T-distribution
-                     {Svy_est(f,j)=log(vbio+0.000001);}
-                     else
-                     {Svy_est(f,j)=vbio;}
-                   }
-                   else  //  Q based on parameters, or in forecast so Q has already been calculated through float approach in the objfun
-                   {
-                     if(Svy_errtype(f)>=0)  //  lognormal or T-distribution
-                     {Svy_est(f,j)=log(vbio+0.000001)+Svy_log_q(f,j);}
-                     else
-                     {Svy_est(f,j)=vbio*Svy_q(f,j);}
-                   }
-                   break;
-                 }
-                 case 3:  //  link is power function
-                 {
-                   vbio=pow(vbio,1.0+Q_parm(Q_setup_parms(f,1)+1));  //  raise vbio to a power
-                   if(Svy_errtype(f)>=0)  //  lognormal or T-distribution
-                   {Svy_est(f,j)=log(vbio+0.000001)+Svy_log_q(f,j);}
-                   else
-                   {Svy_est(f,j)=vbio*Svy_q(f,j);}
-                   break;
-                 }
-               }
-   */
-
                 if (Q_setup(f, 1) == 3) //  link is power function
                 {
                   vbio = pow(vbio, 1.0 + Q_parm(Q_setup_parms(f, 1) + 1));

diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
@@ -2378,6 +2378,21 @@
         ParmLabel += "Impl_err_" + onenum + CRLF(1);
       }
     }
+
+    // check recdev start and end against survey year start and end
+    for (f = 1; f <=Nfleet; f++) {
+      if (Svy_units(f) == 31 || Svy_units(f) == 32 || Svy_units(f) == 33 || Svy_units(f) == 36) { //  select just recruitment surveys
+        if (Svy_styr(f) < recdev_first) {
+          warnstream << "Recruitment survey: " << f << " has data in: " << Svy_styr(f) << ", which is before first early recdev: " << recdev_first << ". Suggest start recdevs earlier";
+          write_message (SUGGEST, 0);
+        }
+        if (Svy_endyr(f) > recdev_end && Fcast_recr_PH_rd <=0 ) {
+          warnstream << "Recruitment survey: " << f << " has data in: " << Svy_endyr(f) << ", which is after last main recdev: " << recdev_end << ". Suggest extend recdev_end, or use pos. phase for fore_recruitments: " << Fcast_recr_PH_rd;
+          write_message (SUGGEST, 0);
+        }
+      }
+    }
+
   }
 
   biasadj_full.initialize();

diff --git a/SS_readdata_330.tpl b/SS_readdata_330.tpl
@@ -833,6 +833,8 @@
           Svy_styr(f) = y; // for dimensioning survey q devs
         if (Svy_endyr(f) == 0 || (y <= endyr && y > Svy_endyr(f)))
           Svy_endyr(f) = y; //  for dimensioning survey q devs
+
+        //  Svy_styr and Svy_endyr for recruitment surveys will be checked against recdev start and end in readcontrol
         if (y >= styr && Svy_data[i](3) > 0)
         {
           Svy_minval(f) = min(Svy_minval(f), Svy_obs(f, j));