Merge pull request #184 from nmfs-stock-synthesis/fix_DM_index

fix for erroroneous limit on D-M parameters

SS_readcontrol_330.tpl

@@ -3106,13 +3106,27 @@
 
 //  SS_Label_Info_4.097 #Read parameters needed for estimating variance of composition data
   {
-    echoinput<<"#Now count parameters for variance of composition data; CANNOT be time-varying"<<endl;
+    echoinput<<"#Now count parameters for D-M variance of composition data; CANNOT be time-varying"<<endl;
     if(Comp_Err_ParmCount>0)
     {
-      echoinput<<Comp_Err_ParmCount<<"  #_parameters are needed"<<endl;
+      echoinput<<Comp_Err_ParmCount<<"  #_parameters are needed: "<<DM_parmlist<<endl;
       Comp_Err_Parm_Start=N_selparm;
+      //  create a D-M parameter only for the first fleet that references that parm number
+
       for(f=1;f<=Comp_Err_ParmCount;f++)
         {N_selparm++; ParCount++; ParmLabel+="ln(DM_theta)_"+NumLbl(f);}
+  /*
+      for (f=1;f<=Nfleet;f++) {
+        if(Comp_Err_L2(f)>0){
+          if (DM_parmlist(f)==1) {
+            N_selparm++; ParCount++; ParmLabel+="ln(DM_theta)_Len_P"+NumLbl(Comp_Err_L2(f))+"("+NumLbl(f)+")";}}
+      	}
+      for (f=1;f<=Nfleet;f++) {
+        if(Comp_Err_A2(f)>0){
+          if (DM_parmlist(f+Nfleet)==1) {
+            N_selparm++; ParCount++; ParmLabel+="ln(DM_theta)_Age_P"+NumLbl(Comp_Err_A2(f))+"("+NumLbl(f)+")";}}
+      	}
+  */
     }
   }
 
@@ -3159,13 +3173,12 @@
    for (f = 1; f <= Nfleet; f++)
    {
       // if Dirichlet was indicated, set fleet for this parameter
-      if (Comp_Err_L(f) >0 && Comp_Err_L2(f) > 0)
+      if (Comp_Err_L2(f) > 0)
       {
         j = Comp_Err_Parm_Start + Comp_Err_L2(f);
         selparm_fleet(j)=f;
       }
-
-      if (Comp_Err_A(f) >0 && Comp_Err_A2(f) > 0)
+      if (Comp_Err_A2(f) > 0)
       {
         j = Comp_Err_Parm_Start + Comp_Err_A2(f);
         selparm_fleet(j)=f;

SS_readdata_330.tpl

@@ -1056,6 +1056,7 @@
   ivector Comp_Err_L2(1,Nfleet)  //  composition error type parameter location
   vector min_sample_size_L(1,Nfleet)  // minimum sample size
   int Comp_Err_ParmCount;  // counts number of fleets that need a parameter for the error estimation
+  ivector DM_parmlist(1,2*Nfleet);
  LOCAL_CALCS
   Comp_Err_ParmCount=0;
   min_tail_L.initialize();
@@ -1064,6 +1065,7 @@
   Comp_Err_L.initialize();
   Comp_Err_L2.initialize();
   min_sample_size_L.initialize();
+  DM_parmlist.initialize();
   
   if(use_length_data>0)
   {
@@ -1092,16 +1094,28 @@
         N_warn++;  warning<<N_warn<<" minimum sample size for length comps must be > 0; minimum sample size set to 0.001 "<<endl;
         min_sample_size_L(f) = 0.001;
       }
-      if (Comp_Err_L2(f) >Nfleet)
+
+      if (Comp_Err_L2(f) >2*Nfleet)
+      {
+        N_warn++; cout<<"fatal input error, see warning "<<endl; warning<<N_warn<<"; length D-M index for fleet: "<<f<<" is: "<<Comp_Err_L2(f)<<" but must be an integer <=2*Nfleet "<<endl;
+        exit(1);
+      }
+      else if(Comp_Err_L2(f)>Comp_Err_ParmCount+1)
       {
-        N_warn++; cout<<"fatal input error, see warning "<<endl; warning<<N_warn<<"; length D-M index for fleet: "<<f<<" is: "<<Comp_Err_L2(f)<<" but must be an integer <=Nfleet "<<endl;
+        N_warn++; cout<<"fatal input error, see warning "<<endl; 
+        warning<<N_warn<<"; length D-M must refer to existing parm num, or increment by 1:  "<<Comp_Err_L2(f)<<endl;
         exit(1);
       }
+      else if(Comp_Err_L2(f)>Comp_Err_ParmCount)
+      {
+        Comp_Err_ParmCount++;
+        DM_parmlist(f)=1;
+      }
+      //  else OK because refers to existing parameter
     }
-    //  get count of needed dirichlet composition parameters
     //  the count for age data will be added after reading the age data setup
-    Comp_Err_ParmCount=max(Comp_Err_L2);
     echoinput<<"number of D-M parameters needed for length comp data: "<<Comp_Err_ParmCount<<endl<<endl;
+
     *(ad_comm::global_datafile) >> nlen_bin;
     echoinput<<nlen_bin<<" nlen_bin_for_data "<<endl;
   }
@@ -1746,15 +1760,24 @@
           N_warn++;  warning<<N_warn<<" minimum sample size for age comps must be > 0; minimum sample size set to 0.001 "<<endl;
           min_sample_size_A(f) = 0.001;
         }
-      if (Comp_Err_A2(f) >Nfleet)
+      if (Comp_Err_A2(f) >2*Nfleet)
+      {
+        N_warn++; cout<<"fatal input error, see warning "<<endl; warning<<N_warn<<"; Age D-M index for fleet: "<<f<<" is: "<<Comp_Err_A2(f)<<" but must be an integer <=2*Nfleet "<<endl;
+        exit(1);
+      }
+      else if(Comp_Err_A2(f)>Comp_Err_ParmCount+1)
       {
-        N_warn++; cout<<"fatal input error, see warning "<<endl; warning<<N_warn<<"; Age D-M index for fleet: "<<f<<" is: "<<Comp_Err_A2(f)<<" but must be an integer <=Nfleet "<<endl;
+        N_warn++; cout<<"fatal input error, see warning "<<endl; 
+        warning<<N_warn<<"; Age D-M must refer to existing parm num, or increment by 1:  "<<Comp_Err_A2(f)<<endl;
         exit(1);
       }
+      else if(Comp_Err_A2(f)>Comp_Err_ParmCount)
+      {
+        Comp_Err_ParmCount++;
+        DM_parmlist(f+Nfleet)=1;
+      }
+      //  else OK because refers to existing parameter
       }
-        //  get count of needed dirichlet composition parameters
-      j=max(Comp_Err_A2);
-      Comp_Err_ParmCount=max(Comp_Err_ParmCount,j);  //  get the maximum parameter number referred to
       echoinput<<"number of D-M parameters needed for length and age comp data: "<<Comp_Err_ParmCount<<endl;
 
       *(ad_comm::global_datafile) >> Lbin_method;

SS_versioninfo_330opt.tpl

@@ -5,7 +5,7 @@ DATA_SECTION
 !!//  SS_Label_Section_1.0 #DATA_SECTION
 
 !!//  SS_Label_Info_1.1.1  #Create string with version info
-!!version_info+="#V3.30.17.00;_2021_06_11;_fast;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_12.3";
+!!version_info+="#V3.30.17.01;_2021_06_15;_fast;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_12.3";
 !!version_info+="#Stock Synthesis (SS) is a work of the U.S. Government and is not subject to copyright protection in the United States.";
 !!version_info+="#Foreign copyrights may apply. See copyright.txt for more information.";
 !!version_info2+="#_user_support_available_at:NMFS.Stock.Synthesis@noaa.gov";

SS_versioninfo_330safe.tpl

@@ -5,7 +5,7 @@ DATA_SECTION
 !!//  SS_Label_Section_1.0 #DATA_SECTION
 
 !!//  SS_Label_Info_1.1.1  #Create string with version info
-!!version_info+="#V3.30.17.00;_2021_06_11;_safe;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_12.3";
+!!version_info+="#V3.30.17.01;_2021_06_15;_safe;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_12.3";
 !!version_info+="#Stock Synthesis (SS) is a work of the U.S. Government and is not subject to copyright protection in the United States.";
 !!version_info+="#Foreign copyrights may apply. See copyright.txt for more information.";
 !!version_info2+="#_user_support_available_at:NMFS.Stock.Synthesis@noaa.gov";

SS_versioninfo_330trans.tpl

@@ -5,7 +5,7 @@ DATA_SECTION
 !!//  SS_Label_Section_1.0 #DATA_SECTION
 
 !!//  SS_Label_Info_1.1.1  #Create string with version info
-!!version_info+="#V3.30.17.00;_2021_06_11;_trans;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_12.3";
+!!version_info+="#V3.30.17.01;_2021_06_15;_trans;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_12.3";
 !!version_info+="#Stock Synthesis (SS) is a work of the U.S. Government and is not subject to copyright protection in the United States.";
 !!version_info+="#Foreign copyrights may apply. See copyright.txt for more information.";
 !!version_info2+="#_user_support_available_at:NMFS.Stock.Synthesis@noaa.gov";

SS_write_ssnew.tpl

@@ -1911,6 +1911,7 @@ FUNCTION void write_nucontrol()
     if(Comp_Err_ParmCount>0)
     {
       report4<<"#_Dirichlet parameters"<<endl;
+      report4<<"#_multiple_fleets_can_refer_to_same_parm;_but_list_cannot_have_gaps"<<endl;
       k=Comp_Err_Parm_Start;
       for(f=1;f<=Comp_Err_ParmCount;f++)
       {
@@ -1921,6 +1922,7 @@ FUNCTION void write_nucontrol()
           report4<<"  #  "<<ParmLabel(NP)<<endl;
       }
     }
+    else
     {
       report4<<"#_No_Dirichlet parameters"<<endl;
     }