Skip to content

fix for tag mirror #268; partial fix for retro-superperiod #265 #270

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
Rick-Methot-NOAA merged 3 commits into from
Mar 11, 2022
Merged

fix for tag mirror #268; partial fix for retro-superperiod #265 #270

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
379a5ed
fix for tag mirror #268; partial fix for retro-superperiod #265
Rick-Methot-NOAA Mar 8, 2022
7c87828
finish fix for tag mirror #268
Rick-Methot-NOAA Mar 9, 2022
6b42bbc
add warning for overdsip out of range
Rick-Methot-NOAA Mar 11, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 9 additions & 1 deletion SS_objfunc.tpl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -512,9 +512,17 @@ FUNCTION void evaluate_the_objective_function()
// SS_Label_Info_25.9 #Fit to tag-recapture
if(Do_TG>0)
{
k=1+2*N_TG;
for (TG=1;TG<=N_TG;TG++)
{
overdisp=TG_parm(2*N_TG+TG);
j=TG+2*N_TG;
if(TG_parm_PH(j)==-1000.)
{ }// do nothing keep k at same value
else
{
if (TG_parm_PH(j)>-1000.) {k=j;} else {k=-1000-TG_parm_PH(j)+2*N_TG;}
}
overdisp=TG_parm(k);
for (TG_t=TG_mixperiod;TG_t<=TG_endtime(TG);TG_t++)
{
TG_recap_exp(TG,TG_t)(1,Nfleet)+=1.0e-6; // add a tiny amount
Expand Down
2 changes: 1 addition & 1 deletion SS_prelim.tpl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -312,7 +312,7 @@ PRELIMINARY_CALCS_SECTION
else
{k++;}
}
if(k!=1) {N_warn++; cout<<"error in length data"; warning<<N_warn<<" "<<" must have only 1 sample with real info in length superperiod "<<j<<endl; exit(1);}
if(k>1) {N_warn++; cout<<"error in length data"; warning<<N_warn<<" "<<" must have only 1 sample with real info in length superperiod "<<j<<endl; exit(1);}
for (i=suprper_l1(f,j);i<=suprper_l2(f,j);i++)
Copy link
Contributor

@k-doering-NOAA k-doering-NOAA Mar 8, 2022

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Next time, it would be nice to break the changes addressing 2 issues into separate commits (although I think 1 PR is fine!)

{
if(header_l(f,i,3)<0) // so one of the obs to be combined
Expand Down
16 changes: 12 additions & 4 deletions SS_readcontrol_330.tpl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3895,6 +3895,12 @@
{TG_parm2(k,7)=-1000; } // phase
}
}

TG_parm_LO=column(TG_parm2,1);
TG_parm_HI=column(TG_parm2,2);
k=3*N_TG+2*Nfleet1;
for (j=1;j<=k;j++) TG_parm_PH(j)=TG_parm2(j,7); // write it out due to no typecast available

echoinput<<"create tag labels "<<endl;
// SS_Label_Info_4.10.1 #Create parameter count and parameter names for tag parameters
onenum=" ";
Expand All @@ -3913,6 +3919,12 @@
{
sprintf(onenum, "%d", j);
ParCount++; ParmLabel+="TG_overdispersion_"+onenum+CRLF(1);
if(TG_parm_LO(2*N_TG+j)<1.0)
{N_warn++; warning<<N_warn<<" overdispersion par_min is <1.0 for TG= "<<j<<"; value = "<<TG_parm_LO(2*N_TG+j)<<"; changed to 1.001 for run"<<endl;
TG_parm_LO(2*N_TG+j)=1.001;}
if(TG_parm2(2*N_TG+j,3)<1.0)
{N_warn++; warning<<N_warn<<" overdispersion parameter is <1.0 for TG= "<<j<<"; value = "<<TG_parm2(2*N_TG+j,3)<<"; changed to 1.001 for run"<<endl;
TG_parm2(2*N_TG+j,3)=1.001;}
}
for (j=1;j<=Nfleet;j++)
{
Expand All @@ -3931,10 +3943,6 @@
}
}

TG_parm_LO=column(TG_parm2,1);
TG_parm_HI=column(TG_parm2,2);
k=3*N_TG+2*Nfleet1;
for (j=1;j<=k;j++) TG_parm_PH(j)=TG_parm2(j,7); // write it out due to no typecast available
echoinput<<" Processed/generated Tag parameters "<<endl<<TG_parm2<<endl;

}
Expand Down
23 changes: 0 additions & 23 deletions SS_tagrecap.tpl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,6 @@ FUNCTION void Tag_Recapture()
TG_rep_decay(f) = TG_parm(k);
}
}

for (TG=1;TG<=N_TG;TG++)
{
firstseas=int(TG_release(TG,4)); // release season
Expand Down Expand Up @@ -75,7 +74,6 @@ FUNCTION void Tag_Recapture()
TG_save(TG,1)=value(TG_init_loss);
TG_save(TG,2)=value(TG_chron_loss);
}

TG_t=0;
for (y=TG_release(TG,3);y<=endyr;y++)
{
Expand Down Expand Up @@ -165,24 +163,3 @@ FUNCTION void Tag_Recapture()
} // end years
} // end loop of tag groups
} // end having tag groups

/*
// SS_Label_Info_25.9 #Fit to tag-recapture
// This code fragment resides in SS_objfunc.tpl
if(Do_TG>0)
{
for (TG=1;TG<=N_TG;TG++)
{
overdisp=TG_parm(2*N_TG+TG);
for (TG_t=TG_mixperiod;TG_t<=TG_endtime(TG);TG_t++)
{
TG_recap_exp(TG,TG_t)(1,Nfleet)+=1.0e-6; // add a tiny amount
TG_recap_exp(TG,TG_t,0) = sum(TG_recap_exp(TG,TG_t)(1,Nfleet));
TG_recap_exp(TG,TG_t)(1,Nfleet)/=TG_recap_exp(TG,TG_t,0);
if(Nfleet>1) TG_like1(TG)-=TG_recap_obs(TG,TG_t,0)* (TG_recap_obs(TG,TG_t)(1,Nfleet) * log(TG_recap_exp(TG,TG_t)(1,Nfleet)));
TG_like2(TG)-=log_negbinomial_density(TG_recap_obs(TG,TG_t,0),TG_recap_exp(TG,TG_t,0),overdisp);
}
}
if(do_once==1) cout<<" did tag obj_fun "<<TG_like1<<endl<<TG_like2<<endl;
}
*/