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first commit of discard body wt output to report 32 #790

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Merged
Rick-Methot-NOAA merged 5 commits into from
Nov 10, 2026
Merged

first commit of discard body wt output to report 32 #790

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076868c
first commit of discard body wt output to report 32
Rick-Methot-NOAA Nov 5, 2026
8555dad
first commit of discard body wt output to report 32
Rick-Methot-NOAA Nov 5, 2026
2ea56bc
Merge branch 'output_disc_bodywt' of https://github.com/nmfs-ost/ss3-…
Rick-Methot-NOAA Nov 6, 2026
5390359
only output when using length-retention
Rick-Methot-NOAA Nov 6, 2026
05d3b5a
trapping for copilot's edge case
Rick-Methot-NOAA Nov 9, 2026
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4 changes: 2 additions & 2 deletions SS_benchfore.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -3043,7 +3043,7 @@ FUNCTION void Get_Forecast()
if (Do_Retain(f) > 0)
{
disc_age(t, disc_fleet_list(f), g) = Hrate(f, t) * elem_prod(elem_prod(natage(t, p, g), sel_num(s, f, g)), Zrate2(p, g)); // selected numbers
disc_age(t, disc_fleet_list(f) + N_retain_fleets, g) = Hrate(f, t) * elem_prod(elem_prod(natage(t, p, g), sel_ret_num(s, f, g)), Zrate2(p, g)); // selected numbers
disc_age(t, disc_fleet_list(f) + N_retain_fleets, g) = Hrate(f, t) * elem_prod(elem_prod(natage(t, p, g), sel_ret_num(s, f, g)), Zrate2(p, g)); // retained numbers
}
} //close gmorph loop
catch_fleet(t, f) *= temp;
Expand Down Expand Up @@ -3212,7 +3212,7 @@ FUNCTION void Get_Forecast()
if (Do_Retain(f) > 0)
{
disc_age(t, disc_fleet_list(f), g) = Hrate(f, t) * elem_prod(elem_prod(natage(t, p, g), sel_num(s, f, g)), Zrate2(p, g)); // selected numbers
disc_age(t, disc_fleet_list(f) + N_retain_fleets, g) = Hrate(f, t) * elem_prod(elem_prod(natage(t, p, g), sel_ret_num(s, f, g)), Zrate2(p, g)); // selected numbers
disc_age(t, disc_fleet_list(f) + N_retain_fleets, g) = Hrate(f, t) * elem_prod(elem_prod(natage(t, p, g), sel_ret_num(s, f, g)), Zrate2(p, g)); // retained numbers
}
} //close gmorph loop
} // close fishery
Expand Down
3 changes: 2 additions & 1 deletion SS_param.tpl
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Expand Up @@ -175,6 +175,7 @@ PARAMETER_SECTION
LOCAL_CALCS
// clang-format on
Ave_Size.initialize();
Wt_Age_t.initialize();
// 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)
{
Expand Down Expand Up @@ -358,7 +359,7 @@ PARAMETER_SECTION
matrix Hrate(1,Nfleet,styr-3*nseas,k) //Harvest Rate for each fleet; this is F
4darray natage(styr-3*nseas,k,1,pop,1,gmorph,0,nages) // add +1 year
4darray catage(styr-3*nseas,k,1,Nfleet,1,gmorph,0,nages)
4darray disc_age(styr-3*nseas,TimeMax_Fcast_std+nseas,1,2*N_retain_fleets,1,gmorph,0,nages);
4darray disc_age(styr-3*nseas,TimeMax_Fcast_std+nseas,1,4*N_retain_fleets,1,gmorph,0,nages); // where 3* holds disc_bodywt and 4* holds ret_bodywt
4darray equ_catage(1,nseas,1,Nfleet,1,gmorph,0,nages)
4darray equ_numbers(1,nseas,1,pop,1,gmorph,0,3*nages)
4darray equ_Z(1,nseas,1,pop,1,gmorph,0,nages)
Expand Down
2 changes: 1 addition & 1 deletion SS_popdyn.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -1305,7 +1305,7 @@ FUNCTION void get_time_series()
if (Do_Retain(f) > 0)
{
disc_age(t, disc_fleet_list(f), g) = Hrate(f, t) * elem_prod(elem_prod(natage(t, p, g), sel_num(s, f, g)), Zrate2(p, g)); // selected numbers
disc_age(t, disc_fleet_list(f) + N_retain_fleets, g) = Hrate(f, t) * elem_prod(elem_prod(natage(t, p, g), sel_ret_num(s, f, g)), Zrate2(p, g)); // selected numbers
disc_age(t, disc_fleet_list(f) + N_retain_fleets, g) = Hrate(f, t) * elem_prod(elem_prod(natage(t, p, g), sel_ret_num(s, f, g)), Zrate2(p, g)); // retained numbers
}
} //close gmorph loop
}
Expand Down
8 changes: 8 additions & 0 deletions SS_selex.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -2026,6 +2026,14 @@ FUNCTION void Make_FishSelex()
{
sel_ret_bio(s, f, g, a) = sel_a(yf, f, gg, a) * (ALK_w(a)(llo, lhi) * sel_l_r_w(llo, lhi));
sel_ret_num(s, f, g, a) = sel_a(yf, f, gg, a) * (ALK_w(a)(llo, lhi) * sel_l_r(yf, f, gg)(llo, lhi));
if (Do_Retain(f) > 0) {
disc_age(tz, disc_fleet_list(f) + 2 * N_retain_fleets, g, a) =
ALK_w(a) * elem_prod(tempvec_l, (1.0 - retain(yf, f)(1, nlength))) /
(ALK_w(a) * elem_prod((1.0 - retain(yf, f)(1, nlength)), sel_l(yf, f, gg)) + 1.0e-09); // mean body wt of discarded fish
disc_age(tz, disc_fleet_list(f) + 3 * N_retain_fleets, g, a) =
ALK_w(a) * elem_prod(tempvec_l, (retain(yf, f)(1, nlength))) /
(ALK_w(a) * elem_prod(retain(yf, f)(1, nlength), sel_l(yf, f, gg)) + 1.0e-09); // mean body wt of retained fish
}
}
else if (a == nages)
{
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5 changes: 5 additions & 0 deletions SS_write_report.tpl
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Expand Up @@ -2987,6 +2987,11 @@ FUNCTION void write_bigoutput()
{
SS2out << "F " << f << " " << y << " " << s << " " << sx(g) << " " << g << " " << y << "_" << f << "_F" << Hrate(f, t) * save_sel_num(t, f, g) << endl;
SS2out << "Fdead " << f << " " << y << " " << s << " " << sx(g) << " " << g << " " << y << "_" << f << "_Fdead" << Hrate(f, t) * save_F_dead(t, f, g) << endl;
// if doing length-based retention, then output the body weight for each partition
if (WTage_rd == 0 && Do_Retain(f) == 1) {
SS2out << "disc_bodywt " << f << " " << y << " " << s << " " << sx(g) << " " << g << " " << y << "_" << f << "_disc_bodywt " << disc_age(t, disc_fleet_list(f) + 2 * N_retain_fleets, g) << endl;
SS2out << "ret_bodywt " << f << " " << y << " " << s << " " << sx(g) << " " << g << " " << y << "_" << f << "_ret_bodywt " << disc_age(t, disc_fleet_list(f) + 3 * N_retain_fleets, g) << endl;
}
}
SS2out << "bodywt " << f << " " << y << " " << s << " " << sx(g) << " " << g << " " << y << "_" << f << "_bodywt" << Wt_Age_t(t, f, g) << endl;
}
Expand Down
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