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deprecate old spawn_recr table #724

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Merged
Rick-Methot-NOAA merged 2 commits into from
Sep 10, 2025
Merged

deprecate old spawn_recr table #724

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840a214
deprecate old spawn_recr table
Rick-Methot-NOAA Sep 9, 2025
ee56269
cleanup code
Rick-Methot-NOAA Sep 10, 2025
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114 changes: 3 additions & 111 deletions SS_write_report.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -1800,117 +1800,7 @@ FUNCTION void write_bigoutput()
var /= (n_rmse(1) + 1.0e-09);

dvariable steepness = SRparm(2);
SS2out << endl
<< pick_report_name(19);
SS2out << " Function: " << SR_fxn << " RecDev_method: " << do_recdev << " sum_recdev: " << sum_recdev << endl
<< SRparm(1) << " Ln(R0) " << mfexp(SRparm(1)) << endl
<< steepness << " steepness" << endl
<< Bmsy / SSB_virgin << " Bmsy/Bzero ";
if (SR_fxn == 8)
{
dvariable Shepherd_c;
dvariable Shepherd_c2;
dvariable Hupper;
Shepherd_c = SRparm(3);
Shepherd_c2 = pow(0.2, Shepherd_c);
Hupper = 1.0 / (5.0 * Shepherd_c2);
temp = 0.2 + (SRparm(2) - 0.2) / (0.8) * (Hupper - 0.2);
SS2out << " Shepherd_c: " << Shepherd_c << " steepness_limit: " << Hupper << " Adjusted_steepness: " << temp;
}
else if (SR_fxn == 9)
{
SS2out << " Ricker_Power: " << SRparm(3);
}

SS2out << endl;
SS2out << sigmaR << " sigmaR" << endl;
SS2out << init_equ_steepness << " # 0/1 to use steepness in initial equ recruitment calculation" << endl;

SS2out << SRparm(N_SRparm2 - 1) << " init_eq: see below" << endl
<< recdev_start << " " << recdev_end << " main_recdev:start_end" << endl
<< recdev_adj(1) << " " << recdev_adj(2, 5) << " breakpoints_for_bias_adjustment_ramp " << endl;

temp = sigmaR * sigmaR; // sigmaR^2
SS2out << "ERA N RMSE RMSE^2/sigmaR^2 mean_BiasAdj est_rho Durbin-Watson" << endl;
SS2out << "main " << n_rmse(1) << " " << rmse(1) << " " << square(rmse(1)) / temp << " " << rmse(2) << " " << cross / var << " " << Durbin;
if (wrote_bigreport == 0) // first time writing bigreport
{
if (rmse(1) < 0.5 * sigmaR && rmse(2) > (0.01 + 2.0 * square(rmse(1)) / temp))
{
warnstream << "Main recdev biasadj is >2 times ratio of rmse to sigmaR";
SS2out << " # " << warnstream.str() ;
write_message (WARN, 0);
}
}
SS2out << endl;

SS2out << "early " << n_rmse(3) << " " << rmse(3) << " " << square(rmse(3)) / temp << " " << rmse(4);
if (wrote_bigreport == 0) // first time writing bigreport
{
if (rmse(3) < 0.5 * sigmaR && rmse(4) > (0.01 + 2.0 * square(rmse(3)) / temp))
{
warnstream << "Early recdev biasadj is >2 times ratio of rmse to sigmaR";
SS2out << " # " << warnstream.str();
write_message (WARN, 0);
}
}
SS2out << endl;

SS2out << "Yr SpawnBio exp_recr with_regime bias_adjusted pred_recr dev biasadjuster era mature_bio mature_num raw_dev" << endl;
SS2out << "S/Rcurve " << SSB_virgin << " " << Recr_virgin << endl;
y = styr - 2;
SS2out << "Virg " << SSB_yr(y) << " " << exp_rec(y) << " - " << 0.0 << " Virg " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " 0.0 " << endl;
y = styr - 1;
SS2out << "Init " << SSB_yr(y) << " " << exp_rec(y) << " - " << 0.0 << " Init " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " " << 0.0 << endl;

if (recdev_first < styr)
{
for (y = recdev_first; y <= styr - 1; y++)
{
SS2out << y << " " << SSB_yr(styr - 1) << " " << exp_rec(styr - 1, 1) << " " << exp_rec(styr - 1, 2) << " " << exp_rec(styr - 1, 3) * mfexp(-biasadj(y) * half_sigmaRsq) << " " << exp_rec(styr - 1, 3) * mfexp(recdev(y) - biasadj(y) * half_sigmaRsq) << " "
<< recdev(y) << " " << biasadj(y) << " Init_age " << SSB_B_yr(styr - 1) << " " << SSB_N_yr(styr - 1) << " " << recdev(y) << endl; // newdev approach uses devs for initial agecomp directly
}
}
for (y = styr; y <= YrMax; y++)
{
SS2out << y << " " << SSB_yr(y) << " " << exp_rec(y) << " ";
if (recdev_do_early > 0 && y >= recdev_early_start && y <= recdev_early_end)
{
SS2out << log(exp_rec(y, 4) / exp_rec(y, 3)) << " " << biasadj(y) << " Early " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " " << recdev(y);
}
else if (y >= recdev_start && y <= recdev_end)
{
SS2out << log(exp_rec(y, 4) / exp_rec(y, 3)) << " " << biasadj(y) << " Main " << SSB_B_yr(y) << " " << SSB_N_yr(y) << " " << recdev(y);
}
else if (Do_Forecast > 0 && y > recdev_end)
{
SS2out << log(exp_rec(y, 4) / exp_rec(y, 3)) << " " << biasadj(y);
if (y <= endyr)
{
SS2out << " Late ";
}
else
{
SS2out << " Fore ";
}
SS2out << SSB_B_yr(y) << " " << SSB_N_yr(y) << " ";
if (do_recdev > 0)
{
SS2out << Fcast_recruitments(y);
}
else
{
SS2out << " 0.0";
}
}
else
{
SS2out << " _ _ Fixed";
}
SS2out << endl;
}

SS2out << endl << "#Expanded_Spawn_Recr_report" << endl << pick_report_name(19) << endl;
SS2out << endl << pick_report_name(19) << endl;
SS2out << SR_fxn << " # SR_Function" << endl;
SS2out << N_SRparm2 << " # N_SRparms" << endl;
SS2out << "#" << endl << "#_SRparm parm_label value phase TV_year" << endl;
Expand Down Expand Up @@ -3164,8 +3054,10 @@ FUNCTION void write_bigoutput()
selmax(f, 2) = float(s);} // save y.s

if (fleet_type(f) <= 2)
{
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;
}
SS2out << "bodywt " << f << " " << y << " " << s << " " << sx(g) << " " << g << " " << y << "_" << f << "_bodywt" << Wt_Age_t(t, f, g) << endl;
}
}
Expand Down
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