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add mean recruitment output to spawn_recr table #699

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Merged
Rick-Methot-NOAA merged 2 commits into from
Aug 12, 2025
Merged

add mean recruitment output to spawn_recr table #699

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3419551
add mean recruitment output to spawn_recr table
Rick-Methot-NOAA Aug 5, 2025
504f285
fix error in year range for mean_recr
Rick-Methot-NOAA Aug 12, 2025
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28 changes: 26 additions & 2 deletions SS_write_report.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -1716,6 +1716,7 @@ FUNCTION void write_bigoutput()
dvector Hrmse(1, k);
dvector Rrmse(1, k);
dvector n_rmse(1, k);
dvector mean_recr_report(1,4);
// following vectors used for index-related quantities
dvector mean_CV(1, k);

Expand All @@ -1735,10 +1736,11 @@ FUNCTION void write_bigoutput()

rmse = 0.0;
n_rmse = 0.0;
mean_recr_report = 0.0;
double cross = 0.0;
double Durbin = 0.0;
double var = 0.0;

warning << recdev_first << " "<<recdev_start << " " << styr << endl;
for (y = recdev_first; y <= recdev_end; y++)
{
temp1 = recdev(y);
Expand All @@ -1759,12 +1761,29 @@ FUNCTION void write_bigoutput()
rmse(1) += value(square(temp1));
n_rmse(1) += 1.;
rmse(2) += biasadj(y);
if (y < styr)
{
mean_recr_report(1) += value(exp_rec(styr - 1, 1));
mean_recr_report(2) += value(exp_rec(styr - 1, 2));
mean_recr_report(3) += value(exp_rec(styr - 1, 3) * mfexp(-biasadj(y) * half_sigmaRsq));
mean_recr_report(4) += value(exp_rec(styr - 1, 3) * mfexp(recdev(y) - biasadj(y) * half_sigmaRsq));
}
else
{
mean_recr_report(1) += value(exp_rec(y, 1));
mean_recr_report(2) += value(exp_rec(y, 2));
mean_recr_report(3) += value(exp_rec(y, 3));
mean_recr_report(4) += value(exp_rec(y, 4));
}
}
}
if (n_rmse(1) > 0. && rmse(1) > 0.)
rmse(1) = sqrt(rmse(1) / n_rmse(1)); // rmse during main period
if (n_rmse(1) > 0.)
{
rmse(2) = rmse(2) / n_rmse(1); // mean biasadj during main period
mean_recr_report /= n_rmse(1); // mean recruitment during main for each of 4 stages of recruitment output
}
if (n_rmse(3) > 0. && rmse(3) > 0.)
rmse(3) = sqrt(rmse(3) / n_rmse(3)); //rmse during early period
if (n_rmse(3) > 0.)
Expand Down Expand Up @@ -1992,7 +2011,12 @@ FUNCTION void write_bigoutput()
write_message (WARN, 0);
}
}
SS2out << endl << "#" << endl << init_equ_steepness << " # Initial_equilibrium:_0/1_to_use_spawner-recruitment_in_initial_equ_recruitment_calculation" << endl << "#" << endl;
SS2out << endl << "#" << endl << "# mean_recruitment_for_main_recdev_years" << endl
<< "# NOTE:_ratio()_is_influenced_by_max_bias_adj;_ratio_should_be_near_1.0" << endl
<< "# SR_exp_recr with_regime bias_adjusted pred_recr ratio(w_reg / pred_rec)" << endl
<< "# " << mean_recr_report << " " << mean_recr_report(2) / mean_recr_report(4) << endl;

SS2out << "#" << endl << init_equ_steepness << " # Initial_equilibrium:_0/1_to_use_spawner-recruitment_in_initial_equ_recruitment_calculation" << endl << "#" << endl;
SS2out << "Yr SpawnBio exp_recr with_regime bias_adjusted pred_recr dev biasadjuster era mature_bio mature_num raw_dev SSBpR(yr) " << endl;

y = styr - 2;
Expand Down
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