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SS_write.tpl
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SS_write.tpl
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// SS_Label_file #17. **SS_write.tpl**
// SS_Label_file # * <u>write_summaryoutput()</u> // append writes to *cumreport.sso*
// SS_Label_file # * <u>write_SS_summary()</u> // writes *ss_summary.sso*
// SS_Label_file # * <u>write_rebuilder_output()</u> // special output
// SS_Label_file # * <u>write_SIStable()</u> // deprecated, see new r4ss routines
// SS_Label_file # * <u>write_Bzero_output()</u> //
// SS_Label_file # * <u>Report_Parm()</u> // used by write_big_report in writing *report.sso*
// SS_Label_file #
/* SS_Label_FUNCTION 36 write_summaryoutput; Writes in append mode to cumreport.sso */
FUNCTION void write_summaryoutput()
{
random_number_generator radm(long(time(&finish)));
time(&finish);
elapsed_time = difftime(finish, start);
report2 << runnumber << " -logL: " << obj_fun << " SSB(Vir_Start_End): " << SSB_yr(styr - 2) << " " << SSB_yr(styr) << " " << SSB_yr(endyr) << endl;
report2 << runnumber << " Files: " << datfilename << " " << ctlfilename;
if (readparfile >= 1)
report2 << " Start_from_ss.par";
report2 << endl
<< runnumber << " N_iter: " << niter << " runtime(sec): " << elapsed_time << " starttime: " << ctime(&start);
report2 << runnumber << version_info(1) << version_info(2) << version_info(3) << endl;
report2 << runnumber << " F_Method: " << F_Method << " Retro_YR: " << retro_yr << " Forecast_Type: " << Do_Forecast << " MSY_Type: " << Do_MSY << endl;
if (N_SC > 0)
{
for (j = 1; j <= N_SC; j++)
report2 << runnumber << " Comment S_" << j << " " << Starter_Comments(j) << endl;
}
if (N_DC > 0)
{
for (j = 1; j <= N_DC; j++)
report2 << runnumber << " Comment D_" << j << " " << Data_Comments(j) << endl;
}
if (N_CC > 0)
{
for (j = 1; j <= N_CC; j++)
report2 << runnumber << " Comment C_" << j << " " << Control_Comments(j) << endl;
}
if (N_FC > 0)
{
for (j = 1; j <= N_FC; j++)
report2 << runnumber << " Comment F_" << j << " " << Forecast_Comments(j) << endl;
}
k = current_phase();
if (k > max_lambda_phase)
k = max_lambda_phase;
report2 << runnumber << " Like_Emph Total 1 " << endl
<< runnumber << " Like_Value Total " << obj_fun << endl;
if (Svy_N > 0)
report2 << runnumber << " Like_Emph Indices All " << column(surv_lambda, k) << endl
<< runnumber << " Like_Value Indices " << surv_like * column(surv_lambda, k) << " " << surv_like << endl;
if (nobs_disc > 0)
report2 << runnumber << " Like_Emph Discard All " << column(disc_lambda, k) << endl
<< runnumber << " Like_Value Discard " << disc_like * column(disc_lambda, k) << " " << disc_like << endl;
if (nobs_mnwt > 0)
report2 << runnumber << " Like_Emph MeanBodyWt All " << column(mnwt_lambda, k) << endl
<< runnumber << " Like_Value MeanBodyWt " << mnwt_like * column(mnwt_lambda, k) << " " << mnwt_like << endl;
if (Nobs_l_tot > 0)
report2 << runnumber << " Like_Emph LenComp All " << column(length_lambda, k) << endl
<< runnumber << " Like_Value LenComp " << length_like_tot * column(length_lambda, k) << " " << length_like_tot << endl;
if (Nobs_a_tot > 0)
report2 << runnumber << " Like_Emph AgeComp All " << column(age_lambda, k) << endl
<< runnumber << " Like_Value AgeComp " << age_like_tot * column(age_lambda, k) << " " << age_like_tot << endl;
if (nobs_ms_tot > 0)
report2 << runnumber << " Like_Emph MeanLAA All " << column(sizeage_lambda, k) << endl
<< runnumber << " Like_Value MeanLAA " << sizeage_like * column(sizeage_lambda, k) << " " << sizeage_like << endl;
if (F_Method > 1)
report2 << runnumber << " Like_Emph Catch All " << column(catch_lambda, k) << endl
<< runnumber << " Like_Value Catch " << catch_like * column(catch_lambda, k) << " " << catch_like << endl;
report2 << runnumber << " Like_Emph init_equ All " << column(init_equ_lambda, k) << endl
<< runnumber << " Like_Value Init_Equ " << equ_catch_like * column(init_equ_lambda, k) << " " << catch_like << endl;
if (SzFreq_Nmeth > 0)
report2 << runnumber << " Like_Emph WeightFreq All " << column(SzFreq_lambda, k) << endl
<< runnumber << " Like_Value WeightFreq " << SzFreq_like * column(SzFreq_lambda, k) << " " << SzFreq_like << endl;
if (Do_Morphcomp > 0)
report2 << runnumber << " Like_Emph Morphcomp All " << Morphcomp_lambda(k) << endl
<< runnumber << " Like_Value Morphcomp " << Morphcomp_like * Morphcomp_lambda(k) << " " << Morphcomp_like << endl;
if (Do_TG > 0)
report2 << runnumber << " Like_Emph Tag_comp All " << column(TG_lambda1, k) << endl
<< runnumber << " Like_Value Tag_comp " << TG_like1 * column(TG_lambda1, k) << " " << TG_like1 << endl;
if (Do_TG > 0)
report2 << runnumber << " Like_Emph Tag_negbin All " << column(TG_lambda2, k) << endl
<< runnumber << " Like_Value Tag_negbin " << TG_like2 * column(TG_lambda2, k) << " " << TG_like2 << endl;
report2 << runnumber << " Like_Comp Recruits Regime Fcast_Recr Biasadj Priors ParmDevs CrashPen" << endl;
report2 << runnumber << " Like_Emph " << recrdev_lambda(k) << " " << regime_lambda(k) << " " << Fcast_recr_lambda << " "
<< parm_prior_lambda(k) << " " << parm_dev_lambda(k) << " " << CrashPen_lambda(k) << endl;
report2 << runnumber << " Like_Value*Emph " << recr_like * recrdev_lambda(k) << " " << regime_like * regime_lambda(k) << " "
<< Fcast_recr_like << " " << parm_like * parm_prior_lambda(k) << " " << sum(parm_dev_like) * parm_dev_lambda(k) << " " << CrashPen * CrashPen_lambda(k) << endl;
report2 << runnumber << " TimeSeries Yr Vir Equ " << years << " ";
k = YrMax;
if (k == endyr)
k = endyr + 1;
for (y = endyr + 1; y <= k; y++)
{
report2 << y << "F ";
}
report2 << endl;
report2 << runnumber << " Timeseries SpawnBio " << SSB_yr(styr - 2, YrMax) << endl;
report2 << runnumber << " Timeseries Recruit " << column(exp_rec, 4) << endl;
report2 << runnumber << " Timeseries TotBio " << column(Smry_Table, 1) << endl;
report2 << runnumber << " Timeseries SmryBio-" << Smry_Age << " " << column(Smry_Table, 2) << endl;
report2 << runnumber << " Timeseries TotCatch " << column(Smry_Table, 4) << endl;
report2 << runnumber << " Timeseries RetCatch " << column(Smry_Table, 5) << endl;
j = 0;
if (max(Do_Retain) > 0)
j = 1;
if (Do_Benchmark > 0)
report2 << runnumber << " Mgmt_Quant " << Mgmt_quant(1, 6 + j) << endl;
report2 << runnumber << " Parm Labels ";
for (i = 1; i <= ParCount; i++)
{
report2 << " " << ParmLabel(i);
}
report2 << endl;
report2 << runnumber << " Parm Values ";
report2 << " " << MGparm << " ";
if (N_parm_dev > 0)
{
for (j = 1; j <= N_parm_dev; j++)
report2 << parm_dev(j) << " ";
}
report2 << SR_parm << " ";
if (recdev_cycle > 0)
report2 << recdev_cycle_parm << " ";
if (recdev_do_early > 0)
report2 << recdev_early << " ";
if (do_recdev == 1)
{
report2 << recdev1 << " ";
}
if (do_recdev == 2)
{
report2 << recdev2 << " ";
}
if (Do_Forecast > 0)
report2 << Fcast_recruitments << " ";
if (Do_Impl_Error > 0)
report2 << Fcast_impl_error << " ";
if (N_init_F > 0)
report2 << init_F << " ";
if (N_Fparm > 0)
report2 << " " << F_rate;
if (Q_Npar2 > 0)
report2 << Q_parm << " ";
if (N_selparm2 > 0)
report2 << selparm << " ";
// if(N_selparm_dev>0) report2<<selparm_dev<<" ";
if (Do_TG > 0)
report2 << TG_parm << " ";
report2 << endl;
NP = 0; // count of number of parameters
report2 << runnumber << " MG_parm ";
for (j = 1; j <= N_MGparm2; j++)
{
NP++;
report2 << " " << ParmLabel(NP);
}
report2 << endl
<< runnumber << " MG_parm " << MGparm << endl;
if (N_parm_dev > 0)
{
report2 << runnumber << " MG_parm_dev ";
for (i = 1; i <= N_parm_dev; i++)
{
for (j = parm_dev_minyr(i); j <= parm_dev_maxyr(i); j++)
{
NP++;
report2 << " " << ParmLabel(NP);
}
report2 << endl
<< runnumber << " MG_parm_dev " << parm_dev(i) << endl;
}
}
report2 << runnumber << " SR_parm ";
for (i = 1; i <= N_SRparm3 + recdev_cycle; i++)
{
NP++;
report2 << " " << ParmLabel(NP);
}
report2 << endl
<< runnumber << " SR_parm " << SR_parm << " ";
if (recdev_cycle > 0)
report2 << recdev_cycle_parm;
report2 << endl;
if (recdev_do_early > 0)
{
report2 << runnumber << " Recr_early ";
for (i = recdev_early_start; i <= recdev_early_end; i++)
{
NP++;
report2 << " " << ParmLabel(NP);
}
report2 << endl
<< runnumber << " Recr_early ";
for (i = recdev_early_start; i <= recdev_early_end; i++)
report2 << " " << recdev(i);
report2 << endl;
}
if (do_recdev > 0)
{
report2 << runnumber << " Recr_main ";
for (i = recdev_start; i <= recdev_end; i++)
{
NP++;
report2 << " " << ParmLabel(NP);
}
report2 << endl
<< runnumber << " Recr_main ";
for (i = recdev_start; i <= recdev_end; i++)
report2 << " " << recdev(i);
report2 << endl;
}
if (Do_Forecast > 0)
{
if (do_recdev > 0)
{
report2 << runnumber << " Recr_fore ";
for (i = recdev_end + 1; i <= YrMax; i++)
{
NP++;
report2 << " " << ParmLabel(NP);
}
report2 << endl
<< runnumber << " Recr_fore ";
for (i = recdev_end + 1; i <= YrMax; i++)
report2 << " " << recdev(i);
report2 << endl;
}
if (Do_Impl_Error > 0)
{
report2 << runnumber << " Impl_err ";
for (i = endyr + 1; i <= YrMax; i++)
{
NP++;
report2 << " " << ParmLabel(NP);
}
report2 << endl
<< runnumber << " Impl_err ";
for (i = endyr + 1; i <= YrMax; i++)
report2 << " " << Fcast_impl_error(i);
report2 << endl;
}
}
report2 << runnumber << " init_F ";
for (i = 1; i <= N_init_F; i++)
{
NP++;
report2 << " " << ParmLabel(NP);
}
report2 << endl
<< runnumber << " init_F ";
for (i = 1; i <= N_init_F; i++)
report2 << " " << init_F(i);
report2 << endl;
if (N_Fparm > 0)
{
report2 << runnumber << " F_rate ";
for (i = 1; i <= N_Fparm; i++)
{
NP++;
report2 << " " << ParmLabel(NP);
}
report2 << endl
<< runnumber << " F_rate ";
for (i = 1; i <= N_Fparm; i++)
report2 << " " << F_rate(i);
report2 << endl;
}
if (Q_Npar2 > 0)
{
report2 << runnumber << " Q_parm ";
for (i = 1; i <= Q_Npar2; i++)
{
NP++;
report2 << " " << ParmLabel(NP);
}
report2 << endl
<< runnumber << " Q_parm ";
for (i = 1; i <= Q_Npar2; i++)
report2 << " " << Q_parm(i);
report2 << endl;
}
if (N_selparm2 > 0)
{
report2 << runnumber << " Sel_parm ";
for (i = 1; i <= N_selparm2; i++)
{
NP++;
report2 << " " << ParmLabel(NP);
}
report2 << endl
<< runnumber << " Sel_parm " << selparm << endl;
}
if (Do_TG > 0)
{
report2 << runnumber << " Tag_parm ";
for (f = 1; f <= 3 * N_TG + 2 * Nfleet1; f++)
{
NP++;
report2 << " " << ParmLabel(NP);
}
report2 << endl
<< runnumber << " Tag_parm " << TG_parm << endl;
}
if (Do_CumReport == 2)
{
if (Svy_N > 0)
for (f = 1; f <= Nfleet; f++)
if (Svy_N_fleet(f) > 0)
{
report2 << runnumber << " Index:" << f << " Yr ";
for (i = 1; i <= Svy_N_fleet(f); i++)
{
ALK_time = Svy_ALK_time(f, i);
report2 << data_time(ALK_time, f, 3) << " ";
}
report2 << endl
<< runnumber << " Index:" << f << " OBS " << Svy_obs(f) << endl;
if (Svy_errtype(f) >= 0) // lognormal or lognormal T-dist
{
report2 << runnumber << " Index:" << f << " EXP " << mfexp(Svy_est(f)) << endl;
}
else // normal error
{
report2 << runnumber << " Index:" << f << " EXP " << Svy_est(f) << endl;
}
}
data_type = 4;
for (f = 1; f <= Nfleet; f++)
if (Nobs_l(f) > 0)
{
report2 << runnumber << " Len:" << f << " YR ";
for (i = 1; i <= Nobs_l(f); i++)
{
t = Len_time_t(f, i);
ALK_time = Len_time_ALK(f, i);
report2 << data_time(ALK_time, f, 3) << " ";
}
report2 << endl
<< runnumber << " Len:" << f << " effN " << neff_l(f) << endl;
}
data_type = 5;
for (f = 1; f <= Nfleet; f++)
if (Nobs_a(f) > 0)
{
report2 << runnumber << " Age:" << f << " YR ";
for (i = 1; i <= Nobs_a(f); i++)
{
t = Age_time_t(f, i);
ALK_time = Age_time_ALK(f, i);
report2 << data_time(ALK_time, f, 3) << " ";
}
report2 << endl
<< runnumber << " Age:" << f << " effN " << neff_a(f) << endl;
}
}
report2 << endl;
cout << " finished appending to cumreport.sso " << endl;
}
FUNCTION void write_SS_summary()
{
SS_smry.open(sso_pathname + "ss_summary.sso");
SS_smry << version_info(1) << version_info(2) << version_info(3) << endl;
SS_smry << datfilename << " #_DataFile " << endl;
SS_smry << ctlfilename << " #_Control " << endl;
SS_smry << "Run_Date: " << ctime(&start);
SS_smry << "Final_phase: " << current_phase() << " N_iterations: " << niter << endl;
k = current_phase();
if (k > max_lambda_phase)
k = max_lambda_phase;
SS_smry << "#_LIKELIHOOD " << endl;
SS_smry << "Label logL*Lambda" << endl;
SS_smry << "TOTAL_LogL " << obj_fun << endl;
if (F_Method > 1)
{
SS_smry << "Catch " << catch_like * column(catch_lambda, k) << endl;
}
if (N_init_F > 0)
SS_smry << "Equil_catch " << equ_catch_like * column(init_equ_lambda, k) << endl;
if (Svy_N > 0)
SS_smry << "Survey " << surv_like * column(surv_lambda, k) << endl;
if (nobs_disc > 0)
SS_smry << "Discard " << disc_like * column(disc_lambda, k) << endl;
if (nobs_mnwt > 0)
SS_smry << "Mean_body_wt " << mnwt_like * column(mnwt_lambda, k) << endl;
if (Nobs_l_tot > 0)
SS_smry << "Length_comp " << length_like_tot * column(length_lambda, k) << endl;
if (Nobs_a_tot > 0)
SS_smry << "Age_comp " << age_like_tot * column(age_lambda, k) << endl;
if (nobs_ms_tot > 0)
SS_smry << "Size_at_age " << sizeage_like * column(sizeage_lambda, k) << endl;
if (SzFreq_Nmeth > 0)
SS_smry << "Gen_Size_Comp " << SzFreq_like * column(SzFreq_lambda, k) << endl;
if (Do_Morphcomp > 0)
SS_smry << "Morphcomp " << Morphcomp_lambda(k) * Morphcomp_like << endl;
if (Do_TG > 0)
{
SS_smry << "Tag_Data_1 " << TG_like1 * column(TG_lambda1, k) << endl;
SS_smry << "Tag_Data_2 " << TG_like2 * column(TG_lambda2, k) << endl;
}
SS_smry << "Recruitment " << recr_like * recrdev_lambda(k) << endl;
SS_smry << "InitEQ_regime " << regime_like * regime_lambda(k) << endl;
SS_smry << "Sum_recdevs " << sum_recdev << endl;
SS_smry << "Forecast_Recruitment " << Fcast_recr_like << endl;
SS_smry << "Parm_priors " << parm_like * parm_prior_lambda(k) << endl;
SS_smry << "Parm_softbounds " << SoftBoundPen << endl;
SS_smry << "Parm_devs " << sum(parm_dev_like) * parm_dev_lambda(k) << endl;
SS_smry << "F_Ballpark " << F_ballpark_lambda(k) * F_ballpark_like << endl;
SS_smry << "Crash_Pen " << CrashPen_lambda(k) * CrashPen << endl;
SS_smry << "#_PARAMETERS" << endl
<< "#label value se active? range" << endl;
NP = 0; // count of number of parameters
active_count = 0;
SS_smry << "#_BIOLOGY" << endl;
for (j = 1; j <= N_MGparm2; j++)
{
NP++;
SS_smry << ParmLabel(NP) << " " << MGparm(j) << " ";
if (active(MGparm(j)))
{
active_count++;
SS_smry << CoVar(active_count, 1) << " Act ";
}
else
{
SS_smry << 0.0 << " Fix ";
}
SS_smry << (MGparm(j) - MGparm_LO(j)) / (MGparm_HI(j) - MGparm_LO(j) + 1.0e-6) << endl;
}
SS_smry << "#_SPAWN_RECR" << endl;
for (j = 1; j <= N_SRparm3; j++)
{
NP++;
SS_smry << ParmLabel(NP) << " " << SR_parm(j) << " ";
if (active(SR_parm(j)))
{
active_count++;
SS_smry << CoVar(active_count, 1) << " Act ";
}
else
{
SS_smry << 0.0 << " Fix ";
}
SS_smry << (SR_parm(j) - SR_parm_LO(j)) / (SR_parm_HI(j) - SR_parm_LO(j) + 1.0e-6) << endl;
}
if (recdev_cycle > 0)
{
for (j = 1; j <= recdev_cycle; j++)
{
NP++;
SS_smry << ParmLabel(NP) << " " << recdev_cycle_parm(j) << " ";
if (active(recdev_cycle_parm(j)))
{
active_count++;
SS_smry << CoVar(active_count, 1) << " Act ";
}
else
{
SS_smry << 0.0 << " Fix ";
}
SS_smry << (recdev_cycle_parm(j) - recdev_cycle_LO(j)) / (recdev_cycle_HI(j) - recdev_cycle_LO(j) + 1.0e-6) << endl;
}
}
if (recdev_do_early > 0)
{
for (j = recdev_early_start; j <= recdev_early_end; j++)
{
NP++;
SS_smry << ParmLabel(NP) << " " << recdev(j) << " ";
if (active(recdev_early))
{
active_count++;
SS_smry << CoVar(active_count, 1) << " Act ";
}
else
{
SS_smry << 0.0 << " Fix ";
}
SS_smry << (recdev(j) - recdev_LO) / (recdev_HI - recdev_LO + 1.0e-6) << endl;
}
}
if (do_recdev > 0)
{
for (j = recdev_start; j <= recdev_end; j++)
{
NP++;
SS_smry << ParmLabel(NP) << " " << recdev(j) << " ";
if (active(recdev1) || active(recdev2))
{
active_count++;
SS_smry << CoVar(active_count, 1) << " Act ";
}
else
{
SS_smry << 0.0 << " Fix ";
}
SS_smry << (recdev(j) - recdev_LO) / (recdev_HI - recdev_LO + 1.0e-6) << endl;
}
}
if (Do_Forecast > 0 && do_recdev > 0)
{
for (j = recdev_end + 1; j <= YrMax; j++)
{
NP++;
SS_smry << ParmLabel(NP) << " " << Fcast_recruitments(j) << " ";
if (active(Fcast_recruitments))
{
active_count++;
SS_smry << CoVar(active_count, 1) << " Act ";
}
else
{
SS_smry << 0.0 << " Fix ";
}
SS_smry << (Fcast_recruitments(j) - recdev_LO) / (recdev_HI - recdev_LO + 1.0e-6) << endl;
}
if (Do_Impl_Error > 0)
{
for (j = endyr + 1; j <= YrMax; j++)
{
NP++;
SS_smry << ParmLabel(NP) << " " << Fcast_impl_error(j) << " ";
if (active(Fcast_impl_error))
{
active_count++;
SS_smry << CoVar(active_count, 1) << " Act ";
}
else
{
SS_smry << 0.0 << " Fix ";
}
SS_smry << (Fcast_impl_error(j) - (-1.)) / (1.0 - (-1.0) + 1.0e-6) << endl;
}
}
}
if (N_init_F > 0)
{
SS_smry << "#_Init_F" << endl;
for (j = 1; j <= N_init_F; j++)
{
NP++;
SS_smry << ParmLabel(NP) << " " << init_F(j) << " ";
if (active(init_F(j)))
{
active_count++;
SS_smry << CoVar(active_count, 1) << " Act ";
}
else
{
SS_smry << 0.0 << " Fix ";
}
SS_smry << (init_F(j) - init_F_LO(j)) / (init_F_HI(j) - init_F_LO(j) + 1.0e-6) << endl;
}
}
if (N_Fparm > 0)
{
SS_smry << "#_F" << endl;
for (j = 1; j <= N_Fparm; j++)
{
NP++;
SS_smry << ParmLabel(NP) << " " << F_rate(j) << " ";
if (active(F_rate(j)))
{
active_count++;
SS_smry << CoVar(active_count, 1) << " Act ";
}
else
{
SS_smry << 0.0 << " Fix ";
}
SS_smry << (F_rate(j) - 0.) / (max_harvest_rate - 0 + 1.0e-6) << endl;
}
}
if (Q_Npar2 > 0)
{
SS_smry << "#_Catchability" << endl;
for (j = 1; j <= Q_Npar2; j++)
{
NP++;
SS_smry << ParmLabel(NP) << " " << Q_parm(j) << " ";
if (active(Q_parm(j)))
{
active_count++;
SS_smry << CoVar(active_count, 1) << " Act ";
}
else
{
SS_smry << 0.0 << " Fix ";
}
SS_smry << (Q_parm(j) - Q_parm_LO(j)) / (Q_parm_HI(j) - Q_parm_LO(j) + 1.0e-6) << endl;
}
}
SS_smry << "#_Selectivity" << endl;
if (N_selparm2 > 0)
for (j = 1; j <= N_selparm2; j++)
{
NP++;
SS_smry << ParmLabel(NP) << " " << selparm(j) << " ";
if (active(selparm(j)))
{
active_count++;
SS_smry << CoVar(active_count, 1) << " Act ";
}
else
{
SS_smry << 0.0 << " Fix ";
}
SS_smry << (selparm(j) - selparm_LO(j)) / (selparm_HI(j) - selparm_LO(j) + 1.0e-6) << endl;
}
if (Do_TG > 0)
{
SS_smry << "#_Tag_Recapture" << endl;
for (j = 1; j <= 3 * N_TG + 2 * Nfleet1; j++)
{
NP++;
SS_smry << ParmLabel(NP) << " " << TG_parm(j) << " ";
if (active(TG_parm(j)))
{
active_count++;
SS_smry << CoVar(active_count, 1) << " Act ";
}
else
{
SS_smry << 0.0 << " Fix ";
}
SS_smry << (TG_parm(j) - TG_parm_LO(j)) / (TG_parm_HI(j) - TG_parm_LO(j) + 1.0e-6) << endl;
}
}
if (N_parm_dev > 0)
{
SS_smry << "#_Parm_Dev" << endl;
for (i = 1; i <= N_parm_dev; i++)
for (j = parm_dev_minyr(i); j <= parm_dev_maxyr(i); j++)
{
NP++;
SS_smry << ParmLabel(NP) << " " << parm_dev(i, j) << " ";
if (parm_dev_PH(i) > 0)
{
active_count++;
SS_smry << CoVar(active_count, 1) << " ACT ";
}
else
{
SS_smry << 0.0 << " FIX ";
}
SS_smry << (parm_dev(i, j) - (-10.)) / (10. - (-10) + 1.0e-6) << endl;
}
}
SS_smry << "#_Derived_Quantities" << endl;
SS_smry << "#_Spawn_Bio" << endl;
for (j = 1; j <= N_STD_Yr; j++)
{
NP++;
active_count++;
SS_smry << ParmLabel(NP) << " " << SSB_std(j) << " " << CoVar(active_count, 1) << endl;
}
SS_smry << "#_Recruitment" << endl;
for (j = 1; j <= N_STD_Yr; j++)
{
NP++;
active_count++;
SS_smry << ParmLabel(NP) << " " << recr_std(j) << " " << CoVar(active_count, 1) << endl;
}
SS_smry << "#_SPR Basis= " << SPR_report_label << endl;
for (j = 1; j <= N_STD_Yr_Ofish; j++)
{
NP++;
active_count++;
SS_smry << ParmLabel(NP) << " " << SPR_std(j) << " " << CoVar(active_count, 1) << endl;
}
SS_smry << "#_F Basis= " << F_report_label << endl;
for (j = 1; j <= N_STD_Yr_F; j++)
{
NP++;
active_count++;
SS_smry << ParmLabel(NP) << " " << F_std(j) << " " << CoVar(active_count, 1) << endl;
}
SS_smry << "#_Depletion Basis= " << depletion_basis_label << endl;
for (j = 1; j <= N_STD_Yr_Dep; j++)
{
NP++;
active_count++;
SS_smry << ParmLabel(NP) << " " << depletion(j) << " " << CoVar(active_count, 1) << endl;
}
SS_smry << "#_Mgmt_Quantity" << endl;
for (j = 1; j <= N_STD_Mgmt_Quant; j++)
{
NP++;
active_count++;
SS_smry << ParmLabel(NP) << " " << Mgmt_quant(j) << " " << CoVar(active_count, 1) << endl;
}
SS_smry << "#_Extra_stdev" << endl;
for (j = 1; j <= Extra_Std_N; j++)
{
NP++;
active_count++;
SS_smry << ParmLabel(NP) << " " << Extra_Std(j) << " " << CoVar(active_count, 1) << endl;
}
if (Do_se_smrybio == 0)
{
SS_smry << "SmryBio_Virgin " << Smry_Table(styr - 2, 2) << " 0.0" << endl;
SS_smry << "SmryBio_Initial " << Smry_Table(styr - 1, 2) << " 0.0" << endl;
for (y = styr; y <= YrMax; y++)
{
SS_smry << "SmryBio_" << y << " " << Smry_Table(y, 2) << " 0.0" << endl;
}
}
SS_smry << "#_survey_stdev " << Svy_N_sdreport << endl;
if (Svy_N_sdreport > 0)
{
k = 0;
for (f = 1; f <= Nfleet; ++f)
{
if (Svy_sdreport(f) > 0)
{
for (j = 1; j <= Svy_N_fleet(f); j++)
{
active_count++;
k++;
NP++;
if (Svy_errtype(f) == -1)
{
SS_smry << ParmLabel(NP) << " " << Svy_sdreport_est(k) << " " << CoVar(active_count, 1) << " #: " << Svy_est(f, j) << " q: " << Svy_q(f, j) << endl;
}
else
{
SS_smry << ParmLabel(NP) << " " << Svy_sdreport_est(k) << " " << CoVar(active_count, 1) << " #exp(): " << mfexp(Svy_est(f, j)) << " q: " << Svy_q(f, j) << endl;
}
}
}
}
}
SS_smry << "#_Biomass" << endl;
SS_smry << "TotBio_Virgin " << Smry_Table(styr - 2, 1) << " 0.0" << endl;
SS_smry << "TotBio_Initial " << Smry_Table(styr - 1, 1) << " 0.0" << endl;
for (y = styr; y <= YrMax; y++)
{
SS_smry << "TotBio_" << y << " " << Smry_Table(y, 1) << " 0.0" << endl;
}
SS_smry << "TotCatch_Virgin " << Smry_Table(styr - 2, 4) << " 0.0" << endl;
SS_smry << "TotCatch_Initial " << Smry_Table(styr - 1, 4) << " 0.0" << endl;
for (y = styr; y <= YrMax; y++)
{
SS_smry << "TotCatch_" << y << " " << Smry_Table(y, 4) << " 0.0" << endl;
}
// report2 <<runnumber<<" Timeseries TotBio "<<column(Smry_Table,1)<<endl;
// report2 <<runnumber<<" Timeseries SmryBio-"<<Smry_Age<<" "<<column(Smry_Table,2)<<endl;
// report2 <<runnumber<<" Timeseries TotCatch "<<column(Smry_Table,4)<<endl;
// report2 <<runnumber<<" Timeseries RetCatch "<<column(Smry_Table,5)<<endl;
SS_smry.close();
echoinput << "Finished SS_summary.sso" << endl;
return;
}
//********************************************************************
/* SS_Label_FUNCTION 37 write_rebuilder_output */
FUNCTION void write_rebuilder_output()
{
if (rundetail > 0 && mceval_counter == 0)
cout << " produce output for rebuilding package" << endl;
rebuilder.open(sso_pathname + "rebuild.sso", ios::app);
rebuild_dat.open(sso_pathname + "rebuild.dat");
if (mceval_counter == 0) // writing to rebuild.dat
{
rebuild_dat << "#Title, #runnumber: " << runnumber << " " << datfilename << " " << ctlfilename << " " << obj_fun << " " << SSB_yr(styr - 2) << " " << SSB_yr(endyr + 1) << " StartTime: " << ctime(&start);
rebuild_dat << "SSv3_default_rebuild.dat" << endl;
rebuild_dat << "# Number of sexes" << endl
<< gender << endl;
rebuild_dat << "# Age range to consider (minimum age; maximum age)" << endl
<< 0 << " " << nages << endl;
rebuild_dat << "# Number of fleets" << endl
<< Nfleet1 << endl;
rebuild_dat << "# First year of projection (Yinit)" << endl
<< Rebuild_Yinit << endl;
rebuild_dat << "# First Year of rebuilding period (Ydecl)" << endl
<< Rebuild_Ydecl << endl;
rebuild_dat << "# Number of simulations" << endl
<< 1000 << endl;
rebuild_dat << "# Maximum number of years" << endl
<< 500 << endl;
rebuild_dat << "# Conduct projections with multiple starting values (0=No;else yes)" << endl
<< 0 << endl;
rebuild_dat << "# Number of parameter vectors" << endl
<< 1000 << endl;
rebuild_dat << "# Is the maximum age a plus-group (1=Yes;2=No)" << endl
<< 1 << endl;
rebuild_dat << "# Generate future recruitments using historical recruitments (1) historical recruits/spawner (2) or a stock-recruitment (3)" << endl
<< 3 << endl;
rebuild_dat << "# Constant fishing mortality (1) or constant Catch (2) projections" << endl
<< 1 << endl;
rebuild_dat << "# Fishing mortality based on SPR (1) or actual rate (2)" << endl
<< 1 << endl;
rebuild_dat << "# Pre-specify the year of recovery (or -1) to ignore" << endl
<< -1 << endl;
rebuild_dat << "# Fecundity-at-age" << endl;
}
// stuff written to both rebuild.dat and rebuild.SSO
//a. "blank line" with run info
if (mceval_phase())
rebuilder << "# mceval phase, cnt=" << mceval_counter << ", StartTime: " << ctime(&start);
else
rebuilder << "# in maximization mode, StartTime: " << ctime(&start);
if (mceval_counter == 0)
rebuild_dat << "#" << age_vector << " #runnumber: " << runnumber << " " << datfilename << " " << ctlfilename << " " << obj_fun << " " << SSB_yr(styr - 2) << " " << SSB_yr(endyr + 1) << endl;
//b. fecundity-at-age
t = styr + (Rebuild_Yinit - styr) * nseas;
dvar_vector tempvec2(0, nages);
dvar_vector tempvec3(0, nages);
tempvec_a.initialize();
tempvec2.initialize();
for (p = 1; p <= pop; p++)
for (g = 1; g <= gmorph; g++)
if (sx(g) == 1)
{
// NEED to adjust for spawning timing within season
tempvec_a += elem_prod(fec(g), natage(t + spawn_seas - 1, p, g));
tempvec2 += natage(t + spawn_seas - 1, p, g);
}
tempvec_a = elem_div(tempvec_a, tempvec2);
rebuilder << tempvec_a << " #female fecundity; weighted by N in year Y_init across morphs and areas" << endl;
if (mceval_counter == 0)
{
rebuild_dat << tempvec_a << " #female fecundity; weighted by N in year Y_init across morphs and areas" << endl;
rebuild_dat << "# Age specific selectivity and weight adjusted for discard and discard mortality" << endl;
}
//c. Weight-at-age and selectivity-at-age (ordered by sex and fleet).
// use the deadfish vectors that account for discard and for mortality of discards
// average across morphs and areas using N_at_Age in year Yinit and across seasons using Fcast_RelF
for (gg = 1; gg <= gender; gg++)
for (f = 1; f <= Nfleet1; f++)
{
tempvec_a.initialize();
tempvec2.initialize();
tempvec3.initialize();
j = 0;
for (s = 1; s <= nseas; s++)
for (p = 1; p <= pop; p++)
if (fleet_area(f) == p && Fcast_RelF_Use(s, f) > 0.0) // active fishery in this area in endyr
{
j = 1;
for (g = 1; g <= gmorph; g++)
if (sx(g) == gg)
{
tempvec_a += elem_prod(Wt_Age_t(t, f, g), natage(t + s - 1, p, g) * Fcast_RelF_Use(s, f)); // body wt
tempvec2 += elem_prod(sel_num(s, f, g), natage(t + s - 1, p, g) * Fcast_RelF_Use(s, f)); //no wt
tempvec3 += natage(t + s - 1, p, g) * Fcast_RelF_Use(s, f);
}
}
if (j == 1)
{
tempvec_a = elem_div(tempvec_a, tempvec3);
tempvec2 = elem_div(tempvec2, tempvec3);
rebuilder << tempvec_a << " #bodywt for gender,fleet: " << gg << " / " << f << " " << fleetname(f) << endl;
rebuilder << tempvec2 << " #selex for gender,fleet: " << gg << " / " << f << " " << fleetname(f) << endl;
if (mceval_counter == 0)
{
rebuild_dat << " #wt and selex for gender,fleet: " << gg << " " << f << " " << fleetname(f) << endl;
rebuild_dat << tempvec_a << endl
<< tempvec2 << endl;
}
}
}
if (mceval_counter == 0)
{
rebuild_dat << "# Sex ratio correction" << endl;
if (gender_rd < 0)
{rebuild_dat << fracfemale << endl;} // where fracfemale is set to the sexratio parameter value
else
{rebuild_dat << "1" << endl;} // value to indicate not used
}
//d. Natural mortality and numbers-at-age for year Yinit (females then males).
if (mceval_counter == 0)
rebuild_dat << "# M and current age-structure in year Yinit: " << Rebuild_Yinit << endl;
for (gg = 1; gg <= gender; gg++)
{
tempvec_a.initialize();
tempvec2.initialize();
tempvec3.initialize();
for (p = 1; p <= pop; p++)
{
for (g = 1; g <= gmorph; g++)
if (sx(g) == gg && use_morph(g) > 0)
{
tempvec_a += elem_prod(natM(t, p, GP3(g)), natage(t, p, g));
tempvec2 += natage(t, p, g); // note, uses season 1 only
}
}
tempvec_a = elem_div(tempvec_a, tempvec2);
rebuilder << tempvec_a << " #mean M for year Yinit: " << Rebuild_Yinit << " sex: " << gg << endl;
rebuilder << tempvec2 << " #numbers for year Yinit: " << Rebuild_Yinit << " sex: " << gg << endl;
if (mceval_counter == 0)
rebuild_dat << " # gender = " << gg << endl
<< tempvec_a << endl
<< tempvec2 << endl;
}
//e. Numbers-at-age for year Ydecl (females then males).
t = styr + (Rebuild_Ydecl - styr) * nseas;
if (mceval_counter == 0)
rebuild_dat << "# Age-structure at Ydeclare= " << Rebuild_Ydecl << endl;
for (gg = 1; gg <= gender; gg++)
{
tempvec_a.initialize();
tempvec2.initialize();
tempvec3.initialize();
for (p = 1; p <= pop; p++)
{
for (g = 1; g <= gmorph; g++)
if (sx(g) == gg && use_morph(g) > 0)
{
tempvec2 += natage(t, p, g);
}
}
rebuilder << tempvec2 << " #numbers for year Ydeclare: " << Rebuild_Ydecl << " sex: " << gg << endl;
if (mceval_counter == 0)
rebuild_dat << tempvec2 << endl;
}
k = endyr;
if (Rebuild_Yinit > k)
k = Rebuild_Yinit;
//f. "blank line" used for header for following lines
rebuilder << "#R0 " << years << " #years" << endl;
//g. recruitment
rebuilder << exp_rec(styr - 2, 4) << " ";
for (y = styr; y <= k; y++)
{
rebuilder << exp_rec(k, 4) << " ";
}
rebuilder << " #Recruits" << endl;
//h. spawnbio
rebuilder << SSB_yr(styr - 2) << " " << SSB_yr(styr, k) << " #SpawnBio" << endl;
//i. steepness; SigmaR; rho
rebuilder << SR_parm(2) << " " << sigmaR << " " << SR_parm(N_SRparm2) << " # spawn-recr steepness, sigmaR, autocorr" << endl;
if (mceval_counter == 0)
{
rebuild_dat << "# Year for Tmin Age-structure (set to Ydecl by SS)" << endl
<< Rebuild_Ydecl << endl;
rebuild_dat << "# recruitment and biomass" << endl
<< "# Number of historical assessment years" << endl