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SS_benchfore.tpl
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SS_benchfore.tpl
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// SS_Label_file #14. **SS_benchfore.tpl**
// SS_Label_file # * <u>setup_Benchmark()</u> // calculates average biology and selectivity over specified range of years for use in benchmark
// SS_Label_file # * <u>get_benchmark()</u> // searches for Fspr, Fmsy, etc. conditioned on average biology and selectivity conditions
// SS_Label_file # * <u>get_forecast()</u> // calculates forecast quantities, includes all popdy characteristics of the time series, writes forecast-report.sso
// SS_Label_file #
FUNCTION void setup_Benchmark() // and forecast
{
// SS_Label_Info_7.5 #Get averages from selected years to use in forecasts
if (Do_Forecast > 0)
{
if (Fcast_timevary_Selex == 1)
{
// SS_Label_Info_7.5.1 #Calc average selectivity to use in forecast; store in endyr+1
temp = float(Fcast_Sel_yr2 - Fcast_Sel_yr1 + 1.);
for (gg = 1; gg <= gender; gg++)
for (f = 1; f <= Nfleet; f++)
{
tempvec_l.initialize();
for (y = Fcast_Sel_yr1; y <= Fcast_Sel_yr2; y++)
{
tempvec_l += sel_l(y, f, gg);
}
for (y = endyr + 1; y <= YrMax; y++)
{
sel_l(y, f, gg) = tempvec_l / temp;
}
tempvec_l.initialize();
for (y = Fcast_Sel_yr1; y <= Fcast_Sel_yr2; y++)
{
tempvec_l += sel_l_r(y, f, gg);
}
for (y = endyr + 1; y <= YrMax; y++)
{
sel_l_r(y, f, gg) = tempvec_l / temp;
}
tempvec_l.initialize();
for (y = Fcast_Sel_yr1; y <= Fcast_Sel_yr2; y++)
{
tempvec_l += discmort2(y, f, gg);
}
for (y = endyr + 1; y <= YrMax; y++)
{
discmort2(y, f, gg) = tempvec_l / temp;
}
if (gg == gender) // vectors processed here have males stacked after females in same row
{
exp_l_temp.initialize();
for (y = Fcast_Sel_yr1; y <= Fcast_Sel_yr2; y++)
{
exp_l_temp += retain(y, f);
}
for (y = endyr + 1; y <= YrMax; y++)
{
retain(y, f) = exp_l_temp / temp;
}
exp_l_temp.initialize();
for (y = Fcast_Sel_yr1; y <= Fcast_Sel_yr2; y++)
{
exp_l_temp += discmort(y, f);
}
for (y = endyr + 1; y <= YrMax; y++)
{
discmort(y, f) = exp_l_temp / temp;
}
}
tempvec_a.initialize();
for (y = Fcast_Sel_yr1; y <= Fcast_Sel_yr2; y++)
{
tempvec_a += sel_a(y, f, gg);
}
for (y = endyr + 1; y <= YrMax; y++)
{
sel_a(y, f, gg) = tempvec_a / temp;
}
tempvec_a.initialize();
for (y = Fcast_Sel_yr1; y <= Fcast_Sel_yr2; y++)
{
tempvec_a += discmort2_a(y, f, gg);
}
for (y = endyr + 1; y <= YrMax; y++)
{
discmort2_a(y, f, gg) = tempvec_a / temp;
}
if (seltype(f + Nfleet, 2) > 0) // using age retention
{
tempvec_a.initialize();
for (y = Fcast_Sel_yr1; y <= Fcast_Sel_yr2; y++)
{
tempvec_a += retain_a(y, f, gg);
}
for (y = endyr + 1; y <= YrMax; y++)
{
retain_a(y, f, gg) = tempvec_a / temp;
}
tempvec_a.initialize();
for (y = Fcast_Sel_yr1; y <= Fcast_Sel_yr2; y++)
{
tempvec_a += discmort_a(y, f, gg);
}
for (y = endyr + 1; y <= YrMax; y++)
{
discmort_a(y, f, gg) = tempvec_a / temp;
}
}
}
}
t = styr + (endyr + 1 - styr) * nseas + spawn_seas - 1;
fec = Wt_Age_t(t, -2);
// for (g=1;g<=gmorph;g++)
// if(use_morph(g)>0 && sx(g)==1)
// {
// fec(g)=save_sel_num(t,0,g);
// }
if (Fcast_Loop_Control(3) == 3) // using mean recr_dist from range of years
{
warnstream << "This option (mean recruitment) may be deprecated; same as forecast option(5), averaging parameters, type 4.";
write_message(WARN, 0);
//get average and store in each fcast years
recr_dist_endyr.initialize();
for (y = Fcast_Rec_yr1; y <= Fcast_Rec_yr2; y++)
for (gp = 1; gp <= N_GP * gender; gp++)
{
recr_dist_endyr(gp) += recr_dist(y, gp);
}
recr_dist_endyr /= float(Fcast_Rec_yr2 - Fcast_Rec_yr1 + 1);
for (y = endyr + 1; y <= YrMax; y++)
{
if (timevary_MG(y, 4) > 0)
{
warnstream << "mean recr_dist for forecast is incompatible with timevary recr_dist in forecast yr: " << y << "; user must adjust manually";
write_message(WARN, 0);
}
recr_dist(y) = recr_dist_endyr;
}
}
else // provide placeholder
{
recr_dist_endyr = recr_dist(endyr);
}
// create average of selected MGparms for use in forecast
for (int parm_type = 1; parm_type <= 12; parm_type++)
{
if(Fcast_MGparm_ave(parm_type, 2) == 1) // do averaging of derived factor
{
double ave_styr = Fcast_MGparm_ave(parm_type,3);
double ave_endyr = Fcast_MGparm_ave(parm_type,4);
double N_ave_yrs = ave_endyr - ave_styr + 1.; // get denominator
switch (parm_type)
{
case 1: // 1=Natural mortality (M),
for (int s = 1; s <= nseas; s++)
for (int g = 1; g <= gmorph; g++)
{
int gpi = GP3(g);
for (int p = 0; p <= pop; p++) // question. Perhaps only do this for area 0 as others filled in later in code
{
tempvec_a.initialize();
for (y = ave_styr; y <= ave_endyr; y++)
{
t = styr + (y - styr) * nseas - 1 + s;
tempvec_a += natM(t, p, gpi);
}
tempvec_a /= N_ave_yrs;
for (int y = endyr + 1; y <= YrMax; y++)
{
t = styr + (y - styr) * nseas - 1 + s;
natM(t, p, gpi) = tempvec_a;
}
}
}
break;
case 2: // 2=growth,
tempvec_a.initialize();
warnstream << "Growth params averaging is not implemented, execution continues. " ;
write_message (WARN, 1);
break;
case 3: // 3=wtlen,
tempvec_a.initialize();
warnstream << "Weight/Length params averaging is not implemented, execution continues. " ;
write_message (WARN, 1);
break;
case 4: // 4=recr_dist&femfrac,
//get average and store in each fcast years
recr_dist_endyr.initialize();
for (y = ave_styr; y <= ave_endyr; y++)
for (gp = 1; gp <= N_GP * gender; gp++)
{
recr_dist_endyr(gp) += recr_dist(y, gp);
}
recr_dist_endyr /= N_ave_yrs;
for (y = endyr + 1; y <= YrMax; y++)
{
if (timevary_MG(y, 4) > 0)
{
warnstream << "mean recr_dist for forecast is incompatible with timevary recr_dist in forecast yr: " << y << "; user must adjust manually";
write_message(WARN, 0);
}
recr_dist(y) = recr_dist_endyr;
}
break;
case 5: // 5=migration,
for (j = 1; j <= do_migr2; j++)
{
tempvec_a.initialize();
for (y = ave_styr; y <= ave_endyr; y++)
{
tempvec_a += migrrate(y, j);
}
tempvec_a /= N_ave_yrs;
for (y = endyr + 1; y <= YrMax; y++)
migrrate(y, j) = tempvec_a;
}
break;
case 6: // 6=ageerror,
tempvec_a.initialize();
warnstream << "Age Error params averaging is not implemented, execution continues. " ;
write_message (WARN, 1);
break;
case 7: // 7=catchmult,
tempvec_a.initialize();
warnstream << "Catch mult params averaging is not implemented, execution continues. " ;
write_message (WARN, 1);
break;
case 8: // 8=hermaphroditism, and
tempvec_a.initialize();
warnstream << "Hermaphroditism params averaging is not implemented, execution continues. " ;
write_message (WARN, 1);
break;
case 9: // 9=maturity&fecundity
tempvec_a.initialize();
warnstream << "Maturity & fecundity params averaging is not implemented, execution continues. " ;
write_message (WARN, 1);
break;
case 10: // 9=selectivity
tempvec_a.initialize();
break;
}
}
}
// SS_Label_Info_7.5.2 #Set-up relative F among fleets and seasons for forecast
if (Fcast_RelF_Basis == 1) // set allocation according to range of years
{
temp = 0.0;
Fcast_RelF_Use.initialize();
for (int ff = 1; ff <= N_catchfleets(0); ff++)
{
f = fish_fleet_area(0, ff);
if (fleet_type(f) == 1 || (fleet_type(f) == 2 && bycatch_setup(f, 3) == 1))
{
for (y = Fcast_RelF_yr1; y <= Fcast_RelF_yr2; y++)
for (s = 1; s <= nseas; s++)
{
t = styr + (y - styr) * nseas + s - 1;
Fcast_RelF_Use(s, f) += Hrate(f, t);
}
}
}
temp = sum(Fcast_RelF_Use);
if (temp > 0.0)
{
Fcast_RelF_Use /= temp;
Fcurr_Fmult = temp / float(Fcast_RelF_yr2 - Fcast_RelF_yr1 + 1);
}
else
{
Fcast_RelF_Use(1, 1) = 1.0;
Fcurr_Fmult = 0.0;
}
}
else // Fcast_RelF_Basis==2 so set to values that were read
{
temp = 0.0;
for (f = 1; f <= Nfleet; f++)
for (s = 1; s <= nseas; s++)
{
temp += Fcast_RelF_Input(s, f);
Fcast_RelF_Use(s, f) = Fcast_RelF_Input(s, f);
}
// Fcast_RelF_Use=Fcast_RelF_Input/temp;
Fcast_RelF_Use /= temp;
Fcurr_Fmult = temp;
}
if (N_bycatch > 0)
{
for (f = 1; f <= Nfleet; f++)
for (s = 1; s <= nseas; s++)
{
if (Fcast_RelF_Use(s, f) == 0. && bycatch_setup(f, 3) > 0)
{
Fcast_RelF_Use(s, f) = 1.0e-6;
warnstream << "setting positive forecast relF for bycatch fleet: " << f;
write_message(ADJUST, 0);
}
}
}
if (N_Fcast_Input_Catches > 0)
{
for (f = 1; f <= Nfleet; f++)
for (s = 1; s <= nseas; s++)
{
if (Fcast_RelF_special(s, f) == 1 && Fcast_RelF_Use(s, f) == 0.0)
{
Fcast_RelF_Use(s, f) = 1.0e-6;
warnstream << "setting positive forecast relF for forecast only fleet: " << f;
write_message(ADJUST, 0);
}
}
}
} // end getting quantities for forecasts
// SS_Label_Info_7.5.3 #Calc average selectivity to use in benchmarks; store in styr-3
// Bmark_Yr(1,6)<<" Benchmark years: beg-end bio; beg-end selex; beg-end alloc"<<endl;
if (Do_Benchmark > 0)
{
// if(save_for_report>0 || last_phase() || current_phase()==max_phase || ((sd_phase() || mceval_phase()) && (initial_params::mc_phase==0)))
{
// calc average biology to use in equil; store in styr-3
temp = float(Bmark_Yr(2) - Bmark_Yr(1) + 1.); // get denominator
for (g = 1; g <= gmorph; g++)
if (use_morph(g) > 0)
{
for (s = 0; s <= nseas - 1; s++) // note -1 baked into the loop index
{
tempvec_a.initialize();
for (t = Bmark_t(1); t <= Bmark_t(2); t += nseas)
{
tempvec_a += Ave_Size(t + s, 1, g);
}
Ave_Size(styr - 3 * nseas + s, 1, g) = tempvec_a / temp;
tempvec_a.initialize();
for (t = Bmark_t(1); t <= Bmark_t(2); t += nseas)
{
tempvec_a += Ave_Size(t + s, mid_subseas, g);
}
Ave_Size(styr - 3 * nseas + s, mid_subseas, g) = tempvec_a / temp;
// get mean natM
int gpi=GP3(g);
for (int p = 0; p <= pop; p++)
{
tempvec_a.initialize();
for (t = Bmark_t(1); t <= Bmark_t(2); t += nseas)
{
tempvec_a += natM(t + s, p, gpi);
}
natM(styr - 3 * nseas + s, p, gpi) = tempvec_a / temp;
if(p>0)
{
int s1 = (p - 1)*nseas + s + 1;
surv1(s1, gpi) = mfexp(-natM(styr - 3 * nseas + s, p, gpi) * seasdur_half(s + 1)); // does all the gpi and ages
surv2(s1, gpi) = square(surv1(s1, gpi));
}
}
for (int kk = -2; kk <= 0; kk++) // get mean fecundity and pop body wt
{
tempvec_a.initialize();
for (t = Bmark_t(1); t <= Bmark_t(2); t += nseas)
{
tempvec_a += Wt_Age_t(t + s, kk, g);
}
Wt_Age_t(styr - 3 * nseas + s, kk, g) = tempvec_a / temp;
}
for (f = 1; f <= Nfleet; f++)
{
tempvec_a.initialize();
for (t = Bmark_t(1); t <= Bmark_t(2); t += nseas)
{
tempvec_a += save_sel_num(t + s, f, g);
}
save_sel_num(styr - 3 * nseas + s, f, g) = tempvec_a / temp;
}
}
}
if (pop > 0)
{
if (do_migration > 0)
{
temp = float(Bmark_Yr(8) - Bmark_Yr(7) + 1.); // get denominator
for (j = 1; j <= do_migr2; j++)
{
tempvec_a.initialize();
for (y = Bmark_Yr(7); y <= Bmark_Yr(8); y++)
{
tempvec_a += migrrate(y, j);
}
migrrate(styr - 3, j) = tempvec_a / temp;
}
}
// recr_dist_unf is accumulated while doing the time_series
// then its mean is calculated in Get_Benchmarks and assigned to recr_dist
// the SR_parm_bench is calculated from Bmark_yrs 9-10 in benchmark code using values stored in SR_parm_byyr
}
// calc average selectivity to use in equil; store in styr-3
temp = float(Bmark_Yr(4) - Bmark_Yr(3) + 1.); // get denominator
for (gg = 1; gg <= gender; gg++)
for (f = 1; f <= Nfleet; f++)
{
tempvec_l.initialize();
for (y = Bmark_Yr(3); y <= Bmark_Yr(4); y++)
{
tempvec_l += sel_l(y, f, gg);
}
sel_l(styr - 3, f, gg) = tempvec_l / temp;
tempvec_l.initialize();
for (y = Bmark_Yr(3); y <= Bmark_Yr(4); y++)
{
tempvec_l += sel_l_r(y, f, gg);
}
sel_l_r(styr - 3, f, gg) = tempvec_l / temp;
if (gg == gender)
{
exp_l_temp.initialize(); // use because dimensioned to nlength2
for (y = Bmark_Yr(3); y <= Bmark_Yr(4); y++)
{
exp_l_temp += retain(y, f);
}
retain(styr - 3, f) = exp_l_temp / temp;
exp_l_temp.initialize();
for (y = Bmark_Yr(3); y <= Bmark_Yr(4); y++)
{
exp_l_temp += discmort(y, f);
}
discmort(styr - 3, f) = exp_l_temp / temp;
}
tempvec_l.initialize();
for (y = Bmark_Yr(3); y <= Bmark_Yr(4); y++)
{
tempvec_l += discmort2(y, f, gg);
}
discmort2(styr - 3, f, gg) = tempvec_l / temp;
tempvec_a.initialize();
for (y = Bmark_Yr(3); y <= Bmark_Yr(4); y++)
{
tempvec_a += sel_a(y, f, gg);
}
sel_a(styr - 3, f, gg) = tempvec_a / temp;
tempvec_a.initialize();
for (y = Bmark_Yr(3); y <= Bmark_Yr(4); y++)
{
tempvec_a += discmort2_a(y, f, gg);
}
discmort2_a(styr - 3, f, gg) = tempvec_a / temp;
if (seltype(f + Nfleet, 2) > 0) // using age retention
{
tempvec_a.initialize();
for (y = Bmark_Yr(3); y <= Bmark_Yr(4); y++)
{
tempvec_a += retain_a(y, f, gg);
}
retain_a(styr - 3, f, gg) = tempvec_a / temp;
tempvec_a.initialize();
for (y = Bmark_Yr(3); y <= Bmark_Yr(4); y++)
{
tempvec_a += discmort_a(y, f, gg);
}
discmort_a(styr - 3, f, gg) = tempvec_a / temp;
}
}
// set-up relative F among fleets and seasons
if (Bmark_RelF_Basis == 1) // set allocation according to range of years
{
temp = 0.0;
Bmark_RelF_Use.initialize();
Bmark_HistF.initialize();
for (y = Bmark_Yr(5); y <= Bmark_Yr(6); y++)
for (f = 1; f <= Nfleet; f++)
if (fleet_type(f) == 1 || (fleet_type(f) == 2 && bycatch_setup(f, 3) == 1))
for (s = 1; s <= nseas; s++)
{
t = styr + (y - styr) * nseas + s - 1;
Bmark_HistF(s, f) += Hrate(f, t);
Bmark_RelF_Use(s, f) += Hrate(f, t);
}
Bmark_HistF /= float(Bmark_Yr(6) - Bmark_Yr(5) + 1.); // average F(s,f) across benchmark years
temp = sum(Bmark_RelF_Use);
// note that the relF calculation below is not conditional on whether a fleet is not bycatch and not non-optimized
// Fmult later calculated as multiplier times Bmark_relF_use and will compensate automatically
if (temp > 0.0)
{
Bmark_RelF_Use /= temp;
}
else
{
Bmark_RelF_Use(1, 1) = 1.0;
}
}
else // Bmark_RelF_Basis==2 so set same as forecast
{
Bmark_RelF_Use = Fcast_RelF_Use;
}
} // end being in a phase for these calcs
} // end getting quantities for benchmarks
}
FUNCTION void Get_Benchmarks(const int show_MSY)
{
//********************************************************************
/* SS_Label_FUNCTION 34 Get_Benchmarks(Find Fspr, MSY) */
int jj;
int Nloops;
int Nloops2;
// int bio_t;
int bio_t_base;
dvariable last_F1;
dvariable Closer;
dvariable Vbio1_unfished;
dvariable SPR_unfished;
dvariable Vbio_MSY;
dvariable Vbio1_MSY;
dvariable junk;
dvariable Nmid_c;
dvariable df;
dvariable BestYield;
dvariable BestF1;
dvariable FF;
dvariable dyld;
dvariable dyldp;
dvariable Fmax;
dvariable bestF1;
dvariable bestF2;
dvariable F01_origin;
dvariable F01_second;
dvariable F01_actual;
dvar_vector F1(1, 3);
dvar_vector F2(1, 3);
dvar_vector yld1(1, 3);
dvar_vector Fmult_save(1, 3);
write_bodywt_save = write_bodywt;
write_bodywt = 0;
Nloops2 = 0;
y = styr - 3; // the average biology from specified benchmark years is stored here
yz = y;
bio_yr = y;
eq_yr = y;
t_base = y + (y - styr) * nseas - 1;
bio_t_base = styr + (bio_yr - styr) * nseas - 1;
// set the Hrate for bycatch fleets so not scaled with other fleets
// bycatch_F(f,s) is created here for use in forecast
for (f = 1; f <= Nfleet; f++)
{
if (fleet_type(f) == 2 && bycatch_setup(f, 3) == 2) // set rate to input value
{
for (s = 1; s <= nseas; s++)
{
t = bio_t_base + s;
Hrate(f, t) = bycatch_setup(f, 4);
bycatch_F(f, s) = bycatch_setup(f, 4);
}
}
else if (fleet_type(f) == 2 && bycatch_setup(f, 3) == 3) // set rate to historical mean
{
for (s = 1; s <= nseas; s++)
{
t = bio_t_base + s;
Hrate(f, t) = 0.0;
for (int yy = bycatch_setup(f, 4); yy <= bycatch_setup(f, 5); yy++)
{
Hrate(f, t) += Hrate(f, styr + (yy - styr) * nseas + s - 1);
}
Hrate(f, t) /= (bycatch_setup(f, 5) - bycatch_setup(f, 4) + 1.);
bycatch_F(f, s) = Hrate(f, t);
}
}
else
{
for (s = 1; s <= nseas; s++)
{
t = bio_t_base + s;
Hrate(f, t) = 0.0;
}
}
}
if (show_MSY == 1)
{
report5 << version_info << endl
<< ctime(&start);
report5 << "Bmark_relF(by_fleet_&seas) (excluding non-scaled bycatch fleets)" << endl
<< Bmark_RelF_Use << endl
<< "#" << endl;
report5 << "Bmark_histF(by_fleet_&seas)" << endl
<< Bmark_HistF << endl
<< "#" << endl;
report5 << "Bycatch_F" << endl
<< trans(bycatch_F) << endl
<< "#" << endl;
report5 << "YPR_mask for including catch: " << endl
<< YPR_mask << endl;
}
if (show_MSY == 2)
{
// do not recalc the age-specific vectors
}
else // recalc age specific biology and selectivity. NOTE: not density-dependent!!
{
for (s = 1; s <= nseas; s++)
{
t = styr - 3 * nseas + s - 1;
subseas = 1; // for begin of season
ALK_idx = (s - 1) * N_subseas + subseas;
ALK_subseas_update(ALK_idx) = 1; // new in 3.30.12 force updating
Make_AgeLength_Key(s, subseas); // begin season
subseas = mid_subseas;
ALK_idx = (s - 1) * N_subseas + subseas;
ALK_subseas_update(ALK_idx) = 1; // new in 3.30.12 force updating
Make_AgeLength_Key(s, subseas);
// SPAWN-RECR: call make_fecundity for benchmarks
if (s == spawn_seas)
{
{
fec = Wt_Age_t(styr - 3 * nseas + s - 1, -2);
}
}
Wt_Age_beg(s) = Wt_Age_t(styr - 3 * nseas + s - 1, 0);
}
// following uses the values of sel_l, sel_a, etc. stored in yr=styr-3
for (s = 1; s <= nseas; s++)
for (g = 1; g <= gmorph; g++)
if (use_morph(g) > 0)
{
ALK_idx = (s - 1) * N_subseas + mid_subseas; // for midseason
Make_FishSelex(); // including sel_dead_num
}
if (show_MSY == 1)
{
report5 << version_info << endl
<< ctime(&start);
report5 << "Bmark_relF(by_fleet_&seas) (excluding non-scaled bycatch fleets)" << endl
<< Bmark_RelF_Use << endl
<< "#" << endl;
report5 << "Bmark_histF(by_fleet_&seas)" << endl
<< Bmark_HistF << endl
<< "#" << endl;
report5 << "Bycatch_F" << endl
<< trans(bycatch_F) << endl
<< "#" << endl;
report5 << "YPR_mask for including catch: " << endl
<< YPR_mask << endl;
report5 << "Fecundity: " << fec(1) << endl;
for (f = 1; f <= Nfleet; f++)
{
if (fleet_type(f) <= 2)
{
for (s = 1; s <= nseas; s++)
{
report5 << f << " " << s << " sel_bio: " << sel_bio(s, f, 1) << endl;
report5 << f << " " << s << " sel_dead_bio: " << sel_dead_bio(s, f, 1) << endl;
}
}
}
for (f = 1; f <= Nfleet; f++)
{
if (fleet_type(f) <= 2)
{
for (s = 1; s <= nseas; s++)
report5 << f << " " << s << " sel_num: " << sel_num(s, f, 1) << endl;
}
}
for (f = 1; f <= Nfleet; f++)
{
if (fleet_type(f) <= 2)
{
for (s = 1; s <= nseas; s++)
report5 << f << " " << s << " sel_dead_num: " << sel_dead_num(s, f, 1) << endl;
}
}
}
}
maxpossF.initialize();
for (g = 1; g <= gmorph; g++)
{
for (s = 1; s <= nseas; s++)
{
tempvec_a.initialize();
for (f = 1; f <= Nfleet; f++)
{
tempvec_a += Bmark_RelF_Use(s, f) * sel_dead_num(s, f, g);
}
temp = max(tempvec_a);
if (temp > maxpossF)
maxpossF = temp;
}
}
maxpossF = max_harvest_rate / maxpossF; // applies to any F_method
// SPAWN-RECR: notes regarding virgin vs. benchmark biology usage in spawn-recr
// the spawner-recruitment function has Bzero based on virgin biology, not benchmark biology
// need to deal with possibility that with time-varying biology, the SSB_virgin calculated from virgin conditions will differ from the SSB_virgin used for benchmark conditions
// note that recr_dist(styr-3), updated at end of ss_popdyn.
for (j = 1; j <= N_SRparm2; j++)
{
if (SR_parm_timevary(j) == 0)
{
SR_parm_work(j) = SR_parm(j);
}
else
{
temp = 0.;
for (int y = Bmark_Yr(9); y <= Bmark_Yr(10); y++)
{
temp += SR_parm_byyr(y, j);
}
SR_parm_work(j) = temp / (Bmark_Yr(10) - Bmark_Yr(9) + 1.);
}
}
Fishon = 0;
Recr_unf = mfexp(SR_parm_work(1));
Do_Equil_Calc(Recr_unf);
SSB_unf = SSB_equil;
SR_parm_work(N_SRparm2 + 1) = SSB_unf;
if (show_MSY == 1)
report5 << "SR_parm for benchmark: " << SR_parm_work << endl
<< "for years: " << Bmark_Yr(9) << " " << Bmark_Yr(10) << " SSB_virgin was: " << SSB_virgin << endl;
if (show_MSY == 1)
report5 << "Repro_output_by_age_for_morph_1: " << fec(1) << endl;
Mgmt_quant(1) = SSB_unf;
Mgmt_quant(2) = totbio;
Mgmt_quant(3) = smrybio;
Mgmt_quant(4) = Recr_unf;
// find Fspr SS_Label_710
{
if (show_MSY == 1)
{
report5 << "#" << endl
<< "find_target_SPR" << endl;
report5 << "SPR_is_spawner_potential_ratio=(fishedSSB/R)/(unfishedSSB/R))" << endl;
report5 << "Iter Fmult ann_F SPR tot_catch";
for (p = 1; p <= pop; p++)
for (gp = 1; gp <= N_GP; gp++)
{
report5 << " SSB_Area:" << p << "_GP:" << gp;
}
report5 << endl;
}
Fmult = 0.;
Nloops = 18;
Closer = 1.;
F1(1) = log(1.0e-3);
last_calc = 0.;
Fchange = -4.0;
equ_Recr = 1.0;
Fishon = 0;
dvariable SPR_target100;
SPR_target100 = SPR_target * 100.;
Do_Equil_Calc(equ_Recr);
SPR_unfished = SSB_unf / Recr_unf; // this corresponds to the biology for benchmark average years, not the virgin SSB_virgin
Vbio1_unfished = smrybio; // gets value from equil_calc
if (show_MSY == 1)
{
report5 << "0 0 0 1 0";
for (p = 1; p <= pop; p++)
for (gp = 1; gp <= N_GP; gp++)
{
report5 << " " << SSB_equil_pop_gp(p, gp);
}
report5 << endl;
}
df = 1.e-5;
Fishon = 1;
for (j = 1; j <= Nloops; j++) // loop find Fspr
{
if (fabs(Fchange) <= 0.25)
{
jj = 3;
F1(2) = F1(1) + df * .5;
F1(3) = F1(2) - df;
}
else
{
jj = 1;
}
for (int ii = jj; ii >= 1; ii--)
{
Fmult = 40.00 / (1.0 + mfexp(-F1(ii)));
for (f = 1; f <= Nfleet; f++)
{
if (fleet_type(f) == 1 || (fleet_type(f) == 2 && bycatch_setup(f, 3) == 1))
{
for (int s = 1; s <= nseas; s++)
{
Hrate(f, bio_t_base + s) = Fmult * Bmark_RelF_Use(s, f);
}
}
// else Hrate for bycatch fleets already set
}
Fishon = 1;
Do_Equil_Calc(equ_Recr);
yld1(ii) = 100. * SSB_equil / SPR_unfished; // spawning potential ratio
}
SPR_actual = yld1(1); // spawning potential ratio
if (jj == 3)
{
Closer *= 0.5;
dyld = (yld1(2) - yld1(3)) / df; // First derivative (to find the root of this)
if (dyld != 0.)
{
last_F1 = F1(1);
F1(1) += (SPR_target100 - SPR_actual) / (dyld + 0.001);
F1(1) = (1. - Closer) * F1(1) + Closer * last_F1;
} // averages with last good value to keep from changing too fast
else
{
F1(1) = (F1(1) + last_F1) * 0.5;
} // go halfway back towards previous value
}
else
{
// if((last_calc-SPR_target)*(SPR_actual-SPR_target)<0.0) {Fchange*=-0.5;} // changed sign, so reverse search direction
temp = (last_calc - SPR_target100) * (SPR_actual - SPR_target100) / (sfabs(last_calc - SPR_target100) * sfabs(SPR_actual - SPR_target100)); // values of -1 or 1
temp1 = temp - 1.; // values of -2 or 0
Fchange *= exp(temp1 / 4.) * temp;
F1(1) += Fchange;
last_calc = SPR_actual;
}
if (show_MSY == 1)
{
report5 << j << " " << Fmult << " " << equ_F_std << " " << SPR_actual / 100. << " " << sum(equ_catch_fleet(2));
for (p = 1; p <= pop; p++)
for (gp = 1; gp <= N_GP; gp++)
{
report5 << " " << SSB_equil_pop_gp(p, gp);
}
report5 << endl;
}
} // end search loop
if (show_MSY == 1)
{
if (fabs(SPR_actual - SPR_target100) >= 0.1)
{
warnstream << "poor convergence in Fspr search " << SPR_target << " " << SPR_actual / 100.;
write_message(WARN, 0);
}
if (SPR_actual / SPR_target100 >= 1.01)
{
warnstream << "Fmult = " << Fmult << " cannot get high enough to achieve low SPR target: " << SPR_target << "; SPR achieved is: " << SPR_actual / 100.;
write_message(WARN, 0);
}
report5 << "seas fleet Hrate encB deadB retB encN deadN retN: " << endl;
for (s = 1; s <= nseas; s++)
for (f = 1; f <= Nfleet; f++)
if (fleet_type(f) <= 2)
{
report5 << s << " " << f << " " << Hrate(f, bio_t_base + s);
for (g = 1; g <= 6; g++)
{
report5 << " " << equ_catch_fleet(g, s, f);
}
report5 << endl;
}
}
// SPAWN-RECR: calc equil spawn-recr in YPR; need to make this area-specific
Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work(2), SR_parm_work(3), SSB_unf, Recr_unf, SSB_equil); // returns 2 element vector containing equilibrium biomass and recruitment at this SPR
Bspr = Equ_SpawnRecr_Result(1);
Bspr_rec = Equ_SpawnRecr_Result(2);
YPR_spr_enc = YPR_enc; // total encountered yield per recruit
YPR_spr_dead = YPR_dead; // total dead yield per recruit
YPR_spr_N_dead = YPR_N_dead;
YPR_spr_ret = YPR_ret;
YPR_spr_cost = Cost;
YPR_spr_revenue = (PricePerF * YPR_val_vec) * Equ_SpawnRecr_Result(2); // vector*vector*scalar
YPR_spr_profit = YPR_spr_revenue - Cost;
SPR_Fmult = Fmult;
if (rundetail > 0 && mceval_counter == 0 && show_MSY == 1)
{
echoinput << "Calculated Fspr " << SPR_Fmult << " " << SPR_actual / 100. << endl;
}
Vbio_spr = totbio;
Vbio1_spr = smrybio;
Mgmt_quant(10) = equ_F_std;
Mgmt_quant(9) = Equ_SpawnRecr_Result(1);
Mgmt_quant(11) = YPR_dead * Equ_SpawnRecr_Result(2);
} // end finding Fspr
if (Do_Benchmark == 2) // Find F0.1
{
equ_Recr = 1.0;
Fishon = 1;
// get slope at origin
// Fmult=0.000001;
Fmult = 0.001;
for (f = 1; f <= Nfleet; f++)
{
if (fleet_type(f) == 1 || (fleet_type(f) == 2 && bycatch_setup(f, 3) == 1))
{
for (int s = 1; s <= nseas; s++)
{
Hrate(f, bio_t_base + s) = Fmult * Bmark_RelF_Use(s, f);
}
}
// else Hrate for bycatch fleets already set
}
Do_Equil_Calc(equ_Recr);
F01_origin = YPR_opt / Fmult;
BTGT_target = 0.1; // now relative to Bmark
Btgttgt = F01_origin * 0.1;
if (show_MSY == 1)
{
report5 << "#" << endl
<< "#Find_F0.1; slope_at_origin_wrt_Fmult: " << F01_origin << " " << YPR_opt << " " << Hrate(1, bio_t_base + 3) << endl;
report5 << "Iter Fmult ann_F SPR YPR YPR_slope YPR_curvature" << endl;
}
Nloops = 20;
Closer = 0.75;
F1(1) = SPR_Fmult * 0.1;
for (j = 1; j <= Nloops; j++) // loop to find F0.1
{
df = 0.01 * F1(1);
F1(2) = F1(1) + df * .5;
F1(3) = F1(2) - df;
for (int ii = 3; ii >= 1; ii--)
{
for (f = 1; f <= Nfleet; f++)
{
if (fleet_type(f) == 1 || (fleet_type(f) == 2 && bycatch_setup(f, 3) == 1))
{
for (int s = 1; s <= nseas; s++)
{
Hrate(f, bio_t_base + s) = F1(ii) * Bmark_RelF_Use(s, f);
}
} // else Hrate for bycatch fleets set above
}
Do_Equil_Calc(equ_Recr);
yld1(ii) = YPR_opt;
}
F01_actual = (yld1(2) - yld1(3)) / (F1(2) - F1(3));
F01_second = ((yld1(2) - yld1(1)) / (F1(2) - F1(1)) - (yld1(1) - yld1(3)) / (F1(1) - F1(3))) / (F1(2) - F1(3));
last_F1 = F1(1);
if (show_MSY == 1)
{
report5 << j << " " << F1(1) << " " << equ_F_std << " " << SSB_equil / SPR_unfished << " " << YPR_opt << " " << F01_actual << " " << F01_second << " last F1 " << last_F1 << " Closer " << Closer << " delta " << (F01_origin * 0.1 - F01_actual) / (F01_second) << endl;
}
F1(1) += (F01_origin * 0.1 - F01_actual) / (F01_second);
F1(1) = (1. - Closer) * F1(1) + Closer * last_F1;
Closer *= 0.75;
} // end search loop
if (show_MSY == 1)
{
if (sfabs(F01_origin * 0.1 - F01_actual) >= 0.001)
{
warnstream << "poor convergence in F0.1 search target= " << F01_origin * 0.1 << " actual= " << F01_actual;
write_message(WARN, 0);