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SS_popdyn.tpl
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SS_popdyn.tpl
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// SS_Label_file #12. **SS_popdyn.tpl**
// SS_Label_file # * <u>setup_recdevs()</u>
// SS_Label_file # * <u>get_initial_conditions()</u> // does virgin and initial year by calling <u>Do_Equil_Calc()</u> with F=0, then F=init_F
// SS_Label_file # * <u>get_time_series()</u> // loops the years, calling biology, selectivity and spawn-recr functions as needed
// SS_Label_file # * <u>Do_Equil_Calc()</u> // does per-recruit calculations and returns SSB/R and Y/R
// SS_Label_file #
FUNCTION void setup_recdevs()
{
// SS_Label_Info_7.1 #Set up recruitment bias_adjustment vector
sigmaR = SR_parm(N_SRparm(SR_fxn) + 1);
two_sigmaRsq = 2.0 * sigmaR * sigmaR;
half_sigmaRsq = 0.5 * sigmaR * sigmaR;
biasadj.initialize();
if (SR_fxn == 4 || do_recdev == 0)
{
// keep all at 0.0 if not using SR fxn
}
// else if (mceval_phase() || initial_params::mc_phase==1 || recdev_adj(5)<0.0)
else if (mceval_phase() || initial_params::mc_phase == 1)
{
// biasadj=1.0;
biasadj = recdev_doit; // sets to 1.0 for the years or initial ages with estimated recruitments
}
else
{
if (recdev_do_early > 0 && recdev_options(2) >= 0) // do logic on basis of recdev_options(2), which is read, not recdev_PH which can be reset to a neg. value
{
for (i = recdev_early_start; i <= recdev_early_end; i++)
{
if (i >= styr - nages)
biasadj(i) = biasadj_full(i);
}
}
if (do_recdev > 0 && recdev_PH_rd >= 0)
{
for (i = recdev_start; i <= recdev_end; i++)
{
if (i >= styr - nages)
biasadj(i) = biasadj_full(i);
}
}
if (Do_Forecast > 0 && recdev_options(3) >= 0)
{
for (i = recdev_end + 1; i <= YrMax; i++)
{
biasadj(i) = biasadj_full(i);
}
}
if (recdev_read > 0)
{
for (j = 1; j <= recdev_read; j++)
{
y = recdev_input(j, 1);
if (y >= recdev_first && y <= YrMax)
biasadj(y) = biasadj_full(y);
}
}
}
sd_offset_rec = sum(biasadj) * sd_offset;
// SS_Label_Info_7.2 #Copy recdev parm vectors into full time series vector
if (recdev_do_early > 0)
{
recdev(recdev_early_start, recdev_early_end) = recdev_early(recdev_early_start, recdev_early_end);
}
if (do_recdev == 1)
{
recdev(recdev_start, recdev_end) = recdev1(recdev_start, recdev_end);
}
else if (do_recdev >= 2)
{
recdev(recdev_start, recdev_end) = recdev2(recdev_start, recdev_end);
}
if (Do_Forecast > 0 && do_recdev > 0)
recdev(recdev_end + 1, YrMax) = Fcast_recruitments(recdev_end + 1, YrMax); // only needed here for reporting
} // end setup for recdevs
FUNCTION void get_initial_conditions()
{
//*********************************************************************
/* SS_Label_Function_23 #get_initial_conditions */
natage.initialize();
catch_fleet.initialize();
annual_catch.initialize();
annual_F.initialize();
Recr.initialize();
save_gparm = 0; // index for saving time-varying changes to biology quantities
if (SzFreq_Nmeth > 0)
SzFreq_exp.initialize();
// SS_Label_Info_23.1 #call biology and selectivity functions for the initial year
// SS_Label_Info_23.1.1 #These rate are calculated once in PRELIMINARY_CALCS_SECTION, so only recalculate if active according to MG_active
y = styr;
yz = styr;
t_base = styr - 1;
recr_dist_unf.initialize();
// Create time varying parameters
// following call is to routine that does this for all timevary parameters
// that are then copied over to replace the base parameter for MG, SRR, Q, Selex, or Tag as needed
make_timevaryparm(); // this fills array parm_timevary for all years; densitydependence must be done year-by-year later
if (MG_active(0) > 0 || save_for_report > 0)
{
get_MGsetup(y);
}
#ifdef DO_ONCE
if (do_once == 1)
echoinput << " MGsetup OK " << endl;
#endif
if (MG_active(2) > 0)
get_growth1(); // seasonal effects and CV
#ifdef DO_ONCE
if (do_once == 1)
echoinput << " growth1 OK" << endl;
#endif
if (MG_active(2) > 0 || do_once == 1)
{
ALK_subseas_update = 1; // to indicate that all ALKs need calculation
get_growth2(y);
t = styr - 1;
for (s = 1; s <= nseas; s++)
{
t++;
for (subseas = 1; subseas <= N_subseas; subseas++) // do all subseasons in first year
{
get_growth3(y, t, s, subseas); // in case needed for Lorenzen M
Make_AgeLength_Key(s, subseas);
}
}
// SS_Label_Info_16.2.4.3 #propagate Ave_Size from early years forward until first year that has time-vary growth
k = styr + 1;
do
{
for (s = 1; s <= nseas; s++)
{
t = styr + (k - styr) * nseas + s - 1;
Ave_Size(t, 1) = Ave_Size(t - nseas, 1);
} // end season loop
k++;
} while (timevary_MG(k, 2) == 0 && k <= YrMax);
if (k <= YrMax)
{
t = styr + (k - styr) * nseas;
Ave_Size(t, 1) = Ave_Size(t - nseas, 1); // prep for time-vary next yr
}
}
if (MG_active(3) > 0)
get_wtlen(); // stores values for all seasons
get_mat_fec(); // does just spawn season and subseason using ALK calculated just above
if (Hermaphro_Option != 0)
get_Hermaphro();
if (do_once>0 || MG_active(1) > 0)
{
get_natmort(); // gets base M (e.g. M1) by season and stores it in natM(t,0). Later, pred_M2 is added by area
for (s = 1; s <= nseas; s++)
{
natM(t_base - 2 * nseas + s) = natM(t_base + s); // copy to virgin
natM(t_base - nseas + s) = natM(t_base + s); // then to init_conditions year
}
}
#ifdef DO_ONCE
if (do_once == 1)
echoinput << "natmort OK" << endl;
#endif
if (MG_active(4) > 0)
get_recr_distribution();
if (y >= Bmark_Yr(7) && y <= Bmark_Yr(8))
{
for (gp = 1; gp <= N_GP; gp++)
for (p = 1; p <= pop; p++)
for (settle = 1; settle <= N_settle_timings; settle++)
if (recr_dist_pattern(gp, settle, p) > 0)
{
recr_dist_unf(gp, settle, p) += recr_dist(y, gp, settle, p);
if (gender == 2)
recr_dist_unf(gp + N_GP, settle, p) += recr_dist(y, gp + N_GP, settle, p);
}
}
if (MG_active(5) > 0)
get_migration();
#ifdef DO_ONCE
if (do_once == 1)
{
echoinput << "migr OK" << endl;
}
#endif
if (MG_active(7) > 0)
{
get_catch_mult(y, catch_mult_pointer);
for (j = styr + 1; j <= YrMax; j++)
{
catch_mult(j) = catch_mult(y);
}
}
if (Use_AgeKeyZero > 0)
{
if (MG_active(6) > 0)
get_age_age(Use_AgeKeyZero, AgeKey_StartAge, AgeKey_Linear1, AgeKey_Linear2); // call function to get the age_age key
if (save_for_report == 1 && store_agekey_add > 0)
{
save_agekey_count = N_ageerr + 1; // first blank key after the used keys
age_age(save_agekey_count) = age_age(Use_AgeKeyZero);
age_err(save_agekey_count) = age_err(Use_AgeKeyZero);
}
#ifdef DO_ONCE
if (do_once == 1)
{
echoinput << "age_err key recalc in " << y << endl;
}
#endif
}
if (save_for_report > 0)
{
get_saveGparm();
}
// SS_Label_Info_23.2 #Calculate selectivity in the initial year
get_selectivity();
#ifdef DO_ONCE
if (do_once == 1)
{
echoinput << "selectivity OK" << endl;
echoinput << "Calculate ALK" << endl;
}
#endif
// SS_Label_Info_23.3 #Loop seasons and subseasons
t = styr - 1;
for (s = 1; s <= nseas; s++)
{
t++;
if (WTage_rd > 0)
{
for (g = 1; g <= gmorph; g++)
if (use_morph(g) > 0)
{
Wt_Age_beg(s, g) = Wt_Age_t(t, 0, g);
Wt_Age_mid(s, g) = Wt_Age_t(t, -1, g);
if (s == spawn_seas)
fec(g) = Wt_Age_t(t, -2, g);
}
}
else if (MG_active(2) > 0 || MG_active(3) > 0 || save_for_report > 0 || do_once == 1)
{
// Make_Fecundity();
if (s == spawn_seas && spawn_seas == 1)
get_mat_fec();
for (g = 1; g <= gmorph; g++)
if (use_morph(g) > 0)
{
subseas = 1;
ALK_idx = (s - 1) * N_subseas + subseas;
Wt_Age_beg(s, g) = (ALK(ALK_idx, g) * wt_len(s, GP(g))); // wt-at-age at beginning of period
subseas = mid_subseas;
ALK_idx = (s - 1) * N_subseas + subseas;
Wt_Age_mid(s, g) = ALK(ALK_idx, g) * wt_len(s, GP(g)); // use for fisheries with no size selectivity
}
}
Wt_Age_t(t, 0) = Wt_Age_beg(s);
for (g = 1; g <= gmorph; g++)
if (use_morph(g) > 0)
{
// SS_Label_Info_23.3.3 #for each platoon, combine size_at_age distribution with length selectivity and weight-at-length to get combined selectivity vectors
Make_FishSelex();
}
// SS_Label_Info_23.3.4 #add predator M2 to M1 to update seasonal, areal natM in styr and calc surv for use in Pope's
if(N_pred>0)
{
// rebase natM to M1, which is stored in the p=0 section of array
for(p = 1; p <= pop; p++)
{
natM(t, p) = natM(t,0);
}
// calc M2
for (f1 = 1; f1 <= N_pred; f1++)
{
f = predator(f1);
pred_M2(f1, t) = mgp_adj(predparm_pointer(f1)); // base with no seasonal effect
if (nseas > 1)
pred_M2(f1, t) *= mgp_adj(predparm_pointer(f1) + s);
pred_M2(f1, t-nseas) = pred_M2(f1, t);
pred_M2(f1, t-nseas-nseas) = pred_M2(f1, t);
p = fleet_area(f); // area this predator occurs in
// a new array for indexing g and gpi could simplify below
// for (gp = 1; gp <= N_GP * gender * N_settle_timings; gp++)
// add each M2 to get total M
for (gp = 1; gp <= N_GP * gender; gp++)
{
g = g_Start(gp); // base platoon
for (settle = 1; settle <= N_settle_timings; settle++)
{
g += N_platoon;
int gpi = GP3(g); // GP*gender*settlement
natM(t, p,gpi) += pred_M2(f1, t) * sel_num(s, f, g);
if (do_once == 1 && p == 1)
echoinput << "init " << y << " s " << s << " t " << t << " area " << 0 << " gp " << gpi << " M1: " << natM(t,0, gpi) << endl;
if (do_once == 1)
echoinput << "init " << y << " s " << s << " t " << t << " area " << p << " gp " << gpi << " M1+M2: " << natM(t, p, gpi) << endl;
}
}
}
natM(t-nseas) = natM(t); //for initial equilibrium
natM(t-nseas-nseas) = natM(t); // for virgin
}
for(p = 1; p <= pop; p++)
{
int s1 = (p - 1) * nseas + s;
surv1(s1) = mfexp( - natM(t,p) * seasdur_half(s));
surv2(s1) = square(surv1(s1));
}
} // end season (s) loop in biology, mortality and selectivity calcs in initial year
#ifdef DO_ONCE
if (do_once == 1)
echoinput << "Begin calculating virgin age struc " << endl;
#endif
// SS_Label_Info_23.4 #calculate unfished (virgin) numbers-at-age
eq_yr = styr - 2;
bio_yr = styr;
Fishon = 0;
virg_fec = fec;
Recr.initialize(); // will store recruitment by area
for (int i = 1; i <= N_SRparm2; i++)
{
SR_parm_byyr(eq_yr, i) = SR_parm(i);
SR_parm_virg(i) = SR_parm(i);
SR_parm_work(i) = SR_parm(i);
}
// SPAWN-RECR: get expected recruitment globally or by area
if (recr_dist_area == 1 || pop == 1) // do global spawn_recruitment calculations
{
Recr_virgin = mfexp(SR_parm(1));
equ_Recr = Recr_virgin;
exp_rec(eq_yr, 1) = Recr_virgin; // expected Recr from s-r parms
exp_rec(eq_yr, 2) = Recr_virgin;
exp_rec(eq_yr, 3) = Recr_virgin;
exp_rec(eq_yr, 4) = Recr_virgin;
Do_Equil_Calc(equ_Recr); // call function to do equilibrium calculation
SSB_virgin = SSB_equil;
SPR_virgin = SSB_equil / Recr_virgin; // spawners per recruit
if(Do_Benchmark==0)
{
Mgmt_quant(1)=SSB_virgin;
SSB_unf=SSB_virgin;
Recr_unf=Recr_virgin;
Mgmt_quant(2)=totbio; // from equil calcs
Mgmt_quant(3)=smrybio; // from equil calcs
Mgmt_quant(4)=Recr_virgin;
}
Smry_Table(styr - 2, 1) = totbio; // from equil calcs
Smry_Table(styr - 2, 2) = smrybio; // from equil calcs
Smry_Table(styr - 2, 3) = smrynum; // from equil calcs
SSB_pop_gp(eq_yr) = SSB_equil_pop_gp; // dimensions of pop x N_GP
if (Hermaphro_Option != 0)
MaleSPB(eq_yr) = MaleSSB_equil_pop_gp;
SSB_yr(eq_yr) = SSB_equil;
SR_parm_byyr(eq_yr, N_SRparm2 + 1) = SSB_equil;
SR_parm_virg(N_SRparm2 + 1) = SSB_equil;
SR_parm_work(N_SRparm2 + 1) = SSB_equil;
t = styr - 2 * nseas - 1;
for (s = 1; s <= nseas; s++)
for (p = 1; p <= pop; p++)
{
for (g = 1; g <= gmorph; g++)
{
if (use_morph(g) > 0)
{
natage(t + s, p, g)(0, nages) = equ_numbers(s, p, g)(0, nages);
Z_rate(t + s, p, g)(0, nages) = equ_Z(s, p, g)(0, nages);
}
}
}
if (save_for_report > 0)
{
SSB_B_yr(eq_yr).initialize();
SSB_N_yr(eq_yr).initialize();
for (s = 1; s <= nseas; s++)
{
for (p = 1; p <= pop; p++)
for (g = 1; g <= gmorph; g++)
if (use_morph(g) > 0)
{
if (s == spawn_seas && sx(g) == 1)
{
SSB_B_yr(eq_yr) += make_mature_bio(GP4(g)) * natage(t + s, p, g);
SSB_N_yr(eq_yr) += make_mature_numbers(GP4(g)) * natage(t + s, p, g);
}
Save_PopAge(t + s, p, g) = natage(t + s, p, g);
Save_PopAge(t + s, p + pop, g) = elem_prod(natage(t + s, p, g), mfexp(-Z_rate(t + s, p, g) * 0.5 * seasdur(s)));
if (Settle_seas(settle_g(g)) == s)
Recr(p, t + 1 + Settle_seas_offset(settle_g(g))) += equ_Recr * recr_dist(y, GP(g), settle_g(g), p) * platoon_distr(GP2(g));
Save_PopBio(t + s, p, g) = elem_prod(natage(t + s, p, g), Wt_Age_beg(s, g));
Save_PopBio(t + s, p + pop, g) = elem_prod(Save_PopAge(t + s, p + pop, g), Wt_Age_mid(s, g));
}
for (int ff = 1; ff <= N_pred; ff++)
{
f = predator(ff);
for (g = 1; g <= 6; g++)
{
catch_fleet(t + s, f, g) = equ_catch_fleet(g, s, f);
}
for (g = 1; g <= gmorph; g++)
{
catage(t + s, f, g) = equ_catage(s, f, g);
}
}
}
}
}
else // area-specific spawn-recruitment
{
}
// SS_Label_Info_23.5 #Calculate equilibrium using initial F
#ifdef DO_ONCE
if (do_once == 1)
echoinput << "Begin calculating initial age structure" << endl;
#endif
eq_yr = styr - 1;
bio_yr = styr;
if (fishery_on_off == 1)
{
Fishon = 1;
}
else
{
Fishon = 0;
}
for (f = 1; f <= N_SRparm2; f++)
{
if (SR_parm_timevary(f) == 0)
{
// no change to SR_parm_work
}
else
{
SR_parm_work(f) = parm_timevary(SR_parm_timevary(f), eq_yr);
}
SR_parm_byyr(eq_yr, f) = SR_parm_work(f);
}
for (s = 1; s <= nseas; s++)
{
t = styr - nseas - 1 + s;
for (int ff = 1; ff <= N_catchfleets(0); ff++)
{
f = fish_fleet_area(0, ff);
if (init_F_loc(s, f) > 0)
{
Hrate(f, t) = init_F(init_F_loc(s, f));
}
}
}
// for the initial equilibrium, R0 and steepness will remain same as for virgin, but a regime shift is allowed
// change with 3.30.12 to allow R0 to change according to a timevary effect
// exp_rec(eq_yr,1)=Recr_virgin;
// R1_exp=Recr_virgin;
R1_exp = mfexp(SR_parm_work(1));
exp_rec(eq_yr, 1) = R1_exp;
// SS_Label_Info_23.5.1 #Apply adjustments to the recruitment level
// SPAWN-RECR: adjust recruitment for the initial equilibrium
regime_change = 1.0;
if (SR_parm_timevary(N_SRparm2 - 1) > 0) // timevary regime exists
{
regime_change = mfexp(SR_parm_work(N_SRparm2 - 1));
}
if (init_equ_steepness == 0) // Adjustments do not include spawner-recruitment steepness
{
// R1=Recr_virgin*regime_change;
R1 = R1_exp * regime_change;
exp_rec(eq_yr, 2) = R1;
exp_rec(eq_yr, 3) = R1;
exp_rec(eq_yr, 4) = R1;
equ_Recr = R1; // equ_Recr is used inside of Do_Equil_Calc
Do_Equil_Calc(equ_Recr);
CrashPen += Equ_penalty;
}
else
{
// SS_Label_Info_23.5.1.2 #Adjustments include spawner-recruitment function
// do initial equilibrium with R1 based on offset from spawner-recruitment curve, using same approach as the benchmark calculations
// first get SPR for this init_F
// SPAWN-RECR: calc initial equilibrium pop, SPB, Recruitment
// equ_Recr=Recr_virgin;
equ_Recr = R1_exp * regime_change;
Do_Equil_Calc(equ_Recr);
CrashPen += Equ_penalty;
SPR_temp = SSB_equil / equ_Recr; // spawners per recruit at initial F
// get equilibrium SSB and recruitment from SPR_temp, Recr_virgin and virgin steepness
Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm(2), SR_parm(3), SSB_virgin, Recr_virgin, SPR_temp); // returns 2 element vector containing equilibrium biomass and recruitment at this SPR
R1_exp = Equ_SpawnRecr_Result(2); // set the expected recruitment equal to this equilibrium
exp_rec(eq_yr, 1) = R1_exp;
equ_Recr = R1_exp * regime_change;
exp_rec(eq_yr, 2) = equ_Recr;
exp_rec(eq_yr, 3) = equ_Recr;
exp_rec(eq_yr, 4) = equ_Recr;
R1 = equ_Recr;
Do_Equil_Calc(equ_Recr); // calculated SSB_equil
CrashPen += Equ_penalty;
}
Smry_Table(styr - 1, 1) = totbio; // from equil calcs
Smry_Table(styr - 1, 2) = smrybio; // from equil calcs
Smry_Table(styr - 1, 3) = smrynum; // from equil calcs
SSB_pop_gp(eq_yr) = SSB_equil_pop_gp; // dimensions of pop x N_GP
if (Hermaphro_Option != 0)
MaleSPB(eq_yr) = MaleSSB_equil_pop_gp;
SSB_yr(eq_yr) = SSB_equil;
SR_parm_byyr(eq_yr, N_SRparm2 + 1) = SSB_equil;
SR_parm_work(N_SRparm2 + 1) = SSB_equil;
SSB_yr(styr) = SSB_equil;
env_data(styr - 1, -1) = 0.0;
env_data(styr - 1, -2) = 0.0;
env_data(styr - 1, -3) = 0.0;
env_data(styr - 1, -4) = 0.0;
/*
// save est_equ_catch which has units (biomass vs numbers) according to that fleet; used in objfun
for (s = 1; s <= nseas; s++)
for (int ff = 1; ff <= N_catchfleets(0); ff++)
{
f = fish_fleet_area(0, ff);
if (catchunits(f) == 1)
{
est_equ_catch(s, f) = equ_catch_fleet(2, s, f);
}
else
{
est_equ_catch(s, f) = equ_catch_fleet(5, s, f);
}
}
*/
// if (save_for_report > 0)
{
for (s = 1; s <= nseas; s++)
{
t = styr - nseas - 1 + s;
for (int ff = 1; ff <= N_catchfleets(0); ff++)
{
f = fish_fleet_area(0, ff);
for (g = 1; g <= 6; g++)
{
catch_fleet(t, f, g) = equ_catch_fleet(g, s, f);
annual_catch(styr - 1, g) += equ_catch_fleet(g, s, f);
}
for (g = 1; g <= gmorph; g++)
{
catage(t, f, g) = equ_catage(s, f, g);
}
}
for (int ff = 1; ff <= N_pred; ff++)
{
f = predator(ff);
for (g = 1; g <= 6; g++)
{
catch_fleet(t, f, g) = equ_catch_fleet(g, s, f);
}
for (g = 1; g <= gmorph; g++)
{
catage(t, f, g) = equ_catage(s, f, g);
}
}
}
for (k = 1; k <= 3; k++)
{
Smry_Table(styr - 1, k + 3) = annual_catch(styr - 1, k);
}
}
for (s = 1; s <= nseas; s++)
{
t = styr - nseas - 1 + s;
a = styr - 1 + s;
for (p = 1; p <= pop; p++)
for (g = 1; g <= gmorph; g++)
{
natage(t, p, g)(0, nages) = equ_numbers(s, p, g)(0, nages);
natage(a, p, g)(0, nages) = equ_numbers(s, p, g)(0, nages);
Z_rate(t, p, g) = equ_Z(s, p, g);
}
}
if (save_for_report > 0)
{
t = styr - nseas - 1;
SSB_B_yr(eq_yr).initialize();
SSB_N_yr(eq_yr).initialize();
for (s = 1; s <= nseas; s++)
for (p = 1; p <= pop; p++)
for (g = 1; g <= gmorph; g++)
if (use_morph(g) > 0)
{
if (s == spawn_seas && sx(g) == 1)
{
SSB_B_yr(eq_yr) += make_mature_bio(GP4(g)) * natage(t + s, p, g);
SSB_N_yr(eq_yr) += make_mature_numbers(GP4(g)) * natage(t + s, p, g);
}
Save_PopAge(t + s, p, g) = natage(t + s, p, g);
Save_PopAge(t + s, p + pop, g) = elem_prod(natage(t + s, p, g), mfexp(-Z_rate(t + s, p, g) * 0.5 * seasdur(s)));
Save_PopBio(t + s, p, g) = elem_prod(natage(t + s, p, g), Wt_Age_beg(s, g));
Save_PopBio(t + s, p + pop, g) = elem_prod(Save_PopAge(t + s, p + pop, g), Wt_Age_mid(s, g));
if (Settle_seas(settle_g(g)) == s)
Recr(p, t + 1 + Settle_seas_offset(settle_g(g))) += equ_Recr * recr_dist(y, GP(g), settle_g(g), p) * platoon_distr(GP2(g));
}
}
if (docheckup == 1)
echoinput << " init equil age comp for styr " << styr << endl
<< natage(styr) << endl
<< endl;
// if recrdevs start before styr, then use them to adjust the initial agecomp
// apply a fraction of the bias adjustment, so bias adjustment gets less linearly as proceed back in time
if (recdev_first < styr)
{
if (do_recdev <= 2 && SR_fxn != 4)
{
for (p = 1; p <= pop; p++)
for (g = 1; g <= gmorph; g++)
for (a = styr - recdev_first; a >= 1; a--)
{
j = styr - a;
natage(styr, p, g, a) *= mfexp(recdev(j) - biasadj(j) * half_sigmaRsq);
}
}
else
{
for (p = 1; p <= pop; p++)
for (g = 1; g <= gmorph; g++)
for (a = styr - recdev_first; a >= 1; a--)
{
j = styr - a;
natage(styr, p, g, a) *= mfexp(recdev(j));
}
}
}
SSB_pop_gp(styr) = SSB_pop_gp(styr - 1); // placeholder in case not calculated early in styr
// note: the above keeps SSB_pop_gp(styr) = SSB_equil. It does not adjust for initial agecomp, but probably should
} // end initial_conditions
//*********************************************************************
FUNCTION void get_time_series()
{
/* SS_Label_Function_24 get_time_series */
dvariable crashtemp;
dvariable crashtemp1;
dvariable interim_tot_catch;
dvariable Z_adjuster;
dvariable R0_use;
dvariable SSB_use;
if (Do_Morphcomp > 0)
Morphcomp_exp.initialize();
// SS_Label_Info_24.0 #Retrieve spawning biomass and recruitment from the initial equilibrium
// SPAWN-RECR: begin of time series, retrieve last spbio and recruitment
SSB_current = SSB_yr(styr); // need these initial assignments in case recruitment distribution occurs before spawnbio&recruits
if (recdev_doit(styr - 1) > 0)
{
Recruits = R1 * mfexp(recdev(styr - 1) - biasadj(styr - 1) * half_sigmaRsq);
}
else
{
Recruits = R1;
}
// SS_Label_Info_24.1 #Loop the years
for (y = styr; y <= endyr; y++)
{
yz = y;
if (STD_Yr_Reverse_F(y) > 0)
F_std(STD_Yr_Reverse_F(y)) = 0.0;
t_base = styr + (y - styr) * nseas - 1;
for (f = 1; f <= N_SRparm2; f++)
{
if (SR_parm_timevary(f) == 0)
{
// no change to SR_parm_work
}
else
{
SR_parm_work(f) = parm_timevary(SR_parm_timevary(f), y);
}
SR_parm_byyr(y, f) = SR_parm_work(f);
}
// SS_Label_Info_24.1.1 #store begin of year quantities for use in density-dependent processes
{
env_data(y, -1) = log(SSB_current / SSB_yr(styr - 1));
if (recdev_doit(y) > 0)
{
env_data(y, -2) = recdev(y);
} // store so can do density-dependence
else
{ // should be 0.0
}
t = t_base + 1; // first season
s = 1;
if (WTage_rd > 0)
{
Wt_Age_beg(s) = Wt_Age_t(t, 0);
Wt_Age_mid(s) = Wt_Age_t(t, -1);
}
else if (timevary_MG(y, 2) > 0 || timevary_MG(y, 3) > 0 || save_for_report == 1)
{
get_growth3(y, t, 1, 1); // before season loop, used for summary biomass
ALK_subseas_update(1) = 1; // do 1st subseas of 1st season; ADD THIS LINE for 3.30.17
Make_AgeLength_Key(s, 1); // this will give wt_age_beg before any time-varying parameter changes for this year
ALK_idx = (s - 1) * N_subseas + 1;
for (g = 1; g <= gmorph; g++)
if (use_morph(g) > 0)
{
Wt_Age_beg(s, g) = (ALK(ALK_idx, g) * wt_len(s, GP(g))); // wt-at-age at beginning of period
}
}
smrybio = 0.0;
smrynum = 0.0;
// do not do totbio here because new recruits have not yet occurred
for (g = 1; g <= gmorph; g++)
if (use_morph(g) > 0)
{
for (p = 1; p <= pop; p++)
{
smrybio += natage(t, p, g)(Smry_Age, nages) * Wt_Age_beg(1, g)(Smry_Age, nages); // calc before recruitment and time-vary biology applied
smrynum += sum(natage(t, p, g)(Smry_Age, nages)); //sums to accumulate across platoons and settlements
}
}
env_data(y, -3) = log(smrybio / Smry_Table(styr - 1, 2));
env_data(y, -4) = log(smrynum / Smry_Table(styr - 1, 3));
Smry_Table(y, 2) = smrybio; // gets used as demoninator for some F_std options
Smry_Table(y, 3) = smrynum;
}
// SS_Label_Info_24.1.1 #skip biology updating if y=styr because already done
if (y > styr)
{
if (do_densitydependent == 1)
make_densitydependent_parm(y); // call to adjust for density dependence
// SS_Label_Info_24.1.1 #Update the time varying biology factors if necessary
if (timevary_MG(y, 0) > 0 || save_for_report > 0)
get_MGsetup(y);
if (timevary_MG(y, 2) > 0)
{
ALK_subseas_update = 1; // indicate that all ALKs will need re-estimation
get_growth2(y); // propagates growth to each season this year and to begin next year
get_growth3(y, t, 1, 1); // cleans up the linear growth range for begin of this year
}
if (timevary_MG(y, 3) > 0)
{
get_wtlen(); // stores values for all seasons
// note that get_mat_fec() will get called in the season loop because it may need the ALK for a later season
// but Maunder's M in get_natmort() may use the fecundity vector, so would be using the most recently calculated Problem??
if (Hermaphro_Option != 0)
get_Hermaphro();
}
if (timevary_MG(y, 1) > 0)
{
get_natmort();
}
else
{
for (s = 1; s <= nseas; s++)
{
natM(t_base + s) = natM(t_base - nseas + s);
} // set M equal to last year's;
// does all areas (p), but if there are predators, then add of pred_M2 occurs in season loop below
}
if (timevary_MG(y, 4) > 0)
get_recr_distribution();
if (y >= Bmark_Yr(7) && y <= Bmark_Yr(8))
{
for (gp = 1; gp <= N_GP; gp++)
for (p = 1; p <= pop; p++)
for (settle = 1; settle <= N_settle_timings; settle++)
if (recr_dist_pattern(gp, settle, p) > 0)
{
recr_dist_unf(gp, settle, p) += recr_dist(y, gp, settle, p);
if (gender == 2)
recr_dist_unf(gp + N_GP, settle, p) += recr_dist(y, gp + N_GP, settle, p);
}
}
if (timevary_MG(y, 5) > 0)
get_migration();
if (timevary_MG(y, 7) > 0)
{
get_catch_mult(y, catch_mult_pointer);
}
if (Use_AgeKeyZero > 0)
{
if (timevary_MG(y, 6) > 0)
{
get_age_age(Use_AgeKeyZero, AgeKey_StartAge, AgeKey_Linear1, AgeKey_Linear2); // call function to get the age_age key
if (save_for_report == 1 && store_agekey_add > 0)
{
save_agekey_count++; // next blank key after the used keys
age_age(save_agekey_count) = age_age(Use_AgeKeyZero);
age_err(save_agekey_count) = age_err(Use_AgeKeyZero);
}
#ifdef DO_ONCE
if (do_once == 1)
echoinput << " ageerr_key recalc in " << y << endl;
#endif
}
}
if (save_for_report > 0)
{
if (timevary_MG(y, 1) > 0 || timevary_MG(y, 2) > 0 || timevary_MG(y, 3) > 0)
{
get_saveGparm();
}
}
}
// SS_Label_Info_24.2 #Loop the seasons
for (s = 1; s <= nseas; s++)
{
if (docheckup == 1)
echoinput << endl
<< "************************************" << endl
<< " year, seas " << y << " " << s << endl;
// SS_Label_Info_24.1.2 #Call selectivity, which does its own internal check for time-varying changes
// note that Make_Fish_selex is called later after the ALK's have been updated
if (s == 1 && y > styr)
get_selectivity();
t = t_base + s;
// SS_Label_Info_24.2.1 #Update the age-length key and the fishery selectivity for this season
// if(timevary_MG(y,2)>0 || timevary_MG(y,3)>0 || save_for_report==1 || WTage_rd>0)
if (timevary_MG(y, 2) > 0 || save_for_report == 1)
{
get_growth3(y, t, s, 1); // first subseas of season=s
Make_AgeLength_Key(s, 1);
get_growth3(y, t, s, mid_subseas); // for midseason
Make_AgeLength_Key(s, mid_subseas);
// SPAWN-RECR: call Make_Fecundity in time series
if (s == spawn_seas)
{
if (spawn_subseas != 1 && spawn_subseas != mid_subseas)
{
subseas = spawn_subseas;
get_growth3(y, t, s, subseas);
Make_AgeLength_Key(s, subseas); // spawn subseas
}
}
}
if (WTage_rd > 0)
{
Wt_Age_beg(s) = Wt_Age_t(t, 0);
Wt_Age_mid(s) = Wt_Age_t(t, -1);
if (s == spawn_seas)
{
fec = Wt_Age_t(t, -2);
}
}
else if (timevary_MG(y, 2) > 0 || timevary_MG(y, 3) > 0 || save_for_report > 0 || do_once == 1)
{
if (s == spawn_seas)
get_mat_fec();
// Make_Fecundity();
ALK_idx = (s - 1) * N_subseas + 1; // subseas=1
int ALK_idx2 = (s - 1) * N_subseas + mid_subseas;
for (g = 1; g <= gmorph; g++)
if (use_morph(g) > 0)
{
Wt_Age_beg(s, g) = (ALK(ALK_idx, g) * wt_len(s, GP(g))); // wt-at-age at beginning of period
Wt_Age_mid(s, g) = ALK(ALK_idx2, g) * wt_len(s, GP(g)); // use for fisheries with no size selectivity
}
}
Wt_Age_t(t, 0) = Wt_Age_beg(s);
if (y > styr) // because styr is done as part of initial conditions
{
for (g = 1; g <= gmorph; g++)
if (use_morph(g) > 0)
{
Make_FishSelex();
}
// rebase natM to M1
for(p = 1; p <= pop; p++)
{
natM(t, p) = natM(t,0);
}
// SS_Label_Info_24.x.x #add predator M2 inside the yr,seas loop
if(N_pred>0)
{
// add pred_M2 by area
for (f1 = 1; f1 <= N_pred; f1++)
{
f = predator(f1);
pred_M2(f1, t) = mgp_adj(predparm_pointer(f1)); // base with no seasonal effect
if (nseas > 1)
pred_M2(f1, t) *= mgp_adj(predparm_pointer(f1) + s);
p = fleet_area(f); // area this predator occurs in
// a new array for indexing g and gpi could simplify below
// for (gp = 1; gp <= N_GP * gender * N_settle_timings; gp++)
for (gp = 1; gp <= N_GP * gender; gp++)
{
g = g_Start(gp); // base platoon
for (settle = 1; settle <= N_settle_timings; settle++)
{
g += N_platoon;
int gpi = GP3(g); // GP*gender*settlement
natM(t, p,gpi) += pred_M2(f1, t) * sel_num(s, f, g);
if (do_once == 1 && p == 1)
echoinput << y << " s " << s << " t " << t << " area " << 0 << " gp " << gpi << " M1: " << natM(t,0, gpi) << endl;
if (do_once == 1)
echoinput << y << " s " << s << " t " << t << " area " << p << " gp " << gpi << " M1+M2: " << natM(t, p, gpi) << endl;
}
}
}
}
for(p = 1; p <= pop; p++)
{
int s1 = (p - 1) * nseas + s;
surv1(s1) = mfexp(-natM(t,p) * seasdur_half(s));
surv2(s1) = square(surv1(s1));
}
}
// SS_Label_Info_24.2.2 #Compute spawning biomass if this is spawning season so recruits could occur later this season
// SPAWN-RECR: calc SPB in time series if spawning is at beginning of the season
if (s == spawn_seas && spawn_time_seas < 0.0001) // compute spawning biomass if spawning at beginning of season so recruits could occur later this season
{
SSB_pop_gp(y).initialize();
SSB_B_yr(y).initialize();
SSB_N_yr(y).initialize();
for (p = 1; p <= pop; p++)
{
for (g = 1; g <= gmorph; g++)
if (sx(g) == 1 && use_morph(g) > 0) // female
{
SSB_pop_gp(y, p, GP4(g)) += fracfemale_mult * fec(g) * natage(t, p, g); // accumulates SSB by area and by growthpattern
SSB_B_yr(y) += fracfemale_mult * make_mature_bio(GP4(g)) * natage(t, p, g);
SSB_N_yr(y) += fracfemale_mult * make_mature_numbers(GP4(g)) * natage(t, p, g);
// SSB_pop_gp(y,p,GP4(g)) += fec(g)*natage(t,p,g); // accumulates SSB by area and by growthpattern
// SSB_B_yr(y) += make_mature_bio(GP4(g))*natage(t,p,g);
// SSB_N_yr(y) += make_mature_numbers(GP4(g))*natage(t,p,g);
}
}
SSB_current = sum(SSB_pop_gp(y));
SSB_yr(y) = SSB_current;
if (Hermaphro_Option != 0) // get male biomass
{
MaleSPB(y).initialize();
for (p = 1; p <= pop; p++)
{
for (g = 1; g <= gmorph; g++)
if (sx(g) == 2 && use_morph(g) > 0) // male; all assumed to be mature
{
MaleSPB(y, p, GP4(g)) += Wt_Age_t(t, 0, g) * natage(t, p, g); // accumulates SSB by area and by growthpattern
}
}
if (Hermaphro_maleSPB > 0.0) // add MaleSPB to female SSB
{
SSB_current += Hermaphro_maleSPB * sum(MaleSPB(y));
SSB_yr(y) = SSB_current;
}
}
// SS_Label_Info_24.2.3 #Get the total recruitment produced by this spawning biomass
// SPAWN-RECR: calc recruitment in time series; need to make this area-specific
if (SR_parm_timevary(1) == 0) // R0 is not time-varying
{