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SS_biofxn.tpl
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SS_biofxn.tpl
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// SS_Label_file #9. **SS_biofxn.tpl**
// SS_Label_file # * <u>get_MGsetup()</u> // get parameter values for this year
// SS_Label_file # * <u>get_growth1()</u> // prep growth quantities
// SS_Label_file # * <u>get_growth2()</u> // growth to beginning of each season of upcoming year
// SS_Label_file # * <u>get_growth3()</u> // growth to particular time point in a season
// SS_Label_file # * <u>get_natmort()</u>
// SS_Label_file # * <u>get_recr_distribution()</u>
// SS_Label_file # * <u>get_wtlen()</u>
// SS_Label_file # * <u>get_mat_fec()</u>
// SS_Label_file # * <u>get_Hermaphro()</u>
// SS_Label_file # * <u>get_migration()</u>
// SS_Label_file # * <u>get_saveGparm()</u>
// SS_Label_file # *
//*********************************************************************
/* SS_Label_Function_14 #Get_MGsetup: apply time-varying factors this year to the MG parameters to create mgp_adj vector */
FUNCTION void get_MGsetup(const int yz)
{
mgp_adj = MGparm; // set all to base parm value
// int y1;
for (f = 1; f <= N_MGparm; f++)
{
if (MGparm_timevary(f) > 0) // timevary
{
mgp_adj(f) = parm_timevary(MGparm_timevary(f), yz);
if (parm_adjust_method == 1 && (save_for_report > 0 || do_once == 1))
{
if (mgp_adj(f) < MGparm_1(f, 1) || mgp_adj(f) > MGparm_1(f, 2))
{
warnstream << "adjusted MGparm out of base parm bounds. Phase: " << current_phase()
<< "; Inter: " << niter << "; parm#: " << f << "; y: " << yz << "; min: "
<< MGparm_1(f, 1) << "; max: " << MGparm_1(f, 2) << "; base: " << MGparm(f)
<< " timevary_val: " << mgp_adj(f) << " " << ParmLabel(f);
write_message (WARN, 0);
}
}
}
} // end parm loop
// SS_Label_Info_14.5 #if MGparm method =1 (no offsets), then do direct assignment if parm value is 0.0. (only for natMort and growth parms)
if (MGparm_def == 1)
{
for (j = 1; j <= N_MGparm; j++)
{
if (MGparm_offset(j) > 0)
mgp_adj(j) = mgp_adj(MGparm_offset(j));
}
}
// SS_Label_Info_19.1 #set wtlen and maturity/fecundity factors equal to annual values from mgp_adj
gp = 0;
for (gg = 1; gg <= gender; gg++)
for (GPat = 1; GPat <= N_GP; GPat++)
{
gp++;
if (gg == 1)
{
for (f = 1; f <= 6; f++)
{
wtlen_p(GPat, f) = mgp_adj(MGparm_point(gg, GPat) + N_M_Grow_parms + f - 1);
}
}
else
{
for (f = 7; f <= 8; f++)
{
wtlen_p(GPat, f) = mgp_adj(MGparm_point(gg, GPat) + N_M_Grow_parms + (f - 6) - 1);
}
}
if (do_once == 1)
echoinput << "get wtlen parms sex: " << gg << " Gpat: " << GPat << " sex*Gpat: " << gp << " " << wtlen_p(GPat) << endl;
}
if (save_for_report > 0)
mgp_save(yz) = value(mgp_adj);
}
//********************************************************************
/* SS_Label_FUNCTION 15 get_growth1; calc some seasonal and CV_growth biology factors that cannot be time-varying */
FUNCTION void get_growth1()
{
// SS_Label_Info_15.1 #create seasonal effects for growth K, and for wt_len parameters
if (MGparm_doseas > 0)
{
if (MGparm_seas_effects(10) > 0) // for seasonal K
{
VBK_seas(0) = 0.0;
for (s = 1; s <= nseas; s++)
{
VBK_seas(s) = mfexp(MGparm(MGparm_seas_effects(10) + s));
VBK_seas(0) += VBK_seas(s) * seasdur(s);
}
}
else
{
VBK_seas = sum(seasdur); // set vector to null effect
}
for (gp = 1; gp <= N_GP; gp++)
for (j = 1; j <= 8; j++)
{
#ifdef DO_ONCE
{
if (do_once == 1)
echoinput << j << " wt_len seas " << MGparm_seas_effects(j) << endl;
}
#endif
if (MGparm_seas_effects(j) > 0)
{
wtlen_seas(0, gp, j) = 0.0;
for (s = 1; s <= nseas; s++)
{
wtlen_seas(s, gp, j) = mfexp(MGparm(MGparm_seas_effects(j) + s));
wtlen_seas(0, gp, j) += wtlen_seas(s, gp, j) * seasdur(s); // this seems not to be used
}
}
else
{
for (s = 0; s <= nseas; s++)
{
wtlen_seas(s, gp, j) = 1.0;
}
}
}
}
else
{
VBK_seas = sum(seasdur); // set vector to null effect
for (s = 1; s <= nseas; s++)
wtlen_seas(s) = 1.0; // set vector to null effect
}
// SS_Label_Info_15.2 #create variability of size-at-age factors using direct assignment or offset approaches
gp = 0;
for (gg = 1; gg <= gender; gg++)
for (g = 1; g <= N_GP; g++)
{
gp++;
Ip = MGparm_point(gg, g);
j = Ip + N_M_Grow_parms - 2; // index for CVmin
k = j + 1; // index for CVmax
switch (MGparm_def) // for CV of size-at-age
{
case 1: // direct
{
if (MGparm(j) > 0)
{
CVLmin(gp) = MGparm(j);
}
else
{
CVLmin(gp) = MGparm(N_M_Grow_parms - 1);
}
if (MGparm(k) > 0)
{
CVLmax(gp) = MGparm(k);
}
else
{
CVLmax(gp) = MGparm(N_M_Grow_parms);
}
break;
}
case 2: // offset
{
if (gp == 1)
{
CVLmin(gp) = MGparm(j);
CVLmax(gp) = MGparm(k);
}
else
{
CVLmin(gp) = CVLmin(1) * mfexp(MGparm(j));
CVLmax(gp) = CVLmax(1) * mfexp(MGparm(k));
}
break;
}
case 3: // offset like SS2 V1.23
{
if (gp == 1)
{
CVLmin(gp) = MGparm(j);
CVLmax(gp) = CVLmin(1) * mfexp(MGparm(k));
}
else
{
CVLmin(gp) = CVLmin(1) * mfexp(MGparm(j));
CVLmax(gp) = CVLmin(gp) * mfexp(MGparm(k));
}
break;
}
} // end switch
if ((CVLmin(gp) != CVLmax(gp)) || active(MGparm(N_M_Grow_parms)) || active(MGparm(k)))
{
CV_const(gp) = 1;
}
else
{
CV_const(gp) = 0;
}
}
}
//********************************************************************
/* SS_Label_Function_ 16 #get_growth2; (do seasonal growth calculations for a selected year) */
FUNCTION void get_growth2(const int y)
{
// called at beginning of each year, so y is known
// if y=styr, then does equilibrium size-at-age according to start year growth parameters
// for any year, calculates for each season the size at the beginning of the next season, with growth increment calculated according to that year's parameters
//Growth Cessation Model code added by Mark Maunder October 2018
//The growth cessation model is described in
//Maunder, M.N., Deriso, R.B., Schaefer, K.M., Fuller, D.W., Aires-da-Silva, A.M., Minte‑Vera, C.V., Campana, S.E. 2018. The growth cessation model: a growth model for species showing a near cessation in growth with application to bigeye tuna (Thunnus obesus). Marine Biology (2018) 165:76.
//Ian Taylor derived the formula for Linf
int k2;
int add_age;
int ALK_idx2; // beginning of first subseas of next season
dvariable plusgroupsize;
dvariable current_size;
dvariable VBK_temp;
dvariable VBK_temp2; // with VBKseas(s) multiplied
dvariable LminR;
dvariable LmaxR;
dvariable LinfR;
dvariable inv_Richards;
dvariable t50;
// SS_Label_Info_16.1 #Create Cohort_Growth offset for the cohort borne (age 0) this year
if (CGD_onoff > 0) // cohort specific growth multiplier
{
temp = mgp_adj(MGP_CGD);
k = min(nages, (YrMax - y));
for (a = 0; a <= k; a++)
{
Cohort_Growth(y + a, a) = temp;
} // so this multiplier on growth_increment is stored on a diagonal into the future
}
// SS_Label_Info_16.2 #Loop growth patterns (sex*N_GP)
gp = 0;
#ifdef DO_ONCE
{
if (do_once == 1)
echoinput << "GROWTH, yr= " << y << endl;
}
#endif
for (gg = 1; gg <= gender; gg++)
for (GPat = 1; GPat <= N_GP; GPat++)
{
gp++;
Ip = MGparm_point(gg, GPat) + N_natMparms;
switch (Grow_type) // create specific growth parameters from the mgp_adj list of current MGparms
{
case 7: // empirical length
{
break;
}
default: // process parameters for all other grow_type
{
// SS_Label_Info_16.2.1 #set Lmin, Lmax, VBK, Richards to this year's values for mgp_adj
if (MGparm_def > 1 && gp > 1) // do offset approach
{
Lmin(gp) = Lmin(1) * mfexp(mgp_adj(Ip));
Lmax_temp(gp) = Lmax_temp(1) * mfexp(mgp_adj(Ip + 1));
VBK(gp) = VBK(1) * mfexp(mgp_adj(Ip + 2)); // assigns to all ages for which VBK is defined
}
else
{
Lmin(gp) = mgp_adj(Ip);
Lmax_temp(gp) = mgp_adj(Ip + 1); // size at A2; could be 999 to indicate Linf
VBK(gp) = -mgp_adj(Ip + 2); // because always used as negative; assigns to all ages for which VBK is defined
}
VBK_temp = VBK(gp, 0); // will be reset to VBK(gp,nages) if using age-specific K
// SS_Label_Info_16.2.2 #Set up age specific k
if (Grow_type == 3) // age specific k
{
j = 1;
for (a = 1; a <= nages; a++)
{
if (a == Age_K_points(j))
{
VBK(gp, a) = VBK(gp, a - 1) * mgp_adj(Ip + 2 + j);
if (j < Age_K_count)
j++;
}
else
{
VBK(gp, a) = VBK(gp, a - 1);
}
}
VBK_temp = VBK(gp, nages);
}
else if (Grow_type == 4) // age specific k reverse order, so age_k_points need to be descending
{
j = 1;
VBK(gp, nages) = VBK_temp;
for (a = nages - 1; a >= 0; a--)
{
if (a == Age_K_points(j))
{
VBK(gp, a) = VBK(gp, a + 1) * mgp_adj(Ip + 2 + j);
if (j < Age_K_count)
j++;
}
else
{
VBK(gp, a) = VBK(gp, a + 1);
}
}
}
else if (Grow_type == 5) // age specific k replacement, so age_k_points need to be descending
{
j = 1;
for (a = nages; a >= 0; a--)
{
if (a == Age_K_points(j))
{
VBK(gp, a) = mgp_adj(Ip + 2 + j) * VBK_temp;
if (j < Age_K_count)
j++;
}
else
{
VBK(gp, a) = VBK_temp;
}
}
VBK_temp = VBK(gp, nages);
}
// get Linf from Lmax
// get Richards or growth cessation parameter if appropriate
if (Grow_type == 2) // Richards
{
if (MGparm_def > 1 && gp > 1)
{
Richards(gp) = Richards(1) * mfexp(mgp_adj(Ip + 3));
}
else
{
Richards(gp) = mgp_adj(Ip + 3);
}
LminR = pow(Lmin(gp), Richards(gp));
inv_Richards = 1.0 / Richards(gp);
if (AFIX2 == 999)
{
L_inf(gp) = Lmax_temp(gp);
LinfR = pow(L_inf(gp), Richards(gp));
}
else
{
LmaxR = pow(Lmax_temp(gp), Richards(gp));
LinfR = LminR + (LmaxR - LminR) / (1. - mfexp(VBK_temp * VBK_seas(0) * (AFIX_delta)));
L_inf(gp) = pow(LinfR, inv_Richards);
}
#ifdef DO_ONCE
if (do_once == 1)
echoinput << " linf " << L_inf(gp) << " VBK: " << VBK_temp << endl;
#endif
}
else if (Grow_type == 8)
{
if (MGparm_def > 1 && gp > 1)
{
Richards(gp) = Richards(1) * mfexp(mgp_adj(Ip + 3));
}
else
{
Richards(gp) = mgp_adj(Ip + 3);
}
L_inf(gp) = Lmax_temp(gp);
VBK_temp = -VBK(gp, 0) * VBK_seas(0);
// t50 is the calculated inflection age for the decline in K
t50 = log(exp((L_inf(gp) - Lmin(gp)) * Richards(gp) / VBK_temp) - 1.0) / Richards(gp);
}
else
{
if (AFIX2 == 999)
{
L_inf(gp) = Lmax_temp(gp);
}
else
{
L_inf(gp) = Lmin(gp) + (Lmax_temp(gp) - Lmin(gp)) / (1. - mfexp(VBK_temp * VBK_seas(0) * (AFIX_delta)));
#ifdef DO_ONCE
if (do_once == 1)
echoinput << VBK_temp << " " << VBK_seas(0) << " " << VBK_temp * VBK_seas(0) << " " << Lmax_temp(gp) << " " << L_inf(gp) << endl;
#endif
}
}
// SS_Label_Info_16.2.3 #Set up Lmin and Lmax in Start Year
if (y == styr)
{
Cohort_Lmin(gp) = Lmin(gp); // sets for all years and ages
}
else if (timevary_MG(y, 2) > 0) // using time-vary growth
{
k = min(nages, (YrMax - y));
for (a = 0; a <= k; a++)
{
Cohort_Lmin(gp, y + a, a) = Lmin(gp);
} // sets for future years so cohort remembers its size at birth; with Lmin(gp) being size at birth this year
}
} // end setup of parametric growth parameters
} // end switch between parametric and non-parametric growth
#ifdef DO_ONCE
if (do_once == 1)
{
echoinput << "sex: " << gg << " GP: " << gp << " Lmin: " << Lmin(gp) << " Linf: " << L_inf(gp) << " VBK_temp: " << VBK_temp << " VBK@age: " << -VBK(gp) << endl;
if (Grow_type == 2)
echoinput << " Richards: " << Richards(gp) << endl;
if (Grow_type == 8)
echoinput << " Cessation_decay: " << Richards(gp) << endl;
}
#endif
// SS_Label_Info_16.2.4 #Loop settlement events because growth starts at time of settlement
g = g_Start(gp); // base platoon
for (settle = 1; settle <= N_settle_timings; settle++)
{
g += N_platoon; // increment by N_platoon because only middle platoon has growth modeled
if (use_morph(g) > 0)
{
if (y == styr)
{
switch (Grow_type)
{
case 7: // non-parametric
{
break;
}
default:
{
// SS_Label_Info_16.2.4.1 #set up the delta in growth variability across ages if needed
if (CV_const(gp) > 0)
{
if (CV_depvar_a == 0)
{
CV_delta(gp) = (CVLmax(gp) - CVLmin(gp)) / (Lmax_temp(gp) - Lmin(gp));
}
else
{
CV_delta(gp) = (CVLmax(gp) - CVLmin(gp)) / (AFIX2_forCV - AFIX);
}
}
else
{
CV_delta(gp) = 0.0;
CV_G(gp) = CVLmin(gp); // sets all seasons and whole age range
}
}
}
// SS_Label_Info_16.2.4.1.1 #if y=styr, get size-at-age in first subseason of first season of this first year
switch (Grow_type)
{
case 1:
{
VBK_temp2 = VBK_temp * VBK_seas(0);
for (a = 0; a <= nages; a++)
{
// Ave_Size(styr,1,g,a) = Lmin(gp) + (Lmin(gp)-L_inf(gp))* (mfexp(VBK_temp2*(real_age(g,1,a)-AFIX))-1.0);
Ave_Size(styr, 1, g, a) = L_inf(gp) + (Lmin(gp) - L_inf(gp)) * mfexp(VBK_temp2 * (real_age(g, 1, a) - AFIX));
} // done ageloop
break;
}
case 2: // Richards
{
Ave_Size(styr, 1, g)(0, first_grow_age(g)) = Lmin(gp);
VBK_temp2 = VBK_temp * VBK_seas(0);
for (a = first_grow_age(g); a <= nages; a++)
{
temp = LinfR + (LminR - LinfR) * mfexp(VBK_temp2 * (real_age(g, 1, a) - AFIX));
Ave_Size(styr, 1, g, a) = pow(temp, inv_Richards);
} // done ageloop
break;
}
case 5:
{
}
case 4:
{
}
case 3: // age-specific K, so need age-by-age calculations
{
ALK_idx = 1;
//VBK_seas(0) accounts for season duration
for (a = 0; a <= nages; a++)
{
k2 = a - 1;
if (lin_grow(g, ALK_idx, a) >= -1.0) // linear segment, or first time point beyond AFIX;
{
Ave_Size(styr, 1, g, a) = Lmin(gp) + (Lmin(gp) - L_inf(gp)) * (mfexp(VBK(gp, 0) * VBK_seas(0) * (real_age(g, 1, a) - AFIX)) - 1.0);
}
else
{
Ave_Size(styr, 1, g, a) = Ave_Size(styr, 1, g, k2) + (mfexp(VBK(gp, k2) * VBK_seas(0)) - 1.0) * (Ave_Size(styr, 1, g, k2) - L_inf(gp));
}
// echoinput<<a<<" "<<lin_grow(g,ALK_idx,a)<<" "<<real_age(g,1,a)-AFIX<<" "<<Ave_Size(styr,1,g,a) <<endl;
} // done ageloop
break;
}
case 8: // Growth Cessation Model
{
// r_max (parameter related to maximum growth rate) = vbktemp
// L0 (mean length at age 0)
// Linf (asymptotic mean length)
// k (steepness of the logistic function that models the reduction in the growth increment) = Richards
VBK_temp2 = VBK_temp * VBK_seas(0);
Ave_Size(styr, 1, g)(0, first_grow_age(g)) = Lmin(gp); //assume first_grow_age(g) = 0
for (a = first_grow_age(g); a <= nages; a++)
{
Ave_Size(styr, 1, g, a) = Lmin(gp) + VBK_temp2 * ((log(exp(-Richards(gp) * t50) + 1) - log(exp(Richards(gp) * (real_age(g, 1, a) - AFIX - t50)) + 1)) / Richards(gp) + real_age(g, 1, a) - AFIX);
} // done ageloop
break;
}
}
#ifdef DO_ONCE
if (do_once == 1)
echoinput << " settlement: " << settle << " g: " << g << endl
<< " L@A initial_year (w/o lin): " << Ave_Size(styr, 1, g)(0, min(6, nages)) << " plusgroup: " << Ave_Size(styr, 1, g, nages) << endl;
#endif
// SS_Label_Info_16.2.4.1.4 #calc approximation to mean size at maxage to account for growth after reaching the maxage (accumulator age)
current_size = Ave_Size(styr, 1, g, nages);
if (Linf_decay > -997.) // decay rate has been read; uses same code for Richards and standard
{
temp1 = 1.0;
temp4 = 1.0;
temp = current_size;
temp2 = mfexp(-Linf_decay); // cannot use natM or Z because growth is calculated first
#ifdef DO_ONCE
if (do_once == 1)
echoinput << " L_inf " << L_inf(gp) << " size@exactly maxage " << current_size << endl;
#endif
if (Grow_type < 3)
{
VBK_temp2 = VBK(gp, 0);
}
else
{
VBK_temp2 = VBK(gp, nages);
}
VBK_temp2 = (1.0 - mfexp(VBK_temp2 * VBK_seas(0)));
for (a = nages + 1; a <= 3 * nages; a++)
{
temp4 *= temp2; // decay numbers at age by exp(-0.xxx)
current_size += (L_inf(gp) - current_size) * VBK_temp2;
temp += temp4 * current_size;
temp1 += temp4; // accumulate numbers to create denominator for mean size calculation
}
Ave_Size(styr, 1, g, nages) = temp / temp1; // this is weighted mean size at nages
}
else if (Linf_decay == -999.) // mimic SS3.24
{
temp = 0.0;
temp1 = 0.0;
temp2 = mfexp(-0.2); // cannot use natM or Z because growth is calculated first
temp3 = L_inf(gp) - current_size; // delta between linf and the size at nages
// frac_ages = age/nages, so is fraction of a lifetime
temp4 = 1.0;
for (a = 0; a <= nages; a++)
{
temp += temp4 * (current_size + frac_ages(a) * temp3); // so grows linearly from size at nages to size at nages+nages
temp1 += temp4; // accumulate numbers to create denominator for mean size calculation
temp4 *= temp2; // decay numbers at age by exp(-0.2)
}
Ave_Size(styr, 1, g, nages) = temp / temp1; // this is weighted mean size at nages
}
else
{
// no adjustment
}
#ifdef DO_ONCE
if (do_once == 1)
echoinput << " adjusted size at maxage " << Ave_Size(styr, 1, g, nages) << " using decay of: " << Linf_decay << endl;
#endif
} // end initial year calcs
// SS_Label_Info_16.2.4.2 #loop seasons for growth calculation
for (s = 1; s <= nseas; s++)
{
t = t_base + s;
ALK_idx = s * N_subseas; // last subseas of season; so checks to see if still in linear phase at end of this season
if (s == nseas)
{
ALK_idx2 = 1; // first subseas of next year
}
else
{
ALK_idx2 = s * N_subseas + 1; // for the beginning of first subseas of next season
}
if (s == nseas)
add_age = 1;
else
add_age = 0; // advance age or not
// growth to next season
VBK_temp2 = (mfexp(VBK_temp * seasdur(s) * VBK_seas(s)) - 1.0);
// warning<<t<<" ave_size_grow2_start "<<Ave_Size(t,1,1)(0,6)<<endl;
switch (Grow_type)
{
case 1:
{
Ave_Size(t + 1, 1, g, 0) = Ave_Size(t, 1, g, 0); // carryforward, but may be overwritten in some circumstances
for (a = 0; a <= nages; a++)
{
if (a == nages)
{
k2 = a;
}
else
{
k2 = a + add_age;
} // where add_age =1 if s=nseas, else 0 (k2 assignment could be in a matrix so not recalculated
// NOTE: there is no seasonal interpolation, or real age adjustment for age-specific K. Maybe someday....
if (lin_grow(g, ALK_idx, a) == -2.0) // so doing growth curve
{
t2 = Ave_Size(t, 1, g, a) - L_inf(gp); // remaining growth potential from first subseas
if (timevary_MG(y, 2) > 0 && t2 > -1.)
{
join1 = 1.0 / (1.0 + mfexp(-(50. * t2 / (1.0 + fabs(t2))))); // note the logit transform is not perfect, so growth near Linf will not be exactly same as with native growth function
t2 *= (1. - join1); // trap to prevent decrease in size-at-age
}
// SS_Label_info_16.2.4.2.1.1 #calc size at end of the season, which will be size at begin of next season using current seasons growth parms
// with k2 adding an age if at the end of the year
if ((a < nages || s < nseas))
Ave_Size(t + 1, 1, g, k2) = Ave_Size(t, 1, g, a) + VBK_temp2 * t2 * Cohort_Growth(y, a);
if (a == nages && s == nseas)
{
plusgroupsize = Ave_Size(t, 1, g, nages) + VBK_temp2 * t2 * Cohort_Growth(y, nages);
}
}
else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX; lin_grow will stay at -1 for all remaining subseas of this season
{
Ave_Size(t + 1, 1, g, k2) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK_temp * (real_age(g, ALK_idx2, k2) - AFIX) * VBK_seas(s)) - 1.0) * Cohort_Growth(y, a);
}
else // in linear phase
{
Ave_Size(t + 1, 1, g, k2) = len_bins(1) + lin_grow(g, ALK_idx, a) * (Cohort_Lmin(gp, y, a) - len_bins(1));
}
// if(y==1990 && g==1) warning<<a<<" "<<lin_grow(g,ALK_idx,a)<<" "<<Ave_Size(t,1,g,a)<<" "<<Ave_Size(t+1,1,g,k2)<<endl;
} // done ageloop
break;
}
case 2: // Richards
{
for (a = 0; a <= nages; a++)
{
if (a == nages)
{
k2 = a;
}
else
{
k2 = a + add_age;
} // where add_age =1 if s=nseas, else 0 (k2 assignment could be in a matrix so not recalculated
// NOTE: there is no seasonal interpolation, or real age adjustment for age-specific K. Maybe someday....
if (lin_grow(g, ALK_idx, a) == -2.0)
{
temp = pow(Ave_Size(t, 1, g, a), Richards(gp));
t2 = temp - LinfR; // remaining growth potential in transformed units
if ((a < nages || s < nseas))
Ave_Size(t + 1, 1, g, k2) =
pow((temp + VBK_temp2 * t2 * Cohort_Growth(y, a)), inv_Richards);
if (a == nages && s == nseas)
plusgroupsize = pow((temp + VBK_temp2 * t2 * Cohort_Growth(y, a)), inv_Richards);
}
else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX; lin_grow will stay at -1 for all remaining subseas of this season
{
// temp=LminR + (LminR-LinfR)*(mfexp(VBK_temp*seasdur(s)*(real_age(g,ALK_idx2,k2)-AFIX))-1.0)*Cohort_Growth(y,a);
temp = LminR + (LminR - LinfR) * (mfexp(VBK_temp * (real_age(g, ALK_idx2, k2) - AFIX) * VBK_seas(s)) - 1.0) * Cohort_Growth(y, a);
Ave_Size(t + 1, 1, g, k2) = pow(temp, inv_Richards);
}
else // in linear phase for subseas
{
Ave_Size(t + 1, 1, g, a) = len_bins(1) + lin_grow(g, ALK_idx, a) * (Cohort_Lmin(gp, y, a) - len_bins(1));
}
} // done ageloop
break;
}
case 8: // Cessation
{
for (a = 0; a <= nages; a++)
{
k2 = a + add_age; // where add_age =1 if s=nseas, else 0 (k2 assignment could be in a matrix so not recalculated
if (a == nages)
k2 = a;
// calculate a full year's growth increment, then multiple by seasdur(s)
if (a < nages || s < nseas)
Ave_Size(t + 1, 1, g, k2) = Ave_Size(t, 1, g, a) +
(VBK_temp - (VBK_temp / Richards(gp)) * (log(exp(Richards(gp) * (real_age(g, 1, a) + 1 - t50)) + 1) - log(exp(Richards(gp) * (real_age(g, 1, a) - t50)) + 1))) * seasdur(s);
if (a == nages && s == nseas)
plusgroupsize = Ave_Size(t, 1, g, nages) +
(VBK_temp - (VBK_temp / Richards(gp)) * (log(exp(Richards(gp) * (real_age(g, 1, a) + 1 - t50)) + 1) - log(exp(Richards(gp) * (real_age(g, 1, a) - t50)) + 1))) * seasdur(s);
/*
echoinput<<a<<" "<<k2<<" "<<grow_inc<<" lin? "<<lin_grow(g,ALK_idx,a)<<" "<<Cohort_Lmin(gp,y,a)<<endl;
if(lin_grow(g,ALK_idx,a)==-2.0)
{
if((a<nages || s<nseas)) Ave_Size(t+1,1,g,k2) = Ave_Size(t,1,g,a)+grow_inc*seasdur(s);
if(a==nages && s==nseas) plusgroupsize = Ave_Size(t,1,g,nages)+grow_inc*seasdur(s);
}
else if(lin_grow(g,ALK_idx,a)==-1.0) // first time point beyond AFIX; lin_grow will stay at -1 for all remaining subseas of this season
{
Ave_Size(t+1,1,g,k2) = Cohort_Lmin(gp,y,a)+grow_inc*seasdur(s);
}
else // in linear phase for subseas
{
Ave_Size(t+1,1,g,a) = len_bins(1)+lin_grow(g,ALK_idx,a)*(Cohort_Lmin(gp,y,a)-len_bins(1));
}
*/
} // done ageloop
break;
}
case 5:
{
}
case 4:
{
}
case 3:
{
// SS_Label_Info_16.2.4.2.1 #standard von Bert growth, loop ages to get size at age at beginning of next season (t+1) which is subseas=1
for (a = 0; a <= nages; a++)
{
if (a < nages)
{
k2 = a + add_age;
}
else
{
k2 = a;
} // where add_age =1 if s=nseas, else 0 (k2 assignment could be in a matrix so not recalculated
// NOTE: there is no seasonal interpolation, or real age adjustment for age-specific K. Maybe someday....
if (lin_grow(g, ALK_idx, a) == -2.0) // so doing growth curve
{
t2 = Ave_Size(t, 1, g, a) - L_inf(gp); // remaining growth potential from first subseas
if (timevary_MG(y, 2) > 0 && t2 > -1.)
{
join1 = 1.0 / (1.0 + mfexp(-(50. * t2 / (1.0 + fabs(t2))))); // note the logit transform is not perfect, so growth near Linf will not be exactly same as with native growth function
t2 *= (1. - join1); // trap to prevent decrease in size-at-age
}
// SS_Label_info_16.2.4.2.1.1 #calc size at end of the season, which will be size at begin of next season using current seasons growth parms
// with k2 adding an age if at the end of the year
if ((a < nages || s < nseas))
Ave_Size(t + 1, 1, g, k2) = Ave_Size(t, 1, g, a) + (mfexp(VBK(gp, a) * seasdur(s) * VBK_seas(s)) - 1.0) * t2 * Cohort_Growth(y, a);
if (a == nages && s == nseas)
plusgroupsize = Ave_Size(t, 1, g, nages) + (mfexp(VBK(gp, nages) * seasdur(s) * VBK_seas(s)) - 1.0) * t2 * Cohort_Growth(y, nages);
}
else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX; lin_grow will stay at -1 for all remaining subseas of this season
{
Ave_Size(t + 1, 1, g, k2) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK(gp, a) * (real_age(g, ALK_idx2, k2) - AFIX) * VBK_seas(s)) - 1.0) * Cohort_Growth(y, a);
}
else // in linear phase
{
Ave_Size(t + 1, 1, g, a) = len_bins(1) + lin_grow(g, ALK_idx, a) * (Cohort_Lmin(gp, y, a) - len_bins(1));
}
} // done ageloop
break;
}
}
// SS_Label_Info_16.2.4.2.1.2 #after age loop, if(s=nseas) get weighted average for size_at_maxage from carryover fish and fish newly moving into this age
// this code needs to execute every year, so need to move to ss_popdyn. Positioned here, it is only updated in years in which growth changes
if (s == nseas)
{
if (y > styr && Linf_decay != -998.)
{
// 3.24 code
#ifdef DO_ONCE
if (do_once == 1)
echoinput << " plus group calc: "
<< " N _entering: " << natage(t, 1, g, nages - 1) << " N_inplus: " << natage(t, 1, g, nages) << " size in: " << Ave_Size(t + 1, 1, g, nages) << " old size: " << plusgroupsize << " ";
#endif
temp = ((natage(t, 1, g, nages - 1) + 0.01) * Ave_Size(t + 1, 1, g, nages) + (natage(t, 1, g, nages) + 0.01) * plusgroupsize) / (natage(t, 1, g, nages - 1) + natage(t, 1, g, nages) + 0.02);
Ave_Size(t + 1, 1, g, nages) = temp;
#ifdef DO_ONCE
if (do_once == 1 && g == 1)
echoinput << " final_val " << Ave_Size(t + 1, 1, g, nages) << endl;
#endif
// early 3.30 code
// temp4= square(natage(t,1,g,nages-1)+0.00000001)/(natage(t-1,1,g,nages-2)+0.00000001);
// temp=temp4*Ave_Size(t+1,1,g,nages)+(natage(t,1,g,nages)-temp4+0.00000001)*plusgroupsize;
// if(do_once==1&&g==1) echoinput<<t<<" plus group calc: "<<" N "<<" "<<natage(t-1,1,g,nages-2)<<" "<<natage(t,1,g,nages-1)<<" "<<natage(t,1,g,nages)<<" T4 "<<temp4<<" N-T4 "<<natage(t,1,g,nages)-temp4+0.00000001<<
// " size in: "<<Ave_Size(t+1,1,g,nages)<<" old size: "<<plusgroupsize<<" ";
// prototype code
// temp4= square(natage(t-1,1,g,nages-1)+0.00000001)/(natage(t-2,1,g,nages-2)+0.00000001);
// temp2=posfun(natage(t,1,g,nages)-temp4+0.00000001,0.0,temp);
// temp=temp4*Ave_Size(t+1,1,g,nages)+(temp2)*plusgroupsize;
// if(do_once==1&&g==1) echoinput<<t<<" plus group calc: "<<" N "<<" "<<natage(t-2,1,g,nages-2)<<" "<<natage(t-1,1,g,nages-1)<<" "<<natage(t,1,g,nages)<<" T4 "<<temp4<<" N-T4 "<<natage(t,1,g,nages)-temp4+0.00000001<<
// " size in: "<<Ave_Size(t+1,1,g,nages)<<" old size: "<<plusgroupsize<<" ";
// Ave_Size(t+1,1,g,nages)=temp/(natage(t,1,g,nages)+0.00000001);
// if(do_once==1&&g==1) echoinput<<" temp "<<temp<<" denom "<<(natage(t,1,g,nages)+0.00000001)<<" Z "<<Z_rate(t-1,1,1,nages-1);
}
else
{
Ave_Size(t + 1, 1, g, nages) = Ave_Size(t, 1, g, nages);
}
}
#ifdef DO_ONCE
if (do_once == 1)
echoinput << " seas: " << s << " size@t+1: " << Ave_Size(t + 1, 1, g)(0, min(6, nages)) << " plusgroup: " << Ave_Size(t + 1, 1, g, nages) << endl;
#endif
} // end of season
/*
// move this code to popdyn in styr so can use adjustments made by growth3
// SS_Label_Info_16.2.4.3 #propagate Ave_Size from early years forward until first year that has time-vary growth
k=y+1;
j=yz+1;
while(timevary_MG(j,2)==0 && k<=YrMax)
{
for (s=1;s<=nseas;s++)
{
t=styr+(k-styr)*nseas+s-1;
Ave_Size(t,1,g)=Ave_Size(t-nseas,1,g);
if(s==1 && k<YrMax)
{
Ave_Size(t+nseas,1,g)=Ave_Size(t,1,g); // prep for time-vary next yr
}
} // end season loop
k++;
if(j<endyr+1) j++;
}
*/
} // end need to consider this GP x settlement combo (usemorph>0)
} // end loop of settlements
Ip += N_M_Grow_parms;
} // end loop of growth patterns, gp
} // end do growth
// *******************************************************************************************************
// SS_Label_Function_16.5 #get_growth3 which calculates mean size-at-age for selected subseason
FUNCTION void get_growth3(const int y, const int t, const int s, const int subseas)
{
// progress mean growth through time series, accounting for seasonality and possible change in parameters
// get mean size at the beginning and end of the season
dvariable LinfR;
dvariable LminR;
dvariable inv_Richards;
dvariable t50;
dvariable VBK_temp2;
ALK_idx = (s - 1) * N_subseas + subseas; // note that this changes a global value
for (g = g_Start(1) + N_platoon; g <= gmorph; g += N_platoon) // looping the middle platoons for each sex*gp
{
if (use_morph(g) > 0)
{
gp = GP(g);
switch (Grow_type)
{
case 1: // regular von B
{
for (a = 0; a <= nages; a++)
{
// SS_Label_Info_16.5.1 #calc subseas size-at-age from begin season size-at-age, accounting for transition from linear to von Bert as necessary
// subseasdur is cumulative time to start of this subseas
if (lin_grow(g, ALK_idx, a) == -2.0) // so doing growth curve
{
t2 = Ave_Size(t, 1, g, a) - L_inf(gp); // remaining growth potential from first subseas
// the constant in join needs to be at least 30 to get rapid transition
// the consequence of (t2>-1.) should be investigated for effect on gradient
if (timevary_MG(y, 2) > 0 && t2 > -1.)
{
join1 = 1.0 / (1.0 + mfexp(-(50. * t2 / (1.0 + fabs(t2))))); // note the logit transform is not perfect, so growth near Linf will not be exactly same as with native growth function
t2 *= (1. - join1); // trap to prevent decrease in size-at-age
}
Ave_Size(t, subseas, g, a) = Ave_Size(t, 1, g, a) + (mfexp(VBK(gp, 0) * subseasdur(s, subseas) * VBK_seas(s)) - 1.0) * t2 * Cohort_Growth(y, a);
}
else if (lin_grow(g, ALK_idx, a) >= 0.0) // in linear phase for subseas
{
Ave_Size(t, subseas, g, a) = len_bins(1) + lin_grow(g, ALK_idx, a) * (Cohort_Lmin(gp, y, a) - len_bins(1));
}
// NOTE: there is no seasonal interpolation, age-specific K uses calendar age, not real age. Maybe someday....
else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX; lin_grow will stay at -1 for all remaining subseas of this season
{
Ave_Size(t, subseas, g, a) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK(gp, 0) * (real_age(g, ALK_idx, a) - AFIX) * VBK_seas(s)) - 1.0) * Cohort_Growth(y, a);
}
}
break;
}
case 2: // Richards
{
LinfR = pow(L_inf(gp), Richards(gp));
LminR = pow(Lmin(gp), Richards(gp));
inv_Richards = 1.0 / Richards(gp);
// uses VBK(nages) because age-specific K not allowed
// and Cohort_Lmin has already had the power function applied
for (a = 0; a <= nages; a++)
{
if (lin_grow(g, ALK_idx, a) == -2.0) // so doing growth curve
{
temp = pow(Ave_Size(t, 1, g, a), Richards(gp));
t2 = temp - LinfR; // remaining growth potential
// disable the shrinkage trap because Richard's parameter could be negative
// join1=1.0/(1.0+mfexp(-(50.*t2/(1.0+fabs(t2))))); // note the logit transform is not perfect, so growth near Linf will not be exactly same as with native growth function
// t2*=(1.-join1); // trap to prevent decrease in size-at-age
temp += (mfexp(VBK(gp, 0) * subseasdur(s, subseas) * VBK_seas(s)) - 1.0) * t2 * Cohort_Growth(y, a);
Ave_Size(t, subseas, g, a) = pow(temp, inv_Richards);
}
else if (lin_grow(g, ALK_idx, a) >= 0.0) // in linear phase for subseas
{
Ave_Size(t, subseas, g, a) = len_bins(1) + lin_grow(g, ALK_idx, a) * (Cohort_Lmin(gp, y, a) - len_bins(1));
}
else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX; lin_grow will stay at -1 for all remaining subseas of this season
{
// temp=Cohort_Lmin(gp,y,a) + (Cohort_Lmin(gp,y,a)-LinfR)*
temp = LminR + (LminR - LinfR) * (mfexp(VBK(gp, 0) * (real_age(g, ALK_idx, a) - AFIX) * VBK_seas(s)) - 1.0) * Cohort_Growth(y, a);
Ave_Size(t, subseas, g, a) = pow(temp, inv_Richards);
}
} // done ageloop
break;
} // done Richards
case 8: // Cessation
{
// VBK_temp2=-VBK_temp*seasdur(s); // negative to restore positive
// t50 is the calculated inflection age for the decline in K
dvariable VBK_temp = -VBK(gp, 0);
t50 = log(exp((L_inf(gp) - Lmin(gp)) * Richards(gp) / (VBK_temp)) - 1.0) / Richards(gp);
for (a = 0; a <= nages; a++)
{
// calculate a full year's growth increment, then multiple by seasdur(s)
Ave_Size(t, subseas, g, a) = Ave_Size(t, 1, g, a) +
(VBK_temp - (VBK_temp / Richards(gp)) * (log(exp(Richards(gp) * (real_age(g, ALK_idx, a) + 1 - t50)) + 1) - log(exp(Richards(gp) * (real_age(g, ALK_idx, a) - t50)) + 1))) * subseasdur(s, subseas);
} // done ageloop
break;
}
case 5: // von B with age-specific K
{
}
case 4: // von B with age-specific K
{
}
case 3: // von B with age-specific K
{
for (a = 0; a <= nages; a++)
{
// SS_Label_Info_16.5.1 #calc subseas size-at-age from begin season size-at-age, accounting for transition from linear to von Bert as necessary
// subseasdur is cumulative time to start of this subseas
if (lin_grow(g, ALK_idx, a) == -2.0) // so doing growth curve
{
t2 = Ave_Size(t, 1, g, a) - L_inf(gp); // remaining growth potential from first subseas
// the constant in join needs to be at least 30 to get rapid transition
// the consequence of (t2>-1.) should be investigated for effect on gradient
if (timevary_MG(y, 2) > 0 && t2 > -1.)
{
join1 = 1.0 / (1.0 + mfexp(-(50. * t2 / (1.0 + fabs(t2))))); // note the logit transform is not perfect, so growth near Linf will not be exactly same as with native growth function
t2 *= (1. - join1); // trap to prevent decrease in size-at-age
}
Ave_Size(t, subseas, g, a) = Ave_Size(t, 1, g, a) + (mfexp(VBK(gp, a) * subseasdur(s, subseas) * VBK_seas(s)) - 1.0) * t2 * Cohort_Growth(y, a);
}
else if (lin_grow(g, ALK_idx, a) >= 0.0) // in linear phase for subseas
{
Ave_Size(t, subseas, g, a) = len_bins(1) + lin_grow(g, ALK_idx, a) * (Cohort_Lmin(gp, y, a) - len_bins(1));
}
// NOTE: there is no seasonal interpolation, age-specific K uses calendar age, not real age. Maybe someday....
else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX; lin_grow will stay at -1 for all remaining subseas of this season
{
Ave_Size(t, subseas, g, a) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK(gp, a) * (real_age(g, ALK_idx, a) - AFIX) * VBK_seas(s)) - 1.0) * Cohort_Growth(y, a);
}
}
break;
}
} // done switch
} // end need this platoon
} // done platoon
} // end calc size-at-age at a particular subseason
FUNCTION void get_natmort()
{
// SS_Label_Function #17 get_natmort for all seasons given this year's parameters
dvariable Loren_M1;
dvariable Loren_temp;
dvariable Loren_temp2;
dvariable Maunder_Mjuv;
dvariable Maunder_lambda;
dvariable Maunder_Lmat;
dvariable Maunder_Mmat;
dvariable Maunder_beta;
dvariable Maunder_L50;
dvar_vector XX_mature(0, nages);
dvariable t_age;
int gpi;
int Do_AveAge;
int K_index;
K_index = VBK(1).indexmax();
Do_AveAge = 0;
t_base = styr + (yz - styr) * nseas - 1; // so looping s=1 to nseas; t=t_base + s
Ip = -N_M_Grow_parms; // start counter for MGparms
// SS_Label_Info_17.1 #loop growth patterns in each gender
gp = 0;
for (gg = 1; gg <= gender; gg++)
for (GPat = 1; GPat <= N_GP; GPat++)
{