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SS_selex.tpl
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SS_selex.tpl
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// SS_Label_file #11. **SS_selex.tpl**
// SS_Label_file # * <u>get_selectivity()</u> // does length and age selectivity and retention for all fleets
// SS_Label_file # * <u>make_fish_selex()</u> // for all fleets in a particular season, does the dot product of length distribution with length selectivity and retention vectors to calculate equivalent mean quantities at age for each platoon
FUNCTION void get_selectivity()
{
//*******************************************************************
/* SS_Label_Function_22 #get_selectivity */
// SS_Label_Info_22.01 #define local variables for selectivity
int fs; // = f-Nfleet to allow reference of actual fleet when looping to 2*Nfleet for the age selectivity calculations
int scaling_offset = 0;
dvariable t1;
dvariable t2;
dvariable t3;
dvariable t4;
dvariable Apical_Selex;
dvariable t1min;
dvariable t1max;
dvariable t1power;
dvariable t2min;
dvariable t2max;
dvariable t2power;
dvariable final;
dvariable sel_maxL;
dvariable lastsel;
dvariable lastSelPoint;
dvariable SelPoint;
dvariable finalSelPoint;
dvariable asc;
dvariable dsc;
dvar_vector sp(1, 199); // temporary vector for selex parms
Ip = 0;
// SS_Label_Info_22.2 #Loop all fisheries and surveys twice; first for size selectivity, then for age selectivity
for (f = 1; f <= 2 * Nfleet; f++)
{
fs = f - Nfleet; //index for saving age selex in the fleet arrays
// SS_Label_Info_22.2.1 #recalculate selectivity for any fleets or surveys with time-vary flag set for this year
if (timevary_sel(y, f) == 1 || save_for_report > 0)
{ // recalculate the selex in this year x type
if (N_selparmvec(f) > 0) // type has parms, so look for adjustments
{
for (j = 1; j <= N_selparmvec(f); j++)
{
if (selparm_timevary(Ip + j) == 0)
{
sp(j) = selparm(Ip + j);
}
else // time-varying
{
sp(j) = parm_timevary(selparm_timevary(Ip + j), y);
if (parm_adjust_method == 1 && (save_for_report > 0 || do_once == 1))
{
if (sp(j) > -999 && (sp(j) < selparm_1(Ip + j, 1) || sp(j) > selparm_1(Ip + j, 2)))
{
warnstream << "Adjusted selparm out of base parm bounds. Phase: " << current_phase() << "; Inter: " << niter << "; fleet: " << f << "; base_parm#: " << Ip + j << "; y: " << y << "; min: " << selparm_1(Ip + j, 1) << "; max: " << selparm_1(Ip + j, 2) << "; base: " << selparm(Ip + j) << " timevary_val: " << sp(j) << " " << ParmLabel(firstselparm + Ip + j);
write_message (ADJUST, 0);
}
}
}
} // end j parm loop
if (docheckup == 1 && f <= Nfleet)
echoinput << " len selex parms for fleet: " << f << " " << endl
<< sp(1, N_selparmvec(f)) << endl;
if (docheckup == 1 && f > Nfleet)
echoinput << " age selex parms for fleet: " << f - Nfleet << " " << endl
<< sp(1, N_selparmvec(f)) << endl;
if (save_for_report > 0 || do_once == 1)
{
for (j = 1; j <= N_selparmvec(f); j++)
save_sp_len(y, f, j) = sp(j);
}
}
if (f <= Nfleet) // do size selectivity, retention, discard mort
{
for (gg = 1; gg <= gender; gg++)
{
if (gg == 1 || (gg == 2 && seltype(f, 3) >= 3))
{
// SS_Label_Info_22.3 #Switch on size selectivity type
switch (seltype(f, 1)) // select the selectivity pattern
{
// SS_Label_Info_22.3.0 #case 0 constant size selectivity
case 0: // *********** constant
{
sel = 1.;
break;
}
// SS_Label_Info_22.3.1 #case 1 logistic size selectivity
case 1:
{
if (seltype(f, 3) < 3 || (gg == 1 && seltype(f, 3) == 3) || (gg == 2 && seltype(f, 3) == 4)) // do the primary gender
{
sel = 1. / (1. + mfexp(neglog19 * (len_bins_m - sp(1)) / sp(2)));
}
else // do the offset gender
{
temp = sp(1) + sp(Maleselparm(f));
temp1 = sp(2) + sp(Maleselparm(f) + 1);
sel = sp(Maleselparm(f) + 2) / (1. + mfexp(neglog19 * (len_bins_m - temp) / temp1));
}
break;
}
// SS_Label_Info_22.3.2 #case 2 size selectivity using double_normal_plateau and lots of bells and whistles; old version of 24 available for back compatibility
case 2:
// SS_Label_Info_22.3.24 #case 24 size selectivity using double_normal_plateau and lots of bells and whistles
case 24:
{
if (seltype(f, 3) < 3 || (gg == 1 && seltype(f, 3) == 3) || (gg == 2 && seltype(f, 3) == 4))
{
peak = sp(1);
upselex = mfexp(sp(3));
downselex = mfexp(sp(4));
final = sp(6);
Apical_Selex = 1.;
}
else
{ // offset male parameters if seltype(f,3)==3, female parameters if seltype(f,3)==4
peak = sp(1) + sp(Maleselparm(f));
upselex = mfexp(sp(3) + sp(Maleselparm(f) + 1));
downselex = mfexp(sp(4) + sp(Maleselparm(f) + 2));
if (sp(6) > -999.)
final = sp(6) + sp(Maleselparm(f) + 3);
Apical_Selex = sp(Maleselparm(f) + 4);
}
if (sp(5) < -1000.)
{
j1 = -1001 - int(value(sp(5))); // selex is nil thru bin j1, so set sp(5) equal to first bin with selex (e.g. -1002 to start selex at bin 2)
sel(1, j1) = 1.0e-06;
}
else
{
j1 = startbin - 1; // start selex at bin equal to min sizecomp databin (=j1+1)
if (sp(5) > -999)
{
point1 = 1.0 / (1.0 + mfexp(-sp(5)));
t1min = mfexp(-(square(len_bins_m(startbin) - peak) / upselex)); // fxn at first bin
}
}
if (sp(6) < -1000.)
{
j2 = -1000 - int(value(sp(6))); // selex is constant beyond this sizebin, so set sp(6) equal to last bin with estimated selex
}
else
{
j2 = nlength;
}
peak2 = peak + binwidth2 + (0.99 * len_bins_m(j2) - peak - binwidth2) / (1. + mfexp(-sp(2)));
if (sp(6) > -999)
{
if (seltype(f, 1) == 24)
{
point2 = Apical_Selex / (1.0 + mfexp(-final)); // The newer way of doing this
}
else
{
point2 = 1.0 / (1.0 + mfexp(-final)); // For back compatibility (old (3.30.18 and earlier) version of pattern 24, now available as 2)
#ifdef DO_ONCE
if (do_once == 1)
{
warnstream << "Selectivity 2 is a back-compatible (SS 3.30.18 and earlier) version of selectivity 24. Recommend using 24.";
write_message (SUGGEST, 0);
}
#endif
}
t2min = mfexp(-(square(len_bins_m(j2) - peak2) / downselex)); // fxn at last bin
}
for (j = j1 + 1; j <= j2; j++)
{
t1 = len_bins_m(j) - peak;
t2 = len_bins_m(j) - peak2;
join1 = 1.0 / (1.0 + mfexp(-(20. * t1 / (1.0 + fabs(t1))))); // note the logit transform on t1 causes range of mfexp to be over -20 to 20
join2 = 1.0 / (1.0 + mfexp(-(20. * t2 / (1.0 + fabs(t2)))));
if (sp(5) > -999)
{
asc = point1 + (Apical_Selex - point1) * (mfexp(-square(t1) / upselex) - t1min) / (1.0 - t1min);
}
else
{
asc = Apical_Selex * mfexp(-square(t1) / upselex);
}
if (sp(6) > -999)
{
dsc = Apical_Selex + (point2 - Apical_Selex) * (mfexp(-square(t2) / downselex) - 1.0) / (t2min - 1.0);
}
else
{
dsc = Apical_Selex * mfexp(-square(t2) / downselex);
}
sel(j) = asc * (1.0 - join1) + join1 * (Apical_Selex * (1.0 - join2) + dsc * join2);
}
if (startbin > 1 && sp(5) >= -1000.)
{
for (j = 1; j <= startbin - 1; j++)
{
sel(j) = square(len_bins_m(j) / len_bins_m(startbin)) * sel(startbin);
}
}
if (j2 < nlength)
{
sel(j2 + 1, nlength) = sel(j2);
}
break;
}
// SS_Label_Info_22.3.3 #case 3 discontinued
case 3:
{
warnstream << "Selectivity pattern 3 discontinued. Use a different pattern.";
write_message (FATAL, 0); // EXIT!
break;
}
// SS_Label_Info_22.3.4 #case 4 discontinued; use pattern 30 to get spawning biomass
case 4:
{
warnstream << "Selectivity pattern 4 discontinued; use pattern 0 and special survey units 30 in data file instead.";
write_message (FATAL, 0); // EXIT!
break;
}
// SS_Label_Info_22.3.5 #case 5 mirror another fleets size selectivity for specified bin range
// use only the specified bin range using mirror_mask created upon read
// must refer to a lower numbered type (f)
case 5:
{
sel = elem_prod(mirror_mask(f), sel_l(y, seltype(f, 4), 1));
break;
}
// SS_Label_Info_22.3.15 #case 15 mirror another fleets size selectivity for all size bins
case 15:
{
sel = sel_l(y, seltype(f, 4), 1);
break;
}
// SS_Label_Info_22.3.6 #case 6 non-parametric size selex pattern
// #43 non-parametric size selex scaled by average of values at low bin through high bin
case 43:
scaling_offset = 2;
[[fallthrough]];
case 6:
{
lastsel = -10.0; // log(selex) for first bin;
lastSelPoint = len_bins_m(1); // first size
finalSelPoint = value(sp(2 + scaling_offset)); // size beyond which selex is constant
SelPoint = value(sp(1 + scaling_offset)); // first size that will get a parameter. Value will get incremented by step interval (temp1)
z = 3 + scaling_offset; // parameter counter
temp1 = (finalSelPoint - SelPoint) / (seltype(f, 4) - 1.0); // step interval
for (j = 1; j <= nlength; j++)
{
if (len_bins_m(j) < SelPoint)
{
tempvec_l(j) = lastsel + (len_bins_m(j) - lastSelPoint) / (SelPoint - lastSelPoint) * (sp(z) - lastsel);
}
else if (len_bins_m(j) == SelPoint)
{
tempvec_l(j) = sp(z);
lastsel = sp(z);
lastSelPoint = SelPoint;
SelPoint += temp1;
if (SelPoint <= finalSelPoint)
{
z++;
}
else
{
SelPoint = finalSelPoint;
}
}
else if (len_bins_m(j) <= finalSelPoint)
{
lastsel = sp(z);
lastSelPoint = SelPoint;
SelPoint += temp1;
if (SelPoint <= finalSelPoint)
{
z++;
}
else
{
SelPoint = finalSelPoint;
}
tempvec_l(j) = lastsel + (len_bins_m(j) - lastSelPoint) / (SelPoint - lastSelPoint) * (sp(z) - lastsel);
}
else
{
tempvec_l(j) = sp(z);
}
#ifdef DO_ONCE
if (do_once == 1)
echoinput << "selex42 " << j << " " << len_bins_m(j) << " " << SelPoint << " " << tempvec_l(j) << endl;
#endif
}
if (scaling_offset == 0)
{
temp = max(tempvec_l);
}
else
{
int low_bin = int(value(sp(1)));
int high_bin = int(value(sp(2)));
if (low_bin < 1)
{
low_bin = 1;
warnstream << "Selex pattern 43; value for low bin is less than 1, so set to 1 ";
write_message (ADJUST, 0);
}
if (high_bin > nlength)
{
high_bin = nlength;
warnstream << " selex pattern 43; value for high bin is greater than " << nlength << ", so set to " << nlength;
write_message (ADJUST, 0);
}
if (high_bin < low_bin)
high_bin = low_bin;
if (low_bin > high_bin)
low_bin = high_bin;
sp(1) = low_bin;
sp(2) = high_bin;
temp = mean(tempvec_l(low_bin, high_bin));
scaling_offset = 0; // reset scaling offset
}
sel = mfexp(tempvec_l - temp);
break;
}
// SS_Label_Info_22.3.7 #case 7 discontinued; use pattern 8 for double logistic
case 7:
{
warnstream << "Selectivity pattern 7 discontinued; use pattern 8 instead for double logistic, but recommend pattern 24. ";
write_message (FATAL, 0); // EXIT!
break;
}
// SS_Label_Info_22.3.8 #case 8 double logistic with eight parameters
case 8:
// 1=peak, 2=init, 3=infl, 4=slope, 5=final, 6=infl2, 7=slope2 8=binwidth; Mirror=1===const_above_Linf
{
#ifdef DO_ONCE
if (do_once == 1)
{
warnstream << "Selectivity pattern 24 is recommended over pattern 8 because it has fewer parameters.";
write_message (SUGGEST, 0);
}
#endif
t1 = minL + (1. / (1. + mfexp(-sp(3)))) * (sp(1) - minL); // INFL
t1min = 1. / (1. + mfexp(-mfexp(sp(4)) * (minL - t1))) * 0.9999; // asc value at minsize
t1max = 1. / (1. + mfexp(-mfexp(sp(4)) * (sp(1) - t1))) * 1.0001; // asc value at peak
t1power = log(0.5) / log((0.5 - t1min) / (t1max - t1min)); // so the parameter will actual correspond to 50% point
if (seltype(f, 4) == 0)
{
sel_maxL = maxL;
}
else
{
sel_maxL = Ave_Size(styr, 1, 1, nages);
}
t2 = (sp(1) + sp(8)) + (1. / (1. + mfexp(-sp(6)))) * (sel_maxL - (sp(1) + sp(8))); // INFL
t2min = 1. / (1. + mfexp(-mfexp(sp(7)) * (sp(1) + sp(8) - t2))) * 0.9999; // asc value at peak+
t2max = 1. / (1. + mfexp(-mfexp(sp(7)) * (sel_maxL - t2))) * 1.0001; // asc value at maxL
t2power = log(0.5) / log((0.5 - t2min) / (t2max - t2min));
final = 1. / (1. + mfexp(-sp(5)));
for (j = 1; j <= nlength; j++) //calculate the value over length bins
{
join1 = 1. / (1. + mfexp(10. * (len_bins_m(j) - sp(1))));
join2 = 1. / (1. + mfexp(10. * (len_bins_m(j) - (sp(1) + sp(8)))));
join3 = 1. / (1. + mfexp(10. * (len_bins_m(j) - sel_maxL)));
upselex = sp(2) + (1. - sp(2)) * pow(((1. / (1. + mfexp(-mfexp(sp(4)) * (len_bins_m(j) - t1))) - t1min) / (t1max - t1min)), t1power);
downselex = (1. + (final - 1.) * pow(fabs((((1. / (1. + mfexp(-mfexp(sp(7)) * (len_bins_m(j) - t2))) - t2min) / (t2max - t2min)))), t2power));
sel(j) = ((((upselex * join1) + 1.0 * (1.0 - join1)) * join2) + downselex * (1 - join2)) * join3 + final * (1 - join3);
} // end size bin loop
break;
} // end New double logistic
// SS_Label_Info_22.3.9 #case 9 old double logistic with 4 parameters
case 9:
{
k1 = int(value(sp(5)));
if (k1 > 1)
sel(1, k1 - 1) = 0.0;
sel(k1, nlength) = elem_prod((1 / (1 + mfexp(-sp(2) * (len_bins_m(k1, nlength) - sp(1))))),
(1 - 1 / (1 + mfexp(-sp(4) * (len_bins_m(k1, nlength) - (sp(1) * sp(6) + sp(3)))))));
sel += 1.0e-6;
sel /= max(sel);
break;
}
// SS_Label_Info_22.3.11 #case 11 selex=1.0 within a range of lengths
case 11:
{
sel = mirror_mask(f); // (y,f,1)
break;
}
// SS_Label_Info_22.3.21 #case 21 non-parametric size selectivity
/* N points; where the first N parameters is vector of sizes for the line segment ends
and second N parameters is selectivity at that size (no transformations) */
case 21: // *******New non-parametric
{
j = 1;
z = 1;
k = seltype(f, 4); // N points
lastsel = 0.0;
lastSelPoint = 0.0;
#ifdef DO_ONCE
if (do_once == 1)
{
if (sp(k) > len_bins(nlength))
{
warnstream << "Selex21: cannot have max selpoint > max_pop_lenbin";
write_message (FATAL, 0); // EXIT!
}
if (sp(k - 1) > len_bins(nlength - 1))
{
warnstream << "Selex21: should not have selpoint(n-1) > pop_lenbin(nlength-1)";
write_message (WARN, 0);
}
}
#endif
while (j <= nlength)
{
if (len_bins(j) <= sp(z))
{
sel(j) = lastsel + (len_bins(j) - lastSelPoint) / (sp(z) - lastSelPoint) * (sp(z + k) - lastsel);
j++;
}
else if (z <= k)
{
lastSelPoint = sp(z);
lastsel = sp(z + k);
z++;
}
else // for sizes beyond last point
{
sel(j) = sp(k + k);
j++;
}
}
break;
}
// SS_Label_Info_22.3.22 #case 22 size selectivity using double_normal_plateau (similar to CASAL)
case 22:
{
peak2 = sp(1) + (0.99 * len_bins(nlength) - sp(1)) / (1. + mfexp(-sp(2)));
upselex = mfexp(sp(3));
downselex = mfexp(sp(4));
for (j = 1; j <= nlength; j++)
{
t1 = len_bins_m(j);
if (t1 < sp(1))
{
sel(j) = mfexp(-square(t1 - sp(1)) / upselex);
}
else if (t1 <= peak2)
{
sel(j) = 1.0;
}
else
{
sel(j) = mfexp(-square(t1 - peak2) / downselex);
}
}
break;
}
// SS_Label_Info_22.3.23 #case 23 size selectivity double_normal_plateau where final value can be greater than 1.0
/* cannot be used with Pope's because can cause selex to be >1.0 */
case 23:
{
if (seltype(f, 3) < 3 || (gg == 1 && seltype(f, 3) == 3) || (gg == 2 && seltype(f, 3) == 4))
{
peak = sp(1);
upselex = mfexp(sp(3));
downselex = mfexp(sp(4));
final = sp(6);
}
else
{ // offset male parameters if seltype(f,3)==3
peak = sp(1) + sp(Maleselparm(f));
upselex = mfexp(sp(3) + sp(Maleselparm(f) + 1));
downselex = mfexp(sp(4) + sp(Maleselparm(f) + 2));
if (sp(6) > -999.)
final = sp(6) + sp(Maleselparm(f) + 3);
}
if (sp(5) < -1000.)
{
j1 = -1001 - int(value(sp(5))); // selex is nil thru bin j1, so set sp(5) equal to first bin with selex (e.g. -1002 to start selex at bin 2)
sel(1, j1) = 1.0e-06;
}
else
{
j1 = startbin - 1; // start selex at bin equal to min sizecomp databin (=j1+1)
if (sp(5) > -999)
{
point1 = 1.0 / (1.0 + mfexp(-sp(5)));
t1min = mfexp(-(square(len_bins_m(startbin) - peak) / upselex)); // fxn at first bin
}
}
if (sp(6) < -1000.)
{
j2 = -1000 - int(value(sp(6))); // selex is constant beyond this sizebin, so set sp(6) equal to last bin with estimated selex
}
else
{
j2 = nlength;
}
peak2 = peak + binwidth2 + (0.99 * len_bins_m(j2) - peak - binwidth2) / (1. + mfexp(-sp(2)));
if (sp(6) > -999)
{
point2 = final;
t2min = mfexp(-(square(len_bins_m(j2) - peak2) / downselex)); // fxn at last bin
}
for (j = j1 + 1; j <= j2; j++)
{
t1 = len_bins_m(j) - peak;
t2 = len_bins_m(j) - peak2;
join1 = 1.0 / (1.0 + mfexp(-(20. * t1 / (1.0 + fabs(t1))))); // note the logit transform on t1 causes range of mfexp to be over -20 to 20
join2 = 1.0 / (1.0 + mfexp(-(20. * t2 / (1.0 + fabs(t2)))));
if (sp(5) > -999)
{
asc = point1 + (1.0 - point1) * (mfexp(-square(t1) / upselex) - t1min) / (1.0 - t1min);
}
else
{
asc = mfexp(-square(t1) / upselex);
}
if (sp(6) > -999)
{
dsc = 1.0 + (point2 - 1.0) * (mfexp(-square(t2) / downselex) - 1.0) / (t2min - 1.0);
}
else
{
dsc = mfexp(-square(t2) / downselex);
}
sel(j) = asc * (1.0 - join1) + join1 * (1.0 - join2 + dsc * join2);
}
if (startbin > 1 && sp(5) >= -1000.)
{
for (j = 1; j <= startbin - 1; j++)
{
sel(j) = square(len_bins_m(j) / len_bins_m(startbin)) * sel(startbin);
}
}
if (j2 < nlength)
{
sel(j2 + 1, nlength) = sel(j2);
}
break;
}
// SS_Label_Info_22.3.25 #case 25 size selectivity using exponential-logistic
case 25:
{
peak = len_bins_m(1) + sp(2) * (len_bins_m(nlength) - len_bins_m(1));
for (j = 1; j <= nlength; j++)
{
sel(j) = mfexp(sp(3) * sp(1) * (peak - len_bins_m(j))) / (1.0 - sp(3) * (1.0 - mfexp(sp(1) * (peak - len_bins_m(j)))));
}
break;
}
// SS_Label_Info_22.3.27 #case 27 size selectivity using cubic spline
// #42 size selectivity using cubic spline scaled by average of values at low bin through high bin
/* first N parameters are the spline knots; second N parameters are ln(selex) at the knot */
/* uses max(raw vector) to achieve scale to 1.0 */
case 42:
scaling_offset = 2;
[[fallthrough]];
case 27:
{
int j2;
// define vectors which form the basis for cubic spline selectivity
// IMPORTANT: these vectors might need to be expanded to fit values for multiple fleets
dvector splineX(1, 200);
dvar_vector splineY(1, 200);
splineX.initialize();
splineY.initialize();
k = seltype(f, 4); // n points to include in cubic spline
for (i = 1; i <= k; i++)
{
splineX(i) = value(sp(i + 3 + scaling_offset)); // "value" required to avoid error, but values should be always fixed anyway
splineY(i) = sp(i + 3 + k + scaling_offset);
}
// calculate last size bin before first knot
z = 1;
while (len_bins_m(z) < splineX(1))
{
z++;
}
j1 = z - 1; // last size bin before first knot
// calculate first size bin beyond last knot
z = nlength;
while (len_bins_m(z) > splineX(k))
{
z--;
}
j2 = z + 1; // first size bin beyond last knot
vcubic_spline_function splinefn = vcubic_spline_function(splineX(1, k), splineY(1, k), sp(2 + scaling_offset), sp(3 + scaling_offset));
tempvec_l = splinefn(len_bins_m); // interpolate selectivity at the mid-point of each population size bin
if (scaling_offset == 0)
{
temp = max(tempvec_l(1, j2));
// if spline code on first parameter line is 10, 11, or 12, then
// scale only based on interval between knots (unless first knot is at first bin)
if ((sp(1) >= 10) & (j1 >= 1))
{
temp = max(tempvec_l(j1, j2));
}
}
else
{
int low_bin = int(value(sp(1)));
int high_bin = int(value(sp(2)));
if (low_bin < 1)
{
low_bin = 1;
warnstream << "Selex pattern 42; value for low bin is less than 1, so set to 1 ";
write_message (ADJUST, 0);
}
if (high_bin > nlength)
{
high_bin = nlength;
warnstream << "Selex pattern 42; value for high bin is greater than " << nlength << ", so set to " << nlength;
write_message (ADJUST, 0);
}
if (high_bin < low_bin)
high_bin = low_bin;
if (low_bin > high_bin)
low_bin = high_bin;
sp(1) = low_bin;
sp(2) = high_bin;
temp = mean(tempvec_l(low_bin, high_bin));
}
tempvec_l -= temp; // rescale to get max of 0.0
tempvec_l(j2 + 1, nlength) = tempvec_l(j2); // set constant above last knot
sel = mfexp(tempvec_l);
// if spline code on third parameter line is 10, 11, or 12, then
// set to zero before the first knot (unless first knot is at first bin)
if ((sp(1 + scaling_offset) >= 10) & (j1 >= 1))
{
sel(1, j1) = 0; // set to 0 before first knot
}
scaling_offset = 0; // reset scaling offset
break;
} // end length-based cubic spline (type 42 or 27)
case 30:
{
warnstream << "Selectivity pattern 30 not valid. Please set up in survey units instead and use pattern 0 for selectivity.";
write_message (FATAL, 0); // EXIT!
break;
}
default: // Selectivity pattern not found
{
warnstream << "Length Selectivity Pattern " << seltype(f, 1) << " not valid.";
write_message (FATAL, 0); // EXIT!
break;
}
} // end select the selectivity pattern
sel_l(y, f, gg) = sel; // Store size-selex in year*type array
} // end direct calc of selex from parameters
// SS_Label_Info_22.4 #Do male relative to female selex
if (gg == 2) // males exist and am now in the male loop
{
if (seltype(f, 1) == 4)
{
sel_l(y, f, 2) = 0.;
} // set males to zero for spawning biomass
else if (seltype(f, 1) == 5) // set males equal to mirrored males
{
// i=int(value(sp(1))); if(i<=0) i=1;
// j=int(value(sp(2))); if(j<=0) j=nlength;
sel_l(y, f, 2) = elem_prod(mirror_mask(f), sel_l(y, seltype(f, 4), 2));
}
else if (seltype(f, 1) == 15) // set males equal to mirrored males
{
sel_l(y, f, 2) = sel_l(y, seltype(f, 4), 2);
}
else if (seltype(f, 3) == 1 || seltype(f, 3) == 2) // do gender selex as offset
{
// k=seltype_Nparam(seltype(f,1)) + 1;
// if(seltype(f,2)>0) k+=seltype(f,2)*4; // first gender offset parm (skip over the retention parameters
// if(seltype(f,1)==6) k += seltype(f,4); // for non-parametric in which N parm is stored in special column
k = Maleselparm(f);
temp = sp(k);
temp1 = 1.;
switch (seltype(f, 3))
{
case 1:
{ // do males relative to females
for (j = 1; j <= nlength; j++)
{
if (len_bins_m(j) <= temp)
{
sel(j) *= mfexp(sp(k + 1) + (len_bins_m(j) - minL_m) / (temp - minL_m) * (sp(k + 2) - sp(k + 1)));
}
else
{
sel(j) *= mfexp(sp(k + 2) + (len_bins_m(j) - temp) / (maxL - temp) * (sp(k + 3) - sp(k + 2)));
}
// if(sel(j)>temp1) temp1=sel(j);
}
sel_l(y, f, 2) = sel;
tempvec_a(1) = max(sel_l(y, f, 1));
tempvec_a(2) = max(sel_l(y, f, 2));
temp1 = max(tempvec_a(1, 2));
sel_l(y, f) /= temp1;
break;
}
case 2:
{ // do females relative to males
sel_l(y, f, 2) = sel;
for (j = 1; j <= nlength; j++)
{
if (len_bins_m(j) <= temp)
{
sel(j) *= mfexp(sp(k + 1) + (len_bins_m(j) - minL_m) / (temp - minL_m) * (sp(k + 2) - sp(k + 1)));
}
else
{
sel(j) *= mfexp(sp(k + 2) + (len_bins_m(j) - temp) / (maxL - temp) * (sp(k + 3) - sp(k + 2)));
}
// if(sel(j)>temp1) temp1=sel(j);
}
sel_l(y, f, 1) = sel;
tempvec_a(1) = max(sel_l(y, f, 1));
tempvec_a(2) = max(sel_l(y, f, 2));
temp1 = max(tempvec_a(1, 2));
sel_l(y, f) /= temp1;
break;
}
} // end switch
} // end do gender selex as offset from other gender
// SS_Label_Info_22.5 #Calculate size-specific retention and discard mortality
else if (seltype(f, 3) != 3 && seltype(f, 3) != 4) // where the "3" and "4" option do the male offset as direct parameters, rathen than do selex as offset
{
sel_l(y, f, 2) = sel;
}
} // end doing males
if (docheckup == 1)
echoinput << gg << " sel-len" << sel_l(y, f, gg) << endl;
} // end loop of genders
// apply 2D_AR adjustment to sex-specific length selectivity
// TwoD_AR_def: read: 1-fleet, 2-ymin, 3-ymax, 4-amin, 5-amax, 6-sigma_amax, 7-use_rho, 8-age/len, 9-dev_phase; 10-before_yrs, 11=after_yrs,
// calc quantities: 12-N_parm_dev, 13-selparm_location
if (TwoD_AR_use(f) > 0)
{
j = TwoD_AR_use(f); // get index for this fleet's effect
if (TwoD_AR_def[j](8) == 1) // age vs length flag
{
z = TwoD_AR_def[j](12); // index of dev vector used
if (docheckup == 1)
echoinput << "2dar for fleet: " << f << " 2DAR: " << j << " dev: " << z << endl;
if (y == styr && (TwoD_AR_before(j) == 3 || TwoD_AR_after(j) == 3)) // if needed, calculate average dev for each length over the range of years
{
TwoD_AR_ave(j).initialize();
for (int yyy = TwoD_AR_ymin(j); yyy <= TwoD_AR_ymax(j); yyy++)
{
k = (yyy - TwoD_AR_ymin(j)) * (TwoD_AR_amax(j) - TwoD_AR_amin(j) + 1); // index of 1st dev in vector created from year and length index
for (int ll = TwoD_AR_amin(j); ll <= TwoD_AR_amax(j); ll++)
{
k++;
TwoD_AR_ave(j, ll) += parm_dev(z, k); // sum devs for each length
}
}
TwoD_AR_ave(j) /= (TwoD_AR_ymax(j) - TwoD_AR_ymin(j) + 1.0);
#ifdef DO_ONCE
if (do_once == 1)
echoinput << "mean 2D AR dev for fleet: " << f << " means: " << TwoD_AR_ave(j) << endl;
#endif
}
if (y < TwoD_AR_ymin(j)) // early years
{
if (TwoD_AR_before(j) == 0) // apply no devs
{
k = -2;
}
else if (TwoD_AR_before(j) == 1) // use first year devs
{
// k=(TwoD_AR_ymin(j)-TwoD_AR_ymin(j))*(TwoD_AR_amax(j)-TwoD_AR_amin(j)+1); // index of 1st dev in vector created from year and length index
k = 0;
}
else if (TwoD_AR_before(j) == 3) // use mean length-specific devs
{
k = -1;
}
}
else if (y <= TwoD_AR_ymax(j)) // in year range for annual devs
{
k = (y - TwoD_AR_ymin(j)) * (TwoD_AR_amax(j) - TwoD_AR_amin(j) + 1); // index of 1st dev in vector created from year and length index
}
else // later years
{
if (TwoD_AR_after(j) == 0) // apply no devs
{
k = -2;
}
else if (TwoD_AR_after(j) == 1) // use last year devs
{
k = (TwoD_AR_ymax(j) - TwoD_AR_ymin(j)) * (TwoD_AR_amax(j) - TwoD_AR_amin(j) + 1);
} // index of 1st dev in vector created from year and length index
else if (TwoD_AR_after(j) == 3) // use mean length-specific devs
{
k = -1;
}
}
if (docheckup == 1)
echoinput << "K value for first dev to use: " << k << endl;
if (k > -2)
{
a1 = TwoD_AR_def[j](13) - 1; // parameter number-1 for sigmasel
dvariable sigmasel;
for (a = TwoD_AR_amin(j); a <= TwoD_AR_amax(j); a++) // loop lengths, using "a" as index
{
if (a <= TwoD_AR_def[j](6)) // so get sigmasel for this length bin
{
a1++;
sigmasel = selparm(a1);
}
if (k >= 0)
{
k++;
if (docheckup == 1)
echoinput << a << " sigmasel: " << sigmasel << endl;
sel_l(y, f, 1, a) *= mfexp(sigmasel * parm_dev(z, k));
if (gender == 2)
sel_l(y, f, 2, a) *= mfexp(sigmasel * parm_dev(z, k));
}
else // use mean devs
{
sel_l(y, f, 1, a) *= mfexp(sigmasel * TwoD_AR_ave(j, a));
if (gender == 2)
sel_l(y, f, 2, a) *= mfexp(sigmasel * TwoD_AR_ave(j, a));
}
}
}
if (docheckup == 1)
echoinput << "len selex after 2D_AR" << endl
<< sel_l(y, f) << endl;
}
}
// SS_Label_Info_22.5.1 #Calculate discmort
// discmort is the size-specific fraction of discarded fish that die
// discmort2 is size-specific fraction that die from being retained or are dead discard
// = elem_prod(sel,(retain + (1-retain)*discmort)) */
if (seltype(f, 2) == 0) // no discard, all retained
{
retain(y, f) = 1.0;
sel_l_r(y, f) = sel_l(y, f);
discmort(y, f) = 1.0;
discmort2(y, f) = sel_l(y, f);
if (gender == 2)
{
discmort_M = 1.0;
retain_M = 1.0;
}
}
else if (seltype(f, 2) == 3) // none retained; all dead
{
retain(y, f) = 0.0;
discmort(y, f) = 1.0;
sel_l_r(y, f) = 0.0;
discmort2(y, f) = sel_l(y, f);
if (gender == 2)
{
discmort_M = 1.0;
retain_M = 0.0;
}
}
else
{
if (seltype(f, 2) < 0) // mirror
{
k = -seltype(f, 2);
retain(y, f) = retain(y, k);
discmort(y, f) = discmort(y, k);
if (seltype(k, 2) == 1)
{
discmort2(y, f) = sel_l(y, f); // all selected fish are dead; this statement does both genders implicitly
}
else
{
discmort2(y, f, 1) = elem_prod(sel_l(y, f, 1), retain(y, f)(1, nlength) + elem_prod((1. - retain(y, f)(1, nlength)), discmort(y, f)(1, nlength)));
}
}
else
{
k = RetainParm(f);
if (sp(k + 2) == -999.)
{
temp1 = 0.0;
}
else if (sp(k + 2) == 999.)
{
temp1 = 1.0;
}
else
{
temp1 = 1.0 / (1.0 + mfexp(-sp(k + 2)));
}
// where maleoffset is a vector of 2*nbins with 0 in length bins for females and 1 for male bins
retain(y, f) = temp1 / (1. + mfexp(-(len_bins_m2 - (sp(k) + male_offset * sp(k + 3))) / sp(k + 1))); // males are at end of vector, so automatically get done
if (seltype(f, 2) == 4)
{
// allow for dome-shaped retention in 3.30 only
retain(y, f) = elem_prod(retain(y, f), (1. - (1. / (1. + mfexp(-(len_bins_m2 - (sp(k + 4) + male_offset * sp(k + 6))) / sp(k + 5))))));
}
if (docheckup == 1 && y == styr)
{
echoinput << "retention parms start at #: " << k << " infl: " << sp(k) << " slope: " << sp(k + 1) << " male_offset " << sp(k + 3) << " asymptote: " << temp1;
if (seltype(f, 2) == 4)
{
// additional dome-shaped retention parameters
echoinput << " " << sp(k + 4) << " " << sp(k + 5) << " " << sp(k + 6);
}
echoinput << "retention " << retain(y, f) << endl;
}
if (seltype(f, 2) == 1) // all discards are dead
{
discmort(y, f) = 1.0;
discmort2(y, f) = sel_l(y, f); // all selected fish are dead; this statement does both genders implicitly
}
else
{
k += N_ret_parm(seltype(f, 2)); // first discard mortality parm
temp = 1. - sp(k + 2);
temp1 = posfun(temp, 0.0, CrashPen);
discmort(y, f) = (1. - temp1 / (1 + mfexp(-(len_bins_m2 - (sp(k) + male_offset * sp(k + 3))) / sp(k + 1)))); // males are at end of vector, so automatically get done
if (docheckup == 1 && y == styr)
echoinput << "discmort " << discmort(y, f) << endl;
discmort2(y, f, 1) = elem_prod(sel_l(y, f, 1), retain(y, f)(1, nlength) + elem_prod((1. - retain(y, f)(1, nlength)), discmort(y, f)(1, nlength)));
}
}
sel_l_r(y, f, 1) = elem_prod(sel_l(y, f, 1), retain(y, f)(1, nlength));
if (gender == 2)
{
discmort_M.shift(nlength1) = discmort(y, f)(nlength1, nlength2);
retain_M.shift(nlength1) = retain(y, f)(nlength1, nlength2);
sel_l_r(y, f, 2) = elem_prod(sel_l(y, f, 2), retain_M.shift(1));
discmort2(y, f, 2) = elem_prod(sel_l(y, f, 2), retain_M.shift(1) + elem_prod((1. - retain_M.shift(1)), discmort_M.shift(1))); // V3.21f
}
}
if (docheckup == 1 && y == styr)
echoinput << "sel-len-r " << sel_l_r(y, f) << endl;
if (docheckup == 1 && y == styr)
echoinput << " dead " << discmort2(y, f) << endl;
} // end loop of fleets for size selex and retention and discard mortality
// SS_Label_Info_22.6 #Do age-selectivity
else
{
for (gg = 1; gg <= gender; gg++)
{
if (gg == 1 || (gg == 2 && seltype(f, 3) >= 3) || (gg == 2 && (seltype(f, 1) == 44 || seltype(f, 1) == 45))) // in age selex
{
// SS_Label_Logic_22.7 #Switch depending on the age-selectivity pattern selected
switch (seltype(f, 1))
{
// SS_Label_Info_22.7.0 #Constant age-specific selex for ages 0 to nages
case 0:
{
sel_a(y, fs, 1)(0, nages) = 1.00;
break;
}
// SS_Label_Info_22.7.10 #Constant age-specific selex for ages 1 to nages
case 10:
{
sel_a(y, fs, 1)(1, nages) = 1.00;
break;