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SS_expval.tpl
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// SS_Label_file #15. **SS_expval.tpl**
// SS_Label_file # * <u>Get_expected_values()</u> // for a specified season and subseason that has data, updates the ALK for that time and calculates expected values for any type of data from any fleet/survey
// SS_Label_file #
//********************************************************************
/* SS_Label_FUNCTION 46 Get_expected_values: check for data */
FUNCTION void Get_expected_values(const int y, const int t);
{
dvariable temp1;
dvar_vector age_exp(0, nages2);
for (subseas = 1; subseas <= N_subseas; subseas++)
{
// make age-length key if needed
ALK_idx = (s - 1) * N_subseas + subseas;
ALK_time = (y - styr) * nseas * N_subseas + (s - 1) * N_subseas + subseas;
if (ALK_subseas_update(ALK_idx) == 1 || have_data(ALK_time, 0, 0, 0) > 0) // need ALK update for growth reasons or for data reasons
{
get_growth3(y, t, s, subseas);
Make_AgeLength_Key(s, subseas);
}
for (f = 1; f <= Nfleet; f++)
{
if (have_data(ALK_time, f, 0, 0) > 0)
{
p = fleet_area(f);
timing = data_time(ALK_time, f, 2) * seasdur(s); // within season elapsed time same for all datatypes of this fleet x time
// make selected age-length sample for this fleet and with this timing
{
exp_AL.initialize();
exp_AL_ret.initialize();
for (g = 1; g <= gmorph; g++)
if (use_morph(g) > 0)
{
gg = sx(g);
if (gg == 2)
{
L1 = nlength1;
L2 = nlength2;
A2 = nages + 1;
} // move over on length dimension to store males
else
{
L1 = 1;
L2 = nlength;
A2 = 0;
}
/*
if(F_Method==1 && surveytime(f)<0.0) // Pope's approximation
{tempvec_a=elem_prod(Nmid(g),sel_a(y,f,gg));} // CHECK Nmid may not exist correctly unless still within the area loop
else if(surveytime(f)<0.0) // mimic fishery catch, but without Hrate so gets available numbers
{tempvec_a=elem_prod(natage(t,p,g),elem_prod(Zrate2(p,g),sel_a(y,f,gg)));}
else // explicit timing
{tempvec_a=elem_prod(natage(t,p,g),elem_prod(mfexp(-Z_rate(t,p,g)*timing),sel_a(y,f,gg)));}
*/
if (timing >= 0.0)
{
tempvec_a = elem_prod(natage(t, p, g), elem_prod(mfexp(-Z_rate(t, p, g) * timing), sel_a(y, f, gg)));
} // explicit timing
else
{
if (F_Method > 1) // mimic fishery catch, so gets mean available numbers
{
tempvec_a = elem_prod(natage(t, p, g), elem_prod(Zrate2(p, g), sel_a(y, f, gg)));
}
else // Pope's approximation
{
Nmid(g) = elem_prod(natage(t, p, g), surv1(s, GP3(g))); // numbers-at-age(g,a) surviving to middle of time period
tempvec_a = elem_prod(Nmid(g), sel_a(y, f, gg));
}
}
tempvec_a = elem_prod(tempvec_a, keep_age(g, ALK_idx));
if (Do_Retain(f) == 0)
{
if (dolen(f) == 1)
{
for (a = 0; a <= nages; a++)
{
temp = tempvec_a(a);
for (z = 1; z <= nlength; z++)
{
exp_AL(a + A2, L1 - 1 + z) += temp * ALK(ALK_idx, g, a, z) * sel_l(y, f, gg, z);
; // note that A2 and L1 depend on what sex g is
}
}
}
else
{
for (a = 0; a <= nages; a++)
{
temp = tempvec_a(a);
for (z = 1; z <= nlength; z++)
{
exp_AL(a + A2, L1 - 1 + z) += temp * ALK(ALK_idx, g, a, z);
}
}
}
exp_AL_ret = exp_AL; // in case user has retain code 2 rather than 0
}
else // need retain matrix
{
if (dolen(f) == 1) // need retention and length
{
for (a = 0; a <= nages; a++)
{
temp = tempvec_a(a);
temp1 = tempvec_a(a) * retain_a(y, f, gg, a);
for (z = 1; z <= nlength; z++)
{
exp_AL(a + A2, L1 - 1 + z) += temp * ALK(ALK_idx, g, a, z) * sel_l(y, f, gg, z); // note that A2 and L1 depend on what sex g is
exp_AL_ret(a + A2, L1 - 1 + z) += temp1 * ALK(ALK_idx, g, a, z) * sel_l(y, f, gg, z) * retain(y, f, L1 - 1 + z); // note that A2 and L1 depend on what sex g is
}
}
}
else // need retention, but no length selex
{
for (a = 0; a <= nages; a++)
{
temp = tempvec_a(a);
temp1 = tempvec_a(a) * retain_a(y, f, gg, a);
for (z = 1; z <= nlength; z++)
{
exp_AL(a + A2, L1 - 1 + z) += temp * ALK(ALK_idx, g, a, z);
exp_AL_ret(a + A2, L1 - 1 + z) += temp1 * ALK(ALK_idx, g, a, z) * retain(y, f, L1 - 1 + z);
}
}
}
}
// code below once erroneously built up catch by morph from exp_AL
// that approach is incorrect, because exp_AL already accumulates the morphs!!!!!
// putting a morph accumulation into the code above would slow computations for everyone in order to have this rarely used feature
// so instead, replicate the above to store directly into morphcomp_exp, rather than into the exp_AL matrix
// note that partition is read with morphcomp data, but it is not used
// fleets with no defined retention function base morphcomp off total catch
// fleets with retention defined, use retained catch
if (have_data(ALK_time, f, 8, 0) > 0) // morphcomp observation
{
int j = have_data(ALK_time, f, 8, 1); // observation number
// {Morphcomp_exp(j,5+GP4(g))+=sum(exp_AL);
if (Do_Retain(f) == 0)
{
if (dolen(f) == 1) // uses length selectivity
{
for (a = 0; a <= nages; a++)
{
temp = tempvec_a(a);
for (z = 1; z <= nlength; z++)
{
Morphcomp_exp(j, 5 + GP4(g)) += temp * ALK(ALK_idx, g, a, z) * sel_l(y, f, gg, z);
; // note that A2 and L1 depend on what sex g is
}
}
}
else
{
for (a = 0; a <= nages; a++)
{
temp = tempvec_a(a);
for (z = 1; z <= nlength; z++)
{
Morphcomp_exp(j, 5 + GP4(g)) += temp * ALK(ALK_idx, g, a, z);
}
}
}
}
else // must base sample on retained catch from a fleet that has retention defined
{
if (dolen(f) == 1) // need retention and length
{
for (a = 0; a <= nages; a++)
{
temp = tempvec_a(a);
temp1 = tempvec_a(a) * retain_a(y, f, gg, a);
for (z = 1; z <= nlength; z++)
{
Morphcomp_exp(j, 5 + GP4(g)) += temp1 * ALK(ALK_idx, g, a, z) * sel_l(y, f, gg, z) * retain(y, f, L1 - 1 + z); // note that A2 and L1 depend on what sex g is
}
}
}
else // need retention, but no length selex
{
for (a = 0; a <= nages; a++)
{
temp = tempvec_a(a);
temp1 = tempvec_a(a) * retain_a(y, f, gg, a);
for (z = 1; z <= nlength; z++)
{
Morphcomp_exp(j, 5 + GP4(g)) += temp1 * ALK(ALK_idx, g, a, z) * retain(y, f, L1 - 1 + z);
}
}
}
}
if (g == gmorph)
{
k = 5 + Morphcomp_nmorph;
Morphcomp_exp(j)(6, k) /= sum(Morphcomp_exp(j)(6, k));
Morphcomp_exp(j)(6, k) += Morphcomp_mincomp;
Morphcomp_exp(j)(6, k) /= 1. + Morphcomp_mincomp * Morphcomp_nmorph;
}
}
} //close gmorph loop
exp_l_temp = colsum(exp_AL); // total size composition
agetemp = rowsum(exp_AL); // total age composition
#ifdef DO_ONCE
if (do_once == 1)
echoinput << "yr " << y << ", seas: " << s << ", fleet:" << f << endl
<< " sampled size " << exp_l_temp << endl
<< " sampled age " << agetemp << endl;
#endif
if (Do_Retain(f) > 0)
{
exp_l_temp_ret = colsum(exp_AL_ret);
exp_truea_ret = rowsum(exp_AL_ret);
#ifdef DO_ONCE
if (do_once == 1)
echoinput << " retained size " << exp_l_temp_ret << endl
<< " retained age " << exp_truea_ret << endl;
;
#endif
}
else
{
exp_truea_ret = agetemp; // covers cases where retention not used, but observations have partition=2
exp_l_temp_ret = exp_l_temp;
}
// end creation of selected A-L
}
if (sum(exp_l_temp) < 1.0e-8)
{
if (do_once == 1)
{
warnstream << current_phase() << " " << niter
<< "warn in first call: Nil selected fish for year, seas, fleet " << y << " " << s << " " << f
<< "; SS may recover; suggest check initial parm. values for selectivity and growth";
write_message (WARN, 0);
}
exp_l_temp += 1.0e-09;
}
for (data_type = 1; data_type <= 9; data_type++)
{
switch (data_type)
{
case (1): // surveyindex
{
/* SS_Label_46.1 expected abundance index */
// NOTE that the Q scaler is factored in later on
j = have_data(ALK_time, f, data_type, 0); // number of observations for this time,f,type
if (j > 0)
{
j = have_data(ALK_time, f, data_type, 1); // for now, only one observations is allowed for surveys
switch (Svy_units(f))
{
case 1: // biomass
{
if (WTage_rd == 1) // using empirical wt-at-age; note that this cannot use GP specific bodyweights
// should sum over all g, but the g is already subsummed when agetemp is created by gender
{
vbio = 0.0;
// warning<<f<<" "<<y<<" "<<s<<" "<<t<<" y_wts "<<Wt_Age_t(y, f, 1)<<endl;
// warning<<f<<" "<<y<<" "<<s<<" "<<t<<" t_wts "<<Wt_Age_t(t, f, 1)<<endl;
if (Do_Retain(f) == 0) // all retained
{
for (a = 0; a <= nages; a++)
vbio += Wt_Age_t(t, f, 1, a) * agetemp(a);
if (gender == 2)
{
for (a = 0; a <= nages; a++)
vbio += Wt_Age_t(t, f, 2, a) * agetemp(a + nages + 1);
}
}
else
{
for (a = 0; a <= nages; a++)
vbio += Wt_Age_t(t, f, 1, a) * exp_truea_ret(a);
if (gender == 2)
{
for (a = 0; a <= nages; a++)
vbio += Wt_Age_t(t, f, 2, a) * exp_truea_ret(a + nages + 1);
}
}
}
else
{
if (Do_Retain(f) == 0)
{
vbio = exp_l_temp * wt_len2(s, 1); // biomass TEMPORARY CODE. Using gp=1 wt at length
}
else
{
vbio = exp_l_temp_ret * wt_len2(s, 1);
}
}
break;
}
case 0: // numbers
{
if (Do_Retain(f) == 0)
{
vbio = sum(exp_l_temp);
}
else
{
vbio = sum(exp_l_temp_ret);
}
break;
}
case 2: // F rate
{
if (fleet_type(f) < 4)
{
vbio = Hrate(f, t);
}
else
{
vbio = pred_M2(predator_rev(f), t);
}
break;
}
case 30: // spawning biomass #30
{
if (pop == 1 || fleet_area(f) == 0)
{
vbio = SSB_current;
}
else
{
vbio = sum(SSB_pop_gp(y, fleet_area(f)));
}
break;
}
case 31: // exp(recruitment deviation) #31
{
vbio = mfexp(recdev(y));
break;
}
case 36: // recruitment deviation #36
{
vbio = recdev(y);
break;
}
case 32: // recruitment without density-dependence (for pre-recruit survey) #32
{
vbio = SSB_current * mfexp(recdev(y));
break;
}
case 33: // recruitment #33
{
vbio = Recruits;
break;
}
case 34: // spawning biomass depletion
{
if (pop == 1 || fleet_area(f) == 0)
{
vbio = (SSB_current + 1.0e-06) / (SSB_virgin + 1.0e-06);
}
else
{
vbio = (sum(SSB_pop_gp(y, fleet_area(f))) + 1.0e-06) / (SSB_virgin + 1.0e-06);
}
break;
}
case 35: // parm deviation #35
{
k = Q_setup(f, 2); // specify which parameter's time-vary vector will be compared to this survey
if (y >= parm_dev_minyr(k) && y <= parm_dev_maxyr(k))
{
vbio = parm_dev(k, y);
// can the mean dev for years with surveys be calculated here?
}
else
{
vbio = 0.0;
}
break;
}
}
Svy_selec_abund(f, j) = vbio; // e.g. the abundance that has been selected through selectivity or other assignment process
// get catchability
// for "float" q, the calculations cannot be done on a year-by-year basis. The calc is done for the whole time series in SS_objfunc.tpl
if (Q_setup(f, 1) == 2) // mirror Q from lower numbered survey
{
Svy_log_q(f, j) = Svy_log_q(Q_setup(f, 2), 1);
Q_parm(Q_setup_parms(f, 1)) = Svy_log_q(f, 1); // base Q So this sets parameter equal to the scaling coefficient and can then have a prior
}
else if (Q_setup(f, 1) == 4) // mirror Q plus an offset
{
Svy_log_q(f, j) = Svy_log_q(Q_setup(f, 2), 1) + Q_parm(Q_setup_parms(f, 1) + 1);
Q_parm(Q_setup_parms(f, 1)) = Svy_log_q(f, 1); // base Q So this sets parameter equal to the scaling coefficient and can then have a prior
}
else // Q from parameter
{
if (Qparm_timevary(Q_setup_parms(f, 1)) == 0) // not time-varying
{
Svy_log_q(f, j) = Q_parm(Q_setup_parms(f, 1)); // set to base parameter value
}
else
{
Svy_log_q(f, j) = parm_timevary(Qparm_timevary(Q_setup_parms(f, 1)), Svy_yr(f, j));
}
}
// SS_Label_Info_25.1.3 #log or not
if (Svy_errtype(f) == -1) // normal
{
Svy_q(f) = Svy_log_q(f); // q already in arithmetic space
}
else if (Svy_errtype(f) >= 0 ) // lognormal, or T-dist
{
Svy_q(f) = mfexp(Svy_log_q(f)); // get q in arithmetic space
}
// Q transformations and offsets
// option 5: add offset, useful when survey units are deviations
// option 3: use power function
// option 6: add offset, then use power function
if (Q_setup(f, 1) == 5 || Q_setup(f, 1) == 6 ) // add offset
{
vbio += Q_parm(Q_setup_parms(f, 1) + 1);
}
if (Q_setup(f, 1) == 3) // link is power function
{
vbio = pow(vbio, 1.0 + Q_parm(Q_setup_parms(f, 1) + 1));
}
if (Q_setup(f, 1) == 6 ) // link is power function
{
vbio = pow(vbio, 1.0 + Q_parm(Q_setup_parms(f, 1) + 2)); // note that this is 2nd parameter after q
}
if (Svy_errtype(f) >= 0) // lognormal or T-distribution
{
Svy_est(f, j) = log(vbio + 0.000001);
}
else
{
Svy_est(f, j) = vbio;
}
// apply catchability, except if float is used.
// With float, catchability is calculated in ss_objfun after all obs have a value for svy_selec_abund
if (Q_setup(f, 5) == 0 || y > endyr) // apply Q if float is not used
// except if y is in forecast, then float Q has already been calculated so can be applied here
{
if (Svy_errtype(f) >= 0) // lognormal or T-dist
{
Svy_est(f, j) += Svy_log_q(f, j);
}
else
{
Svy_est(f, j) *= Svy_q(f, j);
}
}
}
break;
} // end survey index
case (2): // DISCARD_OUTPUT
/* SS_Label_46.2 expected discard amount */
{
if (have_data(ALK_time, f, data_type, 0) > 0) // number of observations
{
j = have_data(ALK_time, f, data_type, 1); // only getting first observation for now
if (fleet_type(f) <= 2)
{
if (catch_ret_obs(f, t) > 0.0 || y > endyr)
{
if (disc_units(f) == 3) // numbers regardless of catchunits for retained catch
{
exp_disc(f, j) = catch_fleet(t, f, 4) - catch_fleet(t, f, 6);
}
else if (catchunits(f) == 1) // biomass units for retained and discarded catch
{
exp_disc(f, j) = catch_fleet(t, f, 1) - catch_fleet(t, f, 3); // discard in biomass
if (disc_units(f) == 2)
exp_disc(f, j) /= (catch_fleet(t, f, 1) + 0.0000001);
}
else // numbers for retained and discarded catch
{
exp_disc(f, j) = catch_fleet(t, f, 4) - catch_fleet(t, f, 6); // discard in numbers
if (disc_units(f) == 2)
exp_disc(f, j) /= (catch_fleet(t, f, 4) + 0.0000001);
}
if (exp_disc(f, j) < 0.0)
{
warnstream << "negative discard occurred for fleet: " << f << "; obs: " << j << "; usually ephemeral issue with bad iteration";
write_message (WARN, 0);
}
}
else
{
exp_disc(f, j) = -1.;
}
}
else if (fleet_type(f) == 4) // predator consumption stored in discard
{
if (disc_units(f) == 3) // numbers
{
exp_disc(f, j) = catch_fleet(t, f, 4); // consumption in numbers
}
else
{
exp_disc(f, j) = catch_fleet(t, f, 1); // consumption in biomass
}
}
else
{
exp_disc(f, j) = -1.;
}
}
break;
} // end discard
case (3): // mean body weight
/* SS_Label_46.3 expected mean body weight */
{
if (have_data(ALK_time, f, data_type, 0) > 0) // number of observations
{
for (int reps = 1; reps <= have_data(ALK_time, f, data_type, 0); reps++)
{
j = have_data(ALK_time, f, data_type, reps); // observation number in overall list
z = mnwtdata(5, j); // type 1=length, 2=weight
int parti = mnwtdata(4, j); // parrtition: 0=all, 1=discard, 2=retained
switch (parti)
{
case 0:
{
if (z == 2)
{
exp_mnwt(j) = (exp_l_temp * wt_len2(s, 1)) / sum(exp_l_temp);
} // total sample
else
{
exp_mnwt(j) = (exp_l_temp * len_bins_m2) / sum(exp_l_temp);
}
break;
}
case 1:
{
if (z == 2)
exp_mnwt(j) = (exp_l_temp - exp_l_temp_ret) * wt_len2(s, 1) / (sum(exp_l_temp) - sum(exp_l_temp_ret)); // discard sample
else
{
exp_mnwt(j) = (exp_l_temp - exp_l_temp_ret) * len_bins_m2 / (sum(exp_l_temp) - sum(exp_l_temp_ret));
}
break;
}
case 2:
{
if (z == 2)
exp_mnwt(j) = (exp_l_temp_ret * wt_len2(s, 1)) / sum(exp_l_temp_ret); // retained only
else
{
exp_mnwt(j) = (exp_l_temp_ret * len_bins_m2) / sum(exp_l_temp_ret);
}
break;
}
}
}
}
break;
}
case (4): // length composition
/* SS_Label_46.4 length composition */
{
if (have_data(ALK_time, f, data_type, 0) > 0)
{
for (j = 1; j <= have_data(ALK_time, f, data_type, 0); j++) // loop all obs of this type
{
i = have_data(ALK_time, f, data_type, j);
if (LenBin_option > 1)
{
if (mkt_l(f, i) == 0)
{
exp_l(f, i) = make_len_bin * exp_l_temp;
} // expected size comp MAtrix * vector = vector
else if (mkt_l(f, i) == 1)
{
exp_l(f, i) = make_len_bin * (exp_l_temp - exp_l_temp_ret);
} // discard sample
else
{
exp_l(f, i) = make_len_bin * exp_l_temp_ret;
} // retained only
}
else // using data_bins same as pop_bins
{
if (mkt_l(f, i) == 0)
{
exp_l(f, i) = exp_l_temp;
} // expected size comp MAtrix * vector = vector
else if (mkt_l(f, i) == 1)
{
exp_l(f, i) = (exp_l_temp - exp_l_temp_ret);
} // discard sample
else
{
exp_l(f, i) = exp_l_temp_ret;
} // retained only
}
if (docheckup == 1)
echoinput << " len obs " << mkt_l(f, i) << " " << tails_l(f, i) << endl
<< obs_l(f, i) << endl
<< exp_l(f, i) << endl;
// code for tail compression, etc in the likelihood section to allow for superyear combinations // mkt=0 Do nothing
} // end lengthcomp loop
}
break;
} // end length composition
case (5): // age composition
/* SS_Label_46.5 age composition */
{
if (have_data(ALK_time, f, data_type, 0) > 0)
{
for (j = 1; j <= have_data(ALK_time, f, data_type, 0); j++) // loop all obs of this type
{
i = have_data(ALK_time, f, data_type, j);
k = ageerr_type_a(f, i); // age-err type
if (use_Lbin_filter(f, i) == 0)
{ // sum across all length bins
if (mkt_a(f, i) == 0)
age_exp = agetemp;
if (mkt_a(f, i) == 1)
age_exp = agetemp - exp_truea_ret; // discard sample
if (mkt_a(f, i) == 2)
age_exp = exp_truea_ret; // retained only
}
else
{ // only use ages from specified range of size bins
// Lbin_filter is a vector with 0 for unselected size bins and 1 for selected bins
if (mkt_a(f, i) == 0)
age_exp = exp_AL * Lbin_filter(f, i);
if (mkt_a(f, i) == 1)
age_exp = (exp_AL - exp_AL_ret) * Lbin_filter(f, i); // discard sample
if (mkt_a(f, i) == 2)
age_exp = exp_AL_ret * Lbin_filter(f, i); // retained only
}
exp_a(f, i) = age_age(k) * age_exp;
if (docheckup == 1)
echoinput << "Lbin " << Lbin_filter(f, i) << endl
<< " obs " << obs_a(f, i) << endl
<< "expected " << age_exp << endl
<< "exp with ageerr " << exp_a(f, i) << endl;
// add code here to store exp_a_true(f,i)=age_exp
// then in data generation the sample can be from true age before ageing error is applied
// if(docheckup==1) echoinput<<" real age "<<age_exp<<endl<<"Lbin "<<Lbin_filter(f,i)<<endl<<" obs "<<obs_a(f,i)<<endl<<" exp with ageerr "<<exp_a(f,i)<<endl;
} // end agecomp loop within fleet/time
}
break;
} // end age composition
case (6): // weight composition (generalized size composition)
/* SS_Label_46.6 weight composition (generalized size composition) */
{
if (SzFreq_Nmeth > 0) // have some sizefreq data
{
if (have_data(ALK_time, f, data_type, 0) > 0)
{
for (j = 1; j <= have_data(ALK_time, f, data_type, 0); j++) // loop all obs of this type
{
iobs = have_data(ALK_time, f, data_type, j); // observation index
SzFreqMethod = SzFreq_obs_hdr(iobs, 6);
SzFreqMethod_seas = nseas * (SzFreqMethod - 1) + s; // index that combines sizefreqmethod and season and used in SzFreqTrans
if (SzFreq_obs_hdr(iobs, 9) > 0) // first occurrence of this method at this time is with fleet = f
{
if (do_once == 1 || (MG_active(3) > 0 && (timevary_MG(y, 3) > 0))) // calc matrix because wtlen parameters have changed
{
for (gg = 1; gg <= gender; gg++)
{
if (gg == 1)
{
z1 = 1;
z2 = nlength;
ibin = 0;
ibinsave = 0;
} // female
else
{
z1 = nlength1;
z2 = nlength2;
ibin = 0;
ibinsave = SzFreq_Nbins(SzFreqMethod);
} // male
topbin = 0.;
botbin = 0.;
// NOTE: wt_len_low is calculated separately for each growth pattern (GPat)
// but the code below still just uses GPat=1 for calculation of the sizefreq transition matrix
switch (SzFreq_units(SzFreqMethod)) // biomass vs. numbers are accumulated in the bins
{
case (1): // units are biomass, so accumulate body weight into the bins; Assume that bin demarcations are also in biomass
{
if (SzFreq_Omit_Small(SzFreqMethod) == 1)
{
while (wt_len_low(s, 1, z1 + 1) < SzFreq_bins(SzFreqMethod, 1) && z1 < z2)
{
z1++;
}
} // ignore tiny fish
if (z1 + 1 >= z2)
{
warnstream << "max population size " << wt_len_low(s, 1, z1) << " is less than first data bin " << SzFreq_bins(SzFreqMethod, 1) << " for SzFreqMethod " << SzFreqMethod;
write_message (FATAL, 0); // EXIT!
}
if (wt_len_low(s, 1, nlength2) < SzFreq_bins(SzFreqMethod, SzFreq_Nbins(SzFreqMethod)))
{
warnstream << "max population size " << wt_len_low(s, 1, nlength2) << " is less than max data bin " << SzFreq_bins(SzFreqMethod, SzFreq_Nbins(SzFreqMethod)) << " for SzFreqMethod " << SzFreqMethod;
write_message (FATAL, 0); // EXIT!
}
for (z = z1; z <= z2; z++)
{
if (ibin == SzFreq_Nbins(SzFreqMethod))
{
SzFreqTrans(SzFreqMethod_seas, z, ibinsave) = wt_len2(s, 1, z);
}
else
{
if (wt_len_low(s, 1, z) >= topbin)
{
ibin++;
ibinsave++;
}
if (ibin > 1)
{
botbin = SzFreq_bins2(SzFreqMethod, ibin);
}
if (ibin == SzFreq_Nbins(SzFreqMethod))
{
SzFreqTrans(SzFreqMethod_seas, z, ibinsave) = wt_len2(s, 1, z);
topbin = 99999.;
}
else
{
topbin = SzFreq_bins2(SzFreqMethod, ibin + 1);
if (wt_len_low(s, 1, z) >= botbin && wt_len_low(s, 1, z + 1) <= topbin)
{
SzFreqTrans(SzFreqMethod_seas, z, ibinsave) = wt_len2(s, 1, z);
}
else
{
temp = (wt_len_low(s, 1, z + 1) - topbin) / wt_len_fd(s, 1, z); // frac in pop bin above (data bin +1)
temp1 = wt_len_low(s, 1, z) + (1. - temp * 0.5) * wt_len_fd(s, 1, z); // approx body wt for these fish
temp2 = wt_len_low(s, 1, z) + (1. - temp) * 0.5 * wt_len_fd(s, 1, z); // approx body wt for fish below
SzFreqTrans(SzFreqMethod_seas, z, ibinsave + 1) = temp * temp1;
SzFreqTrans(SzFreqMethod_seas, z, ibinsave) = (1. - temp) * temp2;
}
}
}
}
if (SzFreq_scale(SzFreqMethod) == 2 && gg == gender) // convert to pounds
{
SzFreqTrans(SzFreqMethod_seas) /= 0.4536;
}
break;
} // end of units in biomass
// NOTE: even though the transition matrix is currently in units of biomass distribution, there is no need to
// normalize to sum to 1.0 here because the normalization will occur after it gets used to create SzFreq_exp
case (2): // units are numbers
{
if (SzFreq_scale(SzFreqMethod) <= 2) // bin demarcations are in weight units (1=kg, 2=lbs), so uses wt_len to compare to bins
{
if (SzFreq_Omit_Small(SzFreqMethod) == 1)
{
while (wt_len_low(s, 1, z1 + 1) < SzFreq_bins(SzFreqMethod, 1) && z1 < z2)
{
z1++;
}
} // ignore tiny fish
if (z1 + 1 >= z2)
{
warnstream << "max population size " << wt_len_low(s, 1, z1) << " is less than first data bin " << SzFreq_bins(SzFreqMethod, 1) << " for SzFreqMethod " << SzFreqMethod;
write_message (FATAL, 0); // EXIT!
}
if (wt_len_low(s, 1, nlength2) < SzFreq_bins(SzFreqMethod, SzFreq_Nbins(SzFreqMethod)))
{
warnstream << "max population size " << wt_len_low(s, 1, nlength2) << " is less than max data bin " << SzFreq_bins(SzFreqMethod, SzFreq_Nbins(SzFreqMethod)) << " for SzFreqMethod " << SzFreqMethod;
write_message (FATAL, 0); // EXIT!
}
for (z = z1; z <= z2; z++)
{
if (ibin == SzFreq_Nbins(SzFreqMethod))
{
SzFreqTrans(SzFreqMethod_seas, z, ibinsave) = 1.;
} //checkup<<" got to last ibin, so put rest of popbins here"<<endl;
else
{
if (wt_len_low(s, 1, z) >= topbin)
{
ibin++;
ibinsave++;
} //checkup<<" incr ibin "<<z<<" "<<ibin<<" "<<len_bins(z)<<" "<<len_bins_dat(ibin);
if (ibin > 1)
{
botbin = SzFreq_bins2(SzFreqMethod, ibin);
}
if (ibin == SzFreq_Nbins(SzFreqMethod)) // checkup<<" got to last ibin, so put rest of popbins here"<<endl;
{
SzFreqTrans(SzFreqMethod_seas, z, ibinsave) = 1.;
topbin = 99999.;
}
else
{
topbin = SzFreq_bins2(SzFreqMethod, ibin + 1);
if (wt_len_low(s, 1, z) >= botbin && wt_len_low(s, 1, z + 1) <= topbin) //checkup<<" pop inside dat, put here"<<endl;
{
SzFreqTrans(SzFreqMethod_seas, z, ibinsave) = 1.;
}
else // checkup<<" overlap"<<endl;
{
SzFreqTrans(SzFreqMethod_seas, z, ibinsave + 1) = (wt_len_low(s, 1, z + 1) - topbin) / wt_len_fd(s, 1, z);
SzFreqTrans(SzFreqMethod_seas, z, ibinsave) = 1. - SzFreqTrans(SzFreqMethod_seas, z, ibinsave + 1);
}
}
}
}
}
else // bin demarcations are in length unit (3=cm, 4=inch) so uses population len_bins to compare to data bins
{
if (SzFreq_Omit_Small(SzFreqMethod) == 1)
{
while (len_bins2(z1 + 1) < SzFreq_bins(SzFreqMethod, 1))
{
z1++;
}
// echoinput<<"accumulate starting at bin: "<<z1<<endl;
} // ignore tiny fish
if (len_bins2(nlength2) < SzFreq_bins(SzFreqMethod, SzFreq_Nbins(SzFreqMethod)))
{
warnstream << "max population len bin " << len_bins2(nlength2) << " is less than max data bin " << SzFreq_bins(SzFreqMethod, SzFreq_Nbins(SzFreqMethod)) << " for SzFreqMethod " << SzFreqMethod;
write_message (FATAL, 0); // EXIT!
}
for (z = z1; z <= z2; z++)
{
if (ibin == SzFreq_Nbins(SzFreqMethod))
{
SzFreqTrans(SzFreqMethod_seas, z, ibinsave) = 1.;
} //checkup<<" got to last ibin, so put rest of popbins here"<<endl;
else
{
if (len_bins2(z) >= topbin)
{
ibin++;
ibinsave++;
} //checkup<<" incr ibin "<<z<<" "<<ibin<<" "<<len_bins(z)<<" "<<len_bins_dat(ibin);
if (ibin > 1)
{
botbin = SzFreq_bins2(SzFreqMethod, ibin);
}
if (ibin == SzFreq_Nbins(SzFreqMethod)) // checkup<<" got to last ibin, so put rest of popbins here"<<endl;
{
SzFreqTrans(SzFreqMethod_seas, z, ibinsave) = 1.;
topbin = 99999.;
}
else
{
topbin = SzFreq_bins2(SzFreqMethod, ibin + 1);
if (len_bins2(z) >= botbin && len_bins2(z + 1) <= topbin) //checkup<<" pop inside dat, put here"<<endl;
{
SzFreqTrans(SzFreqMethod_seas, z, ibinsave) = 1.;
}
else // checkup<<" overlap"<<endl;
{
SzFreqTrans(SzFreqMethod_seas, z, ibinsave + 1) = (len_bins2(z + 1) - topbin) / (len_bins2(z + 1) - len_bins2(z));
SzFreqTrans(SzFreqMethod_seas, z, ibinsave) = 1. - SzFreqTrans(SzFreqMethod_seas, z, ibinsave + 1);
}
}
}
}
}
break;
} // end of units in numbers
}
if (docheckup == 1 && gg == gender)
echoinput << " sizefreq trans_matrix: method/season " << SzFreqMethod << " / " << s << endl
<< trans(SzFreqTrans(SzFreqMethod_seas)) << endl;
} // end gender loop
} // end needing to calc the matrix because it may have changed
} // done calculating the SzFreqTransition matrix for this method
switch (SzFreq_obs_hdr(iobs, 5)) // discard/retained partition
{
case (0):
{
SzFreq_exp(iobs) = trans(SzFreqTrans(SzFreqMethod_seas)) * exp_l_temp;
break;
}
case (1):
{
SzFreq_exp(iobs) = trans(SzFreqTrans(SzFreqMethod_seas)) * (exp_l_temp - exp_l_temp_ret);
break;
}
case (2):
{
SzFreq_exp(iobs) = trans(SzFreqTrans(SzFreqMethod_seas)) * exp_l_temp_ret;
break;
}
}
#ifdef DO_ONCE
if (do_once == 1)
echoinput << y << " " << f << " szfreq_exp_initial " << SzFreq_exp(iobs) << endl;
#endif
if (gender == 2)
{
k = SzFreq_obs_hdr(iobs, 8); // max bins for this method
switch (SzFreq_obs_hdr(iobs, 4)) // combine, select or each gender
{
case (0): // combine genders
{
for (ibin = 1; ibin <= k; ibin++)
SzFreq_exp(iobs, ibin) += SzFreq_exp(iobs, k + ibin);
SzFreq_exp(iobs)(k + 1, 2 * k) = 0.0;
SzFreq_exp(iobs)(1, k) /= sum(SzFreq_exp(iobs)(1, k));
if (SzFreq_mincomp(SzFreqMethod) > 0.0)
{
SzFreq_exp(iobs)(1, k) += SzFreq_mincomp(SzFreqMethod);
SzFreq_exp(iobs)(1, k) /= sum(SzFreq_exp(iobs)(1, k));
}
break;
}
case (1): // female only
{
SzFreq_exp(iobs)(k + 1, 2 * k) = 0.0; // zero out the males so will not interfere with data generation
SzFreq_exp(iobs)(1, k) /= sum(SzFreq_exp(iobs)(1, k));
if (SzFreq_mincomp(SzFreqMethod) > 0.0)
{
SzFreq_exp(iobs)(1, k) += SzFreq_mincomp(SzFreqMethod);
SzFreq_exp(iobs)(1, k) /= sum(SzFreq_exp(iobs)(1, k));
}
break;
}
case (2): // male only
{
ibin = SzFreq_obs_hdr(iobs, 7);
SzFreq_exp(iobs)(1, ibin - 1) = 0.0; // zero out the females so will not interfere with data generation
SzFreq_exp(iobs)(ibin, k) /= sum(SzFreq_exp(iobs)(ibin, k));
if (SzFreq_mincomp(SzFreqMethod) > 0.0)
{
SzFreq_exp(iobs)(ibin, k) += SzFreq_mincomp(SzFreqMethod);
SzFreq_exp(iobs)(ibin, k) /= sum(SzFreq_exp(iobs)(ibin, k));
}
break;
}
case (3): // each gender
{
SzFreq_exp(iobs) /= sum(SzFreq_exp(iobs));
if (SzFreq_mincomp(SzFreqMethod) > 0.0)
{
SzFreq_exp(iobs) += SzFreq_mincomp(SzFreqMethod);
SzFreq_exp(iobs) /= sum(SzFreq_exp(iobs));
}
break;
}
} // end gender switch
} // end have 2 genders
else
{
k = SzFreq_obs_hdr(iobs, 8); // max bins for this method
SzFreq_exp(iobs)(1, k) /= sum(SzFreq_exp(iobs)(1, k));
if (SzFreq_mincomp(SzFreqMethod) > 0.0)
{
SzFreq_exp(iobs)(1, k) += SzFreq_mincomp(SzFreqMethod);
SzFreq_exp(iobs)(1, k) /= sum(SzFreq_exp(iobs)(1, k));
}
}
#ifdef DO_ONCE
if (do_once == 1)
echoinput << y << " " << f << " szfreq_exp_final " << SzFreq_exp(iobs) << endl;
#endif
} // end loop of obs for fleet = f
} // end having some obs for this method in this fleet
} // end use of generalized size freq data
break;
} // end generalized size composition
case (7): // mean size-at-age
/* SS_Label_46.7 mean size at age */
{
if (have_data(ALK_time, f, data_type, 0) > 0)