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Merged
iantaylor-NOAA merged 4 commits into from
Jul 14, 2022
Merged

clean up and add comments for mat_fec calcs #349

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3ca4f6a
clean up and add comments for mat_fec calcs
Rick-Methot-NOAA Jul 13, 2022
47a92a3
tweak the output formatting
Rick-Methot-NOAA Jul 13, 2022
fdbfc45
final set of output tweaks, including control.ss_new
Rick-Methot-NOAA Jul 13, 2022
ad087bd
foolish typo
Rick-Methot-NOAA Jul 13, 2022
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87 changes: 48 additions & 39 deletions SS_biofxn.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -1557,62 +1557,71 @@ FUNCTION void get_mat_fec();
if (WTage_rd == 1)
{
fec(g) = Wt_Age_t(t, -2, g);
make_mature_numbers(g)(First_Mature_Age, nages) = 1.0;
// all other vectors set to contant value of 0.5
}
else
{ // make fecundity from biology
{
if (do_fec_len == 1)
{
// make fecundity from biology

if (do_once == 1)
if (do_once == 1)
echoinput << "fecundity option: " << Fecund_Option << " parms: " << wtlen_p(GPat)(5, 6) << endl;
// fec_len should only get calculated in maturity option = 1, 2, 3, or 6
// maturity option 4 and 5 bypass maturity and read empirical fecundity-at-age

switch (Fecund_Option)
{
case 1: // as eggs/kg (SS original configuration)
switch (Fecund_Option)
{
fec_len(gp) = wtlen_p(GPat, 5) + wtlen_p(GPat, 6) * wt_len(s, gp);
fec_len(gp) = elem_prod(wt_len(s, gp), fec_len(gp));
break;
}
case 2:
{ // as eggs = f(length)
fec_len(gp) = wtlen_p(GPat, 5) * pow(len_bins_m, wtlen_p(GPat, 6));
break;
}
case 3:
{ // as eggs = f(body weight)
fec_len(gp) = wtlen_p(GPat, 5) * pow(wt_len(s, gp), wtlen_p(GPat, 6));
break;
}
case 4:
{ // as eggs = a + b*Len
fec_len(gp) = wtlen_p(GPat, 5) + wtlen_p(GPat, 6) * len_bins_m;
if (wtlen_p(GPat, 5) < 0.0)
case 1: // as eggs/kg (SS original configuration)
{
z = 1;
while (fec_len(gp, z) < 0.0)
fec_len(gp) = wtlen_p(GPat, 5) + wtlen_p(GPat, 6) * wt_len(s, gp);
fec_len(gp) = elem_prod(wt_len(s, gp), fec_len(gp));
break;
}
case 2:
{ // as eggs = f(length)
fec_len(gp) = wtlen_p(GPat, 5) * pow(len_bins_m, wtlen_p(GPat, 6));
break;
}
case 3:
{ // as eggs = f(body weight)
fec_len(gp) = wtlen_p(GPat, 5) * pow(wt_len(s, gp), wtlen_p(GPat, 6));
break;
}
case 4:
{ // as eggs = a + b*Len
fec_len(gp) = wtlen_p(GPat, 5) + wtlen_p(GPat, 6) * len_bins_m;
if (wtlen_p(GPat, 5) < 0.0)
{
fec_len(gp, z) = 0.0;
z++;
z = 1;
while (fec_len(gp, z) < 0.0)
{
fec_len(gp, z) = 0.0;
z++;
}
}
break;
}
break;
}
case 5:
{ // as eggs = a + b*Wt
fec_len(gp) = wtlen_p(GPat, 5) + wtlen_p(GPat, 6) * wt_len(s, gp);
if (wtlen_p(GPat, 5) < 0.0)
{
z = 1;
while (fec_len(gp, z) < 0.0)
case 5:
{ // as eggs = a + b*Wt
fec_len(gp) = wtlen_p(GPat, 5) + wtlen_p(GPat, 6) * wt_len(s, gp);
if (wtlen_p(GPat, 5) < 0.0)
{
fec_len(gp, z) = 0.0;
z++;
z = 1;
while (fec_len(gp, z) < 0.0)
{
fec_len(gp, z) = 0.0;
z++;
}
}
break;
}
break;
}
}
if (do_once == 1)
echoinput << "maturity option: " << Maturity_Option << " parms: " << wtlen_p(GPat)(3, 4) << endl;

switch (Maturity_Option)
{
case 1: // Maturity_Option=1 length logistic
Expand Down
21 changes: 16 additions & 5 deletions SS_param.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -88,11 +88,22 @@ PARAMETER_SECTION
4darray Save_PopBio(styr-3*nseas,TimeMax_Fcast_std+nseas,1,2*pop,1,gmorph,0,nages)

LOCAL_CALCS
// clang-format on
mat_len = 1.0;
mat_age = 1.0;
mat_fec_len = 1.0;
fec_len = 1.0;
// clang-format on
// If empirical wt-at-age is used, maturity and fecundity vectors are set to a distinctive value of 0.5
// If parameters are used, then the calcs could be age-based or length-based or both, so start with default value of 1.0
// These calculations happen in function get_mat_fec() in file SS_biofxn.tpl
if (WTage_rd == 1 || Maturity_Option == 4 || Maturity_Option == 5 ) {
mat_len = 0.5;
mat_age = 0.5;
mat_fec_len = 0.5;
fec_len = 0.5;
}
else {
mat_len = 1.0;
mat_age = 1.0;
mat_fec_len = 1.0;
fec_len = 1.0;
}
// clang-format off
END_CALCS

Expand Down
16 changes: 12 additions & 4 deletions SS_readcontrol_330.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -1066,12 +1066,14 @@
END_CALCS

!!// SS_Label_Info_4.5.2 #Process biology
int do_fec_len // switch based on maturity option to trigger fecundity calcs
init_int Maturity_Option // 1=length logistic; 2=age logistic; 3=read age-maturity
// 4=read age-fecundity; 6=read length-maturity
// 4=read age-fecundity; 5=read age-fec from wtatage.ss; 6=read length-maturity
// options 1, 2, 3, 6 can be used with fecundity options to create fecundity-at-age: fec(g)
// options 4 and 5 read fecundity directly, so the concept of maturity is not defined
LOCAL_CALCS
// clang-format on
echoinput
<< Maturity_Option << " Maturity_Option" << endl;
echoinput << Maturity_Option << " Maturity_Option" << endl;
if (Maturity_Option == 3 || Maturity_Option == 4)
{
k1 = N_GP;
Expand All @@ -1088,6 +1090,12 @@
{
k2 = 0;
}
if (Maturity_Option == 4 || Maturity_Option == 5) {
do_fec_len = 0;
}
else {
do_fec_len = 1;
}

if (Maturity_Option == 5)
{
Expand All @@ -1105,7 +1113,7 @@
END_CALCS
init_matrix Age_Maturity(1,k1,0,nages) // for maturity option 3 or 4
init_matrix Length_Maturity(1,k2,1,nlength) // for maturity option 6
!!if(k1>0) echoinput<<" read Age_Maturity for each GP"<<Age_Maturity<<endl;
!!if(k1>0) echoinput<<" read Age_Maturity(3) or Age_Fecundity(4) for each GP"<<Age_Maturity<<endl;
!!if(k2>0) echoinput<<" read Length_Maturity for each GP"<<Length_Maturity<<endl;

init_int First_Mature_Age // first age with non-zero maturity
Expand Down
8 changes: 6 additions & 2 deletions SS_write_report.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -3268,12 +3268,16 @@ FUNCTION void write_bigoutput()
SS2out << sum(use_morph) << " " << nlength << " " << nages << " " << nseas << " N_Used_morphs;_lengths;_ages;_season;_by_season_in_endyr" << endl;
if (gender == 2)
{
SS2out << "GP Bin Low Mean_Size Wt_len_F Mat_len Spawn Wt_len_M Fecundity" << endl;
SS2out << "GP Bin Len_lo Len_mean Wt_F Mat Mat*Fec Wt_M Fec";
}
else
{
SS2out << "GP Bin Low Mean_Size Wt_len Mat_len Spawn Fecundity" << endl;
SS2out << "GP Bin Len_lo Len_mean Wt_F Mat Mat*Fec Fec";
}
if(Maturity_Option == 4 || Maturity_Option == 5) {
SS2out << " // [Mat, Mat*Fec, and Fec reported as 0.5 because maturity option directly reads age_fecundity]";
}
SS2out << endl;
for (gp = 1; gp <= N_GP; gp++)
for (z = 1; z <= nlength; z++)
{
Expand Down
6 changes: 4 additions & 2 deletions SS_write_ssnew.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -1780,8 +1780,10 @@ FUNCTION void write_nucontrol()
<< Length_Maturity << endl;
}
report4 << First_Mature_Age << " #_First_Mature_Age" << endl;

report4 << Fecund_Option << " #_fecundity option:(1)eggs=Wt*(a+b*Wt);(2)eggs=a*L^b;(3)eggs=a*Wt^b; (4)eggs=a+b*L; (5)eggs=a+b*W" << endl;
if (Maturity_Option == 4 || Maturity_Option == 5) {
report4 << "# NOTE: maturity options 4 and 5 cause fecundity_at_length to be ignored, but parameters still needed " << endl;
}
report4 << Fecund_Option << " #_fecundity_at_length option:(1)eggs=Wt*(a+b*Wt);(2)eggs=a*L^b;(3)eggs=a*Wt^b; (4)eggs=a+b*L; (5)eggs=a+b*W" << endl;
report4 << Hermaphro_Option << " #_hermaphroditism option: 0=none; 1=female-to-male age-specific fxn; -1=male-to-female age-specific fxn" << endl;
if (Hermaphro_Option != 0)
{
Expand Down