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adjust the Lmin test for t0 users; more comments in code #727

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Merged
Rick-Methot-NOAA merged 5 commits into from
Sep 18, 2025
Merged

adjust the Lmin test for t0 users; more comments in code #727

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e10e167
adjust the Lmin test for t0 users; more comments in code
Rick-Methot-NOAA Sep 11, 2025
2d6552b
revised Lmin tests
Rick-Methot-NOAA Sep 13, 2025
9b3fcf9
add neg. length test to report
Rick-Methot-NOAA Sep 15, 2025
0552924
convert lbin_lo to real for compare to len_bins
Rick-Methot-NOAA Sep 16, 2025
7d3a86d
add use_morph(g) to the test
Rick-Methot-NOAA Sep 17, 2025
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25 changes: 19 additions & 6 deletions SS_prelim.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -1285,6 +1285,7 @@

// SS_Label_Info_6.8.3 #Call fxn get_growth2() to calculate size-at-age
get_growth2(styr); // in preliminary calcs
get_growth3(styr, t_base + 1, 1, 1); // this will apply linear below AFIX
gp = 0;
for (gg = 1; gg <= gender; gg++)
for (int GPat = 1; GPat <= N_GP; GPat++)
Expand All @@ -1294,19 +1295,31 @@
for (settle = 1; settle <= N_settle_timings; settle++)
{
g += N_platoon;
echoinput << "sex: " << gg << "; Gpat: " << GPat << " settle: " << settle << "; L-at-Amin: " << Lmin(gp) << "; L at max age: " << Ave_Size(styr, 1, g, nages) << endl;
if (len_bins(1) > Lmin(gp))
if (use_morph(g) > 0)
{
warnstream << "Minimum pop size bin:_" << len_bins(1) << "; is > L at Amin for sex: " << gg
<< "; Gpat: " << GPat << "; L= " << Lmin(gp);
write_message (WARN, 0);
}
echoinput << "sex: " << gg << "; Gpat: " << GPat << " settle: " << settle << "; L-at-Amin: " << Lmin(gp) << "; L at max age: " << Ave_Size(styr, 1, g, nages) << endl;
if (Ave_Size(styr, 1, g, nages) > 0.95 * len_bins(nlength))
{
warnstream << "Maximum pop size bin:_" << len_bins(nlength) << "; is within 5% of L at maxage for sex: " << gg
<< "; Gpat: " << GPat << " settle: " << settle << "; L= " << Ave_Size(styr, 1, g, nages);
write_message (WARN, 0);
}
for (a = 0; a <= nages; a++)
{
if (Ave_Size(styr, 1, g, a) < 0.0)
{
warnstream << "Negative Length calculated for: " << "sex: " << gg << "; Gpat: " << GPat << " settle: " << settle
<< " age: " << a << " Len@age = " << Ave_Size(styr, 1, g, a);
write_message (FATAL, 0);
}
if (a > 0 && Ave_Size(styr, 1, g, a) < Ave_Size(styr, 1, g, a-1))
{
warnstream << "Decreasing Len@age calculated for sex: " << gg << "; Gpat: " << GPat << " settle: " << settle
<< " at age: " << a << " Len@age = " << Ave_Size(styr, 1, g, a) << " < " << Ave_Size(styr, 1, g, a - 1);
write_message (WARN, 0);
}
}
}
}
}

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20 changes: 12 additions & 8 deletions SS_readcontrol_330.tpl
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Expand Up @@ -1614,20 +1614,24 @@
Ip += N_natMparms;
mgp_type(Ip, Ip + N_growparms - 1) = 2; // growth parms

// check on out of bound Lmin values. Only check females because males can be offset from females
// allow for AFIX < 0 because those models are inputting the age at L=0, which must be negative
// check on out of bound Lmin values. Only check females because male parameter can be offset from females
// bypass for AFIX <= 0 because those models are inputting the age at L=0, commonly termed t0
// note that AFIX is age post-settlement
// if AFIX is > 0, then fish settle at age 0.0 at length = len_bins(1), then grow linearly until reaching Lmin at age (post-settlement) = AFIX
// keeping Lmin >= len_bins(1) prevents shrinkage during that linear growth stanza
// additional checks occur in preliminary calcs regarding generating L@age < 0, or generating a decreasing trend in L@age due to linear growth below AFIX

if ( gp == 1 && WTage_rd == 0 && AFIX >= 0.0)
if ( gp == 1 && WTage_rd == 0 && AFIX >= 0.0) // apply test
{
if (MGparm_1(Ip,1) < len_bins(1))
{
warnstream << "parm min for Lmin: " << MGparm_1(Ip,1) << " cannot be less than population min length bin " << len_bins(1);
write_message (FATAL, 0); // EXIT!
warnstream << "parm min for Lmin: " << MGparm_1(Ip,1) << " should not be less than population min length bin " << len_bins(1);
write_message (WARN, 0); // EXIT!
}
if (MGparm_1(Ip,3) < len_bins(1))
if (MGparm_1(Ip,3) < len_bins(1) && MGparm_1(Ip,7) >= 0)
{
warnstream << "parm init value for Lmin: " << MGparm_1(Ip,3) << " cannot be less than population min length bin " << len_bins(1);
write_message (FATAL, 0); // EXIT!
warnstream << "parm init value for Lmin: " << MGparm_1(Ip,3) << " should not be less than population min length bin if Lmin estimated" << len_bins(1);
write_message (WARN, 0); // EXIT!
}
}
// check on estimation of variance parameters for CV_young and CV_old
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4 changes: 2 additions & 2 deletions SS_readdata_330.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -2445,8 +2445,8 @@
imatrix mkt_a(1,Nfleet,1,Nobs_a);
3darray Lbin_filter(1,Nfleet,1,Nobs_a,1,nlength2);
imatrix use_Lbin_filter(1,Nfleet,1,Nobs_a);
imatrix Lbin_lo(1,Nfleet,1,Nobs_a);
imatrix Lbin_hi(1,Nfleet,1,Nobs_a);
matrix Lbin_lo(1,Nfleet,1,Nobs_a);
matrix Lbin_hi(1,Nfleet,1,Nobs_a);
3darray tails_a(1,Nfleet,1,Nobs_a,1,4); // min-max bin for females; min-max bin for males
3darray header_a(1,Nfleet,1,Nobs_a,1,9);
3darray header_a_rd(1,Nfleet,1,Nobs_a,2,3);
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37 changes: 37 additions & 0 deletions SS_write_report.tpl
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Expand Up @@ -3682,6 +3682,43 @@ FUNCTION void write_bigoutput()
SS2out << save_G_parm(g)(1, 2) << " " << sx(save_G_parm(g, 3)) << " " << save_G_parm(g)(3, 22) << endl;
}
}

gp = 0;
for (gg = 1; gg <= gender; gg++)
for (int GPat = 1; GPat <= N_GP; GPat++)
{
gp++;
g = g_Start(gp); // base platoon
for (settle = 1; settle <= N_settle_timings; settle++)
{
g += N_platoon;
if (use_morph(g) > 0)
{
if (Ave_Size(styr, 1, g, nages) > 0.95 * len_bins(nlength))
{
warnstream << "Maximum pop size bin:_" << len_bins(nlength) << "; is within 5% of L at maxage for sex: " << gg
<< "; Gpat: " << GPat << " settle: " << settle << "; L= " << Ave_Size(styr, 1, g, nages);
write_message (WARN, 0);
}
for (a = 0; a <= nages; a++)
{
if (Ave_Size(styr, 1, g, a) < 0.0)
{
warnstream << "Negative Length calculated for: " << "sex: " << gg << "; Gpat: " << GPat << " settle: " << settle
<< " age: " << a << " Len@age = " << Ave_Size(styr, 1, g, a);
write_message (WARN, 0);
}
if (a > 0 && Ave_Size(styr, 1, g, a) < Ave_Size(styr, 1, g, a-1))
{
warnstream << "Decreasing Len@age calculated for sex: " << gg << "; Gpat: " << GPat << " settle: " << settle
<< " at age: " << a << " Len@age = " << Ave_Size(styr, 1, g, a) << " < " << Ave_Size(styr, 1, g, a - 1);
write_message (WARN, 0);
}
}
}
}
}

// REPORT_KEYWORD 46 SEASONAL_BIOLOGY
if (pick_report_use(46) == "Y" && MGparm_doseas > 0)
{
Expand Down
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