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age-based calc of sel_dead_num and bio is repaired #663

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Merged
Rick-Methot-NOAA merged 2 commits into from
Apr 1, 2025
Merged

age-based calc of sel_dead_num and bio is repaired #663

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a26ea63
age-based calc of sel_dead_num and bio is repaired
Rick-Methot-NOAA Apr 1, 2025
2479102
improve some code comments
Rick-Methot-NOAA Apr 1, 2025
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18 changes: 12 additions & 6 deletions SS_selex.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -1955,31 +1955,32 @@ FUNCTION void Make_FishSelex()
sel_num(s, f, g) = sel_a(yf, f, gg); // selected numbers
switch (seltype(f + Nfleet, 2)) // age-retention function
{
case 0:
case 0: // no discarding, so just copy the selected quantities
{
sel_ret_bio(s, f, g) = sel_bio(s, f, g); // retained wt-at-age
sel_ret_num(s, f, g) = sel_num(s, f, g); // retained numbers
sel_dead_bio(s, f, g) = sel_bio(s, f, g); // dead wt
sel_dead_num(s, f, g) = sel_num(s, f, g); // dead numbers
break;
}
case 1:
case 1: // age-based retention function is used; all discarded fish assumed dead and have same bodywt as retained fish
{
sel_ret_bio(s, f, g) = elem_prod(sel_bio(s, f, g), retain_a(y, f, gg)); // retained wt-at-age
sel_ret_num(s, f, g) = elem_prod(sel_num(s, f, g), retain_a(y, f, gg)); // retained numbers
sel_dead_bio(s, f, g) = sel_ret_bio(s, f, g); // dead wt
sel_dead_num(s, f, g) = sel_ret_num(s, f, g); // dead numbers
break;
}
case 2:
case 2: // age-based retention and discard mortality, same body wt as retained fish
{
// details of retention and mortality already taken into account with calc of discmort2_a
sel_ret_bio(s, f, g) = elem_prod(sel_bio(s, f, g), retain_a(y, f, gg)); // retained wt-at-age
sel_ret_num(s, f, g) = elem_prod(sel_num(s, f, g), retain_a(y, f, gg)); // retained numbers
sel_dead_bio(s, f, g) = elem_prod(sel_ret_bio(s, f, g), discmort_a(y, f, gg)); // dead wt
sel_dead_num(s, f, g) = elem_prod(sel_ret_num(s, f, g), discmort_a(y, f, gg)); // dead numbers
sel_dead_bio(s, f, g) = elem_prod(Wt_Age_t(tz, f, g), discmort2_a(y, f, gg)); // dead wt
sel_dead_num(s, f, g) = discmort2_a(y, f, gg); // dead numbers
break;
}
case 3: // all selected fish are dead
case 3: // all selected fish are dead; use this for a discard only fleet
{
sel_ret_bio(s, f, g) = 0.0; // retained wt-at-age
sel_ret_num(s, f, g) = 0.0; // retained numbers
Expand All @@ -1988,6 +1989,11 @@ FUNCTION void Make_FishSelex()
break;
}
}
if (docheckup == 1 && y == styr)
{
echoinput << " sel_ret_bio " << sel_ret_bio(s, f, g) << endl
<< " sel_dead_bio " << sel_dead_bio(s, f, g) << endl;
}
}

else // size_selectivity and possible size retention
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