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new approach for weight composition #752

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5ebff20
first commit for narrow sizebin problem
Rick-Methot-NOAA Jan 30, 2026
a3e4a2e
initial commit of rebin fxn
Rick-Methot-NOAA Feb 3, 2026
7f10ed4
WIP
Rick-Methot-NOAA Feb 4, 2026
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43 changes: 39 additions & 4 deletions SS_expval.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -704,7 +704,7 @@ FUNCTION void Get_expected_values(const int y, const int t);
{
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)
if (SzFreq_Omit_Small(SzFreqMethod) == 1)
{
while (wt_len_low(s, 1, z1 + 1) < SzFreq_bins(SzFreqMethod, 1) && z1 < z2)
{
Expand Down Expand Up @@ -776,6 +776,7 @@ FUNCTION void Get_expected_values(const int y, const int t);
{
if (SzFreq_scale(SzFreqMethod) <= 2) // bin demarcations are in weight units (1=kg, 2=lbs), so uses wt_len to compare to bins
{
warning<<"process_szfreq"<<endl;
if (SzFreq_Omit_Small(SzFreqMethod) == 1)
{
while (wt_len_low(s, 1, z1 + 1) < SzFreq_bins(SzFreqMethod, 1) && z1 < z2)
Expand All @@ -796,8 +797,10 @@ FUNCTION void Get_expected_values(const int y, const int t);

for (z = z1; z <= z2; z++)
{
warning<<z <<" size " << wt_len_low(s, 1, z)<<" bin "<<ibin<< " size_at_bin "<<SzFreq_bins2(SzFreqMethod, ibin)<<" save_ibin " <<ibinsave<<" botbin "<<botbin<<" topbin "<<topbin<< endl;
if (ibin == SzFreq_Nbins(SzFreqMethod))
{
warning<<" last bin "<<ibin<<endl;
SzFreqTrans(SzFreqMethod_seas, z, ibinsave) = 1.;
} //checkup<<" got to last ibin, so put rest of popbins here"<<endl;
else
Expand All @@ -806,25 +809,40 @@ FUNCTION void Get_expected_values(const int y, const int t);
{
ibin++;
ibinsave++;
} //checkup<<" incr ibin "<<z<<" "<<ibin<<" "<<len_bins(z)<<" "<<len_bins_dat(ibin);
warning<<" wt>=topbin, so incr ibin "<<ibin<<" ibinsave "<<ibinsave<<endl;
}
if (ibin > 1)
{
botbin = SzFreq_bins2(SzFreqMethod, ibin);
warning<<" incr botbin to "<<botbin<<endl;

}
if (ibin == SzFreq_Nbins(SzFreqMethod)) // checkup<<" got to last ibin, so put rest of popbins here"<<endl;
if (ibin == SzFreq_Nbins(SzFreqMethod))
{
warning<<" 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);
warning<<"check using topbin = "<<topbin<<endl;
if (wt_len_low(s, 1, z) >= botbin && wt_len_low(s, 1, z + 1) <= topbin) //checkup<<" pop inside dat, put here"<<endl;
{
warning<<"all in bin"<<endl;
SzFreqTrans(SzFreqMethod_seas, z, ibinsave) = 1.;
}
else // checkup<<" overlap"<<endl;
else if (wt_len_low(s, 1, z) >= topbin)
{
// this should have the fish in z size range distributed across all bins >= size(z) until get to overlap
warning<<" size > current bin, increment bin index "<<endl;
ibin++;
ibinsave++;
}
else
{
warning<<" 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);
}
Expand All @@ -835,6 +853,23 @@ FUNCTION void Get_expected_values(const int y, const int t);

else // bin demarcations are in length unit (3=cm, 4=inch) so uses population len_bins to compare to data bins
{
/* wt_len_low(s, 1, z1 + 1) < SzFreq_bins(SzFreqMethod, 1) && z1 < z2)
FUNCTION dvector rebin(const dvector& src_edges, const dvector& src_counts, const dvector& dest_edges)
3darray wt_len_low(1,nseas,1,N_GP,1,nlength2) // wt at lower edge of size bin
*/
dvector freq_in(1, z2-z1); // fill the input
freq_in = 1.;
echoinput << " z1: " << z1 << " z2: " << z2 << endl;
echoinput << " freq_in: " << freq_in << endl;
dvector bins_in(1, z2-z1);
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Vector size and assignment mismatch. bins_in needs z2-z1+2 elements to store bin edges (boundaries) for z2-z1+1 bins. The vector should be sized dvector bins_in(1, z2-z1+2) to accommodate N+1 edges for N bins

Suggested change
dvector bins_in(1, z2-z1);
dvector bins_in(1, z2-z1+2);

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bins_in = len_bins2(z1, z2); // input bins shifted
Comment on lines +860 to +865
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Vector size mismatch. A vector from index 1 to z2-z1 has size z2-z1, but should have size z2-z1+1 to match the number of bins from z1 to z2 inclusive. Should be dvector freq_in(1, z2-z1+1)

Suggested change
dvector freq_in(1, z2-z1); // fill the input
freq_in = 1.;
echoinput << " z1: " << z1 << " z2: " << z2 << endl;
echoinput << " freq_in: " << freq_in << endl;
dvector bins_in(1, z2-z1);
bins_in = len_bins2(z1, z2); // input bins shifted
dvector freq_in(1, z2-z1+1); // fill the input (one element per bin edge from z1 to z2 inclusive)
freq_in = 1.;
echoinput << " z1: " << z1 << " z2: " << z2 << endl;
echoinput << " freq_in: " << freq_in << endl;
dvector bins_in(1, z2-z1+1);
bins_in = len_bins2(z1, z2); // input bins shifted (edges from z1 to z2 inclusive)

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echoinput << " bins_in: " << bins_in << endl;
// dvector bins_out(1, z2-z1) = SzFreq_bins(SzFreqMethod
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Incomplete commented-out code should be removed. This appears to be leftover development code that creates confusion.

Suggested change
// dvector bins_out(1, z2-z1) = SzFreq_bins(SzFreqMethod

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dvector freq_out(1, SzFreq_Nbins(SzFreqMethod));

freq_out = rebin(bins_in, freq_in, SzFreq_bins(SzFreqMethod));
echoinput << " freq_out: " << freq_out << endl;

if (SzFreq_Omit_Small(SzFreqMethod) == 1)
{
while (len_bins2(z1 + 1) < SzFreq_bins(SzFreqMethod, 1))
Expand Down
38 changes: 38 additions & 0 deletions SS_miscfxn.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -120,3 +120,41 @@ FUNCTION dvariable Comp_logL_Dirichlet(const double& Nsamp, const dvariable& dir
logL = sum(gammln(Nsamp * obs_comp + dirichlet_Parm * exp_comp)) - sum(gammln(dirichlet_Parm * exp_comp));
return (logL);
}

FUNCTION dvector rebin(const dvector& src_edges, const dvector& src_counts, const dvector& dest_edges)
{
/*
This implementation takes two vectors representing the boundaries (edges) of the source
and destination bins, and one vector for the source counts.

Rebins frequency data from one set of boundaries to another.
@param src_edges Boundaries of the original bins (size N+1).
@param src_counts Frequency/counts in original bins (size N).
@param dest_edges Boundaries of the new bins (size M+1).
@return Vector of rebinned frequency data (size M).
*/

dvector dest_counts(dest_edges.size() - 1, 0.0);
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Incorrect constructor syntax for dvector initialization. ADMB dvectors use index ranges, not size-based construction. Should be dvector dest_counts(1, dest_edges.size() - 1); dest_counts.initialize();

Suggested change
dvector dest_counts(dest_edges.size() - 1, 0.0);
dvector dest_counts(1, dest_edges.size() - 1);
dest_counts.initialize();

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for (int i = 0; i < dest_counts.size(); ++i) {
double d_low = dest_edges[i];
double d_high = dest_edges[i + 1];

for (int j = 0; j < src_counts.size(); ++j) {
double s_low = src_edges[j];
double s_high = src_edges[j + 1];

// Calculate the overlap between [d_low, d_high] and [s_low, s_high]
double overlap_low = max(d_low, s_low);
double overlap_high = min(d_high, s_high);

if (overlap_low < overlap_high) {
double overlap_width = overlap_high - overlap_low;
double src_bin_width = s_high - s_low;

// Distribute source count proportionally to the overlap area
dest_counts[i] += src_counts[j] * (overlap_width / src_bin_width);
}
}
}
Comment on lines +137 to +158
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ADMB dvector indexing is 1-based by default, not 0-based. This loop should iterate from the vector's indexmin() to indexmax(), or adjust the initialization to use 0-based indexing with dvector dest_counts(0, dest_edges.size() - 2)

Suggested change
dvector dest_counts(dest_edges.size() - 1, 0.0);
for (int i = 0; i < dest_counts.size(); ++i) {
double d_low = dest_edges[i];
double d_high = dest_edges[i + 1];
for (int j = 0; j < src_counts.size(); ++j) {
double s_low = src_edges[j];
double s_high = src_edges[j + 1];
// Calculate the overlap between [d_low, d_high] and [s_low, s_high]
double overlap_low = max(d_low, s_low);
double overlap_high = min(d_high, s_high);
if (overlap_low < overlap_high) {
double overlap_width = overlap_high - overlap_low;
double src_bin_width = s_high - s_low;
// Distribute source count proportionally to the overlap area
dest_counts[i] += src_counts[j] * (overlap_width / src_bin_width);
}
}
}
// dest_counts has one fewer element than dest_edges and follows the same index base.
dvector dest_counts(dest_edges.indexmin(), dest_edges.indexmax() - 1);
dest_counts.initialize();
for (int i = dest_counts.indexmin(); i <= dest_counts.indexmax(); ++i)
{
double d_low = dest_edges(i);
double d_high = dest_edges(i + 1);
for (int j = src_counts.indexmin(); j <= src_counts.indexmax(); ++j)
{
double s_low = src_edges(j);
double s_high = src_edges(j + 1);
// Calculate the overlap between [d_low, d_high] and [s_low, s_high]
double overlap_low = max(d_low, s_low);
double overlap_high = min(d_high, s_high);
if (overlap_low < overlap_high)
{
double overlap_width = overlap_high - overlap_low;
double src_bin_width = s_high - s_low;
// Distribute source count proportionally to the overlap area
dest_counts(i) += src_counts(j) * (overlap_width / src_bin_width);
}
}
}

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Comment on lines +137 to +158
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Same indexing issue as outer loop. ADMB vectors use 1-based indexing by default. Should iterate from src_counts.indexmin() to src_counts.indexmax()

Suggested change
dvector dest_counts(dest_edges.size() - 1, 0.0);
for (int i = 0; i < dest_counts.size(); ++i) {
double d_low = dest_edges[i];
double d_high = dest_edges[i + 1];
for (int j = 0; j < src_counts.size(); ++j) {
double s_low = src_edges[j];
double s_high = src_edges[j + 1];
// Calculate the overlap between [d_low, d_high] and [s_low, s_high]
double overlap_low = max(d_low, s_low);
double overlap_high = min(d_high, s_high);
if (overlap_low < overlap_high) {
double overlap_width = overlap_high - overlap_low;
double src_bin_width = s_high - s_low;
// Distribute source count proportionally to the overlap area
dest_counts[i] += src_counts[j] * (overlap_width / src_bin_width);
}
}
}
// ADMB vectors are 1-based by default; derive index ranges from the edge vectors.
int dest_min = dest_edges.indexmin();
int dest_max = dest_edges.indexmax() - 1; // last bin uses dest_edges(dest_max+1)
dvector dest_counts(dest_min, dest_max);
dest_counts.initialize();
for (int i = dest_min; i <= dest_max; ++i)
{
double d_low = dest_edges(i);
double d_high = dest_edges(i + 1);
int src_min = src_counts.indexmin();
int src_max = src_counts.indexmax();
for (int j = src_min; j <= src_max; ++j)
{
double s_low = src_edges(j);
double s_high = src_edges(j + 1);
// Calculate the overlap between [d_low, d_high] and [s_low, s_high]
double overlap_low = max(d_low, s_low);
double overlap_high = min(d_high, s_high);
if (overlap_low < overlap_high)
{
double overlap_width = overlap_high - overlap_low;
double src_bin_width = s_high - s_low;
// Distribute source count proportionally to the overlap area
dest_counts(i) += src_counts(j) * (overlap_width / src_bin_width);
}
}
}

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return (dest_counts);
}
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