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restore sizecomp bootstrap output #542

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Merged
Rick-Methot-NOAA merged 6 commits into from
Dec 21, 2023
Merged

restore sizecomp bootstrap output #542

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cbac783
restore sizecomp bootstrap output
Rick-Methot-NOAA Dec 19, 2023
a92f602
try different artifact names (#543)
e-perl-NOAA Dec 19, 2023
f2b5205
spellcheck
Rick-Methot-NOAA Dec 19, 2023
5c285fb
restore sizecomp bootstrap output
Rick-Methot-NOAA Dec 19, 2023
e42f8a2
spellcheck
Rick-Methot-NOAA Dec 19, 2023
b66c5ab
Merge branch 'restore-boot-sizecomp' of https://github.com/nmfs-ost/s…
e-perl-NOAA Dec 19, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/build-ss3.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -267,5 +267,5 @@ jobs:
if: success()
uses: actions/upload-artifact@main
with:
name: 'ss3'
name: ss3-${{ matrix.config.os }}
path: SS330/
62 changes: 56 additions & 6 deletions SS_write_ssnew.tpl
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Expand Up @@ -61,7 +61,6 @@ FUNCTION void write_nudata()
newdatfilename = "data_boot_" + anystring2 + ".ss";
}
datinfostring = "bootstrap";
// sprintf(datinfostring, "bootdata:_%d", Nudat);
}
anystring = ssnew_pathname + newdatfilename;
report1.open(anystring);
Expand Down Expand Up @@ -391,7 +390,7 @@ FUNCTION void write_nudata()
{ report1 << j << " ";}
report1 << " # Method" << endl;
report1 << SzFreq_Nbins << " #_Sizefreq N bins" << endl;
report1 << SzFreq_units << " #_Sizetfreq units(1=bio/2=num)" << endl;
report1 << SzFreq_units << " #_Sizefreq units(1=bio/2=num)" << endl;
report1 << SzFreq_scale << " #_Sizefreq scale(1=kg/2=lbs/3=cm/4=inches)" << endl;
report1 << SzFreq_mincomp << " #_Sizefreq: small constant to add to comps" << endl;
report1 << SzFreq_nobs << " #_Sizefreq number of obs per method" << endl;
Expand Down Expand Up @@ -793,7 +792,7 @@ FUNCTION void write_nudata()
{ report1 << j << " ";}
report1 << " # Method" << endl;
report1 << SzFreq_Nbins << " #_Sizefreq N bins" << endl;
report1 << SzFreq_units << " #_Sizetfreq units(1=bio/2=num)" << endl;
report1 << SzFreq_units << " #_Sizefreq units(1=bio/2=num)" << endl;
report1 << SzFreq_scale << " #_Sizefreq scale(1=kg/2=lbs/3=cm/4=inches)" << endl;
report1 << SzFreq_mincomp << " #_Sizefreq: small constant to add to comps" << endl;
report1 << SzFreq_nobs << " #_Sizefreq number of obs per method" << endl;
Expand All @@ -805,7 +804,10 @@ FUNCTION void write_nudata()
<< "#Note: negative value for first bin makes it accumulate all smaller fish vs. truncate small fish" << endl;
for (i = 1; i <= SzFreq_Nmeth; i++)
{ report1 << SzFreq_Omit_Small(i) * SzFreq_bins1(i, 1) << SzFreq_bins1(i)(2, SzFreq_Nbins(i)) << endl; }
report1 << "#_method year month fleet sex partition SampleSize <data> " << endl << SzFreq_obs1 << endl;
report1 << "#_method year month fleet sex partition SampleSize <data> " << endl;
for (iobs = 1; iobs <= SzFreq_totobs; iobs++) {
report1 << SzFreq_obs1(iobs)(1, 7) << " " << SzFreq_exp(iobs) << endl;
}
}

// begin tagging data section #2 (expected values)
Expand Down Expand Up @@ -1306,7 +1308,7 @@ FUNCTION void write_nudata()
{ report1 << j << " ";}
report1 << " # Method" << endl;
report1 << SzFreq_Nbins << " #_Sizefreq N bins" << endl;
report1 << SzFreq_units << " #_Sizetfreq units(1=bio/2=num)" << endl;
report1 << SzFreq_units << " #_Sizefreq units(1=bio/2=num)" << endl;
report1 << SzFreq_scale << " #_Sizefreq scale(1=kg/2=lbs/3=cm/4=inches)" << endl;
report1 << SzFreq_mincomp << " #_Sizefreq: small constant to add to comps" << endl;
report1 << SzFreq_nobs << " #_Sizefreq number of obs per method" << endl;
Expand All @@ -1318,7 +1320,55 @@ FUNCTION void write_nudata()
<< "#Note: negative value for first bin makes it accumulate all smaller fish vs. truncate small fish" << endl;
for (i = 1; i <= SzFreq_Nmeth; i++)
{ report1 << SzFreq_Omit_Small(i) * SzFreq_bins1(i, 1) << SzFreq_bins1(i)(2, SzFreq_Nbins(i)) << endl; }
report1 << "#_method year month fleet sex partition SampleSize <data> " << endl << SzFreq_obs1 << endl;
report1 << "#_method year month fleet sex partition SampleSize <data> " << endl;
j = 2 * max(SzFreq_Nbins);
dvector temp_probs3(1, j);
dvector SzFreq_newdat(1, j);
for (iobs = 1; iobs <= SzFreq_totobs; iobs++)
{
f = SzFreq_obs1(iobs, 1); // sizefreq method
double Nsamp_dat = 50000;
if (SzFreq_obs1(iobs, 7) < Nsamp_dat)
Nsamp_dat = SzFreq_obs1(iobs, 7);
SzFreq_newdat.initialize();

switch (Comp_Err_Sz(f))
{
case 0:
{
Nsamp_DM = Nsamp_dat;
break;
}
case 1: // Dirichlet #1
{
dirichlet_Parm = mfexp(selparm(Comp_Err_parmloc(Comp_Err_Sz2(f),1))); // Thorson's theta from eq 10
// effN_DM = 1/(1+theta) + n*theta/(1+theta)
Nsamp_DM = value(1. / (1. + dirichlet_Parm) + Nsamp_dat * dirichlet_Parm / (1. + dirichlet_Parm));
break;
}
case 2: // Dirichlet #2
{
dirichlet_Parm = mfexp(selparm(Comp_Err_parmloc(Comp_Err_Sz2(f),1))); // Thorson's beta from eq 12
// effN_DM = (n+n*beta)/(n+beta) computed in Fit_LenComp
Nsamp_DM = value((nsamp_l(f, i) + dirichlet_Parm * nsamp_l(f, i)) / (dirichlet_Parm + Nsamp_dat));
break;
}
case 3: // MV_Tweedie
{
// need MV_tweedie
break;
}
}

temp_probs3(1, SzFreq_Setup2(iobs)) = value(SzFreq_exp(iobs));
temp_mult.fill_multinomial(radm, temp_probs3(1, SzFreq_Setup2(iobs))); // create multinomial draws with prob = expected values
for (compindex = 1; compindex <= j; compindex++) // cumulate the multinomial draws by index in the new data
{
SzFreq_newdat(temp_mult(compindex)) += 1.0;
}

report1 << SzFreq_obs1(iobs)(1, 7) << " " << SzFreq_newdat(1, SzFreq_Setup2(iobs)) << endl;
}
}

// begin tagging data section #3 (bootstrap data)
Expand Down