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gmacsbase_20240520AEP.TPL
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gmacsbase_20240520AEP.TPL
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// ==================================================================================== //
// Gmacs: A generalized size-structured stock assessment modeling framework.
//
// Authors: gmacs development team at the
// Alaska Fisheries Science Centre, Seattle
// and the University of Washington.
//
// Info: https://github.com/seacode/gmacs Copyright (C) 2014-2019. All rights reserved.
//
// ACKNOWLEDGEMENTS:
// finacial support provided by NOAA and Bering Sea Fisheries Research Foundation.
//
// INDEXES:
// g/ig = group
// h = sex
// i = year
// j = time step (years)
// k = gear or fleet
// l = index for length class
// m = index for maturity state
// o = index for shell condition.
//
// OUTPUT FILES:
// gmacs.rep Main result file for reading into R etc
// gmacs.std Result file for reading into R etc
// gmacsall.out Result file for all all sorts of purposes.
//
// FOR DEBUGGING INPUT FILES: (for accessing easily with read_admb() function)
// gmacs_files_in.dat Which control and data files were specified for the current run
// gmacs_in.ctl Code-generated copy of control file content (useful for checking read)
// gmacs_in.dat Code-generated copy of data file content (useful for checking read)
// gmacs_in.prj Code-generated copy of projection file content (useful for checking read)
//
// TO ECHO INPUT
// checkfile.rep All of data read in
//
// COMMANDLINE OPTIONS
// The following specify using an ascii pin file fnPin to set parameter values,
// and set usepinfile=1 regardless of the value in gmacs.dat. Pinfile usage can
// also be turned "on" in the gmacs.dat file (in which case the commandline options
// are only usful for specifying a non-default pinfile name).
// If fnPin not given, then fnPin = "gmacs.pin" (the ADMB default).
// -pin fnPin
// -ainp fnPin
// -apin fnPin
// ==================================================================================== //
// ************************************************************************************ //
// Developers
// ************************************************************************************ //
// AEP: Andre E. Punt
// CS: Cody Szuwalski
// JI: Jim Ianelli
// WTS: William T. Stockhausen
// AW: Athol Whitten
// DW: Darcey Webber
// MV: Matthieu Veron
// TJ: Tyler Jackson
// ************************************************************************************ //
// Submodels labeling
// ************************************************************************************ //
// Label 130: Projection inputs
// Label 200: INITIALIZATION_SECTION
// Label 400: calc_objective_function
// Label 401: catch_likelihood
// Label 402: index_likelihhod
// Label 403: length_likelihood
// Label 404: recruitment_likelihood
// Label 405: growth_likelihood
// Label 500: calc_spr_reference_points2
// Label 501: calc_brute_equilibrium
// Label 502: project_biomass_OFL
// Label 503: calc_predicted_project
// Label 504: project_biomass
// Label 505: compute_OFL_and_ABC
// Label 506: project_one_year
// Label 600: CreateOutput
// Label 700: write_eval
// ************************************************************************************ //
DATA_SECTION
!! TheHeader = adstring("## GMACS Version 2.20.13; ** AEP & WTS **; Compiled 2024-05-15");
//-------------------------------
// Sandbox for testing functions |
//-------------------------------
LOCAL_CALCS
{
//
//@brief command line option for sandbox.
//
int on = 0; int opt;//defined for local scope only here
int testingflag = 0;
if ( (on=option_match(ad_comm::argc,ad_comm::argv,"-testing",opt))>-1 )
{
testingflag = 1;
}
if (testingflag==1){
//Testing alternative dat file reader
cout<<"|---------------------------------------|"<<endl;
cout<<"| Testing with alternative dat file |"<<endl;
cout<<"|---------------------------------------|"<<endl;
//cifstream is("TannerCrab_NewDatFile.dat",ios::in);
//DatFileReader* pDFR = new DatFileReader();
//is>>(*pDFR);
//is.close();
//cout<<(*pDFR)<<endl;
exit(1);
}
if (0){
//Testing selectivity using "constant" values
cout<<"|---------------------------------------|"<<endl;
cout<<"| Testing sandbox using constant values |"<<endl;
cout<<"|---------------------------------------|"<<endl;
class gsm::Selex<dvector> *pSLX;
dvector z(1,32);
for (int i=z.indexmin();i<=z.indexmax();i++) z(i) = 27.5+(i-1)*5.0;
cout<<"--Cubic Spline"<<endl;
dvector x_knts(1,5);
x_knts[1]=z[1]; for (int i=1;i<=4;i++) x_knts[i+1] = z[8*i];
dvector y_vals = 1.0/(1.0+exp(-(x_knts-100.0)/30.0));
cout<<"x_knts = "<<x_knts<<endl;
cout<<"y_vals = "<<y_vals<<endl;
pSLX = new class gsm::SelectivitySpline<dvector,dvector>(y_vals,x_knts);
cout<<"z = "<<x_knts<<endl;
cout<<"sel = "<<pSLX->Selectivity(x_knts)<<endl;
cout<<"z = "<<z<<endl;
cout<<"sel = "<<pSLX->Selectivity(z)<<endl;
cout<<"logsel = "<<pSLX->logSelectivity(z)<<endl;
cout<<"logselM1 = "<<pSLX->logSelexMeanOne(z)<<endl;
cout<<"--change knots and y_vals to check reallocation"<<endl;
dvector x_knts1(1,9);
x_knts1[1]=z[1]; for (int i=1;i<=8;i++) x_knts1[i+1] = z[4*i];
dvector y_vals1 = 1.0/(1.0+exp(-(x_knts1-100.0)/30.0));
((gsm::SelectivitySpline<dvector,dvector>*)pSLX)->initSpline(y_vals1,x_knts1);
cout<<"z = "<<x_knts1<<endl;
cout<<"sel = "<<pSLX->Selectivity(x_knts1)<<endl;
cout<<"z = "<<z<<endl;
cout<<"sel = "<<pSLX->Selectivity(z)<<endl;
cout<<"logsel = "<<pSLX->logSelectivity(z)<<endl;
cout<<"logselM1 = "<<pSLX->logSelexMeanOne(z)<<endl;
//exit(1);
cout<<"--DoubleNormal"<<endl;
double p1 = 30.0;
double p2 = 100.0;
double p3 = 50.0;
pSLX = new class gsm::DoubleNormal<dvector,double>(p1,p2,p3);
cout<<z<<endl;
cout<<pSLX->Selectivity(z)<<endl;
cout<<pSLX->logSelectivity(z)<<endl;
cout<<pSLX->logSelexMeanOne(z)<<endl;
cout<<"--DoubleNormal4"<<endl;
p1 = 30.0;
p2 = 100.0;
p3 = 50.0;
double p4 = 130.0;
pSLX = new class gsm::DoubleNormal4<dvector,double>(p1,p2,p3,p4);
cout<<z<<endl;
cout<<pSLX->Selectivity(z)<<endl;
cout<<pSLX->logSelectivity(z)<<endl;
cout<<pSLX->logSelexMeanOne(z)<<endl;
cout<<"--Uniform"<<endl;
pSLX = new class gsm::UniformCurve<dvector>();
cout<<z<<endl;
cout<<pSLX->Selectivity(z)<<endl;
cout<<pSLX->logSelectivity(z)<<endl;
cout<<pSLX->logSelexMeanOne(z)<<endl;
cout<<"--Uniform0"<<endl;
pSLX = new class gsm::Uniform0Curve<dvector>();
cout<<z<<endl;
cout<<pSLX->Selectivity(z)<<endl;
cout<<pSLX->logSelectivity(z)<<endl;
cout<<pSLX->logSelexMeanOne(z)<<endl;
exit(1);
}
}//--end local scope
END_CALCS
//friend_class gmacs_comm;
// |---------------------|
// | SIMULATION CONTROLS |
// |---------------------|
int jitflag;//--jitter indicator from commandline
int simflag;
int rseed;
LOC_CALCS
jitflag = 0;
simflag = 0;
rseed = 0;
int opt,on;
sexes(0) = "undetermined";
sexes(1) = "male";
sexes(2) = "female";
maturestate(0) = "undetermined";
maturestate(1) = "mature";
maturestate(2) = "immature";
shellstate(0) = "undetermined";
shellstate(1) = "new";
shellstate(2) = "old";
catchtypes(0) = "total";
catchtypes(1) = "retained";
catchtypes(2) = "discarded";
unitstypes += "biommass";
unitstypes += "numbers";
seltypes += "selectivity";
seltypes += "retention";
/**
* @brief command line option for simulating data.
**/
if ( (on=option_match(ad_comm::argc,ad_comm::argv,"-sim",opt))>-1 )
{
simflag = 1;
rseed = atoi(ad_comm::argv[on+1]);
}
/**
* @brief command line option for jittering parameter values (overrides gmacs.dat setting).
**/
if ( (on=option_match(ad_comm::argc,ad_comm::argv,"-jitter",opt))>-1 )
{
jitflag = 1;
rseed = atoi(ad_comm::argv[on+1]);//set rseed to 0 to use start time
}
if ( (on=option_match(ad_comm::argc,ad_comm::argv,"-i",opt))>-1 )
{
cout << "\n";
cout << " +----------------------------------------------------------+\n";
cout << " | CONTRIBUTIONS (code and intellectual) |\n";
cout << " +----------------------------------------------------------+\n";
cout << " | Name: Organization: |\n";
cout << " | James Ianelli NOAA-NMFS |\n";
cout << " | D'Arcy Webber Quantifish |\n";
cout << " | Steven Martell SeaState |\n";
cout << " | Jack Turnock NOAA-NMFS |\n";
cout << " | Jie Zheng ADF&G |\n";
cout << " | Hamachan Hamazaki ADF&G |\n";
cout << " | Athol Whitten University of Washington |\n";
cout << " | Andre Punt University of Washington |\n";
cout << " | Dave Fournier Otter Research |\n";
cout << " | John Levitt Mathemetician |\n";
cout << " | William Stockhausen NOAA-NMFS |\n";
cout << " +----------------------------------------------------------+\n";
cout << "\n";
cout << " +----------------------------------------------------------+\n";
cout << " | FINANCIAL SUPPORT |\n";
cout << " +----------------------------------------------------------+\n";
cout << " | Financial support for this project was provided by the |\n";
cout << " | National Marine Fisheries Service, the Bering Sea |\n";
cout << " | Fisheries Research Foundation, ... |\n";
cout << " +----------------------------------------------------------+\n";
cout << "\n";
cout << " +----------------------------------------------------------+\n";
cout << " | DOCUMENTATION |\n";
cout << " +----------------------------------------------------------+\n";
cout << " | online api: http://seacode.github.io/gmacs/index.html |\n";
cout << " +----------------------------------------------------------+\n";
cout << "\n";
exit(1);
}
// Command line option here to do retrospective analysis
if ( (on=option_match(ad_comm::argc,ad_comm::argv, "-retro", opt))>-1 )
{
cout << "\n";
cout << " +----------------------------------------------------------+\n";
cout << " | Running retrospective model with " << ad_comm::argv[on+1] << " recent yrs removed |\n";
cout << " +----------------------------------------------------------+\n";
cout << " | YET TO BE IMPLEMENTED |\n";
cout << " +----------------------------------------------------------+\n";
exit(1);
}
END_CALCS
// create a random number generator for projections
// |------------------------|
// | DATA AND CONTROL FILES |
// |------------------------|
//--read gmacs.dat file
!!WriteFileName(TheHeader);
init_adstring datafile;
init_adstring controlfile;
init_adstring projectfile;
init_adstring weightunit;
init_adstring numbersunit;
init_adstring StockName;
!!WriteFileName(datafile); WriteFileName(controlfile); WriteFileName(projectfile);
!!WriteFileName(weightunit);
!!WriteFileName(numbersunit);
!!WriteFileName(StockName);
init_int IsJittered;
init_number sdJitter;
!! if (jitflag) IsJittered = 1;
!! if (IsJittered==1) cout << "Jittering with sd: " << sdJitter << endl;
!! WriteFileName(IsJittered);
!! WriteFileName(sdJitter);
init_int OutRefPars;
!! WriteFileName(OutRefPars);
init_int OutRecruit;
!! WriteFileName(OutRecruit);
init_int OutSSB;
!! WriteFileName(OutSSB);
init_int Outfbar;
!! WriteFileName(Outfbar);
init_int OutDynB0;
!! WriteFileName(OutDynB0);
init_int nyrRetro; ///> Retrospective end year
!! WriteFileName(nyrRetro);
init_int TurnOffPhase; ///> Maximum phase
init_int StopAfterFnCall ///> Number of function calls to stop after
init_int CalcRefPoints; ///> Set this to zero not to compute reference points
init_int usepinfile ///> Read in a special file (0=normal;1=pin file)
init_int verbose; ///> Flag to print to screen
//check for commandline overide of pinfile use (if set, overrides value from gmacs.dat)
LOCAL_CALCS
if ( (on=option_match(ad_comm::argc,ad_comm::argv,"-verbose",opt))>-1 ){
verbose = atoi(ad_comm::argv[on+1]);
cout<<"#--verbose level set to: "<<verbose<<endl;
}
if ( (on=option_match(ad_comm::argc,ad_comm::argv,"-ainp",opt))>-1 ){
usepinfile = 1;
adstring fnPin = ad_comm::argv[on+1];
if (std::fstream(fnPin)){
ad_comm::change_pinfile_name(fnPin);
cout<<"#Initial parameter values from pin file: "<<fnPin<<endl;
} else {
cout<<"#Initial parameter values from pin file: gmacs.pin"<<endl;
}
}
if ( (on=option_match(ad_comm::argc,ad_comm::argv,"-apin",opt))>-1 ){
usepinfile = 1;
adstring fnPin = ad_comm::argv[on+1];
if (std::fstream(fnPin)){
ad_comm::change_pinfile_name(fnPin);
cout<<"#Initial parameter values from pin file: "<<fnPin<<endl;
} else {
cout<<"#Initial parameter values from pin file: gmacs.pin"<<endl;
}
}
if ( (on=option_match(ad_comm::argc,ad_comm::argv,"-pin",opt))>-1 ){
usepinfile = 1;
adstring fnPin = ad_comm::argv[on+1];
if (std::fstream(fnPin)){
ad_comm::change_pinfile_name(fnPin);
cout<<"#Initial parameter values from pin file: "<<fnPin<<endl;
} else {
cout<<"#Initial parameter values from pin file: gmacs.pin"<<endl;
}
}
END_CALCS
!!gmacs_files << TurnOffPhase << " # Maximum phase (stop the estimation after this phase)" << endl;
!!gmacs_files << StopAfterFnCall << " # Maximum number of function calls" << endl;
!!gmacs_files << CalcRefPoints << " # Calculate reference points (0=no)" << endl;
!!gmacs_files << usepinfile << " # use pin file (0=no, 1=yes)" << endl;
!!gmacs_files << verbose << " # VERBOSE FLAG (0 = off, 1 = on, 2 = objective func; 3 diagnostics)" << endl;
!!echoinput << TurnOffPhase << " # Maximum phase (stop the estimation after this phase)" << endl;
!!echoinput << StopAfterFnCall << " # Maximum number of function calls" << endl;
!!echoinput << CalcRefPoints << " # Calculate reference points (0=no)" << endl;
!!echoinput << usepinfile << " # use pin file (0=no, 1=yes)" << endl;
!!echoinput << verbose << " # VERBOSE FLAG (0 = off, 1 = on, 2 = objective func; 3 diagnostics)" << endl;
init_int dataeof;
!! WriteFileName(dataeof);
!! if ( dataeof != 9999 ) {cout << "Error reading GMACS.DAT" << endl; exit(1);}
!! cout << "end of GMACS.DAT" << endl;
//----------------------------------------------------------------------------
//--read data file
!! ad_comm::change_datafile_name(datafile);
!! cout << "+----------------------+" << endl;
!! cout << "| Reading data file |" << endl;
!! cout << "+----------------------+" << endl;
!! gmacs_data << "# =========================================" << endl;
!! gmacs_data << "# The inputs for catch and index data are CV. To convert from CVs to standard errors of the log and to weights is given by" << endl;
!! gmacs_data << "# sigma = sqrt(ln(1.0+CV^2))" << endl;
!! gmacs_data << "# weight = 1.0/(2*sigma^2)" << endl;
!! gmacs_data << "# CV = sqrt(exp(1/(2*Weight))-1)" << endl;
!! gmacs_data << "# =========================================" << endl << endl;
// |------------------|
// | MODEL DIMENSIONS |
// |------------------|
!! cout << " * Model dimensions" << endl;
!! WRITEDAT(TheHeader);
init_int syr; ///> initial year
init_int nyr; ///> terminal year
int nyrRetroNo;
!! nyrRetroNo = nyrRetro;
!! nyrRetro = nyr-nyrRetro; ///> Adjust to nyear_retro
init_int nseason; ///> time step (years)
init_int nfleet; ///> number of gears (including surveys and fisheries)
init_int nsex; ///> number of sexes
!! if (nsex != 1 && nsex != 2)
!! { cout << "nsex can only be 1 or 2; STOPPING" << endl; exit(1); }
init_int nshell; ///> number of shell conditions
init_int nmature; ///> number of maturity types
init_int nclass; ///> number of size-classes
init_int season_recruitment; ///> Season that recruitment occurs (end of year before growth)
init_int season_growth; ///> Season that growth occurs (end of year after recruitment)
init_int season_ssb; ///> Season to calculate SSB (end of year)
init_int season_N; ///> Season to output N
init_ivector nSizeSex(1,nsex); ///> Number of size-classes by sex
int n_grp; ///> number of sex/newshell/oldshell groups
int nlikes; ///> 1 2 3 4 5
int Nyears;
!! Nyears =(nyrRetro-syr+1);
int Nyears2;
!! Nyears2 =(nyrRetro+1-syr+1);
LOC_CALCS
n_grp = nsex * nshell * nmature;
nlikes = 5; ///> catch, cpue, size comps, recruits, molt increments
gmacs_data << syr << " # Start year" << endl;
gmacs_data << nyrRetro << " # End year (retro)" << endl;
gmacs_data << nseason << " # Number of seasons" << endl;
gmacs_data << nfleet << " # Number of distinct data groups (fleet, among fishing fleets and surveys)" << endl;
gmacs_data << nsex << " # Number of sexes" << endl;
gmacs_data << nshell << " # Number of shell condition types" << endl;
gmacs_data << nmature << " # Number of maturity types" << endl;
gmacs_data << nclass << " # Number of size-classes in the model" << endl;
gmacs_data << season_recruitment << " # Season recruitment occurs" << endl;
gmacs_data << season_growth << " # Season molting and growth occurs" << endl;
gmacs_data << season_ssb << " # Season to calculate SSB (changed to match Feb mating)" << endl;
gmacs_data << season_N << " # Season for N output" << endl;
gmacs_data << "# maximum size-class (males then females)" << endl;
gmacs_data << nSizeSex << endl;
// Check at least one matches nclass
if (max(nSizeSex)!=nclass) { cout << "One of the maximum size-classes needs to match nclass; STOPPING" << endl; exit(1); }
END_CALCS
// Set up index pointers
ivector isex(1,n_grp);
ivector ishell(1,n_grp);
ivector imature(1,n_grp);
3darray pntr_hmo(1,nsex,1,nmature,1,nshell);
LOC_CALCS
int h,m,o;
int hmo=1;
gmacs_data << "# Group definitions: " << n_grp << endl;
gmacs_data << "# Index Sex Shell Maturity" << endl;
for ( h = 1; h <= nsex; h++ )
for ( m = 1; m <= nmature; m++ )
for ( o = 1; o <= nshell; o++ )
{
isex(hmo) = h;
ishell(hmo) = o;
imature(hmo) = m;
gmacs_data << "# " << hmo << " : " << sexes(h) << " ";
if (o==NEW_SHELL) gmacs_data << "New shell(" << o << ") ";
if (o==OLD_SHELL) gmacs_data << "old shell(" << o << ") ";
if (m==IMMATURE) gmacs_data << "Immature(" << m << ") ";
if (m==MATURE) gmacs_data << "Mature(" << m << ") ";
pntr_hmo(h,m,o) = hmo++;
gmacs_data << pntr_hmo(h,m,o) << endl;
}
END_CALCS
init_vector size_breaks(1,nclass+1);
vector mid_points(1,nclass);
!! gmacs_data << "# size_breaks (a vector giving the break points between size intervals with dimension nclass+1)" << endl;
!! gmacs_data << size_breaks << endl;
// |-------------------------------|
// | NATURAL MORTALITY |
// |-------------------------------|
!! cout << " * Natural mortality" << endl;
init_int m_prop_type; ///> 1 for vector by season; 2 for matrix by year and season
!! if (m_prop_type != 1 && m_prop_type != 2)
!! { cout << "m_prop_type can only be 1 or 2; STOPPING" << endl; exit(1); }
int m_dim;
LOC_CALCS
m_dim = 1;
if ( m_prop_type == 2 ) m_dim = nyr - syr + 1;
END_CALCS
init_matrix m_prop_in(1,m_dim,1,nseason);
!! gmacs_data << "# Natural mortality per season input type (1 = vector by season, 2 = matrix by season/year)" << endl << " 2" << endl;
matrix m_prop(syr,nyrRetro,1,nseason);
LOC_CALCS
switch ( m_prop_type )
{
// vector by season
case 1:
for ( int i = syr; i <= nyrRetro; i++ )
for ( int j = 1; j <= nseason; j++ )
m_prop(i,j) = m_prop_in(1,j);
break;
// matrix by year and season
case 2:
for ( int i = syr; i <= nyrRetro; i++ )
for ( int j = 1; j <= nseason; j++ )
m_prop(i,j) = m_prop_in(i-syr+1,j);
break;
}
for ( int i = syr; i <= nyrRetro; i++ )
if ( sum(m_prop(i)) > 1.0000001 || sum(m_prop(i)) < 0.999999 )
{
cout << "Error: the proportion of natural mortality applied each season (in the .dat file) does not sum to 1! It sums to " << sum(m_prop(i)) << endl;
exit(1);
}
gmacs_data << "# Proportion of the total natural mortality to be applied each season" << endl;
for (int i=syr;i<=nyrRetro;i++)
gmacs_data << setw(14) << setprecision(11) << setfixed() << m_prop(i) << " # " << i << endl;
END_CALCS
// |-------------|
// | FLEET NAMES |
// |-------------|
!! for (int ifleet=1;ifleet<=nfleet;ifleet++)
!! {
!! *(ad_comm::global_datafile) >> anystring;
!! fleetname+=anystring;
!! }
!! WRITEDAT(fleetname)
// |-------------|
// | FLEET TYPES |
// |-------------|
init_ivector season_type(1,nseason); ///> Set to 0 for discrete; 1 for continuous
!! gmacs_data << "#Season type: Set to 1 for continuous F and 0 for instantanous F" << endl;
!! gmacs_data << season_type << endl;
// |---------------|
// |--CLASS Subst--|
// |---------------|
LOCAL_CALCS
//class to provide substitutions from/to strings/integers
class Subst{
public:
int fleetID(adstring& flt,adstring_array& fleetname){
int id = 0;
for (int f=fleetname.indexmin();f<=fleetname.indexmax();f++)
if (flt==fleetname[f]) id = f;
return id;
cout<<"Problem assigning fleetID to '"<< flt <<"'."<< endl;
cout<<"Allowed values are ";
for (int f=fleetname.indexmin();f<fleetname.indexmax();f++)
cout<<"'"<<fleetname[f]<<"', ";
cout<<"or '"<<fleetname[fleetname.indexmax()]<<"'."<< endl;
exit(-1);
}
int catchTypeID(adstring& str){
int id = -1;
adstring strp = to_lower(str);
if (strp=="retained") return(RETAINED);
if (strp=="discard") return(DISCARDED);
if (strp=="discarded") return(DISCARDED);
if (strp=="total") return(TOTALCATCH);
cout<<"Problem assigning catchTypeID to '"<< str <<"'."<< endl;
cout<<"Allowed values are 'retained', 'discard', 'discarded' or 'total'."<< endl;
exit(-1);
return(id);
}
int unitsTypeID(adstring& str){
int id = -1;
adstring strp = to_lower(str);
if (strp=="abundance") return(ABUNDANCE);
if (strp=="biomass") return(BIOMASS);
cout<<"Problem assigning unitsTypeID to '"<< str <<"'."<< endl;
cout<<"Allowed values are 'abundance' or 'biomass'."<< endl;
exit(-1);
return(id);
}
int indexTypeID(adstring& str){
int id = -1;
adstring strp = to_lower(str);
if (strp=="sel") return(1);
if (strp=="sel+ret") return(2);
cout<<"Problem assigning indexTypeID to '"<< str <<"'."<< endl;
cout<<"Allowed values are 'sel' or 'sel+ret'."<< endl;
exit(-1);
return(id);
}
int sexID(adstring& str){
int id = -1;
adstring strp = to_lower(str);
if (strp=="males") return(MALES);
if (strp=="females") return(FEMALES);
if (strp=="male") return(MALES);
if (strp=="female") return(FEMALES);
if (strp=="undetermined") return(UNDET_SEX);
return(id);
cout<<"Problem assigning sexID to '"<< str <<"'."<< endl;
cout<<"Allowed values are 'male', 'males', 'female', 'females', or 'undetermined'."<< endl;
exit(-1);
}
int matID(adstring& str){
int id = -1;
adstring strp = to_lower(str);
if (strp=="immature") return(IMMATURE);
if (strp=="mature") return(MATURE);
if (strp=="undetermined") return(UNDET_MATURE);
cout<<"Problem assigning matID to '"<< str << endl;
cout<<"Allowed values are 'immature' or 'mature'."<< endl;
exit(-1);
return(id);
}
int shellID(adstring& str){
int id = -1;
adstring strp = to_lower(str);
if (strp=="new shell") return(NEW_SHELL);
if (strp=="new_shell") return(NEW_SHELL);
if (strp=="old shell") return(OLD_SHELL);
if (strp=="old_shell") return(OLD_SHELL);
if (strp=="undetermined") return(UNDET_SHELL);
cout<<"Problem assigning shellID to '"<< str <<"'."<< endl;
cout<<"Allowed values are 'new shell', 'new_shell', 'old shell', 'old_shell', or 'undetermined'."<< endl;
exit(-1);
return(id);
}
};
Subst substStuff;
END_CALCS
// |--------------|
// | CATCH SERIES |
// |--------------|
!! cout << " * Catch data" << endl;
!! gmacs_data << "\n"<<endl;
!! gmacs_data << "##------------------------------------------------------------" << endl;
!! gmacs_data << "##--CATCH DATA------------------------------------------------" << endl;
!! gmacs_data << "##------------------------------------------------------------" << endl;
init_int fmtCDS_in;
!! gmacs_data << fmtCDS_in << " #--input catch data format (0: old format, 1: new format)" << endl;
init_int nCatchDF;
!! gmacs_data << nCatchDF << " #--Number of catch data frames" << endl;
ivector nCatchRows(1,nCatchDF); // this can't be an init_vector here--incompatible with "new" format
3darray dCatchData(1,nCatchDF); // array of catch data WTS: full allocation delayed until nCatchRows is determined
!!float TempW;
!!float SDlogD;
LOCAL_CALCS
{
cifstream* pGD = ad_comm::global_datafile;
if (fmtCDS_in==0){
//--read in using old format
(*pGD) >> nCatchRows;
gmacs_data << "# Number of lines for each dataframe (this is not correct for retrospective analyses)" << endl;
gmacs_data << nCatchRows << endl;
for (int idf=1;idf<=nCatchDF;idf++) dCatchData(idf).allocate(1,nCatchRows(idf),1,11);//--finish allocation
(*pGD) >> dCatchData;
} else {
//--read in using new format
adstring unitsType,catchType,fleet,sex,maturity, shell;
int iUT,iCT,iF,iX,iM,iS;
for (int idf=1;idf<=nCatchDF;idf++) {
gmacs_data << "#----------------" << endl;
gmacs_data << "# catch dataframe number " << idf << endl;
(*pGD) >> unitsType; iUT = substStuff.unitsTypeID(unitsType);
(*pGD) >> catchType; iCT = substStuff.catchTypeID(catchType);
(*pGD) >> fleet; iF = substStuff.fleetID(fleet,fleetname);
(*pGD) >> sex; iX = substStuff.sexID(sex);
(*pGD) >> maturity; iM = substStuff.matID(maturity);
(*pGD) >> shell; iS = substStuff.shellID(shell);
(*pGD) >> nCatchRows(idf);
gmacs_data << unitsType << " #--units type" << endl;
gmacs_data << catchType << " #--catch type (retained, discard(ed), total)" << endl;
gmacs_data << fleet << " #--fleet name" << endl;
gmacs_data << sex << " #--sex (male(s), female(s), undetermined)" << endl;
gmacs_data << maturity << " #--maturity (immature, mature, undetermined)" << endl;
gmacs_data << shell << " #--shell condition (new shell, old shell, undetermined)" << endl;
gmacs_data << nCatchRows(idf) << " #--number of rows in dataframe" << endl;
dmatrix inpCatchData(1,nCatchRows(idf),1,7);
dCatchData(idf).allocate(1,nCatchRows(idf),1,11);//--finish allocation
(*pGD) >> inpCatchData;
gmacs_data << "#year season value cv multiplier effort discard_mortality" << endl;
gmacs_data << inpCatchData << endl;
for (int irw=1;irw<=nCatchRows(idf);irw++){
dCatchData(idf,irw, 1) = (int) inpCatchData(irw,1);
dCatchData(idf,irw, 2) = (int) inpCatchData(irw,2);
dCatchData(idf,irw, 3) = iF;
dCatchData(idf,irw, 4) = iX;
dCatchData(idf,irw, 5) = inpCatchData(irw,3);
dCatchData(idf,irw, 6) = inpCatchData(irw,4);
dCatchData(idf,irw, 7) = iCT;
dCatchData(idf,irw, 8) = iUT;
dCatchData(idf,irw, 9) = inpCatchData(irw,5);
dCatchData(idf,irw,10) = inpCatchData(irw,6);
dCatchData(idf,irw,11) = inpCatchData(irw,7);
}//--irw
}//--idf
gmacs_data << "#--old format:"<<endl;
}//--end reading new format
gmacs_data << "## Sex: 1 = male, 2 = female, 0 = both" << endl;
gmacs_data << "## Type of catch: 1 = retained, 2 = discard, 0 = total" << endl;
gmacs_data << "## Units of catch: 1 = biomass, 2 = numbers" << endl;
gmacs_data << "## Mult: 1= use data as they are, 2 = multiply by this number (e.g., lbs to kg)" << endl;
gmacs_data << "# Year Season Fleet Sex Obs CV Type Units Mult Effort Discard_mortality" << endl;
for (int iCatOut=1;iCatOut<=nCatchDF;iCatOut++){
for (int irow=1;irow<=nCatchRows(iCatOut); irow++) {
if (dCatchData(iCatOut,irow,1) <= nyrRetro) {
if (fmtCDS_in>0) gmacs_data << "# ";
gmacs_data << (int) dCatchData(iCatOut,irow)(1) << " ";
gmacs_data << (int) dCatchData(iCatOut,irow)(2) << " ";
gmacs_data << (int) dCatchData(iCatOut,irow)(3) << " ";
gmacs_data << (int) dCatchData(iCatOut,irow)(4) << " ";
gmacs_data << dCatchData(iCatOut,irow)(5,6) << " ";
gmacs_data << (int) dCatchData(iCatOut,irow)(7) << " ";
gmacs_data << (int) dCatchData(iCatOut,irow)(8) << " ";
gmacs_data << dCatchData(iCatOut,irow)(9,11) << " ";
anystring = "# " + fleetname(dCatchData(iCatOut,irow,3));
if (dCatchData(iCatOut,irow,4)==MALES) anystring = anystring +"_male";
if (dCatchData(iCatOut,irow,4)==FEMALES) anystring = anystring +"_female";
if (dCatchData(iCatOut,irow,7)==TOTALCATCH) anystring = anystring +"_total";
if (dCatchData(iCatOut,irow,7)==RETAINED) anystring = anystring +"_retained";
if (dCatchData(iCatOut,irow,7)==DISCARDED) anystring = anystring +"_discard";
if (dCatchData(iCatOut,irow,8)==BIOMASS) anystring = anystring +"_biomass";
if (dCatchData(iCatOut,irow,8)==ABUNDANCE) anystring = anystring +"_numbers";
if (dCatchData(iCatOut,irow,6) <= 0) {
cout << "Error: CV of catch is zero (or less) for group " << iCatOut << " row " << irow << endl;
exit(1);
}
gmacs_data << anystring << " ";
SDlogD = sqrt(log(1.0 + square(dCatchData(iCatOut,irow,6))));
TempW = 0.5/(SDlogD*SDlogD);
gmacs_data << "Sd of log = " << SDlogD << "; Weight = " << TempW << " ";
gmacs_data << endl;
}//--dCatchData(iCatOut,irow,1) <= nyrRetro
}//--irow
}//--iCatOut
}
END_CALCS
matrix obs_catch(1,nCatchDF,1,nCatchRows);
matrix obs_effort(1,nCatchDF,1,nCatchRows);
3darray dCatchData_out(1,nCatchDF,syr,nyr,1,11);
matrix obs_catch_out(1,nCatchDF,syr,nyr);
matrix catch_cv(1,nCatchDF,1,nCatchRows);
matrix catch_dm(1,nCatchDF,1,nCatchRows);
matrix catch_mult(1,nCatchDF,1,nCatchRows);
LOC_CALCS
for ( int k = 1; k <= nCatchDF; k++ )
{
catch_mult(k) = column(dCatchData(k),9);
obs_catch(k) = column(dCatchData(k),5);
catch_cv(k) = column(dCatchData(k),6);
catch_dm(k) = column(dCatchData(k),11);
obs_catch(k) = elem_prod(obs_catch(k), catch_mult(k)); ///> rescale catch by multiplier
obs_effort(k) = column(dCatchData(k),10);
}
ECHO(obs_catch);
ECHO(catch_cv);
END_CALCS
// From the catch series determine the number of fishing mortality rate parameters that need to be estimated.
// Note that there are a number of combinations which require an F to be estimated.
ivector nFparams(1,nfleet); ///> The number of deviations required for each fleet
ivector nYparams(1,nfleet); ///> The number of deviations for female Fs
3darray fhit(syr,nyrRetro,1,nseason,1,nfleet); ///> set to 1 for present; 0 for absent
3darray yhit(syr,nyrRetro,1,nseason,1,nfleet); ///> set to 1 for present; 0 for absent
matrix dmr(syr,nyrRetro,1,nfleet); ///> discard mortality - has to be the same for all catch series for each fleet
matrix fhitfut(1,nseason,1,nfleet); ///> set to 1 for present in any year; 0 for absent
LOC_CALCS
nFparams.initialize();
nYparams.initialize();
fhit.initialize();
yhit.initialize();
dmr.initialize();
echoinput<<"\n\nDetermining number of fishing rate parameters to be estimated."<<endl;
for ( int k = 1; k <= nCatchDF; k++ )
{
echoinput<<"catchDF (k) = "<<k<<endl;
for ( int i = 1; i <= nCatchRows(k); i++ )
if (dCatchData(k)(i,1) <= nyrRetro && dCatchData(k)(i,1) >= syr)
{
int y = dCatchData(k)(i,1); ///> year
int j = dCatchData(k)(i,2); ///> season
int g = dCatchData(k)(i,3); ///> fleet
int h = dCatchData(k)(i,4); ///> sex
echoinput<<"Processing i,y,j,g,h (row,year, season, fleet, sex): "<<i<<" "<<y<<" "<<j<<" "<<g<<" "<<h<<endl;
// Check whether the fleet is instantaneous but natural mortality in the relevant period is not zero!
if (season_type(j) == INSTANT_F && m_prop(y,j) > 0)
{
cout << "The proportion of M should be zero for season " << j << " in year " << y << endl;
echoinput << "The proportion of M should be zero for season " << j << " in year " << y << endl;
exit(1);
}
if ( !fhit(y,j,g) )
{
fhit(y,j,g) ++;
nFparams(g) ++;
dmr(y,g) = catch_dm(k)(i);//TODO: presumably dmr could depend on season and sex, as well as year and gear/fleet
}
if ( !yhit(y,j,g) && h == 2 )
{
yhit(y,j,g) ++;
nYparams(g) ++;
dmr(y,g) = catch_dm(k)(i);
}
}
}
for (int g=1;g<=nfleet; g++) { if (nFparams(g) == 0) nFparams(g) = 1; }
for (int g=1;g<=nfleet; g++) { if (nYparams(g) == 0) nYparams(g) = 1; }
ECHO(nFparams); ECHO(nYparams); // ECHO(fhit); ECHO(yhit); ECHO(dmr);
echoinput << "fhit" << endl;
echoinput << "iy(yr) j(season) hit_for_fleet " <<endl;
fhitfut.initialize();
for (int iy=syr;iy<=nyrRetro;iy++)
for (int j=1;j<=nseason;j++)
{
echoinput << iy << " " << j << " ";
for (int g=1;g<=nfleet;g++) echoinput << fhit(iy,j,g) << " ";
for (int g=1;g<=nfleet;g++) if (fhit(iy,j,g)==1) fhitfut(j,g) = 1;
echoinput << endl;
}
echoinput << "fhitfut" << endl;
echoinput << "j(season) hit_for_fleet? " <<endl;
for (int j=1;j<=nseason;j++)
{
echoinput << " " << j << " ";
for (int g=1;g<=nfleet;g++) echoinput << fhitfut(j,g) << " ";
echoinput << endl;
}
echoinput << "yhit" << endl;
echoinput << "iy(yr) j(season) hit_for_fleet? " <<endl;
for (int iy=syr;iy<=nyrRetro;iy++)
for (int j=1;j<=nseason;j++)
{
echoinput << iy << " " << j << " ";
for (int g=1;g<=nfleet;g++) echoinput << yhit(iy,j,g) << " ";
echoinput << endl;
}
ECHO(dmr);
echoinput<<"dmr:"<<endl;
echoinput<<"year fleet dmr"<<endl;
for (int iy=syr;iy<=nyrRetro;iy++)
for (int g=1;g<=nfleet;g++) echoinput<<iy<<" "<<g<<" "<<dmr(iy,g)<<endl;
// Check for errors in discard rate assumptions
for ( int k = 1; k <= nCatchDF; k++ )
for ( int i = 1; i <= nCatchRows(k); i++ )
if (dCatchData(k)(i,1) <= nyrRetro && dCatchData(k)(i,1) >= syr)
{
int y = dCatchData(k)(i,1); ///> year
int g = dCatchData(k)(i,3); ///> fleet
if (catch_dm(k)(i) != dmr(y,g))
{ cout << "ERROR: discard rates do not match: year " << y << " and fleet " << g << " in CatchDF " << k<< endl;
gmacs_data << "ERROR: discard rates do not match: year " << y << " and fleet " << g << " in CatchDF " << k<< endl;
gmacs_data << "k = "<<k<<" i = "<<i<<" y = "<<y<<" g = "<<g<<endl;
gmacs_data << "catch_dm(k)(i) = " <<catch_dm(k)(i) << " dmr(y,g) = " << dmr(y,g) << endl;
exit(1); }
}
// Create the dCatchData_out object for output and plotting in R, this object simply fills in the years that don't have data with zero catch
dCatchData_out.initialize();
obs_catch_out.initialize();
for ( int k = 1; k <= nCatchDF; k++ )
for ( int i = syr; i <= nyrRetro; i++ )
{
dCatchData_out(k,i,1) = i; // Year
int j = 1;
for ( int ii = 1; ii <= nCatchRows(k); ii++ )
{
if ( i == dCatchData(k,ii,1) ) // year index
{
j = ii;
obs_catch_out(k,i) = dCatchData(k,ii,5); // Obs
dCatchData_out(k,i,5) = dCatchData(k,ii,5); // Obs
dCatchData_out(k,i,6) = dCatchData(k,ii,6); // CV
dCatchData_out(k,i,9) = dCatchData(k,j,9); // Mult
dCatchData_out(k,i,10) = dCatchData(k,j,10); // Effort
dCatchData_out(k,i,11) = dCatchData(k,j,11); // Discard mortality
}
}
// Replicate these variables
dCatchData_out(k,i,2) = dCatchData(k,j,2); // Season
dCatchData_out(k,i,3) = dCatchData(k,j,3); // Fleet
dCatchData_out(k,i,4) = dCatchData(k,j,4); // Sex
dCatchData_out(k,i,7) = dCatchData(k,j,7); // Type
dCatchData_out(k,i,8) = dCatchData(k,j,8); // Units
}
END_CALCS
// |----------------------------|
// | RELATIVE ABUNDANCE INDICES |
// |----------------------------|
!! cout << " * Abundance data" << endl;
!! gmacs_data << "\n" << endl;
!! gmacs_data << "##------------------------------------------------------------" << endl;
!! gmacs_data << "##--RELATIVE ABUNDANCE DATA-----------------------------------" << endl;
!! gmacs_data << "##------------------------------------------------------------" << endl;
init_int fmtRAD; ///> Format type (0: old format, 1: new format)
!!gmacs_data << fmtRAD << " #--input format type (0: old format, 1: new format)" << endl;
init_int nSurveys; ///> Number of survey series
!! gmacs_data << nSurveys << " #--Number of dataframes" << endl; //TODO: change name to nSurveyDFs
ivector SurveyType(1,nSurveys); ///> Type of survey
int nSurveyRows; ///> total number of rows in survey dataframes
matrix dSurveyData; ///> survey data
LOCAL_CALCS
{
cifstream* pGD = ad_comm::global_datafile;
if (fmtRAD==0){
//old format
gmacs_data << "# Type of 'survey' catchability (1=Selectivity; 2=Selectivity+Retention), by data frame" << endl;
(*pGD) >> SurveyType;
gmacs_data << SurveyType << endl;
gmacs_data << "# Number of data rows, by data frame" << endl;
(*pGD) >> nSurveyRows;
gmacs_data << "# NOTE: this is not correct for retrospective analyses" << endl;
gmacs_data << nSurveyRows << endl;;
dSurveyData.allocate(1,nSurveyRows,0,9);
(*pGD) >> dSurveyData;
gmacs_data << "# Survey data:"<<endl;
gmacs_data << dSurveyData <<endl;
} else {
//new format
adstring indexType, unitsType, fleet, sexType, matType, shlType;
ivector nrows(1,nSurveys), idIndex(1,nSurveys),idUnits(1,nSurveys);
ivector idFlt(1,nSurveys),idSex(1,nSurveys),idMat(1,nSurveys),idShl(1,nSurveys);
d3_array inpDFs(1,nSurveys);
for (int idf = 1;idf<=nSurveys;idf++){
gmacs_data << "#----------------" << endl;
gmacs_data << "# relative abundance dataframe number " << idf << endl;
(*pGD) >> unitsType; idUnits(idf) = substStuff.unitsTypeID(unitsType);
(*pGD) >> indexType; idIndex(idf) = substStuff.indexTypeID(indexType);
(*pGD) >> fleet; idFlt(idf) = substStuff.fleetID(fleet,fleetname);
(*pGD) >> sexType; idSex(idf) = substStuff.sexID(sexType);
(*pGD) >> matType; idMat(idf) = substStuff.matID(matType);
(*pGD) >> shlType; idShl(idf) = substStuff.shellID(shlType);
(*pGD) >> nrows(idf);
gmacs_data << indexType << " #--abundance index type ('sel' or 'sel+ret')" << endl;
gmacs_data << unitsType << " #--units type ('abundance' or 'biomass')" << endl;
gmacs_data << fleet << " #--fleet name" << endl;
gmacs_data << sexType << " #--sex (male(s), female(s), undetermined)" << endl;
gmacs_data << matType << " #--maturity (immature, mature, undetermined)" << endl;
gmacs_data << shlType << " #--shell condition (new_shell, old_shell, undetermined)" << endl;
inpDFs(idf).allocate(1,nrows(idf),1,7);//--allocate dataframe
(*pGD) >> inpDFs(idf);
gmacs_data << "# q_index year season value cv multiplier CPUE_timing " <<endl;
gmacs_data << inpDFs(idf) <<endl;
}//--idf
nSurveyRows = sum(nrows);
dSurveyData.allocate(1,nSurveyRows,0,9);
int jrw = 1;
for (int idf = 1;idf<=nSurveys;idf++){
SurveyType(idf) = idIndex(idf);
for (int irw = 1;irw<=nrows(idf);irw++){
dSurveyData(jrw, 0) = inpDFs(idf,irw,1); //--q_index
dSurveyData(jrw, 1) = inpDFs(idf,irw,2); //--year
dSurveyData(jrw, 2) = inpDFs(idf,irw,3); //--season
dSurveyData(jrw, 3) = idFlt(idf); //--fleet
dSurveyData(jrw, 4) = idSex(idf); //--sex
dSurveyData(jrw, 5) = idMat(idf); //--maturity
dSurveyData(jrw, 6) = inpDFs(idf,irw,4); //--observed value
dSurveyData(jrw, 7) = inpDFs(idf,irw,5); //--cv
dSurveyData(jrw, 8) = inpDFs(idf,irw,6); //--units scaling
dSurveyData(jrw, 9) = inpDFs(idf,irw,7); //--cpue timing
jrw++;
}//--irw
}//--idf
}//--if (fmtRAD)
}
END_CALCS
vector obs_cpue(1,nSurveyRows);
vector cpue_cv(1,nSurveyRows);
vector cpue_sd(1,nSurveyRows);
vector cpue_cv_add(1,nSurveyRows);
vector cpue_time(1,nSurveyRows);
LOC_CALCS
obs_cpue = column(dSurveyData,6);
cpue_cv = column(dSurveyData,7);
cpue_sd = sqrt(log(1.0 + square(cpue_cv)));
cpue_time = column(dSurveyData,9);
if (fmtRAD) gmacs_data << "# old format:" << endl;
gmacs_data << "## Index: One q is estimated for each index (the number of index values should match nSurveys" << endl;
gmacs_data << "## Sex: 1 = male, 2 = female, 0 = both" << endl;
gmacs_data << "## Maturity: 1 = mature, 2 = immature, 0 = both" << endl;
gmacs_data << "## Units of survey: 1 = biomass, 2 = numbers" << endl;
gmacs_data << "# row Index Year Season Fleet Sex Maturity Obs CV Units CPUE_time" << endl;
for (int irow=1;irow<=nSurveyRows; irow++)
if (((dSurveyData(irow,1) <= nyrRetro) || ((dSurveyData(irow,1) == nyrRetro+1) && (dSurveyData(irow,2) == 1))) && dSurveyData(irow,1) >= syr)
{
gmacs_data << "# " << irow << " " << (int) dSurveyData(irow,0) << " ";
gmacs_data << (int) dSurveyData(irow,1) << " ";//year