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191 spawner recruitment with a b formulation #442

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191 spawner recruitment with a b formulation #442

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1fb37cd
first commit for B-H with ab
Rick-Methot-NOAA Feb 9, 2023
8981777
revise to use WHAM syntax
Rick-Methot-NOAA Feb 14, 2023
5351bb6
Update .gitignore
Rick-Methot-NOAA Feb 14, 2023
cc71b49
Srr=10 now matching SRR=3
Rick-Methot-NOAA May 19, 2023
03b1420
adding reporting for timevary growth
Rick-Methot-NOAA May 20, 2023
63c8681
WIP
Rick-Methot-NOAA May 31, 2023
9201cee
working version with a,b
Rick-Methot-NOAA May 22, 2024
2bb4301
Update .gitignore
May 28, 2024
d01422e
augment spawn_recr report and use to test time-vary SR_parm approach
Rick-Methot-NOAA Jun 12, 2024
92208d4
adding benchmark change
Rick-Methot-NOAA Jun 26, 2024
93eb385
format changes for spawn_recr report
Rick-Methot-NOAA Jul 3, 2024
38ae9ee
fixes to ss_warn
Rick-Methot-NOAA Jul 9, 2024
f034223
WIP-more work needed on benchmark calcs
Rick-Methot-NOAA Aug 14, 2024
0d6d3b6
WIP2-need-to-fix-SPR-passing_to_benchmark
Rick-Methot-NOAA Aug 16, 2024
b4ee3f6
WIP: add switch in benchmark to use correct SPR0
Rick-Methot-NOAA Sep 13, 2024
18fcf7d
refactor SPR to SSBpR; clean-up reference to timevary biology
Rick-Methot-NOAA Sep 17, 2024
f674498
create new switch to control updating of SSBpR0
Rick-Methot-NOAA Sep 20, 2024
e9b838d
too many changes
Rick-Methot-NOAA Oct 4, 2024
33738c4
add HCR_anchor in forecast.ss
Rick-Methot-NOAA Oct 4, 2024
424f3c6
revert change in capitalization of Recr_Virgin
iantaylor-NOAA Oct 18, 2024
27d4095
latest update
Rick-Methot-NOAA Oct 17, 2024
f0bfa6f
go back to g++12.a
e-perl-NOAA Oct 31, 2024
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9 changes: 5 additions & 4 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,11 @@
*.htp
*.obj
*.log
ss.tpl
ss3.tpl
ss_opt.tpl
ss_trans.tpl
Compile/ss.tpl
Compile/ss_opt.tpl
Compile/ss_trans.tpl
Compile/ss3.tpl
Compile/Make_SS_warn.bat
~$*.*
Compile/ss.log
Compile/ss3.log
Expand Down
227 changes: 137 additions & 90 deletions SS_benchfore.tpl
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4 changes: 2 additions & 2 deletions SS_global.tpl
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Expand Up @@ -1270,10 +1270,10 @@ REPORT_SECTION
if (Do_TG > 0)
report << " TG-fleetcomp " << TG_like1 << endl
<< " TG-negbin " << TG_like2 << endl;
report << " -log(L): " << obj_fun << " Spbio: " << value(SSB_yr(styr)) << " " << value(SSB_yr(endyr)) << endl;
report << " -log(L): " << obj_fun << " SSBio: " << value(SSB_yr(styr)) << " " << value(SSB_yr(endyr)) << endl;

report << endl
<< "Year Spbio Recruitment" << endl;
<< "Year SSBio Recruitment" << endl;
report << "Virg " << SSB_yr(styr - 2) << " " << exp_rec(styr - 2, 4) << endl;
report << "Init " << SSB_yr(styr - 1) << " " << exp_rec(styr - 1, 4) << endl;
for (y = styr; y <= endyr; y++)
Expand Down
257 changes: 128 additions & 129 deletions SS_param.tpl
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Expand Up @@ -13,53 +13,52 @@ INITIALIZATION_SECTION
PARAMETER_SECTION
// {
// SS_Label_Info_5.0.1 #Setup convergence critera and max func evaluations
LOCAL_CALCS
// clang-format on
// set the filename to all ADMB output files to "base_modelname.[ext]"
// where base_modelname can be read from command line with command modelname followed by text
// e.g. ss3_win.exe -nohess -stopph 3 modelname ss4you
// if requested modelname.par is not found, then will attempt to read from ss3.par then ss.par
// whatever name is read, the write will be to modelname.par. Which has default of ss3.par
ad_comm::adprogram_name = base_modelname;
echoinput << "Begin setting up parameters" << endl;
cout << "Begin setting up parameters ... ";
if (readparfile >= 1)
{
anystring = base_modelname + ".par";
cout << " read parm file: " << anystring << endl;

LOCAL_CALCS
// clang-format on
// set the filename to all ADMB output files to "base_modelname.[ext]"
// where base_modelname can be read from command line with command modelname followed by text
// e.g. ss3_win.exe -nohess -stopph 3 modelname ss4you
// if requested modelname.par is not found, then will attempt to read from ss3.par then ss.par
// whatever name is read, the write will be to modelname.par. Which has default of ss3.par
ad_comm::adprogram_name = base_modelname;
echoinput << "Begin setting up parameters" << endl;
cout << "Begin setting up parameters ... ";
if (readparfile >= 1) {
anystring = base_modelname + ".par";
cout << " read parm file: " << anystring << endl;

ifstream fin(anystring);
if (fin.fail()) {
cout << " no find, try ss3.par" << endl;
anystring = "ss3.par";
ifstream fin(anystring);
if(fin.fail() ) {
cout << " no find, try ss3.par" << endl;
anystring = "ss3.par";
ifstream fin(anystring);
if(fin.fail() ) {
if (fin.fail()) {
cout << " no find, try ss.par" << endl;
anystring = "ss.par";
ifstream fin(anystring);
if(fin.fail() ) {
warnstream << "could not find ss3.par, ss.par, or requested parfile " << base_modelname << ".par";
write_message(FATAL, 0);
if (fin.fail()) {
warnstream << "could not find ss3.par, ss.par, or requested parfile " << base_modelname << ".par";
write_message(FATAL, 0);
}
}}
cout << " found "<<anystring<<endl;

ad_comm::change_pinfile_name(anystring);
}
}

maximum_function_evaluations.allocate(func_eval.indexmin(), func_eval.indexmax());
maximum_function_evaluations = func_eval;
convergence_criteria.allocate(func_conv.indexmin(), func_conv.indexmax());
convergence_criteria = func_conv;
if (do_ageK == 1) // need for age-specific K
{
k = nages;
} // use for dimension of VBK()
else
{
k = 0;
}
// clang-format off
cout << " found " << anystring << endl;

ad_comm::change_pinfile_name(anystring);
}

maximum_function_evaluations.allocate(func_eval.indexmin(), func_eval.indexmax());
maximum_function_evaluations = func_eval;
convergence_criteria.allocate(func_conv.indexmin(), func_conv.indexmax());
convergence_criteria = func_conv;
if (do_ageK == 1) // need for age-specific K
{
k = nages;
} // use for dimension of VBK()
else {
k = 0;
}
// clang-format off
END_CALCS

!! // SS_Label_Info_5.0.2 #Create dummy_parm that will be estimated even if turn_off_phase is set to 0
Expand Down Expand Up @@ -112,23 +111,25 @@ PARAMETER_SECTION
4darray Save_PopBio(styr-3*nseas,TimeMax_Fcast_std+nseas,1,2*pop,1,gmorph,0,nages)

LOCAL_CALCS
// clang-format on
// If empirical wt-at-age is used, maturity and fecundity vectors are set to a distinctive value of 0.5
// If parameters are used, then the calcs could be age-based or length-based or both, so start with default value of 1.0
// These calculations happen in function get_mat_fec() in file SS_biofxn.tpl
if (WTage_rd == 1 || Maturity_Option == 4 || Maturity_Option == 5 ) {
mat_len = 0.5;
mat_age = 0.5;
mat_fec_len = 0.5;
fec_len = 0.5;
}
else {
mat_len = 1.0;
mat_age = 1.0;
mat_fec_len = 1.0;
fec_len = 1.0;
}
// clang-format off
// clang-format on
// If empirical wt-at-age is used, maturity and fecundity vectors are set to a distinctive value of 0.5
// If parameters are used, then the calcs could be age-based or length-based or both, so start with default value of 1.0
// These calculations happen in function get_mat_fec() in file SS_biofxn.tpl
if (WTage_rd == 1 || Maturity_Option == 4 || Maturity_Option == 5)
{
mat_len = 0.5;
mat_age = 0.5;
mat_fec_len = 0.5;
fec_len = 0.5;
}
else
{
mat_len = 1.0;
mat_age = 1.0;
mat_fec_len = 1.0;
fec_len = 1.0;
}
// clang-format off
END_CALCS

3darray age_age(0,N_ageerr+store_agekey_add,1,n_abins2,0,gender*nages+gender-1)
Expand Down Expand Up @@ -159,42 +160,40 @@ PARAMETER_SECTION
3darray recr_dist_endyr(1,N_GP*gender,1,N_settle_timings,1,pop);
!!// SS_Label_Info_5.1.2 #Create SR_parm vector, recruitment vectors
init_bounded_number_vector SR_parm(1,N_SRparm3,SR_parm_LO,SR_parm_HI,SR_parm_PH)
matrix SR_parm_byyr(styr-3,YrMax,1,N_SRparm2+1) // R0, steepness, parm3, sigmar, rec_dev_offset, R1, rho, SPB Time_vary implementation of spawner-recruitment
matrix SR_parm_byyr(styr-3,YrMax,1,N_SRparm2+1) // R0, steepness, parm3, sigmar, rec_dev_offset, R1, rho, SSB Time_vary implementation of spawner-recruitment
vector SR_parm_virg(1,N_SRparm2+1)
vector SR_parm_work(1,N_SRparm2+1)
number two_sigmaRsq;
number half_sigmaRsq;
number sigmaR;
number SPR_virgin;
number SSBpR_virgin;
number SSBpR_virgin_adj;
number regime_change;
number rho;
number dirichlet_Parm;
LOCAL_CALCS
// clang-format on
Ave_Size.initialize();
// if(SR_parm(N_SRparm2)!=0.0 || SR_parm_PH(N_SRparm2)>0) {SR_autocorr=1;} else {SR_autocorr=0;} // flag for recruitment autocorrelation
if (do_recdev == 1)
{
k = recdev_start;
j = recdev_end;
s = 1;
p = -1;
}
else if (do_recdev >= 2)
{
s = recdev_start;
p = recdev_end;
k = 1;
j = -1;
}
else
{
s = 1;
p = -1;
k = 1;
j = -1;
}
// clang-format off
// clang-format on
Ave_Size.initialize();
// if(SR_parm(N_SRparm2)!=0.0 || SR_parm_PH(N_SRparm2)>0) {SR_autocorr=1;} else {SR_autocorr=0;} // flag for recruitment autocorrelation
if (do_recdev == 1) {
k = recdev_start;
j = recdev_end;
s = 1;
p = -1;
}
else if (do_recdev >= 2) {
s = recdev_start;
p = recdev_end;
k = 1;
j = -1;
}
else {
s = 1;
p = -1;
k = 1;
j = -1;
}
// clang-format off
END_CALCS

// vector biasadj(styr-nages,YrMax) // biasadj as used; depends on whether a recdev is estimated or not
Expand All @@ -210,45 +209,45 @@ PARAMETER_SECTION
vector recdev(recdev_first,YrMax);

LOCAL_CALCS
// clang-format on
if (do_recdev == 0)
{
s = -1;
}
else
{
s = YrMax;
}
if (Do_Impl_Error > 0)
{
k = Fcast_recr_PH2;
j = YrMax;
}
else
{
k = -1;
j = -1;
}
// clang-format off
// clang-format on
if (do_recdev == 0) {
s = -1;
}
else {
s = YrMax;
}
if (Do_Impl_Error > 0) {
k = Fcast_recr_PH2;
j = YrMax;
}
else {
k = -1;
j = -1;
}
// clang-format off
END_CALCS
init_bounded_vector Fcast_recruitments(recdev_end+1,s,recdev_LO,recdev_HI,Fcast_recr_PH2)
init_bounded_vector Fcast_impl_error(endyr+1,j,-1,1,k)
vector ABC_buffer(endyr+1,YrMax);
number HCR_anchor // basis (denominator) for inflection in control rule. Select virgin SSB or benchmark SSB

// SPAWN-RECR: define some spawning biomass and recruitment entities
number SSB_virgin
number Recr_virgin
number SSB_vir_LH

number SSB_unf
number SSB_unf // SSB unfished, based on benchmark biology
number Recr_unf
number SSB_use
number R0_use; // annually updated value if SR_update_SSBpR0_timeseries == 1

number SSB_deplete // SSB that will be used as denominator for depletion calculations and as basis for control rule inflection
number SSB_current; // Spawning biomass
number SSB_equil;

number SPR_trial
number SPR_actual;
number SPR_temp; // used to pass quantity into Equil_SpawnRecr
number SSBpR_temp; // SSB per Recruit; used to pass quantity into Equil_SpawnRecr
number Recruits; // Age0 Recruits
number equ_mat_bio
number equ_mat_num
Expand Down Expand Up @@ -321,7 +320,7 @@ PARAMETER_SECTION
!!k=0;
!!if(Hermaphro_Option!=0) k=1;

3darray MaleSPB(styr-3,YrMax*k,1,pop,1,N_GP) //Male Spawning biomass
3darray MaleSSB(styr-3,YrMax*k,1,pop,1,N_GP) //Male Spawning biomass

matrix SSB_equil_pop_gp(1,pop,1,N_GP);
matrix MaleSSB_equil_pop_gp(1,pop,1,N_GP);
Expand Down Expand Up @@ -387,16 +386,15 @@ PARAMETER_SECTION


LOCAL_CALCS
// clang-format on
if (N_Fparm > 0) // continuous F
{
k = N_Fparm;
}
else
{
k = -1;
}
// clang-format off
// clang-format on
if (N_Fparm > 0) // continuous F
{
k = N_Fparm;
}
else {
k = -1;
}
// clang-format off
END_CALCS
// defining F_rate as number_vector allows for Fparm_PH to be element specific
init_bounded_number_vector F_rate(1,k,0.,max_harvest_rate,Fparm_PH_dim)
Expand All @@ -416,6 +414,7 @@ PARAMETER_SECTION
// note that bycatch_F(1,Nfleet,1,nseas) has similar role
number alpha;
number beta;
number steepness;
number GenTime;
number Yield;
number Adj4010;
Expand Down Expand Up @@ -491,9 +490,9 @@ PARAMETER_SECTION
number overdisp // overdispersion

LOCAL_CALCS
// clang-format on
k = Do_TG * (3 * N_TG + 2 * Nfleet1);
// clang-format off
// clang-format on
k = Do_TG * (3 * N_TG + 2 * Nfleet1);
// clang-format off
END_CALCS

init_bounded_number_vector TG_parm(1,k,TG_parm_LO,TG_parm_HI,TG_parm_PH);
Expand All @@ -506,12 +505,12 @@ PARAMETER_SECTION
matrix parm_timevary(1,timevary_cnt,styr-1,YrMax); // time series of adjusted parm values for block and trend

LOCAL_CALCS
// clang-format on
if (Do_Forecast > 0)
k = TimeMax_Fcast_std + nseas;
else
k = TimeMax + nseas;
// clang-format off
// clang-format on
if (Do_Forecast > 0)
k = TimeMax_Fcast_std + nseas;
else
k = TimeMax + nseas;
// clang-format off
END_CALCS

!!// SS_Label_Info_5.1.7 #Create arrays for storing derived selectivity quantities for use in mortality calculations
Expand Down Expand Up @@ -597,8 +596,8 @@ PARAMETER_SECTION
number equ_M_std

!!// SS_Label_Info_5.1.8 #Create matrix called smry to store derived quantities of interest
matrix Smry_Table(styr-3,YrMax,1,17);
// 1=totbio, 2=smrybio, 3=smrynum, 4=enc_catch, 5=dead_catch, 6=ret_catch, 7=spbio, 8=recruit,
matrix Smry_Table(styr-3,YrMax,1,20+2*gmorph);
// 1=totbio, 2=smrybio, 3=smrynum, 4=enc_catch, 5=dead_catch, 6=ret_catch, 7=SSBio, 8=recruit,
// 9=equ_totbio, 10=equ_smrybio, 11=equ_SSB_virgin, 12=equ_S1, 13=Gentime, 14=YPR, 15=meanage_spawners, 16=meanage_smrynums, 17=meanage_catch


Expand Down
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