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atfgoa.cpp
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atfgoa.cpp
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#include <math.h>
#include <admodel.h>
#include <time.h>
ofstream R_out;
ofstream CheckFile;
time_t start,finish;
long hour,minute,second;
double elapsed_time;
#include <admodel.h>
#include <contrib.h>
extern "C" {
void ad_boundf(int i);
}
#include <atfgoa.htp>
model_data::model_data(int argc,char * argv[]) : ad_comm(argc,argv)
{
pad_evalout = new ofstream("atfgoa2013.mcmc.out");;
styr.allocate("styr");
endyr.allocate("endyr");
styr_fut.allocate("styr_fut");
endyr_fut.allocate("endyr_fut");
phase_F40.allocate("phase_F40");
median_rec.allocate("median_rec");
nages.allocate("nages");
nselages.allocate("nselages");
nselages_srv1.allocate("nselages_srv1");
monot_sel.allocate("monot_sel");
monot_sel_srv1.allocate("monot_sel_srv1");
phase_logistic_sel.allocate("phase_logistic_sel");
phase_selcoffs.allocate("phase_selcoffs");
phase_logistic_sel_srv1.allocate("phase_logistic_sel_srv1");
phase_selcoffs_srv1.allocate("phase_selcoffs_srv1");
wt_like.allocate(1,8,"wt_like");
nlen.allocate("nlen");
nobs_fish.allocate("nobs_fish");
yrs_fish.allocate(1,nobs_fish,"yrs_fish");
nsamples_fish.allocate(1,2,1,nobs_fish,"nsamples_fish");
nobs_srv1.allocate("nobs_srv1");
yrs_srv1.allocate(1,nobs_srv1,"yrs_srv1");
nobs_srv1_length.allocate("nobs_srv1_length");
yrs_srv1_length.allocate(1,nobs_srv1_length,"yrs_srv1_length");
nsamples_srv1_length.allocate(1,2,1,nobs_srv1_length,"nsamples_srv1_length");
nobs_srv1_age.allocate("nobs_srv1_age");
yrs_srv1_age.allocate(1,nobs_srv1_age,"yrs_srv1_age");
like_wght.allocate(1,5,"like_wght");
nsamples_srv1_age.allocate(1,2,1,nobs_srv1_age,"nsamples_srv1_age");
obs_p_srv1_length.allocate(1,2,1,nobs_srv1_length,1,nlen,"obs_p_srv1_length");
obs_p_srv1_age.allocate(1,2,1,nobs_srv1_age,1,nages,"obs_p_srv1_age");
obs_p_fish.allocate(1,2,1,nobs_fish,1,nlen,"obs_p_fish");
catch_bio.allocate(styr,endyr,"catch_bio");
obs_srv1.allocate(1,nobs_srv1,"obs_srv1");
obs_srv1_sd.allocate(1,nobs_srv1,"obs_srv1_sd");
wt.allocate(1,2,1,nages,"wt");
maturity.allocate(1,nages,"maturity");
lenage.allocate(1,2,1,nages,1,nlen,"lenage");
offset_const.allocate("offset_const");
cv_srv1.allocate(1,nobs_srv1);
styr_rec=styr-nages+1;
if(nselages>nages) nselages=nages;
if(nselages_srv1>nages) nselages_srv1=nages;
cv_srv1=elem_div(obs_srv1_sd,obs_srv1);
wt=wt*.001;
test.allocate(1,2,1,3,1,4,1,5);
cout <<"test"<<endl;
cout <<test<<endl;
obs_sexr.allocate(1,nobs_fish);
obs_sexr_srv1.allocate(1,nobs_srv1_age);
obs_sexr_srv1_l.allocate(1,nobs_srv1_length);
}
void model_parameters::initializationfunction(void)
{
mean_log_rec.set_initial_value(18);
log_avg_fmort.set_initial_value(-5.);
q1.set_initial_value(1.);
fmort_dev.set_initial_value(0.00001);
}
model_parameters::model_parameters(int sz,int argc,char * argv[]) :
model_data(argc,argv) , function_minimizer(sz)
{
initializationfunction();
cout <<"line 89"<<endl;
q1.allocate(0.01,20.0,-8,"q1");
mean_log_rec.allocate(1,"mean_log_rec");
rec_dev.allocate(styr_rec,endyr,-15,15,2,"rec_dev");
log_avg_fmort.allocate(1,"log_avg_fmort");
fmort_dev.allocate(styr,endyr,-5.0,3.5,1,"fmort_dev");
log_selcoffs_fish.allocate(1,2,1,nselages,phase_selcoffs,"log_selcoffs_fish");
log_selcoffs_srv1.allocate(1,2,1,nselages_srv1,phase_selcoffs_srv1,"log_selcoffs_srv1");
fish_slope_f.allocate(.1,5.,phase_logistic_sel,"fish_slope_f");
fish_sel50_f.allocate(1.,8.,phase_logistic_sel,"fish_sel50_f");
fish_slope_m.allocate(.05,2.0,phase_logistic_sel,"fish_slope_m");
fish_sel50_m.allocate(1.,25.,phase_logistic_sel,"fish_sel50_m");
srv1_slope_f.allocate(.1,5.,phase_logistic_sel_srv1,"srv1_slope_f");
srv1_sel50_f.allocate(1.,10.,phase_logistic_sel_srv1,"srv1_sel50_f");
srv1_slope_m.allocate(.01,5.,phase_logistic_sel_srv1,"srv1_slope_m");
srv1_sel50_m.allocate(1.,10.,phase_logistic_sel_srv1,"srv1_sel50_m");
sexr_param_fish.allocate(1.0,1.0,-5,"sexr_param_fish");
sexr_param_srv.allocate(.25,1.0,phase_selcoffs_srv1,"sexr_param_srv");
cout <<"line 114"<<endl;
F40.allocate(0.05,.5,phase_F40,"F40");
F35.allocate(0.05,.5,phase_F40,"F35");
log_sel_fish.allocate(1,2,1,nages,"log_sel_fish");
#ifndef NO_AD_INITIALIZE
log_sel_fish.initialize();
#endif
log_sel_srv1.allocate(1,2,1,nages,"log_sel_srv1");
#ifndef NO_AD_INITIALIZE
log_sel_srv1.initialize();
#endif
sel.allocate(1,2,1,nages,"sel");
#ifndef NO_AD_INITIALIZE
sel.initialize();
#endif
sel_srv1.allocate(1,2,1,nages,"sel_srv1");
#ifndef NO_AD_INITIALIZE
sel_srv1.initialize();
#endif
avgsel_fish.allocate(1,2,"avgsel_fish");
#ifndef NO_AD_INITIALIZE
avgsel_fish.initialize();
#endif
avgsel_srv1.allocate(1,2,"avgsel_srv1");
#ifndef NO_AD_INITIALIZE
avgsel_srv1.initialize();
#endif
popn.allocate(1,2,styr,endyr,"popn");
#ifndef NO_AD_INITIALIZE
popn.initialize();
#endif
totn_srv1.allocate(1,2,styr,endyr,"totn_srv1");
#ifndef NO_AD_INITIALIZE
totn_srv1.initialize();
#endif
M.allocate(1,2,"M");
#ifndef NO_AD_INITIALIZE
M.initialize();
#endif
cout <<"line 128"<<endl;
explbiom.allocate(styr,endyr,"explbiom");
#ifndef NO_AD_INITIALIZE
explbiom.initialize();
#endif
pred_bio.allocate(styr,endyr,"pred_bio");
#ifndef NO_AD_INITIALIZE
pred_bio.initialize();
#endif
fspbio.allocate(styr,endyr,"fspbio");
#ifndef NO_AD_INITIALIZE
fspbio.initialize();
#endif
pred_srv1.allocate(styr,endyr,"pred_srv1");
#ifndef NO_AD_INITIALIZE
pred_srv1.initialize();
#endif
cout <<"line 133"<<endl;
pred_p_fish.allocate(1,2,styr,endyr,1,nlen,"pred_p_fish");
#ifndef NO_AD_INITIALIZE
pred_p_fish.initialize();
#endif
pred_p_srv1_age.allocate(1,2,styr,endyr,1,nages,"pred_p_srv1_age");
#ifndef NO_AD_INITIALIZE
pred_p_srv1_age.initialize();
#endif
pred_p_srv1_len.allocate(1,2,styr,endyr,1,nlen,"pred_p_srv1_len");
#ifndef NO_AD_INITIALIZE
pred_p_srv1_len.initialize();
#endif
pred_catch.allocate(styr,endyr,"pred_catch");
#ifndef NO_AD_INITIALIZE
pred_catch.initialize();
#endif
cout <<"line 138"<<endl;
natage.allocate(1,2,styr,endyr,1,nages,"natage");
#ifndef NO_AD_INITIALIZE
natage.initialize();
#endif
catage.allocate(1,2,styr,endyr,1,nages,"catage");
#ifndef NO_AD_INITIALIZE
catage.initialize();
#endif
cout <<"line 141"<<endl;
natlength.allocate(1,2,styr,endyr,1,nlen,"natlength");
#ifndef NO_AD_INITIALIZE
natlength.initialize();
#endif
cout <<"line 142"<<endl;
Z.allocate(1,2,styr,endyr,1,nages,"Z");
#ifndef NO_AD_INITIALIZE
Z.initialize();
#endif
F.allocate(1,2,styr,endyr,1,nages,"F");
#ifndef NO_AD_INITIALIZE
F.initialize();
#endif
S.allocate(1,2,styr,endyr,1,nages,"S");
#ifndef NO_AD_INITIALIZE
S.initialize();
#endif
fmort.allocate(styr,endyr,"fmort");
#ifndef NO_AD_INITIALIZE
fmort.initialize();
#endif
cout <<"line 144"<<endl;
rbar.allocate("rbar");
#ifndef NO_AD_INITIALIZE
rbar.initialize();
#endif
surv.allocate(1,2,"surv");
#ifndef NO_AD_INITIALIZE
surv.initialize();
#endif
offset.allocate(1,3,"offset");
#ifndef NO_AD_INITIALIZE
offset.initialize();
#endif
rec_like.allocate("rec_like");
#ifndef NO_AD_INITIALIZE
rec_like.initialize();
#endif
catch_like.allocate("catch_like");
#ifndef NO_AD_INITIALIZE
catch_like.initialize();
#endif
age_like.allocate(1,3,"age_like");
#ifndef NO_AD_INITIALIZE
age_like.initialize();
#endif
sel_like.allocate(1,4,"sel_like");
#ifndef NO_AD_INITIALIZE
sel_like.initialize();
#endif
fpen.allocate("fpen");
#ifndef NO_AD_INITIALIZE
fpen.initialize();
#endif
surv_like.allocate("surv_like");
#ifndef NO_AD_INITIALIZE
surv_like.initialize();
#endif
recruits.allocate(styr,endyr,"recruits");
biomassrep.allocate(styr,endyr,"biomassrep");
fspbiorep.allocate(styr,endyr,"fspbiorep");
endbiom.allocate("endbiom");
depletion.allocate("depletion");
f.allocate("f");
prior_function_value.allocate("prior_function_value");
likelihood_function_value.allocate("likelihood_function_value");
tmp.allocate("tmp");
#ifndef NO_AD_INITIALIZE
tmp.initialize();
#endif
pred_sexr.allocate(styr,endyr,"pred_sexr");
#ifndef NO_AD_INITIALIZE
pred_sexr.initialize();
#endif
preds_sexr.allocate(styr,endyr,"preds_sexr");
#ifndef NO_AD_INITIALIZE
preds_sexr.initialize();
#endif
cout <<"line 161"<<endl;
sigmar.allocate("sigmar");
#ifndef NO_AD_INITIALIZE
sigmar.initialize();
#endif
ftmp.allocate("ftmp");
#ifndef NO_AD_INITIALIZE
ftmp.initialize();
#endif
SB0.allocate("SB0");
#ifndef NO_AD_INITIALIZE
SB0.initialize();
#endif
SBF40.allocate("SBF40");
#ifndef NO_AD_INITIALIZE
SBF40.initialize();
#endif
SBF35.allocate("SBF35");
#ifndef NO_AD_INITIALIZE
SBF35.initialize();
#endif
sprpen.allocate("sprpen");
#ifndef NO_AD_INITIALIZE
sprpen.initialize();
#endif
Nspr.allocate(1,3,1,nages,"Nspr");
#ifndef NO_AD_INITIALIZE
Nspr.initialize();
#endif
nage_future.allocate(1,2,styr_fut,endyr_fut,1,nages,"nage_future");
#ifndef NO_AD_INITIALIZE
nage_future.initialize();
#endif
F_future.allocate(1,2,styr_fut,endyr_fut,1,nages,"F_future");
#ifndef NO_AD_INITIALIZE
F_future.initialize();
#endif
Z_future.allocate(1,2,styr_fut,endyr_fut,1,nages,"Z_future");
#ifndef NO_AD_INITIALIZE
Z_future.initialize();
#endif
S_future.allocate(1,2,styr_fut,endyr_fut,1,nages,"S_future");
#ifndef NO_AD_INITIALIZE
S_future.initialize();
#endif
catage_future.allocate(1,2,styr_fut,endyr_fut,1,nages,"catage_future");
#ifndef NO_AD_INITIALIZE
catage_future.initialize();
#endif
avg_rec_dev_future.allocate("avg_rec_dev_future");
#ifndef NO_AD_INITIALIZE
avg_rec_dev_future.initialize();
#endif
avg_F_future.allocate(1,3,"avg_F_future");
#ifndef NO_AD_INITIALIZE
avg_F_future.initialize();
#endif
catch_future.allocate(1,5,styr_fut,endyr_fut,"catch_future");
#ifndef NO_AD_INITIALIZE
catch_future.initialize();
#endif
fspbiom_fut.allocate(1,5,styr_fut,endyr_fut,"fspbiom_fut");
future_biomass.allocate(1,5,styr_fut,endyr_fut,"future_biomass");
explbiom_fut.allocate(styr_fut,endyr_fut,"explbiom_fut");
#ifndef NO_AD_INITIALIZE
explbiom_fut.initialize();
#endif
maxsel_fish.allocate("maxsel_fish");
#ifndef NO_AD_INITIALIZE
maxsel_fish.initialize();
#endif
maxsel_srv1.allocate(1,2,"maxsel_srv1");
#ifndef NO_AD_INITIALIZE
maxsel_srv1.initialize();
#endif
B0.allocate("B0");
#ifndef NO_AD_INITIALIZE
B0.initialize();
#endif
B40.allocate("B40");
#ifndef NO_AD_INITIALIZE
B40.initialize();
#endif
B35.allocate("B35");
#ifndef NO_AD_INITIALIZE
B35.initialize();
#endif
AMeanRec.allocate("AMeanRec");
#ifndef NO_AD_INITIALIZE
AMeanRec.initialize();
#endif
like_natm.allocate("like_natm");
#ifndef NO_AD_INITIALIZE
like_natm.initialize();
#endif
like_q.allocate("like_q");
#ifndef NO_AD_INITIALIZE
like_q.initialize();
#endif
cout<<"wt_like"<<endl;
cout<< wt_like <<endl;
}
void model_parameters::preliminary_calculations(void)
{
#if defined(USE_ADPVM)
admaster_slave_variable_interface(*this);
#endif
for(i=1; i<=nobs_fish;i++)
{
obs_sexr(i) = sum(obs_p_fish(2,i))/sum(obs_p_fish(1,i) + obs_p_fish(2,i));
}
for(i=1; i<=nobs_srv1_age;i++)
{
obs_sexr_srv1(i)=(sum(obs_p_srv1_age(2,i)))/(sum(obs_p_srv1_age(1,i))+sum(obs_p_srv1_age(2,i)));
}
for(i=1; i<=nobs_srv1_length;i++)
{
obs_sexr_srv1_l(i)=(sum(obs_p_srv1_length(2,i)(2,nlen+1)))/(sum(obs_p_srv1_length(1,i))+sum(obs_p_srv1_length(2,i)));
}
offset.initialize();
for (i=1; i <= nobs_fish; i++)
{
double sumtot ;
sumtot = sum(obs_p_fish(1,i)+obs_p_fish(2,i));
obs_p_fish(1,i) = obs_p_fish(1,i) / sumtot;
obs_p_fish(2,i) = obs_p_fish(2,i) / sumtot;
for(k=1; k<=2;k++)
offset(1) -= nsamples_fish(k,i)*obs_p_fish(k,i) * log(obs_p_fish(k,i)+.0001);
}
//survey length offset
for (i=1; i <= nobs_srv1_length; i++)
{
double sumtot ;
sumtot = sum(obs_p_srv1_length(1,i)+obs_p_srv1_length(2,i));
obs_p_srv1_length(1,i) = obs_p_srv1_length(1,i) / sumtot;
obs_p_srv1_length(2,i) = obs_p_srv1_length(2,i) / sumtot;
for(k=1; k<=2;k++)
offset(2) -= nsamples_srv1_length(k,i)*obs_p_srv1_length(k,i) * log(obs_p_srv1_length(k,i)+.0001);
}
//survey age offset
for (i=1; i <= nobs_srv1_age; i++)
{
double sumtot ;
sumtot = sum(obs_p_srv1_age(1,i)+obs_p_srv1_age(2,i));
obs_p_srv1_age(1,i) = obs_p_srv1_age(1,i) / sumtot;
obs_p_srv1_age(2,i) = obs_p_srv1_age(2,i) / sumtot;
for(k=1; k<=2;k++)
offset(3) -= nsamples_srv1_age(k,i)*obs_p_srv1_age(k,i) * log(obs_p_srv1_age(k,i)+.0001);
}
M(1)=0.20;
M(2)=0.35;
}
void model_parameters::userfunction(void)
{
f =0.0;
ofstream& evalout= *pad_evalout;
get_selectivity();
get_mortality();
surv(1)=mfexp(-1.0* M(1));
surv(2)=mfexp(-1.0* M(2));
get_numbers_at_age();
get_catch_at_age();
if (active(F40))
compute_spr_rates();
if (last_phase())
{
Future_projections();
}
if (sd_phase() || mceval_phase())
{
if (mceval_phase())
{
evalout << f << " " ;
// loop over years and print in one long row.
for (i=styr;i<=endyr;i++)
evalout<< fspbio(i) << " ";
for (i=styr;i<=endyr;i++)
evalout<< natage(1,i)*wt(1) + natage(2,i)*wt(2) <<" ";
for (i=styr;i<=endyr;i++)
evalout << 2*natage(1,i,1) <<" ";
// hit carriage return on file
evalout << endl;
}
}
evaluate_the_objective_function();
}
void model_parameters::get_selectivity(void)
{
ofstream& evalout= *pad_evalout;
if(active(log_selcoffs_fish))
{
phase_logistic_sel=-2;
for(k=1;k<=2;k++)
{
for (j=1;j<=nselages;j++)
{
log_sel_fish(k,j)=log_selcoffs_fish(k,j);
}
}
//sets selectivity of ages older than nselages to selectivity at nselages
for(k=1;k<=2;k++)
{
for (j=nselages+1;j<=nages;j++)
{
log_sel_fish(k,j)=log_sel_fish(k,j-1);
}
}
for(k=1;k<=2;k++)
{
avgsel_fish(k)=log(mean(mfexp(log_selcoffs_fish(k))));
}
//vector=vector-scalar same as vector-=scalar
//scaling selectivities by subracting the mean so exp(mean(s))=1.
//selectivities can be greater than 1 but mean is 1.
for(k=1;k<=2;k++)
{
log_sel_fish(k)-=log(mean(mfexp(log_sel_fish(k))));
sel(k)=mfexp(log_sel_fish(k));
if(k==2)
{
sel(k)=sel(k)*sexr_param_fish;
}
}
}
else
{
//logistic selectivity curve
for (j=1;j<=nages;j++)
{
if(j<=nselages)
{
sel(1,j)=1./(1.+mfexp(-1.*fish_slope_f*(double(j)-fish_sel50_f)));
sel(2,j)=1./(1.+mfexp(-1.*fish_slope_m*(double(j)-fish_sel50_m)));
}
else
{
sel(1,j)=sel(1,j-1);
sel(2,j)=sel(2,j-1);
}
}
}
if(active(log_selcoffs_srv1))
{
phase_logistic_sel_srv1=-2;
for(k=1;k<=2;k++)
{
for (j=1;j<=nselages_srv1;j++)
{
log_sel_srv1(k,j)=log_selcoffs_srv1(k,j);
}
}
//sets selectivity of ages older than nselages_srv1 to selectivity at nselages_srv1
for(k=1;k<=2;k++)
{
for (j=nselages_srv1+1;j<=nages;j++)
{
log_sel_srv1(k,j)=log_sel_srv1(k,j-1);
}
}
for(k=1;k<=2;k++)
{
avgsel_srv1(k)=log(mean(mfexp(log_selcoffs_srv1(k))));
}
//vector=vector-scalar same as vector-=scalar
//scaling selectivities by subracting the mean so exp(mean(s))=1.
//selectivities can be greater than 1 but mean is 1.
for(k=1;k<=2;k++)
{
log_sel_srv1(k)-=log(mean(mfexp(log_sel_srv1(k))));
sel_srv1(k)=mfexp(log_sel_srv1(k));
if(k==2)
{
sel_srv1(k)=sel_srv1(k)*sexr_param_srv;
}
}
}
else
{
//logistic selectivity curve
for (j=1;j<=nages;j++)
{
if(j<=nselages_srv1)
{
sel_srv1(1,j)=1./(1.+mfexp(-1.*srv1_slope_f*(double(j)-srv1_sel50_f)));
sel_srv1(2,j)=1./(1.+mfexp(-1.*srv1_slope_m*(double(j)-srv1_sel50_m)));
}
else
{
sel_srv1(1,j)=sel_srv1(1,j-1);
sel_srv1(2,j)=sel_srv1(2,j-1);
}
}
}
}
void model_parameters::get_mortality(void)
{
ofstream& evalout= *pad_evalout;
maxsel_fish=max(sel(1));
if(maxsel_fish<max(sel(2)))
maxsel_fish=max(sel(2));
maxsel_srv1(1)=max(sel_srv1(1));
maxsel_srv1(2)=maxsel_srv1(1);
fmort=mfexp(log_avg_fmort+fmort_dev);
for(k=1;k<=2;k++)
{
for (i=styr;i<=endyr;i++)
{
F(k,i)=(sel(k)/maxsel_fish)*fmort(i);
Z(k,i)=F(k,i) + M(k);
}
}
S=mfexp(-1.0*Z);
}
void model_parameters::get_numbers_at_age(void)
{
ofstream& evalout= *pad_evalout;
if(maxsel_srv1(1)<max(sel_srv1(2)))
{
maxsel_srv1(1)=max(sel_srv1(2));
maxsel_srv1(2)=maxsel_srv1(1);
}
int itmp;
//calc initial population
for (j=1;j<nages;j++)
{
itmp=styr+1-j;
natage(1,styr,j)=mfexp(mean_log_rec-(M(1)*double(j-1))+rec_dev(itmp));
natage(2,styr,j)=mfexp(mean_log_rec-(M(2)*double(j-1))+rec_dev(itmp));
}
itmp=styr+1-nages;
natage(1,styr,nages)=mfexp(mean_log_rec+rec_dev(itmp)-(M(1)*(nages-1)))/(1.- surv(1));
natage(2,styr,nages)=mfexp(mean_log_rec+rec_dev(itmp)-(M(2)*(nages-1)))/(1.- surv(2));
// Now do for next several years----------------------------------
for (i=styr+1;i<=endyr;i++)
{
natage(1,i,1)=mfexp(mean_log_rec+rec_dev(i));
natage(2,i,1)=natage(1,i,1);
}
//numbers at age
for(k=1;k<=2;k++)
{
for (i=styr;i< endyr;i++)
{
//subvector - avoids writing a j loop =++ increments the right side
//(1,nages-1) to 1+1 to nages-1+1 then does the assignment x(i)(1,n)
//takes the ith row of x the columns 1 to n
for(j=1;j<nages;j++)
{
natage(k,i+1,j+1)=natage(k,i,j)*S(k,i,j);
}
//accumulates oldest ages
natage(k,i+1,nages)+=natage(k,i,nages)*S(k,i,nages);
popn(k,i)= natage(k,i)*sel(k);
}
popn(k,endyr)=natage(k,endyr)*sel(k);
}
for (i=styr;i<=endyr;i++)
{
for(k=1;k<=2;k++)
{
//population numbers at length
natlength(k,i)=natage(k,i)*lenage(k);
//numbers to rescale age comps and length comps
totn_srv1(k,i)=(natage(k,i)*sel_srv1(k));
}
}
//predicted survey values
fspbio=0.;
for (i=styr;i<=endyr;i++)
{
fspbio(i)+=natage(1,i)*elem_prod(wt(1),maturity);
explbiom(i)=0.;
pred_bio(i)=0.;
pred_srv1(i)=0.;
for(k=1;k<=2;k++)
{
pred_srv1(i)+=q1*(natage(k,i)*elem_prod(sel_srv1(k)/maxsel_srv1(k),wt(k)));
explbiom(i)+=natage(k,i)*elem_prod(sel(k),wt(k))/maxsel_fish;
pred_bio(i)+=natage(k,i)*wt(k);
pred_p_srv1_len(k,i)=elem_prod(sel_srv1(k),natage(k,i))*lenage(k)/(totn_srv1(1,i)+totn_srv1(2,i));
pred_p_srv1_age(k,i)=elem_prod(sel_srv1(k),natage(k,i))/(totn_srv1(1,i)+totn_srv1(2,i));
}
}
biomassrep=pred_bio;
fspbiorep=fspbio;
for(i=styr;i<=endyr;i++)
{
recruits(i)=mfexp(mean_log_rec+rec_dev(i));
}
depletion=pred_bio(endyr)/pred_bio(styr);
endbiom=pred_bio(endyr);
}
void model_parameters::get_catch_at_age(void)
{
ofstream& evalout= *pad_evalout;
for (i=styr; i<=endyr; i++)
{
pred_catch(i)=0.;
for(k=1;k<=2;k++)
{
//--Baranov's equation here-----------------------------------
for (j = 1 ; j<= nages; j++)
{
catage(k,i,j) = natage(k,i,j)*F(k,i,j)*(1.-S(k,i,j))/Z(k,i,j);
pred_catch(i)+=catage(k,i,j)*wt(k,j);
}
pred_p_fish(k,i)=elem_prod(sel(k),natage(k,i))*lenage(k)/(popn(1,i)+popn(2,i));
}
}
}
void model_parameters::Future_projections(void)
{
ofstream& evalout= *pad_evalout;
for(k=1;k<=2;k++)
{
nage_future(k,styr_fut)(2,nages)=++elem_prod(natage(k,endyr)(1,nages-1),S(k,endyr)(1,nages-1));
nage_future(k,styr_fut,nages)+=natage(k,endyr,nages)*S(k,endyr,nages);
}
future_biomass=0.;
catch_future=0.;
fspbiom_fut=0.;
for (int l=1;l<=5;l++)
{
switch (l)
{
case 1:
ftmp=F40;
break;
case 2:
ftmp=F35;
break;
case 3:
ftmp=0.0;
break;
case 4:
ftmp=mean(mfexp(log_avg_fmort+fmort_dev(endyr-4,endyr)));
break;
case 5:
ftmp=mean(mfexp(log_avg_fmort+fmort_dev(endyr-4,endyr)));
break;
}
// Get future F's
for(k=1;k<=2;k++)
{
for (i=endyr+1;i<=endyr_fut;i++)
{
if(l>3){ftmp=mean(mfexp(log_avg_fmort+fmort_dev(endyr-4,endyr)));}
if(i>(endyr+1) && l==5) {ftmp=F35;}
if(i>(endyr+1) && l==4) {ftmp=F40;}
for (j=1;j<=nages;j++)
{
F_future(k,i,j) = (sel(k,j)/maxsel_fish)*ftmp;
Z_future(k,i,j) = F_future(k,i,j)+M(k);
S_future(k,i,j) = mfexp(-1.*Z_future(k,i,j));
}
}
// Future Recruitment (and spawners)
for (i=styr_fut;i<endyr_fut;i++)
{
nage_future(k,i,1) = AMeanRec;
// Now graduate for the next year....
nage_future(k,i+1)(2,nages) = ++elem_prod(nage_future(k,i)(1,nages-1),S_future(k,i)(1,nages-1));
nage_future(k,i+1,nages) += nage_future(k,i,nages)*S_future(k,i,nages);
}
nage_future(k,endyr_fut,1) = AMeanRec;
// Now get catch at future ages
fspbiom_fut(l)=0.;
for (i=styr_fut; i<=endyr_fut; i++)
{
for (j = 1 ; j<= nages; j++)
{
catage_future(k,i,j) = nage_future(k,i,j) * F_future(k,i,j) * ( 1.- S_future(k,i,j) ) / Z_future(k,i,j);
if(k==1)
{
fspbiom_fut(l,i) += nage_future(1,i,j)*wt(1,j)*maturity(j);
}
}
if (l!=3){
catch_future(l,i) += catage_future(k,i)*wt(k);
}
future_biomass(l,i) += nage_future(k,i)*wt(k);
} //end loop over future years
} //end loop over sex
fspbiom_fut(l)=0.;
for(i=styr_fut;i<=endyr_fut;i++)
{
for(j=1;j<=nages;j++)
{
fspbiom_fut(l,i)+= nage_future(1,i,j)*wt(1,j)*maturity(j);
}
}
} //End of loop over F's
}
void model_parameters::compute_spr_rates(void)
{
ofstream& evalout= *pad_evalout;
//Compute SPR Rates and add them to the likelihood for Females
SB0=0.;
SBF40=0.;
SBF35=0.;
AMeanRec=mean(mfexp(mean_log_rec+rec_dev(81,endyr)));
// Initialize the recruit (1) for each F (F40 etc)
for (i=1;i<=3;i++)
Nspr(i,1)=1.;
for (j=2;j<nages;j++)
{
Nspr(1,j)=Nspr(1,j-1)*mfexp(-1.*M(1));
Nspr(2,j)=Nspr(2,j-1)*mfexp(-1.*(M(1)+F40*sel(1,j-1)/maxsel_fish));
Nspr(3,j)=Nspr(3,j-1)*mfexp(-1.*(M(1)+F35*sel(1,j-1)/maxsel_fish));
}
// Now do plus group
Nspr(1,nages)=Nspr(1,nages-1)*mfexp(-1.*M(1))/(1.-mfexp(-1.*M(1)));
Nspr(2,nages)=Nspr(2,nages-1)*mfexp(-1.* (M(1)+F40*sel(1,nages-1)/maxsel_fish))/(1.-mfexp(-1.*(M(1)+F40*sel(1,nages)/maxsel_fish)));
Nspr(3,nages)=Nspr(3,nages-1)*mfexp(-1.* (M(1)+F35*sel(1,nages-1)/maxsel_fish))/(1.-mfexp(-1.*(M(1)+F35*sel(1,nages)/maxsel_fish)));
for (j=1;j<=nages;j++)
{
// Kill them off till- use fraction of the year e.g. april=0.25 - not for atf they spawn in winter so put in 0.0
// Number ProportMat Wt Amount die off prior to spawning (within that year)
SB0 += Nspr(1,j)*maturity(j)*wt(1,j)*mfexp(-0.0*M(1));
SBF40 += Nspr(2,j)*maturity(j)*wt(1,j)*mfexp(-0.0*(M(1)+F40*sel(1,j)/maxsel_fish));
SBF35 += Nspr(3,j)*maturity(j)*wt(1,j)*mfexp(-0.0*(M(1)+F35*sel(1,j)/maxsel_fish));
}
sprpen = 300.*square((SBF40/SB0)-0.4);
sprpen += 300.*square((SBF35/SB0)-0.35);
B0 = AMeanRec*SB0 ;
B40 = AMeanRec*SBF40 ;
B35 = AMeanRec*SBF35 ;
}
void model_parameters::evaluate_the_objective_function(void)
{
ofstream& evalout= *pad_evalout;
age_like=0.; //just having the . as part of the number identifies it as a floating point number (a double)
sel_like=0.;
fpen=0.;
rec_like=0.;
surv_like=0.;
catch_like=0.;
f=0.;
like_natm=0.;
like_q=0.;
if (active(rec_dev))
{
age_like=0.;
int ii;
//recruitment likelihood - norm2 is sum of square values
rec_like=norm2(rec_dev(styr_rec,endyr));
f+=rec_like;
for(k=1;k<=2;k++)
{
for (i=1; i <= nobs_fish; i++)
{
ii=yrs_fish(i);
//fishery length likelihood
for (j=1; j<=nlen; j++)
{
age_like(1)-=nsamples_fish(k,i)*(offset_const+obs_p_fish(k,i,j))*log(pred_p_fish(k,ii,j)+offset_const);
}
}
}
//add the offset to the likelihood
age_like(1)-=offset(1);
//survey
for(k=1;k<=2;k++)
{
for (i=1; i <=nobs_srv1_length; i++)
{
ii=yrs_srv1_length(i);
//survey likelihood
for (j=1; j<=nlen; j++)
{
age_like(2)-=nsamples_srv1_length(k,i)*(offset_const+obs_p_srv1_length(k,i,j))*log(pred_p_srv1_len(k,ii,j)+offset_const);
}
}
}
age_like(2)-=offset(2);
//bracket for active(fish_slope_f)
//survey ages
for(k=1;k<=2;k++)
{
for (i=1; i <=nobs_srv1_age; i++)
{
ii=yrs_srv1_age(i);
//survey likelihood
for (j=1; j<=nages; j++)
{
age_like(3)-=nsamples_srv1_age(k,i)*(offset_const+obs_p_srv1_age(k,i,j))*log(pred_p_srv1_age(k,ii,j)+offset_const);
}
}
}
age_like(3)-=offset(3);
f+=like_wght(1)*age_like(1);
f+=like_wght(2)*age_like(2);
f+=like_wght(3)*age_like(3);
//end of if(active (rec_dev))
}
// Fit to indices (lognormal)
//weight each years estimate by 1/(2*variance) - use cv of biomass in sqrt(log(cv^2+1)) as sd of log(biomass)
surv_like = norm2(elem_div(log(obs_srv1+offset_const)-log(pred_srv1(yrs_srv1)+offset_const),sqrt(2)*sqrt(log(elem_prod(cv_srv1,cv_srv1)+1.0))));
//this subtracts the log(sd) from the likelihood - is a constant so I'm not adding it.
catch_like=norm2(log(catch_bio+offset_const)-log(pred_catch+offset_const));
//selectivity likelihood is penalty on how smooth selectivities are
//here are taking the sum of squares of the second differences
if(active(log_selcoffs_fish))
{
sel_like(1)=wt_like(1)*norm2(first_difference(first_difference(log_sel_fish(1))));
sel_like(3)=wt_like(3)*norm2(first_difference(first_difference(log_sel_fish(2))));
for (j=1;j<nages;j++)
{
if(monot_sel>0.0001)
{
if (log_sel_fish(1,j)>log_sel_fish(1,j+1))
sel_like(1)+=wt_like(5)*square(log_sel_fish(1,j)-log_sel_fish(1,j+1));
if (log_sel_fish(2,j)>log_sel_fish(2,j+1))
sel_like(3)+=wt_like(6)*square(log_sel_fish(2,j)-log_sel_fish(2,j+1));
}
}
f+=1.*(sel_like(1)+sel_like(3));
f+=1.*square(avgsel_fish(1));
f+=1.*square(avgsel_fish(2));
}
if(active(log_selcoffs_srv1))
{
sel_like(2)=wt_like(2)*norm2(first_difference(first_difference(log_sel_srv1(1))));
sel_like(4)=wt_like(4)*norm2(first_difference(first_difference(log_sel_srv1(2))));
for (j=1;j<nages;j++)
{
if(monot_sel_srv1>0.0001)
{
if (log_sel_srv1(1,j)>log_sel_srv1(1,j+1))
sel_like(2)+=wt_like(7)*square(log_sel_srv1(1,j)-log_sel_srv1(1,j+1));
if (log_sel_srv1(2,j)>log_sel_srv1(2,j+1))
sel_like(4)+=wt_like(8)*square(log_sel_srv1(2,j)-log_sel_srv1(2,j+1));
}
}
f+=1.*(sel_like(2)+sel_like(4));
f+=1.*square(avgsel_srv1(1));
f+=1.*square(avgsel_srv1(2));
}
f+=like_wght(5)*surv_like;
f+=like_wght(4)*catch_like;
// Phases less than 3, penalize High F's
if (current_phase()<2)
{
//F's are low for arrowtooth changed the value to compare from .2 to .001
//don't know if makes any difference since the penalty is reduced at the end
fpen=10.*norm2(mfexp(fmort_dev+log_avg_fmort)-.001);
}
else
{
fpen=.01*norm2(mfexp(fmort_dev+log_avg_fmort)-.001);
}
if (active(fmort_dev))
{
fpen+=norm2(fmort_dev);
}
f+=fpen;
f+=sprpen;
}
void model_parameters::report(const dvector& gradients)
{
adstring ad_tmp=initial_params::get_reportfile_name();
ofstream report((char*)(adprogram_name + ad_tmp));
if (!report)
{
cerr << "error trying to open report file" << adprogram_name << ".rep";
return;
}
report << "Estimated numbers of female fish: seq(3,15) " << endl;
report << natage(1) << endl;
report << "Estimated numbers of male fish: seq(3,15) " << endl;
report << natage(2) << endl;
report << "Estimated numbers of female fish by length: '25','27','29','31','33','35','37','39','41.5','44.5','47.5','50.5','53.5','56.5','59.5','62.5','65.5','68.5','72.5','85'" << endl;
report << natlength(1) << endl;
report << "Estimated numbers of male fish by length: '25','27','29','31','33','35','37','39','41.5','44.5','47.5','50.5','53.5','56.5','59.5','62.5','65.5','68.5','72.5','85'" << endl;
report << natlength(2) << endl;
report << "Estimated numbers of female fish by length MD: '24','30','40','52','61','70'" << endl;
for(i=styr;i<=endyr;i++){
report <<sum(natlength(1,i)(1,3))<<" "<<sum(natlength(1,i)(4,8))<<" "<<sum(natlength(1,i)(9,12))<<" "<<sum(natlength(1,i)(13,15))<<" "<<sum(natlength(1,i)(16,18))<<" "<<sum(natlength(1,i)(19,20))<<endl;
}
report << "Estimated numbers of male fish by length MD: '25','35','45','55','65','75'" << endl;
for(i=styr;i<=endyr;i++){
report <<sum(natlength(2,i)(1,3))<<" "<<sum(natlength(2,i)(4,8))<<" "<<sum(natlength(2,i)(9,12))<<" "<<sum(natlength(2,i)(13,15))<<" "<<sum(natlength(2,i)(16,18))<<" "<<sum(natlength(2,i)(19,20))<<endl;
}
report << "Observed Survey 1: '1961','1973','1984','1987','1990','1993','1996','1999','2001','2003','2005','2007','2009','2011','2013'" << endl;
report << obs_srv1 << endl;
report << "Survey catchability Q: 'Q'" << endl;
report << q1 << endl;
report << "natural mortality females, males: 'FemM','MaleM'" << endl;
report << M << endl;
report << "Predicted Survey 1: seq(1961,"<<endyr+1900<<") " << endl;
report << pred_srv1 << endl;
report << "Predicted Biomass : seq(1961,"<<endyr+1900<<")" << endl;
report << pred_bio << endl;
report << "Predicted Exploitable Biomass : seq(1961,"<<endyr+1900<<") " << endl;
report << explbiom << endl;
report << "Female Spawning Biomass : seq(1961,"<<endyr+1900<<") " << endl;
report << fspbio << endl;
report << "Observed Prop fishery females:'year','25','27','29','31','33','35','37','39','41.5','44.5','47.5','50.5','53.5','56.5','59.5','62.5','65.5','68.5','72.5','85'"<< endl;
for (i=1; i<=nobs_fish; i++)
{
report << yrs_fish(i)+1900 << " " << obs_p_fish(1,i) << endl;
}
report << "Predicted length prop fishery females : 'year','25','27','29','31','33','35','37','39','41.5','44.5','47.5','50.5','53.5','56.5','59.5','62.5','65.5','68.5','72.5','85'" << endl;
//report<<pred_p_fish<<endl;
for (i=1; i<=nobs_fish; i++)
{
ii=yrs_fish(i);
report << ii+1900 << " " << pred_p_fish(1,ii) << endl;
}
report << "Observed length Prop fishery males:'year','25','27','29','31','33','35','37','39','41.5','44.5','47.5','50.5','53.5','56.5','59.5','62.5','65.5','68.5','72.5','85'"<< endl;
for (i=1; i<=nobs_fish; i++)
{
report << yrs_fish(i)+1900 << " " << obs_p_fish(2,i) << endl;
}
report << "Predicted length prop fishery males : 'year','25','27','29','31','33','35','37','39','41.5','44.5','47.5','50.5','53.5','56.5','59.5','62.5','65.5','68.5','72.5','85'" << endl;
//report<<pred_p_fish<<endl;
for (i=1; i<=nobs_fish; i++)
{
ii=yrs_fish(i);
report << ii +1900 << " " << pred_p_fish(2,ii) << endl;
}
report << "Observed Length Prop survey females: 'year','25','27','29','31','33','35','37','39','41.5','44.5','47.5','50.5','53.5','56.5','59.5','62.5','65.5','68.5','72.5','85'" << endl;
for (i=1; i<=nobs_srv1_length; i++)
{