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fix bugs
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@Andrea-Havron-NOAA
Andrea-Havron-NOAA committed Aug 1, 2024
1 parent d072377 commit 88b0438
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Showing 6 changed files with 70 additions and 66 deletions.
8 changes: 4 additions & 4 deletions inst/include/common/information.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -158,7 +158,7 @@ class Information {

void setup_priors(){
for(density_components_iterator it = density_components.begin(); it!= density_components.end(); ++it){
std::shared_ptr<DensityComponentBase<Type> > n = (*it).second;
std::shared_ptr<fims_distributions::DensityComponentBase<Type> > n = (*it).second;
if(n->input_type == "prior"){
variable_map_iterator vmit;
vmit = this->variable_map.find(n->key[0]);
Expand All @@ -173,7 +173,7 @@ class Information {
}
void setup_random_effects(){
for(density_components_iterator it = this->density_components.begin(); it!= this->density_components.end(); ++it){
std::shared_ptr<DensityComponentBase<Type> > n = (*it).second;
std::shared_ptr<fims_distributions::DensityComponentBase<Type> > n = (*it).second;
if(n->input_type == "re"){
variable_map_iterator vmit;
vmit = this->variable_map.find(n->key[0]);
Expand All @@ -188,7 +188,7 @@ class Information {
}
void setup_data(){
for(density_components_iterator it = this->density_components.begin(); it!= this->density_components.end(); ++it){
std::shared_ptr<DensityComponentBase<Type> > n = (*it).second;
std::shared_ptr<fims_distributions::DensityComponentBase<Type> > n = (*it).second;
if(n->input_type == "data"){
variable_map_iterator vmit;
vmit = this->variable_map.find(n->key[0]);
Expand Down Expand Up @@ -333,7 +333,7 @@ class Information {
exit(1);
}
// end set selectivity

}

INFO_LOG << "Initializing population objects for "
<< this->populations.size() << " populations." << std::endl;
Expand Down
119 changes: 61 additions & 58 deletions inst/include/common/model.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -34,10 +34,10 @@ class Model { // may need singleton
std::shared_ptr<fims_info::Information<Type> >
fims_information; /**< Create a shared fims_information as a pointer to
Information*/
std::map<uint32_t, std::shared_ptr<DensityComponentBase<Type> > >
std::map<uint32_t, std::shared_ptr<fims_distributions::DensityComponentBase<Type> > >
density_components;
typedef typename std::map<
uint32_t, std::shared_ptr<DensityComponentBase<Type> > >::iterator
uint32_t, std::shared_ptr<fims_distributions::DensityComponentBase<Type> > >::iterator
density_components_iterator;

#ifdef TMB_MODEL
Expand Down Expand Up @@ -92,13 +92,14 @@ class Model { // may need singleton
#endif
// Loop over densities and evaluate joint negative log densities for priors
size_t n_priors = 0;
for(density_components_iterator it = this->density_components.begin(); it!= this->density_components.end(); ++it){
std::shared_ptr<DensityComponentBase<Type> > n = (*it).second;
typename density_components_iterator d_it;
for(d_it = this->density_components.begin(); d_it!= this->density_components.end(); ++d_it){
std::shared_ptr<fims_distributions::DensityComponentBase<Type> > d = (*d_it).second;
#ifdef TMB_MODEL
n->of = this->of;
d->of = this->of;
#endif
if(n->input_type == "prior"){
jnll -= n->evaluate();
if(d->input_type == "prior"){
jnll -= d->evaluate();
n_priors += 1;
}
}
Expand All @@ -109,37 +110,32 @@ class Model { // may need singleton

// Loop over populations and evaluate recruitment component

typename fims_info::Information<Type>::population_iterator it;
typename fims_info::Information<Type>::population_iterator p_it;
MODEL_LOG << "Evaluating recruitment expected values for "
<< this->fims_information->populations.size() << " populations."
<< std::endl;

for (it = this->fims_information->populations.begin();
it != this->fims_information->populations.end(); ++it) {
//(*it).second points to the Population module
MODEL_LOG << "Setting up pointer to population " << (*it).second->id
for (p_it = this->fims_information->populations.begin();
p_it != this->fims_information->populations.end(); ++p_it) {
//(*p_it).second points to the Population module
std::shared_ptr<fims_popdy::Population<Type> > p = (*p_it).second;
MODEL_LOG << "Setting up pointer to population " << p->id
<< "." << std::endl;
// Prepare recruitment
(*it).second->recruitment->Prepare();
p->recruitment->Prepare();
MODEL_LOG << "Recruitment for population successfully prepared"
<< std::endl;
// link to TMB objective function
#ifdef TMB_MODEL
(*it).second->of = this->of;
#endif
// Evaluate population
(*it).second->Evaluate();
}

// Loop over densities and evaluate joint negative log-likelihoods for random effects
size_t n_random_effects = 0;
for(density_components_iterator it = this->density_components.begin(); it!= this->density_components.end(); ++it){
std::shared_ptr<DensityComponentBase<Type> > n = (*it).second;
for(d_it = this->density_components.begin(); d_it!= this->density_components.end(); ++d_it){
std::shared_ptr<fims_distributions::DensityComponentBase<Type> > d = (*d_it).second;
#ifdef TMB_MODEL
n->of = this->of;
d->of = this->of;
#endif
if(n->input_type == "re"){
jnll -= n->evaluate();
if(d->input_type == "re"){
jnll -= d->evaluate();
n_random_effects += 1;
}
}
Expand All @@ -148,69 +144,76 @@ class Model { // may need singleton
<< std::endl;

// Loop over and evaluate populations
typename fims_info::Information<Type>::population_iterator it;
MODEL_LOG << "Evaluating expected values for "
<< this->fims_information->populations.size() << " populations."
<< std::endl;
for (it = this->fims_information->populations.begin();
it != this->fims_information->populations.end(); ++it) {
//(*it).second points to the Population module
for (p_it = this->fims_information->populations.begin();
p_it != this->fims_information->populations.end(); ++it) {
//(*p_it).second points to the Population module
std::shared_ptr<fims_popdy::Population<Type> > p = (*p_it).second;
// link to TMB objective function
#ifdef TMB_MODEL
p->of = this->of;
#endif
// Evaluate population
(*it).second->Evaluate();
p->Evaluate();
}

typename fims_info::Information<Type>::population_iterator f_it;
// Loop over fleets/surveys, and evaluate age comp and index expected values
for (jt = this->fims_information->fleets.begin();
jt != this->fims_information->fleets.end(); ++jt) {
//(*jt).second points to each individual Fleet module
for (f_it = this->fims_information->fleets.begin();
f_it != this->fims_information->fleets.end(); ++f_it) {
//(*f_it).second points to each individual Fleet module
std::shared_ptr<fims_popdy::Fleet<Type> > f = (*f_it).second;
#ifdef TMB_MODEL
(*jt).second->of = this->of;
f->of = this->of;
#endif
MODEL_LOG << "Setting up pointer to fleet " << (*jt).second->id << "."
MODEL_LOG << "Setting up pointer to fleet " << f->id << "."
<< std::endl;
(*jt).second->evaluate_age_comp();
(*jt).second->evaluate_index()
f->evaluate_age_comp();
f->evaluate_index()
}

// Loop over and evaluate data joint negative log-likelihoods
for(density_components_iterator it = this->density_components.begin(); it!= this->density_components.end(); ++it){
std::shared_ptr<DensityComponentBase<Type> > n = (*it).second;
for(d_it = this->density_components.begin(); d_it!= this->density_components.end(); ++d_it){
std::shared_ptr<fims_distributions::DensityComponentBase<Type> > d = (*d_it).second;
#ifdef TMB_MODEL
n->of = this->of;
n->keep = this->keep;
d->of = this->of;
d->keep = this->keep;
#endif
if(n->input_type == "data"){
jnll -= n->evaluate();
if(d->input_type == "data"){
jnll -= d->evaluate();
}
}

// initiate population index for structuring report out objects
int pop_idx = 0;
for (it = this->fims_information->populations.begin();
it != this->fims_information->populations.end(); ++it) {
for (p_it = this->fims_information->populations.begin();
p_it != this->fims_information->populations.end(); ++p_it) {
std::shared_ptr<fims_popdy::Population<Type> > p = (*p_it).second;
#ifdef TMB_MODEL
naa(pop_idx) = vector<Type>((*it).second->numbers_at_age);
ssb(pop_idx) = vector<Type>((*it).second->spawning_biomass);
naa(pop_idx) = vector<Type>(p->numbers_at_age);
ssb(pop_idx) = vector<Type>(p->spawning_biomass);
log_recruit_dev(pop_idx) =
vector<Type>((*it).second->recruitment->log_recruit_devs);
recruitment(pop_idx) = vector<Type>((*it).second->expected_recruitment);
biomass(pop_idx) = vector<Type>((*it).second->biomass);
M(pop_idx) = vector<Type>((*it).second->M);
vector<Type>(p->recruitment->log_recruit_devs);
recruitment(pop_idx) = vector<Type>(p->expected_recruitment);
biomass(pop_idx) = vector<Type>(p->biomass);
M(pop_idx) = vector<Type>(p->M);
#endif
pop_idx += 1;
}

// initiate fleet index for structuring report out objects
int fleet_idx = 0;
for (jt = this->fims_information->fleets.begin();
jt != this->fims_information->fleets.end(); ++jt) {
for (f_it = this->fims_information->fleets.begin();
f_it != this->fims_information->fleets.end(); ++f_it) {
std::shared_ptr<fims_popdy::Fleet<Type> > f = (*f_it).second;
#ifdef TMB_MODEL
exp_index(fleet_idx) = (*jt).second->expected_index;
exp_catch(fleet_idx) = (*jt).second->expected_catch;
F_mort(fleet_idx) = (*jt).second->Fmort;
cnaa(fleet_idx) = (*jt).second->catch_numbers_at_age;
cwaa(fleet_idx) = (*jt).second->catch_weight_at_age;
exp_index(fleet_idx) = f->expected_index;
exp_catch(fleet_idx) = f->expected_catch;
F_mort(fleet_idx) = f->Fmort;
cnaa(fleet_idx) = f->catch_numbers_at_age;
cwaa(fleet_idx) = f->catch_weight_at_age;
#endif
fleet_idx += 1;
}
Expand Down
2 changes: 1 addition & 1 deletion inst/include/distributions/functors/lognormal_lpdf.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ namespace fims_distributions
if(this->x->at(i) != this->x->na_value){
this->lpdf_vec[i] = dnorm(this->x->at(i), logmu[i], logsd[i], true) - this->x->at(i);
} else {
this->lpdf_vec[i] = 0
this->lpdf_vec[i] = 0;
}
} else {
// this->lpdf_vec[i] = this->keep[i] * -dnorm(this->x[i], logmu[i], logsd[i], true);
Expand Down
1 change: 1 addition & 0 deletions inst/include/distributions/functors/multinomial_lpmf.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,7 @@ namespace fims_distributions
}
if(!containsNA){
for (size_t j = 0; j < dims[1]; j++){
size_t idx = (i * dims[1]) + j;
x_vector[j] = this->x->at(i, j);
prob_vector[j] = this->expected_value[idx];
}
Expand Down
2 changes: 1 addition & 1 deletion inst/include/distributions/functors/normal_lpdf.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ struct NormalLPDF : public DensityComponentBase<Type> {
if(this->x->at(i) != this->x->na_value){
this->lpdf_vec[i] = dnorm(this->x->at(i), mu[i], sd[i], true);
} else {
this->lpdf_vec[i] = 0
this->lpdf_vec[i] = 0;
}

} else {
Expand Down
4 changes: 2 additions & 2 deletions inst/include/population_dynamics/fleet/fleet.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -154,7 +154,7 @@ struct Fleet : public fims_model_object::FIMSObject<Type> {
}
}

void const Type evaluate_age_comp() {
void evaluate_age_comp() {
for (size_t y = 0; y < this->nyears; y++) {
Type sum = 0.0;
for (size_t a = 0; a < this->nages; a++) {
Expand All @@ -170,7 +170,7 @@ struct Fleet : public fims_model_object::FIMSObject<Type> {
}
}

void const Type evaluate_index() {
void evaluate_index() {
for(size_t i=0; i<this->expected_index.size(); i++){
expected_index[i] = log(this->expected_index[i]);
}
Expand Down

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