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format C++ code with clang format #461

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Sep 7, 2023
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format C++ code with clang format #461

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151 changes: 93 additions & 58 deletions inst/include/common/information.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -156,19 +156,23 @@ class Information {
*/
bool CreateModel() {
bool valid_model = true;
FIMS_LOG << "Beginning to create FIMS model in information.hpp CreateModel(). " << std::endl;
FIMS_LOG << "Initializing fleet objects for " << this->fleets.size() << " fleets." << std::endl;
FIMS_LOG
<< "Beginning to create FIMS model in information.hpp CreateModel(). "
<< std::endl;
FIMS_LOG << "Initializing fleet objects for " << this->fleets.size()
<< " fleets." << std::endl;
for (fleet_iterator it = this->fleets.begin(); it != this->fleets.end();
++it) {
// Initialize fleet object
std::shared_ptr<fims::Fleet<T> > f = (*it).second;
FIMS_LOG << "Initializing fleet " << f->id << "." << std::endl;
f->Initialize(f->nyears, f->nages);

FIMS_LOG << "Expecting to import " << this->data_objects.size()
<< " data objects." << std::endl;
<< " data objects." << std::endl;

FIMS_LOG << "Checking for available fleet index data objects." << std::endl;
FIMS_LOG << "Checking for available fleet index data objects."
<< std::endl;
// set index data
if (f->observed_index_data_id != -999) {
uint32_t index_id = static_cast<uint32_t>(f->observed_index_data_id);
Expand All @@ -179,7 +183,7 @@ class Information {
f->observed_index_data = (*it).second;
FIMS_LOG << "Index data successfully set." << std::endl;
FIMS_LOG << "Observed input index: \n " << f->observed_index_data
<< std::endl;
<< std::endl;
} else {
valid_model = false;
FIMS_LOG << "Error: Expected data observations not defined for fleet"
Expand All @@ -188,25 +192,26 @@ class Information {

} else {
valid_model = false;
FIMS_LOG << "Error: No index data observed for fleet " << f->id
FIMS_LOG << "Error: No index data observed for fleet " << f->id
<< ". FIMS requires index data for all fleets." << std::endl;
}
// end set index data

FIMS_LOG << "Checking for available fleet age comp data objects." << std::endl;

FIMS_LOG << "Checking for available fleet age comp data objects."
<< std::endl;
// set age composition data
if (f->observed_agecomp_data_id != -999) {
uint32_t agecomp_id =
static_cast<uint32_t>(f->observed_agecomp_data_id);
data_iterator it = this->data_objects.find(agecomp_id);
FIMS_LOG << "Input fleet age comp id = " << agecomp_id
<< "." << std::endl;
FIMS_LOG << "Input fleet age comp id = " << agecomp_id << "."
<< std::endl;

if (it != this->data_objects.end()) {
f->observed_agecomp_data = (*it).second;
FIMS_LOG << "Age comp data successfully set." << std::endl;
FIMS_LOG << "Observed input age comp: \n " << f->observed_agecomp_data
<< std::endl;
<< std::endl;
} else {
valid_model = false;
FIMS_LOG << "Error: Expected data observations not defined for fleet "
Expand All @@ -215,20 +220,22 @@ class Information {

} else {
valid_model = false;
FIMS_LOG << "Error: No age comp data observed for fleet " << f->id
<< ". FIMS requires age comp data for all fleets." << std::endl;
FIMS_LOG << "Error: No age comp data observed for fleet " << f->id
<< ". FIMS requires age comp data for all fleets."
<< std::endl;
}
// end set composition data

FIMS_LOG << "Checking for available fleet selectivity pattern." << std::endl;
FIMS_LOG << "Checking for available fleet selectivity pattern."
<< std::endl;
// set selectivity model
if (f->selectivity_id != -999) {
uint32_t sel_id = static_cast<uint32_t>(
f->selectivity_id); // cast as unsigned integer
selectivity_models_iterator it = this->selectivity_models.find(
sel_id); // if find, set it, otherwise invalid
FIMS_LOG << "Input fleet selectivity pattern id = " << sel_id
<< "." << std::endl;
FIMS_LOG << "Input fleet selectivity pattern id = " << sel_id << "."
<< std::endl;

if (it != this->selectivity_models.end()) {
f->selectivity = (*it).second; // elements in container held in pair
Expand All @@ -237,87 +244,104 @@ class Information {
FIMS_LOG << "Selectivity successfully set." << std::endl;
} else {
valid_model = false;
FIMS_LOG << "Error: Expected selectivity pattern not defined for fleet "
<< f->id << ", selectivity pattern " << sel_id << std::endl;
FIMS_LOG
<< "Error: Expected selectivity pattern not defined for fleet "
<< f->id << ", selectivity pattern " << sel_id << std::endl;
}

} else {
valid_model = false;
FIMS_LOG << "Error: No selectivity pattern defined for fleet " << f->id
<< ". FIMS requires selectivity be defined for all fleets." << std::endl;
FIMS_LOG << "Error: No selectivity pattern defined for fleet " << f->id
<< ". FIMS requires selectivity be defined for all fleets."
<< std::endl;
}
// end set selectivity

FIMS_LOG << "Checking for available index likelihood function." << std::endl;
FIMS_LOG << "Checking for available index likelihood function."
<< std::endl;
// set index likelihood
if (f->index_likelihood_id != -999) {
uint32_t ind_like_id = static_cast<uint32_t>(
f->index_likelihood_id); // cast as unsigned integer
distribution_models_iterator it = this->distribution_models.find(
ind_like_id); // if find, set it, otherwise invalid
FIMS_LOG << "Input index likelihood function id = " << ind_like_id
<< "." << std::endl;
<< "." << std::endl;

if (it != this->distribution_models.end()) {
f->index_likelihood =
(*it).second; // elements in container held in pair (first is
// id, second is object - shared pointer to
// distribution)
FIMS_LOG << "Index likelihood function successfully set." << std::endl;
FIMS_LOG << "Index likelihood function successfully set."
<< std::endl;
} else {
valid_model = false;
FIMS_LOG << "Error: Expected index likelihood function not defined for fleet "
<< f->id << ", likelihood function " << ind_like_id << std::endl;
FIMS_LOG << "Error: Expected index likelihood function not defined "
"for fleet "
<< f->id << ", likelihood function " << ind_like_id
<< std::endl;
}

} else {
valid_model = false;
FIMS_LOG << "Error: No index likelihood function defined for fleet " << f->id
<< ". FIMS requires likelihood functions be defined for all data." << std::endl;
FIMS_LOG
<< "Error: No index likelihood function defined for fleet " << f->id
<< ". FIMS requires likelihood functions be defined for all data."
<< std::endl;
}
// end set index likelihood

FIMS_LOG << "Checking for available age comp likelihood function." << std::endl;
FIMS_LOG << "Checking for available age comp likelihood function."
<< std::endl;
// set agecomp likelihood
if (f->agecomp_likelihood_id != -999) {
uint32_t ac_like_id = static_cast<uint32_t>(
f->agecomp_likelihood_id); // cast as unsigned integer
distribution_models_iterator it = this->distribution_models.find(
ac_like_id); // if find, set it, otherwise invalid
FIMS_LOG << "Input age comp likelihood function id = " << ac_like_id
<< "." << std::endl;
<< "." << std::endl;

if (it != this->distribution_models.end()) {
f->agecomp_likelihood =
(*it).second; // elements in container held in pair (first is
// id, second is object - shared pointer to
// distribution)
FIMS_LOG << "Age comp likelihood function successfully set." << std::endl;
FIMS_LOG << "Age comp likelihood function successfully set."
<< std::endl;
} else {
valid_model = false;
FIMS_LOG << "Error: Expected age comp likelihood function not defined for fleet "
<< f->id << ", likelihood function " << ac_like_id << std::endl;
FIMS_LOG << "Error: Expected age comp likelihood function not "
"defined for fleet "
<< f->id << ", likelihood function " << ac_like_id
<< std::endl;
}

} else {
valid_model = false;
FIMS_LOG << "Error: No age comp likelihood function defined for fleet " << f->id
<< ". FIMS requires likelihood functions be defined for all data." << std::endl;
FIMS_LOG
<< "Error: No age comp likelihood function defined for fleet "
<< f->id
<< ". FIMS requires likelihood functions be defined for all data."
<< std::endl;
}
// end set agecomp likelihood

FIMS_LOG << "Completed initialization for fleet " << f->id << "." << std::endl;
FIMS_LOG << "Completed initialization for fleet " << f->id << "."
<< std::endl;

} // close fleet iterator loop
FIMS_LOG << "Completed initialization of all fleets." << std::endl;

FIMS_LOG << "Initializing population objects for " << this->populations.size() << " populations." << std::endl;

FIMS_LOG << "Initializing population objects for "
<< this->populations.size() << " populations." << std::endl;
for (population_iterator it = this->populations.begin();
it != this->populations.end(); ++it) {

std::shared_ptr<fims::Population<T> > p = (*it).second;

FIMS_LOG << "Setting up links from population " << p->id << " to fleets [ " << std::flush;

FIMS_LOG << "Setting up links from population " << p->id
<< " to fleets [ " << std::flush;
// error check and set population elements
// check me - add another fleet iterator to push information from
for (fleet_iterator it = this->fleets.begin(); it != this->fleets.end();
Expand All @@ -330,32 +354,37 @@ class Information {
p->fleets.push_back(f);
FIMS_LOG << f->id << " " << std::flush;
}
FIMS_LOG << "]" << std::endl;
FIMS_LOG << "]" << std::endl;

FIMS_LOG << "Initializing population " << p->id << "." << std::endl;
p->Initialize(p->nyears, p->nseasons, p->nages);

FIMS_LOG << "Checking for available recruitment function." << std::endl;
// set recruitment
if (p->recruitment_id != -999) {
uint32_t recruitment_uint = static_cast<uint32_t>(p->recruitment_id);
recruitment_models_iterator it =
this->recruitment_models.find(recruitment_uint);
FIMS_LOG << "Input recruitment id = " << recruitment_uint << "." << std::endl;
FIMS_LOG << "Input recruitment id = " << recruitment_uint << "."
<< std::endl;
if (it != this->recruitment_models.end()) {
p->recruitment =
(*it).second; // recruitment defined in population.hpp
FIMS_LOG << "Recruitment function successfully set." << std::endl;
} else {
valid_model = false;
FIMS_LOG << "Error: Expected recruitment function not defined for population "
<< p->id << ", recruitment function " << recruitment_uint << std::endl;
FIMS_LOG << "Error: Expected recruitment function not defined for "
"population "
<< p->id << ", recruitment function " << recruitment_uint
<< std::endl;
}

} else {
valid_model = false;
FIMS_LOG << "Error: No recruitment function defined for population " << p->id
<< ". FIMS requires recruitment functions be defined for all populations."
FIMS_LOG << "Error: No recruitment function defined for population "
<< p->id
<< ". FIMS requires recruitment functions be defined for all "
"populations."
<< std::endl;
}

Expand All @@ -376,14 +405,16 @@ class Information {
FIMS_LOG << "Growth function successfully set." << std::endl;
} else {
valid_model = false;
FIMS_LOG << "Error: Expected growth function not defined for population "
<< p->id << ", growth function " << growth_uint << std::endl;
FIMS_LOG
<< "Error: Expected growth function not defined for population "
<< p->id << ", growth function " << growth_uint << std::endl;
}

} else {
valid_model = false;
FIMS_LOG << "Error: No growth function defined for population " << p->id
<< ". FIMS requires growth functions be defined for all populations."
FIMS_LOG << "Error: No growth function defined for population " << p->id
<< ". FIMS requires growth functions be defined for all "
"populations."
<< std::endl;
}

Expand All @@ -400,17 +431,21 @@ class Information {
FIMS_LOG << "Maturity function successfully set." << std::endl;
} else {
valid_model = false;
FIMS_LOG << "Error: Expected maturity function not defined for population "
<< p->id << ", maturity function " << maturity_uint << std::endl;
FIMS_LOG
<< "Error: Expected maturity function not defined for population "
<< p->id << ", maturity function " << maturity_uint << std::endl;
}

} else {
valid_model = false;
FIMS_LOG << "Error: No maturity function defined for population " << p->id
<< ". FIMS requires maturity functions be defined for all populations."
FIMS_LOG << "Error: No maturity function defined for population "
<< p->id
<< ". FIMS requires maturity functions be defined for all "
"populations."
<< std::endl;
}
FIMS_LOG << "Completed initialization for population " << p->id << "." << std::endl;
FIMS_LOG << "Completed initialization for population " << p->id << "."
<< std::endl;
}
FIMS_LOG << "Completed initialization of all populations." << std::endl;
FIMS_LOG << "Completed FIMS model creation." << std::endl;
Expand Down
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