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Information.hpp
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/*
* File: Information.hpp
*
* Author: Matthew Supernaw
* National Oceanic and Atmospheric Administration
* National Marine Fisheries Service
* Sustainable Fisheries Division
* St. Petersburg, FL, 33701
*
* Created on September 16, 2016, 12:35 PM
*
* This File is part of the NOAA, National Marine Fisheries Service
* Metapopulation Assessment System project.
*
* This software is a "United States Government Work" under the terms of the
* United States Copyright Act. It was written as part of the author's official
* duties as a United States Government employee and thus cannot be copyrighted.
* This software is freely available to the public for use. The National Oceanic
* And Atmospheric Administration and the U.S. Government have not placed any
* restriction on its use or reproduction. Although all reasonable efforts have
* been taken to ensure the accuracy and reliability of the software and data,
* the National Oceanic And Atmospheric Administration and the U.S. Government
* do not and cannot warrant the performance or results that may be obtained by
* using this software or data. The National Oceanic And Atmospheric
* Administration and the U.S. Government disclaim all warranties, express or
* implied, including warranties of performance, merchantability or fitness
* for any particular purpose.
*
* Please cite the author(s) in any work or product based on this material.
*
*/
#ifndef MAS_INFORMATION_HPP
#define MAS_INFORMATION_HPP
#include "Common.hpp"
#include "Area.hpp"
#include "Population.hpp"
#include "Season.hpp"
#include "Movement.hpp"
#include "Selectivity.hpp"
#include "Survey.hpp"
#include "third_party/rapidjson/document.h"
#include "third_party/rapidjson/prettywriter.h"
#include "third_party/rapidjson/stringbuffer.h"
#include "Fleet.hpp"
#include "HarvestControlRule.hpp"
#include <ctime>
//#define MAS_DEBUG
#ifdef MAS_DEBUG
#define INFO_DEBUG std::cout<<"Information.hpp: "<<__func__<<": "<<__LINE__<<std::endl;
#else
#define INFO_DEBUG
#endif
namespace mas {
struct EnsembleUnit {
mas::SubmodelType type;
std::vector<int> units;
rapidjson::Document::MemberIterator val;
};
template<typename REAL_T>
class Information : public mas::ModelObject<REAL_T> {
typedef typename VariableTrait<REAL_T>::variable variable;
typedef typename std::map<int, std::vector<std::shared_ptr<DataObject<REAL_T> > > >::iterator data_iterator;
std::string data_path;
public:
std::map<int, std::vector<std::shared_ptr<DataObject<REAL_T> > > > data_dictionary;
std::vector<std::shared_ptr<DataObject<REAL_T> > > data;
std::string analyst = "NA";
std::string study_name = "NA";
int nyears;
int nseasons = 1;
int first_year;
int last_year;
REAL_T spawning_season_offset = .25;
REAL_T catch_fraction_of_year = .5;
REAL_T survey_fraction_of_year = .5;
std::vector<variable> ages;
std::vector<REAL_T> ages_real;
bool natal_movement = false;
bool valid_configuration = true;
std::unordered_map<int, std::shared_ptr<mas::Area<REAL_T> > > areas;
std::unordered_map<int, std::shared_ptr<mas::Season<REAL_T> > > seasons;
//System sub model objects
std::unordered_map<int, std::shared_ptr<mas::Population<REAL_T> > > populations;
std::unordered_map<int, std::shared_ptr<mas::FishingMortality<REAL_T> > > fishing_mortality_models;
std::unordered_map<int, std::shared_ptr<mas::SelectivityBase<REAL_T> > > selectivity_models;
std::unordered_map<int, std::shared_ptr<mas::Fleet<REAL_T> > > fleets;
// NOTE: why isn't survey_models similar to fleets?
std::unordered_map<int, std::shared_ptr<mas::Survey<REAL_T> > > survey_models;
// per population
std::unordered_map<int, std::shared_ptr<mas::GrowthBase<REAL_T> > > growth_models;
std::unordered_map<int, std::shared_ptr<mas::FecundityBase<REAL_T> > > fecundity_models;
std::unordered_map<int, std::shared_ptr<mas::Movement<REAL_T> > > movement_models;
// per population - area
std::unordered_map<int, std::shared_ptr<mas::NaturalMortality<REAL_T> > > natural_mortality_models;
std::unordered_map<int, std::shared_ptr<mas::RecruitmentBase<REAL_T> > > recruitment_models;
std::unordered_map<int, std::shared_ptr<mas::NLLFunctor<REAL_T> > > likelihood_components;
//System sub model iterators
typedef typename std::unordered_map<int, std::shared_ptr<mas::Season<REAL_T> > >::iterator seasons_iterator;
typedef typename std::unordered_map<int, std::shared_ptr<mas::Area<REAL_T> > >::iterator area_iterator;
typedef typename std::unordered_map<int, std::shared_ptr<mas::Population<REAL_T> > >::iterator population_iterator;
typedef typename std::unordered_map<int, std::shared_ptr<mas::GrowthBase<REAL_T> > >::iterator growth_model_iterator;
typedef typename std::unordered_map<int, std::shared_ptr<mas::RecruitmentBase<REAL_T> > >::iterator recruitment_model_iterator;
typedef typename std::unordered_map<int, std::shared_ptr<mas::NaturalMortality<REAL_T> > >::iterator natural_mortality_model_iterator;
typedef typename std::unordered_map<int, std::shared_ptr<mas::FishingMortality<REAL_T> > >::iterator fishing_mortality_model_iterator;
typedef typename std::unordered_map<int, std::shared_ptr<mas::FecundityBase<REAL_T> > >::iterator fecundity_model_iterator;
typedef typename std::unordered_map<int, std::shared_ptr<mas::Movement<REAL_T> > >::iterator movement_model_iterator;
typedef typename std::unordered_map<int, std::shared_ptr<mas::SelectivityBase<REAL_T> > >::iterator selectivity_model_iterator;
typedef typename std::unordered_map<int, std::shared_ptr<mas::Fleet<REAL_T> > >::iterator fleet_iterator;
typedef typename std::unordered_map<int, std::shared_ptr<mas::Survey<REAL_T> > >::iterator survey_model_iterator;
typedef typename std::unordered_map<int, std::shared_ptr<mas::NLLFunctor<REAL_T> > >::iterator likelihood_components_iterator;
rapidjson::Document config_document;
rapidjson::Document data_document;
std::vector<EnsembleUnit> ensemble_units;
Information() {
}
Information(const Information<REAL_T>& orig) {
}
virtual ~Information() {
}
void ParseConfig(const std::string& path) {
std::time_t result = std::time(nullptr);
mas_log << "MAS Run: " << std::asctime(std::localtime(&result)) << "\n";
INFO_DEBUG;
std::stringstream ss;
std::ifstream config;
config.open(path.c_str());
if (!config.good()) {
std::cerr << "MAS Configuration file \"" << path << "\" not found.\n";
mas::mas_log << "MAS Configuration file \"" << path << "\" not found.\n";
this->valid_configuration = false;
}
INFO_DEBUG;
while (config.good()) {
std::string line;
std::getline(config, line);
ss << line << "\n";
}
this->ParseConfig(ss);
}
void ParseConfig(const std::stringstream& ss) {
INFO_DEBUG;
config_document.Parse(ss.str().c_str());
INFO_DEBUG;
this->ParseConfig(config_document);
}
void ParseConfig(rapidjson::Document& document) {
rapidjson::Document::MemberIterator mit;
for (mit = document.MemberBegin(); mit != document.MemberEnd(); ++mit) {
if (std::string((*mit).name.GetString()) == "analyst") {
INFO_DEBUG;
this->analyst = std::string((*mit).value.GetString());
}
if (std::string((*mit).name.GetString()) == "extended_plus_group") {
INFO_DEBUG;
mas::Subpopulation<REAL_T>::length_weight_key_carryout = static_cast<uint32_t> ((*mit).value.GetInt());
}
#warning should these be here or in the population definition
if (std::string((*mit).name.GetString()) == "catch_season_offset") {
INFO_DEBUG;
this->catch_fraction_of_year = static_cast<REAL_T> ((*mit).value.GetDouble());
}
if (std::string((*mit).name.GetString()) == "survey_season_offset") {
INFO_DEBUG;
this->survey_fraction_of_year = static_cast<REAL_T> ((*mit).value.GetDouble());
}
if (std::string((*mit).name.GetString()) == "spawning_season_offset") {
INFO_DEBUG;
this->spawning_season_offset = static_cast<REAL_T> ((*mit).value.GetDouble());
}
if (std::string((*mit).name.GetString()) == "study_name") {
INFO_DEBUG;
this->study_name = std::string((*mit).value.GetString());
}
if (std::string((*mit).name.GetString()) == "movement_type") {
INFO_DEBUG;
if (std::string((*mit).value.GetString()) == std::string("natal_homing")) {
this->natal_movement = true;
}
}
if (std::string((*mit).name.GetString()) == "data") {
INFO_DEBUG;
this->data_path = std::string((*mit).value.GetString());
}
if (std::string((*mit).name.GetString()) == "years") {
INFO_DEBUG;
this->nyears = (*mit).value.GetInt();
}
if (std::string((*mit).name.GetString()) == "first_year") {
INFO_DEBUG;
this->first_year = (*mit).value.GetInt();
}
if (std::string((*mit).name.GetString()) == "last_year") {
INFO_DEBUG;
this->last_year = (*mit).value.GetInt();
}
if (std::string((*mit).name.GetString()) == "ages") {
INFO_DEBUG;
this->ages.clear();
this->ages_real.clear();
rapidjson::Value& ages = (*mit).value;
if (ages.IsArray()) {
for (int i = 0; i < ages.Size(); i++) {
this->ages.push_back(variable(static_cast<REAL_T> (ages[i].GetDouble())));
this->ages_real.push_back(static_cast<REAL_T> (ages[i].GetDouble()));
}
} else {
std::cout << "Configuration Error: \"ages\" should be a vector.\n";
mas::mas_log << "Configuration Error: \"ages\" should be a vector.\n";
this->valid_configuration = false;
}
mas::GrowthBase<REAL_T>::ages.resize(0);
mas::GrowthBase<REAL_T>::ages_to_intrpolate.clear();
for (int i = 0; i < this->ages.size(); i++) {
mas::GrowthBase<REAL_T>::ages.push_back(this->ages[i]);
mas::GrowthBase<REAL_T>::ages_to_intrpolate.insert(this->ages[i].GetValue());
mas::GrowthBase<REAL_T>::ages_to_intrpolate.insert(this->ages[i].GetValue() + this->catch_fraction_of_year);
mas::GrowthBase<REAL_T>::ages_to_intrpolate.insert(this->ages[i].GetValue() + this->survey_fraction_of_year);
mas::GrowthBase<REAL_T>::ages_to_intrpolate.insert(this->ages[i].GetValue() + this->spawning_season_offset);
}
}
if (std::string((*mit).name.GetString()) == "seasons") {
// HandleSeason(mit);
INFO_DEBUG;
this->nseasons = (*mit).value.GetInt();
}
if (std::string((*mit).name.GetString()) == "recruitment") {
INFO_DEBUG;
HandleRecruitmentModel(mit);
}
if (std::string((*mit).name.GetString()) == "growth") {
INFO_DEBUG;
HandleGrowthModel(mit);
}
if (std::string((*mit).name.GetString()) == "selectivity") {
INFO_DEBUG;
HandleSelectivityModel(mit);
}
if (std::string((*mit).name.GetString()) == "area") {
INFO_DEBUG;
HandleAreaModel(mit);
}
if (std::string((*mit).name.GetString()) == "population") {
INFO_DEBUG;
HandlePopulationModel(mit);
}
if (std::string((*mit).name.GetString()) == "fleet") {
INFO_DEBUG;
HandleFleetModel(mit);
}
if (std::string((*mit).name.GetString()) == "movement") {
INFO_DEBUG;
HandleMovementModel(mit);
}
if (std::string((*mit).name.GetString()) == "natural_mortality") {
INFO_DEBUG;
HandleNaturalMortalityModel(mit);
}
if (std::string((*mit).name.GetString()) == "fishing_mortality") {
INFO_DEBUG;
HandleFishingMortalityModel(mit);
}
if (std::string((*mit).name.GetString()) == "survey") {
INFO_DEBUG;
HandleSurveyModel(mit);
}
if (std::string((*mit).name.GetString()) == "likelihood_component") {
INFO_DEBUG;
HandleLikelihoodComponent(mit);
}
INFO_DEBUG;
}
}
void HandleLikelihoodComponent(rapidjson::Document::MemberIterator& likelihood_component) {
INFO_DEBUG
std::shared_ptr < mas::DataObject<REAL_T > > lambda_data(new mas::DataObject<REAL_T>());
rapidjson::Document::MemberIterator rit;
rit = (*likelihood_component).value.FindMember("model");
if (rit == (*likelihood_component).value.MemberEnd()) {
std::cout << "Configuration Error: Likelihood is required to have a model specified.\n";
mas::mas_log << "Configuration Error: Likelihood is required to have a model specified.\n";
this->valid_configuration = false;
}
std::shared_ptr < mas::NLLFunctor<REAL_T > > model(NULL);
std::string smodel = std::string((*rit).value.GetString());
rit = (*likelihood_component).value.FindMember("id");
int model_id = 0;
if (rit == (*likelihood_component).value.MemberEnd()) {
std::cout << "Configuration Error: Likelihood is required to have a unique identifier\n";
mas::mas_log << "Configuration Error: Likelihood is required to have a unique identifier\n";
this->valid_configuration = false;
} else {
model_id = (*rit).value.GetInt();
}
rit = (*likelihood_component).value.FindMember("lambda");
if (rit != (*likelihood_component).value.MemberEnd()) {
// lambda_data = std::make_shared<mas::DataObject<REAL_T> >();
rapidjson::Document::MemberIterator lit;
rapidjson::Document::MemberIterator lvit;
lit = (*rit).value.FindMember("years");
if (lit != (*rit).value.MemberEnd()) {
lambda_data->imax = (*lit).value.GetInt();
}
lit = (*rit).value.FindMember("seasons");
if (lit != (*rit).value.MemberEnd()) {
lambda_data->jmax = (*lit).value.GetInt();
}
lit = (*rit).value.FindMember("ages");
if (lit != (*rit).value.MemberEnd()) {
lambda_data->kmax = (*lit).value.GetInt();
}
lit = (*rit).value.FindMember("value");
if (lit != (*rit).value.MemberEnd()) {
if ((*lit).value.IsArray()) {
rapidjson::Value& v = (*lit).value;
for (int i = 0; i < v.Size(); i++) {
if (v[i].IsArray()) {
for (int j = 0; j < v[i].Size(); j++) {
if (v[i][j].IsArray()) {
for (int k = 0; k < v[i][j].Size(); k++) {
lambda_data->data.push_back(static_cast<REAL_T> (v[i][j][k].GetDouble()));
}
} else {
lambda_data->data.push_back(static_cast<REAL_T> (v[i][j].GetDouble()));
}
}
} else {
lambda_data->data.push_back(static_cast<REAL_T> (v[i].GetDouble()));
}
}
}
}
}
rapidjson::Document::MemberIterator pit = (*likelihood_component).value.FindMember("parameters");
if (smodel == std::string("dirichlet_multinomial")) {
model = std::make_shared<mas::DirichletMultinomial<REAL_T> >();
mas::DirichletMultinomial<REAL_T>* dirichlet = (mas::DirichletMultinomial<REAL_T>*)model.get();
std::stringstream ss;
ss << "dirichlet_multinomial_beta_" << model_id;
VariableTrait<REAL_T>::SetName(dirichlet->beta, ss.str());
ss.str("");
if (pit == (*likelihood_component).value.MemberEnd()) {
std::cout << "Configuration Waring: Likelihood Component \"Dirichlet-Multinomial \" has no parameter definitions. Defaults will be used\n";
mas::mas_log << "Configuration Waring: Likelihood Component \"Dirichlet-Multinomial \" has no parameter definitions. Defaults will be used\n";
} else {
rapidjson::Document::MemberIterator ppit = (*pit).value.FindMember("beta");
if (ppit == (*pit).value.MemberEnd()) {
std::cout << "Configuration Warning: Likelihood Component \"Dirichlet-Multinomial \" " <<
"does not define \"beta\". Model will use the default value of 0.5 and \"beta\" will not be estimated.\n";
mas::mas_log << "Configuration Warning: Likelihood Component \"Dirichlet-Multinomial \" " <<
"does not define \"beta\". Model will use the default value of 0.5 and \"beta\" will not be estimated.\n";
} else {
bool estimated = false;
int phase = 1;
//1. Get initial value if there is one.
rapidjson::Document::MemberIterator pm = (*ppit).value.FindMember("value");
if (pm == (*ppit).value.MemberEnd()) {
std::cout << "Configuration Warning: Selectivity model \"Dirichlet-Multinomial\" does not provide a initial value for \"beta\".\n";
mas::mas_log << "Configuration Warning: Selectivity model \"Dirichlet-Multinomial\" does not provide a initial value for \"beta\".\n";
} else {
VariableTrait<REAL_T>::SetValue(dirichlet->beta, static_cast<REAL_T> ((*pm).value.GetDouble()));
}
//2. Get min boundary if there is one.
pm = (*ppit).value.FindMember("min");
if (pm != (*ppit).value.MemberEnd()) {
VariableTrait<REAL_T>::SetMinBoundary(dirichlet->beta, static_cast<REAL_T> ((*pm).value.GetDouble()));
}
//3. Get max boundary if there is one.
pm = (*ppit).value.FindMember("max");
if (pm != (*ppit).value.MemberEnd()) {
VariableTrait<REAL_T>::SetMaxBoundary(dirichlet->beta, static_cast<REAL_T> ((*pm).value.GetDouble()));
}
pm = (*ppit).value.FindMember("estimated");
if (pm != (*ppit).value.MemberEnd()) {
std::string e = std::string((*pm).value.GetString());
if (e == "true") {
estimated = true;
}
}
INFO_DEBUG
if (estimated) {
phase = 1;
pm = (*ppit).value.FindMember("phase");
if (pm != (*ppit).value.MemberEnd()) {
phase = (*pm).value.GetInt();
}
//register alpha
dirichlet->Register(dirichlet->beta, phase);
}
}
}
} else if (smodel == std::string("dirichlet_multinomial_robust")) {
model = std::make_shared<mas::DirichletMultinomialRobust<REAL_T> >();
mas::DirichletMultinomialRobust<REAL_T>* dirichlet = (mas::DirichletMultinomialRobust<REAL_T>*)model.get();
rapidjson::Document::MemberIterator eit = (*likelihood_component).value.FindMember("epsilon");
if (eit != (*likelihood_component).value.MemberEnd()) {
dirichlet->epsilon = static_cast<REAL_T> ((*eit).value.GetDouble());
}
std::stringstream ss;
ss << "dirichlet_multinomial_robust_beta_" << model_id;
VariableTrait<REAL_T>::SetName(dirichlet->beta, ss.str());
ss.str("");
if (pit == (*likelihood_component).value.MemberEnd()) {
std::cout << "Configuration Waring: Likelihood Component \"Dirichlet-Multinomial Robust\" has no parameter definitions. Defaults will be used\n";
mas::mas_log << "Configuration Waring: Likelihood Component \"Dirichlet-Multinomial Robust\" has no parameter definitions. Defaults will be used\n";
} else {
rapidjson::Document::MemberIterator ppit = (*pit).value.FindMember("beta");
if (ppit == (*pit).value.MemberEnd()) {
std::cout << "Configuration Warning: Likelihood Component \"Dirichlet-Multinomial Robust\" " <<
"does not define \"beta\". Model will use the default value of 0.5 and \"beta\" will not be estimated.\n";
mas::mas_log << "Configuration Warning: Likelihood Component \"Dirichlet-Multinomial Robust\" " <<
"does not define \"beta\". Model will use the default value of 0.5 and \"beta\" will not be estimated.\n";
} else {
bool estimated = false;
int phase = 1;
//1. Get initial value if there is one.
rapidjson::Document::MemberIterator pm = (*ppit).value.FindMember("value");
if (pm == (*ppit).value.MemberEnd()) {
std::cout << "Configuration Warning: Selectivity model \"Dirichlet-Multinomial Robust\" does not provide a initial value for \"beta\".\n";
mas::mas_log << "Configuration Warning: Selectivity model \"Dirichlet-Multinomial Robust\" does not provide a initial value for \"beta\".\n";
} else {
VariableTrait<REAL_T>::SetValue(dirichlet->beta, static_cast<REAL_T> ((*pm).value.GetDouble()));
}
//2. Get min boundary if there is one.
pm = (*ppit).value.FindMember("min");
if (pm != (*ppit).value.MemberEnd()) {
VariableTrait<REAL_T>::SetMinBoundary(dirichlet->beta, static_cast<REAL_T> ((*pm).value.GetDouble()));
}
//3. Get max boundary if there is one.
pm = (*ppit).value.FindMember("max");
if (pm != (*ppit).value.MemberEnd()) {
VariableTrait<REAL_T>::SetMaxBoundary(dirichlet->beta, static_cast<REAL_T> ((*pm).value.GetDouble()));
}
pm = (*ppit).value.FindMember("estimated");
if (pm != (*ppit).value.MemberEnd()) {
std::string e = std::string((*pm).value.GetString());
if (e == "true") {
estimated = true;
}
}
INFO_DEBUG
if (estimated) {
phase = 1;
pm = (*ppit).value.FindMember("phase");
if (pm != (*ppit).value.MemberEnd()) {
phase = (*pm).value.GetInt();
}
//register alpha
dirichlet->Register(dirichlet->beta, phase);
}
}
}
//no estimable parameters for these component types
} else if (smodel == std::string("multinomial")) {
model = std::make_shared<mas::Multinomial<REAL_T> >();
} else if (smodel == std::string("multinomial_robust")) {
model = std::make_shared<mas::MultinomialRobust<REAL_T> >();
} else if (smodel == std::string("lognormal")) {
model = std::make_shared<mas::Lognormal<REAL_T> >();
rapidjson::Document::MemberIterator eit = (*likelihood_component).value.FindMember("standard_error");
if (eit != (*likelihood_component).value.MemberEnd()) {
mas::Lognormal<REAL_T>* models = (mas::Lognormal<REAL_T>*)model.get();
models->sigma = static_cast<REAL_T> ((*eit).value.GetDouble());
}
}
model->id = model_id;
model->lambda = lambda_data;
likelihood_components_iterator it = this->likelihood_components.find(model->id);
if (it != this->likelihood_components.end()) {
std::cout << "Configuration Error: More than one likelihood components with the same identifier defined. Likelihood components require a unique id.\n";
std::cout << "Configuration Error: More than one likelihood components with the same identifier defined. Likelihood components require a unique id.\n";
this->valid_configuration = false;
} else {
this->likelihood_components[model->id] = model;
}
}
void HandleSurveyModel(rapidjson::Document::MemberIterator & survey_model) {
std::shared_ptr<mas::Survey<REAL_T> > model(new mas::Survey<REAL_T>());
std::stringstream ss;
INFO_DEBUG
rapidjson::Document::MemberIterator rit = (*survey_model).value.FindMember("id");
int model_id = 0;
if (rit == (*survey_model).value.MemberEnd()) {
std::cout << "Configuration Error: Survey is required to have a unique identifier\n";
mas::mas_log << "Configuration Error: Survey is required to have a unique identifier\n";
this->valid_configuration = false;
} else {
model_id = (*rit).value.GetInt();
}
model->id = model_id;
rit = (*survey_model).value.FindMember("name");
if (rit != (*survey_model).value.MemberEnd()) {
model->name = std::string((*rit).value.GetString());
}
rit = (*survey_model).value.FindMember("survey_fraction_of_year");
if (rit != (*survey_model).value.MemberEnd()) {
model->survey_fraction_of_year = (*rit).value.GetDouble();
}
rit = (*survey_model).value.FindMember("CV");
if (rit != (*survey_model).value.MemberEnd()) {
model->CV = (*rit).value.GetDouble();
}
// rit = (*survey_model).value.FindMember("population");
// if (rit == (*survey_model).value.MemberEnd()) {
// std::cout << "Configuration Error: Survey is required to have a population identifier\n";
// mas::mas_log << "Configuration Error: Survey is required to have a population identifier\n";
// this->valid_configuration = false;
// } else {
// model->population = (*rit).value.GetInt();
// }
rit = (*survey_model).value.FindMember("selectivity");
if (rit != (*survey_model).value.MemberEnd()) {
if (!(*rit).value.IsArray()) {
std::cout << "Configuration Error: Surveys are required to have selectivity definitions in a vector\n";
std::cout << "Configuration Error: Surveys are required to have selectivity definitions in a vector\n";
this->valid_configuration = false;
} else {
for (int i = 0; i < (*rit).value.Size(); i++) {
rapidjson::Value& m = (*rit).value[i];
int sid = 0;
int sarea = 0;
int sseason = 0;
REAL_T fraction = 0.5;
rapidjson::Document::MemberIterator vit = m.FindMember("id");
if (vit == m.MemberEnd()) {
std::cout << "Configuration Error: Survey selectivity has no model identifier\n";
std::cout << "Configuration Error: Survey selectivity has no model identifier\n";
this->valid_configuration = false;
} else {
sid = (*vit).value.GetInt();
}
rapidjson::Document::MemberIterator mit = m.FindMember("ensemble");
if (mit != m.MemberEnd()) {
if (!(*mit).value.IsArray()) {
std::cout << "Expected array for survey selectivity ensemble unit, ignored.\n";
mas_log << "Expected array for survey selectivity ensemble unit, ignored.\n";
} else {
EnsembleUnit eunit;
eunit.type = mas::SELECTIVITY;
rapidjson::Value& e = (*mit).value;
eunit.val = vit;
for (int i = 0; i < e.Size(); i++) {
eunit.units.push_back(e[i].GetInt());
}
this->ensemble_units.push_back(eunit);
}
}
mit = m.FindMember("season");
if (mit == m.MemberEnd()) {
std::cout << "Configuration Error: Survey selectivity season has no identifier\n";
std::cout << "Configuration Error: Survey selectivity season has no identifier\n";
this->valid_configuration = false;
} else {
sseason = (*mit).value.GetInt();
}
mit = m.FindMember("fraction");
if (mit == m.MemberEnd()) {
std::cout << "Configuration Warning: Survey selectivity season has no catch fraction. Default is 0.5\n";
std::cout << "Configuration Error: Survey selectivity season has no catch fraction. Default is 0.5\n";
} else {
fraction = (*mit).value.GetDouble();
}
mit = m.FindMember("area");
if (mit == m.MemberEnd()) {
std::cout << "Configuration Error: Survey selectivity area has no identifier\n";
std::cout << "Configuration Error: Survey selectivity area has no identifier\n";
this->valid_configuration = false;
} else {
sarea = (*mit).value.GetInt();
}
model->season_area_selectivity_ids[sseason][sarea] = sid;
model->area_season_selectivity_ids[sarea][sseason] = sid;
model->area_season_survey_fraction[sarea][sseason] = fraction;
model->season_area_survey_fraction[sseason][sarea] = fraction;
}
}
}
rit = (*survey_model).value.FindMember("parameters");
if (rit == (*survey_model).value.MemberEnd()) {
std::cout << "Configuration Error: Survey model \"" << model->id << "\" has no parameter definitions.\n";
mas::mas_log << "Configuration Error: Survey model \"" << model->id << "\" has no parameter definitions.\n";
this->valid_configuration = false;
} else {
bool estimated = false;
int phase = 1;
rapidjson::Document::MemberIterator qit = (*rit).value.FindMember("q");
//1. Get initial value if there is one.
rapidjson::Document::MemberIterator pm = (*qit).value.FindMember("value");
if (pm == (*qit).value.MemberEnd()) {
std::cout << "Configuration Error: Survey model \"" << model->id << "\" does not provide an initial value for \"q\".\n";
mas::mas_log << "Configuration Error: Survey model \"" << model->id << "\" does not provide an initial value for \"q\".\n";
} else {
ss << "survey_q_" << model_id;
VariableTrait<REAL_T>::SetName(model->q, ss.str());
VariableTrait<REAL_T>::SetValue(model->q, static_cast<REAL_T> ((*pm).value.GetDouble()));
}
//2. Get min boundary if there is one.
pm = (*qit).value.FindMember("min");
if (pm != (*qit).value.MemberEnd()) {
VariableTrait<REAL_T>::SetMinBoundary(model->q, static_cast<REAL_T> ((*pm).value.GetDouble()));
}
//3. Get max boundary if there is one.
pm = (*qit).value.FindMember("max");
if (pm != (*qit).value.MemberEnd()) {
VariableTrait<REAL_T>::SetMaxBoundary(model->q, static_cast<REAL_T> ((*pm).value.GetDouble()));
}
pm = (*qit).value.FindMember("estimated");
if (pm != (*qit).value.MemberEnd()) {
std::string e = std::string((*pm).value.GetString());
if (e == "true") {
estimated = true;
}
}
if (estimated) {
phase = 1;
pm = (*qit).value.FindMember("phase");
if (pm != (*qit).value.MemberEnd()) {
phase = (*pm).value.GetInt();
}
//register alpha
model->Register(model->q, phase);
}
}
rit = (*survey_model).value.FindMember("likelihood_components");
if (rit != (*survey_model).value.MemberEnd()) {
if (!(*rit).value.IsArray()) {
std::cout << "Configuration Warning: No Likelihood components defined for survey \"" << model->id << "\". Default will be used\n";
std::cout << "Configuration Warning: No Likelihood components defined for survey \"" << model->id << "\". Default will be used\n";
} else {
for (int i = 0; i < (*rit).value.Size(); i++) {
rapidjson::Value& m = (*rit).value[i];
rapidjson::Document::MemberIterator mit = m.FindMember("id");
if (mit == m.MemberEnd()) {
std::cout << "Configuration Error: Surveys Likelihood component has no model identifier\n";
std::cout << "Configuration Error: Surveys Likelihood component has no model identifier\n";
this->valid_configuration = false;
} else {
rapidjson::Document::MemberIterator mit2 = m.FindMember("component");
if (mit2 == m.MemberEnd()) {
std::cout << "Configuration Error: Surveys Likelihood component has no \"component\" specified.\n";
std::cout << "Configuration Error: Surveys Likelihood component has no \"component\" specified.\n";
this->valid_configuration = false;
} else {
std::string c = std::string((*mit2).value.GetString());
if (c == "age_comp") {
model->survey_age_comp_likelihood_component_id = (*mit).value.GetInt();
} else if (c == "biomass_comp") {
model->survey_biomass_likelihood_component_id = (*mit).value.GetInt();
} else {
std::cout << "Configuration Error: Unknown \"component\" of \" " << c << " \" specified for Survey \"" << model->id << "\" likelihood component definition.\n";
std::cout << "Configuration Error: Unknown \"component\" of \" " << c << " \" specified for Survey \"" << model->id << "\" likelihood component definition.\n";
this->valid_configuration = false;
}
}
}
//
}
}
}
survey_model_iterator fit;
fit = this->survey_models.find(model->id);
if (fit == this->survey_models.end()) {
this->survey_models[model->id] = model;
} else {
std::cout << "Configuration Error: More than one Survey with the same identifier defined. Surveys require a unique id.\n";
mas::mas_log << "Configuration Error: More than one Survey with the same identifier defined. Surveys require a unique id.\n";
}
}
void HandleFishingMortalityModel(rapidjson::Document::MemberIterator & mortality_model) {
INFO_DEBUG
std::shared_ptr<mas::FishingMortality<REAL_T> > model(new mas::FishingMortality<REAL_T>());
bool estimated = false;
bool delta_method = false;
int phase = 1;
bool bounded = false;
REAL_T min = std::numeric_limits<REAL_T>::min();
REAL_T max = std::numeric_limits<REAL_T>::max();
rapidjson::Document::MemberIterator rit = (*mortality_model).value.FindMember("id");
int model_id = 0;
if (rit == (*mortality_model).value.MemberEnd()) {
std::cout << "Configuration Error: Fishing Mortality is required to have a unique identifier\n";
mas::mas_log << "Configuration Error: Fishing Mortality is required to have a unique identifier\n";
this->valid_configuration = false;
} else {
model_id = (*rit).value.GetInt();
}
model->id = model_id;
rapidjson::Document::MemberIterator pit = (*mortality_model).value.FindMember("parameters");
bool is_random = false;
if (pit == (*mortality_model).value.MemberEnd()) {
std::cout << "Configuration Error: Fishing Mortality model has no parameter definitions.\n";
mas::mas_log << "Configuration Error: Fishing Mortality model has no parameter definitions.\n";
this->valid_configuration = false;
} else {
rapidjson::Document::MemberIterator vit = (*pit).value.FindMember("estimated");
if (vit != (*pit).value.MemberEnd()) {
std::string estring = std::string((*vit).value.GetString());
if (estring == "true") {
estimated = true;
}
}
rapidjson::Document::MemberIterator re_it = (*pit).value.FindMember("random_effect");
if (re_it != (*pit).value.MemberEnd()) {
if (std::string((*re_it).value.GetString()) == "true") {
is_random = true;
}
}
vit = (*pit).value.FindMember("delta_method");
if (vit != (*pit).value.MemberEnd()) {
std::string estring = std::string((*vit).value.GetString());
if (estring == "true") {
delta_method = true;
}
}
vit = (*pit).value.FindMember("min");
if (vit != (*pit).value.MemberEnd()) {
min = static_cast<REAL_T> ((*vit).value.GetDouble());
bounded = true;
}
vit = (*pit).value.FindMember("max");
if (vit != (*pit).value.MemberEnd()) {
max = static_cast<REAL_T> ((*vit).value.GetDouble());
bounded = true;
}
vit = (*pit).value.FindMember("phase");
if (vit != (*pit).value.MemberEnd()) {
phase = (*vit).value.GetInt();
}
vit = (*pit).value.FindMember("value");
if (vit == (*pit).value.MemberEnd()) {
std::cout << "Configuration Error: Fishing Mortality model supplied no values\n";
mas::mas_log << "Configuration Error: Fishing Mortality model supplied no values\n";
this->valid_configuration = false;
} else {
if ((*vit).value.IsArray()) {
rapidjson::Value & v = (*vit).value;
if (v.IsArray()) {
model->fishing_mortality.resize(v.Size());
for (int i = 0; i < v.Size(); i++) {
rapidjson::Value & vv = v[i];
model->fishing_mortality[i].resize(vv.Size());
for (int j = 0; j < vv.Size(); j++) {
mas::VariableTrait<REAL_T>::SetValue(model->fishing_mortality[i][j], static_cast<REAL_T> (vv[j].GetDouble()));
if (estimated && !delta_method) {
if (bounded) {
mas::VariableTrait<REAL_T>::SetMinBoundary(model->fishing_mortality[i][j], min);
mas::VariableTrait<REAL_T>::SetMaxBoundary(model->fishing_mortality[i][j], max);
}
std::stringstream ss;
ss << "fishing_mortality[" << i << "][" << j << "]_" << model_id;
mas::VariableTrait<REAL_T>::SetName(model->fishing_mortality[i][j], ss.str());
if (is_random) {
model->RegisterRandom(model->fishing_mortality[i][j]);
} else {
model->Register(model->fishing_mortality[i][j], phase);
}
} else if (delta_method) {
model->fishing_mortality_type = mas::FMETHOD;
}
}
}
} else {
std::cout << "Configuration Error: Fishing Mortality is requires values in a matrix[year,season] not a vector\n";
std::cout << "Configuration Error: Fishing Mortality is requires values in a matrix[year,season] not a vector\n";
this->valid_configuration = false;
}
} else {
std::cout << "Configuration Error: Fishing Mortality is requires values in a matrix[year,season]\n";
std::cout << "Configuration Error: Fishing Mortality is requires values in a matrix[year,season]\n";
this->valid_configuration = false;
}
}
}
fishing_mortality_model_iterator fit = this->fishing_mortality_models.find(model->id);
if (fit == this->fishing_mortality_models.end()) {
if (delta_method) {
model->fishing_mortality_type = mas::FMETHOD;
}
this->fishing_mortality_models[model->id] = model;
} else {
std::cout << "Configuration Error: More than one fishing mortality model with the same identifier defined. Fishing mortality models require a unique id.\n";
mas_log << "Configuration Error: More than one fishing mortality model with the same identifier defined. Fishing mortality models require a unique id.\n";
this->valid_configuration = false;
}
}
void HandleNaturalMortalityModel(rapidjson::Document::MemberIterator & mortality_model) {
INFO_DEBUG
std::shared_ptr<mas::NaturalMortality<REAL_T> > model(new mas::NaturalMortality<REAL_T>());
bool estimated = false;
int phase = 1;
rapidjson::Document::MemberIterator rit = (*mortality_model).value.FindMember("id");
int model_id = 0;
if (rit == (*mortality_model).value.MemberEnd()) {
std::cout << "Configuration Error: Natural Mortality is required to have a unique identifier\n";
mas::mas_log << "Configuration Error: Natural Mortality is required to have a unique identifier\n";
this->valid_configuration = false;
} else {
model_id = (*rit).value.GetInt();
}