/**
* Default constructor
*/
Normal::Normal() {
parameters_.Bind<Double>(PARAM_MU, &mu_, "The normal prior mean (mu) parameter", "");
parameters_.Bind<Double>(PARAM_CV, &cv_, "The normal variance (standard devation) parameter", "")->set_lower_bound(0.0, false);
RegisterAsEstimable(PARAM_MU, &mu_);
RegisterAsEstimable(PARAM_CV, &cv_);
}
/**
* Default constructor
*/
NormalLog::NormalLog() {
parameters_.Bind<Double>(PARAM_MU, &mu_, "Mu", "");
parameters_.Bind<Double>(PARAM_SIGMA, &sigma_, "Sigma", "")->set_lower_bound(0.0, false);
RegisterAsEstimable(PARAM_MU, &mu_);
RegisterAsEstimable(PARAM_SIGMA, &sigma_);
}
/**
* Default constructor
*/
Lognormal::Lognormal() {
parameters_.Bind<Double>(PARAM_MU, &mu_, "The lognormal prior mean (mu) parameter", "")->set_lower_bound(0.0, false);
parameters_.Bind<Double>(PARAM_CV, &cv_, "The Lognormal variance (CV) parameter", "")->set_lower_bound(0.0, false);
RegisterAsEstimable(PARAM_MU, &mu_);
RegisterAsEstimable(PARAM_CV, &cv_);
}
/**
* Default constructor
*/
Normal::Normal() {
parameters_.Bind<Double>(PARAM_MU, &mu_, "Mu", "");
parameters_.Bind<Double>(PARAM_CV, &cv_, "Cv", "")->set_lower_bound(0.0, false);
RegisterAsEstimable(PARAM_MU, &mu_);
RegisterAsEstimable(PARAM_CV, &cv_);
}
/**
* Default constructor
*/
Linear::Linear(Model* model) : TimeVarying(model) {
parameters_.Bind<Double>(PARAM_SLOPE, &slope_, "The slope of the linear trend (additive unit per year)", "");
parameters_.Bind<Double>(PARAM_INTERCEPT, &intercept_, "The intercept of the linear trend value for the first year", "");
RegisterAsEstimable(PARAM_SLOPE, &slope_);
RegisterAsEstimable(PARAM_INTERCEPT, &intercept_);
}
/**
* Default constructor
*
* Bind any parameters that are allowed to be loaded from the configuration files.
* Set bounds on registered parameters
* Register any parameters that can be an estimated or utilised in other run modes (e.g profiling, yields, projections etc)
* Set some initial values
*
* Note: The constructor is parsed to generate Latex for the documentation.
*/
AgeLength::AgeLength(Model* model) : model_(model) {
parameters_.Bind<string>(PARAM_LABEL, &label_, "Label of the age length relationship", "");
parameters_.Bind<string>(PARAM_TYPE, &type_, "Type of age length relationship", "");
parameters_.Bind<Double>(PARAM_TIME_STEP_PROPORTIONS, &time_step_proportions_, "the fraction of the year applied in each time step that is added to the age for the purposes of evaluating the length, i.e., a value of 0.5 for a time step will evaluate the length of individuals at age+0.5 in that time step", "", true);
parameters_.Bind<string>(PARAM_DISTRIBUTION, &distribution_, "The assumed distribution for the growth curve", "", PARAM_NORMAL);
parameters_.Bind<Double>(PARAM_CV_FIRST, &cv_first_ , "CV for the first age class", "",Double(0.0))->set_lower_bound(0.0);
parameters_.Bind<Double>(PARAM_CV_LAST, &cv_last_ , "CV for last age class", "",Double(0.0))->set_lower_bound(0.0);
parameters_.Bind<bool>(PARAM_CASAL_SWITCH, &casal_normal_cdf_ , "If true, use the (less accurate) equation for the cumulative normal function as was used in the legacy version of CASAL.", "",false);
RegisterAsEstimable(PARAM_CV_FIRST, &cv_first_);
RegisterAsEstimable(PARAM_CV_LAST, &cv_last_);
}
/**
* Explicit constructor
*/
LogisticProducing::LogisticProducing(Model* model)
: Selectivity(model) {
parameters_.Bind<unsigned>(PARAM_L, &low_, "Low", "");
parameters_.Bind<unsigned>(PARAM_H, &high_, "High", "");
parameters_.Bind<Double>(PARAM_A50, &a50_, "A50", "");
parameters_.Bind<Double>(PARAM_ATO95, &ato95_, "Ato95", "");
parameters_.Bind<Double>(PARAM_ALPHA, &alpha_, "Alpha", "", 1.0);
RegisterAsEstimable(PARAM_A50, &a50_);
RegisterAsEstimable(PARAM_ATO95, &ato95_);
RegisterAsEstimable(PARAM_ALPHA, &alpha_);
}
/**
* default constructor
*/
MortalityEventBiomass::MortalityEventBiomass(Model* model)
: Process(model),
partition_(model) {
parameters_.Bind<string>(PARAM_CATEGORIES, &category_labels_, "Category labels", "");
parameters_.Bind<string>(PARAM_SELECTIVITIES, &selectivity_labels_, "The labels of the selectivities for each of the categories", "");
parameters_.Bind<unsigned>(PARAM_YEARS, &years_, "Years in which to apply the mortality process", "");
parameters_.Bind<Double>(PARAM_CATCHES, &catches_, "The biomass of removals (catches) to apply for each year", "");
parameters_.Bind<Double>(PARAM_U_MAX, &u_max_, "Maximum exploitation rate ($Umax$)", "", 0.99);
parameters_.Bind<string>(PARAM_PENALTY, &penalty_label_, "The label of the penalty to apply if the total biomass of removals cannot be taken", "", "");
RegisterAsEstimable(PARAM_U_MAX, &u_max_);
RegisterAsEstimable(PARAM_CATCHES, &catch_years_);
process_type_ = ProcessType::kMortality;
partition_structure_ = PartitionStructure::kAge;
}
/**
* Explicit Constructor
*/
AllValuesBounded::AllValuesBounded(Model* model)
: Selectivity(model) {
parameters_.Bind<unsigned>(PARAM_L, &low_, "L", "");
parameters_.Bind<unsigned>(PARAM_H, &high_, "H", "");
parameters_.Bind<Double>(PARAM_V, &v_, "V", "");
RegisterAsEstimable(PARAM_V, &v_);
}
/**
* Default constructor
*
* Bind any parameters that are allowed to be loaded from the configuration files.
* Set bounds on registered parameters
* Register any parameters that can be an estimated or utilised in other run modes (e.g profiling, yields, projections etc)
* Set some initial values
*
* Note: The constructor is parsed to generate Latex for the documentation.
*/
MortalityPreySuitability::MortalityPreySuitability(Model* model)
: Process(model) {
process_type_ = ProcessType::kMortality;
partition_structure_ = PartitionStructure::kAge;
parameters_.Bind<string>(PARAM_PREY_CATEGORIES, &prey_category_labels_, "Prey Categories labels", "");
parameters_.Bind<string>(PARAM_PREDATOR_CATEGORIES, &predator_category_labels_, "Predator Categories labels", "");
parameters_.Bind<Double>(PARAM_CONSUMPTION_RATE, &consumption_rate_, "Predator consumption rate", "")->set_range(0.0, 1.0);
parameters_.Bind<Double>(PARAM_ELECTIVITIES, &electivities_, "Prey Electivities", "")->set_range(0.0, 1.0);
parameters_.Bind<Double>(PARAM_U_MAX, &u_max_, "Umax", "")->set_range(0.0, 1.0);
parameters_.Bind<string>(PARAM_PREY_SELECTIVITIES, &prey_selectivity_labels_, "Selectivities for prey categories", "");
parameters_.Bind<string>(PARAM_PREDATOR_SELECTIVITIES, &predator_selectivity_labels_, "Selectivities for predator categories", "");
parameters_.Bind<string>(PARAM_PENALTY, & penalty_label_, "Label of penalty to be applied", "","");
parameters_.Bind<unsigned>(PARAM_YEARS, &years_, "Year that process occurs", "");
RegisterAsEstimable(PARAM_CONSUMPTION_RATE, &consumption_rate_);
RegisterAsEstimable(PARAM_ELECTIVITIES, &electivities_);
}
/**
* Default Constructor
*/
SurvivalConstantRate::SurvivalConstantRate(Model* model)
: Process(model),
partition_(model) {
LOG_TRACE();
process_type_ = ProcessType::kMortality;
partition_structure_ = PartitionStructure::kAge;
parameters_.Bind<string>(PARAM_CATEGORIES, &category_labels_, "List of categories", "");
parameters_.Bind<Double>(PARAM_S, &s_input_, "Survival rates", "");
parameters_.Bind<Double>(PARAM_TIME_STEP_RATIO, &ratios_, "Time step ratios for S", "", true);
parameters_.Bind<string>(PARAM_SELECTIVITIES, &selectivity_names_, "Selectivity label", "");
RegisterAsEstimable(PARAM_S, &s_);
}
/**
* Default Constructor
*/
TransitionCategory::TransitionCategory(Model* model)
: Process(model),
from_partition_(model),
to_partition_(model) {
LOG_TRACE();
parameters_.Bind<string>(PARAM_FROM, &from_category_names_, "From", "");
parameters_.Bind<string>(PARAM_TO, &to_category_names_, "To", "");
parameters_.Bind<Double>(PARAM_PROPORTIONS, &proportions_, "Proportions", "");
parameters_.Bind<string>(PARAM_SELECTIVITIES, &selectivity_names_, "Selectivity names", "");
RegisterAsEstimable(PARAM_PROPORTIONS, &proportions_by_category_);
process_type_ = ProcessType::kTransition;
partition_structure_ = PartitionStructure::kAge;
}
/**
* Default constructor
*
* Bind any parameters that are allowed to be loaded from the configuration files.
* Set bounds on registered parameters
* Register any parameters that can be an estimated or utilised in other run modes (e.g profiling, yields, projections etc)
* Set some initial values
*
* Note: The constructor is parsed to generate Latex for the documentation.
*/
DerivedQuantity::DerivedQuantity(Model* model)
: model_(model),
partition_(model) {
parameters_.Bind<string>(PARAM_LABEL, &label_, "Label of the derived quantity", "");
parameters_.Bind<string>(PARAM_TYPE, &type_, "Type of derived quantity", "");
parameters_.Bind<string>(PARAM_TIME_STEP, &time_step_label_, "The time step in which to calculate the derived quantity after", "");
parameters_.Bind<string>(PARAM_CATEGORIES, &category_labels_, "The list of categories to use when calculating the derived quantity", "");
parameters_.Bind<string>(PARAM_SELECTIVITIES, &selectivity_labels_, "A list of one selectivity", "");
parameters_.Bind<Double>(PARAM_TIME_STEP_PROPORTION, &time_step_proportion_, "Proportion through the mortality block of the time step when calculated", "", Double(0.5))->set_range(0.0, 1.0);
parameters_.Bind<string>(PARAM_TIME_STEP_PROPORTION_METHOD, &proportion_method_, "Method for interpolating for the proportion through the mortality block", "", PARAM_WEIGHTED_SUM)
->set_allowed_values({ PARAM_WEIGHTED_SUM, PARAM_WEIGHTED_PRODUCT });
RegisterAsEstimable(PARAM_VALUES, &override_values_);
create_missing_estimables_[PARAM_VALUES] = true;
mean_proportion_method_ = true;
}
/**
* Default constructor
*
* Bind any parameters that are allowed to be loaded from the configuration files.
* Set bounds on registered parameters
* Register any parameters that can be an estimated or utilised in other run modes (e.g profiling, yields, projections etc)
* Set some initial values
*
* Note: The constructor is parsed to generate Latex for the documentation.
*/
DerivedQuantity::DerivedQuantity(Model* model)
: model_(model),
partition_(model) {
parameters_.Bind<string>(PARAM_LABEL, &label_, "Label", "");
parameters_.Bind<string>(PARAM_TYPE, &type_, "Type", "");
parameters_.Bind<string>(PARAM_TIME_STEP, &time_step_label_, "The time step to calculate the derived quantity after", "");
parameters_.Bind<string>(PARAM_CATEGORIES, &category_labels_, "The list of categories to use when calculating the derived quantity", "");
parameters_.Bind<string>(PARAM_SELECTIVITIES, &selectivity_labels_, "The list of selectivities to use when calculating the derived quantity. 1 per category", "");
parameters_.Bind<Double>(PARAM_TIME_STEP_PROPORTION, &time_step_proportion_, "", "", Double(1.0));
parameters_.Bind<string>(PARAM_TIME_STEP_PROPORTION_METHOD, &proportion_method_, "", "", PARAM_WEIGHTED_SUM)
->set_allowed_values({ PARAM_WEIGHTED_SUM, PARAM_WEIGHTED_PRODUCT });
RegisterAsEstimable(PARAM_VALUES, &override_values_);
create_missing_estimables_[PARAM_VALUES] = true;
mean_proportion_method_ = true;
}
/**
* Default constructor
*/
Constant::Constant(Model* model) : TimeVarying(model) {
parameters_.Bind<Double>(PARAM_VALUE, &values_, "Value to assign to estimable", "");
RegisterAsEstimable(PARAM_VALUE, ¶meter_by_year_);
}
/**
* Default constructor
*
* Bind any parameters that are allowed to be loaded from the configuration files.
* Set bounds on registered parameters
* Register any parameters that can be an estimated or utilised in other run modes (e.g profiling, yields, projections etc)
* Set some initial values
*
* Note: The constructor is parsed to generate Latex for the documentation.
*/
Free::Free() {
parameters_.Bind<Double>(PARAM_Q, &q_, "The catchability amount", "");
RegisterAsEstimable(PARAM_Q, &q_);
}
