IOSKJ::Parameters Class Reference

#include <parameters.hpp>

Inheritance diagram for IOSKJ::Parameters:

Classes
struct	Logliker
struct	Names
struct	Randomiser
struct	Restrictor
struct	SteepnessBeta
struct	Values
struct	Variabler
struct	VectorGetter
struct	VectorSetter

Public Member Functions
template<class Mirror >
void	reflect (Mirror &mirror)
void	read (void)
void	write (void)
void	set (uint time, Model &model, bool catches_apply=true) const
Parameters &	randomise (void)
Parameters &	bounce (void)
double	loglike (void)
std::vector< std::string >	names (void)
Frame	values (void)
std::vector< double >	vector (void)
void	vector (const std::vector< double > &vector)

Public Attributes
Variable< Uniform >	spawners_unfished
Variable< Uniform >	spawners_ma
Variable< Uniform >	spawners_ea
Variable< SteepnessBeta >	recruits_steepness
Variable< Uniform >	recruits_sd
Variable< Uniform >	recruits_autocorr
Array< Variable< Normal >, RecdevYear >	recruits_deviations
Variable< Uniform >	spawning_0
Variable< Uniform >	spawning_1
Variable< Uniform >	spawning_2
Variable< Uniform >	spawning_3
Variable< Fixed >	weight_a
Variable< Fixed >	weight_b
Variable< TruncatedNormal >	maturity_inflection
Variable< TruncatedNormal >	maturity_steepness
Variable< Uniform >	mortality_mean
Variable< Fixed >	growth_rate_1
Variable< Fixed >	growth_rate_2
Variable< Fixed >	growth_assymptote
Variable< Fixed >	growth_stanza_inflection
Variable< Fixed >	growth_stanza_steepness
Variable< Fixed >	growth_age_0
Variable< Fixed >	growth_cv_0
Variable< Fixed >	growth_cv_old
Variable< Uniform >	movement_we_ma
Variable< Uniform >	movement_we_ea
Variable< Uniform >	movement_ma_ea
Variable< Uniform >	movement_length_inflection
Variable< Uniform >	movement_length_steepness
Array< Variable< Uniform >, Method, SelectivityKnot >	selectivities
Array< Variable< Fixed >, Year, Quarter, Region, Method >	catches

Detailed Description

Class for defining model parameters, their priors, transformations etc. See the set() method which "binds" parameters defined here to model variables.

Member Function Documentation

Parameters& IOSKJ::Parameters::bounce ( void  )

inline

Bounce values of parameters off bounds to ensure that they are within bounds but not bunched up against them

double IOSKJ::Parameters::loglike ( void  )

inline

Calculate prior likelihoods for parameters

std::vector<std::string> IOSKJ::Parameters::names ( void  )

inline

Get the names of variables

Parameters& IOSKJ::Parameters::randomise ( void  )

inline

Randomise the values of variables

template<class Mirror >

void IOSKJ::Parameters::reflect ( Mirror &  mirror )

inline

Reflection

void IOSKJ::Parameters::set ( uint  time, Model &  model, bool  catches_apply = true  ) const

inline

Set model variables

catches_apply Turn off application of catches (e.g. in hindcasts of procedures)

Frame IOSKJ::Parameters::values ( void  )

inline

Get the values of variables

std::vector<double> IOSKJ::Parameters::vector ( void  )

inline

Get the values of variables as a vector

void IOSKJ::Parameters::vector ( const std::vector< double > &  vector )

inline

Set the values of variables from a vector

Member Data Documentation

Array<Variable<Fixed>,Year,Quarter,Region,Method> IOSKJ::Parameters::catches

Catches by year, quarter, region and method

Variable<Fixed> IOSKJ::Parameters::growth_rate_1

Growth rate parameters

Variable<TruncatedNormal> IOSKJ::Parameters::maturity_inflection

Maturity parameters

Variable<Uniform> IOSKJ::Parameters::mortality_mean

Mortality parameters

Variable<Uniform> IOSKJ::Parameters::movement_we_ma

Movement parameters

Variable<Uniform> IOSKJ::Parameters::recruits_autocorr

Autocorrelation of recruitment deviations

Thorson et al 2014 estimated values between 0.371-0.466 across orders and overall value of 0.426

Array<Variable<Normal>,RecdevYear> IOSKJ::Parameters::recruits_deviations

Recruitment deviations

Variable<Uniform> IOSKJ::Parameters::recruits_sd

Standard deviation of recruitment deviations

Array<Variable<Uniform>,Method,SelectivityKnot> IOSKJ::Parameters::selectivities

Selectivity parameters

Variable<Uniform> IOSKJ::Parameters::spawners_ma

Relative recruitment in each of the smaller regions

These are relative to the unfished spawning biomass going to WE region. All proportions are then normalised in the model initialisation so that they sum to one.

Variable<Uniform> IOSKJ::Parameters::spawners_unfished

Overall unfished spawning biomass

Variable<Uniform> IOSKJ::Parameters::spawning_0

Proportion of mature fish spawning by quarter

Variable<Fixed> IOSKJ::Parameters::weight_a

Length-weight parameters

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The documentation for this class was generated from the following file:

• parameters.hpp