#include <model.hpp>

Public Member Functions
void	initialise (void)

void	update (uint time)

void	equilibrium (void)

void	pristine_go (void)

Frame	yield_curve (double step=0.01)

Frame	yield_per_recruit (void)

void	msy_go (void)

void	msy_find (void)

void	status_go (const double &status)

void	b40_find (void)

void	write (void)

Variable getting methods
double	biomass_status (void) const

Parameter setting methods
void	movement_uniform (void)

void	spawning_uniform (void)

Dynamics setting methods
void	exploitation_rate_set (double value)

double	exploitation_rate_get (void) const

void	fishing_mortality_set (double value)

double	fishing_mortality_get (void) const

void	catches_set (double catches_, double error=0.2)

void	effort_set (double effort_)

Public Attributes
Array< double, Region, Age >	numbers

Array< double, Region >	biomass

Array< double, Region >	biomass_spawners

Array< double, Region >	biomass_spawners_unfished

double	msy

double	e_msy

double	f_msy

double	biomass_spawners_msy

int	msy_trials

double	e_40

double	f_40

double	biomass_spawners_40

Spawning and stock-recruitment
Array< double, Quarter >	spawning

Array< double, Region, Quarter >	biomass_spawning

Array< double, Region, Quarter >	biomass_spawning_unfished

Array< double, Region >	recruits_unfished

double	recruits_steepness

bool	recruits_relation_on = true

Array< double, Region >	recruits_determ

bool	recruits_variation_on = true

double	recruits_sd

Normal	recruits_distrib

double	recruits_autocorr

double	recruits_deviation = 0

double	recruits_multiplier = 1

Array< double, Region >	recruits

Growth
double	growth_rate_1

double	growth_rate_2

double	growth_assymptote

double	growth_stanza_inflection

double	growth_stanza_steepness

double	growth_age_0

double	growth_cv_0

double	growth_cv_old

Array< double, Size >	length_size

Array< Normal, Age >	length_age

Array< double, Age, Size >	age_size

Weight
double	weight_length_a

double	weight_length_b

Array< double, Size >	weight_size

Array< double, Age >	weight_age

Maturity
double	maturity_length_inflection

double	maturity_length_steepness

Array< double, Size >	maturity_size

Array< double, Age >	maturity_age

Natural mortality
double	mortality_mean

Array< double, Age >	mortality_shape

Array< double, Age >	mortality

Array< double, Age >	survival

Movement
Array< double, RegionFrom, Region >	movement_region

double	movement_length_inflection

double	movement_length_steepness

Array< double, Size >	movement_size

Array< double, Age >	movement_age

Data related "nuisance" parameters
Array< double, Quarter >	m_pl_quarter = {0.97,0.87,0.97,1.19}

Selectivity and exploitation
Array< double, SelectivityKnot >	selectivity_lengths = {20,30,40,50,60,70,80}

Array< double, Method, SelectivityKnot >	selectivity_values

Array< double, Method, Size >	selectivity_size

Array< double, Method, Age >	selectivity_age

enum IOSKJ::Model::{ exploit_none = 0, exploit_rate = 1, exploit_catch = 2, exploit_effort = 3 }	exploit

Array< double, Region, Method >	biomass_vulnerable

Array< double, Region, Method >	cpue

Array< GeometricMean, Region, Method >	cpue_base

Array< double, Region, Method >	catches

Array< double, Region, Method >	effort

Array< double, Region, Method >	catchability

Array< GeometricMean, Region, Method >	catchability_estim

Array< double, Region, Method >	exploitation_rate_specified

Array< double, Region, Method >	catches_taken

Array< double, Region, Method >	exploitation_rate

Array< double, Region, Age >	escapement

Detailed Description

Model of the Indian Ocean skipjack tuna fishery. This class encapsulates the dynamics of both the fish population and fishing.

Test:: equilibrium_stable

Test that when there is no substantial change in equilibrium conditions given further simulation.

Test:: equilibrium_uniform

Test that when there is no movement and equal reruitment distribution that the equilibrium biomass is equal in all areas

Test:: recruiment_variation

Test that recruitment variation has the right mean and standard deviation.

Test:: exploitation_specified

Member Function Documentation

void IOSKJ::Model::b40_find ( void )

inline

Calculate a status related re

double IOSKJ::Model::biomass_status ( void ) const

inline

Get the stock status (spawning biomass as a fraction of pristine)

void IOSKJ::Model::catches_set	(	double	catches_,
		double	error = `0.2`
	)

inline

Set the catch by region/method assuming a certain allocation, currently based on the period 2003-2012 (see data/nominal-catches-quarter.R)

Note that currently this does not allow for seasonal variation, assumes an equal split across quarters

void IOSKJ::Model::effort_set ( double effort_ )

inline

Set the number of effort units by region/method

void IOSKJ::Model::equilibrium ( void )

inline

Move the population to a deterministic equilibrium by iterating over time until biomass in each region remains stable

double IOSKJ::Model::exploitation_rate_get ( void ) const

inline

Get overall exploitation rate.

void IOSKJ::Model::exploitation_rate_set ( double value )

inline

Set overall exploitation rate. Used in testing and in equilibrium exploitation e.g. MSY/BMSY calculations

Currently assumes an equal explotation rate is applied to the three main methods in each region (W/PS,M/PL,E/GN). An alternative would be to assume equal exploitation rates in each region and use current partial exploitation rates by method within each region.

double IOSKJ::Model::fishing_mortality_get ( void ) const

inline

Get overall instantaneous rate of fishing mortality (F). Like exploitation_rate_get but gives F instead of exp. rate.

void IOSKJ::Model::fishing_mortality_set ( double value )

inline

Set overall instantaneous rate of fishing mortality (F). Like exploitation_rate_set but uses F instead of exp. rate.

void IOSKJ::Model::initialise ( void )

inline

Initialise various model variables based on current parameter values

void IOSKJ::Model::movement_uniform ( void )

inline

Set movement parameters so that there is uniform movement.

All movement_regions elements set to 1/(number of regions). All sizes move. Mainly used for testing

void IOSKJ::Model::msy_find ( void )

inline

Calculate MSY related reference points

void IOSKJ::Model::msy_go ( void )

inline

Take this model to a equilibirum state associated with MSY

void IOSKJ::Model::spawning_uniform ( void )

inline

Set spawning seasonality parameters so that there is uniform spawning.

All elements set to 1. Mainly used for testing.

void IOSKJ::Model::status_go ( const double & status )

inline

Take this model to a equilibrium state associated with a proportion of B0

void IOSKJ::Model::update ( uint time )

inline

Perform a single time step

void IOSKJ::Model::write ( void )

inline

Write model attributes to files for examination

Frame IOSKJ::Model::yield_curve ( double step = 0.01 )

inline

Generate a yield curve

Frame IOSKJ::Model::yield_per_recruit ( void )

inline

Generate a yield per recruit curve

This is really a biomass-per-recruit curve.

Member Data Documentation

Array<double,Age,Size> IOSKJ::Model::age_size

Proportion of fish of each age in each size bin

Array<double,Region> IOSKJ::Model::biomass

Total biomass by region

Array<double,Region> IOSKJ::Model::biomass_spawners

Total biomass of spawners

Array<double,Region> IOSKJ::Model::biomass_spawners_unfished

Unfished equlibrium spawners (biomass)

This differs from biomass_spawning_unfished in that it is not affected by the proportion spawning in a season

Array<double,Region,Quarter> IOSKJ::Model::biomass_spawning

The total spawning biomass by region

Array<double,Region,Quarter> IOSKJ::Model::biomass_spawning_unfished

Unfished spawning biomass by region and quarter. It is necessary to have this by quarter because the proportion of mature fish that spawn varies by quarter.

Array<double,Region,Method> IOSKJ::Model::biomass_vulnerable

Vulnerable biomass by region and method

Array<double,Region,Method> IOSKJ::Model::catchability

Estimated catchability by region and method

Array<double,Region,Method> IOSKJ::Model::catches

Catches by region and method

Array<double,Region,Method> IOSKJ::Model::catches_taken

Catches by region and method given maximimum exploitation rate of one. This variable is useful for penalising against impossible dynamics.

Array<double,Region,Method> IOSKJ::Model::cpue

CPUE. Simply biomass_vulnerable scaled to its geometric mean for the period 1985-2013

double IOSKJ::Model::e_40

40B0 related variables

Array<double,Region,Method> IOSKJ::Model::effort

Effort by region and method

Currently these are nominal units relative to the period 2004-2013

Array<double,Region,Age> IOSKJ::Model::escapement

Escapement (i.e. survival form exploitation)

Array<double,Region,Method> IOSKJ::Model::exploitation_rate

Exploitation rate by region and method for current time step

Array<double,Region,Method> IOSKJ::Model::exploitation_rate_specified

The exploitation rate specified, for example, when calculating MSY/Bmsy

double IOSKJ::Model::growth_rate_1

Parameters of the two-stanza vonBertallanffy

Array<Normal,Age> IOSKJ::Model::length_age

Length distribution for each age group

Array<double,Size> IOSKJ::Model::length_size

Length associated with each size

Array<double,Quarter> IOSKJ::Model::m_pl_quarter = {0.97,0.87,0.97,1.19}

Lengths at each selectivity knot

The default values below are simply the means of the observed standardised CPUE index by quarter.

double IOSKJ::Model::maturity_length_inflection

Maturity at length logistic function

Array<double,Size> IOSKJ::Model::maturity_size

Maturity at size and age

Array<double,Age> IOSKJ::Model::mortality

Instantaneous rate of natural mortality at age

double IOSKJ::Model::mortality_mean

Mean instantaneous rate of natural mortality across ages

Array<double,Age> IOSKJ::Model::mortality_shape

Initial value:

= {
        1.25, 1.25, 1.25, 1.25,
        1.25, 1.25, 1.25, 1.25, 
        0.80, 0.80, 0.80, 0.80, 
        0.45, 0.45, 0.45, 0.45, 
        1.50, 1.50, 1.50, 1.50, 
        1.50, 1.50, 1.50, 1.50  
    }

Relative morality by age. These are used to calculate a mortality at age by multiplying by mortality_mean. These are from Everson 2011 IOTC–2011–WPTT13–30

double IOSKJ::Model::movement_length_inflection

Movement proportion at size logistic function

Array<double,RegionFrom,Region> IOSKJ::Model::movement_region

Movement maximum proportion moving from one region to another

double IOSKJ::Model::msy

MSY related variables

Array<double,Region,Age> IOSKJ::Model::numbers

Fish numbers by region and age

Array<double,Region> IOSKJ::Model::recruits

Total number of recruits at time t

double IOSKJ::Model::recruits_autocorr

Autocorrelation in recruitment deviations

Array<double,Region> IOSKJ::Model::recruits_determ

Deterministic recruitment at time t

double IOSKJ::Model::recruits_deviation = 0

Recruitment deviation at time t

Normal IOSKJ::Model::recruits_distrib

Underlying distribution for generation recr deviations

double IOSKJ::Model::recruits_multiplier = 1

Recruitment multiplier at time t

bool IOSKJ::Model::recruits_relation_on = true

Flag to turn on/off recruitment relation (if off then recruits_unfished is used)

double IOSKJ::Model::recruits_sd

Standard deviation of recruitment deviations

double IOSKJ::Model::recruits_steepness

Steepness of stock-recruit relation

Array<double,Region> IOSKJ::Model::recruits_unfished

Unfished equlibrium recruitment (numbers) by region

bool IOSKJ::Model::recruits_variation_on = true

Flag to turn on/off recruitment variation

Array<double,SelectivityKnot> IOSKJ::Model::selectivity_lengths = {20,30,40,50,60,70,80}

Lengths at each selectivity knot

Array<double,Method,Size> IOSKJ::Model::selectivity_size

Selectivities by method and size

Array<double,Method,SelectivityKnot> IOSKJ::Model::selectivity_values

Proportion selected at each selectivity knot for each method

Array<double,Quarter> IOSKJ::Model::spawning

The spawning fraction by quarter

Array<double,Age> IOSKJ::Model::survival

Quarterly rate of survival from natural mortality at age

double IOSKJ::Model::weight_length_a

Weight at length power funciton

Array<double,Size> IOSKJ::Model::weight_size

Weight at size

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

model.hpp

Public Member Functions

Public Attributes

Selectivity and exploitation

Detailed Description

Member Function Documentation

Member Data Documentation