fims_popdy::RecruitmentBase< Type > Struct Template Reference

Base class for all recruitment functors. More...

#include <recruitment_base.hpp>

Inheritance diagram for fims_popdy::RecruitmentBase< Type >:

Public Member Functions
	RecruitmentBase ()
	Constructor.
void	Prepare ()
	Prepares the recruitment deviations vector.
virtual const Type	evaluate_mean (const Type &spawners, const Type &ssbzero)=0
	Calculates the expected recruitment for a given spawning input.
virtual const Type	evaluate_process (size_t pos)=0
	Handle error in recruitment.
void	PrepareConstrainedDeviations ()
	Prepare constrained recruitment deviations. Based on ADMB sum-to-zero constraint implementation. We still need to add an additional penalty to the PrepareConstrainedDeviations method. More discussion can be found here: https://groups.google.com/a/ADMB-project.org/g/users/c/63YJmYGEPuE.
Public Member Functions inherited from fims_model_object::FIMSObject< Type >
uint32_t	GetId () const
	Getter that returns the unique id for parameters in the model.
bool	CheckDimensions (size_t actual, size_t expected)
	Check the dimensions of an object.
virtual void	create_report_vectors (std::map< std::string, fims::Vector< fims::Vector< Type > > > &report_vectors)
	Create a map of report vectors for the object. used to populate the report_vectors map in FisheryModelBase.
virtual void	get_report_vector_count (std::map< std::string, size_t > &report_vector_count)
	Get the report vector count object. used to get the length of each report vector for populating the UncertaintyReportInfo struct in FisheryModelBase.

Public Attributes
fims::Vector< Type >	log_recruit_devs
bool	constrain_deviations = false
fims::Vector< Type >	log_rzero
fims::Vector< Type >	log_r
fims::Vector< Type >	log_expected_recruitment
bool	estimate_log_recruit_devs = true
int	process_id = -999
std::shared_ptr< fims_popdy::RecruitmentBase< Type > >	process
std::shared_ptr< fims_popdy::RecruitmentBase< Type > >	recruitment
Public Attributes inherited from fims_model_object::FIMSObject< Type >
uint32_t	id
std::vector< Type * >	parameters
std::vector< Type * >	random_effects_parameters
std::vector< Type * >	fixed_effects_parameters

Static Public Attributes
static uint32_t	id_g = 0

Detailed Description

template<class Type>
struct fims_popdy::RecruitmentBase< Type >

Base class for all recruitment functors.

Template Parameters

Type	The type of the recruitment functor.

Member Function Documentation

evaluate_mean()

template<class Type >

virtual const Type fims_popdy::RecruitmentBase< Type >::evaluate_mean ( const Type &  spawners, const Type &  ssbzero  )

pure virtual

Calculates the expected recruitment for a given spawning input.

Parameters

spawners	A measure for spawning output.
ssbzero	A measure for spawning output in unfished population.

Implemented in fims_popdy::LogDevs< Type >, fims_popdy::LogR< Type >, and fims_popdy::SRBevertonHolt< Type >.

evaluate_process()

template<class Type >

virtual const Type fims_popdy::RecruitmentBase< Type >::evaluate_process ( size_t  pos )

pure virtual

Handle error in recruitment.

Parameters

pos	Position index, e.g., which year.

Implemented in fims_popdy::LogDevs< Type >, fims_popdy::LogR< Type >, and fims_popdy::SRBevertonHolt< Type >.

Member Data Documentation

constrain_deviations

template<class Type >

bool fims_popdy::RecruitmentBase< Type >::constrain_deviations = false

A flag to indicate if recruitment deviations are summing to zero or not

estimate_log_recruit_devs

template<class Type >

bool fims_popdy::RecruitmentBase< Type >::estimate_log_recruit_devs = true

A flag to indicate if recruitment deviations are estimated or not

id_g

template<class Type >

uint32_t fims_popdy::RecruitmentBase< Type >::id_g = 0

static

reference id for recruitment object

log_expected_recruitment

template<class Type >

fims::Vector<Type> fims_popdy::RecruitmentBase< Type >::log_expected_recruitment

Expectation of the recruitment process

log_r

template<class Type >

fims::Vector<Type> fims_popdy::RecruitmentBase< Type >::log_r

Natural log of recruitment used for random effects

log_recruit_devs

template<class Type >

fims::Vector<Type> fims_popdy::RecruitmentBase< Type >::log_recruit_devs

A vector of the natural log of recruitment deviations

log_rzero

template<class Type >

fims::Vector<Type> fims_popdy::RecruitmentBase< Type >::log_rzero

Natural log of unexploited recruitment.

process

template<class Type >

std::shared_ptr<fims_popdy::RecruitmentBase<Type> > fims_popdy::RecruitmentBase< Type >::process

shared pointer to recruitment processmodule

process_id

template<class Type >

int fims_popdy::RecruitmentBase< Type >::process_id = -999

id of recruitment process model object

recruitment

template<class Type >

std::shared_ptr<fims_popdy::RecruitmentBase<Type> > fims_popdy::RecruitmentBase< Type >::recruitment

shared pointer to recruitment module

---

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

• inst/include/population_dynamics/recruitment/functors/recruitment_base.hpp