fims_popdy::LogDevs< Type > Struct Template Reference

Log Devs class that returns the log of the input added to the log of the recruitment deviations. More...

#include <log_devs.hpp>

Inheritance diagram for fims_popdy::LogDevs< Type >:

Public Member Functions
virtual const Type	evaluate_process (size_t pos)
	Log of the recruitment deviations approach to adding error to expected recruitment.
virtual const Type	evaluate_mean (const Type &spawners, const Type &phi_0)
	Evaluates expected recruitment from the stock–recruitment relationship before recruitment-process deviations are applied.
Public Member Functions inherited from fims_popdy::RecruitmentBase< Type >
	RecruitmentBase ()
	Constructor.
void	Prepare ()
	Prepares the recruitment deviations vector.
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.

Additional Inherited Members
Public Attributes inherited from fims_popdy::RecruitmentBase< Type >
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 inherited from fims_popdy::RecruitmentBase< Type >
static uint32_t	id_g = 0

Detailed Description

template<typename Type>
struct fims_popdy::LogDevs< Type >

Log Devs class that returns the log of the input added to the log of the recruitment deviations.

Member Function Documentation

evaluate_mean()

template<typename Type >

virtual const Type fims_popdy::LogDevs< Type >::evaluate_mean ( const Type &  spawners, const Type &  phi_0  )

inlinevirtual

Evaluates expected recruitment from the stock–recruitment relationship before recruitment-process deviations are applied.

Recruitment is evaluated for the first age represented in the input data. For example, if the weight-at-age and age-composition data start at age 1, recruitment is evaluated for age-1 fish rather than age-0 fish. The recruitment age is not set directly by this function; it is determined by the age structure of the input data.

Recruitment functors that do not define a stock–recruitment mean return the default value of zero.

Parameters

spawners	Spawning output at the time step being evaluated, such as spawning biomass or another model-specific measure of reproductive output.
phi_0	Spawners per recruit at unfished equilibrium, used to scale the stock–recruitment relationship relative to unfished conditions.

Returns

Expected recruitment before recruitment-process deviations or random effects are applied.

Implements fims_popdy::RecruitmentBase< Type >.

evaluate_process()

template<typename Type >

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

inlinevirtual

Log of the recruitment deviations approach to adding error to expected recruitment.

The Log Recruitment Deviation implementation: \( \text{log expected recruitment} + log_devs \)

Parameters

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

Implements fims_popdy::RecruitmentBase< Type >.

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

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