From 45853a19539bcf5b8a4e39847504f9fa6b3c18c6 Mon Sep 17 00:00:00 2001 From: Christine Stawitz Date: Tue, 31 Oct 2023 23:19:29 +0000 Subject: [PATCH] Docs: run Doxygen --- docs/annotated.html | 92 +- docs/classEWAAGrowthInterface.html | 4 +- docs/classes.html | 20 +- ...lassfims__info_1_1Information-members.html | 126 ++ docs/classfims__info_1_1Information.html | 1022 ++++++++++ docs/classfims__model_1_1Model-members.html | 93 + docs/classfims__model_1_1Model.html | 202 ++ docs/classfims__popdy_1_1Subpopulation.html | 95 + docs/data__object_8hpp_source.html | 148 +- docs/def_8hpp_source.html | 2 +- docs/distributions__base_8hpp.html | 4 +- docs/distributions__base_8hpp_source.html | 26 +- docs/double__logistic_8hpp_source.html | 36 +- docs/ewaa_8hpp_source.html | 22 +- docs/fims__math_8hpp.html | 146 +- docs/fims__math_8hpp_source.html | 72 +- docs/fleet_8hpp.html | 4 +- docs/fleet_8hpp_source.html | 236 +-- docs/functions.html | 8 +- docs/functions_b.html | 2 +- docs/functions_c.html 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Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 12]
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 ▼Nfims
 CDataObject
 Cfims_log
 CInformationStores FIMS model information and creates model. Contains all objects and data pre-model construction
 CModelModel class. FIMS objective function
 CFIMSObjectFIMSObject struct that defines member types and returns the unique id
 CDistributionsBaseBase class for all module_name functors
 CFleetBase class for all fleets
 CEWAAgrowthEWAAgrowth class that returns the EWAA function value
 CGrowthBaseBase class for all growth functors
 CLogisticMaturityLogisticMaturity class that returns the logistic function value from fims_math
 CMaturityBaseBase class for all maturity functors
 CPopulationPopulation class. Contains subpopulations that are divided into generic partitions (eg. sex, area)
 CSubpopulation
 CRecruitmentBaseBase class for all recruitment functors
 CSRBevertonHoltBevertonHolt class that returns the Beverton Holt SR from fims_math
 CDoubleLogisticSelectivityDoubleLogisticSelectivity class that returns the double logistic function value from fims_math
 CLogisticSelectivityLogisticSelectivity class that returns the logistic function value from fims_math
 CSelectivityBaseBase class for all selectivity functors
 CAgeCompDataInterfaceRcpp interface for age comp data as an S4 object. To instantiate from R: acomp <- new(fims$AgeComp)
 CBevertonHoltRecruitmentInterfaceRcpp interface for Beverton-Holt as an S4 object. To instantiate from R: beverton_holt <- new(fims$beverton_holt)
 CDataInterfaceBaseRcpp interface for Data as an S4 object. To instantiate from R: fleet <- new(fims$Data)
 CDistributionsInterfaceBaseDistributions Rcpp Interface
 CDlnormDistributionsInterfaceRcpp interface for Dlnorm as an S4 object. To instantiate from R: dlnorm_ <- new(fims$TMBDlnormDistribution)
 CDmultinomDistributionsInterfaceRcpp interface for Dmultinom as an S4 object. To instantiate from R: dmultinom_ <- new(fims$TMBDmultinomDistribution)
 CDnormDistributionsInterfaceRcpp interface for Dnorm as an S4 object. To instantiate from R: dnorm_ <- new(fims$TMBDnormDistribution)
 CDoubleLogisticSelectivityInterfaceRcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity <- new(fims$logistic_selectivity)
 CEWAAGrowthInterfaceRcpp interface for EWAAgrowth as an S4 object. To instantiate from R: ewaa <- new(fims$EWAAgrowth)
 CFIMSRcppInterfaceBaseBase class for all interface objects
 CFleetInterfaceRcpp interface for Fleet as an S4 object. To instantiate from R: fleet <- new(fims$Fleet)
 CFleetInterfaceBaseRcpp interface that serves as the parent class for Rcpp fleet interfaces. This type should be inherited and not called from R directly
 CGrowthInterfaceBaseRcpp interface that serves as the parent class for Rcpp growth interfaces. This type should be inherited and not called from R directly
 CIndexDataInterfaceRcpp interface for data as an S4 object. To instantiate from R: fleet <- new(fims$Index)
 CJsonParserParses JSON strings and generates JSON values
 CJsonValueRepresents a JSON value
 CLogisticMaturityInterfaceRcpp interface for logistic maturity as an S4 object. To instantiate from R: logistic_maturity <- new(fims$logistic_maturity)
 CLogisticSelectivityInterfaceRcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity <- new(fims$logistic_selectivity)
 CMaturityInterfaceBaseMaturityInterfaceBase class should be inherited to define different Rcpp interfaces for each possible maturity function
 CNLLInterfaceBaseNLLInterfaceBase class should be inherited to define different Rcpp interfaces for each possible negative log-likelihood function
 CParameterRcppInterface class that defines the interface between R and C++ for parameter types
 CPopulationInterfaceRcpp interface for a new Population. To instantiate from R: population <- new(fims$population)
 CPopulationInterfaceBasePopulationInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Population function
 CRecruitmentInterfaceBaseRecruitmentInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Recruitment function
 CSelectivityInterfaceBaseSelectivityInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Selectivity function
 Cfims_log
 ▼Nfims_data_object
 CDataObject
 ▼Nfims_distributions
 CDistributionsBaseBase class for all module_name functors
 ▼Nfims_info
 CInformationStores FIMS model information and creates model. Contains all objects and data pre-model construction
 ▼Nfims_model
 CModelModel class. FIMS objective function
 ▼Nfims_model_object
 CFIMSObjectFIMSObject struct that defines member types and returns the unique id
 ▼Nfims_popdy
 CFleetBase class for all fleets
 CEWAAgrowthEWAAgrowth class that returns the EWAA function value
 CGrowthBaseBase class for all growth functors
 CLogisticMaturityLogisticMaturity class that returns the logistic function value from fims_math
 CMaturityBaseBase class for all maturity functors
 CPopulationPopulation class. Contains subpopulations that are divided into generic partitions (eg. sex, area)
 CSubpopulation
 CRecruitmentBaseBase class for all recruitment functors
 CSRBevertonHoltBevertonHolt class that returns the Beverton Holt SR from fims_math
 CDoubleLogisticSelectivityDoubleLogisticSelectivity class that returns the double logistic function value from fims_math
 CLogisticSelectivityLogisticSelectivity class that returns the logistic function value from fims_math
 CSelectivityBaseBase class for all selectivity functors
 CAgeCompDataInterfaceRcpp interface for age comp data as an S4 object. To instantiate from R: acomp <- new(fims$AgeComp)
 CBevertonHoltRecruitmentInterfaceRcpp interface for Beverton-Holt as an S4 object. To instantiate from R: beverton_holt <- new(fims$beverton_holt)
 CDataInterfaceBaseRcpp interface for Data as an S4 object. To instantiate from R: fleet <- new(fims$Data)
 CDistributionsInterfaceBaseDistributions Rcpp Interface
 CDlnormDistributionsInterfaceRcpp interface for Dlnorm as an S4 object. To instantiate from R: dlnorm_ <- new(fims$TMBDlnormDistribution)
 CDmultinomDistributionsInterfaceRcpp interface for Dmultinom as an S4 object. To instantiate from R: dmultinom_ <- new(fims$TMBDmultinomDistribution)
 CDnormDistributionsInterfaceRcpp interface for Dnorm as an S4 object. To instantiate from R: dnorm_ <- new(fims$TMBDnormDistribution)
 CDoubleLogisticSelectivityInterfaceRcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity <- new(fims$logistic_selectivity)
 CEWAAGrowthInterfaceRcpp interface for EWAAgrowth as an S4 object. To instantiate from R: ewaa <- new(fims$EWAAgrowth)
 CFIMSRcppInterfaceBaseBase class for all interface objects
 CFleetInterfaceRcpp interface for Fleet as an S4 object. To instantiate from R: fleet <- new(fims$Fleet)
 CFleetInterfaceBaseRcpp interface that serves as the parent class for Rcpp fleet interfaces. This type should be inherited and not called from R directly
 CGrowthInterfaceBaseRcpp interface that serves as the parent class for Rcpp growth interfaces. This type should be inherited and not called from R directly
 CIndexDataInterfaceRcpp interface for data as an S4 object. To instantiate from R: fleet <- new(fims$Index)
 CJsonParserParses JSON strings and generates JSON values
 CJsonValueRepresents a JSON value
 CLogisticMaturityInterfaceRcpp interface for logistic maturity as an S4 object. To instantiate from R: logistic_maturity <- new(fims$logistic_maturity)
 CLogisticSelectivityInterfaceRcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity <- new(fims$logistic_selectivity)
 CMaturityInterfaceBaseMaturityInterfaceBase class should be inherited to define different Rcpp interfaces for each possible maturity function
 CNLLInterfaceBaseNLLInterfaceBase class should be inherited to define different Rcpp interfaces for each possible negative log-likelihood function
 CParameterRcppInterface class that defines the interface between R and C++ for parameter types
 CPopulationInterfaceRcpp interface for a new Population. To instantiate from R: population <- new(fims$population)
 CPopulationInterfaceBasePopulationInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Population function
 CRecruitmentInterfaceBaseRecruitmentInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Recruitment function
 CSelectivityInterfaceBaseSelectivityInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Selectivity function
diff --git a/docs/classEWAAGrowthInterface.html b/docs/classEWAAGrowthInterface.html index 03d31ce..3a42e50 100644 --- a/docs/classEWAAGrowthInterface.html +++ b/docs/classEWAAGrowthInterface.html @@ -176,8 +176,8 @@

Parameters
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weightsT vector of weights
agesT vector of ages
weightsType vector of weights
agesType vector of ages
diff --git a/docs/classes.html b/docs/classes.html index 666d51f..e929951 100644 --- a/docs/classes.html +++ b/docs/classes.html @@ -82,40 +82,40 @@
BevertonHoltRecruitmentInterface
D
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DataInterfaceBase
DataObject (fims)
DistributionsBase (fims)
DistributionsInterfaceBase
DlnormDistributionsInterface
DmultinomDistributionsInterface
DnormDistributionsInterface
DoubleLogisticSelectivity (fims)
DoubleLogisticSelectivityInterface
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DataInterfaceBase
DataObject (fims_data_object)
DistributionsBase (fims_distributions)
DistributionsInterfaceBase
DlnormDistributionsInterface
DmultinomDistributionsInterface
DnormDistributionsInterface
DoubleLogisticSelectivity (fims_popdy)
DoubleLogisticSelectivityInterface
E
-
EWAAgrowth (fims)
EWAAGrowthInterface
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EWAAgrowth (fims_popdy)
EWAAGrowthInterface
F
-
fims_log (fims)
FIMSObject (fims)
FIMSRcppInterfaceBase
Fleet (fims)
FleetInterface
FleetInterfaceBase
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fims_log (fims)
FIMSObject (fims_model_object)
FIMSRcppInterfaceBase
Fleet (fims_popdy)
FleetInterface
FleetInterfaceBase
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GrowthBase (fims)
GrowthInterfaceBase
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GrowthBase (fims_popdy)
GrowthInterfaceBase
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IndexDataInterface
Information (fims)
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IndexDataInterface
Information (fims_info)
J
JsonParser
JsonValue
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LogisticMaturity (fims)
LogisticMaturityInterface
LogisticSelectivity (fims)
LogisticSelectivityInterface
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LogisticMaturity (fims_popdy)
LogisticMaturityInterface
LogisticSelectivity (fims_popdy)
LogisticSelectivityInterface
M
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MaturityBase (fims)
MaturityInterfaceBase
Model (fims)
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MaturityBase (fims_popdy)
MaturityInterfaceBase
Model (fims_model)
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NLLInterfaceBase
P
-
Parameter
Population (fims)
PopulationInterface
PopulationInterfaceBase
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Parameter
Population (fims_popdy)
PopulationInterface
PopulationInterfaceBase
R
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RecruitmentBase (fims)
RecruitmentInterfaceBase
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RecruitmentBase (fims_popdy)
RecruitmentInterfaceBase
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SelectivityBase (fims)
SelectivityInterfaceBase
SRBevertonHolt (fims)
Subpopulation (fims)
+
SelectivityBase (fims_popdy)
SelectivityInterfaceBase
SRBevertonHolt (fims_popdy)
Subpopulation (fims_popdy)
diff --git a/docs/classfims__info_1_1Information-members.html b/docs/classfims__info_1_1Information-members.html new file mode 100644 index 0000000..f8289fb --- /dev/null +++ b/docs/classfims__info_1_1Information-members.html @@ -0,0 +1,126 @@ + + + + + + + +FIMS: Member List + + + + + + + + + + + +
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FIMS +
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fims_info::Information< Type > Member List
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This is the complete list of members for fims_info::Information< Type >, including all inherited members.

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CreateModel()fims_info::Information< Type >inline
data_iterator typedeffims_info::Information< Type >
data_objectsfims_info::Information< Type >
distribution_modelsfims_info::Information< Type >
distribution_models_iterator typedeffims_info::Information< Type >
fims_informationfims_info::Information< Type >static
fixed_effects_parametersfims_info::Information< Type >
fleet_iterator typedeffims_info::Information< Type >
fleetsfims_info::Information< Type >
GetFixedEffectsParameters()fims_info::Information< Type >inline
GetInstance()fims_info::Information< Type >inlinestatic
GetNages() constfims_info::Information< Type >inline
GetNseasons() constfims_info::Information< Type >inline
GetNyears() constfims_info::Information< Type >inline
GetParameters()fims_info::Information< Type >inline
GetRandomEffectsParameters()fims_info::Information< Type >inline
growth_modelsfims_info::Information< Type >
growth_models_iterator typedeffims_info::Information< Type >
Information() (defined in fims_info::Information< Type >)fims_info::Information< Type >inline
maturity_modelsfims_info::Information< Type >
maturity_models_iterator typedeffims_info::Information< Type >
nagesfims_info::Information< Type >
nseasonsfims_info::Information< Type >
nyearsfims_info::Information< Type >
parametersfims_info::Information< Type >
population_iterator typedeffims_info::Information< Type >
populationsfims_info::Information< Type >
random_effects_parametersfims_info::Information< Type >
recruitment_modelsfims_info::Information< Type >
recruitment_models_iterator typedeffims_info::Information< Type >
RegisterParameter(Type &p)fims_info::Information< Type >inline
RegisterRandomEffect(Type &re)fims_info::Information< Type >inline
selectivity_modelsfims_info::Information< Type >
selectivity_models_iterator typedeffims_info::Information< Type >
SetNages(size_t nages)fims_info::Information< Type >inline
SetNseasons(size_t nseasons)fims_info::Information< Type >inline
SetNyears(size_t nyears)fims_info::Information< Type >inline
~Information() (defined in fims_info::Information< Type >)fims_info::Information< Type >inlinevirtual
+ +
+Generated by doxygen 1.9.1 +
+ + diff --git a/docs/classfims__info_1_1Information.html b/docs/classfims__info_1_1Information.html new file mode 100644 index 0000000..5e28fd8 --- /dev/null +++ b/docs/classfims__info_1_1Information.html @@ -0,0 +1,1022 @@ + + + + + + + +FIMS: fims_info::Information< Type > Class Template Reference + + + + + + + + + + + +
+
+ + + + + + +
+
FIMS +
+
+
+ + + + + + + + +
+
+ + +
+ +
+ + +
+
+
+Public Types | +Public Member Functions | +Static Public Member Functions | +Public Attributes | +Static Public Attributes | +List of all members
+
+
fims_info::Information< Type > Class Template Reference
+
+
+ +

Stores FIMS model information and creates model. Contains all objects and data pre-model construction. + More...

+ +

#include <information.hpp>

+ + + + + + + + + + + + + + + + + + +

+Public Types

typedef std::map< uint32_t, std::shared_ptr< fims_data_object::DataObject< Type > > >::iterator data_iterator
 
typedef std::map< uint32_t, std::shared_ptr< fims_popdy::RecruitmentBase< Type > > >::iterator recruitment_models_iterator
 
typedef std::map< uint32_t, std::shared_ptr< fims_popdy::SelectivityBase< Type > > >::iterator selectivity_models_iterator
 
typedef std::map< uint32_t, std::shared_ptr< fims_popdy::GrowthBase< Type > > >::iterator growth_models_iterator
 
typedef std::map< uint32_t, std::shared_ptr< fims_popdy::MaturityBase< Type > > >::iterator maturity_models_iterator
 
typedef std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > >::iterator fleet_iterator
 
typedef std::map< uint32_t, std::shared_ptr< fims_popdy::Population< Type > > >::iterator population_iterator
 
typedef std::map< uint32_t, std::shared_ptr< fims_distributions::DistributionsBase< Type > > >::iterator distribution_models_iterator
 
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+Public Member Functions

void RegisterParameter (Type &p)
 
void RegisterRandomEffect (Type &re)
 
bool CreateModel ()
 
size_t GetNages () const
 Get the Nages object. More...
 
void SetNages (size_t nages)
 Set the Nages object. More...
 
size_t GetNseasons () const
 Get the Nseasons object. More...
 
void SetNseasons (size_t nseasons)
 Set the Nseasons object. More...
 
size_t GetNyears () const
 Get the Nyears object. More...
 
void SetNyears (size_t nyears)
 Set the Nyears object. More...
 
std::vector< Type * > & GetParameters ()
 Get the Parameters object. More...
 
std::vector< Type * > & GetFixedEffectsParameters ()
 Get the Fixed Effects Parameters object. More...
 
std::vector< Type * > & GetRandomEffectsParameters ()
 Get the Random Effects Parameters object. More...
 
+ + + +

+Static Public Member Functions

static std::shared_ptr< Information< Type > > GetInstance ()
 
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+Public Attributes

size_t nyears
 
size_t nseasons = 1
 
size_t nages
 
std::vector< Type * > parameters
 
std::vector< Type * > random_effects_parameters
 
std::vector< Type * > fixed_effects_parameters
 
std::map< uint32_t, std::shared_ptr< fims_data_object::DataObject< Type > > > data_objects
 
std::map< uint32_t, std::shared_ptr< fims_popdy::RecruitmentBase< Type > > > recruitment_models
 
std::map< uint32_t, std::shared_ptr< fims_popdy::SelectivityBase< Type > > > selectivity_models
 
std::map< uint32_t, std::shared_ptr< fims_popdy::GrowthBase< Type > > > growth_models
 
std::map< uint32_t, std::shared_ptr< fims_popdy::MaturityBase< Type > > > maturity_models
 
std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > > fleets
 
std::map< uint32_t, std::shared_ptr< fims_popdy::Population< Type > > > populations
 
std::map< uint32_t, std::shared_ptr< fims_distributions::DistributionsBase< Type > > > distribution_models
 
+ + + +

+Static Public Attributes

static std::shared_ptr< Information< Type > > fims_information
 
+

Detailed Description

+

template<typename Type>
+class fims_info::Information< Type >

+ +

Stores FIMS model information and creates model. Contains all objects and data pre-model construction.

+

Member Typedef Documentation

+ +

◆ data_iterator

+ +
+
+
+template<typename Type >
+ + + + +
typedef std::map<uint32_t, std::shared_ptr<fims_data_object::DataObject<Type> > >::iterator fims_info::Information< Type >::data_iterator
+
+

iterator for the data objects

+ +
+
+ +

◆ distribution_models_iterator

+ +
+
+
+template<typename Type >
+ + + + +
typedef std::map<uint32_t, std::shared_ptr<fims_distributions::DistributionsBase<Type> > >::iterator fims_info::Information< Type >::distribution_models_iterator
+
+

iterator for distribution objects>

+ +
+
+ +

◆ fleet_iterator

+ +
+
+
+template<typename Type >
+ + + + +
typedef std::map<uint32_t, std::shared_ptr<fims_popdy::Fleet<Type> > >::iterator fims_info::Information< Type >::fleet_iterator
+
+

iterator for fleet objects>

+ +
+
+ +

◆ growth_models_iterator

+ +
+
+
+template<typename Type >
+ + + + +
typedef std::map<uint32_t, std::shared_ptr<fims_popdy::GrowthBase<Type> > >::iterator fims_info::Information< Type >::growth_models_iterator
+
+

iterator for growth objects>

+ +
+
+ +

◆ maturity_models_iterator

+ +
+
+
+template<typename Type >
+ + + + +
typedef std::map<uint32_t, std::shared_ptr<fims_popdy::MaturityBase<Type> > >::iterator fims_info::Information< Type >::maturity_models_iterator
+
+

iterator for maturity objects>

+ +
+
+ +

◆ population_iterator

+ +
+
+
+template<typename Type >
+ + + + +
typedef std::map<uint32_t, std::shared_ptr<fims_popdy::Population<Type> > >::iterator fims_info::Information< Type >::population_iterator
+
+

iterator for population objects>

+ +
+
+ +

◆ recruitment_models_iterator

+ +
+
+
+template<typename Type >
+ + + + +
typedef std::map<uint32_t, std::shared_ptr<fims_popdy::RecruitmentBase<Type> > >::iterator fims_info::Information< Type >::recruitment_models_iterator
+
+

iterator for recruitment objects>

+ +
+
+ +

◆ selectivity_models_iterator

+ +
+
+
+template<typename Type >
+ + + + +
typedef std::map<uint32_t, std::shared_ptr<fims_popdy::SelectivityBase<Type> > >::iterator fims_info::Information< Type >::selectivity_models_iterator
+
+

iterator for selectivity objects>

+ +
+
+

Member Function Documentation

+ +

◆ CreateModel()

+ +
+
+
+template<typename Type >
+ + + + + +
+ + + + + + + +
bool fims_info::Information< Type >::CreateModel ()
+ 		+inline
+
+

Create the generalized stock assessment model that will evaluate the objective function. Does error checking to make sure the program has all necessary components for the model and that they're in the right dimensions.

+
Returns
+ +
+
+ +

◆ GetFixedEffectsParameters()

+ +
+
+
+template<typename Type >
+ + + + + +
+ + + + + + + +
std::vector<Type*>& fims_info::Information< Type >::GetFixedEffectsParameters ()
+ 		+inline
+
+ +

Get the Fixed Effects Parameters object.

+
Returns
std::vector<Type*>&
+ +
+
+ +

◆ GetInstance()

+ +
+
+
+template<typename Type >
+ + + + + +
+ + + + + + + +
static std::shared_ptr<Information<Type> > fims_info::Information< Type >::GetInstance ()
+ 		+inlinestatic
+
+

Returns a single Information object for type T.

+
Returns
singleton for type T
+ +
+
+ +

◆ GetNages()

+ +
+
+
+template<typename Type >
+ + + + + +
+ + + + + + + +
size_t fims_info::Information< Type >::GetNages () const
+ 		+inline
+
+ +

Get the Nages object.

+
Returns
size_t
+ +
+
+ +

◆ GetNseasons()

+ +
+
+
+template<typename Type >
+ + + + + +
+ + + + + + + +
size_t fims_info::Information< Type >::GetNseasons () const
+ 		+inline
+
+ +

Get the Nseasons object.

+
Returns
size_t
+ +
+
+ +

◆ GetNyears()

+ +
+
+
+template<typename Type >
+ + + + + +
+ + + + + + + +
size_t fims_info::Information< Type >::GetNyears () const
+ 		+inline
+
+ +

Get the Nyears object.

+
Returns
size_t
+ +
+
+ +

◆ GetParameters()

+ +
+
+
+template<typename Type >
+ + + + + +
+ + + + + + + +
std::vector<Type*>& fims_info::Information< Type >::GetParameters ()
+ 		+inline
+
+ +

Get the Parameters object.

+
Returns
std::vector<Type*>&
+ +
+
+ +

◆ GetRandomEffectsParameters()

+ +
+
+
+template<typename Type >
+ + + + + +
+ + + + + + + +
std::vector<Type*>& fims_info::Information< Type >::GetRandomEffectsParameters ()
+ 		+inline
+
+ +

Get the Random Effects Parameters object.

+
Returns
std::vector<Type*>&
+ +
+
+ +

◆ RegisterParameter()

+ +
+
+
+template<typename Type >
+ + + + + +
+ + + + + + + + +
void fims_info::Information< Type >::RegisterParameter (Type & p)
+ 		+inline
+
+

Register a parameter as estimable.

+
Parameters
+ + +
p
+
+
+ +
+
+ +

◆ RegisterRandomEffect()

+ +
+
+
+template<typename Type >
+ + + + + +
+ + + + + + + + +
void fims_info::Information< Type >::RegisterRandomEffect (Type & re)
+ 		+inline
+
+

Register a random effect as estimable.

+
Parameters
+ + +
re
+
+
+ +
+
+ +

◆ SetNages()

+ +
+
+
+template<typename Type >
+ + + + + +
+ + + + + + + + +
void fims_info::Information< Type >::SetNages (size_t nages)
+ 		+inline
+
+ +

Set the Nages object.

+
Parameters
+ + +
nages
+
+
+ +
+
+ +

◆ SetNseasons()

+ +
+
+
+template<typename Type >
+ + + + + +
+ + + + + + + + +
void fims_info::Information< Type >::SetNseasons (size_t nseasons)
+ 		+inline
+
+ +

Set the Nseasons object.

+
Parameters
+ + +
nseasons
+
+
+ +
+
+ +

◆ SetNyears()

+ +
+
+
+template<typename Type >
+ + + + + +
+ + + + + + + + +
void fims_info::Information< Type >::SetNyears (size_t nyears)
+ 		+inline
+
+ +

Set the Nyears object.

+
Parameters
+ + +
nyears
+
+
+ +
+
+

Member Data Documentation

+ +

◆ data_objects

+ +
+
+
+template<typename Type >
+ + + + +
std::map<uint32_t, std::shared_ptr<fims_data_object::DataObject<Type> > > fims_info::Information< Type >::data_objects
+
+

map that holds data objects >

+ +
+
+ +

◆ distribution_models

+ +
+
+
+template<typename Type >
+ + + + +
std::map<uint32_t, std::shared_ptr<fims_distributions::DistributionsBase<Type> > > fims_info::Information< Type >::distribution_models
+
+

hash map to link each object to its shared location in memory

+ +
+
+ +

◆ fims_information

+ +
+
+
+template<typename Type >
+ + + + + +
+ + + + +
std::shared_ptr< Information< Type > > fims_info::Information< Type >::fims_information
+ 		+static
+
+Initial value:
=
+
nullptr
+

singleton instance >

+ +
+
+ +

◆ fixed_effects_parameters

+ +
+
+
+template<typename Type >
+ + + + +
std::vector<Type*> fims_info::Information< Type >::fixed_effects_parameters
+
+

list of all fixed effects parameters >

+ +
+
+ +

◆ fleets

+ +
+
+
+template<typename Type >
+ + + + +
std::map<uint32_t, std::shared_ptr<fims_popdy::Fleet<Type> > > fims_info::Information< Type >::fleets
+
+

hash map to link each object to its shared location in memory

+ +
+
+ +

◆ growth_models

+ +
+
+
+template<typename Type >
+ + + + +
std::map<uint32_t, std::shared_ptr<fims_popdy::GrowthBase<Type> > > fims_info::Information< Type >::growth_models
+
+

hash map to link each object to its shared location in memory

+ +
+
+ +

◆ maturity_models

+ +
+
+
+template<typename Type >
+ + + + +
std::map<uint32_t, std::shared_ptr<fims_popdy::MaturityBase<Type> > > fims_info::Information< Type >::maturity_models
+
+

hash map to link each object to its shared location in memory

+ +
+
+ +

◆ nages

+ +
+
+
+template<typename Type >
+ + + + +
size_t fims_info::Information< Type >::nages
+
+

number of ages>

+ +
+
+ +

◆ nseasons

+ +
+
+
+template<typename Type >
+ + + + +
size_t fims_info::Information< Type >::nseasons = 1
+
+

number of seasons >

+ +
+
+ +

◆ nyears

+ +
+
+
+template<typename Type >
+ + + + +
size_t fims_info::Information< Type >::nyears
+
+

number of years >

+ +
+
+ +

◆ parameters

+ +
+
+
+template<typename Type >
+ + + + +
std::vector<Type*> fims_info::Information< Type >::parameters
+
+

list of all estimated parameters >

+ +
+
+ +

◆ populations

+ +
+
+
+template<typename Type >
+ + + + +
std::map<uint32_t, std::shared_ptr<fims_popdy::Population<Type> > > fims_info::Information< Type >::populations
+
+

hash map to link each object to its shared location in memory

+ +
+
+ +

◆ random_effects_parameters

+ +
+
+
+template<typename Type >
+ + + + +
std::vector<Type*> fims_info::Information< Type >::random_effects_parameters
+
+

list of all random effects parameters >

+ +
+
+ +

◆ recruitment_models

+ +
+
+
+template<typename Type >
+ + + + +
std::map<uint32_t, std::shared_ptr<fims_popdy::RecruitmentBase<Type> > > fims_info::Information< Type >::recruitment_models
+
+

hash map to link each object to its shared location in memory

+ +
+
+ +

◆ selectivity_models

+ +
+
+
+template<typename Type >
+ + + + +
std::map<uint32_t, std::shared_ptr<fims_popdy::SelectivityBase<Type> > > fims_info::Information< Type >::selectivity_models
+
+

hash map to link each object to its shared location in memory

+ +
+
+
The documentation for this class was generated from the following file: +
+ +
+Generated by doxygen 1.9.1 +
+ + diff --git a/docs/classfims__model_1_1Model-members.html b/docs/classfims__model_1_1Model-members.html new file mode 100644 index 0000000..1a9d1fb --- /dev/null +++ b/docs/classfims__model_1_1Model-members.html @@ -0,0 +1,93 @@ + + + + + + + +FIMS: Member List + + + + + + + + + + + +
+
+ + + + + + +
+
FIMS +
+
+
+ + + + + + + + +
+
+ + +
+ +
+ + +
+
+
+
fims_model::Model< Type > Member List
+
+
+ +

This is the complete list of members for fims_model::Model< Type >, including all inherited members.

+ + + + + + +
Evaluate()fims_model::Model< Type >inline
fims_informationfims_model::Model< Type >
fims_modelfims_model::Model< Type >static
GetInstance()fims_model::Model< Type >inlinestatic
~Model() (defined in fims_model::Model< Type >)fims_model::Model< Type >inlinevirtual
+ +
+Generated by doxygen 1.9.1 +
+ + diff --git a/docs/classfims__model_1_1Model.html b/docs/classfims__model_1_1Model.html new file mode 100644 index 0000000..d6dffdb --- /dev/null +++ b/docs/classfims__model_1_1Model.html @@ -0,0 +1,202 @@ + + + + + + + +FIMS: fims_model::Model< Type > Class Template Reference + + + + + + + + + + + +
+
+ + + + + + +
+
FIMS +
+
+
+ + + + + + + + +
+
+ + +
+ +
+ + +
+
+
+Public Member Functions | +Static Public Member Functions | +Public Attributes | +Static Public Attributes | +List of all members
+
+
fims_model::Model< Type > Class Template Reference
+
+
+ +

Model class. FIMS objective function. + More...

+ +

#include <model.hpp>

+ + + + + +

+Public Member Functions

+const Type Evaluate ()
 Evaluate. Calculates the joint negative log-likelihood function.
 
+ + + +

+Static Public Member Functions

static std::shared_ptr< Model< Type > > GetInstance ()
 
+ + + +

+Public Attributes

std::shared_ptr< fims_info::Information< Type > > fims_information
 
+ + + +

+Static Public Attributes

static std::shared_ptr< Model< Type > > fims_model
 
+

Detailed Description

+

template<typename Type>
+class fims_model::Model< Type >

+ +

Model class. FIMS objective function.

+

Member Function Documentation

+ +

◆ GetInstance()

+ +
+
+
+template<typename Type >
+ + + + + +
+ + + + + + + +
static std::shared_ptr<Model<Type> > fims_model::Model< Type >::GetInstance ()
+ 		+inlinestatic
+
+

Returns a single Information object for type Type.

+
Returns
singleton for type Type
+ +
+
+

Member Data Documentation

+ +

◆ fims_information

+ +
+
+
+template<typename Type >
+ + + + +
std::shared_ptr<fims_info::Information<Type> > fims_model::Model< Type >::fims_information
+
+

Create a shared fims_information as a pointer to Information

+ +
+
+ +

◆ fims_model

+ +
+
+
+template<typename Type >
+ + + + + +
+ + + + +
std::shared_ptr< Model< Type > > fims_model::Model< Type >::fims_model
+ 		+static
+
+Initial value:
=
+
nullptr
+

Create a shared fims_model as a pointer to Model

+ +
+
+
The documentation for this class was generated from the following file: +
+ +
+Generated by doxygen 1.9.1 +
+ + diff --git a/docs/classfims__popdy_1_1Subpopulation.html b/docs/classfims__popdy_1_1Subpopulation.html new file mode 100644 index 0000000..730d1e4 --- /dev/null +++ b/docs/classfims__popdy_1_1Subpopulation.html @@ -0,0 +1,95 @@ + + + + + + + +FIMS: fims_popdy::Subpopulation< Type > Class Template Reference + + + + + + + + + + + +
+
+ + + + + + +
+
FIMS +
+
+
+ + + + + + + + +
+
+ + +
+ +
+ + +
+
+
+
fims_popdy::Subpopulation< Type > Class Template Reference
+
+
+ +

#include <subpopulation.hpp>

+

Detailed Description

+

template<typename Type>
+class fims_popdy::Subpopulation< Type >

+ +

Subpopulation class. This class represents a generic partition of a population (eg., sex, area).

+
The documentation for this class was generated from the following file: +
+ +
+Generated by doxygen 1.9.1 +
+ + diff --git a/docs/data__object_8hpp_source.html b/docs/data__object_8hpp_source.html index ed3d230..160a454 100644 --- a/docs/data__object_8hpp_source.html +++ b/docs/data__object_8hpp_source.html @@ -115,126 +115,126 @@
37 
38 #include "model_object.hpp"
39 
-
40 namespace fims {
+
40 namespace fims_data_object {
41 
45 template <typename Type>
-
46 struct DataObject : public fims::FIMSObject<Type> {
-
47  static uint32_t id_g;
-
48  std::vector<Type> data;
-
49  size_t dimensions;
-
50  size_t imax;
-
51  size_t jmax;
-
52  size_t kmax;
-
53  size_t lmax;
-
58  DataObject(size_t imax) : dimensions(1), imax(imax) {
-
59  data.resize(imax);
+
46 struct DataObject : public fims_model_object::FIMSObject<Type> {
+
47  static uint32_t id_g;
+
48  std::vector<Type> data;
+
49  size_t dimensions;
+
50  size_t imax;
+
51  size_t jmax;
+
52  size_t kmax;
+
53  size_t lmax;
+
58  DataObject(size_t imax) : dimensions(1), imax(imax) {
+
59  data.resize(imax);
60 
-
61  this->id = DataObject<Type>::id_g++;
+
61  this->id = DataObject<Type>::id_g++;
62  }
63 
-
67  DataObject(size_t imax, size_t jmax) : dimensions(2), imax(imax), jmax(jmax) {
-
68  data.resize(imax * jmax);
-
69  this->id = DataObject<Type>::id_g++;
+
67  DataObject(size_t imax, size_t jmax) : dimensions(2), imax(imax), jmax(jmax) {
+
68  data.resize(imax * jmax);
+
69  this->id = DataObject<Type>::id_g++;
70  }
71 
-
75  DataObject(size_t imax, size_t jmax, size_t kmax)
-
76  : dimensions(3), imax(imax), jmax(jmax), kmax(kmax) {
-
77  data.resize(imax * jmax * kmax);
-
78  this->id = DataObject<Type>::id_g++;
+
75  DataObject(size_t imax, size_t jmax, size_t kmax)
+
76  : dimensions(3), imax(imax), jmax(jmax), kmax(kmax) {
+
77  data.resize(imax * jmax * kmax);
+
78  this->id = DataObject<Type>::id_g++;
79  }
80 
-
84  DataObject(size_t imax, size_t jmax, size_t kmax, size_t lmax)
-
85  : dimensions(4), imax(imax), jmax(jmax), kmax(kmax), lmax(lmax) {
-
86  data.resize(imax * jmax * kmax * lmax);
-
87  this->id = DataObject<Type>::id_g++;
+
84  DataObject(size_t imax, size_t jmax, size_t kmax, size_t lmax)
+
85  : dimensions(4), imax(imax), jmax(jmax), kmax(kmax), lmax(lmax) {
+
86  data.resize(imax * jmax * kmax * lmax);
+
87  this->id = DataObject<Type>::id_g++;
88  }
89 
-
95  inline Type operator()(size_t i) { return data[i]; }
+
95  inline Type operator()(size_t i) { return data[i]; }
96 
-
103  inline Type& at(size_t i) {
+
103  inline Type& at(size_t i) {
104  if (i >= this->data.size()) {
105  throw std::overflow_error("DataObject error:i index out of bounds");
106  }
-
107  return data[i];
+
107  return data[i];
108  }
109 
-
116  inline const Type operator()(size_t i, size_t j) {
-
117  return data[i * jmax + j];
+
116  inline const Type operator()(size_t i, size_t j) {
+
117  return data[i * jmax + j];
118  }
119 
-
127  inline Type& at(size_t i, size_t j) {
-
128  if ((i * jmax + j) >= this->data.size()) {
+
127  inline Type& at(size_t i, size_t j) {
+
128  if ((i * jmax + j) >= this->data.size()) {
129  throw std::overflow_error("DataObject error: index out of bounds");
130  }
-
131  return data[i * jmax + j];
+
131  return data[i * jmax + j];
132  }
133 
-
141  inline const Type operator()(size_t i, size_t j, size_t k) {
-
142  return data[i * jmax * kmax + j * kmax + k];
+
141  inline const Type operator()(size_t i, size_t j, size_t k) {
+
142  return data[i * jmax * kmax + j * kmax + k];
143  }
144 
-
153  inline Type& at(size_t i, size_t j, size_t k) {
-
154  if ((i * jmax * kmax + j * kmax + k) >= this->data.size()) {
+
153  inline Type& at(size_t i, size_t j, size_t k) {
+
154  if ((i * jmax * kmax + j * kmax + k) >= this->data.size()) {
155  throw std::overflow_error("DataObject error: index out of bounds");
156  }
-
157  return data[i * jmax * kmax + j * kmax + k];
+
157  return data[i * jmax * kmax + j * kmax + k];
158  }
159 
-
168  inline const Type operator()(size_t i, size_t j, size_t k, size_t l) {
-
169  return data[i * jmax * kmax * lmax + j * kmax * lmax + k * lmax + l];
+
168  inline const Type operator()(size_t i, size_t j, size_t k, size_t l) {
+
169  return data[i * jmax * kmax * lmax + j * kmax * lmax + k * lmax + l];
170  }
171 
-
181  inline Type& at(size_t i, size_t j, size_t k, size_t l) {
-
182  if ((i * jmax * kmax * lmax + j * kmax * lmax + k * lmax + l) >=
+
181  inline Type& at(size_t i, size_t j, size_t k, size_t l) {
+
182  if ((i * jmax * kmax * lmax + j * kmax * lmax + k * lmax + l) >=
183  this->data.size()) {
184  throw std::overflow_error("DataObject error: index out of bounds");
185  }
-
186  return data[i * jmax * kmax * lmax + j * kmax * lmax + k * lmax + l];
+
186  return data[i * jmax * kmax * lmax + j * kmax * lmax + k * lmax + l];
187  }
188 
-
194  size_t get_dimensions() const { return dimensions; }
+
194  size_t get_dimensions() const { return dimensions; }
195 
-
201  size_t get_imax() const { return imax; }
+
201  size_t get_imax() const { return imax; }
202 
-
208  size_t get_jmax() const { return jmax; }
+
208  size_t get_jmax() const { return jmax; }
209 
-
215  size_t get_kmax() const { return kmax; }
+
215  size_t get_kmax() const { return kmax; }
216 
-
222  size_t get_lmax() const { return lmax; }
+
222  size_t get_lmax() const { return lmax; }
223 };
224 
225 template <typename Type>
-
226 uint32_t DataObject<Type>::id_g = 0;
+
226 uint32_t DataObject<Type>::id_g = 0;
227 
-
228 } // namespace fims
+
228 } // namespace fims_data_object
229 
230 #endif
-
fims::DataObject
Definition: data_object.hpp:46
-
fims::DataObject::DataObject
DataObject(size_t imax, size_t jmax, size_t kmax, size_t lmax)
Definition: data_object.hpp:84
-
fims::DataObject::id_g
static uint32_t id_g
Definition: data_object.hpp:47
-
fims::DataObject::operator()
const Type operator()(size_t i, size_t j, size_t k)
Definition: data_object.hpp:141
-
fims::DataObject::DataObject
DataObject(size_t imax, size_t jmax, size_t kmax)
Definition: data_object.hpp:75
-
fims::DataObject::at
Type & at(size_t i, size_t j)
Definition: data_object.hpp:127
-
fims::DataObject::get_kmax
size_t get_kmax() const
Get the kmax object.
Definition: data_object.hpp:215
-
fims::DataObject::at
Type & at(size_t i, size_t j, size_t k, size_t l)
Definition: data_object.hpp:181
-
fims::DataObject::get_imax
size_t get_imax() const
Get the imax object.
Definition: data_object.hpp:201
-
fims::DataObject::at
Type & at(size_t i, size_t j, size_t k)
Definition: data_object.hpp:153
-
fims::DataObject::lmax
size_t lmax
Definition: data_object.hpp:53
-
fims::DataObject::imax
size_t imax
Definition: data_object.hpp:50
-
fims::DataObject::DataObject
DataObject(size_t imax, size_t jmax)
Definition: data_object.hpp:67
-
fims::DataObject::dimensions
size_t dimensions
Definition: data_object.hpp:49
-
fims::DataObject::get_dimensions
size_t get_dimensions() const
Get the dimensions object.
Definition: data_object.hpp:194
-
fims::DataObject::data
std::vector< Type > data
Definition: data_object.hpp:48
-
fims::DataObject::DataObject
DataObject(size_t imax)
Definition: data_object.hpp:58
-
fims::DataObject::get_jmax
size_t get_jmax() const
Get the jmax object.
Definition: data_object.hpp:208
-
fims::DataObject::operator()
Type operator()(size_t i)
Definition: data_object.hpp:95
-
fims::DataObject::jmax
size_t jmax
Definition: data_object.hpp:51
-
fims::DataObject::get_lmax
size_t get_lmax() const
Get the lmax object.
Definition: data_object.hpp:222
-
fims::DataObject::at
Type & at(size_t i)
Definition: data_object.hpp:103
-
fims::DataObject::operator()
const Type operator()(size_t i, size_t j)
Definition: data_object.hpp:116
-
fims::DataObject::kmax
size_t kmax
Definition: data_object.hpp:52
-
fims::DataObject::operator()
const Type operator()(size_t i, size_t j, size_t k, size_t l)
Definition: data_object.hpp:168
-
fims::FIMSObject
FIMSObject struct that defines member types and returns the unique id.
Definition: model_object.hpp:25
+
fims_data_object::DataObject
Definition: data_object.hpp:46
+
fims_data_object::DataObject::get_dimensions
size_t get_dimensions() const
Get the dimensions object.
Definition: data_object.hpp:194
+
fims_data_object::DataObject::lmax
size_t lmax
Definition: data_object.hpp:53
+
fims_data_object::DataObject::operator()
Type operator()(size_t i)
Definition: data_object.hpp:95
+
fims_data_object::DataObject::get_imax
size_t get_imax() const
Get the imax object.
Definition: data_object.hpp:201
+
fims_data_object::DataObject::at
Type & at(size_t i)
Definition: data_object.hpp:103
+
fims_data_object::DataObject::at
Type & at(size_t i, size_t j)
Definition: data_object.hpp:127
+
fims_data_object::DataObject::kmax
size_t kmax
Definition: data_object.hpp:52
+
fims_data_object::DataObject::operator()
const Type operator()(size_t i, size_t j)
Definition: data_object.hpp:116
+
fims_data_object::DataObject::DataObject
DataObject(size_t imax, size_t jmax, size_t kmax)
Definition: data_object.hpp:75
+
fims_data_object::DataObject::data
std::vector< Type > data
Definition: data_object.hpp:48
+
fims_data_object::DataObject::operator()
const Type operator()(size_t i, size_t j, size_t k)
Definition: data_object.hpp:141
+
fims_data_object::DataObject::get_jmax
size_t get_jmax() const
Get the jmax object.
Definition: data_object.hpp:208
+
fims_data_object::DataObject::get_lmax
size_t get_lmax() const
Get the lmax object.
Definition: data_object.hpp:222
+
fims_data_object::DataObject::DataObject
DataObject(size_t imax)
Definition: data_object.hpp:58
+
fims_data_object::DataObject::imax
size_t imax
Definition: data_object.hpp:50
+
fims_data_object::DataObject::DataObject
DataObject(size_t imax, size_t jmax, size_t kmax, size_t lmax)
Definition: data_object.hpp:84
+
fims_data_object::DataObject::DataObject
DataObject(size_t imax, size_t jmax)
Definition: data_object.hpp:67
+
fims_data_object::DataObject::operator()
const Type operator()(size_t i, size_t j, size_t k, size_t l)
Definition: data_object.hpp:168
+
fims_data_object::DataObject::at
Type & at(size_t i, size_t j, size_t k)
Definition: data_object.hpp:153
+
fims_data_object::DataObject::get_kmax
size_t get_kmax() const
Get the kmax object.
Definition: data_object.hpp:215
+
fims_data_object::DataObject::dimensions
size_t dimensions
Definition: data_object.hpp:49
+
fims_data_object::DataObject::at
Type & at(size_t i, size_t j, size_t k, size_t l)
Definition: data_object.hpp:181
+
fims_data_object::DataObject::jmax
size_t jmax
Definition: data_object.hpp:51
+
fims_data_object::DataObject::id_g
static uint32_t id_g
Definition: data_object.hpp:47
+
fims_model_object::FIMSObject
FIMSObject struct that defines member types and returns the unique id.
Definition: model_object.hpp:25
diff --git a/docs/def_8hpp_source.html b/docs/def_8hpp_source.html index 3ba9983..0af1770 100644 --- a/docs/def_8hpp_source.html +++ b/docs/def_8hpp_source.html @@ -122,7 +122,7 @@
54 
55 #ifdef STD_LIB
56 
-
61 template <typename T>
+
61 template <typename Type>
62 struct ModelTraits {
63  typedef double real_t;
64  typedef double variable_t;
diff --git a/docs/distributions__base_8hpp.html b/docs/distributions__base_8hpp.html index 056f22a..b0ab1e2 100644 --- a/docs/distributions__base_8hpp.html +++ b/docs/distributions__base_8hpp.html @@ -85,8 +85,8 @@ - - + +

Classes

struct  fims::DistributionsBase< Type >
 Base class for all module_name functors. More...
struct  fims_distributions::DistributionsBase< Type >
 Base class for all module_name functors. More...
 

Detailed Description

diff --git a/docs/distributions__base_8hpp_source.html b/docs/distributions__base_8hpp_source.html index c4b0670..55b822e 100644 --- a/docs/distributions__base_8hpp_source.html +++ b/docs/distributions__base_8hpp_source.html @@ -83,33 +83,33 @@
17 #include "../../common/model_object.hpp"
18 #include "../../interface/interface.hpp"
19 
-
20 namespace fims {
+
20 namespace fims_distributions {
21 
27 template <typename Type>
-
28 struct DistributionsBase : public FIMSObject<Type> {
+
28 struct DistributionsBase : public fims_model_object::FIMSObject<Type> {
29  // id_g is the ID of the instance of the DistributionsBase class.
30  // this is like a memory tracker.
31  // Assigning each one its own ID is a way to keep track of
32  // all the instances of the DistributionsBase class.
-
33  static uint32_t id_g;
+
33  static uint32_t id_g;
34 
-
37  DistributionsBase() { this->id = DistributionsBase::id_g++; }
+
37  DistributionsBase() { this->id = DistributionsBase::id_g++; }
38 
-
39  virtual ~DistributionsBase() {}
-
45  virtual const Type evaluate(const bool& do_log) = 0;
+
39  virtual ~DistributionsBase() {}
+
45  virtual const Type evaluate(const bool& do_log) = 0;
46 };
47 
50 template <typename Type>
-
51 uint32_t DistributionsBase<Type>::id_g = 0;
+
51 uint32_t DistributionsBase<Type>::id_g = 0;
52 
-
53 } // namespace fims
+
53 } // namespace fims_distributions
54 
55 #endif /* DISTRIBUTIONS_BASE_HPP */
-
fims::DistributionsBase
Base class for all module_name functors.
Definition: distributions_base.hpp:28
-
fims::DistributionsBase::DistributionsBase
DistributionsBase()
Constructor.
Definition: distributions_base.hpp:37
-
fims::DistributionsBase::id_g
static uint32_t id_g
Default id of the singleton distribution class.
Definition: distributions_base.hpp:33
-
fims::DistributionsBase::evaluate
virtual const Type evaluate(const bool &do_log)=0
Generic probability density function. Calculates the pdf at the independent variable value.
-
fims::FIMSObject
FIMSObject struct that defines member types and returns the unique id.
Definition: model_object.hpp:25
+
fims_distributions::DistributionsBase
Base class for all module_name functors.
Definition: distributions_base.hpp:28
+
fims_distributions::DistributionsBase::evaluate
virtual const Type evaluate(const bool &do_log)=0
Generic probability density function. Calculates the pdf at the independent variable value.
+
fims_distributions::DistributionsBase::id_g
static uint32_t id_g
Default id of the singleton distribution class.
Definition: distributions_base.hpp:33
+
fims_distributions::DistributionsBase::DistributionsBase
DistributionsBase()
Constructor.
Definition: distributions_base.hpp:37
+
fims_model_object::FIMSObject
FIMSObject struct that defines member types and returns the unique id.
Definition: model_object.hpp:25
diff --git a/docs/double__logistic_8hpp_source.html b/docs/double__logistic_8hpp_source.html index fb7d2ad..1ba24f8 100644 --- a/docs/double__logistic_8hpp_source.html +++ b/docs/double__logistic_8hpp_source.html @@ -89,33 +89,33 @@
11 #include "../../../common/fims_math.hpp"
12 #include "selectivity_base.hpp"
13 
-
14 namespace fims {
+
14 namespace fims_popdy {
15 
20 template <typename Type>
-
21 struct DoubleLogisticSelectivity : public SelectivityBase<Type> {
-
22  Type median_asc;
-
25  Type slope_asc;
-
28  Type median_desc;
-
31  Type slope_desc;
-
35  DoubleLogisticSelectivity() : SelectivityBase<Type>() {}
+
21 struct DoubleLogisticSelectivity : public SelectivityBase<Type> {
+
22  Type median_asc;
+
25  Type slope_asc;
+
28  Type median_desc;
+
31  Type slope_desc;
+
35  DoubleLogisticSelectivity() : SelectivityBase<Type>() {}
36 
-
37  virtual ~DoubleLogisticSelectivity() {}
-
49  virtual const Type evaluate(const Type &x) {
-
50  return fims::double_logistic<Type>(median_asc, slope_asc, median_desc,
-
51  slope_desc, x);
+
37  virtual ~DoubleLogisticSelectivity() {}
+
49  virtual const Type evaluate(const Type &x) {
+
50  return fims_math::double_logistic<Type>(median_asc, slope_asc, median_desc,
+
51  slope_desc, x);
52  }
53 };
54 
55 } // namespace fims
56 
57 #endif /* POPULATION_DYNAMICS_SELECTIVITY_DOUBLE_LOGISTIC_HPP */
-
fims::DoubleLogisticSelectivity
DoubleLogisticSelectivity class that returns the double logistic function value from fims_math.
Definition: double_logistic.hpp:21
-
fims::DoubleLogisticSelectivity::evaluate
virtual const Type evaluate(const Type &x)
Method of the double logistic selectivity class that implements the double logistic function from FIM...
Definition: double_logistic.hpp:49
-
fims::DoubleLogisticSelectivity::slope_asc
Type slope_asc
Definition: double_logistic.hpp:25
-
fims::DoubleLogisticSelectivity::slope_desc
Type slope_desc
Definition: double_logistic.hpp:31
-
fims::DoubleLogisticSelectivity::median_desc
Type median_desc
Definition: double_logistic.hpp:28
-
fims::DoubleLogisticSelectivity::median_asc
Type median_asc
Definition: double_logistic.hpp:22
-
fims::SelectivityBase
Base class for all selectivity functors.
Definition: selectivity_base.hpp:27
+
fims_popdy::DoubleLogisticSelectivity
DoubleLogisticSelectivity class that returns the double logistic function value from fims_math.
Definition: double_logistic.hpp:21
+
fims_popdy::DoubleLogisticSelectivity::median_asc
Type median_asc
Definition: double_logistic.hpp:22
+
fims_popdy::DoubleLogisticSelectivity::median_desc
Type median_desc
Definition: double_logistic.hpp:28
+
fims_popdy::DoubleLogisticSelectivity::slope_asc
Type slope_asc
Definition: double_logistic.hpp:25
+
fims_popdy::DoubleLogisticSelectivity::slope_desc
Type slope_desc
Definition: double_logistic.hpp:31
+
fims_popdy::DoubleLogisticSelectivity::evaluate
virtual const Type evaluate(const Type &x)
Method of the double logistic selectivity class that implements the double logistic function from FIM...
Definition: double_logistic.hpp:49
+
fims_popdy::SelectivityBase
Base class for all selectivity functors.
Definition: selectivity_base.hpp:27
diff --git a/docs/ewaa_8hpp_source.html b/docs/ewaa_8hpp_source.html index f07adc4..9a3426b 100644 --- a/docs/ewaa_8hpp_source.html +++ b/docs/ewaa_8hpp_source.html @@ -92,31 +92,31 @@
14 
15 #include "growth_base.hpp"
16 
-
17 namespace fims {
+
17 namespace fims_popdy {
18 
22 template <typename Type>
-
23 struct EWAAgrowth : public GrowthBase<Type> {
+
23 struct EWAAgrowth : public GrowthBase<Type> {
24  // add submodule class members here
25  // these include parameters of the submodule
26  // a map looks up values based on a reference key
27  // in this case, our key is age (first double), and
28  // the value is the weight at that age (second double)
-
29  std::map<double, double> ewaa;
-
32  EWAAgrowth() : GrowthBase<Type>() {}
+
29  std::map<double, double> ewaa;
+
32  EWAAgrowth() : GrowthBase<Type>() {}
33 
-
34  virtual ~EWAAgrowth() {}
+
34  virtual ~EWAAgrowth() {}
35 
-
41  virtual const Type evaluate(const double& a) {
-
42  Type ret = ewaa[a];
+
41  virtual const Type evaluate(const double& a) {
+
42  Type ret = ewaa[a];
43  return ret;
44  }
45 };
46 } // namespace fims
47 #endif /* POPULATION_DYNAMICS_GROWTH_EWAA_HPP */
-
fims::EWAAgrowth
EWAAgrowth class that returns the EWAA function value.
Definition: ewaa.hpp:23
-
fims::EWAAgrowth::evaluate
virtual const Type evaluate(const double &a)
Returns the weight at age a (in kg) from the input vector.
Definition: ewaa.hpp:41
-
fims::EWAAgrowth::ewaa
std::map< double, double > ewaa
Definition: ewaa.hpp:29
-
fims::GrowthBase
Base class for all growth functors.
Definition: growth_base.hpp:27
+
fims_popdy::EWAAgrowth
EWAAgrowth class that returns the EWAA function value.
Definition: ewaa.hpp:23
+
fims_popdy::EWAAgrowth::ewaa
std::map< double, double > ewaa
Definition: ewaa.hpp:29
+
fims_popdy::EWAAgrowth::evaluate
virtual const Type evaluate(const double &a)
Returns the weight at age a (in kg) from the input vector.
Definition: ewaa.hpp:41
+
fims_popdy::GrowthBase
Base class for all growth functors.
Definition: growth_base.hpp:27
diff --git a/docs/fims__math_8hpp.html b/docs/fims__math_8hpp.html index b4af46c..06c6f9f 100644 --- a/docs/fims__math_8hpp.html +++ b/docs/fims__math_8hpp.html @@ -85,51 +85,51 @@ - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + +

Functions

template<class T >
const T fims::logistic (const T &median, const T &slope, const T &x)
 The general logistic function. More...
 
template<class T >
const T fims::logit (const T &a, const T &b, const T &x)
 A logit function for bounding of parameters. More...
 
template<class T >
const T fims::inv_logit (const T &a, const T &b, const T &logit_x)
 An inverse logit function for bounding of parameters. More...
 
template<class T >
const T fims::double_logistic (const T &median_asc, const T &slope_asc, const T &median_desc, const T &slope_desc, const T &x)
 The general double logistic function. More...
 
template<class T >
const T fims::ad_fabs (const T &x, T C=1e-5)
 
template<typename T >
const T fims::ad_min (const T &a, const T &b, T C=1e-5)
 
template<typename Type >
const Type fims::ad_max (const Type &a, const Type &b, Type C=1e-5)
 
template<class Type >
const Type fims_math::logistic (const Type &median, const Type &slope, const Type &x)
 The general logistic function. More...
 
template<class Type >
const Type fims_math::logit (const Type &a, const Type &b, const Type &x)
 A logit function for bounding of parameters. More...
 
template<class Type >
const Type fims_math::inv_logit (const Type &a, const Type &b, const Type &logit_x)
 An inverse logit function for bounding of parameters. More...
 
template<class Type >
const Type fims_math::double_logistic (const Type &median_asc, const Type &slope_asc, const Type &median_desc, const Type &slope_desc, const Type &x)
 The general double logistic function. More...
 
template<class Type >
const Type fims_math::ad_fabs (const Type &x, Type C=1e-5)
 
template<typename Type >
const Type fims_math::ad_min (const Type &a, const Type &b, Type C=1e-5)
 
template<typename Type >
const Type fims_math::ad_max (const Type &a, const Type &b, Type C=1e-5)
 

Function Documentation

- -

◆ ad_fabs()

+ +

◆ ad_fabs()

-template<class T >
+template<class Type >
- + - + - + @@ -153,8 +153,8 @@

-

◆ ad_max()

+ +

◆ ad_max()

@@ -165,7 +165,7 @@

const T fims::ad_fabs const Type fims_math::ad_fabs (const T & const Type &  x,
T Type  C = 1e-5 
- + @@ -195,7 +195,7 @@

Returns the maximum between a and b in a continuous manner using:

-

(a + b + fims::ad_fabs(a - b)) *.5; Reference: fims::ad_fabs() This is an approximation with minimal error.

+

(a + b + fims_math::ad_fabs(a - b)) *.5; Reference: fims_math::ad_fabs() This is an approximation with minimal error.

Parameters

const Type fims::ad_max const Type fims_math::ad_max ( const Type &  a,
@@ -208,33 +208,33 @@

-

◆ ad_min()

+ +

◆ ad_min()

-template<typename T >
+template<typename Type >

a
- + - + - + - + @@ -250,7 +250,7 @@

Returns the minimum between a and b in a continuous manner using:

-

(a + b - fims::ad_fabs(a - b))*.5; Reference: fims::ad_fabs()

+

(a + b - fims_math::ad_fabs(a - b))*.5; Reference: fims_math::ad_fabs()

This is an approximation with minimal error.

Parameters

const T fims::ad_min const Type fims_math::ad_min (const T & const Type &  a,
const T & const Type &  b,
T Type  C = 1e-5 
@@ -264,45 +264,45 @@

-

◆ double_logistic()

+ +

◆ double_logistic()

-template<class T >
+template<class Type >

- + - + - + - + - + - + @@ -334,33 +334,33 @@

-

◆ inv_logit()

+ +

◆ inv_logit()

-template<class T >
+template<class Type >

const T fims::double_logistic const Type fims_math::double_logistic (const T & const Type &  median_asc,
const T & const Type &  slope_asc,
const T & const Type &  median_desc,
const T & const Type &  slope_desc,
const T & const Type &  x 
- + - + - + - + @@ -389,33 +389,33 @@

-

◆ logistic()

+ +

◆ logistic()

-template<class T >
+template<class Type >

const T fims::inv_logit const Type fims_math::inv_logit (const T & const Type &  a,
const T & const Type &  b,
const T & const Type &  logit_x 
- + - + - + - + @@ -445,33 +445,33 @@

-

◆ logit()

+ +

◆ logit()

-template<class T >
+template<class Type >

const T fims::logistic const Type fims_math::logistic (const T & const Type &  median,
const T & const Type &  slope,
const T & const Type &  x 
- + - + - + - + diff --git a/docs/fims__math_8hpp_source.html b/docs/fims__math_8hpp_source.html index 11ba25f..168fbe3 100644 --- a/docs/fims__math_8hpp_source.html +++ b/docs/fims__math_8hpp_source.html @@ -98,15 +98,15 @@
21 
22 #include "../interface/interface.hpp"
23 
-
24 namespace fims {
+
24 namespace fims_math {
25 #ifdef STD_LIB
-
33 template <class T>
-
34 inline const T exp(const T &x) {
+
33 template <class Type>
+
34 inline const Type exp(const Type &x) {
35  return std::exp(x);
36 }
37 
-
44 template <class T>
-
45 inline const T log(const T &x) {
+
44 template <class Type>
+
45 inline const Type log(const Type &x) {
46  return std::log(x);
47 }
48 #endif
@@ -114,8 +114,8 @@
50 #ifdef TMB_MODEL
51 // #include <TMB.hpp>
52 
-
61 template <class T>
-
62 inline const T exp(const T &x) {
+
61 template <class Type>
+
62 inline const Type exp(const Type &x) {
63  using ::exp;
64  return exp(x);
65 }
@@ -125,8 +125,8 @@
69  return std::exp(x);
70 }
71 
-
80 template <class T>
-
81 inline const T log(const T &x) {
+
80 template <class Type>
+
81 inline const Type log(const Type &x) {
82  return log(x);
83 }
84 
@@ -137,54 +137,54 @@
89 
90 #endif
91 
-
102 template <class T>
-
103 inline const T logistic(const T &median, const T &slope, const T &x) {
+
102 template <class Type>
+
103 inline const Type logistic(const Type &median, const Type &slope, const Type &x) {
104  return (1.0) / (1.0 + exp(-1.0 * slope * (x - median)));
105 }
106 
-
117 template <class T>
-
118 inline const T logit(const T &a, const T &b, const T &x) {
-
119  return -fims::log(b - x) + fims::log(x - a);
+
117 template <class Type>
+
118 inline const Type logit(const Type &a, const Type &b, const Type &x) {
+
119  return -fims_math::log(b - x) + fims_math::log(x - a);
120 }
121 
-
132 template <class T>
-
133 inline const T inv_logit(const T &a, const T &b, const T &logit_x) {
-
134  return a + (b - a) / (1 + fims::exp(-logit_x));
+
132 template <class Type>
+
133 inline const Type inv_logit(const Type &a, const Type &b, const Type &logit_x) {
+
134  return a + (b - a) / (1 + fims_math::exp(-logit_x));
135 }
136 
-
156 template <class T>
-
157 inline const T double_logistic(const T &median_asc, const T &slope_asc,
-
158  const T &median_desc, const T &slope_desc,
-
159  const T &x) {
+
156 template <class Type>
+
157 inline const Type double_logistic(const Type &median_asc, const Type &slope_asc,
+
158  const Type &median_desc, const Type &slope_desc,
+
159  const Type &x) {
160  return (1.0) / (1.0 + exp(-1.0 * slope_asc * (x - median_asc))) *
161  (1.0 - (1.0) / (1.0 + exp(-1.0 * slope_desc * (x - median_desc))));
162 }
163 
-
177 template <class T>
-
178 const T ad_fabs(const T &x, T C = 1e-5) {
+
177 template <class Type>
+
178 const Type ad_fabs(const Type &x, Type C = 1e-5) {
179  return sqrt((x * x) + C); //, .5);
180 }
181 
-
196 template <typename T>
-
197 inline const T ad_min(const T &a, const T &b, T C = 1e-5) {
-
198  return (a + b - fims::ad_fabs(a - b, C)) * .5;
+
196 template <typename Type>
+
197 inline const Type ad_min(const Type &a, const Type &b, Type C = 1e-5) {
+
198  return (a + b - fims_math::ad_fabs(a - b, C)) * .5;
199 }
200 
213 template <typename Type>
-
214 inline const Type ad_max(const Type &a, const Type &b, Type C = 1e-5) {
-
215  return (a + b + fims::ad_fabs(a - b, C)) * static_cast<Type>(.5);
+
214 inline const Type ad_max(const Type &a, const Type &b, Type C = 1e-5) {
+
215  return (a + b + fims_math::ad_fabs(a - b, C)) * static_cast<Type>(.5);
216 }
217 
-
218 } // namespace fims
+
218 } // namespace fims_math
219 
220 #endif /* FIMS_MATH_HPP */
-
fims::logistic
const T logistic(const T &median, const T &slope, const T &x)
The general logistic function.
Definition: fims_math.hpp:103
-
fims::logit
const T logit(const T &a, const T &b, const T &x)
A logit function for bounding of parameters.
Definition: fims_math.hpp:118
-
fims::ad_max
const Type ad_max(const Type &a, const Type &b, Type C=1e-5)
Definition: fims_math.hpp:214
-
fims::ad_min
const T ad_min(const T &a, const T &b, T C=1e-5)
Definition: fims_math.hpp:197
-
fims::ad_fabs
const T ad_fabs(const T &x, T C=1e-5)
Definition: fims_math.hpp:178
-
fims::double_logistic
const T double_logistic(const T &median_asc, const T &slope_asc, const T &median_desc, const T &slope_desc, const T &x)
The general double logistic function.
Definition: fims_math.hpp:157
-
fims::inv_logit
const T inv_logit(const T &a, const T &b, const T &logit_x)
An inverse logit function for bounding of parameters.
Definition: fims_math.hpp:133
+
fims_math::logistic
const Type logistic(const Type &median, const Type &slope, const Type &x)
The general logistic function.
Definition: fims_math.hpp:103
+
fims_math::logit
const Type logit(const Type &a, const Type &b, const Type &x)
A logit function for bounding of parameters.
Definition: fims_math.hpp:118
+
fims_math::ad_min
const Type ad_min(const Type &a, const Type &b, Type C=1e-5)
Definition: fims_math.hpp:197
+
fims_math::ad_max
const Type ad_max(const Type &a, const Type &b, Type C=1e-5)
Definition: fims_math.hpp:214
+
fims_math::double_logistic
const Type double_logistic(const Type &median_asc, const Type &slope_asc, const Type &median_desc, const Type &slope_desc, const Type &x)
The general double logistic function.
Definition: fims_math.hpp:157
+
fims_math::inv_logit
const Type inv_logit(const Type &a, const Type &b, const Type &logit_x)
An inverse logit function for bounding of parameters.
Definition: fims_math.hpp:133
+
fims_math::ad_fabs
const Type ad_fabs(const Type &x, Type C=1e-5)
Definition: fims_math.hpp:178
diff --git a/docs/fleet_8hpp.html b/docs/fleet_8hpp.html index 1d544db..3b17203 100644 --- a/docs/fleet_8hpp.html +++ b/docs/fleet_8hpp.html @@ -87,8 +87,8 @@
const T fims::logit const Type fims_math::logit (const T & const Type &  a,
const T & const Type &  b,
const T & const Type &  x 
- - + +

Classes

struct  fims::Fleet< Type >
 Base class for all fleets. More...
struct  fims_popdy::Fleet< Type >
 Base class for all fleets. More...
 

Detailed Description

diff --git a/docs/fleet_8hpp_source.html b/docs/fleet_8hpp_source.html index 4e0fef2..1216556 100644 --- a/docs/fleet_8hpp_source.html +++ b/docs/fleet_8hpp_source.html @@ -85,136 +85,136 @@
15 #include "../../distributions/distributions.hpp"
16 #include "../selectivity/selectivity.hpp"
17 
-
18 namespace fims {
+
18 namespace fims_popdy {
19 
24 template <class Type>
-
25 struct Fleet : public FIMSObject<Type> {
-
26  static uint32_t id_g;
-
27  size_t nyears;
-
28  size_t nages;
-
29  using ParameterVector =
-
30  typename ModelTraits<Type>::ParameterVector;
+
25 struct Fleet : public fims_model_object::FIMSObject<Type> {
+
26  static uint32_t id_g;
+
27  size_t nyears;
+
28  size_t nages;
+
29  using ParameterVector =
+
30  typename fims::ModelTraits<Type>::ParameterVector;
33  // This likelihood index is not currently being used as only one likelihood
34  // distribution is available. These are for a future update M2+.
-
35  int fleet_index_likelihood_id_m =
+
35  int fleet_index_likelihood_id_m =
36  -999;
-
39  std::shared_ptr<fims::DistributionsBase<Type>>
-
40  index_likelihood;
+
39  std::shared_ptr<fims_distributions::DistributionsBase<Type>>
+
40  index_likelihood;
42  // This likelihood index is not currently being used as only one likelihood
43  // distribution is available. These are for a future update M2+.
-
44  int fleet_agecomp_likelihood_id_m =
+
44  int fleet_agecomp_likelihood_id_m =
45  -999;
-
46  std::shared_ptr<fims::DistributionsBase<Type>>
-
47  agecomp_likelihood;
+
46  std::shared_ptr<fims_distributions::DistributionsBase<Type>>
+
47  agecomp_likelihood;
49  // selectivity
-
50  int fleet_selectivity_id_m = -999;
-
51  std::shared_ptr<fims::SelectivityBase<Type>>
-
52  selectivity;
-
54  int fleet_observed_index_data_id_m = -999;
-
55  std::shared_ptr<fims::DataObject<Type>>
-
56  observed_index_data;
-
58  int fleet_observed_agecomp_data_id_m = -999;
-
59  std::shared_ptr<fims::DataObject<Type>>
-
60  observed_agecomp_data;
+
50  int fleet_selectivity_id_m = -999;
+
51  std::shared_ptr<SelectivityBase<Type>>
+
52  selectivity;
+
54  int fleet_observed_index_data_id_m = -999;
+
55  std::shared_ptr<fims_data_object::DataObject<Type>>
+
56  observed_index_data;
+
58  int fleet_observed_agecomp_data_id_m = -999;
+
59  std::shared_ptr<fims_data_object::DataObject<Type>>
+
60  observed_agecomp_data;
62  // Mortality and catchability
-
63  ParameterVector log_Fmort;
-
64  Type log_q;
-
66  Type log_obs_error;
-
68  ParameterVector Fmort;
-
69  Type q;
+
63  ParameterVector log_Fmort;
+
64  Type log_q;
+
66  Type log_obs_error;
+
68  ParameterVector Fmort;
+
69  Type q;
71  // derived quantities
-
72  std::vector<Type> catch_at_age;
-
73  std::vector<Type> catch_index;
-
74  std::vector<Type> age_composition;
+
72  std::vector<Type> catch_at_age;
+
73  std::vector<Type> catch_index;
+
74  std::vector<Type> age_composition;
76  // derived quantities
-
77  std::vector<Type> expected_catch;
-
78  std::vector<Type> expected_index;
-
79  std::vector<Type> catch_numbers_at_age;
-
80  std::vector<Type> catch_weight_at_age;
-
81  bool is_survey = false;
+
77  std::vector<Type> expected_catch;
+
78  std::vector<Type> expected_index;
+
79  std::vector<Type> catch_numbers_at_age;
+
80  std::vector<Type> catch_weight_at_age;
+
81  bool is_survey = false;
83 #ifdef TMB_MODEL
84  ::objective_function<Type> *of;
85 #endif
86 
-
90  Fleet() { this->id = Fleet::id_g++; }
+
90  Fleet() { this->id = Fleet::id_g++; }
91 
-
95  virtual ~Fleet() {}
+
95  virtual ~Fleet() {}
96 
-
102  void Initialize(int nyears, int nages) {
-
103  this->nyears = nyears;
-
104  this->nages = nages;
+
102  void Initialize(int nyears, int nages) {
+
103  this->nyears = nyears;
+
104  this->nages = nages;
105 
-
106  catch_at_age.resize(nyears * nages);
-
107  catch_weight_at_age.resize(nyears * nages);
-
108  catch_index.resize(nyears); // assume index is for all ages.
-
109  age_composition.resize(nyears * nages);
-
110  expected_catch.resize(nyears);
-
111  expected_index.resize(nyears); // assume index is for all ages.
-
112  catch_numbers_at_age.resize(nyears * nages);
+
106  catch_at_age.resize(nyears * nages);
+
107  catch_weight_at_age.resize(nyears * nages);
+
108  catch_index.resize(nyears); // assume index is for all ages.
+
109  age_composition.resize(nyears * nages);
+
110  expected_catch.resize(nyears);
+
111  expected_index.resize(nyears); // assume index is for all ages.
+
112  catch_numbers_at_age.resize(nyears * nages);
113 
-
114  log_Fmort.resize(nyears);
-
115  Fmort.resize(nyears);
+
114  log_Fmort.resize(nyears);
+
115  Fmort.resize(nyears);
116  }
117 
-
123  void Prepare() {
+
123  void Prepare() {
124  // for(size_t fleet_ = 0; fleet_ <= this->nfleets; fleet_++) {
-
125  // this -> Fmort[fleet_] = fims::exp(this -> log_Fmort[fleet_]);
+
125  // this -> Fmort[fleet_] = fims_math::exp(this -> log_Fmort[fleet_]);
126 
127  // derived quantities
-
128  std::fill(catch_at_age.begin(), catch_at_age.end(),
+
128  std::fill(catch_at_age.begin(), catch_at_age.end(),
129  0);
-
130  std::fill(catch_index.begin(), catch_index.end(),
+
130  std::fill(catch_index.begin(), catch_index.end(),
131  0);
-
132  std::fill(age_composition.begin(), age_composition.end(), 0);
-
133  std::fill(expected_catch.begin(), expected_catch.end(),
+
132  std::fill(age_composition.begin(), age_composition.end(), 0);
+
133  std::fill(expected_catch.begin(), expected_catch.end(),
134  0);
-
135  std::fill(expected_index.begin(), expected_index.end(),
+
135  std::fill(expected_index.begin(), expected_index.end(),
136  0);
-
137  std::fill(catch_numbers_at_age.begin(), catch_numbers_at_age.end(),
+
137  std::fill(catch_numbers_at_age.begin(), catch_numbers_at_age.end(),
138  0);
-
139  std::fill(catch_weight_at_age.begin(), catch_weight_at_age.end(),
+
139  std::fill(catch_weight_at_age.begin(), catch_weight_at_age.end(),
140  0);
-
141  this->q = fims::exp(this->log_q);
-
142  for (size_t year = 0; year < this->nyears; year++) {
+
141  this->q = fims_math::exp(this->log_q);
+
142  for (size_t year = 0; year < this->nyears; year++) {
143  FIMS_LOG << "input F mort " << this->log_Fmort[year] << std::endl;
144  FIMS_LOG << "input q " << this->log_q << std::endl;
-
145  this->Fmort[year] = fims::exp(this->log_Fmort[year]);
+
145  this->Fmort[year] = fims_math::exp(this->log_Fmort[year]);
146  }
147  }
148 
-
149  virtual const Type evaluate_age_comp_nll() {
+
149  virtual const Type evaluate_age_comp_nll() {
150  Type nll = 0.0;
151 #ifdef TMB_MODEL
-
152  fims::Dmultinom<Type> dmultinom;
-
153  size_t dims = this->observed_agecomp_data->get_imax() *
-
154  this->observed_agecomp_data->get_jmax();
+
152  fims_distributions::Dmultinom<Type> dmultinom;
+
153  size_t dims = this->observed_agecomp_data->get_imax() *
+
154  this->observed_agecomp_data->get_jmax();
155  if (dims != this->catch_numbers_at_age.size()) {
-
156  fims_log::get("fleet.log") << "Error: observed age comp is of size "
+
156  fims::fims_log::get("fleet.log") << "Error: observed age comp is of size "
157  << dims << " and expected is of size "
158  << this->age_composition.size() << std::endl;
159  } else {
-
160  for (size_t y = 0; y < this->nyears; y++) {
+
160  for (size_t y = 0; y < this->nyears; y++) {
161  // EigenVector declares a vector type from the Eigen library, which is
162  // the expected type for TMB's dmultinom
-
163  using Vector = typename ModelTraits<Type>::EigenVector;
+
163  using Vector = typename fims::ModelTraits<Type>::EigenVector;
164  Vector observed_acomp;
165  Vector expected_acomp;
166 
167  observed_acomp.resize(this->nages);
168  expected_acomp.resize(this->nages);
169  Type sum = 0.0;
-
170  for (size_t a = 0; a < this->nages; a++) {
+
170  for (size_t a = 0; a < this->nages; a++) {
171  size_t i_age_year = y * this->nages + a;
172  sum += this->catch_numbers_at_age[i_age_year];
173  }
174 
-
175  for (size_t a = 0; a < this->nages; a++) {
+
175  for (size_t a = 0; a < this->nages; a++) {
176  size_t i_age_year = y * this->nages + a;
177  expected_acomp[a] = this->catch_numbers_at_age[i_age_year] /
178  sum; // probabilities for ages
179 
-
180  observed_acomp[a] = this->observed_agecomp_data->at(y, a);
-
181  fims_log::get("fleet.log")
+
180  observed_acomp[a] = this->observed_agecomp_data->at(y, a);
+
181  fims::fims_log::get("fleet.log")
182  << " age " << a << " in year " << y
183  << "has expected: " << expected_acomp[a]
184  << " and observed: " << observed_acomp[a] << std::endl;
@@ -229,23 +229,23 @@
193  return nll;
194  }
195 
-
196  virtual const Type evaluate_index_nll() {
+
196  virtual const Type evaluate_index_nll() {
197  Type nll = 0.0;
199 #ifdef TMB_MODEL
-
200  fims::Dnorm<Type> dnorm;
-
201  dnorm.sd = fims::exp(this->log_obs_error);
+
200  fims_distributions::Dnorm<Type> dnorm;
+
201  dnorm.sd = fims_math::exp(this->log_obs_error);
202  for (size_t i = 0; i < this->expected_index.size(); i++) {
-
203  dnorm.x = fims::log(this->observed_index_data->at(i));
-
204  dnorm.mean = fims::log(this->expected_index[i]);
+
203  dnorm.x = fims_math::log(this->observed_index_data->at(i));
+
204  dnorm.mean = fims_math::log(this->expected_index[i]);
205  nll -= dnorm.evaluate(true);
-
206  fims_log::get("fleet.log")
+
206  fims::fims_log::get("fleet.log")
207  << "observed likelihood component: " << i << " is "
-
208  << this->observed_index_data->at(i)
+
208  << this->observed_index_data->at(i)
209  << " and expected is: " << this->expected_index[i] << std::endl;
210  }
-
211  fims_log::get("fleet.log")
+
211  fims::fims_log::get("fleet.log")
212  << " log obs error is: " << this->log_obs_error << std::endl;
-
213  fims_log::get("fleet.log") << " sd is: " << dnorm.sd << std::endl;
+
213  fims::fims_log::get("fleet.log") << " sd is: " << dnorm.sd << std::endl;
214 #endif
215  return nll;
216  }
@@ -253,48 +253,48 @@
218 
219 // default id of the singleton fleet class
220 template <class Type>
-
221 uint32_t Fleet<Type>::id_g = 0;
+
221 uint32_t Fleet<Type>::id_g = 0;
222 
-
223 } // end namespace fims
+
223 } // end namespace fims_popdy
224 
225 #endif /* FIMS_POPULATION_DYNAMICS_FLEET_HPP */
fims::fims_log::get
static std::ofstream & get(const std::string &l)
Definition: def.hpp:41
FIMS_LOG
std::ofstream FIMS_LOG("fims.log")
-
fims::FIMSObject
FIMSObject struct that defines member types and returns the unique id.
Definition: model_object.hpp:25
-
fims::Fleet
Base class for all fleets.
Definition: fleet.hpp:25
-
fims::Fleet::is_survey
bool is_survey
Definition: fleet.hpp:81
-
fims::Fleet::~Fleet
virtual ~Fleet()
Destructor.
Definition: fleet.hpp:95
-
fims::Fleet::fleet_index_likelihood_id_m
int fleet_index_likelihood_id_m
Definition: fleet.hpp:35
-
fims::Fleet::expected_index
std::vector< Type > expected_index
Definition: fleet.hpp:78
-
fims::Fleet::catch_numbers_at_age
std::vector< Type > catch_numbers_at_age
Definition: fleet.hpp:79
-
fims::Fleet::observed_agecomp_data
std::shared_ptr< fims::DataObject< Type > > observed_agecomp_data
Definition: fleet.hpp:60
-
fims::Fleet::log_Fmort
ParameterVector log_Fmort
Definition: fleet.hpp:63
-
fims::Fleet::catch_weight_at_age
std::vector< Type > catch_weight_at_age
Definition: fleet.hpp:80
-
fims::Fleet::log_obs_error
Type log_obs_error
Definition: fleet.hpp:66
-
fims::Fleet::catch_at_age
std::vector< Type > catch_at_age
Definition: fleet.hpp:72
-
fims::Fleet::expected_catch
std::vector< Type > expected_catch
Definition: fleet.hpp:77
-
fims::Fleet::Fmort
ParameterVector Fmort
Definition: fleet.hpp:68
-
fims::Fleet::fleet_selectivity_id_m
int fleet_selectivity_id_m
Definition: fleet.hpp:50
-
fims::Fleet::Fleet
Fleet()
Constructor.
Definition: fleet.hpp:90
-
fims::Fleet::catch_index
std::vector< Type > catch_index
Definition: fleet.hpp:73
-
fims::Fleet::age_composition
std::vector< Type > age_composition
Definition: fleet.hpp:74
-
fims::Fleet::agecomp_likelihood
std::shared_ptr< fims::DistributionsBase< Type > > agecomp_likelihood
Definition: fleet.hpp:47
-
fims::Fleet::nages
size_t nages
Definition: fleet.hpp:28
-
fims::Fleet::fleet_agecomp_likelihood_id_m
int fleet_agecomp_likelihood_id_m
Definition: fleet.hpp:44
-
fims::Fleet::q
Type q
Definition: fleet.hpp:69
-
fims::Fleet::log_q
Type log_q
Definition: fleet.hpp:64
-
fims::Fleet::nyears
size_t nyears
Definition: fleet.hpp:27
-
fims::Fleet::observed_index_data
std::shared_ptr< fims::DataObject< Type > > observed_index_data
Definition: fleet.hpp:56
-
fims::Fleet::index_likelihood
std::shared_ptr< fims::DistributionsBase< Type > > index_likelihood
Definition: fleet.hpp:40
-
fims::Fleet::fleet_observed_index_data_id_m
int fleet_observed_index_data_id_m
Definition: fleet.hpp:54
-
fims::Fleet::Initialize
void Initialize(int nyears, int nages)
Intialize Fleet Class.
Definition: fleet.hpp:102
-
fims::Fleet::evaluate_index_nll
virtual const Type evaluate_index_nll()
Definition: fleet.hpp:196
-
fims::Fleet::fleet_observed_agecomp_data_id_m
int fleet_observed_agecomp_data_id_m
Definition: fleet.hpp:58
-
fims::Fleet::selectivity
std::shared_ptr< fims::SelectivityBase< Type > > selectivity
Definition: fleet.hpp:52
-
fims::Fleet::Prepare
void Prepare()
Prepare to run the fleet module. Called at each model itartion, and used to exponentiate the log q an...
Definition: fleet.hpp:123
-
fims::Fleet::id_g
static uint32_t id_g
Definition: fleet.hpp:26
-
fims::Fleet::ParameterVector
typename ModelTraits< Type >::ParameterVector ParameterVector
Definition: fleet.hpp:31
-
fims::Fleet::evaluate_age_comp_nll
virtual const Type evaluate_age_comp_nll()
Definition: fleet.hpp:149
+
fims_model_object::FIMSObject
FIMSObject struct that defines member types and returns the unique id.
Definition: model_object.hpp:25
+
fims_popdy::Fleet
Base class for all fleets.
Definition: fleet.hpp:25
+
fims_popdy::Fleet::is_survey
bool is_survey
Definition: fleet.hpp:81
+
fims_popdy::Fleet::log_Fmort
ParameterVector log_Fmort
Definition: fleet.hpp:63
+
fims_popdy::Fleet::catch_index
std::vector< Type > catch_index
Definition: fleet.hpp:73
+
fims_popdy::Fleet::log_obs_error
Type log_obs_error
Definition: fleet.hpp:66
+
fims_popdy::Fleet::Fleet
Fleet()
Constructor.
Definition: fleet.hpp:90
+
fims_popdy::Fleet::selectivity
std::shared_ptr< SelectivityBase< Type > > selectivity
Definition: fleet.hpp:52
+
fims_popdy::Fleet::id_g
static uint32_t id_g
Definition: fleet.hpp:26
+
fims_popdy::Fleet::nages
size_t nages
Definition: fleet.hpp:28
+
fims_popdy::Fleet::catch_numbers_at_age
std::vector< Type > catch_numbers_at_age
Definition: fleet.hpp:79
+
fims_popdy::Fleet::evaluate_index_nll
virtual const Type evaluate_index_nll()
Definition: fleet.hpp:196
+
fims_popdy::Fleet::fleet_selectivity_id_m
int fleet_selectivity_id_m
Definition: fleet.hpp:50
+
fims_popdy::Fleet::q
Type q
Definition: fleet.hpp:69
+
fims_popdy::Fleet::catch_at_age
std::vector< Type > catch_at_age
Definition: fleet.hpp:72
+
fims_popdy::Fleet::observed_agecomp_data
std::shared_ptr< fims_data_object::DataObject< Type > > observed_agecomp_data
Definition: fleet.hpp:60
+
fims_popdy::Fleet::expected_catch
std::vector< Type > expected_catch
Definition: fleet.hpp:77
+
fims_popdy::Fleet::log_q
Type log_q
Definition: fleet.hpp:64
+
fims_popdy::Fleet::fleet_observed_agecomp_data_id_m
int fleet_observed_agecomp_data_id_m
Definition: fleet.hpp:58
+
fims_popdy::Fleet::observed_index_data
std::shared_ptr< fims_data_object::DataObject< Type > > observed_index_data
Definition: fleet.hpp:56
+
fims_popdy::Fleet::index_likelihood
std::shared_ptr< fims_distributions::DistributionsBase< Type > > index_likelihood
Definition: fleet.hpp:40
+
fims_popdy::Fleet::evaluate_age_comp_nll
virtual const Type evaluate_age_comp_nll()
Definition: fleet.hpp:149
+
fims_popdy::Fleet::expected_index
std::vector< Type > expected_index
Definition: fleet.hpp:78
+
fims_popdy::Fleet::fleet_index_likelihood_id_m
int fleet_index_likelihood_id_m
Definition: fleet.hpp:35
+
fims_popdy::Fleet::Prepare
void Prepare()
Prepare to run the fleet module. Called at each model itartion, and used to exponentiate the log q an...
Definition: fleet.hpp:123
+
fims_popdy::Fleet::~Fleet
virtual ~Fleet()
Destructor.
Definition: fleet.hpp:95
+
fims_popdy::Fleet::catch_weight_at_age
std::vector< Type > catch_weight_at_age
Definition: fleet.hpp:80
+
fims_popdy::Fleet::Initialize
void Initialize(int nyears, int nages)
Intialize Fleet Class.
Definition: fleet.hpp:102
+
fims_popdy::Fleet::agecomp_likelihood
std::shared_ptr< fims_distributions::DistributionsBase< Type > > agecomp_likelihood
Definition: fleet.hpp:47
+
fims_popdy::Fleet::age_composition
std::vector< Type > age_composition
Definition: fleet.hpp:74
+
fims_popdy::Fleet::ParameterVector
typename fims::ModelTraits< Type >::ParameterVector ParameterVector
Definition: fleet.hpp:31
+
fims_popdy::Fleet::nyears
size_t nyears
Definition: fleet.hpp:27
+
fims_popdy::Fleet::Fmort
ParameterVector Fmort
Definition: fleet.hpp:68
+
fims_popdy::Fleet::fleet_observed_index_data_id_m
int fleet_observed_index_data_id_m
Definition: fleet.hpp:54
+
fims_popdy::Fleet::fleet_agecomp_likelihood_id_m
int fleet_agecomp_likelihood_id_m
Definition: fleet.hpp:44
diff --git a/docs/functions.html b/docs/functions.html index 43f2751..56d116b 100644 --- a/docs/functions.html +++ b/docs/functions.html @@ -79,24 +79,24 @@

- a -

diff --git a/docs/functions_b.html b/docs/functions_b.html index 9916d23..ad01a06 100644 --- a/docs/functions_b.html +++ b/docs/functions_b.html @@ -72,7 +72,7 @@

- b -

diff --git a/docs/functions_c.html b/docs/functions_c.html index 04a514d..727776b 100644 --- a/docs/functions_c.html +++ b/docs/functions_c.html @@ -72,67 +72,67 @@

- c -

diff --git a/docs/functions_d.html b/docs/functions_d.html index 5823542..30bd53a 100644 --- a/docs/functions_d.html +++ b/docs/functions_d.html @@ -72,34 +72,34 @@

- d -

diff --git a/docs/functions_e.html b/docs/functions_e.html index 2719e9b..c4c5767 100644 --- a/docs/functions_e.html +++ b/docs/functions_e.html @@ -87,7 +87,7 @@

- e -

    : FleetInterface
  • estimate_recruit_deviations -: fims::RecruitmentBase< Type > +: fims_popdy::RecruitmentBase< Type >
  • estimated_m : Parameter @@ -100,22 +100,26 @@

    - e -

      , DnormDistributionsInterface , DoubleLogisticSelectivityInterface , EWAAGrowthInterface -, fims::DistributionsBase< Type > -, fims::DoubleLogisticSelectivity< Type > -, fims::EWAAgrowth< Type > -, fims::GrowthBase< Type > -, fims::LogisticMaturity< Type > -, fims::LogisticSelectivity< Type > -, fims::MaturityBase< Type > +, fims_distributions::DistributionsBase< Type >
    • Evaluate() -: fims::Model< Type > -, fims::Population< Type > +: fims_model::Model< Type >
    • evaluate() -: fims::RecruitmentBase< Type > -, fims::SelectivityBase< Type > -, fims::SRBevertonHolt< Type > +: fims_popdy::DoubleLogisticSelectivity< Type > +, fims_popdy::EWAAgrowth< Type > +, fims_popdy::GrowthBase< Type > +, fims_popdy::LogisticMaturity< Type > +, fims_popdy::LogisticSelectivity< Type > +, fims_popdy::MaturityBase< Type > +
      • +
    • Evaluate() +: fims_popdy::Population< Type > +
      • +
    • evaluate() +: fims_popdy::RecruitmentBase< Type > +, fims_popdy::SelectivityBase< Type > +, fims_popdy::SRBevertonHolt< Type > , GrowthInterfaceBase , LogisticMaturityInterface , LogisticSelectivityInterface @@ -125,33 +129,33 @@

      - e -

      diff --git a/docs/functions_f.html b/docs/functions_f.html index 4a9ecca..d7ed0d7 100644 --- a/docs/functions_f.html +++ b/docs/functions_f.html @@ -72,8 +72,8 @@

      - f -

      • fims_information -: fims::Information< T > -, fims::Model< Type > +: fims_info::Information< Type > +, fims_model::Model< Type >
      • fims_interface_objects : FIMSRcppInterfaceBase @@ -82,42 +82,42 @@

        - f -

        diff --git a/docs/functions_func.html b/docs/functions_func.html index 044bad6..e456b4c 100644 --- a/docs/functions_func.html +++ b/docs/functions_func.html @@ -79,59 +79,59 @@

        - a -

        - c -

        @@ -141,10 +141,10 @@

        - d -

        @@ -158,22 +158,26 @@

        - e -

          , DnormDistributionsInterface , DoubleLogisticSelectivityInterface , EWAAGrowthInterface -, fims::DistributionsBase< Type > -, fims::DoubleLogisticSelectivity< Type > -, fims::EWAAgrowth< Type > -, fims::GrowthBase< Type > -, fims::LogisticMaturity< Type > -, fims::LogisticSelectivity< Type > -, fims::MaturityBase< Type > +, fims_distributions::DistributionsBase< Type >
        • Evaluate() -: fims::Model< Type > -, fims::Population< Type > +: fims_model::Model< Type >
        • evaluate() -: fims::RecruitmentBase< Type > -, fims::SelectivityBase< Type > -, fims::SRBevertonHolt< Type > +: fims_popdy::DoubleLogisticSelectivity< Type > +, fims_popdy::EWAAgrowth< Type > +, fims_popdy::GrowthBase< Type > +, fims_popdy::LogisticMaturity< Type > +, fims_popdy::LogisticSelectivity< Type > +, fims_popdy::MaturityBase< Type > +
          • +
        • Evaluate() +: fims_popdy::Population< Type > +
          • +
        • evaluate() +: fims_popdy::RecruitmentBase< Type > +, fims_popdy::SelectivityBase< Type > +, fims_popdy::SRBevertonHolt< Type > , GrowthInterfaceBase , LogisticMaturityInterface , LogisticSelectivityInterface @@ -183,14 +187,14 @@

          - e -

            , SelectivityInterfaceBase
          • evaluate_age_comp_nll() -: fims::Fleet< Type > +: fims_popdy::Fleet< Type >
          • evaluate_index_nll() -: fims::Fleet< Type > +: fims_popdy::Fleet< Type >
          • evaluate_nll() : BevertonHoltRecruitmentInterface -, fims::RecruitmentBase< Type > +, fims_popdy::RecruitmentBase< Type > , NLLInterfaceBase , RecruitmentInterfaceBase
            • @@ -199,7 +203,7 @@

            - e -

              - f -

              @@ -209,7 +213,7 @@

              - g -

                : fims::fims_log
              • get_dimensions() -: fims::DataObject< Type > +: fims_data_object::DataObject< Type >
              • get_id() : AgeCompDataInterface @@ -235,16 +239,16 @@

                - g -

                  , SelectivityInterfaceBase
                • get_imax() -: fims::DataObject< Type > +: fims_data_object::DataObject< Type >
                • get_jmax() -: fims::DataObject< Type > +: fims_data_object::DataObject< Type >
                • get_kmax() -: fims::DataObject< Type > +: fims_data_object::DataObject< Type >
                • get_lmax() -: fims::DataObject< Type > +: fims_data_object::DataObject< Type >
                • GetArray() : JsonValue @@ -256,35 +260,35 @@

                  - g -

                    : JsonValue
                  • GetFixedEffectsParameters() -: fims::Information< T > +: fims_info::Information< Type >
                  • GetId() -: fims::FIMSObject< T > +: fims_model_object::FIMSObject< Type >
                  • GetInstance() -: fims::Information< T > -, fims::Model< Type > +: fims_info::Information< Type > +, fims_model::Model< Type >
                  • GetInt() : JsonValue
                  • GetNages() -: fims::Information< T > +: fims_info::Information< Type >
                  • GetNseasons() -: fims::Information< T > +: fims_info::Information< Type >
                  • GetNyears() -: fims::Information< T > +: fims_info::Information< Type >
                  • GetObject() : JsonValue
                  • GetParameters() -: fims::Information< T > +: fims_info::Information< Type >
                  • GetRandomEffectsParameters() -: fims::Information< T > +: fims_info::Information< Type >
                  • GetString() : JsonValue @@ -293,7 +297,7 @@

                    - g -

                    @@ -303,8 +307,8 @@

                    - i -

                    @@ -321,14 +325,14 @@

                    - m -

                    - o -

                    @@ -341,35 +345,35 @@

                    - p -

                    - r -

                    - s -

                    • SelectivityBase() -: fims::SelectivityBase< Type > +: fims_popdy::SelectivityBase< Type >
                    • SetAgeCompLikelihood() : FleetInterface @@ -384,13 +388,13 @@

                      - s -

                        : PopulationInterface
                      • SetNages() -: fims::Information< T > +: fims_info::Information< Type >
                      • SetNseasons() -: fims::Information< T > +: fims_info::Information< Type >
                      • SetNyears() -: fims::Information< T > +: fims_info::Information< Type >
                      • SetObservedAgeCompData() : FleetInterface @@ -425,7 +429,7 @@

                        - ~ -

                          : DataInterfaceBase
                        • ~Fleet() -: fims::Fleet< Type > +: fims_popdy::Fleet< Type >
                        • ~IndexDataInterface() : IndexDataInterface diff --git a/docs/functions_g.html b/docs/functions_g.html index 230384d..8528b44 100644 --- a/docs/functions_g.html +++ b/docs/functions_g.html @@ -75,7 +75,7 @@

                          - g -

                            : fims::fims_log
                          • get_dimensions() -: fims::DataObject< Type > +: fims_data_object::DataObject< Type >
                          • get_id() : AgeCompDataInterface @@ -101,16 +101,16 @@

                            - g -

                              , SelectivityInterfaceBase
                            • get_imax() -: fims::DataObject< Type > +: fims_data_object::DataObject< Type >
                            • get_jmax() -: fims::DataObject< Type > +: fims_data_object::DataObject< Type >
                            • get_kmax() -: fims::DataObject< Type > +: fims_data_object::DataObject< Type >
                            • get_lmax() -: fims::DataObject< Type > +: fims_data_object::DataObject< Type >
                            • GetArray() : JsonValue @@ -122,35 +122,35 @@

                              - g -

                                : JsonValue
                              • GetFixedEffectsParameters() -: fims::Information< T > +: fims_info::Information< Type >
                              • GetId() -: fims::FIMSObject< T > +: fims_model_object::FIMSObject< Type >
                              • GetInstance() -: fims::Information< T > -, fims::Model< Type > +: fims_info::Information< Type > +, fims_model::Model< Type >
                              • GetInt() : JsonValue
                              • GetNages() -: fims::Information< T > +: fims_info::Information< Type >
                              • GetNseasons() -: fims::Information< T > +: fims_info::Information< Type >
                              • GetNyears() -: fims::Information< T > +: fims_info::Information< Type >
                              • GetObject() : JsonValue
                              • GetParameters() -: fims::Information< T > +: fims_info::Information< Type >
                              • GetRandomEffectsParameters() -: fims::Information< T > +: fims_info::Information< Type >
                              • GetString() : JsonValue @@ -159,20 +159,20 @@

                                - g -

                                diff --git a/docs/functions_i.html b/docs/functions_i.html index aa0d117..b9cfda0 100644 --- a/docs/functions_i.html +++ b/docs/functions_i.html @@ -74,7 +74,7 @@

                                - i -

                                • id : DataInterfaceBase , DistributionsInterfaceBase -, fims::FIMSObject< T > +, fims_model_object::FIMSObject< Type > , FleetInterfaceBase , GrowthInterfaceBase , MaturityInterfaceBase @@ -86,14 +86,14 @@

                                  - i -

                                  • id_g : DataInterfaceBase , DistributionsInterfaceBase -, fims::DataObject< Type > -, fims::DistributionsBase< Type > -, fims::Fleet< Type > -, fims::GrowthBase< Type > -, fims::MaturityBase< Type > -, fims::Population< Type > -, fims::RecruitmentBase< Type > -, fims::SelectivityBase< Type > +, fims_data_object::DataObject< Type > +, fims_distributions::DistributionsBase< Type > +, fims_popdy::Fleet< Type > +, fims_popdy::GrowthBase< Type > +, fims_popdy::MaturityBase< Type > +, fims_popdy::Population< Type > +, fims_popdy::RecruitmentBase< Type > +, fims_popdy::SelectivityBase< Type > , FleetInterfaceBase , GrowthInterfaceBase , MaturityInterfaceBase @@ -103,20 +103,20 @@

                                    - i -

                                      , SelectivityInterfaceBase
                                    • imax -: fims::DataObject< Type > +: fims_data_object::DataObject< Type >
                                    • index_data : IndexDataInterface
                                    • index_likelihood -: fims::Fleet< Type > +: fims_popdy::Fleet< Type >
                                    • IndexDataInterface() : IndexDataInterface
                                    • Initialize() -: fims::Fleet< Type > -, fims::Population< Type > +: fims_popdy::Fleet< Type > +, fims_popdy::Population< Type >
                                    • initialized : EWAAGrowthInterface @@ -125,7 +125,7 @@

                                      - i -

                                      diff --git a/docs/functions_j.html b/docs/functions_j.html index 6dc8ae8..42203a4 100644 --- a/docs/functions_j.html +++ b/docs/functions_j.html @@ -72,7 +72,7 @@

                                      - j -

                                      • jmax -: fims::DataObject< Type > +: fims_data_object::DataObject< Type >
                                      • JsonValue() : JsonValue diff --git a/docs/functions_k.html b/docs/functions_k.html index 386905d..8e2d877 100644 --- a/docs/functions_k.html +++ b/docs/functions_k.html @@ -72,7 +72,7 @@

                                        - k -

                                        diff --git a/docs/functions_l.html b/docs/functions_l.html index 622e31e..9070623 100644 --- a/docs/functions_l.html +++ b/docs/functions_l.html @@ -83,39 +83,39 @@

                                        - l -

                                        diff --git a/docs/functions_m.html b/docs/functions_m.html index d8612da..3616e11 100644 --- a/docs/functions_m.html +++ b/docs/functions_m.html @@ -72,26 +72,26 @@

                                        - m -

                                        • M -: fims::Population< Type > +: fims_popdy::Population< Type >
                                        • make_map() : EWAAGrowthInterface
                                        • maturity -: fims::Population< Type > +: fims_popdy::Population< Type >
                                        • maturity_id -: fims::Population< Type > +: fims_popdy::Population< Type > , PopulationInterface
                                        • maturity_models -: fims::Information< T > +: fims_info::Information< Type >
                                        • maturity_models_iterator -: fims::Information< T > +: fims_info::Information< Type >
                                        • MaturityBase() -: fims::MaturityBase< Type > +: fims_popdy::MaturityBase< Type >
                                        • max_m : Parameter @@ -103,27 +103,27 @@

                                          - m -

                                          diff --git a/docs/functions_n.html b/docs/functions_n.html index 7ed45ad..5dbd57f 100644 --- a/docs/functions_n.html +++ b/docs/functions_n.html @@ -72,28 +72,28 @@

                                          - n -

                                          • nages -: fims::Fleet< Type > -, fims::Information< T > -, fims::Population< Type > +: fims_info::Information< Type > +, fims_popdy::Fleet< Type > +, fims_popdy::Population< Type > , FleetInterface , PopulationInterface
                                          • nfleets -: fims::Population< Type > +: fims_popdy::Population< Type > , PopulationInterface
                                          • nseasons -: fims::Information< T > -, fims::Population< Type > +: fims_info::Information< Type > +, fims_popdy::Population< Type > , PopulationInterface
                                          • numbers_at_age -: fims::Population< Type > +: fims_popdy::Population< Type >
                                          • nyears -: fims::Fleet< Type > -, fims::Information< T > -, fims::Population< Type > +: fims_info::Information< Type > +, fims_popdy::Fleet< Type > +, fims_popdy::Population< Type > , FleetInterface , PopulationInterface
                                            • diff --git a/docs/functions_o.html b/docs/functions_o.html index db6c0b8..f047e74 100644 --- a/docs/functions_o.html +++ b/docs/functions_o.html @@ -72,16 +72,16 @@

                                            - o -

                                            diff --git a/docs/functions_p.html b/docs/functions_p.html index 66f5536..789ee78 100644 --- a/docs/functions_p.html +++ b/docs/functions_p.html @@ -78,38 +78,38 @@

                                            - p -

                                            diff --git a/docs/functions_q.html b/docs/functions_q.html index 8aeb365..516e8d2 100644 --- a/docs/functions_q.html +++ b/docs/functions_q.html @@ -72,7 +72,7 @@

                                            - q -

                                            diff --git a/docs/functions_r.html b/docs/functions_r.html index c95fd01..596f963 100644 --- a/docs/functions_r.html +++ b/docs/functions_r.html @@ -72,8 +72,8 @@

                                            - r -

                                            • random_effects_parameters -: fims::FIMSObject< T > -, fims::Information< T > +: fims_info::Information< Type > +, fims_model_object::FIMSObject< Type >
                                            • random_F : FleetInterface @@ -82,32 +82,32 @@

                                              - r -

                                              diff --git a/docs/functions_s.html b/docs/functions_s.html index a43df32..e5a7b74 100644 --- a/docs/functions_s.html +++ b/docs/functions_s.html @@ -78,16 +78,16 @@

                                              - s -

                                                : DlnormDistributionsInterface
                                              • selectivity -: fims::Fleet< Type > +: fims_popdy::Fleet< Type >
                                              • selectivity_models -: fims::Information< T > +: fims_info::Information< Type >
                                              • selectivity_models_iterator -: fims::Information< T > +: fims_info::Information< Type >
                                              • SelectivityBase() -: fims::SelectivityBase< Type > +: fims_popdy::SelectivityBase< Type >
                                              • SetAgeCompLikelihood() : FleetInterface @@ -102,13 +102,13 @@

                                                - s -

                                                  : PopulationInterface
                                                • SetNages() -: fims::Information< T > +: fims_info::Information< Type >
                                                • SetNseasons() -: fims::Information< T > +: fims_info::Information< Type >
                                                • SetNyears() -: fims::Information< T > +: fims_info::Information< Type >
                                                • SetObservedAgeCompData() : FleetInterface @@ -126,21 +126,21 @@

                                                  - s -

                                                  diff --git a/docs/functions_type.html b/docs/functions_type.html index 517efc9..020b5ef 100644 --- a/docs/functions_type.html +++ b/docs/functions_type.html @@ -70,32 +70,32 @@
                                                   
                                                  diff --git a/docs/functions_u.html b/docs/functions_u.html index 4123519..d375cec 100644 --- a/docs/functions_u.html +++ b/docs/functions_u.html @@ -72,13 +72,13 @@

                                                  - u -

                                                  diff --git a/docs/functions_vars.html b/docs/functions_vars.html index 9813033..d56cf8d 100644 --- a/docs/functions_vars.html +++ b/docs/functions_vars.html @@ -75,14 +75,14 @@

                                                  - a -

                                                    : AgeCompDataInterface
                                                  • age_composition -: fims::Fleet< Type > +: fims_popdy::Fleet< Type >
                                                  • agecomp_likelihood -: fims::Fleet< Type > +: fims_popdy::Fleet< Type >
                                                  • ages : EWAAGrowthInterface -, fims::Population< Type > +, fims_popdy::Population< Type > , PopulationInterface
                                                  • amax @@ -93,45 +93,45 @@

                                                    - a -

                                                      - b -

                                                      - c -

                                                      - d -

                                                      @@ -153,35 +153,35 @@

                                                      - e -

                                                      - f -

                                                      • fims_information -: fims::Information< T > -, fims::Model< Type > +: fims_info::Information< Type > +, fims_model::Model< Type >
                                                      • fims_interface_objects : FIMSRcppInterfaceBase @@ -190,50 +190,50 @@

                                                        - f -

                                                        - g -

                                                        @@ -242,7 +242,7 @@

                                                        - i -

                                                        • id : DataInterfaceBase , DistributionsInterfaceBase -, fims::FIMSObject< T > +, fims_model_object::FIMSObject< Type > , FleetInterfaceBase , GrowthInterfaceBase , MaturityInterfaceBase @@ -254,14 +254,14 @@

                                                          - i -

                                                          • id_g : DataInterfaceBase , DistributionsInterfaceBase -, fims::DataObject< Type > -, fims::DistributionsBase< Type > -, fims::Fleet< Type > -, fims::GrowthBase< Type > -, fims::MaturityBase< Type > -, fims::Population< Type > -, fims::RecruitmentBase< Type > -, fims::SelectivityBase< Type > +, fims_data_object::DataObject< Type > +, fims_distributions::DistributionsBase< Type > +, fims_popdy::Fleet< Type > +, fims_popdy::GrowthBase< Type > +, fims_popdy::MaturityBase< Type > +, fims_popdy::Population< Type > +, fims_popdy::RecruitmentBase< Type > +, fims_popdy::SelectivityBase< Type > , FleetInterfaceBase , GrowthInterfaceBase , MaturityInterfaceBase @@ -271,13 +271,13 @@

                                                            - i -

                                                              , SelectivityInterfaceBase
                                                            • imax -: fims::DataObject< Type > +: fims_data_object::DataObject< Type >
                                                            • index_data : IndexDataInterface
                                                            • index_likelihood -: fims::Fleet< Type > +: fims_popdy::Fleet< Type >
                                                            • initialized : EWAAGrowthInterface @@ -286,7 +286,7 @@

                                                              - i -

                                                              @@ -294,14 +294,14 @@

                                                              - i -

                                                                - j -

                                                                - k -

                                                                @@ -319,56 +319,56 @@

                                                                - l -

                                                                - m -

                                                                • M -: fims::Population< Type > +: fims_popdy::Population< Type >
                                                                • maturity -: fims::Population< Type > +: fims_popdy::Population< Type >
                                                                • maturity_id -: fims::Population< Type > +: fims_popdy::Population< Type > , PopulationInterface
                                                                • maturity_models -: fims::Information< T > +: fims_info::Information< Type >
                                                                • max_m : Parameter @@ -380,55 +380,55 @@

                                                                  - m -

                                                                  - n -

                                                                  • nages -: fims::Fleet< Type > -, fims::Information< T > -, fims::Population< Type > +: fims_info::Information< Type > +, fims_popdy::Fleet< Type > +, fims_popdy::Population< Type > , FleetInterface , PopulationInterface
                                                                  • nfleets -: fims::Population< Type > +: fims_popdy::Population< Type > , PopulationInterface
                                                                  • nseasons -: fims::Information< T > -, fims::Population< Type > +: fims_info::Information< Type > +, fims_popdy::Population< Type > , PopulationInterface
                                                                  • numbers_at_age -: fims::Population< Type > +: fims_popdy::Population< Type >
                                                                  • nyears -: fims::Fleet< Type > -, fims::Information< T > -, fims::Population< Type > +: fims_info::Information< Type > +, fims_popdy::Fleet< Type > +, fims_popdy::Population< Type > , FleetInterface , PopulationInterface
                                                                    • @@ -437,13 +437,13 @@

                                                                    - n -

                                                                      - o -

                                                                      @@ -453,35 +453,35 @@

                                                                      - p -

                                                                      - q -

                                                                      - r -

                                                                      • random_effects_parameters -: fims::FIMSObject< T > -, fims::Information< T > +: fims_info::Information< Type > +, fims_model_object::FIMSObject< Type >
                                                                      • random_F : FleetInterface @@ -490,17 +490,17 @@

                                                                        - r -

                                                                        @@ -513,40 +513,40 @@

                                                                        - s -

                                                                        - u -

                                                                        @@ -560,7 +560,7 @@

                                                                        - v -

                                                                          - w -

                                                                          • weight_at_age -: fims::Population< Type > +: fims_popdy::Population< Type >
                                                                          • weights : EWAAGrowthInterface @@ -579,7 +579,7 @@

                                                                            - x -

                                                                              - y -

                                                                              • years -: fims::Population< Type > +: fims_popdy::Population< Type >
                                                                              • ymax : AgeCompDataInterface diff --git a/docs/functions_w.html b/docs/functions_w.html index 49f9464..4df7c7c 100644 --- a/docs/functions_w.html +++ b/docs/functions_w.html @@ -72,7 +72,7 @@

                                                                                - w -

                                                                                • weight_at_age -: fims::Population< Type > +: fims_popdy::Population< Type >
                                                                                • weights : EWAAGrowthInterface diff --git a/docs/functions_y.html b/docs/functions_y.html index 8930cea..994f59a 100644 --- a/docs/functions_y.html +++ b/docs/functions_y.html @@ -72,7 +72,7 @@

                                                                                  - y -

                                                                                  • years -: fims::Population< Type > +: fims_popdy::Population< Type >
                                                                                  • ymax : AgeCompDataInterface diff --git a/docs/functions_~.html b/docs/functions_~.html index 111a85f..3be2f99 100644 --- a/docs/functions_~.html +++ b/docs/functions_~.html @@ -78,7 +78,7 @@

                                                                                    - ~ -

                                                                                      : DataInterfaceBase
                                                                                    • ~Fleet() -: fims::Fleet< Type > +: fims_popdy::Fleet< Type >
                                                                                    • ~IndexDataInterface() : IndexDataInterface diff --git a/docs/growth__base_8hpp_source.html b/docs/growth__base_8hpp_source.html index a370ed8..ec97fe0 100644 --- a/docs/growth__base_8hpp_source.html +++ b/docs/growth__base_8hpp_source.html @@ -94,33 +94,33 @@
                                                                                      16 
                                                                                      17 #include "../../../common/model_object.hpp"
                                                                                      18 
                                                                                      -
                                                                                      19 namespace fims {
                                                                                      +
                                                                                      19 namespace fims_popdy {
                                                                                      20 
                                                                                      26 template <typename Type>
                                                                                      -
                                                                                      27 struct GrowthBase : public FIMSObject<Type> {
                                                                                      +
                                                                                      27 struct GrowthBase : public fims_model_object::FIMSObject<Type> {
                                                                                      28  // id_g is the ID of the instance of the growthBase class.
                                                                                      29  // this is like a memory tracker.
                                                                                      30  // Assigning each one its own ID is a way to keep track of
                                                                                      31  // all the instances of the growthBase class.
                                                                                      -
                                                                                      32  static uint32_t id_g;
                                                                                      -
                                                                                      37  GrowthBase() { this->id = GrowthBase::id_g++; }
                                                                                      +
                                                                                      32  static uint32_t id_g;
                                                                                      +
                                                                                      37  GrowthBase() { this->id = GrowthBase::id_g++; }
                                                                                      38 
                                                                                      -
                                                                                      39  virtual ~GrowthBase() {}
                                                                                      +
                                                                                      39  virtual ~GrowthBase() {}
                                                                                      40 
                                                                                      -
                                                                                      45  virtual const Type evaluate(const double& a) = 0;
                                                                                      +
                                                                                      45  virtual const Type evaluate(const double& a) = 0;
                                                                                      46 };
                                                                                      47 
                                                                                      48 template <typename Type>
                                                                                      -
                                                                                      49 uint32_t GrowthBase<Type>::id_g = 0;
                                                                                      +
                                                                                      49 uint32_t GrowthBase<Type>::id_g = 0;
                                                                                      50 
                                                                                      51 } // namespace fims
                                                                                      52 
                                                                                      53 #endif /* POPULATION_DYNAMICS_GROWTH_BASE_HPP */
                                                                                      -
                                                                                      fims::FIMSObject
                                                                                      FIMSObject struct that defines member types and returns the unique id.
                                                                                      Definition: model_object.hpp:25
                                                                                      -
                                                                                      fims::GrowthBase
                                                                                      Base class for all growth functors.
                                                                                      Definition: growth_base.hpp:27
                                                                                      -
                                                                                      fims::GrowthBase::GrowthBase
                                                                                      GrowthBase()
                                                                                      Constructor.
                                                                                      Definition: growth_base.hpp:37
                                                                                      -
                                                                                      fims::GrowthBase::id_g
                                                                                      static uint32_t id_g
                                                                                      Definition: growth_base.hpp:32
                                                                                      -
                                                                                      fims::GrowthBase::evaluate
                                                                                      virtual const Type evaluate(const double &a)=0
                                                                                      Calculates the growth at the independent variable value.
                                                                                      +
                                                                                      fims_model_object::FIMSObject
                                                                                      FIMSObject struct that defines member types and returns the unique id.
                                                                                      Definition: model_object.hpp:25
                                                                                      +
                                                                                      fims_popdy::GrowthBase
                                                                                      Base class for all growth functors.
                                                                                      Definition: growth_base.hpp:27
                                                                                      +
                                                                                      fims_popdy::GrowthBase::id_g
                                                                                      static uint32_t id_g
                                                                                      Definition: growth_base.hpp:32
                                                                                      +
                                                                                      fims_popdy::GrowthBase::GrowthBase
                                                                                      GrowthBase()
                                                                                      Constructor.
                                                                                      Definition: growth_base.hpp:37
                                                                                      +
                                                                                      fims_popdy::GrowthBase::evaluate
                                                                                      virtual const Type evaluate(const double &a)=0
                                                                                      Calculates the growth at the independent variable value.
                                                                                      diff --git a/docs/hierarchy.html b/docs/hierarchy.html index cf01cfb..3ae1490 100644 --- a/docs/hierarchy.html +++ b/docs/hierarchy.html @@ -75,49 +75,48 @@
                                                                                      This inheritance list is sorted roughly, but not completely, alphabetically:
                                                                                      [detail level 123]
                                                                                      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                       Cfims::fims_log
                                                                                       Cfims::FIMSObject< T >FIMSObject struct that defines member types and returns the unique id
                                                                                       ▼Cfims::FIMSObject< Type >
                                                                                       Cfims::DataObject< Type >
                                                                                       Cfims::DistributionsBase< Type >Base class for all module_name functors
                                                                                       Cfims::Fleet< Type >Base class for all fleets
                                                                                       ▼Cfims::GrowthBase< Type >Base class for all growth functors
                                                                                       Cfims::EWAAgrowth< Type >EWAAgrowth class that returns the EWAA function value
                                                                                       ▼Cfims::MaturityBase< Type >Base class for all maturity functors
                                                                                       Cfims::LogisticMaturity< Type >LogisticMaturity class that returns the logistic function value from fims_math
                                                                                       Cfims::Population< Type >Population class. Contains subpopulations that are divided into generic partitions (eg. sex, area)
                                                                                       ▼Cfims::RecruitmentBase< Type >Base class for all recruitment functors
                                                                                       Cfims::SRBevertonHolt< Type >BevertonHolt class that returns the Beverton Holt SR from fims_math
                                                                                       ▼Cfims::SelectivityBase< Type >Base class for all selectivity functors
                                                                                       Cfims::DoubleLogisticSelectivity< Type >DoubleLogisticSelectivity class that returns the double logistic function value from fims_math
                                                                                       Cfims::LogisticSelectivity< Type >LogisticSelectivity class that returns the logistic function value from fims_math
                                                                                       ▼CFIMSRcppInterfaceBaseBase class for all interface objects
                                                                                       ▼CDataInterfaceBaseRcpp interface for Data as an S4 object. To instantiate from R: fleet <- new(fims$Data)
                                                                                       CAgeCompDataInterfaceRcpp interface for age comp data as an S4 object. To instantiate from R: acomp <- new(fims$AgeComp)
                                                                                       CIndexDataInterfaceRcpp interface for data as an S4 object. To instantiate from R: fleet <- new(fims$Index)
                                                                                       ▼CDistributionsInterfaceBaseDistributions Rcpp Interface
                                                                                       CDlnormDistributionsInterfaceRcpp interface for Dlnorm as an S4 object. To instantiate from R: dlnorm_ <- new(fims$TMBDlnormDistribution)
                                                                                       CDmultinomDistributionsInterfaceRcpp interface for Dmultinom as an S4 object. To instantiate from R: dmultinom_ <- new(fims$TMBDmultinomDistribution)
                                                                                       CDnormDistributionsInterfaceRcpp interface for Dnorm as an S4 object. To instantiate from R: dnorm_ <- new(fims$TMBDnormDistribution)
                                                                                       ▼CFleetInterfaceBaseRcpp interface that serves as the parent class for Rcpp fleet interfaces. This type should be inherited and not called from R directly
                                                                                       CFleetInterfaceRcpp interface for Fleet as an S4 object. To instantiate from R: fleet <- new(fims$Fleet)
                                                                                       ▼CGrowthInterfaceBaseRcpp interface that serves as the parent class for Rcpp growth interfaces. This type should be inherited and not called from R directly
                                                                                       CEWAAGrowthInterfaceRcpp interface for EWAAgrowth as an S4 object. To instantiate from R: ewaa <- new(fims$EWAAgrowth)
                                                                                       ▼CMaturityInterfaceBaseMaturityInterfaceBase class should be inherited to define different Rcpp interfaces for each possible maturity function
                                                                                       CLogisticMaturityInterfaceRcpp interface for logistic maturity as an S4 object. To instantiate from R: logistic_maturity <- new(fims$logistic_maturity)
                                                                                       CNLLInterfaceBaseNLLInterfaceBase class should be inherited to define different Rcpp interfaces for each possible negative log-likelihood function
                                                                                       ▼CPopulationInterfaceBasePopulationInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Population function
                                                                                       CPopulationInterfaceRcpp interface for a new Population. To instantiate from R: population <- new(fims$population)
                                                                                       ▼CRecruitmentInterfaceBaseRecruitmentInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Recruitment function
                                                                                       CBevertonHoltRecruitmentInterfaceRcpp interface for Beverton-Holt as an S4 object. To instantiate from R: beverton_holt <- new(fims$beverton_holt)
                                                                                       ▼CSelectivityInterfaceBaseSelectivityInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Selectivity function
                                                                                       CDoubleLogisticSelectivityInterfaceRcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity <- new(fims$logistic_selectivity)
                                                                                       CLogisticSelectivityInterfaceRcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity <- new(fims$logistic_selectivity)
                                                                                       Cfims::Information< T >Stores FIMS model information and creates model. Contains all objects and data pre-model construction
                                                                                       CJsonParserParses JSON strings and generates JSON values
                                                                                       CJsonValueRepresents a JSON value
                                                                                       Cfims::Model< Type >Model class. FIMS objective function
                                                                                       CParameterRcppInterface class that defines the interface between R and C++ for parameter types
                                                                                       Cfims::Subpopulation< T >
                                                                                       ▼Cfims_model_object::FIMSObject< Type >FIMSObject struct that defines member types and returns the unique id
                                                                                       Cfims_data_object::DataObject< Type >
                                                                                       Cfims_distributions::DistributionsBase< Type >Base class for all module_name functors
                                                                                       Cfims_popdy::Fleet< Type >Base class for all fleets
                                                                                       ▼Cfims_popdy::GrowthBase< Type >Base class for all growth functors
                                                                                       Cfims_popdy::EWAAgrowth< Type >EWAAgrowth class that returns the EWAA function value
                                                                                       ▼Cfims_popdy::MaturityBase< Type >Base class for all maturity functors
                                                                                       Cfims_popdy::LogisticMaturity< Type >LogisticMaturity class that returns the logistic function value from fims_math
                                                                                       Cfims_popdy::Population< Type >Population class. Contains subpopulations that are divided into generic partitions (eg. sex, area)
                                                                                       ▼Cfims_popdy::RecruitmentBase< Type >Base class for all recruitment functors
                                                                                       Cfims_popdy::SRBevertonHolt< Type >BevertonHolt class that returns the Beverton Holt SR from fims_math
                                                                                       ▼Cfims_popdy::SelectivityBase< Type >Base class for all selectivity functors
                                                                                       Cfims_popdy::DoubleLogisticSelectivity< Type >DoubleLogisticSelectivity class that returns the double logistic function value from fims_math
                                                                                       Cfims_popdy::LogisticSelectivity< Type >LogisticSelectivity class that returns the logistic function value from fims_math
                                                                                       ▼CFIMSRcppInterfaceBaseBase class for all interface objects
                                                                                       ▼CDataInterfaceBaseRcpp interface for Data as an S4 object. To instantiate from R: fleet <- new(fims$Data)
                                                                                       CAgeCompDataInterfaceRcpp interface for age comp data as an S4 object. To instantiate from R: acomp <- new(fims$AgeComp)
                                                                                       CIndexDataInterfaceRcpp interface for data as an S4 object. To instantiate from R: fleet <- new(fims$Index)
                                                                                       ▼CDistributionsInterfaceBaseDistributions Rcpp Interface
                                                                                       CDlnormDistributionsInterfaceRcpp interface for Dlnorm as an S4 object. To instantiate from R: dlnorm_ <- new(fims$TMBDlnormDistribution)
                                                                                       CDmultinomDistributionsInterfaceRcpp interface for Dmultinom as an S4 object. To instantiate from R: dmultinom_ <- new(fims$TMBDmultinomDistribution)
                                                                                       CDnormDistributionsInterfaceRcpp interface for Dnorm as an S4 object. To instantiate from R: dnorm_ <- new(fims$TMBDnormDistribution)
                                                                                       ▼CFleetInterfaceBaseRcpp interface that serves as the parent class for Rcpp fleet interfaces. This type should be inherited and not called from R directly
                                                                                       CFleetInterfaceRcpp interface for Fleet as an S4 object. To instantiate from R: fleet <- new(fims$Fleet)
                                                                                       ▼CGrowthInterfaceBaseRcpp interface that serves as the parent class for Rcpp growth interfaces. This type should be inherited and not called from R directly
                                                                                       CEWAAGrowthInterfaceRcpp interface for EWAAgrowth as an S4 object. To instantiate from R: ewaa <- new(fims$EWAAgrowth)
                                                                                       ▼CMaturityInterfaceBaseMaturityInterfaceBase class should be inherited to define different Rcpp interfaces for each possible maturity function
                                                                                       CLogisticMaturityInterfaceRcpp interface for logistic maturity as an S4 object. To instantiate from R: logistic_maturity <- new(fims$logistic_maturity)
                                                                                       CNLLInterfaceBaseNLLInterfaceBase class should be inherited to define different Rcpp interfaces for each possible negative log-likelihood function
                                                                                       ▼CPopulationInterfaceBasePopulationInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Population function
                                                                                       CPopulationInterfaceRcpp interface for a new Population. To instantiate from R: population <- new(fims$population)
                                                                                       ▼CRecruitmentInterfaceBaseRecruitmentInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Recruitment function
                                                                                       CBevertonHoltRecruitmentInterfaceRcpp interface for Beverton-Holt as an S4 object. To instantiate from R: beverton_holt <- new(fims$beverton_holt)
                                                                                       ▼CSelectivityInterfaceBaseSelectivityInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Selectivity function
                                                                                       CDoubleLogisticSelectivityInterfaceRcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity <- new(fims$logistic_selectivity)
                                                                                       CLogisticSelectivityInterfaceRcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity <- new(fims$logistic_selectivity)
                                                                                       Cfims_info::Information< Type >Stores FIMS model information and creates model. Contains all objects and data pre-model construction
                                                                                       CJsonParserParses JSON strings and generates JSON values
                                                                                       CJsonValueRepresents a JSON value
                                                                                       Cfims_model::Model< Type >Model class. FIMS objective function
                                                                                       CParameterRcppInterface class that defines the interface between R and C++ for parameter types
                                                                                       Cfims_popdy::Subpopulation< Type >
                                                                                      diff --git a/docs/information_8hpp.html b/docs/information_8hpp.html index 9d0704c..51a9294 100644 --- a/docs/information_8hpp.html +++ b/docs/information_8hpp.html @@ -94,8 +94,8 @@ - - + +

                                                                                      Classes

                                                                                      class  fims::Information< T >
                                                                                       Stores FIMS model information and creates model. Contains all objects and data pre-model construction. More...
                                                                                      class  fims_info::Information< Type >
                                                                                       Stores FIMS model information and creates model. Contains all objects and data pre-model construction. More...
                                                                                       

                                                                                      Detailed Description

                                                                                      diff --git a/docs/information_8hpp_source.html b/docs/information_8hpp_source.html index 8fe53bc..9cb7502 100644 --- a/docs/information_8hpp_source.html +++ b/docs/information_8hpp_source.html @@ -93,102 +93,102 @@
                                                                                      22 #include "def.hpp"
                                                                                      23 #include "model_object.hpp"
                                                                                      24 
                                                                                      -
                                                                                      25 namespace fims {
                                                                                      +
                                                                                      25 namespace fims_info {
                                                                                      26 
                                                                                      -
                                                                                      31 template <typename T>
                                                                                      -
                                                                                      32 class Information {
                                                                                      +
                                                                                      31 template <typename Type>
                                                                                      +
                                                                                      32 class Information {
                                                                                      33  public:
                                                                                      -
                                                                                      34  size_t nyears;
                                                                                      -
                                                                                      35  size_t nseasons = 1;
                                                                                      -
                                                                                      36  size_t nages;
                                                                                      -
                                                                                      38  static std::shared_ptr<Information<T> >
                                                                                      -
                                                                                      39  fims_information;
                                                                                      -
                                                                                      40  std::vector<T*> parameters;
                                                                                      -
                                                                                      41  std::vector<T*>
                                                                                      -
                                                                                      42  random_effects_parameters;
                                                                                      -
                                                                                      43  std::vector<T*>
                                                                                      -
                                                                                      44  fixed_effects_parameters;
                                                                                      +
                                                                                      34  size_t nyears;
                                                                                      +
                                                                                      35  size_t nseasons = 1;
                                                                                      +
                                                                                      36  size_t nages;
                                                                                      +
                                                                                      38  static std::shared_ptr<Information<Type> >
                                                                                      +
                                                                                      39  fims_information;
                                                                                      +
                                                                                      40  std::vector<Type*> parameters;
                                                                                      +
                                                                                      41  std::vector<Type*>
                                                                                      +
                                                                                      42  random_effects_parameters;
                                                                                      +
                                                                                      43  std::vector<Type*>
                                                                                      +
                                                                                      44  fixed_effects_parameters;
                                                                                      46  // data objects
                                                                                      -
                                                                                      47  std::map<uint32_t, std::shared_ptr<fims::DataObject<T> > >
                                                                                      -
                                                                                      48  data_objects;
                                                                                      +
                                                                                      47  std::map<uint32_t, std::shared_ptr<fims_data_object::DataObject<Type> > >
                                                                                      +
                                                                                      48  data_objects;
                                                                                      49  typedef typename std::map<uint32_t,
                                                                                      -
                                                                                      50  std::shared_ptr<fims::DataObject<T> > >::iterator
                                                                                      -
                                                                                      51  data_iterator;
                                                                                      +
                                                                                      50  std::shared_ptr<fims_data_object::DataObject<Type> > >::iterator
                                                                                      +
                                                                                      51  data_iterator;
                                                                                      53  // life history modules
                                                                                      -
                                                                                      54  std::map<uint32_t, std::shared_ptr<fims::RecruitmentBase<T> > >
                                                                                      -
                                                                                      55  recruitment_models;
                                                                                      +
                                                                                      54  std::map<uint32_t, std::shared_ptr<fims_popdy::RecruitmentBase<Type> > >
                                                                                      +
                                                                                      55  recruitment_models;
                                                                                      57  typedef
                                                                                      58  typename std::map<uint32_t,
                                                                                      -
                                                                                      59  std::shared_ptr<fims::RecruitmentBase<T> > >::iterator
                                                                                      -
                                                                                      60  recruitment_models_iterator;
                                                                                      -
                                                                                      63  std::map<uint32_t, std::shared_ptr<fims::SelectivityBase<T> > >
                                                                                      -
                                                                                      64  selectivity_models;
                                                                                      +
                                                                                      59  std::shared_ptr<fims_popdy::RecruitmentBase<Type> > >::iterator
                                                                                      +
                                                                                      60  recruitment_models_iterator;
                                                                                      +
                                                                                      63  std::map<uint32_t, std::shared_ptr<fims_popdy::SelectivityBase<Type> > >
                                                                                      +
                                                                                      64  selectivity_models;
                                                                                      66  typedef
                                                                                      67  typename std::map<uint32_t,
                                                                                      -
                                                                                      68  std::shared_ptr<fims::SelectivityBase<T> > >::iterator
                                                                                      -
                                                                                      69  selectivity_models_iterator;
                                                                                      -
                                                                                      72  std::map<uint32_t, std::shared_ptr<fims::GrowthBase<T> > >
                                                                                      -
                                                                                      73  growth_models;
                                                                                      +
                                                                                      68  std::shared_ptr<fims_popdy::SelectivityBase<Type> > >::iterator
                                                                                      +
                                                                                      69  selectivity_models_iterator;
                                                                                      +
                                                                                      72  std::map<uint32_t, std::shared_ptr<fims_popdy::GrowthBase<Type> > >
                                                                                      +
                                                                                      73  growth_models;
                                                                                      75  typedef typename std::map<uint32_t,
                                                                                      -
                                                                                      76  std::shared_ptr<fims::GrowthBase<T> > >::iterator
                                                                                      -
                                                                                      77  growth_models_iterator;
                                                                                      -
                                                                                      80  std::map<uint32_t, std::shared_ptr<fims::MaturityBase<T> > >
                                                                                      -
                                                                                      81  maturity_models;
                                                                                      +
                                                                                      76  std::shared_ptr<fims_popdy::GrowthBase<Type> > >::iterator
                                                                                      +
                                                                                      77  growth_models_iterator;
                                                                                      +
                                                                                      80  std::map<uint32_t, std::shared_ptr<fims_popdy::MaturityBase<Type> > >
                                                                                      +
                                                                                      81  maturity_models;
                                                                                      83  typedef typename std::map<uint32_t,
                                                                                      -
                                                                                      84  std::shared_ptr<fims::MaturityBase<T> > >::iterator
                                                                                      -
                                                                                      85  maturity_models_iterator;
                                                                                      +
                                                                                      84  std::shared_ptr<fims_popdy::MaturityBase<Type> > >::iterator
                                                                                      +
                                                                                      85  maturity_models_iterator;
                                                                                      88  // fleet modules
                                                                                      -
                                                                                      89  std::map<uint32_t, std::shared_ptr<fims::Fleet<T> > >
                                                                                      -
                                                                                      90  fleets;
                                                                                      +
                                                                                      89  std::map<uint32_t, std::shared_ptr<fims_popdy::Fleet<Type> > >
                                                                                      +
                                                                                      90  fleets;
                                                                                      92  typedef
                                                                                      -
                                                                                      93  typename std::map<uint32_t, std::shared_ptr<fims::Fleet<T> > >::iterator
                                                                                      -
                                                                                      94  fleet_iterator;
                                                                                      +
                                                                                      93  typename std::map<uint32_t, std::shared_ptr<fims_popdy::Fleet<Type> > >::iterator
                                                                                      +
                                                                                      94  fleet_iterator;
                                                                                      97  // populations
                                                                                      -
                                                                                      98  std::map<uint32_t, std::shared_ptr<fims::Population<T> > >
                                                                                      -
                                                                                      99  populations;
                                                                                      +
                                                                                      98  std::map<uint32_t, std::shared_ptr<fims_popdy::Population<Type> > >
                                                                                      +
                                                                                      99  populations;
                                                                                      101  typedef typename std::map<uint32_t,
                                                                                      -
                                                                                      102  std::shared_ptr<fims::Population<T> > >::iterator
                                                                                      -
                                                                                      103  population_iterator;
                                                                                      +
                                                                                      102  std::shared_ptr<fims_popdy::Population<Type> > >::iterator
                                                                                      +
                                                                                      103  population_iterator;
                                                                                      106  // distributions
                                                                                      -
                                                                                      107  std::map<uint32_t, std::shared_ptr<fims::DistributionsBase<T> > >
                                                                                      -
                                                                                      108  distribution_models;
                                                                                      +
                                                                                      107  std::map<uint32_t, std::shared_ptr<fims_distributions::DistributionsBase<Type> > >
                                                                                      +
                                                                                      108  distribution_models;
                                                                                      110  typedef
                                                                                      111  typename std::map<uint32_t,
                                                                                      -
                                                                                      112  std::shared_ptr<fims::DistributionsBase<T> > >::iterator
                                                                                      -
                                                                                      113  distribution_models_iterator;
                                                                                      -
                                                                                      116  Information() {}
                                                                                      +
                                                                                      112  std::shared_ptr<fims_distributions::DistributionsBase<Type> > >::iterator
                                                                                      +
                                                                                      113  distribution_models_iterator;
                                                                                      +
                                                                                      116  Information() {}
                                                                                      117 
                                                                                      -
                                                                                      118  virtual ~Information() {}
                                                                                      +
                                                                                      118  virtual ~Information() {}
                                                                                      119 
                                                                                      -
                                                                                      125  static std::shared_ptr<Information<T> > GetInstance() {
                                                                                      -
                                                                                      126  if (Information<T>::fims_information == nullptr) {
                                                                                      -
                                                                                      127  Information<T>::fims_information =
                                                                                      -
                                                                                      128  std::make_shared<fims::Information<T> >();
                                                                                      +
                                                                                      125  static std::shared_ptr<Information<Type> > GetInstance() {
                                                                                      +
                                                                                      126  if (Information<Type>::fims_information == nullptr) {
                                                                                      +
                                                                                      127  Information<Type>::fims_information =
                                                                                      +
                                                                                      128  std::make_shared<fims_info::Information<Type> >();
                                                                                      129  }
                                                                                      -
                                                                                      130  return Information<T>::fims_information;
                                                                                      +
                                                                                      130  return Information<Type>::fims_information;
                                                                                      131  }
                                                                                      132 
                                                                                      -
                                                                                      138  void RegisterParameter(T& p) { this->fixed_effects_parameters.push_back(&p); }
                                                                                      +
                                                                                      138  void RegisterParameter(Type& p) { this->fixed_effects_parameters.push_back(&p); }
                                                                                      139 
                                                                                      -
                                                                                      145  void RegisterRandomEffect(T& re) {
                                                                                      -
                                                                                      146  this->random_effects_parameters.push_back(&re);
                                                                                      +
                                                                                      145  void RegisterRandomEffect(Type& re) {
                                                                                      +
                                                                                      146  this->random_effects_parameters.push_back(&re);
                                                                                      147  }
                                                                                      148 
                                                                                      -
                                                                                      157  bool CreateModel() {
                                                                                      +
                                                                                      157  bool CreateModel() {
                                                                                      158  bool valid_model = true;
                                                                                      159  FIMS_LOG
                                                                                      160  << "Beginning to create FIMS model in information.hpp CreateModel(). "
                                                                                      161  << std::endl;
                                                                                      -
                                                                                      162  FIMS_LOG << "Initializing fleet objects for " << this->fleets.size()
                                                                                      +
                                                                                      162  FIMS_LOG << "Initializing fleet objects for " << this->fleets.size()
                                                                                      163  << " fleets." << std::endl;
                                                                                      -
                                                                                      164  for (fleet_iterator it = this->fleets.begin(); it != this->fleets.end();
                                                                                      +
                                                                                      164  for (fleet_iterator it = this->fleets.begin(); it != this->fleets.end();
                                                                                      165  ++it) {
                                                                                      166  // Initialize fleet object
                                                                                      -
                                                                                      167  std::shared_ptr<fims::Fleet<T> > f = (*it).second;
                                                                                      +
                                                                                      167  std::shared_ptr<fims_popdy::Fleet<Type> > f = (*it).second;
                                                                                      168  FIMS_LOG << "Initializing fleet " << f->id << "." << std::endl;
                                                                                      169  f->Initialize(f->nyears, f->nages);
                                                                                      170 
                                                                                      -
                                                                                      171  FIMS_LOG << "Expecting to import " << this->data_objects.size()
                                                                                      +
                                                                                      171  FIMS_LOG << "Expecting to import " << this->data_objects.size()
                                                                                      172  << " data objects." << std::endl;
                                                                                      173 
                                                                                      174  FIMS_LOG << "Checking for available fleet index data objects."
                                                                                      @@ -197,11 +197,11 @@
                                                                                      177  if (f->fleet_observed_index_data_id_m != -999) {
                                                                                      178  uint32_t observed_index_id =
                                                                                      179  static_cast<uint32_t>(f->fleet_observed_index_data_id_m);
                                                                                      -
                                                                                      180  data_iterator it = this->data_objects.find(observed_index_id);
                                                                                      +
                                                                                      180  data_iterator it = this->data_objects.find(observed_index_id);
                                                                                      181  FIMS_LOG << "Input fleet index id = " << observed_index_id << "."
                                                                                      182  << std::endl;
                                                                                      183 
                                                                                      -
                                                                                      184  if (it != this->data_objects.end()) {
                                                                                      +
                                                                                      184  if (it != this->data_objects.end()) {
                                                                                      185  f->observed_index_data = (*it).second;
                                                                                      186  FIMS_LOG << "Index data successfully set." << std::endl;
                                                                                      187  FIMS_LOG << "Observed input index: \n " << f->observed_index_data
                                                                                      @@ -225,11 +225,11 @@
                                                                                      205  if (f->fleet_observed_agecomp_data_id_m != -999) {
                                                                                      206  uint32_t observed_agecomp_id =
                                                                                      207  static_cast<uint32_t>(f->fleet_observed_agecomp_data_id_m);
                                                                                      -
                                                                                      208  data_iterator it = this->data_objects.find(observed_agecomp_id);
                                                                                      +
                                                                                      208  data_iterator it = this->data_objects.find(observed_agecomp_id);
                                                                                      209  FIMS_LOG << "Input fleet age comp id = " << observed_agecomp_id << "."
                                                                                      210  << std::endl;
                                                                                      211 
                                                                                      -
                                                                                      212  if (it != this->data_objects.end()) {
                                                                                      +
                                                                                      212  if (it != this->data_objects.end()) {
                                                                                      213  f->observed_agecomp_data = (*it).second;
                                                                                      214  FIMS_LOG << "Age comp data successfully set." << std::endl;
                                                                                      215  FIMS_LOG << "Observed input age comp: \n " << f->observed_agecomp_data
                                                                                      @@ -254,12 +254,12 @@
                                                                                      234  if (f->fleet_selectivity_id_m != -999) {
                                                                                      235  uint32_t sel_id = static_cast<uint32_t>(
                                                                                      236  f->fleet_selectivity_id_m); // cast as unsigned integer
                                                                                      -
                                                                                      237  selectivity_models_iterator it = this->selectivity_models.find(
                                                                                      +
                                                                                      237  selectivity_models_iterator it = this->selectivity_models.find(
                                                                                      238  sel_id); // if find, set it, otherwise invalid
                                                                                      239  FIMS_LOG << "Input fleet selectivity pattern id = " << sel_id << "."
                                                                                      240  << std::endl;
                                                                                      241 
                                                                                      -
                                                                                      242  if (it != this->selectivity_models.end()) {
                                                                                      +
                                                                                      242  if (it != this->selectivity_models.end()) {
                                                                                      243  f->selectivity = (*it).second; // elements in container held in pair
                                                                                      244  // (first is id, second is object -
                                                                                      245  // shared pointer to distribution)
                                                                                      @@ -285,12 +285,12 @@
                                                                                      265  if (f->fleet_index_likelihood_id_m != -999) {
                                                                                      266  uint32_t ind_like_id = static_cast<uint32_t>(
                                                                                      267  f->fleet_index_likelihood_id_m); // cast as unsigned integer
                                                                                      -
                                                                                      268  distribution_models_iterator it = this->distribution_models.find(
                                                                                      +
                                                                                      268  distribution_models_iterator it = this->distribution_models.find(
                                                                                      269  ind_like_id); // if find, set it, otherwise invalid
                                                                                      270  FIMS_LOG << "Input index likelihood function id = " << ind_like_id
                                                                                      271  << "." << std::endl;
                                                                                      272 
                                                                                      -
                                                                                      273  if (it != this->distribution_models.end()) {
                                                                                      +
                                                                                      273  if (it != this->distribution_models.end()) {
                                                                                      274  f->index_likelihood =
                                                                                      275  (*it).second; // elements in container held in pair (first is
                                                                                      276  // id, second is object - shared pointer to
                                                                                      @@ -320,12 +320,12 @@
                                                                                      300  if (f->fleet_agecomp_likelihood_id_m != -999) {
                                                                                      301  uint32_t ac_like_id = static_cast<uint32_t>(
                                                                                      302  f->fleet_agecomp_likelihood_id_m); // cast as unsigned integer
                                                                                      -
                                                                                      303  distribution_models_iterator it = this->distribution_models.find(
                                                                                      +
                                                                                      303  distribution_models_iterator it = this->distribution_models.find(
                                                                                      304  ac_like_id); // if find, set it, otherwise invalid
                                                                                      305  FIMS_LOG << "Input age comp likelihood function id = " << ac_like_id
                                                                                      306  << "." << std::endl;
                                                                                      307 
                                                                                      -
                                                                                      308  if (it != this->distribution_models.end()) {
                                                                                      +
                                                                                      308  if (it != this->distribution_models.end()) {
                                                                                      309  f->agecomp_likelihood =
                                                                                      310  (*it).second; // elements in container held in pair (first is
                                                                                      311  // id, second is object - shared pointer to
                                                                                      @@ -357,19 +357,19 @@
                                                                                      337  FIMS_LOG << "Completed initialization of all fleets." << std::endl;
                                                                                      338 
                                                                                      339  FIMS_LOG << "Initializing population objects for "
                                                                                      -
                                                                                      340  << this->populations.size() << " populations." << std::endl;
                                                                                      -
                                                                                      341  for (population_iterator it = this->populations.begin();
                                                                                      -
                                                                                      342  it != this->populations.end(); ++it) {
                                                                                      -
                                                                                      343  std::shared_ptr<fims::Population<T> > p = (*it).second;
                                                                                      +
                                                                                      340  << this->populations.size() << " populations." << std::endl;
                                                                                      +
                                                                                      341  for (population_iterator it = this->populations.begin();
                                                                                      +
                                                                                      342  it != this->populations.end(); ++it) {
                                                                                      +
                                                                                      343  std::shared_ptr<fims_popdy::Population<Type> > p = (*it).second;
                                                                                      344 
                                                                                      345  FIMS_LOG << "Setting up links from population " << p->id
                                                                                      346  << " to fleets [ " << std::flush;
                                                                                      347  // error check and set population elements
                                                                                      348  // check me - add another fleet iterator to push information from
                                                                                      -
                                                                                      349  for (fleet_iterator it = this->fleets.begin(); it != this->fleets.end();
                                                                                      +
                                                                                      349  for (fleet_iterator it = this->fleets.begin(); it != this->fleets.end();
                                                                                      350  ++it) {
                                                                                      351  // Initialize fleet object
                                                                                      -
                                                                                      352  std::shared_ptr<fims::Fleet<T> > f = (*it).second;
                                                                                      +
                                                                                      352  std::shared_ptr<fims_popdy::Fleet<Type> > f = (*it).second;
                                                                                      353  // population to the individual fleets This is to pass catch at age
                                                                                      354  // from population to fleets?
                                                                                      355  // any shared member in p (population is pushed into fleets)
                                                                                      @@ -385,11 +385,11 @@
                                                                                      365  // set recruitment
                                                                                      366  if (p->recruitment_id != -999) {
                                                                                      367  uint32_t recruitment_uint = static_cast<uint32_t>(p->recruitment_id);
                                                                                      -
                                                                                      368  recruitment_models_iterator it =
                                                                                      -
                                                                                      369  this->recruitment_models.find(recruitment_uint);
                                                                                      +
                                                                                      368  recruitment_models_iterator it =
                                                                                      +
                                                                                      369  this->recruitment_models.find(recruitment_uint);
                                                                                      370  FIMS_LOG << "Input recruitment id = " << recruitment_uint << "."
                                                                                      371  << std::endl;
                                                                                      -
                                                                                      372  if (it != this->recruitment_models.end()) {
                                                                                      +
                                                                                      372  if (it != this->recruitment_models.end()) {
                                                                                      373  p->recruitment =
                                                                                      374  (*it).second; // recruitment defined in population.hpp
                                                                                      375  FIMS_LOG << "Recruitment function successfully set." << std::endl;
                                                                                      @@ -414,13 +414,13 @@
                                                                                      394  // set growth
                                                                                      395  if (p->growth_id != -999) {
                                                                                      396  uint32_t growth_uint = static_cast<uint32_t>(p->growth_id);
                                                                                      -
                                                                                      397  growth_models_iterator it = this->growth_models.find(
                                                                                      +
                                                                                      397  growth_models_iterator it = this->growth_models.find(
                                                                                      398  growth_uint); // growth_models is specified in information.hpp
                                                                                      399  // and used in rcpp
                                                                                      400  // at the head of information.hpp; are the
                                                                                      401  // dimensions of ages defined in rcpp or where?
                                                                                      402  FIMS_LOG << "Input growth id = " << growth_uint << "." << std::endl;
                                                                                      -
                                                                                      403  if (it != this->growth_models.end()) {
                                                                                      +
                                                                                      403  if (it != this->growth_models.end()) {
                                                                                      404  p->growth =
                                                                                      405  (*it).second; // growth defined in population.hpp (the object
                                                                                      406  // is called p, growth is within p)
                                                                                      @@ -444,11 +444,11 @@
                                                                                      424  // set maturity
                                                                                      425  if (p->maturity_id != -999) {
                                                                                      426  uint32_t maturity_uint = static_cast<uint32_t>(p->maturity_id);
                                                                                      -
                                                                                      427  maturity_models_iterator it = this->maturity_models.find(
                                                                                      +
                                                                                      427  maturity_models_iterator it = this->maturity_models.find(
                                                                                      428  maturity_uint); // >maturity_models is specified in
                                                                                      429  // information.hpp and used in rcpp
                                                                                      430  FIMS_LOG << "Input maturity id = " << maturity_uint << "." << std::endl;
                                                                                      -
                                                                                      431  if (it != this->maturity_models.end()) {
                                                                                      +
                                                                                      431  if (it != this->maturity_models.end()) {
                                                                                      432  p->maturity = (*it).second; // >maturity defined in population.hpp
                                                                                      433  FIMS_LOG << "Maturity function successfully set." << std::endl;
                                                                                      434  } else {
                                                                                      @@ -474,73 +474,73 @@
                                                                                      454  return valid_model;
                                                                                      455  }
                                                                                      456 
                                                                                      -
                                                                                      462  size_t GetNages() const { return nages; }
                                                                                      +
                                                                                      462  size_t GetNages() const { return nages; }
                                                                                      463 
                                                                                      -
                                                                                      469  void SetNages(size_t nages) { this->nages = nages; }
                                                                                      +
                                                                                      469  void SetNages(size_t nages) { this->nages = nages; }
                                                                                      470 
                                                                                      -
                                                                                      476  size_t GetNseasons() const { return nseasons; }
                                                                                      +
                                                                                      476  size_t GetNseasons() const { return nseasons; }
                                                                                      477 
                                                                                      -
                                                                                      483  void SetNseasons(size_t nseasons) { this->nseasons = nseasons; }
                                                                                      +
                                                                                      483  void SetNseasons(size_t nseasons) { this->nseasons = nseasons; }
                                                                                      484 
                                                                                      -
                                                                                      490  size_t GetNyears() const { return nyears; }
                                                                                      +
                                                                                      490  size_t GetNyears() const { return nyears; }
                                                                                      491 
                                                                                      -
                                                                                      497  void SetNyears(size_t nyears) { this->nyears = nyears; }
                                                                                      +
                                                                                      497  void SetNyears(size_t nyears) { this->nyears = nyears; }
                                                                                      498 
                                                                                      -
                                                                                      504  std::vector<T*>& GetParameters() { return parameters; }
                                                                                      +
                                                                                      504  std::vector<Type*>& GetParameters() { return parameters; }
                                                                                      505 
                                                                                      -
                                                                                      511  std::vector<T*>& GetFixedEffectsParameters() {
                                                                                      -
                                                                                      512  return fixed_effects_parameters;
                                                                                      +
                                                                                      511  std::vector<Type*>& GetFixedEffectsParameters() {
                                                                                      +
                                                                                      512  return fixed_effects_parameters;
                                                                                      513  }
                                                                                      514 
                                                                                      -
                                                                                      520  std::vector<T*>& GetRandomEffectsParameters() {
                                                                                      -
                                                                                      521  return random_effects_parameters;
                                                                                      +
                                                                                      520  std::vector<Type*>& GetRandomEffectsParameters() {
                                                                                      +
                                                                                      521  return random_effects_parameters;
                                                                                      522  }
                                                                                      523 };
                                                                                      524 
                                                                                      -
                                                                                      525 template <typename T>
                                                                                      -
                                                                                      526 std::shared_ptr<Information<T> > Information<T>::fims_information =
                                                                                      +
                                                                                      525 template <typename Type>
                                                                                      +
                                                                                      526 std::shared_ptr<Information<Type> > Information<Type>::fims_information =
                                                                                      527  nullptr; // singleton instance
                                                                                      528 
                                                                                      -
                                                                                      529 } // namespace fims
                                                                                      +
                                                                                      529 } // namespace fims_info
                                                                                      530 
                                                                                      531 #endif /* FIMS_COMMON_INFORMATION_HPP */
                                                                                      -
                                                                                      fims::Information
                                                                                      Stores FIMS model information and creates model. Contains all objects and data pre-model construction...
                                                                                      Definition: information.hpp:32
                                                                                      -
                                                                                      fims::Information::fleets
                                                                                      std::map< uint32_t, std::shared_ptr< fims::Fleet< T > > > fleets
                                                                                      Definition: information.hpp:90
                                                                                      -
                                                                                      fims::Information::selectivity_models
                                                                                      std::map< uint32_t, std::shared_ptr< fims::SelectivityBase< T > > > selectivity_models
                                                                                      Definition: information.hpp:64
                                                                                      -
                                                                                      fims::Information::maturity_models
                                                                                      std::map< uint32_t, std::shared_ptr< fims::MaturityBase< T > > > maturity_models
                                                                                      Definition: information.hpp:81
                                                                                      -
                                                                                      fims::Information::recruitment_models_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims::RecruitmentBase< T > > >::iterator recruitment_models_iterator
                                                                                      Definition: information.hpp:60
                                                                                      -
                                                                                      fims::Information::distribution_models
                                                                                      std::map< uint32_t, std::shared_ptr< fims::DistributionsBase< T > > > distribution_models
                                                                                      Definition: information.hpp:108
                                                                                      -
                                                                                      fims::Information::maturity_models_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims::MaturityBase< T > > >::iterator maturity_models_iterator
                                                                                      Definition: information.hpp:85
                                                                                      -
                                                                                      fims::Information::GetFixedEffectsParameters
                                                                                      std::vector< T * > & GetFixedEffectsParameters()
                                                                                      Get the Fixed Effects Parameters object.
                                                                                      Definition: information.hpp:511
                                                                                      -
                                                                                      fims::Information::data_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims::DataObject< T > > >::iterator data_iterator
                                                                                      Definition: information.hpp:51
                                                                                      -
                                                                                      fims::Information::growth_models
                                                                                      std::map< uint32_t, std::shared_ptr< fims::GrowthBase< T > > > growth_models
                                                                                      Definition: information.hpp:73
                                                                                      -
                                                                                      fims::Information::GetParameters
                                                                                      std::vector< T * > & GetParameters()
                                                                                      Get the Parameters object.
                                                                                      Definition: information.hpp:504
                                                                                      -
                                                                                      fims::Information::RegisterRandomEffect
                                                                                      void RegisterRandomEffect(T &re)
                                                                                      Definition: information.hpp:145
                                                                                      -
                                                                                      fims::Information::nages
                                                                                      size_t nages
                                                                                      Definition: information.hpp:36
                                                                                      -
                                                                                      fims::Information::growth_models_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims::GrowthBase< T > > >::iterator growth_models_iterator
                                                                                      Definition: information.hpp:77
                                                                                      -
                                                                                      fims::Information::fixed_effects_parameters
                                                                                      std::vector< T * > fixed_effects_parameters
                                                                                      Definition: information.hpp:44
                                                                                      -
                                                                                      fims::Information::SetNages
                                                                                      void SetNages(size_t nages)
                                                                                      Set the Nages object.
                                                                                      Definition: information.hpp:469
                                                                                      -
                                                                                      fims::Information::GetNyears
                                                                                      size_t GetNyears() const
                                                                                      Get the Nyears object.
                                                                                      Definition: information.hpp:490
                                                                                      -
                                                                                      fims::Information::nyears
                                                                                      size_t nyears
                                                                                      Definition: information.hpp:34
                                                                                      -
                                                                                      fims::Information::CreateModel
                                                                                      bool CreateModel()
                                                                                      Definition: information.hpp:157
                                                                                      -
                                                                                      fims::Information::selectivity_models_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims::SelectivityBase< T > > >::iterator selectivity_models_iterator
                                                                                      Definition: information.hpp:69
                                                                                      -
                                                                                      fims::Information::SetNseasons
                                                                                      void SetNseasons(size_t nseasons)
                                                                                      Set the Nseasons object.
                                                                                      Definition: information.hpp:483
                                                                                      -
                                                                                      fims::Information::RegisterParameter
                                                                                      void RegisterParameter(T &p)
                                                                                      Definition: information.hpp:138
                                                                                      -
                                                                                      fims::Information::populations
                                                                                      std::map< uint32_t, std::shared_ptr< fims::Population< T > > > populations
                                                                                      Definition: information.hpp:99
                                                                                      -
                                                                                      fims::Information::population_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims::Population< T > > >::iterator population_iterator
                                                                                      Definition: information.hpp:103
                                                                                      -
                                                                                      fims::Information::data_objects
                                                                                      std::map< uint32_t, std::shared_ptr< fims::DataObject< T > > > data_objects
                                                                                      Definition: information.hpp:48
                                                                                      -
                                                                                      fims::Information::GetRandomEffectsParameters
                                                                                      std::vector< T * > & GetRandomEffectsParameters()
                                                                                      Get the Random Effects Parameters object.
                                                                                      Definition: information.hpp:520
                                                                                      -
                                                                                      fims::Information::recruitment_models
                                                                                      std::map< uint32_t, std::shared_ptr< fims::RecruitmentBase< T > > > recruitment_models
                                                                                      Definition: information.hpp:55
                                                                                      -
                                                                                      fims::Information::GetNages
                                                                                      size_t GetNages() const
                                                                                      Get the Nages object.
                                                                                      Definition: information.hpp:462
                                                                                      -
                                                                                      fims::Information::GetInstance
                                                                                      static std::shared_ptr< Information< T > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      -
                                                                                      fims::Information::distribution_models_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims::DistributionsBase< T > > >::iterator distribution_models_iterator
                                                                                      Definition: information.hpp:113
                                                                                      -
                                                                                      fims::Information::fleet_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims::Fleet< T > > >::iterator fleet_iterator
                                                                                      Definition: information.hpp:94
                                                                                      -
                                                                                      fims::Information::GetNseasons
                                                                                      size_t GetNseasons() const
                                                                                      Get the Nseasons object.
                                                                                      Definition: information.hpp:476
                                                                                      -
                                                                                      fims::Information::fims_information
                                                                                      static std::shared_ptr< Information< T > > fims_information
                                                                                      Definition: information.hpp:39
                                                                                      -
                                                                                      fims::Information::parameters
                                                                                      std::vector< T * > parameters
                                                                                      Definition: information.hpp:40
                                                                                      -
                                                                                      fims::Information::random_effects_parameters
                                                                                      std::vector< T * > random_effects_parameters
                                                                                      Definition: information.hpp:42
                                                                                      -
                                                                                      fims::Information::SetNyears
                                                                                      void SetNyears(size_t nyears)
                                                                                      Set the Nyears object.
                                                                                      Definition: information.hpp:497
                                                                                      -
                                                                                      fims::Information::nseasons
                                                                                      size_t nseasons
                                                                                      Definition: information.hpp:35
                                                                                      +
                                                                                      fims_info::Information
                                                                                      Stores FIMS model information and creates model. Contains all objects and data pre-model construction...
                                                                                      Definition: information.hpp:32
                                                                                      +
                                                                                      fims_info::Information::selectivity_models_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims_popdy::SelectivityBase< Type > > >::iterator selectivity_models_iterator
                                                                                      Definition: information.hpp:69
                                                                                      +
                                                                                      fims_info::Information::population_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims_popdy::Population< Type > > >::iterator population_iterator
                                                                                      Definition: information.hpp:103
                                                                                      +
                                                                                      fims_info::Information::populations
                                                                                      std::map< uint32_t, std::shared_ptr< fims_popdy::Population< Type > > > populations
                                                                                      Definition: information.hpp:99
                                                                                      +
                                                                                      fims_info::Information::random_effects_parameters
                                                                                      std::vector< Type * > random_effects_parameters
                                                                                      Definition: information.hpp:42
                                                                                      +
                                                                                      fims_info::Information::nages
                                                                                      size_t nages
                                                                                      Definition: information.hpp:36
                                                                                      +
                                                                                      fims_info::Information::fleets
                                                                                      std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > > fleets
                                                                                      Definition: information.hpp:90
                                                                                      +
                                                                                      fims_info::Information::growth_models
                                                                                      std::map< uint32_t, std::shared_ptr< fims_popdy::GrowthBase< Type > > > growth_models
                                                                                      Definition: information.hpp:73
                                                                                      +
                                                                                      fims_info::Information::distribution_models_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims_distributions::DistributionsBase< Type > > >::iterator distribution_models_iterator
                                                                                      Definition: information.hpp:113
                                                                                      +
                                                                                      fims_info::Information::distribution_models
                                                                                      std::map< uint32_t, std::shared_ptr< fims_distributions::DistributionsBase< Type > > > distribution_models
                                                                                      Definition: information.hpp:108
                                                                                      +
                                                                                      fims_info::Information::RegisterParameter
                                                                                      void RegisterParameter(Type &p)
                                                                                      Definition: information.hpp:138
                                                                                      +
                                                                                      fims_info::Information::RegisterRandomEffect
                                                                                      void RegisterRandomEffect(Type &re)
                                                                                      Definition: information.hpp:145
                                                                                      +
                                                                                      fims_info::Information::SetNyears
                                                                                      void SetNyears(size_t nyears)
                                                                                      Set the Nyears object.
                                                                                      Definition: information.hpp:497
                                                                                      +
                                                                                      fims_info::Information::GetNages
                                                                                      size_t GetNages() const
                                                                                      Get the Nages object.
                                                                                      Definition: information.hpp:462
                                                                                      +
                                                                                      fims_info::Information::fleet_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > >::iterator fleet_iterator
                                                                                      Definition: information.hpp:94
                                                                                      +
                                                                                      fims_info::Information::growth_models_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims_popdy::GrowthBase< Type > > >::iterator growth_models_iterator
                                                                                      Definition: information.hpp:77
                                                                                      +
                                                                                      fims_info::Information::nseasons
                                                                                      size_t nseasons
                                                                                      Definition: information.hpp:35
                                                                                      +
                                                                                      fims_info::Information::selectivity_models
                                                                                      std::map< uint32_t, std::shared_ptr< fims_popdy::SelectivityBase< Type > > > selectivity_models
                                                                                      Definition: information.hpp:64
                                                                                      +
                                                                                      fims_info::Information::CreateModel
                                                                                      bool CreateModel()
                                                                                      Definition: information.hpp:157
                                                                                      +
                                                                                      fims_info::Information::GetNseasons
                                                                                      size_t GetNseasons() const
                                                                                      Get the Nseasons object.
                                                                                      Definition: information.hpp:476
                                                                                      +
                                                                                      fims_info::Information::GetFixedEffectsParameters
                                                                                      std::vector< Type * > & GetFixedEffectsParameters()
                                                                                      Get the Fixed Effects Parameters object.
                                                                                      Definition: information.hpp:511
                                                                                      +
                                                                                      fims_info::Information::maturity_models_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims_popdy::MaturityBase< Type > > >::iterator maturity_models_iterator
                                                                                      Definition: information.hpp:85
                                                                                      +
                                                                                      fims_info::Information::parameters
                                                                                      std::vector< Type * > parameters
                                                                                      Definition: information.hpp:40
                                                                                      +
                                                                                      fims_info::Information::nyears
                                                                                      size_t nyears
                                                                                      Definition: information.hpp:34
                                                                                      +
                                                                                      fims_info::Information::maturity_models
                                                                                      std::map< uint32_t, std::shared_ptr< fims_popdy::MaturityBase< Type > > > maturity_models
                                                                                      Definition: information.hpp:81
                                                                                      +
                                                                                      fims_info::Information::GetParameters
                                                                                      std::vector< Type * > & GetParameters()
                                                                                      Get the Parameters object.
                                                                                      Definition: information.hpp:504
                                                                                      +
                                                                                      fims_info::Information::GetRandomEffectsParameters
                                                                                      std::vector< Type * > & GetRandomEffectsParameters()
                                                                                      Get the Random Effects Parameters object.
                                                                                      Definition: information.hpp:520
                                                                                      +
                                                                                      fims_info::Information::GetNyears
                                                                                      size_t GetNyears() const
                                                                                      Get the Nyears object.
                                                                                      Definition: information.hpp:490
                                                                                      +
                                                                                      fims_info::Information::recruitment_models_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims_popdy::RecruitmentBase< Type > > >::iterator recruitment_models_iterator
                                                                                      Definition: information.hpp:60
                                                                                      +
                                                                                      fims_info::Information::data_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims_data_object::DataObject< Type > > >::iterator data_iterator
                                                                                      Definition: information.hpp:51
                                                                                      +
                                                                                      fims_info::Information::GetInstance
                                                                                      static std::shared_ptr< Information< Type > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      +
                                                                                      fims_info::Information::fims_information
                                                                                      static std::shared_ptr< Information< Type > > fims_information
                                                                                      Definition: information.hpp:39
                                                                                      +
                                                                                      fims_info::Information::recruitment_models
                                                                                      std::map< uint32_t, std::shared_ptr< fims_popdy::RecruitmentBase< Type > > > recruitment_models
                                                                                      Definition: information.hpp:55
                                                                                      +
                                                                                      fims_info::Information::fixed_effects_parameters
                                                                                      std::vector< Type * > fixed_effects_parameters
                                                                                      Definition: information.hpp:44
                                                                                      +
                                                                                      fims_info::Information::SetNseasons
                                                                                      void SetNseasons(size_t nseasons)
                                                                                      Set the Nseasons object.
                                                                                      Definition: information.hpp:483
                                                                                      +
                                                                                      fims_info::Information::SetNages
                                                                                      void SetNages(size_t nages)
                                                                                      Set the Nages object.
                                                                                      Definition: information.hpp:469
                                                                                      +
                                                                                      fims_info::Information::data_objects
                                                                                      std::map< uint32_t, std::shared_ptr< fims_data_object::DataObject< Type > > > data_objects
                                                                                      Definition: information.hpp:48
                                                                                      FIMS_LOG
                                                                                      std::ofstream FIMS_LOG("fims.log")
                                                                                      diff --git a/docs/maturity_2functors_2logistic_8hpp_source.html b/docs/maturity_2functors_2logistic_8hpp_source.html index 2b515c5..9ac791f 100644 --- a/docs/maturity_2functors_2logistic_8hpp_source.html +++ b/docs/maturity_2functors_2logistic_8hpp_source.html @@ -91,27 +91,27 @@
                                                                                      13 #include "../../../common/fims_math.hpp"
                                                                                      14 #include "maturity_base.hpp"
                                                                                      15 
                                                                                      -
                                                                                      16 namespace fims {
                                                                                      +
                                                                                      16 namespace fims_popdy {
                                                                                      17 
                                                                                      22 template <typename Type>
                                                                                      -
                                                                                      23 struct LogisticMaturity : public MaturityBase<Type> {
                                                                                      -
                                                                                      24  Type median;
                                                                                      -
                                                                                      26  Type slope;
                                                                                      -
                                                                                      29  LogisticMaturity() : MaturityBase<Type>() {}
                                                                                      +
                                                                                      23 struct LogisticMaturity : public MaturityBase<Type> {
                                                                                      +
                                                                                      24  Type median;
                                                                                      +
                                                                                      26  Type slope;
                                                                                      +
                                                                                      29  LogisticMaturity() : MaturityBase<Type>() {}
                                                                                      30 
                                                                                      -
                                                                                      40  virtual const Type evaluate(const Type& x) {
                                                                                      -
                                                                                      41  return fims::logistic<Type>(median, slope, x);
                                                                                      +
                                                                                      40  virtual const Type evaluate(const Type & x) {
                                                                                      +
                                                                                      41  return fims_math::logistic<Type>(median, slope, x);
                                                                                      42  }
                                                                                      43 };
                                                                                      44 
                                                                                      45 } // namespace fims
                                                                                      46 
                                                                                      47 #endif /* POPULATION_DYNAMICS_MATURITY_LOGISTIC_HPP */
                                                                                      -
                                                                                      fims::LogisticMaturity
                                                                                      LogisticMaturity class that returns the logistic function value from fims_math.
                                                                                      Definition: logistic.hpp:23
                                                                                      -
                                                                                      fims::LogisticMaturity::slope
                                                                                      Type slope
                                                                                      Definition: logistic.hpp:26
                                                                                      -
                                                                                      fims::LogisticMaturity::evaluate
                                                                                      virtual const Type evaluate(const Type &x)
                                                                                      Method of the logistic maturity class that implements the logistic function from FIMS math.
                                                                                      Definition: logistic.hpp:40
                                                                                      -
                                                                                      fims::LogisticMaturity::median
                                                                                      Type median
                                                                                      Definition: logistic.hpp:24
                                                                                      -
                                                                                      fims::MaturityBase
                                                                                      Base class for all maturity functors.
                                                                                      Definition: maturity_base.hpp:27
                                                                                      +
                                                                                      fims_popdy::LogisticMaturity
                                                                                      LogisticMaturity class that returns the logistic function value from fims_math.
                                                                                      Definition: logistic.hpp:23
                                                                                      +
                                                                                      fims_popdy::LogisticMaturity::slope
                                                                                      Type slope
                                                                                      Definition: logistic.hpp:26
                                                                                      +
                                                                                      fims_popdy::LogisticMaturity::evaluate
                                                                                      virtual const Type evaluate(const Type &x)
                                                                                      Method of the logistic maturity class that implements the logistic function from FIMS math.
                                                                                      Definition: logistic.hpp:40
                                                                                      +
                                                                                      fims_popdy::LogisticMaturity::median
                                                                                      Type median
                                                                                      Definition: logistic.hpp:24
                                                                                      +
                                                                                      fims_popdy::MaturityBase
                                                                                      Base class for all maturity functors.
                                                                                      Definition: maturity_base.hpp:27
                                                                                      diff --git a/docs/maturity__base_8hpp_source.html b/docs/maturity__base_8hpp_source.html index bba1137..27db796 100644 --- a/docs/maturity__base_8hpp_source.html +++ b/docs/maturity__base_8hpp_source.html @@ -94,35 +94,35 @@
                                                                                      16 
                                                                                      17 #include "../../../common/model_object.hpp"
                                                                                      18 
                                                                                      -
                                                                                      19 namespace fims {
                                                                                      +
                                                                                      19 namespace fims_popdy {
                                                                                      20 
                                                                                      26 template <typename Type>
                                                                                      -
                                                                                      27 struct MaturityBase : public FIMSObject<Type> {
                                                                                      +
                                                                                      27 struct MaturityBase : public fims_model_object::FIMSObject<Type> {
                                                                                      28  // id_g is the ID of the instance of the MaturityBase class.
                                                                                      29  // this is like a memory tracker.
                                                                                      30  // Assigning each one its own ID is a way to keep track of
                                                                                      31  // all the instances of the MaturityBase class.
                                                                                      -
                                                                                      32  static uint32_t id_g;
                                                                                      -
                                                                                      36  MaturityBase() {
                                                                                      +
                                                                                      32  static uint32_t id_g;
                                                                                      +
                                                                                      36  MaturityBase() {
                                                                                      37  // increment id of the singleton maturity class
                                                                                      -
                                                                                      38  this->id = MaturityBase::id_g++;
                                                                                      +
                                                                                      38  this->id = MaturityBase::id_g++;
                                                                                      39  }
                                                                                      40 
                                                                                      -
                                                                                      46  virtual const Type evaluate(const Type& x) = 0;
                                                                                      +
                                                                                      46  virtual const Type evaluate(const Type& x) = 0;
                                                                                      47 };
                                                                                      48 
                                                                                      49 // default id of the singleton maturity class
                                                                                      50 template <typename Type>
                                                                                      -
                                                                                      51 uint32_t MaturityBase<Type>::id_g = 0;
                                                                                      +
                                                                                      51 uint32_t MaturityBase<Type>::id_g = 0;
                                                                                      52 
                                                                                      53 } // namespace fims
                                                                                      54 
                                                                                      55 #endif /* POPULATION_DYNAMICS_MATURITY_BASE_HPP */
                                                                                      -
                                                                                      fims::FIMSObject
                                                                                      FIMSObject struct that defines member types and returns the unique id.
                                                                                      Definition: model_object.hpp:25
                                                                                      -
                                                                                      fims::MaturityBase
                                                                                      Base class for all maturity functors.
                                                                                      Definition: maturity_base.hpp:27
                                                                                      -
                                                                                      fims::MaturityBase::id_g
                                                                                      static uint32_t id_g
                                                                                      Definition: maturity_base.hpp:32
                                                                                      -
                                                                                      fims::MaturityBase::MaturityBase
                                                                                      MaturityBase()
                                                                                      Constructor.
                                                                                      Definition: maturity_base.hpp:36
                                                                                      -
                                                                                      fims::MaturityBase::evaluate
                                                                                      virtual const Type evaluate(const Type &x)=0
                                                                                      Calculates the maturity.
                                                                                      +
                                                                                      fims_model_object::FIMSObject
                                                                                      FIMSObject struct that defines member types and returns the unique id.
                                                                                      Definition: model_object.hpp:25
                                                                                      +
                                                                                      fims_popdy::MaturityBase
                                                                                      Base class for all maturity functors.
                                                                                      Definition: maturity_base.hpp:27
                                                                                      +
                                                                                      fims_popdy::MaturityBase::evaluate
                                                                                      virtual const Type evaluate(const Type &x)=0
                                                                                      Calculates the maturity.
                                                                                      +
                                                                                      fims_popdy::MaturityBase::id_g
                                                                                      static uint32_t id_g
                                                                                      Definition: maturity_base.hpp:32
                                                                                      +
                                                                                      fims_popdy::MaturityBase::MaturityBase
                                                                                      MaturityBase()
                                                                                      Constructor.
                                                                                      Definition: maturity_base.hpp:36
                                                                                      diff --git a/docs/model_8hpp_source.html b/docs/model_8hpp_source.html index 7221c12..636adfe 100644 --- a/docs/model_8hpp_source.html +++ b/docs/model_8hpp_source.html @@ -99,40 +99,40 @@
                                                                                      21 
                                                                                      22 #include "information.hpp"
                                                                                      23 
                                                                                      -
                                                                                      24 namespace fims {
                                                                                      +
                                                                                      24 namespace fims_model {
                                                                                      25 
                                                                                      29 template <typename Type>
                                                                                      -
                                                                                      30 class Model { // may need singleton
                                                                                      +
                                                                                      30 class Model { // may need singleton
                                                                                      31  public:
                                                                                      32  static std::shared_ptr<Model<Type> >
                                                                                      -
                                                                                      33  fims_model;
                                                                                      -
                                                                                      34  std::shared_ptr<Information<Type> >
                                                                                      -
                                                                                      35  fims_information;
                                                                                      +
                                                                                      33  fims_model;
                                                                                      +
                                                                                      34  std::shared_ptr<fims_info::Information<Type> >
                                                                                      +
                                                                                      35  fims_information;
                                                                                      38 #ifdef TMB_MODEL
                                                                                      39  ::objective_function<Type> *of;
                                                                                      40 #endif
                                                                                      41 
                                                                                      42  // constructor
                                                                                      -
                                                                                      43  virtual ~Model() {}
                                                                                      +
                                                                                      43  virtual ~Model() {}
                                                                                      44 
                                                                                      -
                                                                                      50  static std::shared_ptr<Model<Type> > GetInstance() {
                                                                                      -
                                                                                      51  if (Model<Type>::fims_model == nullptr) {
                                                                                      -
                                                                                      52  Model<Type>::fims_model = std::make_shared<fims::Model<Type> >();
                                                                                      -
                                                                                      53  Model<Type>::fims_model->fims_information =
                                                                                      -
                                                                                      54  fims::Information<Type>::GetInstance();
                                                                                      +
                                                                                      50  static std::shared_ptr<Model<Type> > GetInstance() {
                                                                                      +
                                                                                      51  if (Model<Type>::fims_model == nullptr) {
                                                                                      +
                                                                                      52  Model<Type>::fims_model = std::make_shared<fims_model::Model<Type> >();
                                                                                      +
                                                                                      53  Model<Type>::fims_model->fims_information =
                                                                                      +
                                                                                      54  fims_info::Information<Type>::GetInstance();
                                                                                      55  }
                                                                                      -
                                                                                      56  return Model<Type>::fims_model;
                                                                                      +
                                                                                      56  return Model<Type>::fims_model;
                                                                                      57  }
                                                                                      58 
                                                                                      -
                                                                                      62  const Type Evaluate() {
                                                                                      +
                                                                                      62  const Type Evaluate() {
                                                                                      63  // jnll = negative-log-likelihood (the objective function)
                                                                                      64  Type jnll = 0.0;
                                                                                      65  Type rec_nll = 0.0; // recrutiment nll
                                                                                      66  Type age_comp_nll = 0.0; // age composition nll
                                                                                      67  Type index_nll = 0.0; // survey and fishery cacth nll
                                                                                      68 
                                                                                      -
                                                                                      69  int n_fleets = fims_information->fleets.size();
                                                                                      -
                                                                                      70  int n_pops = fims_information->populations.size();
                                                                                      +
                                                                                      69  int n_fleets = fims_information->fleets.size();
                                                                                      +
                                                                                      70  int n_pops = fims_information->populations.size();
                                                                                      71 
                                                                                      72 // Create vector lists to store output for reporting
                                                                                      73 #ifdef TMB_MODEL
                                                                                      @@ -155,9 +155,9 @@
                                                                                      90 
                                                                                      91  // Loop over populations, evaluate, and sum up the recruitment likelihood
                                                                                      92  // component
                                                                                      -
                                                                                      93  typename fims::Information<Type>::population_iterator it;
                                                                                      -
                                                                                      94  for (it = this->fims_information->populations.begin();
                                                                                      -
                                                                                      95  it != this->fims_information->populations.end(); ++it) {
                                                                                      +
                                                                                      93  typename fims_info::Information<Type>::population_iterator it;
                                                                                      +
                                                                                      94  for (it = this->fims_information->populations.begin();
                                                                                      +
                                                                                      95  it != this->fims_information->populations.end(); ++it) {
                                                                                      96  //(*it).second points to each individual Population module
                                                                                      97  FIMS_LOG << "inside pop loop" << std::endl;
                                                                                      98  // Prepare recruitment
                                                                                      @@ -175,9 +175,9 @@
                                                                                      110  }
                                                                                      111 
                                                                                      112  // Loop over fleets/surveys, and sum up age comp and index nlls
                                                                                      -
                                                                                      113  typename fims::Information<Type>::fleet_iterator jt;
                                                                                      -
                                                                                      114  for (jt = this->fims_information->fleets.begin();
                                                                                      -
                                                                                      115  jt != this->fims_information->fleets.end(); ++jt) {
                                                                                      +
                                                                                      113  typename fims_info::Information<Type>::fleet_iterator jt;
                                                                                      +
                                                                                      114  for (jt = this->fims_information->fleets.begin();
                                                                                      +
                                                                                      115  jt != this->fims_information->fleets.end(); ++jt) {
                                                                                      116  //(*jt).second points to each individual Fleet module
                                                                                      117 #ifdef TMB_MODEL
                                                                                      118  (*jt).second->of = this->of;
                                                                                      @@ -190,8 +190,8 @@
                                                                                      125 
                                                                                      126  // initiate population index for structuring report out objects
                                                                                      127  int pop_idx = 0;
                                                                                      -
                                                                                      128  for (it = this->fims_information->populations.begin();
                                                                                      -
                                                                                      129  it != this->fims_information->populations.end(); ++it) {
                                                                                      +
                                                                                      128  for (it = this->fims_information->populations.begin();
                                                                                      +
                                                                                      129  it != this->fims_information->populations.end(); ++it) {
                                                                                      130 #ifdef TMB_MODEL
                                                                                      131  naa(pop_idx) = vector<Type>((*it).second->numbers_at_age);
                                                                                      132  ssb(pop_idx) = vector<Type>((*it).second->spawning_biomass);
                                                                                      @@ -206,8 +206,8 @@
                                                                                      141 
                                                                                      142  // initiate fleet index for structuring report out objects
                                                                                      143  int fleet_idx = 0;
                                                                                      -
                                                                                      144  for (jt = this->fims_information->fleets.begin();
                                                                                      -
                                                                                      145  jt != this->fims_information->fleets.end(); ++jt) {
                                                                                      +
                                                                                      144  for (jt = this->fims_information->fleets.begin();
                                                                                      +
                                                                                      145  jt != this->fims_information->fleets.end(); ++jt) {
                                                                                      146 #ifdef TMB_MODEL
                                                                                      147  exp_index(fleet_idx) = vector<Type>((*jt).second->expected_index);
                                                                                      148  exp_catch(fleet_idx) = vector<Type>((*jt).second->expected_catch);
                                                                                      @@ -265,20 +265,20 @@
                                                                                      200 
                                                                                      201 // Create singleton instance of Model class
                                                                                      202 template <typename Type>
                                                                                      -
                                                                                      203 std::shared_ptr<Model<Type> > Model<Type>::fims_model =
                                                                                      +
                                                                                      203 std::shared_ptr<Model<Type> > Model<Type>::fims_model =
                                                                                      204  nullptr; // singleton instance
                                                                                      -
                                                                                      205 } // namespace fims
                                                                                      +
                                                                                      205 } // namespace fims_model
                                                                                      206 
                                                                                      207 #endif /* FIMS_COMMON_MODEL_HPP */
                                                                                      -
                                                                                      fims::Information::population_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims::Population< T > > >::iterator population_iterator
                                                                                      Definition: information.hpp:103
                                                                                      -
                                                                                      fims::Information::GetInstance
                                                                                      static std::shared_ptr< Information< T > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      -
                                                                                      fims::Information::fleet_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims::Fleet< T > > >::iterator fleet_iterator
                                                                                      Definition: information.hpp:94
                                                                                      -
                                                                                      fims::Information::fims_information
                                                                                      static std::shared_ptr< Information< T > > fims_information
                                                                                      Definition: information.hpp:39
                                                                                      -
                                                                                      fims::Model
                                                                                      Model class. FIMS objective function.
                                                                                      Definition: model.hpp:30
                                                                                      -
                                                                                      fims::Model::fims_information
                                                                                      std::shared_ptr< Information< Type > > fims_information
                                                                                      Definition: model.hpp:35
                                                                                      -
                                                                                      fims::Model::Evaluate
                                                                                      const Type Evaluate()
                                                                                      Evaluate. Calculates the joint negative log-likelihood function.
                                                                                      Definition: model.hpp:62
                                                                                      -
                                                                                      fims::Model::fims_model
                                                                                      static std::shared_ptr< Model< Type > > fims_model
                                                                                      Definition: model.hpp:33
                                                                                      -
                                                                                      fims::Model::GetInstance
                                                                                      static std::shared_ptr< Model< Type > > GetInstance()
                                                                                      Definition: model.hpp:50
                                                                                      +
                                                                                      fims_info::Information::population_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims_popdy::Population< Type > > >::iterator population_iterator
                                                                                      Definition: information.hpp:103
                                                                                      +
                                                                                      fims_info::Information::fleet_iterator
                                                                                      std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > >::iterator fleet_iterator
                                                                                      Definition: information.hpp:94
                                                                                      +
                                                                                      fims_info::Information::GetInstance
                                                                                      static std::shared_ptr< Information< Type > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      +
                                                                                      fims_info::Information::fims_information
                                                                                      static std::shared_ptr< Information< Type > > fims_information
                                                                                      Definition: information.hpp:39
                                                                                      +
                                                                                      fims_model::Model
                                                                                      Model class. FIMS objective function.
                                                                                      Definition: model.hpp:30
                                                                                      +
                                                                                      fims_model::Model::fims_model
                                                                                      static std::shared_ptr< Model< Type > > fims_model
                                                                                      Definition: model.hpp:33
                                                                                      +
                                                                                      fims_model::Model::Evaluate
                                                                                      const Type Evaluate()
                                                                                      Evaluate. Calculates the joint negative log-likelihood function.
                                                                                      Definition: model.hpp:62
                                                                                      +
                                                                                      fims_model::Model::fims_information
                                                                                      std::shared_ptr< fims_info::Information< Type > > fims_information
                                                                                      Definition: model.hpp:35
                                                                                      +
                                                                                      fims_model::Model::GetInstance
                                                                                      static std::shared_ptr< Model< Type > > GetInstance()
                                                                                      Definition: model.hpp:50
                                                                                      FIMS_LOG
                                                                                      std::ofstream FIMS_LOG("fims.log")
                                                                                      diff --git a/docs/model__object_8hpp_source.html b/docs/model__object_8hpp_source.html index fa7c5f2..0b4ee2d 100644 --- a/docs/model__object_8hpp_source.html +++ b/docs/model__object_8hpp_source.html @@ -94,30 +94,30 @@
                                                                                      16 
                                                                                      17 #include "def.hpp"
                                                                                      18 
                                                                                      -
                                                                                      19 namespace fims {
                                                                                      +
                                                                                      19 namespace fims_model_object {
                                                                                      20 
                                                                                      -
                                                                                      24 template <typename T>
                                                                                      -
                                                                                      25 struct FIMSObject {
                                                                                      -
                                                                                      26  uint32_t id;
                                                                                      -
                                                                                      27  std::vector<T*> parameters;
                                                                                      -
                                                                                      28  std::vector<T*>
                                                                                      -
                                                                                      29  random_effects_parameters;
                                                                                      -
                                                                                      30  std::vector<T*>
                                                                                      -
                                                                                      31  fixed_effects_parameters;
                                                                                      -
                                                                                      33  virtual ~FIMSObject() {}
                                                                                      -
                                                                                      37  uint32_t GetId() const { return id; }
                                                                                      +
                                                                                      24 template <typename Type>
                                                                                      +
                                                                                      25 struct FIMSObject {
                                                                                      +
                                                                                      26  uint32_t id;
                                                                                      +
                                                                                      27  std::vector<Type*> parameters;
                                                                                      +
                                                                                      28  std::vector<Type*>
                                                                                      +
                                                                                      29  random_effects_parameters;
                                                                                      +
                                                                                      30  std::vector<Type*>
                                                                                      +
                                                                                      31  fixed_effects_parameters;
                                                                                      +
                                                                                      33  virtual ~FIMSObject() {}
                                                                                      +
                                                                                      37  uint32_t GetId() const { return id; }
                                                                                      38 };
                                                                                      39 
                                                                                      -
                                                                                      40 } // namespace fims
                                                                                      +
                                                                                      40 } // namespace fims_model_object
                                                                                      41 
                                                                                      42 #endif /* FIMS_COMMON_MODEL_OBJECT_HPP */
                                                                                      -
                                                                                      fims::FIMSObject
                                                                                      FIMSObject struct that defines member types and returns the unique id.
                                                                                      Definition: model_object.hpp:25
                                                                                      -
                                                                                      fims::FIMSObject::parameters
                                                                                      std::vector< T * > parameters
                                                                                      Definition: model_object.hpp:27
                                                                                      -
                                                                                      fims::FIMSObject::fixed_effects_parameters
                                                                                      std::vector< T * > fixed_effects_parameters
                                                                                      Definition: model_object.hpp:31
                                                                                      -
                                                                                      fims::FIMSObject::GetId
                                                                                      uint32_t GetId() const
                                                                                      Getter that returns the unique id for parameters in the model.
                                                                                      Definition: model_object.hpp:37
                                                                                      -
                                                                                      fims::FIMSObject::id
                                                                                      uint32_t id
                                                                                      Definition: model_object.hpp:26
                                                                                      -
                                                                                      fims::FIMSObject::random_effects_parameters
                                                                                      std::vector< T * > random_effects_parameters
                                                                                      Definition: model_object.hpp:29
                                                                                      +
                                                                                      fims_model_object::FIMSObject
                                                                                      FIMSObject struct that defines member types and returns the unique id.
                                                                                      Definition: model_object.hpp:25
                                                                                      +
                                                                                      fims_model_object::FIMSObject::id
                                                                                      uint32_t id
                                                                                      Definition: model_object.hpp:26
                                                                                      +
                                                                                      fims_model_object::FIMSObject::GetId
                                                                                      uint32_t GetId() const
                                                                                      Getter that returns the unique id for parameters in the model.
                                                                                      Definition: model_object.hpp:37
                                                                                      +
                                                                                      fims_model_object::FIMSObject::random_effects_parameters
                                                                                      std::vector< Type * > random_effects_parameters
                                                                                      Definition: model_object.hpp:29
                                                                                      +
                                                                                      fims_model_object::FIMSObject::parameters
                                                                                      std::vector< Type * > parameters
                                                                                      Definition: model_object.hpp:27
                                                                                      +
                                                                                      fims_model_object::FIMSObject::fixed_effects_parameters
                                                                                      std::vector< Type * > fixed_effects_parameters
                                                                                      Definition: model_object.hpp:31
                                                                                      diff --git a/docs/population_8hpp_source.html b/docs/population_8hpp_source.html index aac379c..adc1bc0 100644 --- a/docs/population_8hpp_source.html +++ b/docs/population_8hpp_source.html @@ -100,126 +100,126 @@
                                                                                      22 #include "../../interface/interface.hpp"
                                                                                      23 #include "../maturity/maturity.hpp"
                                                                                      24 
                                                                                      -
                                                                                      25 namespace fims {
                                                                                      +
                                                                                      25 namespace fims_popdy {
                                                                                      26 /*TODO:
                                                                                      27 Review, add functions to evaluate, push vectors back to fleet (or point to fleet
                                                                                      28 directly?)
                                                                                      29  */
                                                                                      30 
                                                                                      35 template <typename Type>
                                                                                      -
                                                                                      36 struct Population : public FIMSObject<Type> {
                                                                                      -
                                                                                      37  using ParameterVector =
                                                                                      -
                                                                                      38  typename ModelTraits<Type>::ParameterVector;
                                                                                      -
                                                                                      40  static uint32_t id_g;
                                                                                      -
                                                                                      41  size_t nyears;
                                                                                      -
                                                                                      42  size_t nseasons;
                                                                                      -
                                                                                      43  size_t nages;
                                                                                      -
                                                                                      44  size_t nfleets;
                                                                                      +
                                                                                      36 struct Population : public fims_model_object::FIMSObject<Type> {
                                                                                      +
                                                                                      37  using ParameterVector =
                                                                                      +
                                                                                      38  typename fims::ModelTraits<Type>::ParameterVector;
                                                                                      +
                                                                                      40  static uint32_t id_g;
                                                                                      +
                                                                                      41  size_t nyears;
                                                                                      +
                                                                                      42  size_t nseasons;
                                                                                      +
                                                                                      43  size_t nages;
                                                                                      +
                                                                                      44  size_t nfleets;
                                                                                      46  // constants
                                                                                      -
                                                                                      47  const Type proportion_female =
                                                                                      +
                                                                                      47  const Type proportion_female =
                                                                                      48  0.5;
                                                                                      50  // parameters are estimated; after initialize in create_model, push_back to
                                                                                      51  // parameter list - in information.hpp (same for initial F in fleet)
                                                                                      -
                                                                                      52  std::vector<Type> log_init_naa;
                                                                                      -
                                                                                      53  ParameterVector log_M;
                                                                                      +
                                                                                      52  std::vector<Type> log_init_naa;
                                                                                      +
                                                                                      53  ParameterVector log_M;
                                                                                      55  // Transformed values
                                                                                      -
                                                                                      56  std::vector<Type> M;
                                                                                      -
                                                                                      58  std::vector<double> ages;
                                                                                      -
                                                                                      59  std::vector<double> years;
                                                                                      -
                                                                                      60  ParameterVector mortality_F;
                                                                                      +
                                                                                      56  std::vector<Type> M;
                                                                                      +
                                                                                      58  std::vector<double> ages;
                                                                                      +
                                                                                      59  std::vector<double> years;
                                                                                      +
                                                                                      60  ParameterVector mortality_F;
                                                                                      62  std::vector<Type>
                                                                                      -
                                                                                      63  mortality_Z;
                                                                                      +
                                                                                      63  mortality_Z;
                                                                                      65  // derived quantities
                                                                                      66  std::vector<Type>
                                                                                      -
                                                                                      67  weight_at_age;
                                                                                      +
                                                                                      67  weight_at_age;
                                                                                      68  // fecundity removed because we don't need it yet
                                                                                      -
                                                                                      69  std::vector<Type> numbers_at_age;
                                                                                      +
                                                                                      69  std::vector<Type> numbers_at_age;
                                                                                      71  std::vector<Type>
                                                                                      -
                                                                                      72  unfished_numbers_at_age;
                                                                                      +
                                                                                      72  unfished_numbers_at_age;
                                                                                      74  std::vector<Type>
                                                                                      -
                                                                                      75  biomass;
                                                                                      -
                                                                                      76  std::vector<Type> spawning_biomass;
                                                                                      -
                                                                                      77  std::vector<Type> unfished_biomass;
                                                                                      -
                                                                                      79  std::vector<Type> unfished_spawning_biomass;
                                                                                      -
                                                                                      81  std::vector<Type> proportion_mature_at_age;
                                                                                      -
                                                                                      83  std::vector<Type> expected_numbers_at_age;
                                                                                      -
                                                                                      85  std::vector<Type> expected_catch;
                                                                                      -
                                                                                      86  std::vector<Type> expected_recruitment;
                                                                                      -
                                                                                      88  int recruitment_id = -999;
                                                                                      -
                                                                                      89  std::shared_ptr<fims::RecruitmentBase<Type>>
                                                                                      -
                                                                                      90  recruitment;
                                                                                      +
                                                                                      75  biomass;
                                                                                      +
                                                                                      76  std::vector<Type> spawning_biomass;
                                                                                      +
                                                                                      77  std::vector<Type> unfished_biomass;
                                                                                      +
                                                                                      79  std::vector<Type> unfished_spawning_biomass;
                                                                                      +
                                                                                      81  std::vector<Type> proportion_mature_at_age;
                                                                                      +
                                                                                      83  std::vector<Type> expected_numbers_at_age;
                                                                                      +
                                                                                      85  std::vector<Type> expected_catch;
                                                                                      +
                                                                                      86  std::vector<Type> expected_recruitment;
                                                                                      +
                                                                                      88  int recruitment_id = -999;
                                                                                      +
                                                                                      89  std::shared_ptr<RecruitmentBase<Type>>
                                                                                      +
                                                                                      90  recruitment;
                                                                                      92  // growth
                                                                                      -
                                                                                      93  int growth_id = -999;
                                                                                      -
                                                                                      94  std::shared_ptr<fims::GrowthBase<Type>>
                                                                                      -
                                                                                      95  growth;
                                                                                      +
                                                                                      93  int growth_id = -999;
                                                                                      +
                                                                                      94  std::shared_ptr<GrowthBase<Type>>
                                                                                      +
                                                                                      95  growth;
                                                                                      97  // maturity
                                                                                      -
                                                                                      98  int maturity_id = -999;
                                                                                      -
                                                                                      99  std::shared_ptr<fims::MaturityBase<Type>>
                                                                                      -
                                                                                      100  maturity;
                                                                                      +
                                                                                      98  int maturity_id = -999;
                                                                                      +
                                                                                      99  std::shared_ptr<MaturityBase<Type>>
                                                                                      +
                                                                                      100  maturity;
                                                                                      102  // fleet
                                                                                      -
                                                                                      103  int fleet_id = -999;
                                                                                      -
                                                                                      104  std::vector<std::shared_ptr<fims::Fleet<Type>>>
                                                                                      -
                                                                                      105  fleets;
                                                                                      +
                                                                                      103  int fleet_id = -999;
                                                                                      +
                                                                                      104  std::vector<std::shared_ptr<Fleet<Type>>>
                                                                                      +
                                                                                      105  fleets;
                                                                                      107  // Define objective function object to be able to REPORT and ADREPORT
                                                                                      108 #ifdef TMB_MODEL
                                                                                      -
                                                                                      109  ::objective_function<Type> *of;
                                                                                      +
                                                                                      109  ::objective_function<Type> *of; // :: references global namespace, defined in src/FIMS.cpp, available anywhere in the R package
                                                                                      110 #endif
                                                                                      111 
                                                                                      112  // this -> means you're referring to a class member (member of self)
                                                                                      113 
                                                                                      -
                                                                                      114  Population() { this->id = Population::id_g++; }
                                                                                      +
                                                                                      114  Population() { this->id = Population::id_g++; }
                                                                                      115 
                                                                                      -
                                                                                      123  void Initialize(int nyears, int nseasons, int nages) {
                                                                                      -
                                                                                      124  this->nyears = nyears;
                                                                                      -
                                                                                      125  this->nseasons = nseasons;
                                                                                      -
                                                                                      126  this->nages = nages;
                                                                                      +
                                                                                      123  void Initialize(int nyears, int nseasons, int nages) {
                                                                                      +
                                                                                      124  this->nyears = nyears;
                                                                                      +
                                                                                      125  this->nseasons = nseasons;
                                                                                      +
                                                                                      126  this->nages = nages;
                                                                                      127 
                                                                                      128  // size all the vectors to length of nages
                                                                                      -
                                                                                      129  nfleets = fleets.size();
                                                                                      -
                                                                                      130  expected_catch.resize(nyears * nfleets);
                                                                                      -
                                                                                      131  years.resize(nyears);
                                                                                      -
                                                                                      132  mortality_F.resize(nyears * nages);
                                                                                      -
                                                                                      133  mortality_Z.resize(nyears * nages);
                                                                                      -
                                                                                      134  proportion_mature_at_age.resize((nyears + 1) * nages);
                                                                                      -
                                                                                      135  weight_at_age.resize(nages);
                                                                                      -
                                                                                      136  unfished_numbers_at_age.resize((nyears + 1) * nages);
                                                                                      -
                                                                                      137  numbers_at_age.resize((nyears + 1) * nages);
                                                                                      -
                                                                                      138  biomass.resize((nyears + 1));
                                                                                      -
                                                                                      139  unfished_biomass.resize((nyears + 1));
                                                                                      -
                                                                                      140  unfished_spawning_biomass.resize((nyears + 1));
                                                                                      -
                                                                                      141  spawning_biomass.resize((nyears + 1));
                                                                                      -
                                                                                      142  expected_recruitment.resize((nyears + 1));
                                                                                      -
                                                                                      143  M.resize(nyears * nages);
                                                                                      -
                                                                                      144  ages.resize(nages);
                                                                                      -
                                                                                      145  log_init_naa.resize(nages);
                                                                                      -
                                                                                      146  log_M.resize(nyears * nages);
                                                                                      +
                                                                                      129  nfleets = fleets.size();
                                                                                      +
                                                                                      130  expected_catch.resize(nyears * nfleets);
                                                                                      +
                                                                                      131  years.resize(nyears);
                                                                                      +
                                                                                      132  mortality_F.resize(nyears * nages);
                                                                                      +
                                                                                      133  mortality_Z.resize(nyears * nages);
                                                                                      +
                                                                                      134  proportion_mature_at_age.resize((nyears + 1) * nages);
                                                                                      +
                                                                                      135  weight_at_age.resize(nages);
                                                                                      +
                                                                                      136  unfished_numbers_at_age.resize((nyears + 1) * nages);
                                                                                      +
                                                                                      137  numbers_at_age.resize((nyears + 1) * nages);
                                                                                      +
                                                                                      138  biomass.resize((nyears + 1));
                                                                                      +
                                                                                      139  unfished_biomass.resize((nyears + 1));
                                                                                      +
                                                                                      140  unfished_spawning_biomass.resize((nyears + 1));
                                                                                      +
                                                                                      141  spawning_biomass.resize((nyears + 1));
                                                                                      +
                                                                                      142  expected_recruitment.resize((nyears + 1));
                                                                                      +
                                                                                      143  M.resize(nyears * nages);
                                                                                      +
                                                                                      144  ages.resize(nages);
                                                                                      +
                                                                                      145  log_init_naa.resize(nages);
                                                                                      +
                                                                                      146  log_M.resize(nyears * nages);
                                                                                      147  }
                                                                                      148 
                                                                                      -
                                                                                      154  void Prepare() {
                                                                                      +
                                                                                      154  void Prepare() {
                                                                                      155  FIMS_LOG << " population prepare " << this->nages << std::endl;
                                                                                      156  FIMS_LOG << "nfleets: " << this->nfleets << std::endl;
                                                                                      157  FIMS_LOG << "nseasons: " << this->nseasons << std::endl;
                                                                                      158  FIMS_LOG << "nyears: " << this->nyears << std::endl;
                                                                                      159 
                                                                                      -
                                                                                      160  for (size_t fleet = 0; fleet < this->nfleets; fleet++) {
                                                                                      -
                                                                                      161  this->fleets[fleet]->Prepare();
                                                                                      +
                                                                                      160  for (size_t fleet = 0; fleet < this->nfleets; fleet++) {
                                                                                      +
                                                                                      161  this->fleets[fleet]->Prepare();
                                                                                      162  }
                                                                                      163 
                                                                                      -
                                                                                      164  std::fill(biomass.begin(), biomass.end(), 0);
                                                                                      -
                                                                                      165  std::fill(unfished_spawning_biomass.begin(),
                                                                                      -
                                                                                      166  unfished_spawning_biomass.end(), 0);
                                                                                      -
                                                                                      167  std::fill(spawning_biomass.begin(), spawning_biomass.end(), 0);
                                                                                      -
                                                                                      168  std::fill(expected_catch.begin(), expected_catch.end(), 0);
                                                                                      -
                                                                                      169  std::fill(expected_recruitment.begin(), expected_recruitment.end(), 0.0);
                                                                                      -
                                                                                      170  std::fill(proportion_mature_at_age.begin(), proportion_mature_at_age.end(),
                                                                                      +
                                                                                      164  std::fill(biomass.begin(), biomass.end(), 0);
                                                                                      +
                                                                                      165  std::fill(unfished_spawning_biomass.begin(),
                                                                                      +
                                                                                      166  unfished_spawning_biomass.end(), 0);
                                                                                      +
                                                                                      167  std::fill(spawning_biomass.begin(), spawning_biomass.end(), 0);
                                                                                      +
                                                                                      168  std::fill(expected_catch.begin(), expected_catch.end(), 0);
                                                                                      +
                                                                                      169  std::fill(expected_recruitment.begin(), expected_recruitment.end(), 0.0);
                                                                                      +
                                                                                      170  std::fill(proportion_mature_at_age.begin(), proportion_mature_at_age.end(),
                                                                                      171  0.0);
                                                                                      -
                                                                                      172  std::fill(mortality_Z.begin(), mortality_Z.end(), 0.0);
                                                                                      +
                                                                                      172  std::fill(mortality_Z.begin(), mortality_Z.end(), 0.0);
                                                                                      173 
                                                                                      174  // Transformation Section
                                                                                      -
                                                                                      175  for (size_t age = 0; age < this->nages; age++) {
                                                                                      -
                                                                                      176  for (size_t year = 0; year < this->nyears; year++) {
                                                                                      +
                                                                                      175  for (size_t age = 0; age < this->nages; age++) {
                                                                                      +
                                                                                      176  for (size_t year = 0; year < this->nyears; year++) {
                                                                                      177  size_t i_age_year = age * this->nyears + year;
                                                                                      -
                                                                                      178  this->M[i_age_year] = fims::exp(this->log_M[i_age_year]);
                                                                                      +
                                                                                      178  this->M[i_age_year] = fims_math::exp(this->log_M[i_age_year]);
                                                                                      179  // mortality_F is a ParameterVector and therefore needs to be filled
                                                                                      180  // within a loop
                                                                                      181  this->mortality_F[i_age_year] = 0.0;
                                                                                      @@ -227,459 +227,460 @@
                                                                                      183  }
                                                                                      184  }
                                                                                      185 
                                                                                      -
                                                                                      196  inline void CalculateInitialNumbersAA(
                                                                                      +
                                                                                      196  inline void CalculateInitialNumbersAA(
                                                                                      197  size_t i_age_year, size_t a) { // inline all function unless complicated
                                                                                      -
                                                                                      198  this->numbers_at_age[i_age_year] = fims::exp(this->log_init_naa[a]);
                                                                                      +
                                                                                      198  this->numbers_at_age[i_age_year] = fims_math::exp(this->log_init_naa[a]);
                                                                                      199  }
                                                                                      200 
                                                                                      -
                                                                                      208  void CalculateMortality(size_t i_age_year, size_t year, size_t age) {
                                                                                      -
                                                                                      209  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                                      -
                                                                                      210  if (this->fleets[fleet_]->is_survey == false) {
                                                                                      +
                                                                                      208  void CalculateMortality(size_t i_age_year, size_t year, size_t age) {
                                                                                      +
                                                                                      209  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                                      +
                                                                                      210  if (this->fleets[fleet_]->is_survey == false) {
                                                                                      211  this->mortality_F[i_age_year] +=
                                                                                      -
                                                                                      212  this->fleets[fleet_]->Fmort[year] *
                                                                                      -
                                                                                      213  this->fleets[fleet_]->selectivity->evaluate(ages[age]);
                                                                                      -
                                                                                      214  FIMS_LOG << " sel age " << ages[age] << "for fleet " << fleet_ << " is "
                                                                                      -
                                                                                      215  << this->fleets[fleet_]->selectivity->evaluate(ages[age])
                                                                                      -
                                                                                      216  << " F mort year " << year << " "
                                                                                      -
                                                                                      217  << this->fleets[fleet_]->Fmort[year] << std::endl;
                                                                                      -
                                                                                      218  }
                                                                                      -
                                                                                      219  }
                                                                                      -
                                                                                      220  FIMS_LOG << "M in calculate mortality is " << this->M[i_age_year]
                                                                                      -
                                                                                      221  << std::endl;
                                                                                      -
                                                                                      222  this->mortality_Z[i_age_year] =
                                                                                      -
                                                                                      223  this->M[i_age_year] + this->mortality_F[i_age_year];
                                                                                      -
                                                                                      224  }
                                                                                      -
                                                                                      225 
                                                                                      -
                                                                                      233  inline void CalculateNumbersAA(size_t i_age_year, size_t i_agem1_yearm1,
                                                                                      -
                                                                                      234  size_t age) {
                                                                                      -
                                                                                      235  // using Z from previous age/year
                                                                                      -
                                                                                      236  this->numbers_at_age[i_age_year] =
                                                                                      -
                                                                                      237  this->numbers_at_age[i_agem1_yearm1] *
                                                                                      -
                                                                                      238  (fims::exp(-this->mortality_Z[i_agem1_yearm1]));
                                                                                      -
                                                                                      239  FIMS_LOG << " z at i_agem1_yearm1 = " << i_agem1_yearm1 << " is "
                                                                                      -
                                                                                      240  << this->mortality_Z[i_agem1_yearm1] << std::endl;
                                                                                      -
                                                                                      241  // Plus group calculation
                                                                                      -
                                                                                      242  if (age == (this->nages - 1)) {
                                                                                      -
                                                                                      243  this->numbers_at_age[i_age_year] =
                                                                                      -
                                                                                      244  this->numbers_at_age[i_age_year] +
                                                                                      -
                                                                                      245  this->numbers_at_age[i_agem1_yearm1 + 1] *
                                                                                      -
                                                                                      246  (fims::exp(-this->mortality_Z[i_agem1_yearm1 + 1]));
                                                                                      -
                                                                                      247  }
                                                                                      -
                                                                                      248  }
                                                                                      -
                                                                                      249 
                                                                                      -
                                                                                      257  inline void CalculateUnfishedNumbersAA(size_t i_age_year,
                                                                                      -
                                                                                      258  size_t i_agem1_yearm1, size_t age) {
                                                                                      -
                                                                                      259  // using M from previous age/year
                                                                                      -
                                                                                      260  this->unfished_numbers_at_age[i_age_year] =
                                                                                      -
                                                                                      261  this->unfished_numbers_at_age[i_agem1_yearm1] *
                                                                                      -
                                                                                      262  (fims::exp(-this->M[i_agem1_yearm1]));
                                                                                      -
                                                                                      263  FIMS_LOG << "survival rate at index " << i_agem1_yearm1 << " is "
                                                                                      -
                                                                                      264  << fims::exp(-(this->M[i_agem1_yearm1])) << std::endl;
                                                                                      -
                                                                                      265  // Plus group calculation
                                                                                      -
                                                                                      266  if (age == (this->nages - 1)) {
                                                                                      -
                                                                                      267  this->unfished_numbers_at_age[i_age_year] =
                                                                                      -
                                                                                      268  this->unfished_numbers_at_age[i_age_year] +
                                                                                      -
                                                                                      269  this->unfished_numbers_at_age[i_agem1_yearm1 + 1] *
                                                                                      -
                                                                                      270  (fims::exp(-this->M[i_agem1_yearm1 + 1]));
                                                                                      -
                                                                                      271  }
                                                                                      -
                                                                                      272  }
                                                                                      -
                                                                                      273 
                                                                                      -
                                                                                      281  void CalculateBiomass(size_t i_age_year, size_t year, size_t age) {
                                                                                      -
                                                                                      282  this->biomass[year] +=
                                                                                      -
                                                                                      283  this->numbers_at_age[i_age_year] * growth->evaluate(ages[age]);
                                                                                      -
                                                                                      284  FIMS_LOG << " age " << ages[age] << std::endl;
                                                                                      -
                                                                                      285  FIMS_LOG << "growth evaluate: " << growth->evaluate(ages[age])
                                                                                      -
                                                                                      286  << " biomass inputs----- +++\n";
                                                                                      -
                                                                                      287  }
                                                                                      -
                                                                                      288 
                                                                                      -
                                                                                      297  void CalculateUnfishedBiomass(size_t i_age_year, size_t year, size_t age) {
                                                                                      -
                                                                                      298  this->unfished_biomass[year] += this->unfished_numbers_at_age[i_age_year] *
                                                                                      -
                                                                                      299  this->growth->evaluate(ages[age]);
                                                                                      -
                                                                                      300  }
                                                                                      -
                                                                                      301 
                                                                                      -
                                                                                      309  void CalculateSpawningBiomass(size_t i_age_year, size_t year, size_t age) {
                                                                                      -
                                                                                      310  this->spawning_biomass[year] += this->proportion_female *
                                                                                      -
                                                                                      311  this->numbers_at_age[i_age_year] *
                                                                                      -
                                                                                      312  this->proportion_mature_at_age[i_age_year] *
                                                                                      -
                                                                                      313  growth->evaluate(ages[age]);
                                                                                      -
                                                                                      314  FIMS_LOG << " proportion female " << this->proportion_female << " "
                                                                                      -
                                                                                      315  << " mature age " << age << " is "
                                                                                      -
                                                                                      316  << this->proportion_mature_at_age[i_age_year] << " "
                                                                                      -
                                                                                      317  << " numbers at age " << this->numbers_at_age[i_age_year] << " "
                                                                                      -
                                                                                      318  << " growth " << growth->evaluate(ages[age]) << " "
                                                                                      -
                                                                                      319  << " spawning biomass " << this->spawning_biomass[year] << " "
                                                                                      -
                                                                                      320  << " spawning biomass inputs----- +++\n";
                                                                                      -
                                                                                      321  }
                                                                                      -
                                                                                      322 
                                                                                      -
                                                                                      331  void CalculateUnfishedSpawningBiomass(size_t i_age_year, size_t year,
                                                                                      -
                                                                                      332  size_t age) {
                                                                                      -
                                                                                      333  this->unfished_spawning_biomass[year] +=
                                                                                      -
                                                                                      334  this->proportion_female * this->unfished_numbers_at_age[i_age_year] *
                                                                                      -
                                                                                      335  this->proportion_mature_at_age[i_age_year] *
                                                                                      -
                                                                                      336  this->growth->evaluate(ages[age]);
                                                                                      -
                                                                                      337  }
                                                                                      -
                                                                                      338 
                                                                                      -
                                                                                      344  Type CalculateSBPR0() {
                                                                                      -
                                                                                      345  std::vector<Type> numbers_spr(this->nages, 1.0);
                                                                                      -
                                                                                      346  Type phi_0 = 0.0;
                                                                                      -
                                                                                      347  phi_0 += numbers_spr[0] * this->proportion_female *
                                                                                      -
                                                                                      348  this->proportion_mature_at_age[0] *
                                                                                      -
                                                                                      349  this->growth->evaluate(ages[0]);
                                                                                      -
                                                                                      350  for (size_t a = 1; a < (this->nages - 1); a++) {
                                                                                      -
                                                                                      351  numbers_spr[a] = numbers_spr[a - 1] * fims::exp(-this->M[a]);
                                                                                      -
                                                                                      352  phi_0 += numbers_spr[a] * this->proportion_female *
                                                                                      -
                                                                                      353  this->proportion_mature_at_age[a] *
                                                                                      -
                                                                                      354  this->growth->evaluate(ages[a]);
                                                                                      -
                                                                                      355  }
                                                                                      -
                                                                                      356 
                                                                                      -
                                                                                      357  numbers_spr[this->nages - 1] =
                                                                                      -
                                                                                      358  (numbers_spr[nages - 2] * fims::exp(-this->M[nages - 2])) /
                                                                                      -
                                                                                      359  (1 - fims::exp(-this->M[this->nages - 1]));
                                                                                      -
                                                                                      360  phi_0 += numbers_spr[this->nages - 1] * this->proportion_female *
                                                                                      -
                                                                                      361  this->proportion_mature_at_age[this->nages - 1] *
                                                                                      -
                                                                                      362  this->growth->evaluate(ages[this->nages - 1]);
                                                                                      -
                                                                                      363  return phi_0;
                                                                                      -
                                                                                      364  }
                                                                                      -
                                                                                      365 
                                                                                      -
                                                                                      372  void CalculateRecruitment(size_t i_age_year, size_t year) {
                                                                                      -
                                                                                      373  FIMS_LOG << "recruitment 1" << std::endl;
                                                                                      -
                                                                                      374  Type phi0 = CalculateSBPR0();
                                                                                      -
                                                                                      375  FIMS_LOG << "recruitment 2" << std::endl;
                                                                                      -
                                                                                      376  FIMS_LOG << "phi0 = " << phi0 << std::endl;
                                                                                      -
                                                                                      377  FIMS_LOG << "spawning biomass = " << this->spawning_biomass[year]
                                                                                      -
                                                                                      378  << std::endl;
                                                                                      -
                                                                                      379  FIMS_LOG << "rec devs = " << this->recruitment->recruit_deviations[year - 1]
                                                                                      -
                                                                                      380  << std::endl;
                                                                                      -
                                                                                      381  FIMS_LOG << "rec eval = "
                                                                                      -
                                                                                      382  << this->recruitment->evaluate(this->spawning_biomass[year - 1],
                                                                                      -
                                                                                      383  phi0)
                                                                                      -
                                                                                      384  << std::endl;
                                                                                      -
                                                                                      385  this->numbers_at_age[i_age_year] =
                                                                                      -
                                                                                      386  this->recruitment->evaluate(this->spawning_biomass[year - 1], phi0) *
                                                                                      -
                                                                                      387  this->recruitment->recruit_deviations[year];
                                                                                      -
                                                                                      388  this->expected_recruitment[year] = this->numbers_at_age[i_age_year];
                                                                                      -
                                                                                      389  FIMS_LOG << " numbers at age at indexya " << i_age_year << " is "
                                                                                      -
                                                                                      390  << this->numbers_at_age[i_age_year] << std::endl;
                                                                                      -
                                                                                      391  }
                                                                                      -
                                                                                      392 
                                                                                      -
                                                                                      399  void CalculateCatch(size_t year, size_t age) {
                                                                                      -
                                                                                      400  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                                      -
                                                                                      401  if (this->fleets[fleet_]->is_survey == false) {
                                                                                      -
                                                                                      402  size_t index_yf = year * this->nfleets +
                                                                                      -
                                                                                      403  fleet_; // index by fleet and years to dimension fold
                                                                                      -
                                                                                      404  size_t i_age_year = year * this->nages + age;
                                                                                      -
                                                                                      405 
                                                                                      -
                                                                                      406  FIMS_LOG << " fleet " << fleet_ << " year " << year << " age " << age
                                                                                      -
                                                                                      407  << std::endl;
                                                                                      -
                                                                                      408  this->expected_catch[index_yf] +=
                                                                                      -
                                                                                      409  this->fleets[fleet_]->catch_weight_at_age[i_age_year];
                                                                                      -
                                                                                      410 
                                                                                      -
                                                                                      411  FIMS_LOG << "expected catch: " << this->expected_catch[index_yf]
                                                                                      -
                                                                                      412  << std::endl;
                                                                                      -
                                                                                      413  FIMS_LOG << "----------------------------------------------"
                                                                                      -
                                                                                      414  << std::endl;
                                                                                      -
                                                                                      415 
                                                                                      -
                                                                                      416  fleets[fleet_]->expected_catch[year] +=
                                                                                      -
                                                                                      417  this->fleets[fleet_]->catch_weight_at_age[i_age_year];
                                                                                      -
                                                                                      418  }
                                                                                      -
                                                                                      419  }
                                                                                      -
                                                                                      420  }
                                                                                      -
                                                                                      421 
                                                                                      -
                                                                                      429  void CalculateIndex(size_t i_age_year, size_t year, size_t age) {
                                                                                      -
                                                                                      430  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                                      -
                                                                                      431  Type index_;
                                                                                      -
                                                                                      432  // I = qN (N is total numbers), I is an index in numbers
                                                                                      -
                                                                                      433  if (this->fleets[fleet_]->is_survey == false) {
                                                                                      -
                                                                                      434  index_ = this->fleets[fleet_]->catch_numbers_at_age[i_age_year] *
                                                                                      -
                                                                                      435  growth->evaluate(ages[age]);
                                                                                      -
                                                                                      436  } else {
                                                                                      -
                                                                                      437  FIMS_LOG << "fleet " << fleet_ << " is a survey" << std::endl;
                                                                                      -
                                                                                      438  index_ = this->fleets[fleet_]->q *
                                                                                      -
                                                                                      439  this->fleets[fleet_]->selectivity->evaluate(ages[age]) *
                                                                                      -
                                                                                      440  this->numbers_at_age[i_age_year] *
                                                                                      -
                                                                                      441  growth->evaluate(ages[age]); // this->weight_at_age[age];
                                                                                      -
                                                                                      442  }
                                                                                      -
                                                                                      443  fleets[fleet_]->expected_index[year] += index_;
                                                                                      -
                                                                                      444  FIMS_LOG << " expected index in year " << year << " is "
                                                                                      -
                                                                                      445  << fleets[fleet_]->expected_index[year] << std::endl;
                                                                                      -
                                                                                      446  }
                                                                                      -
                                                                                      447  }
                                                                                      -
                                                                                      448 
                                                                                      -
                                                                                      458  void CalculateCatchNumbersAA(size_t i_age_year, size_t year, size_t age) {
                                                                                      -
                                                                                      459  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                                      -
                                                                                      460  // make an intermediate value in order to set multiple members (of
                                                                                      -
                                                                                      461  // current and fleet objects) to that value.
                                                                                      -
                                                                                      462  Type catch_; // catch_ is used to avoid using the c++ keyword catch
                                                                                      -
                                                                                      463  // Baranov Catch Equation
                                                                                      -
                                                                                      464  if (this->fleets[fleet_]->is_survey == false) {
                                                                                      -
                                                                                      465  catch_ = (this->fleets[fleet_]->Fmort[year] *
                                                                                      -
                                                                                      466  this->fleets[fleet_]->selectivity->evaluate(ages[age])) /
                                                                                      -
                                                                                      467  this->mortality_Z[i_age_year] *
                                                                                      -
                                                                                      468  this->numbers_at_age[i_age_year] *
                                                                                      -
                                                                                      469  (1 - fims::exp(-(this->mortality_Z[i_age_year])));
                                                                                      -
                                                                                      470  } else {
                                                                                      -
                                                                                      471  catch_ = (this->fleets[fleet_]->selectivity->evaluate(ages[age])) *
                                                                                      -
                                                                                      472  this->numbers_at_age[i_age_year];
                                                                                      -
                                                                                      473  }
                                                                                      -
                                                                                      474  FIMS_LOG << " F " << fleet_ << " " << this->fleets[fleet_]->Fmort[year]
                                                                                      -
                                                                                      475  << std::endl;
                                                                                      -
                                                                                      476  FIMS_LOG << " selectivity "
                                                                                      -
                                                                                      477  << this->fleets[fleet_]->selectivity->evaluate(ages[age])
                                                                                      -
                                                                                      478  << std::endl;
                                                                                      -
                                                                                      479  FIMS_LOG << " catch " << catch_ << std::endl;
                                                                                      -
                                                                                      480  // this->catch_numbers_at_age[i_age_yearf] += catch_;
                                                                                      -
                                                                                      481  // catch_numbers_at_age for the fleet module has different
                                                                                      -
                                                                                      482  // dimensions (year/age, not year/fleet/age)
                                                                                      -
                                                                                      483  this->fleets[fleet_]->catch_numbers_at_age[i_age_year] += catch_;
                                                                                      -
                                                                                      484  }
                                                                                      -
                                                                                      485  }
                                                                                      -
                                                                                      486 
                                                                                      -
                                                                                      494  void CalculateCatchWeightAA(size_t year, size_t age) {
                                                                                      -
                                                                                      495  int i_age_year = year * this->nages + age;
                                                                                      -
                                                                                      496  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                                      -
                                                                                      497  FIMS_LOG << " fleet " << fleet_ << std::endl;
                                                                                      -
                                                                                      498  FIMS_LOG << " catchnaa "
                                                                                      -
                                                                                      499  << this->fleets[fleet_]->catch_numbers_at_age[year] << std::endl;
                                                                                      -
                                                                                      500  FIMS_LOG << " weight " << this->growth->evaluate(ages[age]) << std::endl;
                                                                                      -
                                                                                      501  this->fleets[fleet_]->catch_weight_at_age[i_age_year] =
                                                                                      -
                                                                                      502  this->fleets[fleet_]->catch_numbers_at_age[i_age_year] *
                                                                                      -
                                                                                      503  this->growth->evaluate(ages[age]); // this->weight_at_age[age];
                                                                                      -
                                                                                      504  FIMS_LOG << " catch_waa "
                                                                                      -
                                                                                      505  << this->fleets[fleet_]->catch_weight_at_age[i_age_year]
                                                                                      -
                                                                                      506  << std::endl;
                                                                                      -
                                                                                      507  }
                                                                                      -
                                                                                      508  }
                                                                                      -
                                                                                      509 
                                                                                      -
                                                                                      517  void CalculateMaturityAA(size_t i_age_year, size_t age) {
                                                                                      -
                                                                                      518  // this->maturity is pointing to the maturity module, which has
                                                                                      -
                                                                                      519  // an evaluate function. -> can be nested.
                                                                                      -
                                                                                      520  FIMS_LOG << " age " << age << std::endl;
                                                                                      -
                                                                                      521  FIMS_LOG << " ages size " << this->ages.size() << std::endl;
                                                                                      -
                                                                                      522  FIMS_LOG << " i_age_year " << i_age_year << std::endl;
                                                                                      -
                                                                                      523  FIMS_LOG << "p mature" << this->proportion_mature_at_age[i_age_year]
                                                                                      -
                                                                                      524  << std::endl;
                                                                                      -
                                                                                      525  FIMS_LOG << this->ages[age] << std::endl;
                                                                                      -
                                                                                      526  this->proportion_mature_at_age[i_age_year] =
                                                                                      -
                                                                                      527  this->maturity->evaluate(ages[age]);
                                                                                      -
                                                                                      528 
                                                                                      -
                                                                                      529  FIMS_LOG << "p mature set to " << this->proportion_mature_at_age[i_age_year]
                                                                                      -
                                                                                      530  << std::endl;
                                                                                      -
                                                                                      531  }
                                                                                      -
                                                                                      532 
                                                                                      -
                                                                                      537  void Evaluate() {
                                                                                      -
                                                                                      538  /*
                                                                                      -
                                                                                      539  Sets derived vectors to zero
                                                                                      -
                                                                                      540  Performs parameters transformations
                                                                                      -
                                                                                      541  Sets recruitment deviations to mean 0.
                                                                                      -
                                                                                      542  */
                                                                                      -
                                                                                      543  Prepare();
                                                                                      -
                                                                                      544  /*
                                                                                      -
                                                                                      545  start at year=0, age=0;
                                                                                      -
                                                                                      546  here year 0 is the estimated initial stock structure and age 0 are recruits
                                                                                      -
                                                                                      547  loops start at zero with if statements inside to specify unique code for
                                                                                      -
                                                                                      548  initial structure and recruitment 0 loops. Could also have started loops at
                                                                                      -
                                                                                      549  1 with initial structure and recruitment setup outside the loops.
                                                                                      -
                                                                                      550 
                                                                                      -
                                                                                      551  year loop is extended to <= nyears because SSB is calculted as the start of
                                                                                      -
                                                                                      552  the year value and by extending one extra year we get estimates of the
                                                                                      -
                                                                                      553  population structure at the end of the final year. An alternative approach
                                                                                      -
                                                                                      554  would be to keep initial numbers at age in it's own vector and each year to
                                                                                      -
                                                                                      555  include the population structure at the end of the year. This is likely a
                                                                                      -
                                                                                      556  null point given that we are planning to modify to an event/stanza based
                                                                                      -
                                                                                      557  structure in later milestones which will elimitate this confusion by
                                                                                      -
                                                                                      558  explicity referencing the exact date (or period of averaging) at which any
                                                                                      -
                                                                                      559  calculation or output is being made.
                                                                                      -
                                                                                      560  */
                                                                                      -
                                                                                      561  for (size_t y = 0; y <= this->nyears; y++) {
                                                                                      -
                                                                                      562  for (size_t a = 0; a < this->nages; a++) {
                                                                                      -
                                                                                      563  /*
                                                                                      -
                                                                                      564  index naming defines the dimensional folding structure
                                                                                      -
                                                                                      565  i.e. i_age_year is referencing folding over years and ages.
                                                                                      -
                                                                                      566  */
                                                                                      -
                                                                                      567  size_t i_age_year = y * this->nages + a;
                                                                                      -
                                                                                      568  /*
                                                                                      -
                                                                                      569  Mortality rates are not estimated in the final year which is
                                                                                      -
                                                                                      570  used to show expected stock structure at the end of the model period.
                                                                                      -
                                                                                      571  This is because biomass in year i represents biomass at the start of
                                                                                      -
                                                                                      572  the year.
                                                                                      -
                                                                                      573  Should we add complexity to track more values such as start,
                                                                                      -
                                                                                      574  mid, and end biomass in all years where, start biomass=end biomass of
                                                                                      -
                                                                                      575  the previous year? Referenced above, this is probably not worth
                                                                                      -
                                                                                      576  exploring as later milestone changes will eliminate this confusion.
                                                                                      -
                                                                                      577  */
                                                                                      -
                                                                                      578  if (y < this->nyears) {
                                                                                      -
                                                                                      579  /*
                                                                                      -
                                                                                      580  First thing we need is total mortality aggregated across all fleets
                                                                                      -
                                                                                      581  to inform the subsequent catch and change in numbers at age
                                                                                      -
                                                                                      582  calculations. This is only calculated for years < nyears as these are
                                                                                      -
                                                                                      583  the model estimated years with data. The year loop extends to
                                                                                      -
                                                                                      584  y=nyears so that population numbers at age and SSB can be calculated
                                                                                      -
                                                                                      585  at the end of the last year of the model
                                                                                      -
                                                                                      586  */
                                                                                      -
                                                                                      587  CalculateMortality(i_age_year, y, a);
                                                                                      -
                                                                                      588  }
                                                                                      -
                                                                                      589  CalculateMaturityAA(i_age_year, a);
                                                                                      -
                                                                                      590  /* if statements needed because some quantities are only needed
                                                                                      -
                                                                                      591  for the first year and/or age, so these steps are included here.
                                                                                      -
                                                                                      592  */
                                                                                      -
                                                                                      593  if (y == 0) {
                                                                                      -
                                                                                      594  // Initial numbers at age is a user input or estimated parameter
                                                                                      -
                                                                                      595  // vector.
                                                                                      -
                                                                                      596  CalculateInitialNumbersAA(i_age_year, a);
                                                                                      -
                                                                                      597 
                                                                                      -
                                                                                      598  if (a == 0) {
                                                                                      -
                                                                                      599  // this->numbers_at_age[i_age_year] = this->recruitment->rzero;
                                                                                      -
                                                                                      600  this->unfished_numbers_at_age[i_age_year] =
                                                                                      -
                                                                                      601  fims::exp(this->recruitment->log_rzero);
                                                                                      -
                                                                                      602  } else {
                                                                                      -
                                                                                      603  CalculateUnfishedNumbersAA(i_age_year, a - 1, a);
                                                                                      -
                                                                                      604  }
                                                                                      -
                                                                                      605 
                                                                                      -
                                                                                      606  /*
                                                                                      -
                                                                                      607  Fished and unfished biomass vectors are summing biomass at
                                                                                      -
                                                                                      608  age across ages.
                                                                                      -
                                                                                      609  */
                                                                                      -
                                                                                      610 
                                                                                      -
                                                                                      611  CalculateBiomass(i_age_year, y, a);
                                                                                      -
                                                                                      612 
                                                                                      -
                                                                                      613  CalculateUnfishedBiomass(i_age_year, y, a);
                                                                                      -
                                                                                      614 
                                                                                      -
                                                                                      615  /*
                                                                                      -
                                                                                      616  Fished and unfished spawning biomass vectors are summing biomass at
                                                                                      -
                                                                                      617  age across ages to allow calculation of recruitment in the next year.
                                                                                      -
                                                                                      618  */
                                                                                      -
                                                                                      619 
                                                                                      -
                                                                                      620  CalculateSpawningBiomass(i_age_year, y, a);
                                                                                      -
                                                                                      621 
                                                                                      -
                                                                                      622  CalculateUnfishedSpawningBiomass(i_age_year, y, a);
                                                                                      -
                                                                                      623 
                                                                                      -
                                                                                      624  /*
                                                                                      -
                                                                                      625  Expected recruitment in year 0 is numbers at age 0 in year 0.
                                                                                      -
                                                                                      626  */
                                                                                      -
                                                                                      627 
                                                                                      -
                                                                                      628  this->expected_recruitment[i_age_year] =
                                                                                      -
                                                                                      629  this->numbers_at_age[i_age_year];
                                                                                      -
                                                                                      630 
                                                                                      -
                                                                                      631  } else {
                                                                                      -
                                                                                      632  if (a == 0) {
                                                                                      -
                                                                                      633  // Set the nrecruits for age a=0 year y (use pointers instead of
                                                                                      -
                                                                                      634  // functional returns) assuming fecundity = 1 and 50:50 sex ratio
                                                                                      -
                                                                                      635  FIMS_LOG << "Recruitment: " << std::endl;
                                                                                      -
                                                                                      636  CalculateRecruitment(i_age_year, y);
                                                                                      -
                                                                                      637  this->unfished_numbers_at_age[i_age_year] =
                                                                                      -
                                                                                      638  fims::exp(this->recruitment->log_rzero);
                                                                                      -
                                                                                      639 
                                                                                      -
                                                                                      640  } else {
                                                                                      -
                                                                                      641  size_t i_agem1_yearm1 = (y - 1) * nages + (a - 1);
                                                                                      -
                                                                                      642  CalculateNumbersAA(i_age_year, i_agem1_yearm1, a);
                                                                                      -
                                                                                      643  CalculateUnfishedNumbersAA(i_age_year, i_agem1_yearm1, a);
                                                                                      -
                                                                                      644  }
                                                                                      -
                                                                                      645  CalculateBiomass(i_age_year, y, a);
                                                                                      -
                                                                                      646  CalculateSpawningBiomass(i_age_year, y, a);
                                                                                      -
                                                                                      647 
                                                                                      -
                                                                                      648  FIMS_LOG << "index ya: " << i_age_year << std::endl;
                                                                                      -
                                                                                      649  CalculateUnfishedBiomass(i_age_year, y, a);
                                                                                      -
                                                                                      650  CalculateUnfishedSpawningBiomass(i_age_year, y, a);
                                                                                      -
                                                                                      651  }
                                                                                      -
                                                                                      652 
                                                                                      -
                                                                                      653  /*
                                                                                      -
                                                                                      654  Here composition, total catch, and index values are calculated for all
                                                                                      -
                                                                                      655  years with reference data. They are not calculated for y=nyears as there
                                                                                      -
                                                                                      656  is this is just to get final population structure at the end of the
                                                                                      -
                                                                                      657  terminal year.
                                                                                      -
                                                                                      658  */
                                                                                      -
                                                                                      659  if (y < this->nyears) {
                                                                                      -
                                                                                      660  FIMS_LOG << i_age_year << std::endl;
                                                                                      -
                                                                                      661  CalculateCatchNumbersAA(i_age_year, y, a);
                                                                                      -
                                                                                      662 
                                                                                      -
                                                                                      663  CalculateCatchWeightAA(y, a);
                                                                                      -
                                                                                      664  FIMS_LOG << "year " << y << " and age " << a << std::endl;
                                                                                      -
                                                                                      665  CalculateCatch(y, a);
                                                                                      -
                                                                                      666  CalculateIndex(i_age_year, y, a);
                                                                                      -
                                                                                      667  }
                                                                                      -
                                                                                      668  }
                                                                                      -
                                                                                      669  }
                                                                                      -
                                                                                      670  FIMS_LOG << "NAA\n";
                                                                                      -
                                                                                      671  for (size_t i = 0; i < nyears; i++) {
                                                                                      -
                                                                                      672  for (size_t j = 0; j < nages; j++) {
                                                                                      -
                                                                                      673  FIMS_LOG << numbers_at_age[i * nages + j] << "\t";
                                                                                      -
                                                                                      674  }
                                                                                      -
                                                                                      675  FIMS_LOG << "\n";
                                                                                      -
                                                                                      676  }
                                                                                      -
                                                                                      677 
                                                                                      -
                                                                                      678  FIMS_LOG << "CAA\n";
                                                                                      -
                                                                                      679  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                                      -
                                                                                      680  FIMS_LOG << "Fleet " << fleet_ + 1 << "\n";
                                                                                      -
                                                                                      681  for (size_t i = 0; i < nyears; i++) {
                                                                                      -
                                                                                      682  for (size_t j = 0; j < nages; j++) {
                                                                                      -
                                                                                      683  FIMS_LOG << fleets[fleet_]->catch_numbers_at_age[i * nages + j]
                                                                                      -
                                                                                      684  << "\t";
                                                                                      -
                                                                                      685  }
                                                                                      -
                                                                                      686  FIMS_LOG << "\n";
                                                                                      -
                                                                                      687  }
                                                                                      -
                                                                                      688  }
                                                                                      -
                                                                                      689  }
                                                                                      -
                                                                                      690 };
                                                                                      -
                                                                                      691 template <class Type>
                                                                                      -
                                                                                      692 uint32_t Population<Type>::id_g = 0;
                                                                                      -
                                                                                      693 
                                                                                      -
                                                                                      694 } // namespace fims
                                                                                      -
                                                                                      695 
                                                                                      -
                                                                                      696 #endif /* FIMS_POPULATION_DYNAMICS_POPULATION_HPP */
                                                                                      +
                                                                                      212  this->fleets[fleet_]->Fmort[year] *
                                                                                      +
                                                                                      213  // evaluate is a member function of the selectivity class
                                                                                      +
                                                                                      214  this->fleets[fleet_]->selectivity->evaluate(ages[age]);
                                                                                      +
                                                                                      215  FIMS_LOG << " sel age " << ages[age] << "for fleet " << fleet_ << " is "
                                                                                      +
                                                                                      216  << this->fleets[fleet_]->selectivity->evaluate(ages[age])
                                                                                      +
                                                                                      217  << " F mort year " << year << " "
                                                                                      +
                                                                                      218  << this->fleets[fleet_]->Fmort[year] << std::endl;
                                                                                      +
                                                                                      219  }
                                                                                      +
                                                                                      220  }
                                                                                      +
                                                                                      221  FIMS_LOG << "M in calculate mortality is " << this->M[i_age_year]
                                                                                      +
                                                                                      222  << std::endl;
                                                                                      +
                                                                                      223  this->mortality_Z[i_age_year] =
                                                                                      +
                                                                                      224  this->M[i_age_year] + this->mortality_F[i_age_year];
                                                                                      +
                                                                                      225  }
                                                                                      +
                                                                                      226 
                                                                                      +
                                                                                      234  inline void CalculateNumbersAA(size_t i_age_year, size_t i_agem1_yearm1,
                                                                                      +
                                                                                      235  size_t age) {
                                                                                      +
                                                                                      236  // using Z from previous age/year
                                                                                      +
                                                                                      237  this->numbers_at_age[i_age_year] =
                                                                                      +
                                                                                      238  this->numbers_at_age[i_agem1_yearm1] *
                                                                                      +
                                                                                      239  (fims_math::exp(-this->mortality_Z[i_agem1_yearm1]));
                                                                                      +
                                                                                      240  FIMS_LOG << " z at i_agem1_yearm1 = " << i_agem1_yearm1 << " is "
                                                                                      +
                                                                                      241  << this->mortality_Z[i_agem1_yearm1] << std::endl;
                                                                                      +
                                                                                      242  // Plus group calculation
                                                                                      +
                                                                                      243  if (age == (this->nages - 1)) {
                                                                                      +
                                                                                      244  this->numbers_at_age[i_age_year] =
                                                                                      +
                                                                                      245  this->numbers_at_age[i_age_year] +
                                                                                      +
                                                                                      246  this->numbers_at_age[i_agem1_yearm1 + 1] *
                                                                                      +
                                                                                      247  (fims_math::exp(-this->mortality_Z[i_agem1_yearm1 + 1]));
                                                                                      +
                                                                                      248  }
                                                                                      +
                                                                                      249  }
                                                                                      +
                                                                                      250 
                                                                                      +
                                                                                      258  inline void CalculateUnfishedNumbersAA(size_t i_age_year,
                                                                                      +
                                                                                      259  size_t i_agem1_yearm1, size_t age) {
                                                                                      +
                                                                                      260  // using M from previous age/year
                                                                                      +
                                                                                      261  this->unfished_numbers_at_age[i_age_year] =
                                                                                      +
                                                                                      262  this->unfished_numbers_at_age[i_agem1_yearm1] *
                                                                                      +
                                                                                      263  (fims_math::exp(-this->M[i_agem1_yearm1]));
                                                                                      +
                                                                                      264  FIMS_LOG << "survival rate at index " << i_agem1_yearm1 << " is "
                                                                                      +
                                                                                      265  << fims_math::exp(-(this->M[i_agem1_yearm1])) << std::endl;
                                                                                      +
                                                                                      266  // Plus group calculation
                                                                                      +
                                                                                      267  if (age == (this->nages - 1)) {
                                                                                      +
                                                                                      268  this->unfished_numbers_at_age[i_age_year] =
                                                                                      +
                                                                                      269  this->unfished_numbers_at_age[i_age_year] +
                                                                                      +
                                                                                      270  this->unfished_numbers_at_age[i_agem1_yearm1 + 1] *
                                                                                      +
                                                                                      271  (fims_math::exp(-this->M[i_agem1_yearm1 + 1]));
                                                                                      +
                                                                                      272  }
                                                                                      +
                                                                                      273  }
                                                                                      +
                                                                                      274 
                                                                                      +
                                                                                      282  void CalculateBiomass(size_t i_age_year, size_t year, size_t age) {
                                                                                      +
                                                                                      283  this->biomass[year] +=
                                                                                      +
                                                                                      284  this->numbers_at_age[i_age_year] * growth->evaluate(ages[age]);
                                                                                      +
                                                                                      285  FIMS_LOG << " age " << ages[age] << std::endl;
                                                                                      +
                                                                                      286  FIMS_LOG << "growth evaluate: " << growth->evaluate(ages[age])
                                                                                      +
                                                                                      287  << " biomass inputs----- +++\n";
                                                                                      +
                                                                                      288  }
                                                                                      +
                                                                                      289 
                                                                                      +
                                                                                      298  void CalculateUnfishedBiomass(size_t i_age_year, size_t year, size_t age) {
                                                                                      +
                                                                                      299  this->unfished_biomass[year] += this->unfished_numbers_at_age[i_age_year] *
                                                                                      +
                                                                                      300  this->growth->evaluate(ages[age]);
                                                                                      +
                                                                                      301  }
                                                                                      +
                                                                                      302 
                                                                                      +
                                                                                      310  void CalculateSpawningBiomass(size_t i_age_year, size_t year, size_t age) {
                                                                                      +
                                                                                      311  this->spawning_biomass[year] += this->proportion_female *
                                                                                      +
                                                                                      312  this->numbers_at_age[i_age_year] *
                                                                                      +
                                                                                      313  this->proportion_mature_at_age[i_age_year] *
                                                                                      +
                                                                                      314  growth->evaluate(ages[age]);
                                                                                      +
                                                                                      315  FIMS_LOG << " proportion female " << this->proportion_female << " "
                                                                                      +
                                                                                      316  << " mature age " << age << " is "
                                                                                      +
                                                                                      317  << this->proportion_mature_at_age[i_age_year] << " "
                                                                                      +
                                                                                      318  << " numbers at age " << this->numbers_at_age[i_age_year] << " "
                                                                                      +
                                                                                      319  << " growth " << growth->evaluate(ages[age]) << " "
                                                                                      +
                                                                                      320  << " spawning biomass " << this->spawning_biomass[year] << " "
                                                                                      +
                                                                                      321  << " spawning biomass inputs----- +++\n";
                                                                                      +
                                                                                      322  }
                                                                                      +
                                                                                      323 
                                                                                      +
                                                                                      332  void CalculateUnfishedSpawningBiomass(size_t i_age_year, size_t year,
                                                                                      +
                                                                                      333  size_t age) {
                                                                                      +
                                                                                      334  this->unfished_spawning_biomass[year] +=
                                                                                      +
                                                                                      335  this->proportion_female * this->unfished_numbers_at_age[i_age_year] *
                                                                                      +
                                                                                      336  this->proportion_mature_at_age[i_age_year] *
                                                                                      +
                                                                                      337  this->growth->evaluate(ages[age]);
                                                                                      +
                                                                                      338  }
                                                                                      +
                                                                                      339 
                                                                                      +
                                                                                      345  Type CalculateSBPR0() {
                                                                                      +
                                                                                      346  std::vector<Type> numbers_spr(this->nages, 1.0);
                                                                                      +
                                                                                      347  Type phi_0 = 0.0;
                                                                                      +
                                                                                      348  phi_0 += numbers_spr[0] * this->proportion_female *
                                                                                      +
                                                                                      349  this->proportion_mature_at_age[0] *
                                                                                      +
                                                                                      350  this->growth->evaluate(ages[0]);
                                                                                      +
                                                                                      351  for (size_t a = 1; a < (this->nages - 1); a++) {
                                                                                      +
                                                                                      352  numbers_spr[a] = numbers_spr[a - 1] * fims_math::exp(-this->M[a]);
                                                                                      +
                                                                                      353  phi_0 += numbers_spr[a] * this->proportion_female *
                                                                                      +
                                                                                      354  this->proportion_mature_at_age[a] *
                                                                                      +
                                                                                      355  this->growth->evaluate(ages[a]);
                                                                                      +
                                                                                      356  }
                                                                                      +
                                                                                      357 
                                                                                      +
                                                                                      358  numbers_spr[this->nages - 1] =
                                                                                      +
                                                                                      359  (numbers_spr[nages - 2] * fims_math::exp(-this->M[nages - 2])) /
                                                                                      +
                                                                                      360  (1 - fims_math::exp(-this->M[this->nages - 1]));
                                                                                      +
                                                                                      361  phi_0 += numbers_spr[this->nages - 1] * this->proportion_female *
                                                                                      +
                                                                                      362  this->proportion_mature_at_age[this->nages - 1] *
                                                                                      +
                                                                                      363  this->growth->evaluate(ages[this->nages - 1]);
                                                                                      +
                                                                                      364  return phi_0;
                                                                                      +
                                                                                      365  }
                                                                                      +
                                                                                      366 
                                                                                      +
                                                                                      373  void CalculateRecruitment(size_t i_age_year, size_t year) {
                                                                                      +
                                                                                      374  FIMS_LOG << "recruitment 1" << std::endl;
                                                                                      +
                                                                                      375  Type phi0 = CalculateSBPR0();
                                                                                      +
                                                                                      376  FIMS_LOG << "recruitment 2" << std::endl;
                                                                                      +
                                                                                      377  FIMS_LOG << "phi0 = " << phi0 << std::endl;
                                                                                      +
                                                                                      378  FIMS_LOG << "spawning biomass = " << this->spawning_biomass[year]
                                                                                      +
                                                                                      379  << std::endl;
                                                                                      +
                                                                                      380  FIMS_LOG << "rec devs = " << this->recruitment->recruit_deviations[year - 1]
                                                                                      +
                                                                                      381  << std::endl;
                                                                                      +
                                                                                      382  FIMS_LOG << "rec eval = "
                                                                                      +
                                                                                      383  << this->recruitment->evaluate(this->spawning_biomass[year - 1],
                                                                                      +
                                                                                      384  phi0)
                                                                                      +
                                                                                      385  << std::endl;
                                                                                      +
                                                                                      386  this->numbers_at_age[i_age_year] =
                                                                                      +
                                                                                      387  this->recruitment->evaluate(this->spawning_biomass[year - 1], phi0) *
                                                                                      +
                                                                                      388  this->recruitment->recruit_deviations[year];
                                                                                      +
                                                                                      389  this->expected_recruitment[year] = this->numbers_at_age[i_age_year];
                                                                                      +
                                                                                      390  FIMS_LOG << " numbers at age at indexya " << i_age_year << " is "
                                                                                      +
                                                                                      391  << this->numbers_at_age[i_age_year] << std::endl;
                                                                                      +
                                                                                      392  }
                                                                                      +
                                                                                      393 
                                                                                      +
                                                                                      400  void CalculateCatch(size_t year, size_t age) {
                                                                                      +
                                                                                      401  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                                      +
                                                                                      402  if (this->fleets[fleet_]->is_survey == false) {
                                                                                      +
                                                                                      403  size_t index_yf = year * this->nfleets +
                                                                                      +
                                                                                      404  fleet_; // index by fleet and years to dimension fold
                                                                                      +
                                                                                      405  size_t i_age_year = year * this->nages + age;
                                                                                      +
                                                                                      406 
                                                                                      +
                                                                                      407  FIMS_LOG << " fleet " << fleet_ << " year " << year << " age " << age
                                                                                      +
                                                                                      408  << std::endl;
                                                                                      +
                                                                                      409  this->expected_catch[index_yf] +=
                                                                                      +
                                                                                      410  this->fleets[fleet_]->catch_weight_at_age[i_age_year];
                                                                                      +
                                                                                      411 
                                                                                      +
                                                                                      412  FIMS_LOG << "expected catch: " << this->expected_catch[index_yf]
                                                                                      +
                                                                                      413  << std::endl;
                                                                                      +
                                                                                      414  FIMS_LOG << "----------------------------------------------"
                                                                                      +
                                                                                      415  << std::endl;
                                                                                      +
                                                                                      416 
                                                                                      +
                                                                                      417  fleets[fleet_]->expected_catch[year] +=
                                                                                      +
                                                                                      418  this->fleets[fleet_]->catch_weight_at_age[i_age_year];
                                                                                      +
                                                                                      419  }
                                                                                      +
                                                                                      420  }
                                                                                      +
                                                                                      421  }
                                                                                      +
                                                                                      422 
                                                                                      +
                                                                                      430  void CalculateIndex(size_t i_age_year, size_t year, size_t age) {
                                                                                      +
                                                                                      431  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                                      +
                                                                                      432  Type index_;
                                                                                      +
                                                                                      433  // I = qN (N is total numbers), I is an index in numbers
                                                                                      +
                                                                                      434  if (this->fleets[fleet_]->is_survey == false) {
                                                                                      +
                                                                                      435  index_ = this->fleets[fleet_]->catch_numbers_at_age[i_age_year] *
                                                                                      +
                                                                                      436  growth->evaluate(ages[age]);
                                                                                      +
                                                                                      437  } else {
                                                                                      +
                                                                                      438  FIMS_LOG << "fleet " << fleet_ << " is a survey" << std::endl;
                                                                                      +
                                                                                      439  index_ = this->fleets[fleet_]->q *
                                                                                      +
                                                                                      440  this->fleets[fleet_]->selectivity->evaluate(ages[age]) *
                                                                                      +
                                                                                      441  this->numbers_at_age[i_age_year] *
                                                                                      +
                                                                                      442  growth->evaluate(ages[age]); // this->weight_at_age[age];
                                                                                      +
                                                                                      443  }
                                                                                      +
                                                                                      444  fleets[fleet_]->expected_index[year] += index_;
                                                                                      +
                                                                                      445  FIMS_LOG << " expected index in year " << year << " is "
                                                                                      +
                                                                                      446  << fleets[fleet_]->expected_index[year] << std::endl;
                                                                                      +
                                                                                      447  }
                                                                                      +
                                                                                      448  }
                                                                                      +
                                                                                      449 
                                                                                      +
                                                                                      459  void CalculateCatchNumbersAA(size_t i_age_year, size_t year, size_t age) {
                                                                                      +
                                                                                      460  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                                      +
                                                                                      461  // make an intermediate value in order to set multiple members (of
                                                                                      +
                                                                                      462  // current and fleet objects) to that value.
                                                                                      +
                                                                                      463  Type catch_; // catch_ is used to avoid using the c++ keyword catch
                                                                                      +
                                                                                      464  // Baranov Catch Equation
                                                                                      +
                                                                                      465  if (this->fleets[fleet_]->is_survey == false) {
                                                                                      +
                                                                                      466  catch_ = (this->fleets[fleet_]->Fmort[year] *
                                                                                      +
                                                                                      467  this->fleets[fleet_]->selectivity->evaluate(ages[age])) /
                                                                                      +
                                                                                      468  this->mortality_Z[i_age_year] *
                                                                                      +
                                                                                      469  this->numbers_at_age[i_age_year] *
                                                                                      +
                                                                                      470  (1 - fims_math::exp(-(this->mortality_Z[i_age_year])));
                                                                                      +
                                                                                      471  } else {
                                                                                      +
                                                                                      472  catch_ = (this->fleets[fleet_]->selectivity->evaluate(ages[age])) *
                                                                                      +
                                                                                      473  this->numbers_at_age[i_age_year];
                                                                                      +
                                                                                      474  }
                                                                                      +
                                                                                      475  FIMS_LOG << " F " << fleet_ << " " << this->fleets[fleet_]->Fmort[year]
                                                                                      +
                                                                                      476  << std::endl;
                                                                                      +
                                                                                      477  FIMS_LOG << " selectivity "
                                                                                      +
                                                                                      478  << this->fleets[fleet_]->selectivity->evaluate(ages[age])
                                                                                      +
                                                                                      479  << std::endl;
                                                                                      +
                                                                                      480  FIMS_LOG << " catch " << catch_ << std::endl;
                                                                                      +
                                                                                      481  // this->catch_numbers_at_age[i_age_yearf] += catch_;
                                                                                      +
                                                                                      482  // catch_numbers_at_age for the fleet module has different
                                                                                      +
                                                                                      483  // dimensions (year/age, not year/fleet/age)
                                                                                      +
                                                                                      484  this->fleets[fleet_]->catch_numbers_at_age[i_age_year] += catch_;
                                                                                      +
                                                                                      485  }
                                                                                      +
                                                                                      486  }
                                                                                      +
                                                                                      487 
                                                                                      +
                                                                                      495  void CalculateCatchWeightAA(size_t year, size_t age) {
                                                                                      +
                                                                                      496  int i_age_year = year * this->nages + age;
                                                                                      +
                                                                                      497  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                                      +
                                                                                      498  FIMS_LOG << " fleet " << fleet_ << std::endl;
                                                                                      +
                                                                                      499  FIMS_LOG << " catchnaa "
                                                                                      +
                                                                                      500  << this->fleets[fleet_]->catch_numbers_at_age[year] << std::endl;
                                                                                      +
                                                                                      501  FIMS_LOG << " weight " << this->growth->evaluate(ages[age]) << std::endl;
                                                                                      +
                                                                                      502  this->fleets[fleet_]->catch_weight_at_age[i_age_year] =
                                                                                      +
                                                                                      503  this->fleets[fleet_]->catch_numbers_at_age[i_age_year] *
                                                                                      +
                                                                                      504  this->growth->evaluate(ages[age]); // this->weight_at_age[age];
                                                                                      +
                                                                                      505  FIMS_LOG << " catch_waa "
                                                                                      +
                                                                                      506  << this->fleets[fleet_]->catch_weight_at_age[i_age_year]
                                                                                      +
                                                                                      507  << std::endl;
                                                                                      +
                                                                                      508  }
                                                                                      +
                                                                                      509  }
                                                                                      +
                                                                                      510 
                                                                                      +
                                                                                      518  void CalculateMaturityAA(size_t i_age_year, size_t age) {
                                                                                      +
                                                                                      519  // this->maturity is pointing to the maturity module, which has
                                                                                      +
                                                                                      520  // an evaluate function. -> can be nested.
                                                                                      +
                                                                                      521  FIMS_LOG << " age " << age << std::endl;
                                                                                      +
                                                                                      522  FIMS_LOG << " ages size " << this->ages.size() << std::endl;
                                                                                      +
                                                                                      523  FIMS_LOG << " i_age_year " << i_age_year << std::endl;
                                                                                      +
                                                                                      524  FIMS_LOG << "p mature" << this->proportion_mature_at_age[i_age_year]
                                                                                      +
                                                                                      525  << std::endl;
                                                                                      +
                                                                                      526  FIMS_LOG << this->ages[age] << std::endl;
                                                                                      +
                                                                                      527  this->proportion_mature_at_age[i_age_year] =
                                                                                      +
                                                                                      528  this->maturity->evaluate(ages[age]);
                                                                                      +
                                                                                      529 
                                                                                      +
                                                                                      530  FIMS_LOG << "p mature set to " << this->proportion_mature_at_age[i_age_year]
                                                                                      +
                                                                                      531  << std::endl;
                                                                                      +
                                                                                      532  }
                                                                                      +
                                                                                      533 
                                                                                      +
                                                                                      538  void Evaluate() {
                                                                                      +
                                                                                      539  /*
                                                                                      +
                                                                                      540  Sets derived vectors to zero
                                                                                      +
                                                                                      541  Performs parameters transformations
                                                                                      +
                                                                                      542  Sets recruitment deviations to mean 0.
                                                                                      +
                                                                                      543  */
                                                                                      +
                                                                                      544  Prepare();
                                                                                      +
                                                                                      545  /*
                                                                                      +
                                                                                      546  start at year=0, age=0;
                                                                                      +
                                                                                      547  here year 0 is the estimated initial stock structure and age 0 are recruits
                                                                                      +
                                                                                      548  loops start at zero with if statements inside to specify unique code for
                                                                                      +
                                                                                      549  initial structure and recruitment 0 loops. Could also have started loops at
                                                                                      +
                                                                                      550  1 with initial structure and recruitment setup outside the loops.
                                                                                      +
                                                                                      551 
                                                                                      +
                                                                                      552  year loop is extended to <= nyears because SSB is calculted as the start of
                                                                                      +
                                                                                      553  the year value and by extending one extra year we get estimates of the
                                                                                      +
                                                                                      554  population structure at the end of the final year. An alternative approach
                                                                                      +
                                                                                      555  would be to keep initial numbers at age in it's own vector and each year to
                                                                                      +
                                                                                      556  include the population structure at the end of the year. This is likely a
                                                                                      +
                                                                                      557  null point given that we are planning to modify to an event/stanza based
                                                                                      +
                                                                                      558  structure in later milestones which will elimitate this confusion by
                                                                                      +
                                                                                      559  explicity referencing the exact date (or period of averaging) at which any
                                                                                      +
                                                                                      560  calculation or output is being made.
                                                                                      +
                                                                                      561  */
                                                                                      +
                                                                                      562  for (size_t y = 0; y <= this->nyears; y++) {
                                                                                      +
                                                                                      563  for (size_t a = 0; a < this->nages; a++) {
                                                                                      +
                                                                                      564  /*
                                                                                      +
                                                                                      565  index naming defines the dimensional folding structure
                                                                                      +
                                                                                      566  i.e. i_age_year is referencing folding over years and ages.
                                                                                      +
                                                                                      567  */
                                                                                      +
                                                                                      568  size_t i_age_year = y * this->nages + a;
                                                                                      +
                                                                                      569  /*
                                                                                      +
                                                                                      570  Mortality rates are not estimated in the final year which is
                                                                                      +
                                                                                      571  used to show expected stock structure at the end of the model period.
                                                                                      +
                                                                                      572  This is because biomass in year i represents biomass at the start of
                                                                                      +
                                                                                      573  the year.
                                                                                      +
                                                                                      574  Should we add complexity to track more values such as start,
                                                                                      +
                                                                                      575  mid, and end biomass in all years where, start biomass=end biomass of
                                                                                      +
                                                                                      576  the previous year? Referenced above, this is probably not worth
                                                                                      +
                                                                                      577  exploring as later milestone changes will eliminate this confusion.
                                                                                      +
                                                                                      578  */
                                                                                      +
                                                                                      579  if (y < this->nyears) {
                                                                                      +
                                                                                      580  /*
                                                                                      +
                                                                                      581  First thing we need is total mortality aggregated across all fleets
                                                                                      +
                                                                                      582  to inform the subsequent catch and change in numbers at age
                                                                                      +
                                                                                      583  calculations. This is only calculated for years < nyears as these are
                                                                                      +
                                                                                      584  the model estimated years with data. The year loop extends to
                                                                                      +
                                                                                      585  y=nyears so that population numbers at age and SSB can be calculated
                                                                                      +
                                                                                      586  at the end of the last year of the model
                                                                                      +
                                                                                      587  */
                                                                                      +
                                                                                      588  CalculateMortality(i_age_year, y, a);
                                                                                      +
                                                                                      589  }
                                                                                      +
                                                                                      590  CalculateMaturityAA(i_age_year, a);
                                                                                      +
                                                                                      591  /* if statements needed because some quantities are only needed
                                                                                      +
                                                                                      592  for the first year and/or age, so these steps are included here.
                                                                                      +
                                                                                      593  */
                                                                                      +
                                                                                      594  if (y == 0) {
                                                                                      +
                                                                                      595  // Initial numbers at age is a user input or estimated parameter
                                                                                      +
                                                                                      596  // vector.
                                                                                      +
                                                                                      597  CalculateInitialNumbersAA(i_age_year, a);
                                                                                      +
                                                                                      598 
                                                                                      +
                                                                                      599  if (a == 0) {
                                                                                      +
                                                                                      600  // this->numbers_at_age[i_age_year] = this->recruitment->rzero;
                                                                                      +
                                                                                      601  this->unfished_numbers_at_age[i_age_year] =
                                                                                      +
                                                                                      602  fims_math::exp(this->recruitment->log_rzero);
                                                                                      +
                                                                                      603  } else {
                                                                                      +
                                                                                      604  CalculateUnfishedNumbersAA(i_age_year, a - 1, a);
                                                                                      +
                                                                                      605  }
                                                                                      +
                                                                                      606 
                                                                                      +
                                                                                      607  /*
                                                                                      +
                                                                                      608  Fished and unfished biomass vectors are summing biomass at
                                                                                      +
                                                                                      609  age across ages.
                                                                                      +
                                                                                      610  */
                                                                                      +
                                                                                      611 
                                                                                      +
                                                                                      612  CalculateBiomass(i_age_year, y, a);
                                                                                      +
                                                                                      613 
                                                                                      +
                                                                                      614  CalculateUnfishedBiomass(i_age_year, y, a);
                                                                                      +
                                                                                      615 
                                                                                      +
                                                                                      616  /*
                                                                                      +
                                                                                      617  Fished and unfished spawning biomass vectors are summing biomass at
                                                                                      +
                                                                                      618  age across ages to allow calculation of recruitment in the next year.
                                                                                      +
                                                                                      619  */
                                                                                      +
                                                                                      620 
                                                                                      +
                                                                                      621  CalculateSpawningBiomass(i_age_year, y, a);
                                                                                      +
                                                                                      622 
                                                                                      +
                                                                                      623  CalculateUnfishedSpawningBiomass(i_age_year, y, a);
                                                                                      +
                                                                                      624 
                                                                                      +
                                                                                      625  /*
                                                                                      +
                                                                                      626  Expected recruitment in year 0 is numbers at age 0 in year 0.
                                                                                      +
                                                                                      627  */
                                                                                      +
                                                                                      628 
                                                                                      +
                                                                                      629  this->expected_recruitment[i_age_year] =
                                                                                      +
                                                                                      630  this->numbers_at_age[i_age_year];
                                                                                      +
                                                                                      631 
                                                                                      +
                                                                                      632  } else {
                                                                                      +
                                                                                      633  if (a == 0) {
                                                                                      +
                                                                                      634  // Set the nrecruits for age a=0 year y (use pointers instead of
                                                                                      +
                                                                                      635  // functional returns) assuming fecundity = 1 and 50:50 sex ratio
                                                                                      +
                                                                                      636  FIMS_LOG << "Recruitment: " << std::endl;
                                                                                      +
                                                                                      637  CalculateRecruitment(i_age_year, y);
                                                                                      +
                                                                                      638  this->unfished_numbers_at_age[i_age_year] =
                                                                                      +
                                                                                      639  fims_math::exp(this->recruitment->log_rzero);
                                                                                      +
                                                                                      640 
                                                                                      +
                                                                                      641  } else {
                                                                                      +
                                                                                      642  size_t i_agem1_yearm1 = (y - 1) * nages + (a - 1);
                                                                                      +
                                                                                      643  CalculateNumbersAA(i_age_year, i_agem1_yearm1, a);
                                                                                      +
                                                                                      644  CalculateUnfishedNumbersAA(i_age_year, i_agem1_yearm1, a);
                                                                                      +
                                                                                      645  }
                                                                                      +
                                                                                      646  CalculateBiomass(i_age_year, y, a);
                                                                                      +
                                                                                      647  CalculateSpawningBiomass(i_age_year, y, a);
                                                                                      +
                                                                                      648 
                                                                                      +
                                                                                      649  FIMS_LOG << "index ya: " << i_age_year << std::endl;
                                                                                      +
                                                                                      650  CalculateUnfishedBiomass(i_age_year, y, a);
                                                                                      +
                                                                                      651  CalculateUnfishedSpawningBiomass(i_age_year, y, a);
                                                                                      +
                                                                                      652  }
                                                                                      +
                                                                                      653 
                                                                                      +
                                                                                      654  /*
                                                                                      +
                                                                                      655  Here composition, total catch, and index values are calculated for all
                                                                                      +
                                                                                      656  years with reference data. They are not calculated for y=nyears as there
                                                                                      +
                                                                                      657  is this is just to get final population structure at the end of the
                                                                                      +
                                                                                      658  terminal year.
                                                                                      +
                                                                                      659  */
                                                                                      +
                                                                                      660  if (y < this->nyears) {
                                                                                      +
                                                                                      661  FIMS_LOG << i_age_year << std::endl;
                                                                                      +
                                                                                      662  CalculateCatchNumbersAA(i_age_year, y, a);
                                                                                      +
                                                                                      663 
                                                                                      +
                                                                                      664  CalculateCatchWeightAA(y, a);
                                                                                      +
                                                                                      665  FIMS_LOG << "year " << y << " and age " << a << std::endl;
                                                                                      +
                                                                                      666  CalculateCatch(y, a);
                                                                                      +
                                                                                      667  CalculateIndex(i_age_year, y, a);
                                                                                      +
                                                                                      668  }
                                                                                      +
                                                                                      669  }
                                                                                      +
                                                                                      670  }
                                                                                      +
                                                                                      671  FIMS_LOG << "NAA\n";
                                                                                      +
                                                                                      672  for (size_t i = 0; i < nyears; i++) {
                                                                                      +
                                                                                      673  for (size_t j = 0; j < nages; j++) {
                                                                                      +
                                                                                      674  FIMS_LOG << numbers_at_age[i * nages + j] << "\t";
                                                                                      +
                                                                                      675  }
                                                                                      +
                                                                                      676  FIMS_LOG << "\n";
                                                                                      +
                                                                                      677  }
                                                                                      +
                                                                                      678 
                                                                                      +
                                                                                      679  FIMS_LOG << "CAA\n";
                                                                                      +
                                                                                      680  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                                      +
                                                                                      681  FIMS_LOG << "Fleet " << fleet_ + 1 << "\n";
                                                                                      +
                                                                                      682  for (size_t i = 0; i < nyears; i++) {
                                                                                      +
                                                                                      683  for (size_t j = 0; j < nages; j++) {
                                                                                      +
                                                                                      684  FIMS_LOG << fleets[fleet_]->catch_numbers_at_age[i * nages + j]
                                                                                      +
                                                                                      685  << "\t";
                                                                                      +
                                                                                      686  }
                                                                                      +
                                                                                      687  FIMS_LOG << "\n";
                                                                                      +
                                                                                      688  }
                                                                                      +
                                                                                      689  }
                                                                                      +
                                                                                      690  }
                                                                                      +
                                                                                      691 };
                                                                                      +
                                                                                      692 template <class Type>
                                                                                      +
                                                                                      693 uint32_t Population<Type>::id_g = 0;
                                                                                      +
                                                                                      694 
                                                                                      +
                                                                                      695 } // namespace fims
                                                                                      +
                                                                                      696 
                                                                                      +
                                                                                      697 #endif /* FIMS_POPULATION_DYNAMICS_POPULATION_HPP */
                                                                                      FIMS_LOG
                                                                                      std::ofstream FIMS_LOG("fims.log")
                                                                                      -
                                                                                      fims::FIMSObject
                                                                                      FIMSObject struct that defines member types and returns the unique id.
                                                                                      Definition: model_object.hpp:25
                                                                                      -
                                                                                      fims::Population
                                                                                      Population class. Contains subpopulations that are divided into generic partitions (eg....
                                                                                      Definition: population.hpp:36
                                                                                      -
                                                                                      fims::Population::CalculateUnfishedNumbersAA
                                                                                      void CalculateUnfishedNumbersAA(size_t i_age_year, size_t i_agem1_yearm1, size_t age)
                                                                                      Calculates unfished numbers at age at year and age specific indices.
                                                                                      Definition: population.hpp:257
                                                                                      -
                                                                                      fims::Population::maturity
                                                                                      std::shared_ptr< fims::MaturityBase< Type > > maturity
                                                                                      Definition: population.hpp:100
                                                                                      -
                                                                                      fims::Population::expected_recruitment
                                                                                      std::vector< Type > expected_recruitment
                                                                                      Definition: population.hpp:86
                                                                                      -
                                                                                      fims::Population::CalculateCatchWeightAA
                                                                                      void CalculateCatchWeightAA(size_t year, size_t age)
                                                                                      Calculates expected catch weight at age for each fleet for a given year and age.
                                                                                      Definition: population.hpp:494
                                                                                      -
                                                                                      fims::Population::Evaluate
                                                                                      void Evaluate()
                                                                                      Executes the population loop.
                                                                                      Definition: population.hpp:537
                                                                                      -
                                                                                      fims::Population::CalculateNumbersAA
                                                                                      void CalculateNumbersAA(size_t i_age_year, size_t i_agem1_yearm1, size_t age)
                                                                                      Calculates numbers at age at year and age specific indices.
                                                                                      Definition: population.hpp:233
                                                                                      -
                                                                                      fims::Population::CalculateIndex
                                                                                      void CalculateIndex(size_t i_age_year, size_t year, size_t age)
                                                                                      Adds to the expected population indices by fleet.
                                                                                      Definition: population.hpp:429
                                                                                      -
                                                                                      fims::Population::weight_at_age
                                                                                      std::vector< Type > weight_at_age
                                                                                      Definition: population.hpp:67
                                                                                      -
                                                                                      fims::Population::recruitment
                                                                                      std::shared_ptr< fims::RecruitmentBase< Type > > recruitment
                                                                                      Definition: population.hpp:90
                                                                                      -
                                                                                      fims::Population::M
                                                                                      std::vector< Type > M
                                                                                      Definition: population.hpp:56
                                                                                      -
                                                                                      fims::Population::CalculateCatchNumbersAA
                                                                                      void CalculateCatchNumbersAA(size_t i_age_year, size_t year, size_t age)
                                                                                      Calculates catch in numbers at age for each fleet for a given year and age, then adds the value to th...
                                                                                      Definition: population.hpp:458
                                                                                      -
                                                                                      fims::Population::ages
                                                                                      std::vector< double > ages
                                                                                      Definition: population.hpp:58
                                                                                      -
                                                                                      fims::Population::nages
                                                                                      size_t nages
                                                                                      Definition: population.hpp:43
                                                                                      -
                                                                                      fims::Population::maturity_id
                                                                                      int maturity_id
                                                                                      Definition: population.hpp:98
                                                                                      -
                                                                                      fims::Population::proportion_female
                                                                                      const Type proportion_female
                                                                                      Definition: population.hpp:47
                                                                                      -
                                                                                      fims::Population::unfished_spawning_biomass
                                                                                      std::vector< Type > unfished_spawning_biomass
                                                                                      Definition: population.hpp:79
                                                                                      -
                                                                                      fims::Population::CalculateCatch
                                                                                      void CalculateCatch(size_t year, size_t age)
                                                                                      Adds to exiting expected total catch by fleet in weight.
                                                                                      Definition: population.hpp:399
                                                                                      -
                                                                                      fims::Population::biomass
                                                                                      std::vector< Type > biomass
                                                                                      Definition: population.hpp:75
                                                                                      -
                                                                                      fims::Population::fleets
                                                                                      std::vector< std::shared_ptr< fims::Fleet< Type > > > fleets
                                                                                      Definition: population.hpp:105
                                                                                      -
                                                                                      fims::Population::growth_id
                                                                                      int growth_id
                                                                                      Definition: population.hpp:93
                                                                                      -
                                                                                      fims::Population::proportion_mature_at_age
                                                                                      std::vector< Type > proportion_mature_at_age
                                                                                      Definition: population.hpp:81
                                                                                      -
                                                                                      fims::Population::CalculateRecruitment
                                                                                      void CalculateRecruitment(size_t i_age_year, size_t year)
                                                                                      Calculates expected recruitment for a given year.
                                                                                      Definition: population.hpp:372
                                                                                      -
                                                                                      fims::Population::log_init_naa
                                                                                      std::vector< Type > log_init_naa
                                                                                      Definition: population.hpp:52
                                                                                      -
                                                                                      fims::Population::nyears
                                                                                      size_t nyears
                                                                                      Definition: population.hpp:41
                                                                                      -
                                                                                      fims::Population::log_M
                                                                                      ParameterVector log_M
                                                                                      Definition: population.hpp:53
                                                                                      -
                                                                                      fims::Population::mortality_F
                                                                                      ParameterVector mortality_F
                                                                                      Definition: population.hpp:60
                                                                                      -
                                                                                      fims::Population::growth
                                                                                      std::shared_ptr< fims::GrowthBase< Type > > growth
                                                                                      Definition: population.hpp:95
                                                                                      -
                                                                                      fims::Population::CalculateInitialNumbersAA
                                                                                      void CalculateInitialNumbersAA(size_t i_age_year, size_t a)
                                                                                      Calculates initial numbers at age for index and age.
                                                                                      Definition: population.hpp:196
                                                                                      -
                                                                                      fims::Population::CalculateMaturityAA
                                                                                      void CalculateMaturityAA(size_t i_age_year, size_t age)
                                                                                      Calculates expected proportion of individuals mature at a selected ageage.
                                                                                      Definition: population.hpp:517
                                                                                      -
                                                                                      fims::Population::Initialize
                                                                                      void Initialize(int nyears, int nseasons, int nages)
                                                                                      Initialize values. Called once at the start of model run.
                                                                                      Definition: population.hpp:123
                                                                                      -
                                                                                      fims::Population::nseasons
                                                                                      size_t nseasons
                                                                                      Definition: population.hpp:42
                                                                                      -
                                                                                      fims::Population::years
                                                                                      std::vector< double > years
                                                                                      Definition: population.hpp:59
                                                                                      -
                                                                                      fims::Population::numbers_at_age
                                                                                      std::vector< Type > numbers_at_age
                                                                                      Definition: population.hpp:69
                                                                                      -
                                                                                      fims::Population::Prepare
                                                                                      void Prepare()
                                                                                      Prepare to run the population loop. Called at each model iteration, and used to zero out derived quan...
                                                                                      Definition: population.hpp:154
                                                                                      -
                                                                                      fims::Population::CalculateUnfishedSpawningBiomass
                                                                                      void CalculateUnfishedSpawningBiomass(size_t i_age_year, size_t year, size_t age)
                                                                                      Adds to existing yearly unfished spawning biomass estimates the biomass for a specified year and age.
                                                                                      Definition: population.hpp:331
                                                                                      -
                                                                                      fims::Population::unfished_biomass
                                                                                      std::vector< Type > unfished_biomass
                                                                                      Definition: population.hpp:77
                                                                                      -
                                                                                      fims::Population::id_g
                                                                                      static uint32_t id_g
                                                                                      Definition: population.hpp:40
                                                                                      -
                                                                                      fims::Population::unfished_numbers_at_age
                                                                                      std::vector< Type > unfished_numbers_at_age
                                                                                      Definition: population.hpp:72
                                                                                      -
                                                                                      fims::Population::expected_numbers_at_age
                                                                                      std::vector< Type > expected_numbers_at_age
                                                                                      Definition: population.hpp:83
                                                                                      -
                                                                                      fims::Population::CalculateBiomass
                                                                                      void CalculateBiomass(size_t i_age_year, size_t year, size_t age)
                                                                                      Calculates biomass.
                                                                                      Definition: population.hpp:281
                                                                                      -
                                                                                      fims::Population::spawning_biomass
                                                                                      std::vector< Type > spawning_biomass
                                                                                      Definition: population.hpp:76
                                                                                      -
                                                                                      fims::Population::fleet_id
                                                                                      int fleet_id
                                                                                      Definition: population.hpp:103
                                                                                      -
                                                                                      fims::Population::CalculateSpawningBiomass
                                                                                      void CalculateSpawningBiomass(size_t i_age_year, size_t year, size_t age)
                                                                                      Calculates spawning biomass.
                                                                                      Definition: population.hpp:309
                                                                                      -
                                                                                      fims::Population::ParameterVector
                                                                                      typename ModelTraits< Type >::ParameterVector ParameterVector
                                                                                      Definition: population.hpp:39
                                                                                      -
                                                                                      fims::Population::expected_catch
                                                                                      std::vector< Type > expected_catch
                                                                                      Definition: population.hpp:85
                                                                                      -
                                                                                      fims::Population::CalculateMortality
                                                                                      void CalculateMortality(size_t i_age_year, size_t year, size_t age)
                                                                                      Calculates total mortality at an index, year, and age.
                                                                                      Definition: population.hpp:208
                                                                                      -
                                                                                      fims::Population::mortality_Z
                                                                                      std::vector< Type > mortality_Z
                                                                                      Definition: population.hpp:63
                                                                                      -
                                                                                      fims::Population::CalculateSBPR0
                                                                                      Type CalculateSBPR0()
                                                                                      Calculates equilibrium spawning biomass per recruit.
                                                                                      Definition: population.hpp:344
                                                                                      -
                                                                                      fims::Population::nfleets
                                                                                      size_t nfleets
                                                                                      Definition: population.hpp:44
                                                                                      -
                                                                                      fims::Population::CalculateUnfishedBiomass
                                                                                      void CalculateUnfishedBiomass(size_t i_age_year, size_t year, size_t age)
                                                                                      Adds to existing yearly unfished biomass estimates the biomass for a specified year and age.
                                                                                      Definition: population.hpp:297
                                                                                      -
                                                                                      fims::Population::recruitment_id
                                                                                      int recruitment_id
                                                                                      recruitment
                                                                                      Definition: population.hpp:88
                                                                                      +
                                                                                      fims_model_object::FIMSObject
                                                                                      FIMSObject struct that defines member types and returns the unique id.
                                                                                      Definition: model_object.hpp:25
                                                                                      +
                                                                                      fims_popdy::Population
                                                                                      Population class. Contains subpopulations that are divided into generic partitions (eg....
                                                                                      Definition: population.hpp:36
                                                                                      +
                                                                                      fims_popdy::Population::unfished_numbers_at_age
                                                                                      std::vector< Type > unfished_numbers_at_age
                                                                                      Definition: population.hpp:72
                                                                                      +
                                                                                      fims_popdy::Population::growth
                                                                                      std::shared_ptr< GrowthBase< Type > > growth
                                                                                      Definition: population.hpp:95
                                                                                      +
                                                                                      fims_popdy::Population::M
                                                                                      std::vector< Type > M
                                                                                      Definition: population.hpp:56
                                                                                      +
                                                                                      fims_popdy::Population::nseasons
                                                                                      size_t nseasons
                                                                                      Definition: population.hpp:42
                                                                                      +
                                                                                      fims_popdy::Population::proportion_female
                                                                                      const Type proportion_female
                                                                                      Definition: population.hpp:47
                                                                                      +
                                                                                      fims_popdy::Population::numbers_at_age
                                                                                      std::vector< Type > numbers_at_age
                                                                                      Definition: population.hpp:69
                                                                                      +
                                                                                      fims_popdy::Population::maturity
                                                                                      std::shared_ptr< MaturityBase< Type > > maturity
                                                                                      Definition: population.hpp:100
                                                                                      +
                                                                                      fims_popdy::Population::expected_numbers_at_age
                                                                                      std::vector< Type > expected_numbers_at_age
                                                                                      Definition: population.hpp:83
                                                                                      +
                                                                                      fims_popdy::Population::expected_catch
                                                                                      std::vector< Type > expected_catch
                                                                                      Definition: population.hpp:85
                                                                                      +
                                                                                      fims_popdy::Population::growth_id
                                                                                      int growth_id
                                                                                      Definition: population.hpp:93
                                                                                      +
                                                                                      fims_popdy::Population::nyears
                                                                                      size_t nyears
                                                                                      Definition: population.hpp:41
                                                                                      +
                                                                                      fims_popdy::Population::nfleets
                                                                                      size_t nfleets
                                                                                      Definition: population.hpp:44
                                                                                      +
                                                                                      fims_popdy::Population::CalculateUnfishedSpawningBiomass
                                                                                      void CalculateUnfishedSpawningBiomass(size_t i_age_year, size_t year, size_t age)
                                                                                      Adds to existing yearly unfished spawning biomass estimates the biomass for a specified year and age.
                                                                                      Definition: population.hpp:332
                                                                                      +
                                                                                      fims_popdy::Population::CalculateNumbersAA
                                                                                      void CalculateNumbersAA(size_t i_age_year, size_t i_agem1_yearm1, size_t age)
                                                                                      Calculates numbers at age at year and age specific indices.
                                                                                      Definition: population.hpp:234
                                                                                      +
                                                                                      fims_popdy::Population::CalculateSpawningBiomass
                                                                                      void CalculateSpawningBiomass(size_t i_age_year, size_t year, size_t age)
                                                                                      Calculates spawning biomass.
                                                                                      Definition: population.hpp:310
                                                                                      +
                                                                                      fims_popdy::Population::ParameterVector
                                                                                      typename fims::ModelTraits< Type >::ParameterVector ParameterVector
                                                                                      Definition: population.hpp:39
                                                                                      +
                                                                                      fims_popdy::Population::Evaluate
                                                                                      void Evaluate()
                                                                                      Executes the population loop.
                                                                                      Definition: population.hpp:538
                                                                                      +
                                                                                      fims_popdy::Population::ages
                                                                                      std::vector< double > ages
                                                                                      Definition: population.hpp:58
                                                                                      +
                                                                                      fims_popdy::Population::proportion_mature_at_age
                                                                                      std::vector< Type > proportion_mature_at_age
                                                                                      Definition: population.hpp:81
                                                                                      +
                                                                                      fims_popdy::Population::unfished_spawning_biomass
                                                                                      std::vector< Type > unfished_spawning_biomass
                                                                                      Definition: population.hpp:79
                                                                                      +
                                                                                      fims_popdy::Population::CalculateMaturityAA
                                                                                      void CalculateMaturityAA(size_t i_age_year, size_t age)
                                                                                      Calculates expected proportion of individuals mature at a selected ageage.
                                                                                      Definition: population.hpp:518
                                                                                      +
                                                                                      fims_popdy::Population::biomass
                                                                                      std::vector< Type > biomass
                                                                                      Definition: population.hpp:75
                                                                                      +
                                                                                      fims_popdy::Population::CalculateRecruitment
                                                                                      void CalculateRecruitment(size_t i_age_year, size_t year)
                                                                                      Calculates expected recruitment for a given year.
                                                                                      Definition: population.hpp:373
                                                                                      +
                                                                                      fims_popdy::Population::Initialize
                                                                                      void Initialize(int nyears, int nseasons, int nages)
                                                                                      Initialize values. Called once at the start of model run.
                                                                                      Definition: population.hpp:123
                                                                                      +
                                                                                      fims_popdy::Population::CalculateBiomass
                                                                                      void CalculateBiomass(size_t i_age_year, size_t year, size_t age)
                                                                                      Calculates biomass.
                                                                                      Definition: population.hpp:282
                                                                                      +
                                                                                      fims_popdy::Population::spawning_biomass
                                                                                      std::vector< Type > spawning_biomass
                                                                                      Definition: population.hpp:76
                                                                                      +
                                                                                      fims_popdy::Population::fleet_id
                                                                                      int fleet_id
                                                                                      Definition: population.hpp:103
                                                                                      +
                                                                                      fims_popdy::Population::mortality_F
                                                                                      ParameterVector mortality_F
                                                                                      Definition: population.hpp:60
                                                                                      +
                                                                                      fims_popdy::Population::recruitment_id
                                                                                      int recruitment_id
                                                                                      recruitment
                                                                                      Definition: population.hpp:88
                                                                                      +
                                                                                      fims_popdy::Population::CalculateUnfishedBiomass
                                                                                      void CalculateUnfishedBiomass(size_t i_age_year, size_t year, size_t age)
                                                                                      Adds to existing yearly unfished biomass estimates the biomass for a specified year and age.
                                                                                      Definition: population.hpp:298
                                                                                      +
                                                                                      fims_popdy::Population::recruitment
                                                                                      std::shared_ptr< RecruitmentBase< Type > > recruitment
                                                                                      Definition: population.hpp:90
                                                                                      +
                                                                                      fims_popdy::Population::log_M
                                                                                      ParameterVector log_M
                                                                                      Definition: population.hpp:53
                                                                                      +
                                                                                      fims_popdy::Population::id_g
                                                                                      static uint32_t id_g
                                                                                      Definition: population.hpp:40
                                                                                      +
                                                                                      fims_popdy::Population::maturity_id
                                                                                      int maturity_id
                                                                                      Definition: population.hpp:98
                                                                                      +
                                                                                      fims_popdy::Population::nages
                                                                                      size_t nages
                                                                                      Definition: population.hpp:43
                                                                                      +
                                                                                      fims_popdy::Population::CalculateCatchWeightAA
                                                                                      void CalculateCatchWeightAA(size_t year, size_t age)
                                                                                      Calculates expected catch weight at age for each fleet for a given year and age.
                                                                                      Definition: population.hpp:495
                                                                                      +
                                                                                      fims_popdy::Population::unfished_biomass
                                                                                      std::vector< Type > unfished_biomass
                                                                                      Definition: population.hpp:77
                                                                                      +
                                                                                      fims_popdy::Population::CalculateUnfishedNumbersAA
                                                                                      void CalculateUnfishedNumbersAA(size_t i_age_year, size_t i_agem1_yearm1, size_t age)
                                                                                      Calculates unfished numbers at age at year and age specific indices.
                                                                                      Definition: population.hpp:258
                                                                                      +
                                                                                      fims_popdy::Population::expected_recruitment
                                                                                      std::vector< Type > expected_recruitment
                                                                                      Definition: population.hpp:86
                                                                                      +
                                                                                      fims_popdy::Population::CalculateCatchNumbersAA
                                                                                      void CalculateCatchNumbersAA(size_t i_age_year, size_t year, size_t age)
                                                                                      Calculates catch in numbers at age for each fleet for a given year and age, then adds the value to th...
                                                                                      Definition: population.hpp:459
                                                                                      +
                                                                                      fims_popdy::Population::fleets
                                                                                      std::vector< std::shared_ptr< Fleet< Type > > > fleets
                                                                                      Definition: population.hpp:105
                                                                                      +
                                                                                      fims_popdy::Population::CalculateIndex
                                                                                      void CalculateIndex(size_t i_age_year, size_t year, size_t age)
                                                                                      Adds to the expected population indices by fleet.
                                                                                      Definition: population.hpp:430
                                                                                      +
                                                                                      fims_popdy::Population::CalculateMortality
                                                                                      void CalculateMortality(size_t i_age_year, size_t year, size_t age)
                                                                                      Calculates total mortality at an index, year, and age.
                                                                                      Definition: population.hpp:208
                                                                                      +
                                                                                      fims_popdy::Population::CalculateCatch
                                                                                      void CalculateCatch(size_t year, size_t age)
                                                                                      Adds to exiting expected total catch by fleet in weight.
                                                                                      Definition: population.hpp:400
                                                                                      +
                                                                                      fims_popdy::Population::years
                                                                                      std::vector< double > years
                                                                                      Definition: population.hpp:59
                                                                                      +
                                                                                      fims_popdy::Population::mortality_Z
                                                                                      std::vector< Type > mortality_Z
                                                                                      Definition: population.hpp:63
                                                                                      +
                                                                                      fims_popdy::Population::CalculateInitialNumbersAA
                                                                                      void CalculateInitialNumbersAA(size_t i_age_year, size_t a)
                                                                                      Calculates initial numbers at age for index and age.
                                                                                      Definition: population.hpp:196
                                                                                      +
                                                                                      fims_popdy::Population::CalculateSBPR0
                                                                                      Type CalculateSBPR0()
                                                                                      Calculates equilibrium spawning biomass per recruit.
                                                                                      Definition: population.hpp:345
                                                                                      +
                                                                                      fims_popdy::Population::weight_at_age
                                                                                      std::vector< Type > weight_at_age
                                                                                      Definition: population.hpp:67
                                                                                      +
                                                                                      fims_popdy::Population::Prepare
                                                                                      void Prepare()
                                                                                      Prepare to run the population loop. Called at each model iteration, and used to zero out derived quan...
                                                                                      Definition: population.hpp:154
                                                                                      +
                                                                                      fims_popdy::Population::log_init_naa
                                                                                      std::vector< Type > log_init_naa
                                                                                      Definition: population.hpp:52
                                                                                      diff --git a/docs/rcpp__data_8hpp_source.html b/docs/rcpp__data_8hpp_source.html index ab37c57..9bc5391 100644 --- a/docs/rcpp__data_8hpp_source.html +++ b/docs/rcpp__data_8hpp_source.html @@ -132,8 +132,8 @@
                                                                                      85 
                                                                                      86  template <typename Type>
                                                                                      87  bool add_to_fims_tmb_internal() {
                                                                                      -
                                                                                      88  std::shared_ptr<fims::DataObject<Type>> age_comp_data =
                                                                                      -
                                                                                      89  std::make_shared<fims::DataObject<Type>>(this->ymax, this->amax);
                                                                                      +
                                                                                      88  std::shared_ptr<fims_data_object::DataObject<Type>> age_comp_data =
                                                                                      +
                                                                                      89  std::make_shared<fims_data_object::DataObject<Type>>(this->ymax, this->amax);
                                                                                      90 
                                                                                      91  age_comp_data->id = this->id;
                                                                                      92  for (int y = 0; y < ymax; y++) {
                                                                                      @@ -143,8 +143,8 @@
                                                                                      96  }
                                                                                      97  }
                                                                                      98 
                                                                                      -
                                                                                      99  std::shared_ptr<fims::Information<Type>> info =
                                                                                      -
                                                                                      100  fims::Information<Type>::GetInstance();
                                                                                      +
                                                                                      99  std::shared_ptr<fims_info::Information<Type>> info =
                                                                                      +
                                                                                      100  fims_info::Information<Type>::GetInstance();
                                                                                      101 
                                                                                      102  info->data_objects[this->id] = age_comp_data;
                                                                                      103 
                                                                                      @@ -177,8 +177,8 @@
                                                                                      147 
                                                                                      148  template <typename Type>
                                                                                      149  bool add_to_fims_tmb_internal() {
                                                                                      -
                                                                                      150  std::shared_ptr<fims::DataObject<Type>> data =
                                                                                      -
                                                                                      151  std::make_shared<fims::DataObject<Type>>(this->ymax);
                                                                                      +
                                                                                      150  std::shared_ptr<fims_data_object::DataObject<Type>> data =
                                                                                      +
                                                                                      151  std::make_shared<fims_data_object::DataObject<Type>>(this->ymax);
                                                                                      152 
                                                                                      153  data->id = this->id;
                                                                                      154 
                                                                                      @@ -186,8 +186,8 @@
                                                                                      156  data->at(y) = this->index_data[y];
                                                                                      157  }
                                                                                      158 
                                                                                      -
                                                                                      159  std::shared_ptr<fims::Information<Type>> info =
                                                                                      -
                                                                                      160  fims::Information<Type>::GetInstance();
                                                                                      +
                                                                                      159  std::shared_ptr<fims_info::Information<Type>> info =
                                                                                      +
                                                                                      160  fims_info::Information<Type>::GetInstance();
                                                                                      161 
                                                                                      162  info->data_objects[this->id] = data;
                                                                                      163  return true;
                                                                                      @@ -230,7 +230,7 @@
                                                                                      IndexDataInterface::index_data
                                                                                      Rcpp::NumericVector index_data
                                                                                      Definition: rcpp_data.hpp:130
                                                                                      IndexDataInterface::~IndexDataInterface
                                                                                      virtual ~IndexDataInterface()
                                                                                      destructor
                                                                                      Definition: rcpp_data.hpp:140
                                                                                      IndexDataInterface::get_id
                                                                                      virtual uint32_t get_id()
                                                                                      get the ID of the interface base object
                                                                                      Definition: rcpp_data.hpp:144
                                                                                      -
                                                                                      fims::Information::GetInstance
                                                                                      static std::shared_ptr< Information< T > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      +
                                                                                      fims_info::Information::GetInstance
                                                                                      static std::shared_ptr< Information< Type > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      diff --git a/docs/rcpp__fleet_8hpp_source.html b/docs/rcpp__fleet_8hpp_source.html index f2efbb1..c0306ec 100644 --- a/docs/rcpp__fleet_8hpp_source.html +++ b/docs/rcpp__fleet_8hpp_source.html @@ -163,11 +163,11 @@
                                                                                      132 #ifdef TMB_MODEL
                                                                                      133  template <typename Type>
                                                                                      134  bool add_to_fims_tmb_internal() {
                                                                                      -
                                                                                      135  std::shared_ptr<fims::Information<Type> > info =
                                                                                      -
                                                                                      136  fims::Information<Type>::GetInstance();
                                                                                      +
                                                                                      135  std::shared_ptr<fims_info::Information<Type> > info =
                                                                                      +
                                                                                      136  fims_info::Information<Type>::GetInstance();
                                                                                      137 
                                                                                      -
                                                                                      138  std::shared_ptr<fims::Fleet<Type> > fleet =
                                                                                      -
                                                                                      139  std::make_shared<fims::Fleet<Type> >();
                                                                                      +
                                                                                      138  std::shared_ptr<fims_popdy::Fleet<Type> > fleet =
                                                                                      +
                                                                                      139  std::make_shared<fims_popdy::Fleet<Type> >();
                                                                                      140 
                                                                                      141  // set relative info
                                                                                      142  fleet->id = this->id;
                                                                                      @@ -252,7 +252,7 @@
                                                                                      Parameter
                                                                                      RcppInterface class that defines the interface between R and C++ for parameter types.
                                                                                      Definition: rcpp_interface_base.hpp:26
                                                                                      Parameter::estimated_m
                                                                                      bool estimated_m
                                                                                      Definition: rcpp_interface_base.hpp:35
                                                                                      Parameter::value_m
                                                                                      double value_m
                                                                                      Definition: rcpp_interface_base.hpp:28
                                                                                      -
                                                                                      fims::Information::GetInstance
                                                                                      static std::shared_ptr< Information< T > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      +
                                                                                      fims_info::Information::GetInstance
                                                                                      static std::shared_ptr< Information< Type > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      diff --git a/docs/rcpp__growth_8hpp_source.html b/docs/rcpp__growth_8hpp_source.html index c55f7b5..16fbea6 100644 --- a/docs/rcpp__growth_8hpp_source.html +++ b/docs/rcpp__growth_8hpp_source.html @@ -139,7 +139,7 @@
                                                                                      89  }
                                                                                      90 
                                                                                      95  virtual double evaluate(double age) {
                                                                                      -
                                                                                      96  fims::EWAAgrowth<double> EWAAGrowth;
                                                                                      +
                                                                                      96  fims_popdy::EWAAgrowth<double> EWAAGrowth;
                                                                                      97 
                                                                                      98  if (initialized == false) {
                                                                                      99  this->ewaa = make_map(this->ages, this->weights);
                                                                                      @@ -151,18 +151,18 @@
                                                                                      105  } else {
                                                                                      106  Rcpp::stop("this empirical weight at age object is already initialized");
                                                                                      107  }
                                                                                      -
                                                                                      108  EWAAGrowth.ewaa = this->ewaa;
                                                                                      -
                                                                                      109  return EWAAGrowth.evaluate(age);
                                                                                      +
                                                                                      108  EWAAGrowth.ewaa = this->ewaa;
                                                                                      +
                                                                                      109  return EWAAGrowth.evaluate(age);
                                                                                      110  }
                                                                                      111 #ifdef TMB_MODEL
                                                                                      112 
                                                                                      113  template <typename Type>
                                                                                      114  bool add_to_fims_tmb_internal() {
                                                                                      -
                                                                                      115  std::shared_ptr<fims::Information<Type> > info =
                                                                                      -
                                                                                      116  fims::Information<Type>::GetInstance();
                                                                                      +
                                                                                      115  std::shared_ptr<fims_info::Information<Type> > info =
                                                                                      +
                                                                                      116  fims_info::Information<Type>::GetInstance();
                                                                                      117 
                                                                                      -
                                                                                      118  std::shared_ptr<fims::EWAAgrowth<Type> > ewaa_growth =
                                                                                      -
                                                                                      119  std::make_shared<fims::EWAAgrowth<Type> >();
                                                                                      +
                                                                                      118  std::shared_ptr<fims_popdy::EWAAgrowth<Type> > ewaa_growth =
                                                                                      +
                                                                                      119  std::make_shared<fims_popdy::EWAAgrowth<Type> >();
                                                                                      120 
                                                                                      121  // set relative info
                                                                                      122  ewaa_growth->id = this->id;
                                                                                      @@ -203,10 +203,10 @@
                                                                                      GrowthInterfaceBase::id_g
                                                                                      static uint32_t id_g
                                                                                      Definition: rcpp_growth.hpp:26
                                                                                      GrowthInterfaceBase::id
                                                                                      uint32_t id
                                                                                      Definition: rcpp_growth.hpp:27
                                                                                      GrowthInterfaceBase::get_id
                                                                                      virtual uint32_t get_id()=0
                                                                                      get_id method for child growth interface objects to inherit
                                                                                      -
                                                                                      fims::Information::GetInstance
                                                                                      static std::shared_ptr< Information< T > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      -
                                                                                      fims::EWAAgrowth
                                                                                      EWAAgrowth class that returns the EWAA function value.
                                                                                      Definition: ewaa.hpp:23
                                                                                      -
                                                                                      fims::EWAAgrowth::evaluate
                                                                                      virtual const Type evaluate(const double &a)
                                                                                      Returns the weight at age a (in kg) from the input vector.
                                                                                      Definition: ewaa.hpp:41
                                                                                      -
                                                                                      fims::EWAAgrowth::ewaa
                                                                                      std::map< double, double > ewaa
                                                                                      Definition: ewaa.hpp:29
                                                                                      +
                                                                                      fims_info::Information::GetInstance
                                                                                      static std::shared_ptr< Information< Type > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      +
                                                                                      fims_popdy::EWAAgrowth
                                                                                      EWAAgrowth class that returns the EWAA function value.
                                                                                      Definition: ewaa.hpp:23
                                                                                      +
                                                                                      fims_popdy::EWAAgrowth::ewaa
                                                                                      std::map< double, double > ewaa
                                                                                      Definition: ewaa.hpp:29
                                                                                      +
                                                                                      fims_popdy::EWAAgrowth::evaluate
                                                                                      virtual const Type evaluate(const double &a)
                                                                                      Returns the weight at age a (in kg) from the input vector.
                                                                                      Definition: ewaa.hpp:41
                                                                                      diff --git a/docs/rcpp__interface_8hpp_source.html b/docs/rcpp__interface_8hpp_source.html index 2294e9a..07c9386 100644 --- a/docs/rcpp__interface_8hpp_source.html +++ b/docs/rcpp__interface_8hpp_source.html @@ -107,23 +107,23 @@
                                                                                      32  }
                                                                                      33 
                                                                                      34  // base model
                                                                                      -
                                                                                      35  std::shared_ptr<fims::Information<TMB_FIMS_REAL_TYPE>> d0 =
                                                                                      -
                                                                                      36  fims::Information<TMB_FIMS_REAL_TYPE>::GetInstance();
                                                                                      +
                                                                                      35  std::shared_ptr<fims_info::Information<TMB_FIMS_REAL_TYPE>> d0 =
                                                                                      +
                                                                                      36  fims_info::Information<TMB_FIMS_REAL_TYPE>::GetInstance();
                                                                                      37  d0->CreateModel();
                                                                                      38 
                                                                                      39  // first-order derivative
                                                                                      -
                                                                                      40  std::shared_ptr<fims::Information<TMB_FIMS_FIRST_ORDER>> d1 =
                                                                                      -
                                                                                      41  fims::Information<TMB_FIMS_FIRST_ORDER>::GetInstance();
                                                                                      +
                                                                                      40  std::shared_ptr<fims_info::Information<TMB_FIMS_FIRST_ORDER>> d1 =
                                                                                      +
                                                                                      41  fims_info::Information<TMB_FIMS_FIRST_ORDER>::GetInstance();
                                                                                      42  d1->CreateModel();
                                                                                      43 
                                                                                      44  // second-order derivative
                                                                                      -
                                                                                      45  std::shared_ptr<fims::Information<TMB_FIMS_SECOND_ORDER>> d2 =
                                                                                      -
                                                                                      46  fims::Information<TMB_FIMS_SECOND_ORDER>::GetInstance();
                                                                                      +
                                                                                      45  std::shared_ptr<fims_info::Information<TMB_FIMS_SECOND_ORDER>> d2 =
                                                                                      +
                                                                                      46  fims_info::Information<TMB_FIMS_SECOND_ORDER>::GetInstance();
                                                                                      47  d2->CreateModel();
                                                                                      48 
                                                                                      49  // third-order derivative
                                                                                      -
                                                                                      50  std::shared_ptr<fims::Information<TMB_FIMS_THIRD_ORDER>> d3 =
                                                                                      -
                                                                                      51  fims::Information<TMB_FIMS_THIRD_ORDER>::GetInstance();
                                                                                      +
                                                                                      50  std::shared_ptr<fims_info::Information<TMB_FIMS_THIRD_ORDER>> d3 =
                                                                                      +
                                                                                      51  fims_info::Information<TMB_FIMS_THIRD_ORDER>::GetInstance();
                                                                                      52  d3->CreateModel();
                                                                                      53 
                                                                                      54  return true;
                                                                                      @@ -131,8 +131,8 @@
                                                                                      56 
                                                                                      57 Rcpp::NumericVector get_fixed_parameters_vector() {
                                                                                      58  // base model
                                                                                      -
                                                                                      59  std::shared_ptr<fims::Information<TMB_FIMS_REAL_TYPE>> d0 =
                                                                                      -
                                                                                      60  fims::Information<TMB_FIMS_REAL_TYPE>::GetInstance();
                                                                                      +
                                                                                      59  std::shared_ptr<fims_info::Information<TMB_FIMS_REAL_TYPE>> d0 =
                                                                                      +
                                                                                      60  fims_info::Information<TMB_FIMS_REAL_TYPE>::GetInstance();
                                                                                      61 
                                                                                      62  Rcpp::NumericVector p;
                                                                                      63 
                                                                                      @@ -145,8 +145,8 @@
                                                                                      70 
                                                                                      71 Rcpp::NumericVector get_random_parameters_vector() {
                                                                                      72  // base model
                                                                                      -
                                                                                      73  std::shared_ptr<fims::Information<TMB_FIMS_REAL_TYPE>> d0 =
                                                                                      -
                                                                                      74  fims::Information<TMB_FIMS_REAL_TYPE>::GetInstance();
                                                                                      +
                                                                                      73  std::shared_ptr<fims_info::Information<TMB_FIMS_REAL_TYPE>> d0 =
                                                                                      +
                                                                                      74  fims_info::Information<TMB_FIMS_REAL_TYPE>::GetInstance();
                                                                                      75 
                                                                                      76  Rcpp::NumericVector p;
                                                                                      77 
                                                                                      @@ -159,8 +159,8 @@
                                                                                      84 
                                                                                      85 template <typename Type>
                                                                                      86 void clear_internal() {
                                                                                      -
                                                                                      87  std::shared_ptr<fims::Information<Type>> d0 =
                                                                                      -
                                                                                      88  fims::Information<Type>::GetInstance();
                                                                                      +
                                                                                      87  std::shared_ptr<fims_info::Information<Type>> d0 =
                                                                                      +
                                                                                      88  fims_info::Information<Type>::GetInstance();
                                                                                      89  d0->fixed_effects_parameters.clear();
                                                                                      90  d0->random_effects_parameters.clear();
                                                                                      91 }
                                                                                      @@ -471,7 +471,7 @@
                                                                                      RecruitmentInterfaceBase::id_g
                                                                                      static uint32_t id_g
                                                                                      Definition: rcpp_recruitment.hpp:25
                                                                                      SelectivityInterfaceBase::live_objects
                                                                                      static std::map< uint32_t, SelectivityInterfaceBase * > live_objects
                                                                                      Definition: rcpp_selectivity.hpp:29
                                                                                      SelectivityInterfaceBase::id_g
                                                                                      static uint32_t id_g
                                                                                      Definition: rcpp_selectivity.hpp:25
                                                                                      -
                                                                                      fims::Information::GetInstance
                                                                                      static std::shared_ptr< Information< T > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      +
                                                                                      fims_info::Information::GetInstance
                                                                                      static std::shared_ptr< Information< Type > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      diff --git a/docs/rcpp__maturity_8hpp_source.html b/docs/rcpp__maturity_8hpp_source.html index 5980611..73fc215 100644 --- a/docs/rcpp__maturity_8hpp_source.html +++ b/docs/rcpp__maturity_8hpp_source.html @@ -131,21 +131,21 @@
                                                                                      71  virtual uint32_t get_id() { return this->id; }
                                                                                      72 
                                                                                      77  virtual double evaluate(double x) {
                                                                                      -
                                                                                      78  fims::LogisticMaturity<double> LogisticMat;
                                                                                      -
                                                                                      79  LogisticMat.median = this->median.value_m;
                                                                                      -
                                                                                      80  LogisticMat.slope = this->slope.value_m;
                                                                                      -
                                                                                      81  return LogisticMat.evaluate(x);
                                                                                      +
                                                                                      78  fims_popdy::LogisticMaturity<double> LogisticMat;
                                                                                      +
                                                                                      79  LogisticMat.median = this->median.value_m;
                                                                                      +
                                                                                      80  LogisticMat.slope = this->slope.value_m;
                                                                                      +
                                                                                      81  return LogisticMat.evaluate(x);
                                                                                      82  }
                                                                                      83 
                                                                                      84 #ifdef TMB_MODEL
                                                                                      85 
                                                                                      86  template <typename Type>
                                                                                      87  bool add_to_fims_tmb_internal() {
                                                                                      -
                                                                                      88  std::shared_ptr<fims::Information<Type> > info =
                                                                                      -
                                                                                      89  fims::Information<Type>::GetInstance();
                                                                                      +
                                                                                      88  std::shared_ptr<fims_info::Information<Type> > info =
                                                                                      +
                                                                                      89  fims_info::Information<Type>::GetInstance();
                                                                                      90 
                                                                                      -
                                                                                      91  std::shared_ptr<fims::LogisticMaturity<Type> > maturity =
                                                                                      -
                                                                                      92  std::make_shared<fims::LogisticMaturity<Type> >();
                                                                                      +
                                                                                      91  std::shared_ptr<fims_popdy::LogisticMaturity<Type> > maturity =
                                                                                      +
                                                                                      92  std::make_shared<fims_popdy::LogisticMaturity<Type> >();
                                                                                      93 
                                                                                      94  // set relative info
                                                                                      95  maturity->id = this->id;
                                                                                      @@ -203,11 +203,11 @@
                                                                                      Parameter::estimated_m
                                                                                      bool estimated_m
                                                                                      Definition: rcpp_interface_base.hpp:35
                                                                                      Parameter::value_m
                                                                                      double value_m
                                                                                      Definition: rcpp_interface_base.hpp:28
                                                                                      Parameter::is_random_effect_m
                                                                                      bool is_random_effect_m
                                                                                      Definition: rcpp_interface_base.hpp:33
                                                                                      -
                                                                                      fims::Information::GetInstance
                                                                                      static std::shared_ptr< Information< T > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      -
                                                                                      fims::LogisticMaturity
                                                                                      LogisticMaturity class that returns the logistic function value from fims_math.
                                                                                      Definition: logistic.hpp:23
                                                                                      -
                                                                                      fims::LogisticMaturity::slope
                                                                                      Type slope
                                                                                      Definition: logistic.hpp:26
                                                                                      -
                                                                                      fims::LogisticMaturity::evaluate
                                                                                      virtual const Type evaluate(const Type &x)
                                                                                      Method of the logistic maturity class that implements the logistic function from FIMS math.
                                                                                      Definition: logistic.hpp:40
                                                                                      -
                                                                                      fims::LogisticMaturity::median
                                                                                      Type median
                                                                                      Definition: logistic.hpp:24
                                                                                      +
                                                                                      fims_info::Information::GetInstance
                                                                                      static std::shared_ptr< Information< Type > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      +
                                                                                      fims_popdy::LogisticMaturity
                                                                                      LogisticMaturity class that returns the logistic function value from fims_math.
                                                                                      Definition: logistic.hpp:23
                                                                                      +
                                                                                      fims_popdy::LogisticMaturity::slope
                                                                                      Type slope
                                                                                      Definition: logistic.hpp:26
                                                                                      +
                                                                                      fims_popdy::LogisticMaturity::evaluate
                                                                                      virtual const Type evaluate(const Type &x)
                                                                                      Method of the logistic maturity class that implements the logistic function from FIMS math.
                                                                                      Definition: logistic.hpp:40
                                                                                      +
                                                                                      fims_popdy::LogisticMaturity::median
                                                                                      Type median
                                                                                      Definition: logistic.hpp:24
                                                                                      diff --git a/docs/rcpp__population_8hpp_source.html b/docs/rcpp__population_8hpp_source.html index 93d08de..0a48972 100644 --- a/docs/rcpp__population_8hpp_source.html +++ b/docs/rcpp__population_8hpp_source.html @@ -147,19 +147,19 @@
                                                                                      97  }
                                                                                      98 
                                                                                      100  virtual void evaluate() {
                                                                                      -
                                                                                      101  fims::Population<double> population;
                                                                                      -
                                                                                      102  return population.Evaluate();
                                                                                      +
                                                                                      101  fims_popdy::Population<double> population;
                                                                                      +
                                                                                      102  return population.Evaluate();
                                                                                      103  }
                                                                                      104 
                                                                                      105 #ifdef TMB_MODEL
                                                                                      106 
                                                                                      107  template <typename Type>
                                                                                      108  bool add_to_fims_tmb_internal() {
                                                                                      -
                                                                                      109  std::shared_ptr<fims::Information<Type> > info =
                                                                                      -
                                                                                      110  fims::Information<Type>::GetInstance();
                                                                                      +
                                                                                      109  std::shared_ptr<fims_info::Information<Type> > info =
                                                                                      +
                                                                                      110  fims_info::Information<Type>::GetInstance();
                                                                                      111 
                                                                                      -
                                                                                      112  std::shared_ptr<fims::Population<Type> > population =
                                                                                      -
                                                                                      113  std::make_shared<fims::Population<Type> >();
                                                                                      +
                                                                                      112  std::shared_ptr<fims_popdy::Population<Type> > population =
                                                                                      +
                                                                                      113  std::make_shared<fims_popdy::Population<Type> >();
                                                                                      114 
                                                                                      115  // set relative info
                                                                                      116  population->id = this->id;
                                                                                      @@ -241,9 +241,9 @@
                                                                                      PopulationInterface::estimate_M
                                                                                      bool estimate_M
                                                                                      Definition: rcpp_population.hpp:67
                                                                                      PopulationInterface::SetGrowth
                                                                                      void SetGrowth(uint32_t growth_id)
                                                                                      Set the unique id for the growth object.
                                                                                      Definition: rcpp_population.hpp:88
                                                                                      PopulationInterface::log_M
                                                                                      Rcpp::NumericVector log_M
                                                                                      Definition: rcpp_population.hpp:63
                                                                                      -
                                                                                      fims::Information::GetInstance
                                                                                      static std::shared_ptr< Information< T > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      -
                                                                                      fims::Population
                                                                                      Population class. Contains subpopulations that are divided into generic partitions (eg....
                                                                                      Definition: population.hpp:36
                                                                                      -
                                                                                      fims::Population::Evaluate
                                                                                      void Evaluate()
                                                                                      Executes the population loop.
                                                                                      Definition: population.hpp:537
                                                                                      +
                                                                                      fims_info::Information::GetInstance
                                                                                      static std::shared_ptr< Information< Type > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      +
                                                                                      fims_popdy::Population
                                                                                      Population class. Contains subpopulations that are divided into generic partitions (eg....
                                                                                      Definition: population.hpp:36
                                                                                      +
                                                                                      fims_popdy::Population::Evaluate
                                                                                      void Evaluate()
                                                                                      Executes the population loop.
                                                                                      Definition: population.hpp:538
                                                                                      diff --git a/docs/rcpp__recruitment_8hpp_source.html b/docs/rcpp__recruitment_8hpp_source.html index 0f93f8b..874c659 100644 --- a/docs/rcpp__recruitment_8hpp_source.html +++ b/docs/rcpp__recruitment_8hpp_source.html @@ -139,42 +139,42 @@
                                                                                      84  virtual uint32_t get_id() { return this->id; }
                                                                                      85 
                                                                                      86  virtual double evaluate(double spawners, double ssbzero) {
                                                                                      -
                                                                                      87  fims::SRBevertonHolt<double> BevHolt;
                                                                                      +
                                                                                      87  fims_popdy::SRBevertonHolt<double> BevHolt;
                                                                                      88 
                                                                                      -
                                                                                      89  BevHolt.logit_steep = this->logit_steep.value_m;
                                                                                      +
                                                                                      89  BevHolt.logit_steep = this->logit_steep.value_m;
                                                                                      90  if (this->logit_steep.value_m == 1.0) {
                                                                                      91  warning(
                                                                                      92  "Steepness is subject to a logit transformation, so its value is "
                                                                                      93  "0.7848469. Fixing it at 1.0 is not currently possible.");
                                                                                      94  }
                                                                                      95 
                                                                                      -
                                                                                      96  BevHolt.log_rzero = this->log_rzero.value_m;
                                                                                      +
                                                                                      96  BevHolt.log_rzero = this->log_rzero.value_m;
                                                                                      97 
                                                                                      -
                                                                                      98  return BevHolt.evaluate(spawners, ssbzero);
                                                                                      +
                                                                                      98  return BevHolt.evaluate(spawners, ssbzero);
                                                                                      99  }
                                                                                      100 
                                                                                      101  virtual double evaluate_nll() {
                                                                                      -
                                                                                      102  fims::SRBevertonHolt<double> NLL;
                                                                                      +
                                                                                      102  fims_popdy::SRBevertonHolt<double> NLL;
                                                                                      103 
                                                                                      -
                                                                                      104  NLL.log_sigma_recruit = this->log_sigma_recruit.value_m;
                                                                                      -
                                                                                      105  NLL.recruit_deviations.resize(deviations.size()); // Vector from TMB
                                                                                      +
                                                                                      104  NLL.log_sigma_recruit = this->log_sigma_recruit.value_m;
                                                                                      +
                                                                                      105  NLL.recruit_deviations.resize(deviations.size()); // Vector from TMB
                                                                                      106  for (int i = 0; i < deviations.size(); i++) {
                                                                                      -
                                                                                      107  NLL.recruit_deviations[i] = deviations[i];
                                                                                      +
                                                                                      107  NLL.recruit_deviations[i] = deviations[i];
                                                                                      108  }
                                                                                      109  FIMS_LOG << "Rec devs being passed to C++ are " << deviations << std::endl;
                                                                                      -
                                                                                      110  NLL.estimate_recruit_deviations = this->estimate_deviations;
                                                                                      -
                                                                                      111  return NLL.evaluate_nll();
                                                                                      +
                                                                                      110  NLL.estimate_recruit_deviations = this->estimate_deviations;
                                                                                      +
                                                                                      111  return NLL.evaluate_nll();
                                                                                      112  }
                                                                                      113 
                                                                                      114 #ifdef TMB_MODEL
                                                                                      115 
                                                                                      116  template <typename Type>
                                                                                      117  bool add_to_fims_tmb_internal() {
                                                                                      -
                                                                                      118  std::shared_ptr<fims::Information<Type> > info =
                                                                                      -
                                                                                      119  fims::Information<Type>::GetInstance();
                                                                                      +
                                                                                      118  std::shared_ptr<fims_info::Information<Type> > info =
                                                                                      +
                                                                                      119  fims_info::Information<Type>::GetInstance();
                                                                                      120 
                                                                                      -
                                                                                      121  std::shared_ptr<fims::SRBevertonHolt<Type> > recruitment =
                                                                                      -
                                                                                      122  std::make_shared<fims::SRBevertonHolt<Type> >();
                                                                                      +
                                                                                      121  std::shared_ptr<fims_popdy::SRBevertonHolt<Type> > recruitment =
                                                                                      +
                                                                                      122  std::make_shared<fims_popdy::SRBevertonHolt<Type> >();
                                                                                      123 
                                                                                      124  // set relative info
                                                                                      125  recruitment->id = this->id;
                                                                                      @@ -258,16 +258,16 @@
                                                                                      RecruitmentInterfaceBase::RecruitmentInterfaceBase
                                                                                      RecruitmentInterfaceBase()
                                                                                      Definition: rcpp_recruitment.hpp:36
                                                                                      RecruitmentInterfaceBase::id_g
                                                                                      static uint32_t id_g
                                                                                      Definition: rcpp_recruitment.hpp:25
                                                                                      RecruitmentInterfaceBase::evaluate_nll
                                                                                      virtual double evaluate_nll()=0
                                                                                      evaluate recruitment nll
                                                                                      -
                                                                                      fims::Information::GetInstance
                                                                                      static std::shared_ptr< Information< T > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      +
                                                                                      fims_info::Information::GetInstance
                                                                                      static std::shared_ptr< Information< Type > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      FIMS_LOG
                                                                                      std::ofstream FIMS_LOG("fims.log")
                                                                                      -
                                                                                      fims::RecruitmentBase::log_rzero
                                                                                      Type log_rzero
                                                                                      Definition: recruitment_base.hpp:41
                                                                                      -
                                                                                      fims::RecruitmentBase::log_sigma_recruit
                                                                                      Type log_sigma_recruit
                                                                                      Definition: recruitment_base.hpp:39
                                                                                      -
                                                                                      fims::RecruitmentBase::recruit_deviations
                                                                                      ModelTraits< Type >::ParameterVector recruit_deviations
                                                                                      Definition: recruitment_base.hpp:35
                                                                                      -
                                                                                      fims::RecruitmentBase::evaluate_nll
                                                                                      virtual const Type evaluate_nll()
                                                                                      Calculates the negative log likelihood of recruitment deviations.
                                                                                      Definition: recruitment_base.hpp:72
                                                                                      -
                                                                                      fims::RecruitmentBase::estimate_recruit_deviations
                                                                                      bool estimate_recruit_deviations
                                                                                      Definition: recruitment_base.hpp:43
                                                                                      -
                                                                                      fims::SRBevertonHolt
                                                                                      BevertonHolt class that returns the Beverton Holt SR from fims_math.
                                                                                      Definition: sr_beverton_holt.hpp:27
                                                                                      -
                                                                                      fims::SRBevertonHolt::evaluate
                                                                                      virtual const Type evaluate(const Type &spawners, const Type &phi_0)
                                                                                      Beverton Holt implementation of the stock recruitment function.
                                                                                      Definition: sr_beverton_holt.hpp:47
                                                                                      -
                                                                                      fims::SRBevertonHolt::logit_steep
                                                                                      Type logit_steep
                                                                                      Definition: sr_beverton_holt.hpp:31
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase::estimate_recruit_deviations
                                                                                      bool estimate_recruit_deviations
                                                                                      Definition: recruitment_base.hpp:43
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase::evaluate_nll
                                                                                      virtual const Type evaluate_nll()
                                                                                      Calculates the negative log likelihood of recruitment deviations.
                                                                                      Definition: recruitment_base.hpp:72
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase::recruit_deviations
                                                                                      fims::ModelTraits< Type >::ParameterVector recruit_deviations
                                                                                      Definition: recruitment_base.hpp:35
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase::log_sigma_recruit
                                                                                      Type log_sigma_recruit
                                                                                      Definition: recruitment_base.hpp:39
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase::log_rzero
                                                                                      Type log_rzero
                                                                                      Definition: recruitment_base.hpp:41
                                                                                      +
                                                                                      fims_popdy::SRBevertonHolt
                                                                                      BevertonHolt class that returns the Beverton Holt SR from fims_math.
                                                                                      Definition: sr_beverton_holt.hpp:27
                                                                                      +
                                                                                      fims_popdy::SRBevertonHolt::logit_steep
                                                                                      Type logit_steep
                                                                                      Definition: sr_beverton_holt.hpp:31
                                                                                      +
                                                                                      fims_popdy::SRBevertonHolt::evaluate
                                                                                      virtual const Type evaluate(const Type &spawners, const Type &phi_0)
                                                                                      Beverton Holt implementation of the stock recruitment function.
                                                                                      Definition: sr_beverton_holt.hpp:47
                                                                                      diff --git a/docs/rcpp__selectivity_8hpp_source.html b/docs/rcpp__selectivity_8hpp_source.html index ce68a69..15d14b3 100644 --- a/docs/rcpp__selectivity_8hpp_source.html +++ b/docs/rcpp__selectivity_8hpp_source.html @@ -131,21 +131,21 @@
                                                                                      71  virtual uint32_t get_id() { return this->id; }
                                                                                      72 
                                                                                      77  virtual double evaluate(double x) {
                                                                                      -
                                                                                      78  fims::LogisticSelectivity<double> LogisticSel;
                                                                                      -
                                                                                      79  LogisticSel.median = this->median.value_m;
                                                                                      -
                                                                                      80  LogisticSel.slope = this->slope.value_m;
                                                                                      -
                                                                                      81  return LogisticSel.evaluate(x);
                                                                                      +
                                                                                      78  fims_popdy::LogisticSelectivity<double> LogisticSel;
                                                                                      +
                                                                                      79  LogisticSel.median = this->median.value_m;
                                                                                      +
                                                                                      80  LogisticSel.slope = this->slope.value_m;
                                                                                      +
                                                                                      81  return LogisticSel.evaluate(x);
                                                                                      82  }
                                                                                      83 
                                                                                      84 #ifdef TMB_MODEL
                                                                                      85 
                                                                                      86  template <typename Type>
                                                                                      87  bool add_to_fims_tmb_internal() {
                                                                                      -
                                                                                      88  std::shared_ptr<fims::Information<Type> > info =
                                                                                      -
                                                                                      89  fims::Information<Type>::GetInstance();
                                                                                      +
                                                                                      88  std::shared_ptr<fims_info::Information<Type> > info =
                                                                                      +
                                                                                      89  fims_info::Information<Type>::GetInstance();
                                                                                      90 
                                                                                      -
                                                                                      91  std::shared_ptr<fims::LogisticSelectivity<Type> > selectivity =
                                                                                      -
                                                                                      92  std::make_shared<fims::LogisticSelectivity<Type> >();
                                                                                      +
                                                                                      91  std::shared_ptr<fims_popdy::LogisticSelectivity<Type> > selectivity =
                                                                                      +
                                                                                      92  std::make_shared<fims_popdy::LogisticSelectivity<Type> >();
                                                                                      93 
                                                                                      94  // set relative info
                                                                                      95  selectivity->id = this->id;
                                                                                      @@ -198,23 +198,23 @@
                                                                                      150  virtual uint32_t get_id() { return this->id; }
                                                                                      151 
                                                                                      156  virtual double evaluate(double x) {
                                                                                      -
                                                                                      157  fims::DoubleLogisticSelectivity<double> DoubleLogisticSel;
                                                                                      -
                                                                                      158  DoubleLogisticSel.median_asc = this->median_asc.value_m;
                                                                                      -
                                                                                      159  DoubleLogisticSel.slope_asc = this->slope_asc.value_m;
                                                                                      -
                                                                                      160  DoubleLogisticSel.median_desc = this->median_desc.value_m;
                                                                                      -
                                                                                      161  DoubleLogisticSel.slope_desc = this->slope_desc.value_m;
                                                                                      -
                                                                                      162  return DoubleLogisticSel.evaluate(x);
                                                                                      +
                                                                                      157  fims_popdy::DoubleLogisticSelectivity<double> DoubleLogisticSel;
                                                                                      +
                                                                                      158  DoubleLogisticSel.median_asc = this->median_asc.value_m;
                                                                                      +
                                                                                      159  DoubleLogisticSel.slope_asc = this->slope_asc.value_m;
                                                                                      +
                                                                                      160  DoubleLogisticSel.median_desc = this->median_desc.value_m;
                                                                                      +
                                                                                      161  DoubleLogisticSel.slope_desc = this->slope_desc.value_m;
                                                                                      +
                                                                                      162  return DoubleLogisticSel.evaluate(x);
                                                                                      163  }
                                                                                      164 
                                                                                      165 #ifdef TMB_MODEL
                                                                                      166 
                                                                                      167  template <typename Type>
                                                                                      168  bool add_to_fims_tmb_internal() {
                                                                                      -
                                                                                      169  std::shared_ptr<fims::Information<Type> > info =
                                                                                      -
                                                                                      170  fims::Information<Type>::GetInstance();
                                                                                      +
                                                                                      169  std::shared_ptr<fims_info::Information<Type> > info =
                                                                                      +
                                                                                      170  fims_info::Information<Type>::GetInstance();
                                                                                      171 
                                                                                      -
                                                                                      172  std::shared_ptr<fims::DoubleLogisticSelectivity<Type> > selectivity =
                                                                                      -
                                                                                      173  std::make_shared<fims::DoubleLogisticSelectivity<Type> >();
                                                                                      +
                                                                                      172  std::shared_ptr<fims_popdy::DoubleLogisticSelectivity<Type> > selectivity =
                                                                                      +
                                                                                      173  std::make_shared<fims_popdy::DoubleLogisticSelectivity<Type> >();
                                                                                      174 
                                                                                      175  // set relative info
                                                                                      176  selectivity->id = this->id;
                                                                                      @@ -295,17 +295,17 @@
                                                                                      SelectivityInterfaceBase::id_g
                                                                                      static uint32_t id_g
                                                                                      Definition: rcpp_selectivity.hpp:25
                                                                                      SelectivityInterfaceBase::evaluate
                                                                                      virtual double evaluate(double x)=0
                                                                                      evaluate the function
                                                                                      SelectivityInterfaceBase::id
                                                                                      uint32_t id
                                                                                      Definition: rcpp_selectivity.hpp:26
                                                                                      -
                                                                                      fims::Information::GetInstance
                                                                                      static std::shared_ptr< Information< T > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      -
                                                                                      fims::DoubleLogisticSelectivity
                                                                                      DoubleLogisticSelectivity class that returns the double logistic function value from fims_math.
                                                                                      Definition: double_logistic.hpp:21
                                                                                      -
                                                                                      fims::DoubleLogisticSelectivity::evaluate
                                                                                      virtual const Type evaluate(const Type &x)
                                                                                      Method of the double logistic selectivity class that implements the double logistic function from FIM...
                                                                                      Definition: double_logistic.hpp:49
                                                                                      -
                                                                                      fims::DoubleLogisticSelectivity::slope_asc
                                                                                      Type slope_asc
                                                                                      Definition: double_logistic.hpp:25
                                                                                      -
                                                                                      fims::DoubleLogisticSelectivity::slope_desc
                                                                                      Type slope_desc
                                                                                      Definition: double_logistic.hpp:31
                                                                                      -
                                                                                      fims::DoubleLogisticSelectivity::median_desc
                                                                                      Type median_desc
                                                                                      Definition: double_logistic.hpp:28
                                                                                      -
                                                                                      fims::DoubleLogisticSelectivity::median_asc
                                                                                      Type median_asc
                                                                                      Definition: double_logistic.hpp:22
                                                                                      -
                                                                                      fims::LogisticSelectivity
                                                                                      LogisticSelectivity class that returns the logistic function value from fims_math.
                                                                                      Definition: logistic.hpp:24
                                                                                      -
                                                                                      fims::LogisticSelectivity::median
                                                                                      Type median
                                                                                      Definition: logistic.hpp:25
                                                                                      -
                                                                                      fims::LogisticSelectivity::slope
                                                                                      Type slope
                                                                                      Definition: logistic.hpp:27
                                                                                      -
                                                                                      fims::LogisticSelectivity::evaluate
                                                                                      virtual const Type evaluate(const Type &x)
                                                                                      Method of the logistic selectivity class that implements the logistic function from FIMS math.
                                                                                      Definition: logistic.hpp:43
                                                                                      +
                                                                                      fims_info::Information::GetInstance
                                                                                      static std::shared_ptr< Information< Type > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      +
                                                                                      fims_popdy::DoubleLogisticSelectivity
                                                                                      DoubleLogisticSelectivity class that returns the double logistic function value from fims_math.
                                                                                      Definition: double_logistic.hpp:21
                                                                                      +
                                                                                      fims_popdy::DoubleLogisticSelectivity::median_asc
                                                                                      Type median_asc
                                                                                      Definition: double_logistic.hpp:22
                                                                                      +
                                                                                      fims_popdy::DoubleLogisticSelectivity::median_desc
                                                                                      Type median_desc
                                                                                      Definition: double_logistic.hpp:28
                                                                                      +
                                                                                      fims_popdy::DoubleLogisticSelectivity::slope_asc
                                                                                      Type slope_asc
                                                                                      Definition: double_logistic.hpp:25
                                                                                      +
                                                                                      fims_popdy::DoubleLogisticSelectivity::slope_desc
                                                                                      Type slope_desc
                                                                                      Definition: double_logistic.hpp:31
                                                                                      +
                                                                                      fims_popdy::DoubleLogisticSelectivity::evaluate
                                                                                      virtual const Type evaluate(const Type &x)
                                                                                      Method of the double logistic selectivity class that implements the double logistic function from FIM...
                                                                                      Definition: double_logistic.hpp:49
                                                                                      +
                                                                                      fims_popdy::LogisticSelectivity
                                                                                      LogisticSelectivity class that returns the logistic function value from fims_math.
                                                                                      Definition: logistic.hpp:24
                                                                                      +
                                                                                      fims_popdy::LogisticSelectivity::median
                                                                                      Type median
                                                                                      Definition: logistic.hpp:25
                                                                                      +
                                                                                      fims_popdy::LogisticSelectivity::slope
                                                                                      Type slope
                                                                                      Definition: logistic.hpp:27
                                                                                      +
                                                                                      fims_popdy::LogisticSelectivity::evaluate
                                                                                      virtual const Type evaluate(const Type &x)
                                                                                      Method of the logistic selectivity class that implements the logistic function from FIMS math.
                                                                                      Definition: logistic.hpp:43
                                                                                      diff --git a/docs/rcpp__tmb__distribution_8hpp_source.html b/docs/rcpp__tmb__distribution_8hpp_source.html index 2926732..32ce5b6 100644 --- a/docs/rcpp__tmb__distribution_8hpp_source.html +++ b/docs/rcpp__tmb__distribution_8hpp_source.html @@ -131,7 +131,7 @@
                                                                                      74  virtual ~DnormDistributionsInterface() {}
                                                                                      75 
                                                                                      83  virtual double evaluate(bool do_log) {
                                                                                      -
                                                                                      84  fims::Dnorm<double> dnorm;
                                                                                      +
                                                                                      84  fims_distributions::Dnorm<double> dnorm;
                                                                                      85  dnorm.x = this->x.value_m;
                                                                                      86  dnorm.mean = this->mean.value_m;
                                                                                      87  dnorm.sd = this->sd.value_m;
                                                                                      @@ -142,11 +142,11 @@
                                                                                      92 
                                                                                      93  template <typename Type>
                                                                                      94  bool add_to_fims_tmb_internal() {
                                                                                      -
                                                                                      95  std::shared_ptr<fims::Information<Type>> info =
                                                                                      -
                                                                                      96  fims::Information<Type>::GetInstance();
                                                                                      +
                                                                                      95  std::shared_ptr<fims_info::Information<Type>> info =
                                                                                      +
                                                                                      96  fims_info::Information<Type>::GetInstance();
                                                                                      97 
                                                                                      -
                                                                                      98  std::shared_ptr<fims::Dnorm<Type>> distribution =
                                                                                      -
                                                                                      99  std::make_shared<fims::Dnorm<Type>>();
                                                                                      +
                                                                                      98  std::shared_ptr<fims_distributions::Dnorm<Type>> distribution =
                                                                                      +
                                                                                      99  std::make_shared<fims_distributions::Dnorm<Type>>();
                                                                                      100 
                                                                                      101  // interface to data/parameter value
                                                                                      102  distribution->id = this->id;
                                                                                      @@ -184,7 +184,7 @@
                                                                                      147  virtual uint32_t get_id() { return this->id; }
                                                                                      148 
                                                                                      156  virtual double evaluate(bool do_log) {
                                                                                      -
                                                                                      157  fims::Dlnorm<double> dlnorm;
                                                                                      +
                                                                                      157  fims_distributions::Dlnorm<double> dlnorm;
                                                                                      158  dlnorm.x = this->x.value_m;
                                                                                      159  dlnorm.meanlog = this->meanlog.value_m;
                                                                                      160  dlnorm.sdlog = this->sdlog.value_m;
                                                                                      @@ -195,11 +195,11 @@
                                                                                      165 
                                                                                      166  template <typename Type>
                                                                                      167  bool add_to_fims_tmb_internal() {
                                                                                      -
                                                                                      168  std::shared_ptr<fims::Information<Type>> info =
                                                                                      -
                                                                                      169  fims::Information<Type>::GetInstance();
                                                                                      +
                                                                                      168  std::shared_ptr<fims_info::Information<Type>> info =
                                                                                      +
                                                                                      169  fims_info::Information<Type>::GetInstance();
                                                                                      170 
                                                                                      -
                                                                                      171  std::shared_ptr<fims::Dlnorm<Type>> distribution =
                                                                                      -
                                                                                      172  std::make_shared<fims::Dlnorm<Type>>();
                                                                                      +
                                                                                      171  std::shared_ptr<fims_distributions::Dlnorm<Type>> distribution =
                                                                                      +
                                                                                      172  std::make_shared<fims_distributions::Dlnorm<Type>>();
                                                                                      173 
                                                                                      174  // set relative info
                                                                                      175  distribution->id = this->id;
                                                                                      @@ -237,7 +237,7 @@
                                                                                      218  virtual uint32_t get_id() { return this->id; }
                                                                                      219 
                                                                                      227  virtual double evaluate(bool do_log) {
                                                                                      -
                                                                                      228  fims::Dmultinom<double> dmultinom;
                                                                                      +
                                                                                      228  fims_distributions::Dmultinom<double> dmultinom;
                                                                                      229  // Decale TMBVector in this scope
                                                                                      230  typedef typename fims::ModelTraits<TMB_FIMS_REAL_TYPE>::EigenVector Vector;
                                                                                      231  dmultinom.x = Vector(x.size()); // Vector from TMB
                                                                                      @@ -254,11 +254,11 @@
                                                                                      242  template <typename Type>
                                                                                      243  bool add_to_fims_tmb_internal() {
                                                                                      244  typedef typename fims::ModelTraits<Type>::EigenVector Vector;
                                                                                      -
                                                                                      245  std::shared_ptr<fims::Information<Type>> info =
                                                                                      -
                                                                                      246  fims::Information<Type>::GetInstance();
                                                                                      +
                                                                                      245  std::shared_ptr<fims_info::Information<Type>> info =
                                                                                      +
                                                                                      246  fims_info::Information<Type>::GetInstance();
                                                                                      247 
                                                                                      -
                                                                                      248  std::shared_ptr<fims::Dmultinom<Type>> distribution =
                                                                                      -
                                                                                      249  std::make_shared<fims::Dmultinom<Type>>();
                                                                                      +
                                                                                      248  std::shared_ptr<fims_distributions::Dmultinom<Type>> distribution =
                                                                                      +
                                                                                      249  std::make_shared<fims_distributions::Dmultinom<Type>>();
                                                                                      250 
                                                                                      251  distribution->id = this->id;
                                                                                      252  distribution->x = Vector(x.size());
                                                                                      @@ -314,7 +314,7 @@
                                                                                      FIMSRcppInterfaceBase::add_to_fims_tmb
                                                                                      virtual bool add_to_fims_tmb()
                                                                                      virtual method to inherit to add objects to the TMB model
                                                                                      Definition: rcpp_interface_base.hpp:67
                                                                                      Parameter
                                                                                      RcppInterface class that defines the interface between R and C++ for parameter types.
                                                                                      Definition: rcpp_interface_base.hpp:26
                                                                                      Parameter::value_m
                                                                                      double value_m
                                                                                      Definition: rcpp_interface_base.hpp:28
                                                                                      -
                                                                                      fims::Information::GetInstance
                                                                                      static std::shared_ptr< Information< T > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      +
                                                                                      fims_info::Information::GetInstance
                                                                                      static std::shared_ptr< Information< Type > > GetInstance()
                                                                                      Definition: information.hpp:125
                                                                                      diff --git a/docs/recruitment__base_8hpp.html b/docs/recruitment__base_8hpp.html index 7570635..fef0993 100644 --- a/docs/recruitment__base_8hpp.html +++ b/docs/recruitment__base_8hpp.html @@ -87,8 +87,8 @@ - - + +

                                                                                      Classes

                                                                                      struct  fims::RecruitmentBase< Type >
                                                                                       Base class for all recruitment functors. More...
                                                                                      struct  fims_popdy::RecruitmentBase< Type >
                                                                                       Base class for all recruitment functors. More...
                                                                                       

                                                                                      Detailed Description

                                                                                      diff --git a/docs/recruitment__base_8hpp_source.html b/docs/recruitment__base_8hpp_source.html index 4c16f8f..6a3bc1a 100644 --- a/docs/recruitment__base_8hpp_source.html +++ b/docs/recruitment__base_8hpp_source.html @@ -82,42 +82,42 @@
                                                                                      16 
                                                                                      17 #include <cmath> // for using std::pow and M_PI
                                                                                      18 
                                                                                      -
                                                                                      19 #include "../../../common/fims_math.hpp" // for using fims::log()
                                                                                      +
                                                                                      19 #include "../../../common/fims_math.hpp" // for using fims_math::log()
                                                                                      20 #include "../../../common/model_object.hpp"
                                                                                      21 #include "../../../distributions/distributions.hpp"
                                                                                      22 
                                                                                      -
                                                                                      23 namespace fims {
                                                                                      +
                                                                                      23 namespace fims_popdy {
                                                                                      24 
                                                                                      30 template <class Type>
                                                                                      -
                                                                                      31 struct RecruitmentBase : public FIMSObject<Type> {
                                                                                      -
                                                                                      32  static uint32_t id_g;
                                                                                      -
                                                                                      34  typename ModelTraits<Type>::ParameterVector
                                                                                      -
                                                                                      35  recruit_deviations;
                                                                                      -
                                                                                      36  bool constrain_deviations = false;
                                                                                      -
                                                                                      39  Type log_sigma_recruit;
                                                                                      -
                                                                                      41  Type log_rzero;
                                                                                      -
                                                                                      43  bool estimate_recruit_deviations =
                                                                                      +
                                                                                      31 struct RecruitmentBase : public fims_model_object::FIMSObject<Type> {
                                                                                      +
                                                                                      32  static uint32_t id_g;
                                                                                      +
                                                                                      34  typename fims::ModelTraits<Type>::ParameterVector
                                                                                      +
                                                                                      35  recruit_deviations;
                                                                                      +
                                                                                      36  bool constrain_deviations = false;
                                                                                      +
                                                                                      39  Type log_sigma_recruit;
                                                                                      +
                                                                                      41  Type log_rzero;
                                                                                      +
                                                                                      43  bool estimate_recruit_deviations =
                                                                                      44  true;
                                                                                      -
                                                                                      49  RecruitmentBase() { this->id = RecruitmentBase::id_g++; }
                                                                                      +
                                                                                      49  RecruitmentBase() { this->id = RecruitmentBase::id_g++; }
                                                                                      50 
                                                                                      -
                                                                                      51  virtual ~RecruitmentBase() {}
                                                                                      +
                                                                                      51  virtual ~RecruitmentBase() {}
                                                                                      52 
                                                                                      -
                                                                                      57  void Prepare() { this->PrepareConstrainedDeviations(); }
                                                                                      +
                                                                                      57  void Prepare() { this->PrepareConstrainedDeviations(); }
                                                                                      58 
                                                                                      -
                                                                                      65  virtual const Type evaluate(
                                                                                      +
                                                                                      65  virtual const Type evaluate(
                                                                                      66  const Type &spawners,
                                                                                      67  const Type &ssbzero) = 0; // need to add input parameter values
                                                                                      68 
                                                                                      -
                                                                                      72  virtual const Type evaluate_nll() {
                                                                                      +
                                                                                      72  virtual const Type evaluate_nll() {
                                                                                      73  Type nll = 0.0;
                                                                                      75  if (!this->estimate_recruit_deviations) {
                                                                                      76  return nll;
                                                                                      77  } else {
                                                                                      78 #ifdef TMB_MODEL
                                                                                      -
                                                                                      79  fims::Dnorm<Type> dnorm;
                                                                                      -
                                                                                      80  dnorm.sd = fims::exp(this->log_sigma_recruit);
                                                                                      -
                                                                                      81  for (size_t i = 0; i < this->recruit_deviations.size(); i++) {
                                                                                      -
                                                                                      82  dnorm.x = fims::log(this->recruit_deviations[i]);
                                                                                      +
                                                                                      79  fims_distributions::Dnorm<Type> dnorm;
                                                                                      +
                                                                                      80  dnorm.sd = fims_math::exp(this->log_sigma_recruit);
                                                                                      +
                                                                                      81  for (size_t i = 0; i < this->recruit_deviations.size(); i++) {
                                                                                      +
                                                                                      82  dnorm.x = fims_math::log(this->recruit_deviations[i]);
                                                                                      83  dnorm.mean = 0.0;
                                                                                      84  nll -= dnorm.evaluate(true);
                                                                                      85  }
                                                                                      @@ -126,44 +126,44 @@
                                                                                      88  }
                                                                                      89  }
                                                                                      90 
                                                                                      -
                                                                                      97  void PrepareConstrainedDeviations() {
                                                                                      +
                                                                                      97  void PrepareConstrainedDeviations() {
                                                                                      98  if (!this->constrain_deviations) {
                                                                                      99  return;
                                                                                      100  }
                                                                                      101 
                                                                                      102  Type sum = 0.0;
                                                                                      103 
                                                                                      -
                                                                                      104  for (size_t i = 0; i < this->recruit_deviations.size(); i++) {
                                                                                      -
                                                                                      105  sum += this->recruit_deviations[i];
                                                                                      +
                                                                                      104  for (size_t i = 0; i < this->recruit_deviations.size(); i++) {
                                                                                      +
                                                                                      105  sum += this->recruit_deviations[i];
                                                                                      106  }
                                                                                      107 
                                                                                      108  FIMS_LOG << "recruit_deviations: \n";
                                                                                      -
                                                                                      109  for (size_t i = 0; i < this->recruit_deviations.size(); i++) {
                                                                                      -
                                                                                      110  this->recruit_deviations[i] -= sum / (this->recruit_deviations.size());
                                                                                      -
                                                                                      111  FIMS_LOG << this->recruit_deviations[i] << std::endl;
                                                                                      +
                                                                                      109  for (size_t i = 0; i < this->recruit_deviations.size(); i++) {
                                                                                      +
                                                                                      110  this->recruit_deviations[i] -= sum / (this->recruit_deviations.size());
                                                                                      +
                                                                                      111  FIMS_LOG << this->recruit_deviations[i] << std::endl;
                                                                                      112  }
                                                                                      113  }
                                                                                      114 };
                                                                                      115 
                                                                                      116 template <class Type>
                                                                                      -
                                                                                      117 uint32_t RecruitmentBase<Type>::id_g = 0;
                                                                                      +
                                                                                      117 uint32_t RecruitmentBase<Type>::id_g = 0;
                                                                                      118 } // namespace fims
                                                                                      119 
                                                                                      120 #endif /* FIMS_POPULATION_DYNAMICS_RECRUITMENT_BASE_HPP */
                                                                                      FIMS_LOG
                                                                                      std::ofstream FIMS_LOG("fims.log")
                                                                                      -
                                                                                      fims::FIMSObject
                                                                                      FIMSObject struct that defines member types and returns the unique id.
                                                                                      Definition: model_object.hpp:25
                                                                                      -
                                                                                      fims::RecruitmentBase
                                                                                      Base class for all recruitment functors.
                                                                                      Definition: recruitment_base.hpp:31
                                                                                      -
                                                                                      fims::RecruitmentBase::RecruitmentBase
                                                                                      RecruitmentBase()
                                                                                      Constructor.
                                                                                      Definition: recruitment_base.hpp:49
                                                                                      -
                                                                                      fims::RecruitmentBase::id_g
                                                                                      static uint32_t id_g
                                                                                      Definition: recruitment_base.hpp:32
                                                                                      -
                                                                                      fims::RecruitmentBase::PrepareConstrainedDeviations
                                                                                      void PrepareConstrainedDeviations()
                                                                                      Prepare constrained recruitment deviations. Based on ADMB sum-to-zero constraint implementation....
                                                                                      Definition: recruitment_base.hpp:97
                                                                                      -
                                                                                      fims::RecruitmentBase::log_rzero
                                                                                      Type log_rzero
                                                                                      Definition: recruitment_base.hpp:41
                                                                                      -
                                                                                      fims::RecruitmentBase::evaluate
                                                                                      virtual const Type evaluate(const Type &spawners, const Type &ssbzero)=0
                                                                                      Calculates the expected recruitment for a given spawning input.
                                                                                      -
                                                                                      fims::RecruitmentBase::log_sigma_recruit
                                                                                      Type log_sigma_recruit
                                                                                      Definition: recruitment_base.hpp:39
                                                                                      -
                                                                                      fims::RecruitmentBase::recruit_deviations
                                                                                      ModelTraits< Type >::ParameterVector recruit_deviations
                                                                                      Definition: recruitment_base.hpp:35
                                                                                      -
                                                                                      fims::RecruitmentBase::evaluate_nll
                                                                                      virtual const Type evaluate_nll()
                                                                                      Calculates the negative log likelihood of recruitment deviations.
                                                                                      Definition: recruitment_base.hpp:72
                                                                                      -
                                                                                      fims::RecruitmentBase::Prepare
                                                                                      void Prepare()
                                                                                      Prepares the recruitment deviations vector.
                                                                                      Definition: recruitment_base.hpp:57
                                                                                      -
                                                                                      fims::RecruitmentBase::constrain_deviations
                                                                                      bool constrain_deviations
                                                                                      Definition: recruitment_base.hpp:36
                                                                                      -
                                                                                      fims::RecruitmentBase::estimate_recruit_deviations
                                                                                      bool estimate_recruit_deviations
                                                                                      Definition: recruitment_base.hpp:43
                                                                                      +
                                                                                      fims_model_object::FIMSObject
                                                                                      FIMSObject struct that defines member types and returns the unique id.
                                                                                      Definition: model_object.hpp:25
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase
                                                                                      Base class for all recruitment functors.
                                                                                      Definition: recruitment_base.hpp:31
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase::estimate_recruit_deviations
                                                                                      bool estimate_recruit_deviations
                                                                                      Definition: recruitment_base.hpp:43
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase::id_g
                                                                                      static uint32_t id_g
                                                                                      Definition: recruitment_base.hpp:32
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase::PrepareConstrainedDeviations
                                                                                      void PrepareConstrainedDeviations()
                                                                                      Prepare constrained recruitment deviations. Based on ADMB sum-to-zero constraint implementation....
                                                                                      Definition: recruitment_base.hpp:97
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase::evaluate_nll
                                                                                      virtual const Type evaluate_nll()
                                                                                      Calculates the negative log likelihood of recruitment deviations.
                                                                                      Definition: recruitment_base.hpp:72
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase::recruit_deviations
                                                                                      fims::ModelTraits< Type >::ParameterVector recruit_deviations
                                                                                      Definition: recruitment_base.hpp:35
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase::Prepare
                                                                                      void Prepare()
                                                                                      Prepares the recruitment deviations vector.
                                                                                      Definition: recruitment_base.hpp:57
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase::evaluate
                                                                                      virtual const Type evaluate(const Type &spawners, const Type &ssbzero)=0
                                                                                      Calculates the expected recruitment for a given spawning input.
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase::log_sigma_recruit
                                                                                      Type log_sigma_recruit
                                                                                      Definition: recruitment_base.hpp:39
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase::constrain_deviations
                                                                                      bool constrain_deviations
                                                                                      Definition: recruitment_base.hpp:36
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase::log_rzero
                                                                                      Type log_rzero
                                                                                      Definition: recruitment_base.hpp:41
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase::RecruitmentBase
                                                                                      RecruitmentBase()
                                                                                      Constructor.
                                                                                      Definition: recruitment_base.hpp:49
                                                                                      diff --git a/docs/search/all_0.js b/docs/search/all_0.js index 08d631e..1e4c5ce 100644 --- a/docs/search/all_0.js +++ b/docs/search/all_0.js @@ -1,15 +1,15 @@ var searchData= [ - ['ad_5ffabs_0',['ad_fabs',['../fims__math_8hpp.html#ad478fc97fc94719ab6aa77b6afc9c025',1,'fims']]], - ['ad_5fmax_1',['ad_max',['../fims__math_8hpp.html#a8235ee7ae8ea25ceca47019643813402',1,'fims']]], - ['ad_5fmin_2',['ad_min',['../fims__math_8hpp.html#acf57604ca0cfae434810d51a52371600',1,'fims']]], + ['ad_5ffabs_0',['ad_fabs',['../fims__math_8hpp.html#abda4b1b8b7ea34fcde2a05e78217d522',1,'fims_math']]], + ['ad_5fmax_1',['ad_max',['../fims__math_8hpp.html#a54cfbb09833fa0de10e18203526e8321',1,'fims_math']]], + ['ad_5fmin_2',['ad_min',['../fims__math_8hpp.html#a4c3897f03cbc7860a4b73b21f58558f6',1,'fims_math']]], 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['proportion_5fmature_5fat_5fage_497',['proportion_mature_at_age',['../structfims__popdy_1_1Population.html#a479fa5993d1d6597b65f8d0459d550a5',1,'fims_popdy::Population']]] ]; diff --git a/docs/search/variables_f.js b/docs/search/variables_f.js index 711e99a..42ce8af 100644 --- a/docs/search/variables_f.js +++ b/docs/search/variables_f.js @@ -1,4 +1,4 @@ var searchData= [ - ['q_500',['q',['../structfims_1_1Fleet.html#a9f228a0756981b92ad43393d083981e6',1,'fims::Fleet']]] + ['q_498',['q',['../structfims__popdy_1_1Fleet.html#a3d3b3fd71ba4856b080c263024bfe2d7',1,'fims_popdy::Fleet']]] ]; diff --git a/docs/selectivity_2functors_2logistic_8hpp_source.html b/docs/selectivity_2functors_2logistic_8hpp_source.html index 4564807..35388e4 100644 --- a/docs/selectivity_2functors_2logistic_8hpp_source.html +++ b/docs/selectivity_2functors_2logistic_8hpp_source.html @@ -92,29 +92,29 @@
                                                                                      14 #include "../../../common/fims_math.hpp"
                                                                                      15 #include "selectivity_base.hpp"
                                                                                      16 
                                                                                      -
                                                                                      17 namespace fims {
                                                                                      +
                                                                                      17 namespace fims_popdy {
                                                                                      18 
                                                                                      23 template <typename Type>
                                                                                      -
                                                                                      24 struct LogisticSelectivity : public SelectivityBase<Type> {
                                                                                      -
                                                                                      25  Type median;
                                                                                      -
                                                                                      27  Type slope;
                                                                                      -
                                                                                      30  LogisticSelectivity() : SelectivityBase<Type>() {}
                                                                                      +
                                                                                      24 struct LogisticSelectivity : public SelectivityBase<Type> {
                                                                                      +
                                                                                      25  Type median;
                                                                                      +
                                                                                      27  Type slope;
                                                                                      +
                                                                                      30  LogisticSelectivity() : SelectivityBase<Type>() {}
                                                                                      31 
                                                                                      -
                                                                                      32  virtual ~LogisticSelectivity() {}
                                                                                      +
                                                                                      32  virtual ~LogisticSelectivity() {}
                                                                                      33 
                                                                                      -
                                                                                      43  virtual const Type evaluate(const Type& x) {
                                                                                      -
                                                                                      44  return fims::logistic<Type>(median, slope, x);
                                                                                      +
                                                                                      43  virtual const Type evaluate(const Type& x) {
                                                                                      +
                                                                                      44  return fims_math::logistic<Type>(median, slope, x);
                                                                                      45  }
                                                                                      46 };
                                                                                      47 
                                                                                      48 } // namespace fims
                                                                                      49 
                                                                                      50 #endif /* POPULATION_DYNAMICS_SELECTIVITY_LOGISTIC_HPP */
                                                                                      -
                                                                                      fims::LogisticSelectivity
                                                                                      LogisticSelectivity class that returns the logistic function value from fims_math.
                                                                                      Definition: logistic.hpp:24
                                                                                      -
                                                                                      fims::LogisticSelectivity::median
                                                                                      Type median
                                                                                      Definition: logistic.hpp:25
                                                                                      -
                                                                                      fims::LogisticSelectivity::slope
                                                                                      Type slope
                                                                                      Definition: logistic.hpp:27
                                                                                      -
                                                                                      fims::LogisticSelectivity::evaluate
                                                                                      virtual const Type evaluate(const Type &x)
                                                                                      Method of the logistic selectivity class that implements the logistic function from FIMS math.
                                                                                      Definition: logistic.hpp:43
                                                                                      -
                                                                                      fims::SelectivityBase
                                                                                      Base class for all selectivity functors.
                                                                                      Definition: selectivity_base.hpp:27
                                                                                      +
                                                                                      fims_popdy::LogisticSelectivity
                                                                                      LogisticSelectivity class that returns the logistic function value from fims_math.
                                                                                      Definition: logistic.hpp:24
                                                                                      +
                                                                                      fims_popdy::LogisticSelectivity::median
                                                                                      Type median
                                                                                      Definition: logistic.hpp:25
                                                                                      +
                                                                                      fims_popdy::LogisticSelectivity::slope
                                                                                      Type slope
                                                                                      Definition: logistic.hpp:27
                                                                                      +
                                                                                      fims_popdy::LogisticSelectivity::evaluate
                                                                                      virtual const Type evaluate(const Type &x)
                                                                                      Method of the logistic selectivity class that implements the logistic function from FIMS math.
                                                                                      Definition: logistic.hpp:43
                                                                                      +
                                                                                      fims_popdy::SelectivityBase
                                                                                      Base class for all selectivity functors.
                                                                                      Definition: selectivity_base.hpp:27
                                                                                      diff --git a/docs/selectivity__base_8hpp_source.html b/docs/selectivity__base_8hpp_source.html index 9bde107..4623a25 100644 --- a/docs/selectivity__base_8hpp_source.html +++ b/docs/selectivity__base_8hpp_source.html @@ -94,38 +94,38 @@
                                                                                      16 
                                                                                      17 #include "../../../common/model_object.hpp"
                                                                                      18 
                                                                                      -
                                                                                      19 namespace fims {
                                                                                      +
                                                                                      19 namespace fims_popdy {
                                                                                      20 
                                                                                      26 template <typename Type>
                                                                                      -
                                                                                      27 struct SelectivityBase : public FIMSObject<Type> {
                                                                                      +
                                                                                      27 struct SelectivityBase : public fims_model_object::FIMSObject<Type> {
                                                                                      28  // id_g is the ID of the instance of the SelectivityBase class.
                                                                                      29  // this is like a memory tracker.
                                                                                      30  // Assigning each one its own ID is a way to keep track of
                                                                                      31  // all the instances of the SelectivityBase class.
                                                                                      32  static uint32_t
                                                                                      -
                                                                                      33  id_g;
                                                                                      -
                                                                                      37  SelectivityBase() {
                                                                                      +
                                                                                      33  id_g;
                                                                                      +
                                                                                      37  SelectivityBase() {
                                                                                      38  // increment id of the singleton selectivity class
                                                                                      -
                                                                                      39  this->id = SelectivityBase::id_g++;
                                                                                      +
                                                                                      39  this->id = SelectivityBase::id_g++;
                                                                                      40  }
                                                                                      41 
                                                                                      -
                                                                                      42  virtual ~SelectivityBase() {}
                                                                                      +
                                                                                      42  virtual ~SelectivityBase() {}
                                                                                      43 
                                                                                      -
                                                                                      49  virtual const Type evaluate(const Type& x) = 0;
                                                                                      +
                                                                                      49  virtual const Type evaluate(const Type& x) = 0;
                                                                                      50 };
                                                                                      51 
                                                                                      52 // default id of the singleton selectivity class
                                                                                      53 template <typename Type>
                                                                                      -
                                                                                      54 uint32_t SelectivityBase<Type>::id_g = 0;
                                                                                      +
                                                                                      54 uint32_t SelectivityBase<Type>::id_g = 0;
                                                                                      55 
                                                                                      56 } // namespace fims
                                                                                      57 
                                                                                      58 #endif /* POPULATION_DYNAMICS_SELECTIVITY_BASE_HPP */
                                                                                      -
                                                                                      fims::FIMSObject
                                                                                      FIMSObject struct that defines member types and returns the unique id.
                                                                                      Definition: model_object.hpp:25
                                                                                      -
                                                                                      fims::SelectivityBase
                                                                                      Base class for all selectivity functors.
                                                                                      Definition: selectivity_base.hpp:27
                                                                                      -
                                                                                      fims::SelectivityBase::id_g
                                                                                      static uint32_t id_g
                                                                                      Definition: selectivity_base.hpp:33
                                                                                      -
                                                                                      fims::SelectivityBase::evaluate
                                                                                      virtual const Type evaluate(const Type &x)=0
                                                                                      Calculates the selectivity.
                                                                                      -
                                                                                      fims::SelectivityBase::SelectivityBase
                                                                                      SelectivityBase()
                                                                                      Constructor.
                                                                                      Definition: selectivity_base.hpp:37
                                                                                      +
                                                                                      fims_model_object::FIMSObject
                                                                                      FIMSObject struct that defines member types and returns the unique id.
                                                                                      Definition: model_object.hpp:25
                                                                                      +
                                                                                      fims_popdy::SelectivityBase
                                                                                      Base class for all selectivity functors.
                                                                                      Definition: selectivity_base.hpp:27
                                                                                      +
                                                                                      fims_popdy::SelectivityBase::evaluate
                                                                                      virtual const Type evaluate(const Type &x)=0
                                                                                      Calculates the selectivity.
                                                                                      +
                                                                                      fims_popdy::SelectivityBase::id_g
                                                                                      static uint32_t id_g
                                                                                      Definition: selectivity_base.hpp:33
                                                                                      +
                                                                                      fims_popdy::SelectivityBase::SelectivityBase
                                                                                      SelectivityBase()
                                                                                      Constructor.
                                                                                      Definition: selectivity_base.hpp:37
                                                                                      diff --git a/docs/sr__beverton__holt_8hpp_source.html b/docs/sr__beverton__holt_8hpp_source.html index d5fb07d..51cc435 100644 --- a/docs/sr__beverton__holt_8hpp_source.html +++ b/docs/sr__beverton__holt_8hpp_source.html @@ -93,19 +93,19 @@
                                                                                      15 
                                                                                      16 #include "recruitment_base.hpp"
                                                                                      17 
                                                                                      -
                                                                                      18 namespace fims {
                                                                                      +
                                                                                      18 namespace fims_popdy {
                                                                                      19 
                                                                                      26 template <typename Type>
                                                                                      -
                                                                                      27 struct SRBevertonHolt : public RecruitmentBase<Type> {
                                                                                      +
                                                                                      27 struct SRBevertonHolt : public RecruitmentBase<Type> {
                                                                                      28  // Here we define the members that will be used in the Beverton Holt SR
                                                                                      29  // function. These members are needed by Beverton Holt but will not be common
                                                                                      30  // to all recruitment functions like spawners is below.
                                                                                      -
                                                                                      31  Type logit_steep;
                                                                                      -
                                                                                      34  SRBevertonHolt() : RecruitmentBase<Type>() {}
                                                                                      +
                                                                                      31  Type logit_steep;
                                                                                      +
                                                                                      34  SRBevertonHolt() : RecruitmentBase<Type>() {}
                                                                                      35 
                                                                                      -
                                                                                      36  virtual ~SRBevertonHolt() {}
                                                                                      +
                                                                                      36  virtual ~SRBevertonHolt() {}
                                                                                      37 
                                                                                      -
                                                                                      47  virtual const Type evaluate(const Type& spawners, const Type& phi_0) {
                                                                                      +
                                                                                      47  virtual const Type evaluate(const Type& spawners, const Type& phi_0) {
                                                                                      48  Type recruits;
                                                                                      49  Type steep;
                                                                                      50  Type steep_lo = 0.2;
                                                                                      @@ -113,8 +113,8 @@
                                                                                      52  Type rzero;
                                                                                      53 
                                                                                      54  // Transform input parameters
                                                                                      -
                                                                                      55  steep = fims::inv_logit(steep_lo, steep_hi, this->logit_steep);
                                                                                      -
                                                                                      56  rzero = fims::exp(this->log_rzero);
                                                                                      +
                                                                                      55  steep = fims_math::inv_logit(steep_lo, steep_hi, this->logit_steep);
                                                                                      +
                                                                                      56  rzero = fims_math::exp(this->log_rzero);
                                                                                      57 
                                                                                      58  recruits = (0.8 * rzero * steep * spawners) /
                                                                                      59  (0.2 * phi_0 * rzero * (1.0 - steep) + spawners * (steep - 0.2));
                                                                                      @@ -126,13 +126,12 @@
                                                                                      65 } // namespace fims
                                                                                      66 
                                                                                      67 #endif /* FIMS_POPULATION_DYNAMICS_RECRUITMENT_SR_BEVERTON_HOLT_HPP */
                                                                                      -
                                                                                      fims::inv_logit
                                                                                      const T inv_logit(const T &a, const T &b, const T &logit_x)
                                                                                      An inverse logit function for bounding of parameters.
                                                                                      Definition: fims_math.hpp:133
                                                                                      recruitment_base.hpp
                                                                                      -
                                                                                      fims::RecruitmentBase
                                                                                      Base class for all recruitment functors.
                                                                                      Definition: recruitment_base.hpp:31
                                                                                      -
                                                                                      fims::RecruitmentBase::log_rzero
                                                                                      Type log_rzero
                                                                                      Definition: recruitment_base.hpp:41
                                                                                      -
                                                                                      fims::SRBevertonHolt
                                                                                      BevertonHolt class that returns the Beverton Holt SR from fims_math.
                                                                                      Definition: sr_beverton_holt.hpp:27
                                                                                      -
                                                                                      fims::SRBevertonHolt::evaluate
                                                                                      virtual const Type evaluate(const Type &spawners, const Type &phi_0)
                                                                                      Beverton Holt implementation of the stock recruitment function.
                                                                                      Definition: sr_beverton_holt.hpp:47
                                                                                      -
                                                                                      fims::SRBevertonHolt::logit_steep
                                                                                      Type logit_steep
                                                                                      Definition: sr_beverton_holt.hpp:31
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase
                                                                                      Base class for all recruitment functors.
                                                                                      Definition: recruitment_base.hpp:31
                                                                                      +
                                                                                      fims_popdy::RecruitmentBase::log_rzero
                                                                                      Type log_rzero
                                                                                      Definition: recruitment_base.hpp:41
                                                                                      +
                                                                                      fims_popdy::SRBevertonHolt
                                                                                      BevertonHolt class that returns the Beverton Holt SR from fims_math.
                                                                                      Definition: sr_beverton_holt.hpp:27
                                                                                      +
                                                                                      fims_popdy::SRBevertonHolt::logit_steep
                                                                                      Type logit_steep
                                                                                      Definition: sr_beverton_holt.hpp:31
                                                                                      +
                                                                                      fims_popdy::SRBevertonHolt::evaluate
                                                                                      virtual const Type evaluate(const Type &spawners, const Type &phi_0)
                                                                                      Beverton Holt implementation of the stock recruitment function.
                                                                                      Definition: sr_beverton_holt.hpp:47
                                                                                      diff --git a/docs/structfims__data__object_1_1DataObject-members.html b/docs/structfims__data__object_1_1DataObject-members.html new file mode 100644 index 0000000..1c9377d --- /dev/null +++ b/docs/structfims__data__object_1_1DataObject-members.html @@ -0,0 +1,118 @@ + + + + + + + +FIMS: Member List + + + + + + + + + + + +
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                                                                                      FIMS +
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                                                                                      +
                                                                                      +
                                                                                      fims_data_object::DataObject< Type > Member List
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      This is the complete list of members for fims_data_object::DataObject< Type >, including all inherited members.

                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      at(size_t i)fims_data_object::DataObject< Type >inline
                                                                                      at(size_t i, size_t j)fims_data_object::DataObject< Type >inline
                                                                                      at(size_t i, size_t j, size_t k)fims_data_object::DataObject< Type >inline
                                                                                      at(size_t i, size_t j, size_t k, size_t l)fims_data_object::DataObject< Type >inline
                                                                                      datafims_data_object::DataObject< Type >
                                                                                      DataObject(size_t imax)fims_data_object::DataObject< Type >inline
                                                                                      DataObject(size_t imax, size_t jmax)fims_data_object::DataObject< Type >inline
                                                                                      DataObject(size_t imax, size_t jmax, size_t kmax)fims_data_object::DataObject< Type >inline
                                                                                      DataObject(size_t imax, size_t jmax, size_t kmax, size_t lmax)fims_data_object::DataObject< Type >inline
                                                                                      dimensionsfims_data_object::DataObject< Type >
                                                                                      fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      get_dimensions() constfims_data_object::DataObject< Type >inline
                                                                                      get_imax() constfims_data_object::DataObject< Type >inline
                                                                                      get_jmax() constfims_data_object::DataObject< Type >inline
                                                                                      get_kmax() constfims_data_object::DataObject< Type >inline
                                                                                      get_lmax() constfims_data_object::DataObject< Type >inline
                                                                                      GetId() constfims_model_object::FIMSObject< Type >inline
                                                                                      idfims_model_object::FIMSObject< Type >
                                                                                      id_gfims_data_object::DataObject< Type >static
                                                                                      imaxfims_data_object::DataObject< Type >
                                                                                      jmaxfims_data_object::DataObject< Type >
                                                                                      kmaxfims_data_object::DataObject< Type >
                                                                                      lmaxfims_data_object::DataObject< Type >
                                                                                      operator()(size_t i)fims_data_object::DataObject< Type >inline
                                                                                      operator()(size_t i, size_t j)fims_data_object::DataObject< Type >inline
                                                                                      operator()(size_t i, size_t j, size_t k)fims_data_object::DataObject< Type >inline
                                                                                      operator()(size_t i, size_t j, size_t k, size_t l)fims_data_object::DataObject< Type >inline
                                                                                      parametersfims_model_object::FIMSObject< Type >
                                                                                      random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
                                                                                      + + diff --git a/docs/structfims__data__object_1_1DataObject.html b/docs/structfims__data__object_1_1DataObject.html new file mode 100644 index 0000000..f4b0d5d --- /dev/null +++ b/docs/structfims__data__object_1_1DataObject.html @@ -0,0 +1,1018 @@ + + + + + + + +FIMS: fims_data_object::DataObject< Type > Struct Template Reference + + + + + + + + + + + +
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                                                                                      FIMS +
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                                                                                      +Public Member Functions | +Public Attributes | +Static Public Attributes | +List of all members
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                                                                                      fims_data_object::DataObject< Type > Struct Template Reference
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      #include <data_object.hpp>

                                                                                      +
                                                                                      +Inheritance diagram for fims_data_object::DataObject< Type >:
                                                                                      +
                                                                                      +
                                                                                      + + +fims_model_object::FIMSObject< Type > + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

                                                                                      +Public Member Functions

                                                                                       DataObject (size_t imax)
                                                                                       
                                                                                       DataObject (size_t imax, size_t jmax)
                                                                                       
                                                                                       DataObject (size_t imax, size_t jmax, size_t kmax)
                                                                                       
                                                                                       DataObject (size_t imax, size_t jmax, size_t kmax, size_t lmax)
                                                                                       
                                                                                      Type operator() (size_t i)
                                                                                       
                                                                                      Type & at (size_t i)
                                                                                       
                                                                                      const Type operator() (size_t i, size_t j)
                                                                                       
                                                                                      Type & at (size_t i, size_t j)
                                                                                       
                                                                                      const Type operator() (size_t i, size_t j, size_t k)
                                                                                       
                                                                                      Type & at (size_t i, size_t j, size_t k)
                                                                                       
                                                                                      const Type operator() (size_t i, size_t j, size_t k, size_t l)
                                                                                       
                                                                                      Type & at (size_t i, size_t j, size_t k, size_t l)
                                                                                       
                                                                                      size_t get_dimensions () const
                                                                                       Get the dimensions object. More...
                                                                                       
                                                                                      size_t get_imax () const
                                                                                       Get the imax object. More...
                                                                                       
                                                                                      size_t get_jmax () const
                                                                                       Get the jmax object. More...
                                                                                       
                                                                                      size_t get_kmax () const
                                                                                       Get the kmax object. More...
                                                                                       
                                                                                      size_t get_lmax () const
                                                                                       Get the lmax object. More...
                                                                                       
                                                                                      - 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.
                                                                                       
                                                                                      + + + + + + + + + + + + + + + + + + + + + + +

                                                                                      +Public Attributes

                                                                                      std::vector< Type > data
                                                                                       
                                                                                      size_t dimensions
                                                                                       
                                                                                      size_t imax
                                                                                       
                                                                                      size_t jmax
                                                                                       
                                                                                      size_t kmax
                                                                                       
                                                                                      size_t lmax
                                                                                       
                                                                                      - 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<typename Type>
                                                                                      +struct fims_data_object::DataObject< Type >

                                                                                      + +

                                                                                      Container to hold user supplied data.

                                                                                      +

                                                                                      Constructor & Destructor Documentation

                                                                                      + +

                                                                                      ◆ DataObject() [1/4]

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + +
                                                                                      fims_data_object::DataObject< Type >::DataObject (size_t imax)
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      +

                                                                                      Constructs a one-dimensional data object.

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ DataObject() [2/4]

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + +
                                                                                      fims_data_object::DataObject< Type >::DataObject (size_t imax,
                                                                                      size_t jmax 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      +

                                                                                      Constructs a two-dimensional data object.

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ DataObject() [3/4]

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      fims_data_object::DataObject< Type >::DataObject (size_t imax,
                                                                                      size_t jmax,
                                                                                      size_t kmax 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      +

                                                                                      Constructs a three-dimensional data object.

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ DataObject() [4/4]

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      fims_data_object::DataObject< Type >::DataObject (size_t imax,
                                                                                      size_t jmax,
                                                                                      size_t kmax,
                                                                                      size_t lmax 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      +

                                                                                      Constructs a four-dimensional data object.

                                                                                      + +
                                                                                      +
                                                                                      +

                                                                                      Member Function Documentation

                                                                                      + +

                                                                                      ◆ at() [1/4]

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + +
                                                                                      Type& fims_data_object::DataObject< Type >::at (size_t i)
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      +

                                                                                      Retrieve element from 1d data set. Throws an exception if index is out of bounds.

                                                                                      Parameters
                                                                                      + + +
                                                                                      idimension of 1d data set
                                                                                      +
                                                                                      +
                                                                                      +
                                                                                      Returns
                                                                                      the reference to the value of the vector at position i
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ at() [2/4]

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + +
                                                                                      Type& fims_data_object::DataObject< Type >::at (size_t i,
                                                                                      size_t j 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      +

                                                                                      Retrieve element from 2d data set. Throws an exception if index is out of bounds.

                                                                                      Parameters
                                                                                      + + + +
                                                                                      i1st dimension of 2d data set
                                                                                      j2nd dimension of 2d data set
                                                                                      +
                                                                                      +
                                                                                      +
                                                                                      Returns
                                                                                      the reference to the value of the matrix at position i, j
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ at() [3/4]

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      Type& fims_data_object::DataObject< Type >::at (size_t i,
                                                                                      size_t j,
                                                                                      size_t k 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      +

                                                                                      Retrieve element from 3d data set. Throws an exception if index is out of bounds.

                                                                                      Parameters
                                                                                      + + + + +
                                                                                      i1st dimension of 3d data set
                                                                                      j2nd dimension of 3d data set
                                                                                      k3rd dimension of 3d data set
                                                                                      +
                                                                                      +
                                                                                      +
                                                                                      Returns
                                                                                      the reference to the value of the array at position i, j, k
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ at() [4/4]

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      Type& fims_data_object::DataObject< Type >::at (size_t i,
                                                                                      size_t j,
                                                                                      size_t k,
                                                                                      size_t l 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      +

                                                                                      Retrieve element from 3d data set. Throws an exception if index is out of bounds.

                                                                                      Parameters
                                                                                      + + + + + +
                                                                                      i1st dimension of 4d data set
                                                                                      j2nd dimension of 4d data set
                                                                                      k3rd dimension of 4d data set
                                                                                      l4th dimension of 4d data set
                                                                                      +
                                                                                      +
                                                                                      +
                                                                                      Returns
                                                                                      the reference to the value of the array at position i, j, k, l
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ get_dimensions()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + +
                                                                                      size_t fims_data_object::DataObject< Type >::get_dimensions () const
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Get the dimensions object.

                                                                                      +
                                                                                      Returns
                                                                                      size_t
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ get_imax()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + +
                                                                                      size_t fims_data_object::DataObject< Type >::get_imax () const
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Get the imax object.

                                                                                      +
                                                                                      Returns
                                                                                      size_t
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ get_jmax()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + +
                                                                                      size_t fims_data_object::DataObject< Type >::get_jmax () const
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Get the jmax object.

                                                                                      +
                                                                                      Returns
                                                                                      size_t
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ get_kmax()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + +
                                                                                      size_t fims_data_object::DataObject< Type >::get_kmax () const
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Get the kmax object.

                                                                                      +
                                                                                      Returns
                                                                                      size_t
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ get_lmax()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + +
                                                                                      size_t fims_data_object::DataObject< Type >::get_lmax () const
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Get the lmax object.

                                                                                      +
                                                                                      Returns
                                                                                      size_t
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ operator()() [1/4]

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + +
                                                                                      Type fims_data_object::DataObject< Type >::operator() (size_t i)
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      +

                                                                                      Retrieve element from 1d data set.

                                                                                      Parameters
                                                                                      + + +
                                                                                      idimension of 1d data set
                                                                                      +
                                                                                      +
                                                                                      +
                                                                                      Returns
                                                                                      the value of the vector at position i
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ operator()() [2/4]

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + +
                                                                                      const Type fims_data_object::DataObject< Type >::operator() (size_t i,
                                                                                      size_t j 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      +

                                                                                      Retrieve element from 2d data set.

                                                                                      Parameters
                                                                                      + + + +
                                                                                      i1st dimension of 2d data set
                                                                                      j2nd dimension of 2d data set
                                                                                      +
                                                                                      +
                                                                                      +
                                                                                      Returns
                                                                                      the value of the matrix at position i, j
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ operator()() [3/4]

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      const Type fims_data_object::DataObject< Type >::operator() (size_t i,
                                                                                      size_t j,
                                                                                      size_t k 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      +

                                                                                      Retrieve element from 3d data set.

                                                                                      Parameters
                                                                                      + + + + +
                                                                                      i1st dimension of 3d data set
                                                                                      j2nd dimension of 3d data set
                                                                                      k3rd dimension of 3d data set
                                                                                      +
                                                                                      +
                                                                                      +
                                                                                      Returns
                                                                                      the value of the array at position i, j, k
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ operator()() [4/4]

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      const Type fims_data_object::DataObject< Type >::operator() (size_t i,
                                                                                      size_t j,
                                                                                      size_t k,
                                                                                      size_t l 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      +

                                                                                      Retrieve element from 4d data set.

                                                                                      Parameters
                                                                                      + + + + + +
                                                                                      i1st dimension of 4d data set
                                                                                      j2nd dimension of 4d data set
                                                                                      k3rd dimension of 4d data set
                                                                                      l4th dimension of 4d data set
                                                                                      +
                                                                                      +
                                                                                      +
                                                                                      Returns
                                                                                      the value of the array at position i, j, k, l
                                                                                      + +
                                                                                      +
                                                                                      +

                                                                                      Member Data Documentation

                                                                                      + +

                                                                                      ◆ data

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_data_object::DataObject< Type >::data
                                                                                      +
                                                                                      +

                                                                                      vector of the data >

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ dimensions

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      size_t fims_data_object::DataObject< Type >::dimensions
                                                                                      +
                                                                                      +

                                                                                      dimension of the Data object >

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ id_g

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + +
                                                                                      uint32_t fims_data_object::DataObject< Type >::id_g = 0
                                                                                      +                                                                                       		+static
                                                                                      +
                                                                                      +

                                                                                      id of the Data Object >

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ imax

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      size_t fims_data_object::DataObject< Type >::imax
                                                                                      +
                                                                                      +

                                                                                      1st dimension of data object >

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ jmax

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      size_t fims_data_object::DataObject< Type >::jmax
                                                                                      +
                                                                                      +

                                                                                      2nd dimension of data object>

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ kmax

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      size_t fims_data_object::DataObject< Type >::kmax
                                                                                      +
                                                                                      +

                                                                                      3rd dimension of data object>

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ lmax

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      size_t fims_data_object::DataObject< Type >::lmax
                                                                                      +
                                                                                      +

                                                                                      4th dimension of data object>

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      The documentation for this struct was generated from the following file: +
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
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                                                                                      + + + + + + +
                                                                                      +
                                                                                      FIMS +
                                                                                      +
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                                                                                      + + + + + + + + +
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                                                                                      + + +
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                                                                                      + + +
                                                                                      +
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                                                                                      +
                                                                                      fims_distributions::DistributionsBase< Type > Member List
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      This is the complete list of members for fims_distributions::DistributionsBase< Type >, including all inherited members.

                                                                                      + + + + + + + + + + + +
                                                                                      DistributionsBase()fims_distributions::DistributionsBase< Type >inline
                                                                                      evaluate(const bool &do_log)=0fims_distributions::DistributionsBase< Type >pure virtual
                                                                                      fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      GetId() constfims_model_object::FIMSObject< Type >inline
                                                                                      idfims_model_object::FIMSObject< Type >
                                                                                      id_gfims_distributions::DistributionsBase< Type >static
                                                                                      parametersfims_model_object::FIMSObject< Type >
                                                                                      random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      ~DistributionsBase() (defined in fims_distributions::DistributionsBase< Type >)fims_distributions::DistributionsBase< Type >inlinevirtual
                                                                                      ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
                                                                                      + + diff --git a/docs/structfims__distributions_1_1DistributionsBase.html b/docs/structfims__distributions_1_1DistributionsBase.html new file mode 100644 index 0000000..cad5d20 --- /dev/null +++ b/docs/structfims__distributions_1_1DistributionsBase.html @@ -0,0 +1,189 @@ + + + + + + + +FIMS: fims_distributions::DistributionsBase< Type > Struct Template Reference + + + + + + + + + + + +
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                                                                                      fims_distributions::DistributionsBase< Type > Struct Template Referenceabstract
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      Base class for all module_name functors. + More...

                                                                                      + +

                                                                                      #include <distributions_base.hpp>

                                                                                      +
                                                                                      +Inheritance diagram for fims_distributions::DistributionsBase< Type >:
                                                                                      +
                                                                                      +
                                                                                      + + +fims_model_object::FIMSObject< Type > + +
                                                                                      + + + + + + + + + + + + +

                                                                                      +Public Member Functions

                                                                                      + DistributionsBase ()
                                                                                       Constructor.
                                                                                       
                                                                                      virtual const Type evaluate (const bool &do_log)=0
                                                                                       Generic probability density function. Calculates the pdf at the independent variable value. More...
                                                                                       
                                                                                      - 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.
                                                                                       
                                                                                      + + + + +

                                                                                      +Static Public Attributes

                                                                                      +static uint32_t id_g = 0
                                                                                       Default id of the singleton distribution class.
                                                                                       
                                                                                      + + + + + + + + + + +

                                                                                      +Additional Inherited Members

                                                                                      - 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
                                                                                       
                                                                                      +

                                                                                      Detailed Description

                                                                                      +

                                                                                      template<typename Type>
                                                                                      +struct fims_distributions::DistributionsBase< Type >

                                                                                      + +

                                                                                      Base class for all module_name functors.

                                                                                      +
                                                                                      Template Parameters
                                                                                      + + +
                                                                                      TypeThe type of the module_name functor.
                                                                                      +
                                                                                      +
                                                                                      +

                                                                                      Member Function Documentation

                                                                                      + +

                                                                                      ◆ evaluate()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + +
                                                                                      virtual const Type fims_distributions::DistributionsBase< Type >::evaluate (const bool & do_log)
                                                                                      +                                                                                       		+pure virtual
                                                                                      +
                                                                                      + +

                                                                                      Generic probability density function. Calculates the pdf at the independent variable value.

                                                                                      +
                                                                                      Parameters
                                                                                      + + +
                                                                                      do_logBoolean; if true, log densities are returned
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      The documentation for this struct was generated from the following file: +
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
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                                                                                      fims_model_object::FIMSObject< Type > Member List
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                                                                                      + +

                                                                                      This is the complete list of members for fims_model_object::FIMSObject< Type >, including all inherited members.

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                                                                                      fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      GetId() constfims_model_object::FIMSObject< Type >inline
                                                                                      idfims_model_object::FIMSObject< Type >
                                                                                      parametersfims_model_object::FIMSObject< Type >
                                                                                      random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
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                                                                                      fims_model_object::FIMSObject< Type > Struct Template Reference
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                                                                                      + +

                                                                                      FIMSObject struct that defines member types and returns the unique id. + More...

                                                                                      + +

                                                                                      #include <model_object.hpp>

                                                                                      +
                                                                                      +Inheritance diagram for fims_model_object::FIMSObject< Type >:
                                                                                      +
                                                                                      +
                                                                                      + + +fims_data_object::DataObject< Type > +fims_distributions::DistributionsBase< Type > +fims_popdy::Fleet< Type > +fims_popdy::GrowthBase< Type > +fims_popdy::MaturityBase< Type > +fims_popdy::Population< Type > +fims_popdy::RecruitmentBase< Type > +fims_popdy::SelectivityBase< Type > + +
                                                                                      + + + + + +

                                                                                      +Public Member Functions

                                                                                      +uint32_t GetId () const
                                                                                       Getter that returns the unique id for parameters in the model.
                                                                                       
                                                                                      + + + + + + + + + +

                                                                                      +Public Attributes

                                                                                      uint32_t id
                                                                                       
                                                                                      std::vector< Type * > parameters
                                                                                       
                                                                                      std::vector< Type * > random_effects_parameters
                                                                                       
                                                                                      std::vector< Type * > fixed_effects_parameters
                                                                                       
                                                                                      +

                                                                                      Detailed Description

                                                                                      +

                                                                                      template<typename Type>
                                                                                      +struct fims_model_object::FIMSObject< Type >

                                                                                      + +

                                                                                      FIMSObject struct that defines member types and returns the unique id.

                                                                                      +

                                                                                      Member Data Documentation

                                                                                      + +

                                                                                      ◆ fixed_effects_parameters

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type*> fims_model_object::FIMSObject< Type >::fixed_effects_parameters
                                                                                      +
                                                                                      +

                                                                                      list of fixed effects parameters

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ id

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      uint32_t fims_model_object::FIMSObject< Type >::id
                                                                                      +
                                                                                      +

                                                                                      unique identifier assigned for all fims objects

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ parameters

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type*> fims_model_object::FIMSObject< Type >::parameters
                                                                                      +
                                                                                      +

                                                                                      list of estimable parameters

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ random_effects_parameters

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type*> fims_model_object::FIMSObject< Type >::random_effects_parameters
                                                                                      +
                                                                                      +

                                                                                      list of all random effects parameters

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      The documentation for this struct was generated from the following file: +
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
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                                                                                      fims_popdy::DoubleLogisticSelectivity< Type > Member List
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      This is the complete list of members for fims_popdy::DoubleLogisticSelectivity< Type >, including all inherited members.

                                                                                      + + + + + + + + + + + + + + + + + +
                                                                                      DoubleLogisticSelectivity() (defined in fims_popdy::DoubleLogisticSelectivity< Type >)fims_popdy::DoubleLogisticSelectivity< Type >inline
                                                                                      evaluate(const Type &x)fims_popdy::DoubleLogisticSelectivity< Type >inlinevirtual
                                                                                      fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      GetId() constfims_model_object::FIMSObject< Type >inline
                                                                                      idfims_model_object::FIMSObject< Type >
                                                                                      id_gfims_popdy::SelectivityBase< Type >static
                                                                                      median_ascfims_popdy::DoubleLogisticSelectivity< Type >
                                                                                      median_descfims_popdy::DoubleLogisticSelectivity< Type >
                                                                                      parametersfims_model_object::FIMSObject< Type >
                                                                                      random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      SelectivityBase()fims_popdy::SelectivityBase< Type >inline
                                                                                      slope_ascfims_popdy::DoubleLogisticSelectivity< Type >
                                                                                      slope_descfims_popdy::DoubleLogisticSelectivity< Type >
                                                                                      ~DoubleLogisticSelectivity() (defined in fims_popdy::DoubleLogisticSelectivity< Type >)fims_popdy::DoubleLogisticSelectivity< Type >inlinevirtual
                                                                                      ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                                      ~SelectivityBase() (defined in fims_popdy::SelectivityBase< Type >)fims_popdy::SelectivityBase< Type >inlinevirtual
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
                                                                                      + + diff --git a/docs/structfims__popdy_1_1DoubleLogisticSelectivity.html b/docs/structfims__popdy_1_1DoubleLogisticSelectivity.html new file mode 100644 index 0000000..9448954 --- /dev/null +++ b/docs/structfims__popdy_1_1DoubleLogisticSelectivity.html @@ -0,0 +1,264 @@ + + + + + + + +FIMS: fims_popdy::DoubleLogisticSelectivity< Type > Struct Template Reference + + + + + + + + + + + +
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                                                                                      fims_popdy::DoubleLogisticSelectivity< Type > Struct Template Reference
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      DoubleLogisticSelectivity class that returns the double logistic function value from fims_math. + More...

                                                                                      + +

                                                                                      #include <double_logistic.hpp>

                                                                                      +
                                                                                      +Inheritance diagram for fims_popdy::DoubleLogisticSelectivity< Type >:
                                                                                      +
                                                                                      +
                                                                                      + + +fims_popdy::SelectivityBase< Type > +fims_model_object::FIMSObject< Type > + +
                                                                                      + + + + + + + + + + + + + +

                                                                                      +Public Member Functions

                                                                                      virtual const Type evaluate (const Type &x)
                                                                                       Method of the double logistic selectivity class that implements the double logistic function from FIMS math. More...
                                                                                       
                                                                                      - Public Member Functions inherited from fims_popdy::SelectivityBase< Type >
                                                                                      + SelectivityBase ()
                                                                                       Constructor.
                                                                                       
                                                                                      - 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.
                                                                                       
                                                                                      + + + + + + + + + + + + + + + + + + +

                                                                                      +Public Attributes

                                                                                      Type median_asc
                                                                                       
                                                                                      Type slope_asc
                                                                                       
                                                                                      Type median_desc
                                                                                       
                                                                                      Type slope_desc
                                                                                       
                                                                                      - 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
                                                                                       
                                                                                      + + + + +

                                                                                      +Additional Inherited Members

                                                                                      - Static Public Attributes inherited from fims_popdy::SelectivityBase< Type >
                                                                                      static uint32_t id_g = 0
                                                                                       
                                                                                      +

                                                                                      Detailed Description

                                                                                      +

                                                                                      template<typename Type>
                                                                                      +struct fims_popdy::DoubleLogisticSelectivity< Type >

                                                                                      + +

                                                                                      DoubleLogisticSelectivity class that returns the double logistic function value from fims_math.

                                                                                      +

                                                                                      Member Function Documentation

                                                                                      + +

                                                                                      ◆ evaluate()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + +
                                                                                      virtual const Type fims_popdy::DoubleLogisticSelectivity< Type >::evaluate (const Type & x)
                                                                                      +                                                                                       		+inlinevirtual
                                                                                      +
                                                                                      + +

                                                                                      Method of the double logistic selectivity class that implements the double logistic function from FIMS math.

                                                                                      +

                                                                                      \( \frac{1.0}{ 1.0 + exp(-1.0 * slope_{asc} (x - median_{asc}))} \left(1-\frac{1.0}{ 1.0 + exp(-1.0 * slope_{desc} (x - median_{desc}))} \right)\)

                                                                                      +
                                                                                      Parameters
                                                                                      + + +
                                                                                      xThe independent variable in the double logistic function (e.g., age or size in selectivity).
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      Implements fims_popdy::SelectivityBase< Type >.

                                                                                      + +
                                                                                      +
                                                                                      +

                                                                                      Member Data Documentation

                                                                                      + +

                                                                                      ◆ median_asc

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      Type fims_popdy::DoubleLogisticSelectivity< Type >::median_asc
                                                                                      +
                                                                                      +

                                                                                      50% quantile of the value of the quantity of interest (x) on the ascending limb of the double logistic curve; e.g. age at which 50% of the fish are selected

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ median_desc

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      Type fims_popdy::DoubleLogisticSelectivity< Type >::median_desc
                                                                                      +
                                                                                      +

                                                                                      50% quantile of the value of the quantity of interest (x) on the descending limb of the double logistic curve; e.g. age at which 50% of the fish are selected

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ slope_asc

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      Type fims_popdy::DoubleLogisticSelectivity< Type >::slope_asc
                                                                                      +
                                                                                      +

                                                                                      scalar multiplier of difference between quantity of interest value (x) and median on the ascending limb of the double logistic curve

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ slope_desc

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      Type fims_popdy::DoubleLogisticSelectivity< Type >::slope_desc
                                                                                      +
                                                                                      +

                                                                                      scalar multiplier of difference between quantity of interest value (x) and median on the descending limb of the double logistic curve

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      The documentation for this struct was generated from the following file: +
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
                                                                                      + + diff --git a/docs/structfims__popdy_1_1DoubleLogisticSelectivity.png b/docs/structfims__popdy_1_1DoubleLogisticSelectivity.png new file mode 100644 index 0000000000000000000000000000000000000000..c6a00c61f08bf595cb99a1f07283ffdeb2e3bfe6 GIT binary patch literal 1556 zcmbu9X;4#F7=~}4D5$6fTZIuQ8okC1t566*m?8u&;0*;7q68_6$Rd;_>*Zp38q%kH zkPU1LNQ*wN-dA>K0YL5%Wb(aTC`!oi4xBxBH3LgyL@D||P~Jia{1u=9RA zC*WaX;FCGk%;ps0o=BdxPD>NFvish$7#&`$)O2bbP;G9D};PfkeEB`i*G9a;3O`Z;c}Tf*~eRGrpAV`yo3CN2a$-PBHo zsHf9>r>xFE855@9kfBa?wZ?Kkqi5(Lnl!IFFNmRSc!AUfziZZcS#qG2aihOdhSV9JIxDQii|e~HcKo`!(4RmIQ-YGb!ApkQsGk2>S~oF?NS zRj`EwS)g2`pyT=f75$e*R!!klcOuoDXz?S;+$B}&ox^{6$6wqRe6>H+X9#H7{H134 z_H<+@M;W7B;tqY^364krl}1ln#2 z7qdtGTQif77xP^Rg{rAz*&>;nSe-B*No+#`fsM`Q7yMcgAuRO?@7gRByY15t==Ptn z6|)nPmD^-Gk&4+P;Zv+DxCgQfvUp$y4|j~)m$~RMSUUYl0T83adTviS(We zYDditO7g_by2Ih`XRQ)kJ*n(D!IVuVc!YgEr+D5i+{lw*m%jO0!pa!UzLA78d;|Aa zBAhy=6%*H&NloaDwPE5S9G7`m)zhtUw|Je5iv7d3kKyY4!0pcF9`1EyvFxrD^TWzT zUqu0=EZkt;eA?Zv?Hr?whIW~n)}N_<*mN#J*p + + + + + + +FIMS: Member List + + + + + + + + + + + +
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                                                                                      fims_popdy::EWAAgrowth< Type > Member List
                                                                                      +
                                                                                      +
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                                                                                      This is the complete list of members for fims_popdy::EWAAgrowth< Type >, including all inherited members.

                                                                                      + + + + + + + + + + + + + + +
                                                                                      evaluate(const double &a)fims_popdy::EWAAgrowth< Type >inlinevirtual
                                                                                      ewaafims_popdy::EWAAgrowth< Type >
                                                                                      EWAAgrowth() (defined in fims_popdy::EWAAgrowth< Type >)fims_popdy::EWAAgrowth< Type >inline
                                                                                      fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      GetId() constfims_model_object::FIMSObject< Type >inline
                                                                                      GrowthBase()fims_popdy::GrowthBase< Type >inline
                                                                                      idfims_model_object::FIMSObject< Type >
                                                                                      id_gfims_popdy::GrowthBase< Type >static
                                                                                      parametersfims_model_object::FIMSObject< Type >
                                                                                      random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      ~EWAAgrowth() (defined in fims_popdy::EWAAgrowth< Type >)fims_popdy::EWAAgrowth< Type >inlinevirtual
                                                                                      ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                                      ~GrowthBase() (defined in fims_popdy::GrowthBase< Type >)fims_popdy::GrowthBase< Type >inlinevirtual
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
                                                                                      + + diff --git a/docs/structfims__popdy_1_1EWAAgrowth.html b/docs/structfims__popdy_1_1EWAAgrowth.html new file mode 100644 index 0000000..8be24e5 --- /dev/null +++ b/docs/structfims__popdy_1_1EWAAgrowth.html @@ -0,0 +1,206 @@ + + + + + + + +FIMS: fims_popdy::EWAAgrowth< Type > Struct Template Reference + + + + + + + + + + + +
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                                                                                      FIMS +
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                                                                                      +Public Member Functions | +Public Attributes | +List of all members
                                                                                      +
                                                                                      +
                                                                                      fims_popdy::EWAAgrowth< Type > Struct Template Reference
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      EWAAgrowth class that returns the EWAA function value. + More...

                                                                                      + +

                                                                                      #include <ewaa.hpp>

                                                                                      +
                                                                                      +Inheritance diagram for fims_popdy::EWAAgrowth< Type >:
                                                                                      +
                                                                                      +
                                                                                      + + +fims_popdy::GrowthBase< Type > +fims_model_object::FIMSObject< Type > + +
                                                                                      + + + + + + + + + + + + + +

                                                                                      +Public Member Functions

                                                                                      virtual const Type evaluate (const double &a)
                                                                                       Returns the weight at age a (in kg) from the input vector. More...
                                                                                       
                                                                                      - Public Member Functions inherited from fims_popdy::GrowthBase< Type >
                                                                                      + GrowthBase ()
                                                                                       Constructor.
                                                                                       
                                                                                      - 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.
                                                                                       
                                                                                      + + + + + + + + + + + + +

                                                                                      +Public Attributes

                                                                                      std::map< double, double > ewaa
                                                                                       
                                                                                      - 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
                                                                                       
                                                                                      + + + + +

                                                                                      +Additional Inherited Members

                                                                                      - Static Public Attributes inherited from fims_popdy::GrowthBase< Type >
                                                                                      static uint32_t id_g = 0
                                                                                       
                                                                                      +

                                                                                      Detailed Description

                                                                                      +

                                                                                      template<typename Type>
                                                                                      +struct fims_popdy::EWAAgrowth< Type >

                                                                                      + +

                                                                                      EWAAgrowth class that returns the EWAA function value.

                                                                                      +

                                                                                      Member Function Documentation

                                                                                      + +

                                                                                      ◆ evaluate()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + +
                                                                                      virtual const Type fims_popdy::EWAAgrowth< Type >::evaluate (const double & a)
                                                                                      +                                                                                       		+inlinevirtual
                                                                                      +
                                                                                      + +

                                                                                      Returns the weight at age a (in kg) from the input vector.

                                                                                      +
                                                                                      Parameters
                                                                                      + + +
                                                                                      aage of the fish, the age vector must start at zero
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      Implements fims_popdy::GrowthBase< Type >.

                                                                                      + +
                                                                                      +
                                                                                      +

                                                                                      Member Data Documentation

                                                                                      + +

                                                                                      ◆ ewaa

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::map<double, double> fims_popdy::EWAAgrowth< Type >::ewaa
                                                                                      +
                                                                                      +

                                                                                      map of doubles for EWAA values by age, where age starts at zero >

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      The documentation for this struct was generated from the following file:
                                                                                        +
                                                                                      • inst/include/population_dynamics/growth/functors/ewaa.hpp
                                                                                        • +
                                                                                      +
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
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                                                                                      fims_popdy::Fleet< Type > Member List
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      This is the complete list of members for fims_popdy::Fleet< Type >, including all inherited members.

                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      age_compositionfims_popdy::Fleet< Type >
                                                                                      agecomp_likelihoodfims_popdy::Fleet< Type >
                                                                                      catch_at_agefims_popdy::Fleet< Type >
                                                                                      catch_indexfims_popdy::Fleet< Type >
                                                                                      catch_numbers_at_agefims_popdy::Fleet< Type >
                                                                                      catch_weight_at_agefims_popdy::Fleet< Type >
                                                                                      evaluate_age_comp_nll()fims_popdy::Fleet< Type >inlinevirtual
                                                                                      evaluate_index_nll()fims_popdy::Fleet< Type >inlinevirtual
                                                                                      expected_catchfims_popdy::Fleet< Type >
                                                                                      expected_indexfims_popdy::Fleet< Type >
                                                                                      fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      Fleet()fims_popdy::Fleet< Type >inline
                                                                                      fleet_agecomp_likelihood_id_mfims_popdy::Fleet< Type >
                                                                                      fleet_index_likelihood_id_mfims_popdy::Fleet< Type >
                                                                                      fleet_observed_agecomp_data_id_mfims_popdy::Fleet< Type >
                                                                                      fleet_observed_index_data_id_mfims_popdy::Fleet< Type >
                                                                                      fleet_selectivity_id_mfims_popdy::Fleet< Type >
                                                                                      Fmortfims_popdy::Fleet< Type >
                                                                                      GetId() constfims_model_object::FIMSObject< Type >inline
                                                                                      idfims_model_object::FIMSObject< Type >
                                                                                      id_gfims_popdy::Fleet< Type >static
                                                                                      index_likelihoodfims_popdy::Fleet< Type >
                                                                                      Initialize(int nyears, int nages)fims_popdy::Fleet< Type >inline
                                                                                      is_surveyfims_popdy::Fleet< Type >
                                                                                      log_Fmortfims_popdy::Fleet< Type >
                                                                                      log_obs_errorfims_popdy::Fleet< Type >
                                                                                      log_qfims_popdy::Fleet< Type >
                                                                                      nagesfims_popdy::Fleet< Type >
                                                                                      nyearsfims_popdy::Fleet< Type >
                                                                                      observed_agecomp_datafims_popdy::Fleet< Type >
                                                                                      observed_index_datafims_popdy::Fleet< Type >
                                                                                      parametersfims_model_object::FIMSObject< Type >
                                                                                      ParameterVector typedeffims_popdy::Fleet< Type >
                                                                                      Prepare()fims_popdy::Fleet< Type >inline
                                                                                      qfims_popdy::Fleet< Type >
                                                                                      random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      selectivityfims_popdy::Fleet< Type >
                                                                                      ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                                      ~Fleet()fims_popdy::Fleet< Type >inlinevirtual
                                                                                      + +
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                                                                                      + + diff --git a/docs/structfims__popdy_1_1Fleet.html b/docs/structfims__popdy_1_1Fleet.html new file mode 100644 index 0000000..63263f3 --- /dev/null +++ b/docs/structfims__popdy_1_1Fleet.html @@ -0,0 +1,830 @@ + + + + + + + +FIMS: fims_popdy::Fleet< Type > Struct Template Reference + + + + + + + + + + + +
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                                                                                      fims_popdy::Fleet< Type > Struct Template Reference
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      Base class for all fleets. + More...

                                                                                      + +

                                                                                      #include <fleet.hpp>

                                                                                      +
                                                                                      +Inheritance diagram for fims_popdy::Fleet< Type >:
                                                                                      +
                                                                                      +
                                                                                      + + +fims_model_object::FIMSObject< Type > + +
                                                                                      + + + + +

                                                                                      +Public Types

                                                                                      using ParameterVector = typename fims::ModelTraits< Type >::ParameterVector
                                                                                       
                                                                                      + + + + + + + + + + + + + + + + + + + + + +

                                                                                      +Public Member Functions

                                                                                      + Fleet ()
                                                                                       Constructor.
                                                                                       
                                                                                      +virtual ~Fleet ()
                                                                                       Destructor.
                                                                                       
                                                                                      void Initialize (int nyears, int nages)
                                                                                       Intialize Fleet Class. More...
                                                                                       
                                                                                      void Prepare ()
                                                                                       Prepare to run the fleet module. Called at each model itartion, and used to exponentiate the log q and Fmort parameters prior to evaluation. More...
                                                                                       
                                                                                      virtual const Type evaluate_age_comp_nll ()
                                                                                       
                                                                                      virtual const Type evaluate_index_nll ()
                                                                                       
                                                                                      - 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.
                                                                                       
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

                                                                                      +Public Attributes

                                                                                      size_t nyears
                                                                                       
                                                                                      size_t nages
                                                                                       
                                                                                      int fleet_index_likelihood_id_m
                                                                                       
                                                                                      std::shared_ptr< fims_distributions::DistributionsBase< Type > > index_likelihood
                                                                                       
                                                                                      int fleet_agecomp_likelihood_id_m
                                                                                       
                                                                                      std::shared_ptr< fims_distributions::DistributionsBase< Type > > agecomp_likelihood
                                                                                       
                                                                                      int fleet_selectivity_id_m = -999
                                                                                       
                                                                                      std::shared_ptr< SelectivityBase< Type > > selectivity
                                                                                       
                                                                                      int fleet_observed_index_data_id_m = -999
                                                                                       
                                                                                      std::shared_ptr< fims_data_object::DataObject< Type > > observed_index_data
                                                                                       
                                                                                      int fleet_observed_agecomp_data_id_m = -999
                                                                                       
                                                                                      std::shared_ptr< fims_data_object::DataObject< Type > > observed_agecomp_data
                                                                                       
                                                                                      ParameterVector log_Fmort
                                                                                       
                                                                                      Type log_q
                                                                                       
                                                                                      Type log_obs_error
                                                                                       
                                                                                      ParameterVector Fmort
                                                                                       
                                                                                      Type q
                                                                                       
                                                                                      std::vector< Type > catch_at_age
                                                                                       
                                                                                      std::vector< Type > catch_index
                                                                                       
                                                                                      std::vector< Type > age_composition
                                                                                       
                                                                                      std::vector< Type > expected_catch
                                                                                       
                                                                                      std::vector< Type > expected_index
                                                                                       
                                                                                      std::vector< Type > catch_numbers_at_age
                                                                                       
                                                                                      std::vector< Type > catch_weight_at_age
                                                                                       
                                                                                      bool is_survey = false
                                                                                       
                                                                                      - 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::Fleet< Type >

                                                                                      + +

                                                                                      Base class for all fleets.

                                                                                      +
                                                                                      Template Parameters
                                                                                      + + +
                                                                                      TypeThe type of the fleet object.
                                                                                      +
                                                                                      +
                                                                                      +

                                                                                      Member Typedef Documentation

                                                                                      + +

                                                                                      ◆ ParameterVector

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      using fims_popdy::Fleet< Type >::ParameterVector = typename fims::ModelTraits<Type>::ParameterVector
                                                                                      +
                                                                                      +

                                                                                      vector of fleet parameters

                                                                                      + +
                                                                                      +
                                                                                      +

                                                                                      Member Function Documentation

                                                                                      + +

                                                                                      ◆ evaluate_age_comp_nll()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + +
                                                                                      virtual const Type fims_popdy::Fleet< Type >::evaluate_age_comp_nll ()
                                                                                      +                                                                                       		+inlinevirtual
                                                                                      +
                                                                                      +

                                                                                      < The negative log likelihood value

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ evaluate_index_nll()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + +
                                                                                      virtual const Type fims_popdy::Fleet< Type >::evaluate_index_nll ()
                                                                                      +                                                                                       		+inlinevirtual
                                                                                      +
                                                                                      +

                                                                                      < The negative log likelihood value

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ Initialize()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + +
                                                                                      void fims_popdy::Fleet< Type >::Initialize (int nyears,
                                                                                      int nages 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Intialize Fleet Class.

                                                                                      +
                                                                                      Parameters
                                                                                      + + + +
                                                                                      nyearsThe number of years in the model.
                                                                                      nagesThe number of ages in the model.
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ Prepare()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + +
                                                                                      void fims_popdy::Fleet< Type >::Prepare ()
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Prepare to run the fleet module. Called at each model itartion, and used to exponentiate the log q and Fmort parameters prior to evaluation.

                                                                                      +

                                                                                      <derived quantity catch at age

                                                                                      +

                                                                                      <derived quantity catch index

                                                                                      +

                                                                                      <model expected total catch

                                                                                      +

                                                                                      <model expected index of abundance

                                                                                      +

                                                                                      <model expected catch at age

                                                                                      +

                                                                                      <model expected weight at age

                                                                                      + +
                                                                                      +
                                                                                      +

                                                                                      Member Data Documentation

                                                                                      + +

                                                                                      ◆ age_composition

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Fleet< Type >::age_composition
                                                                                      +
                                                                                      +

                                                                                      derived quantity age composition

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ agecomp_likelihood

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      std::shared_ptr<fims_distributions::DistributionsBase<Type> > fims_popdy::Fleet< Type >::agecomp_likelihood
                                                                                      +
                                                                                      +

                                                                                      agecomp likelihood component

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ catch_at_age

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Fleet< Type >::catch_at_age
                                                                                      +
                                                                                      +

                                                                                      derived quantity catch at age

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ catch_index

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Fleet< Type >::catch_index
                                                                                      +
                                                                                      +

                                                                                      derived quantity catch index

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ catch_numbers_at_age

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Fleet< Type >::catch_numbers_at_age
                                                                                      +
                                                                                      +

                                                                                      model expected catch at age

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ catch_weight_at_age

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Fleet< Type >::catch_weight_at_age
                                                                                      +
                                                                                      +

                                                                                      model expected weight at age

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ expected_catch

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Fleet< Type >::expected_catch
                                                                                      +
                                                                                      +

                                                                                      model expected total catch

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ expected_index

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Fleet< Type >::expected_index
                                                                                      +
                                                                                      +

                                                                                      model expected index of abundance

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ fleet_agecomp_likelihood_id_m

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      int fims_popdy::Fleet< Type >::fleet_agecomp_likelihood_id_m
                                                                                      +
                                                                                      +Initial value:
                                                                                      =
                                                                                      +
                                                                                      -999
                                                                                      +

                                                                                      id of agecomp likelihood component

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ fleet_index_likelihood_id_m

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      int fims_popdy::Fleet< Type >::fleet_index_likelihood_id_m
                                                                                      +
                                                                                      +Initial value:
                                                                                      =
                                                                                      +
                                                                                      -999
                                                                                      +

                                                                                      id of index likelihood component. The "fleet_" prefix indicates it belongs to the Fleet struct, and the "_m" postfix signifies that it's a member variable.

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ fleet_observed_agecomp_data_id_m

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      int fims_popdy::Fleet< Type >::fleet_observed_agecomp_data_id_m = -999
                                                                                      +
                                                                                      +

                                                                                      id of age comp data

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ fleet_observed_index_data_id_m

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      int fims_popdy::Fleet< Type >::fleet_observed_index_data_id_m = -999
                                                                                      +
                                                                                      +

                                                                                      id of index data

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ fleet_selectivity_id_m

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      int fims_popdy::Fleet< Type >::fleet_selectivity_id_m = -999
                                                                                      +
                                                                                      +

                                                                                      id of selectivity component

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ Fmort

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      ParameterVector fims_popdy::Fleet< Type >::Fmort
                                                                                      +
                                                                                      +

                                                                                      transformed parameter: Fishing mortality

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ id_g

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + + +
                                                                                      + + + + +
                                                                                      uint32_t fims_popdy::Fleet< Type >::id_g = 0
                                                                                      +                                                                                       		+static
                                                                                      +
                                                                                      +

                                                                                      reference id for fleet object

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ index_likelihood

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      std::shared_ptr<fims_distributions::DistributionsBase<Type> > fims_popdy::Fleet< Type >::index_likelihood
                                                                                      +
                                                                                      +

                                                                                      index likelihood component

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ is_survey

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      bool fims_popdy::Fleet< Type >::is_survey = false
                                                                                      +
                                                                                      +

                                                                                      is this fleet object a survey

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ log_Fmort

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      ParameterVector fims_popdy::Fleet< Type >::log_Fmort
                                                                                      +
                                                                                      +

                                                                                      estimated parameter: log Fishing mortality

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ log_obs_error

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      Type fims_popdy::Fleet< Type >::log_obs_error
                                                                                      +
                                                                                      +

                                                                                      estimated parameter: observation error associated with index

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ log_q

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      Type fims_popdy::Fleet< Type >::log_q
                                                                                      +
                                                                                      +

                                                                                      estimated parameter: catchability of the fleet

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ nages

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      size_t fims_popdy::Fleet< Type >::nages
                                                                                      +
                                                                                      +

                                                                                      the number of ages in the model

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ nyears

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      size_t fims_popdy::Fleet< Type >::nyears
                                                                                      +
                                                                                      +

                                                                                      the number of years in the model

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ observed_agecomp_data

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      std::shared_ptr<fims_data_object::DataObject<Type> > fims_popdy::Fleet< Type >::observed_agecomp_data
                                                                                      +
                                                                                      +

                                                                                      observed agecomp data

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ observed_index_data

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      std::shared_ptr<fims_data_object::DataObject<Type> > fims_popdy::Fleet< Type >::observed_index_data
                                                                                      +
                                                                                      +

                                                                                      observed index data

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ q

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      Type fims_popdy::Fleet< Type >::q
                                                                                      +
                                                                                      +

                                                                                      transofrmed parameter: the catchability of the fleet

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ selectivity

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      std::shared_ptr<SelectivityBase<Type> > fims_popdy::Fleet< Type >::selectivity
                                                                                      +
                                                                                      +

                                                                                      selectivity component

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      The documentation for this struct was generated from the following file:
                                                                                        +
                                                                                      • inst/include/population_dynamics/fleet/fleet.hpp
                                                                                        • +
                                                                                      +
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
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                                                                                      +
                                                                                      + + + + + + +
                                                                                      +
                                                                                      FIMS +
                                                                                      +
                                                                                      +
                                                                                      + + + + + + + + +
                                                                                      +
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                                                                                      + + +
                                                                                      +
                                                                                      +
                                                                                      +
                                                                                      fims_popdy::GrowthBase< Type > Member List
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      This is the complete list of members for fims_popdy::GrowthBase< Type >, including all inherited members.

                                                                                      + + + + + + + + + + + +
                                                                                      evaluate(const double &a)=0fims_popdy::GrowthBase< Type >pure virtual
                                                                                      fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      GetId() constfims_model_object::FIMSObject< Type >inline
                                                                                      GrowthBase()fims_popdy::GrowthBase< Type >inline
                                                                                      idfims_model_object::FIMSObject< Type >
                                                                                      id_gfims_popdy::GrowthBase< Type >static
                                                                                      parametersfims_model_object::FIMSObject< Type >
                                                                                      random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                                      ~GrowthBase() (defined in fims_popdy::GrowthBase< Type >)fims_popdy::GrowthBase< Type >inlinevirtual
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
                                                                                      + + diff --git a/docs/structfims__popdy_1_1GrowthBase.html b/docs/structfims__popdy_1_1GrowthBase.html new file mode 100644 index 0000000..cbb6ad7 --- /dev/null +++ b/docs/structfims__popdy_1_1GrowthBase.html @@ -0,0 +1,216 @@ + + + + + + + +FIMS: fims_popdy::GrowthBase< Type > Struct Template Reference + + + + + + + + + + + +
                                                                                      +
                                                                                      + + + + + + +
                                                                                      +
                                                                                      FIMS +
                                                                                      +
                                                                                      +
                                                                                      + + + + + + + + +
                                                                                      +
                                                                                      + + +
                                                                                      + +
                                                                                      + + +
                                                                                      +
                                                                                      +
                                                                                      +Public Member Functions | +Static Public Attributes | +List of all members
                                                                                      +
                                                                                      +
                                                                                      fims_popdy::GrowthBase< Type > Struct Template Referenceabstract
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      Base class for all growth functors. + More...

                                                                                      + +

                                                                                      #include <growth_base.hpp>

                                                                                      +
                                                                                      +Inheritance diagram for fims_popdy::GrowthBase< Type >:
                                                                                      +
                                                                                      +
                                                                                      + + +fims_model_object::FIMSObject< Type > +fims_popdy::EWAAgrowth< Type > + +
                                                                                      + + + + + + + + + + + + +

                                                                                      +Public Member Functions

                                                                                      + GrowthBase ()
                                                                                       Constructor.
                                                                                       
                                                                                      virtual const Type evaluate (const double &a)=0
                                                                                       Calculates the growth at the independent variable value. More...
                                                                                       
                                                                                      - 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.
                                                                                       
                                                                                      + + + +

                                                                                      +Static Public Attributes

                                                                                      static uint32_t id_g = 0
                                                                                       
                                                                                      + + + + + + + + + + +

                                                                                      +Additional Inherited Members

                                                                                      - 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
                                                                                       
                                                                                      +

                                                                                      Detailed Description

                                                                                      +

                                                                                      template<typename Type>
                                                                                      +struct fims_popdy::GrowthBase< Type >

                                                                                      + +

                                                                                      Base class for all growth functors.

                                                                                      +
                                                                                      Template Parameters
                                                                                      + + +
                                                                                      TypeThe type of the growth functor.
                                                                                      +
                                                                                      +
                                                                                      +

                                                                                      Member Function Documentation

                                                                                      + +

                                                                                      ◆ evaluate()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + +
                                                                                      virtual const Type fims_popdy::GrowthBase< Type >::evaluate (const double & a)
                                                                                      +                                                                                       		+pure virtual
                                                                                      +
                                                                                      + +

                                                                                      Calculates the growth at the independent variable value.

                                                                                      +
                                                                                      Parameters
                                                                                      + + +
                                                                                      aThe age at which to return weight of the fish (in kg).
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      Implemented in fims_popdy::EWAAgrowth< Type >.

                                                                                      + +
                                                                                      +
                                                                                      +

                                                                                      Member Data Documentation

                                                                                      + +

                                                                                      ◆ id_g

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + +
                                                                                      uint32_t fims_popdy::GrowthBase< Type >::id_g = 0
                                                                                      +                                                                                       		+static
                                                                                      +
                                                                                      +

                                                                                      reference id for growth object

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      The documentation for this struct was generated from the following file: +
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
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                                                                                      fims_popdy::LogisticMaturity< Type > Member List
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                                                                                      This is the complete list of members for fims_popdy::LogisticMaturity< Type >, including all inherited members.

                                                                                      + + + + + + + + + + + + + +
                                                                                      evaluate(const Type &x)fims_popdy::LogisticMaturity< Type >inlinevirtual
                                                                                      fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      GetId() constfims_model_object::FIMSObject< Type >inline
                                                                                      idfims_model_object::FIMSObject< Type >
                                                                                      id_gfims_popdy::MaturityBase< Type >static
                                                                                      LogisticMaturity() (defined in fims_popdy::LogisticMaturity< Type >)fims_popdy::LogisticMaturity< Type >inline
                                                                                      MaturityBase()fims_popdy::MaturityBase< Type >inline
                                                                                      medianfims_popdy::LogisticMaturity< Type >
                                                                                      parametersfims_model_object::FIMSObject< Type >
                                                                                      random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      slopefims_popdy::LogisticMaturity< Type >
                                                                                      ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                                      + +
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                                                                                      fims_popdy::LogisticMaturity< Type > Struct Template Reference
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      LogisticMaturity class that returns the logistic function value from fims_math. + More...

                                                                                      + +

                                                                                      #include <logistic.hpp>

                                                                                      +
                                                                                      +Inheritance diagram for fims_popdy::LogisticMaturity< Type >:
                                                                                      +
                                                                                      +
                                                                                      + + +fims_popdy::MaturityBase< Type > +fims_model_object::FIMSObject< Type > + +
                                                                                      + + + + + + + + + + + + + +

                                                                                      +Public Member Functions

                                                                                      virtual const Type evaluate (const Type &x)
                                                                                       Method of the logistic maturity class that implements the logistic function from FIMS math. More...
                                                                                       
                                                                                      - Public Member Functions inherited from fims_popdy::MaturityBase< Type >
                                                                                      + MaturityBase ()
                                                                                       Constructor.
                                                                                       
                                                                                      - 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.
                                                                                       
                                                                                      + + + + + + + + + + + + + + +

                                                                                      +Public Attributes

                                                                                      Type median
                                                                                       
                                                                                      Type slope
                                                                                       
                                                                                      - 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
                                                                                       
                                                                                      + + + + +

                                                                                      +Additional Inherited Members

                                                                                      - Static Public Attributes inherited from fims_popdy::MaturityBase< Type >
                                                                                      static uint32_t id_g = 0
                                                                                       
                                                                                      +

                                                                                      Detailed Description

                                                                                      +

                                                                                      template<typename Type>
                                                                                      +struct fims_popdy::LogisticMaturity< Type >

                                                                                      + +

                                                                                      LogisticMaturity class that returns the logistic function value from fims_math.

                                                                                      +

                                                                                      Member Function Documentation

                                                                                      + +

                                                                                      ◆ evaluate()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + +
                                                                                      virtual const Type fims_popdy::LogisticMaturity< Type >::evaluate (const Type & x)
                                                                                      +                                                                                       		+inlinevirtual
                                                                                      +
                                                                                      + +

                                                                                      Method of the logistic maturity class that implements the logistic function from FIMS math.

                                                                                      +

                                                                                      +\[ \frac{1.0}{ 1.0 + exp(-1.0 * slope (x - median))} \] +

                                                                                      +
                                                                                      Parameters
                                                                                      + + +
                                                                                      xThe independent variable in the logistic function (e.g., age or size at maturity).
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      Implements fims_popdy::MaturityBase< Type >.

                                                                                      + +
                                                                                      +
                                                                                      +

                                                                                      Member Data Documentation

                                                                                      + +

                                                                                      ◆ median

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      Type fims_popdy::LogisticMaturity< Type >::median
                                                                                      +
                                                                                      +

                                                                                      50% quantile of the value of the quantity of interest (x); e.g. age at which 50% of the fish are mature

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ slope

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      Type fims_popdy::LogisticMaturity< Type >::slope
                                                                                      +
                                                                                      +

                                                                                      scalar multiplier of difference between quantity of interest value (x) and median

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      The documentation for this struct was generated from the following file:
                                                                                        +
                                                                                      • inst/include/population_dynamics/maturity/functors/logistic.hpp
                                                                                        • +
                                                                                      +
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
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                                                                                      fims_popdy::LogisticSelectivity< Type > Member List
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      This is the complete list of members for fims_popdy::LogisticSelectivity< Type >, including all inherited members.

                                                                                      + + + + + + + + + + + + + + + +
                                                                                      evaluate(const Type &x)fims_popdy::LogisticSelectivity< Type >inlinevirtual
                                                                                      fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      GetId() constfims_model_object::FIMSObject< Type >inline
                                                                                      idfims_model_object::FIMSObject< Type >
                                                                                      id_gfims_popdy::SelectivityBase< Type >static
                                                                                      LogisticSelectivity() (defined in fims_popdy::LogisticSelectivity< Type >)fims_popdy::LogisticSelectivity< Type >inline
                                                                                      medianfims_popdy::LogisticSelectivity< Type >
                                                                                      parametersfims_model_object::FIMSObject< Type >
                                                                                      random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      SelectivityBase()fims_popdy::SelectivityBase< Type >inline
                                                                                      slopefims_popdy::LogisticSelectivity< Type >
                                                                                      ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                                      ~LogisticSelectivity() (defined in fims_popdy::LogisticSelectivity< Type >)fims_popdy::LogisticSelectivity< Type >inlinevirtual
                                                                                      ~SelectivityBase() (defined in fims_popdy::SelectivityBase< Type >)fims_popdy::SelectivityBase< Type >inlinevirtual
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                                                                                      +
                                                                                      fims_popdy::LogisticSelectivity< Type > Struct Template Reference
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      LogisticSelectivity class that returns the logistic function value from fims_math. + More...

                                                                                      + +

                                                                                      #include <logistic.hpp>

                                                                                      +
                                                                                      +Inheritance diagram for fims_popdy::LogisticSelectivity< Type >:
                                                                                      +
                                                                                      +
                                                                                      + + +fims_popdy::SelectivityBase< Type > +fims_model_object::FIMSObject< Type > + +
                                                                                      + + + + + + + + + + + + + +

                                                                                      +Public Member Functions

                                                                                      virtual const Type evaluate (const Type &x)
                                                                                       Method of the logistic selectivity class that implements the logistic function from FIMS math. More...
                                                                                       
                                                                                      - Public Member Functions inherited from fims_popdy::SelectivityBase< Type >
                                                                                      + SelectivityBase ()
                                                                                       Constructor.
                                                                                       
                                                                                      - 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.
                                                                                       
                                                                                      + + + + + + + + + + + + + + +

                                                                                      +Public Attributes

                                                                                      Type median
                                                                                       
                                                                                      Type slope
                                                                                       
                                                                                      - 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
                                                                                       
                                                                                      + + + + +

                                                                                      +Additional Inherited Members

                                                                                      - Static Public Attributes inherited from fims_popdy::SelectivityBase< Type >
                                                                                      static uint32_t id_g = 0
                                                                                       
                                                                                      +

                                                                                      Detailed Description

                                                                                      +

                                                                                      template<typename Type>
                                                                                      +struct fims_popdy::LogisticSelectivity< Type >

                                                                                      + +

                                                                                      LogisticSelectivity class that returns the logistic function value from fims_math.

                                                                                      +

                                                                                      Member Function Documentation

                                                                                      + +

                                                                                      ◆ evaluate()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + +
                                                                                      virtual const Type fims_popdy::LogisticSelectivity< Type >::evaluate (const Type & x)
                                                                                      +                                                                                       		+inlinevirtual
                                                                                      +
                                                                                      + +

                                                                                      Method of the logistic selectivity class that implements the logistic function from FIMS math.

                                                                                      +

                                                                                      +\[ \frac{1.0}{ 1.0 + exp(-1.0 * slope (x - median))} \] +

                                                                                      +
                                                                                      Parameters
                                                                                      + + +
                                                                                      xThe independent variable in the logistic function (e.g., age or size in selectivity).
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      Implements fims_popdy::SelectivityBase< Type >.

                                                                                      + +
                                                                                      +
                                                                                      +

                                                                                      Member Data Documentation

                                                                                      + +

                                                                                      ◆ median

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      Type fims_popdy::LogisticSelectivity< Type >::median
                                                                                      +
                                                                                      +

                                                                                      50% quantile of the value of the quantity of interest (x); e.g. age at which 50% of the fish are selected

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ slope

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      Type fims_popdy::LogisticSelectivity< Type >::slope
                                                                                      +
                                                                                      +

                                                                                      scalar multiplier of difference between quantity of interest value (x) and median

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      The documentation for this struct was generated from the following file:
                                                                                        +
                                                                                      • inst/include/population_dynamics/selectivity/functors/logistic.hpp
                                                                                        • +
                                                                                      +
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
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                                                                                      fims_popdy::MaturityBase< Type > Member List
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                                                                                      This is the complete list of members for fims_popdy::MaturityBase< Type >, including all inherited members.

                                                                                      + + + + + + + + + + +
                                                                                      evaluate(const Type &x)=0fims_popdy::MaturityBase< Type >pure virtual
                                                                                      fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      GetId() constfims_model_object::FIMSObject< Type >inline
                                                                                      idfims_model_object::FIMSObject< Type >
                                                                                      id_gfims_popdy::MaturityBase< Type >static
                                                                                      MaturityBase()fims_popdy::MaturityBase< Type >inline
                                                                                      parametersfims_model_object::FIMSObject< Type >
                                                                                      random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
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                                                                                      + + diff --git a/docs/structfims__popdy_1_1MaturityBase.html b/docs/structfims__popdy_1_1MaturityBase.html new file mode 100644 index 0000000..138b3d5 --- /dev/null +++ b/docs/structfims__popdy_1_1MaturityBase.html @@ -0,0 +1,216 @@ + + + + + + + +FIMS: fims_popdy::MaturityBase< Type > Struct Template Reference + + + + + + + + + + + +
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                                                                                      +Public Member Functions | +Static Public Attributes | +List of all members
                                                                                      +
                                                                                      +
                                                                                      fims_popdy::MaturityBase< Type > Struct Template Referenceabstract
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      Base class for all maturity functors. + More...

                                                                                      + +

                                                                                      #include <maturity_base.hpp>

                                                                                      +
                                                                                      +Inheritance diagram for fims_popdy::MaturityBase< Type >:
                                                                                      +
                                                                                      +
                                                                                      + + +fims_model_object::FIMSObject< Type > +fims_popdy::LogisticMaturity< Type > + +
                                                                                      + + + + + + + + + + + + +

                                                                                      +Public Member Functions

                                                                                      + MaturityBase ()
                                                                                       Constructor.
                                                                                       
                                                                                      virtual const Type evaluate (const Type &x)=0
                                                                                       Calculates the maturity. More...
                                                                                       
                                                                                      - 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.
                                                                                       
                                                                                      + + + +

                                                                                      +Static Public Attributes

                                                                                      static uint32_t id_g = 0
                                                                                       
                                                                                      + + + + + + + + + + +

                                                                                      +Additional Inherited Members

                                                                                      - 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
                                                                                       
                                                                                      +

                                                                                      Detailed Description

                                                                                      +

                                                                                      template<typename Type>
                                                                                      +struct fims_popdy::MaturityBase< Type >

                                                                                      + +

                                                                                      Base class for all maturity functors.

                                                                                      +
                                                                                      Template Parameters
                                                                                      + + +
                                                                                      TypeThe type of the maturity functor.
                                                                                      +
                                                                                      +
                                                                                      +

                                                                                      Member Function Documentation

                                                                                      + +

                                                                                      ◆ evaluate()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + +
                                                                                      virtual const Type fims_popdy::MaturityBase< Type >::evaluate (const Type & x)
                                                                                      +                                                                                       		+pure virtual
                                                                                      +
                                                                                      + +

                                                                                      Calculates the maturity.

                                                                                      +
                                                                                      Parameters
                                                                                      + + +
                                                                                      xThe independent variable in the maturity function (e.g., logistic maturity at age or size).
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      Implemented in fims_popdy::LogisticMaturity< Type >.

                                                                                      + +
                                                                                      +
                                                                                      +

                                                                                      Member Data Documentation

                                                                                      + +

                                                                                      ◆ id_g

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + +
                                                                                      uint32_t fims_popdy::MaturityBase< Type >::id_g = 0
                                                                                      +                                                                                       		+static
                                                                                      +
                                                                                      +

                                                                                      The ID of the instance of the MaturityBase class

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      The documentation for this struct was generated from the following file: +
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
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                                                                                      fims_popdy::Population< Type > Member List
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      This is the complete list of members for fims_popdy::Population< Type >, including all inherited members.

                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      agesfims_popdy::Population< Type >
                                                                                      biomassfims_popdy::Population< Type >
                                                                                      CalculateBiomass(size_t i_age_year, size_t year, size_t age)fims_popdy::Population< Type >inline
                                                                                      CalculateCatch(size_t year, size_t age)fims_popdy::Population< Type >inline
                                                                                      CalculateCatchNumbersAA(size_t i_age_year, size_t year, size_t age)fims_popdy::Population< Type >inline
                                                                                      CalculateCatchWeightAA(size_t year, size_t age)fims_popdy::Population< Type >inline
                                                                                      CalculateIndex(size_t i_age_year, size_t year, size_t age)fims_popdy::Population< Type >inline
                                                                                      CalculateInitialNumbersAA(size_t i_age_year, size_t a)fims_popdy::Population< Type >inline
                                                                                      CalculateMaturityAA(size_t i_age_year, size_t age)fims_popdy::Population< Type >inline
                                                                                      CalculateMortality(size_t i_age_year, size_t year, size_t age)fims_popdy::Population< Type >inline
                                                                                      CalculateNumbersAA(size_t i_age_year, size_t i_agem1_yearm1, size_t age)fims_popdy::Population< Type >inline
                                                                                      CalculateRecruitment(size_t i_age_year, size_t year)fims_popdy::Population< Type >inline
                                                                                      CalculateSBPR0()fims_popdy::Population< Type >inline
                                                                                      CalculateSpawningBiomass(size_t i_age_year, size_t year, size_t age)fims_popdy::Population< Type >inline
                                                                                      CalculateUnfishedBiomass(size_t i_age_year, size_t year, size_t age)fims_popdy::Population< Type >inline
                                                                                      CalculateUnfishedNumbersAA(size_t i_age_year, size_t i_agem1_yearm1, size_t age)fims_popdy::Population< Type >inline
                                                                                      CalculateUnfishedSpawningBiomass(size_t i_age_year, size_t year, size_t age)fims_popdy::Population< Type >inline
                                                                                      Evaluate()fims_popdy::Population< Type >inline
                                                                                      expected_catchfims_popdy::Population< Type >
                                                                                      expected_numbers_at_agefims_popdy::Population< Type >
                                                                                      expected_recruitmentfims_popdy::Population< Type >
                                                                                      fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      fleet_idfims_popdy::Population< Type >
                                                                                      fleetsfims_popdy::Population< Type >
                                                                                      GetId() constfims_model_object::FIMSObject< Type >inline
                                                                                      growthfims_popdy::Population< Type >
                                                                                      growth_idfims_popdy::Population< Type >
                                                                                      idfims_model_object::FIMSObject< Type >
                                                                                      id_gfims_popdy::Population< Type >static
                                                                                      Initialize(int nyears, int nseasons, int nages)fims_popdy::Population< Type >inline
                                                                                      log_init_naafims_popdy::Population< Type >
                                                                                      log_Mfims_popdy::Population< Type >
                                                                                      Mfims_popdy::Population< Type >
                                                                                      maturityfims_popdy::Population< Type >
                                                                                      maturity_idfims_popdy::Population< Type >
                                                                                      mortality_Ffims_popdy::Population< Type >
                                                                                      mortality_Zfims_popdy::Population< Type >
                                                                                      nagesfims_popdy::Population< Type >
                                                                                      nfleetsfims_popdy::Population< Type >
                                                                                      nseasonsfims_popdy::Population< Type >
                                                                                      numbers_at_agefims_popdy::Population< Type >
                                                                                      nyearsfims_popdy::Population< Type >
                                                                                      parametersfims_model_object::FIMSObject< Type >
                                                                                      ParameterVector typedeffims_popdy::Population< Type >
                                                                                      Population() (defined in fims_popdy::Population< Type >)fims_popdy::Population< Type >inline
                                                                                      Prepare()fims_popdy::Population< Type >inline
                                                                                      proportion_femalefims_popdy::Population< Type >
                                                                                      proportion_mature_at_agefims_popdy::Population< Type >
                                                                                      random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      recruitmentfims_popdy::Population< Type >
                                                                                      recruitment_idfims_popdy::Population< Type >
                                                                                      spawning_biomassfims_popdy::Population< Type >
                                                                                      unfished_biomassfims_popdy::Population< Type >
                                                                                      unfished_numbers_at_agefims_popdy::Population< Type >
                                                                                      unfished_spawning_biomassfims_popdy::Population< Type >
                                                                                      weight_at_agefims_popdy::Population< Type >
                                                                                      yearsfims_popdy::Population< Type >
                                                                                      ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
                                                                                      + + diff --git a/docs/structfims__popdy_1_1Population.html b/docs/structfims__popdy_1_1Population.html new file mode 100644 index 0000000..3f755cd --- /dev/null +++ b/docs/structfims__popdy_1_1Population.html @@ -0,0 +1,1645 @@ + + + + + + + +FIMS: fims_popdy::Population< Type > Struct Template Reference + + + + + + + + + + + +
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                                                                                      FIMS +
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                                                                                      +
                                                                                      +
                                                                                      +Public Types | +Public Member Functions | +Public Attributes | +Static Public Attributes | +List of all members
                                                                                      +
                                                                                      +
                                                                                      fims_popdy::Population< Type > Struct Template Reference
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      Population class. Contains subpopulations that are divided into generic partitions (eg. sex, area). + More...

                                                                                      + +

                                                                                      #include <population.hpp>

                                                                                      +
                                                                                      +Inheritance diagram for fims_popdy::Population< Type >:
                                                                                      +
                                                                                      +
                                                                                      + + +fims_model_object::FIMSObject< Type > + +
                                                                                      + + + + +

                                                                                      +Public Types

                                                                                      using ParameterVector = typename fims::ModelTraits< Type >::ParameterVector
                                                                                       
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

                                                                                      +Public Member Functions

                                                                                      void Initialize (int nyears, int nseasons, int nages)
                                                                                       Initialize values. Called once at the start of model run. More...
                                                                                       
                                                                                      +void Prepare ()
                                                                                       Prepare to run the population loop. Called at each model iteration, and used to zero out derived quantities, values that were summed, etc.
                                                                                       
                                                                                      void CalculateInitialNumbersAA (size_t i_age_year, size_t a)
                                                                                       Calculates initial numbers at age for index and age. More...
                                                                                       
                                                                                      void CalculateMortality (size_t i_age_year, size_t year, size_t age)
                                                                                       Calculates total mortality at an index, year, and age. More...
                                                                                       
                                                                                      void CalculateNumbersAA (size_t i_age_year, size_t i_agem1_yearm1, size_t age)
                                                                                       Calculates numbers at age at year and age specific indices. More...
                                                                                       
                                                                                      void CalculateUnfishedNumbersAA (size_t i_age_year, size_t i_agem1_yearm1, size_t age)
                                                                                       Calculates unfished numbers at age at year and age specific indices. More...
                                                                                       
                                                                                      void CalculateBiomass (size_t i_age_year, size_t year, size_t age)
                                                                                       Calculates biomass. More...
                                                                                       
                                                                                      void CalculateUnfishedBiomass (size_t i_age_year, size_t year, size_t age)
                                                                                       Adds to existing yearly unfished biomass estimates the biomass for a specified year and age. More...
                                                                                       
                                                                                      void CalculateSpawningBiomass (size_t i_age_year, size_t year, size_t age)
                                                                                       Calculates spawning biomass. More...
                                                                                       
                                                                                      void CalculateUnfishedSpawningBiomass (size_t i_age_year, size_t year, size_t age)
                                                                                       Adds to existing yearly unfished spawning biomass estimates the biomass for a specified year and age. More...
                                                                                       
                                                                                      Type CalculateSBPR0 ()
                                                                                       Calculates equilibrium spawning biomass per recruit. More...
                                                                                       
                                                                                      void CalculateRecruitment (size_t i_age_year, size_t year)
                                                                                       Calculates expected recruitment for a given year. More...
                                                                                       
                                                                                      void CalculateCatch (size_t year, size_t age)
                                                                                       Adds to exiting expected total catch by fleet in weight. More...
                                                                                       
                                                                                      void CalculateIndex (size_t i_age_year, size_t year, size_t age)
                                                                                       Adds to the expected population indices by fleet. More...
                                                                                       
                                                                                      void CalculateCatchNumbersAA (size_t i_age_year, size_t year, size_t age)
                                                                                       Calculates catch in numbers at age for each fleet for a given year and age, then adds the value to the expected catch in numbers at age for each fleet. More...
                                                                                       
                                                                                      void CalculateCatchWeightAA (size_t year, size_t age)
                                                                                       Calculates expected catch weight at age for each fleet for a given year and age. More...
                                                                                       
                                                                                      void CalculateMaturityAA (size_t i_age_year, size_t age)
                                                                                       Calculates expected proportion of individuals mature at a selected ageage. More...
                                                                                       
                                                                                      +void Evaluate ()
                                                                                       Executes the population loop.
                                                                                       
                                                                                      - 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.
                                                                                       
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

                                                                                      +Public Attributes

                                                                                      size_t nyears
                                                                                       
                                                                                      size_t nseasons
                                                                                       
                                                                                      size_t nages
                                                                                       
                                                                                      size_t nfleets
                                                                                       
                                                                                      const Type proportion_female
                                                                                       
                                                                                      std::vector< Type > log_init_naa
                                                                                       
                                                                                      ParameterVector log_M
                                                                                       
                                                                                      std::vector< Type > M
                                                                                       
                                                                                      std::vector< double > ages
                                                                                       
                                                                                      std::vector< double > years
                                                                                       
                                                                                      ParameterVector mortality_F
                                                                                       
                                                                                      std::vector< Type > mortality_Z
                                                                                       
                                                                                      std::vector< Type > weight_at_age
                                                                                       
                                                                                      std::vector< Type > numbers_at_age
                                                                                       
                                                                                      std::vector< Type > unfished_numbers_at_age
                                                                                       
                                                                                      std::vector< Type > biomass
                                                                                       
                                                                                      std::vector< Type > spawning_biomass
                                                                                       
                                                                                      std::vector< Type > unfished_biomass
                                                                                       
                                                                                      std::vector< Type > unfished_spawning_biomass
                                                                                       
                                                                                      std::vector< Type > proportion_mature_at_age
                                                                                       
                                                                                      std::vector< Type > expected_numbers_at_age
                                                                                       
                                                                                      std::vector< Type > expected_catch
                                                                                       
                                                                                      std::vector< Type > expected_recruitment
                                                                                       
                                                                                      int recruitment_id = -999
                                                                                       recruitment More...
                                                                                       
                                                                                      std::shared_ptr< RecruitmentBase< Type > > recruitment
                                                                                       
                                                                                      int growth_id = -999
                                                                                       
                                                                                      std::shared_ptr< GrowthBase< Type > > growth
                                                                                       
                                                                                      int maturity_id = -999
                                                                                       
                                                                                      std::shared_ptr< MaturityBase< Type > > maturity
                                                                                       
                                                                                      int fleet_id = -999
                                                                                       
                                                                                      std::vector< std::shared_ptr< Fleet< Type > > > fleets
                                                                                       
                                                                                      - 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<typename Type>
                                                                                      +struct fims_popdy::Population< Type >

                                                                                      + +

                                                                                      Population class. Contains subpopulations that are divided into generic partitions (eg. sex, area).

                                                                                      +

                                                                                      Member Typedef Documentation

                                                                                      + +

                                                                                      ◆ ParameterVector

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      using fims_popdy::Population< Type >::ParameterVector = typename fims::ModelTraits<Type>::ParameterVector
                                                                                      +
                                                                                      +

                                                                                      the vector of population parameters

                                                                                      + +
                                                                                      +
                                                                                      +

                                                                                      Member Function Documentation

                                                                                      + +

                                                                                      ◆ CalculateBiomass()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      void fims_popdy::Population< Type >::CalculateBiomass (size_t i_age_year,
                                                                                      size_t year,
                                                                                      size_t age 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Calculates biomass.

                                                                                      +
                                                                                      Parameters
                                                                                      + + + + +
                                                                                      i_age_yeardimension folded index for age and year
                                                                                      yearthe year biomass is being aggregated for
                                                                                      agethe age who's biomass is being added into total biomass
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ CalculateCatch()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + +
                                                                                      void fims_popdy::Population< Type >::CalculateCatch (size_t year,
                                                                                      size_t age 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Adds to exiting expected total catch by fleet in weight.

                                                                                      +
                                                                                      Parameters
                                                                                      + + + +
                                                                                      yearthe year of expected total catch
                                                                                      agethe age of catch that is being added into total catch
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ CalculateCatchNumbersAA()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      void fims_popdy::Population< Type >::CalculateCatchNumbersAA (size_t i_age_year,
                                                                                      size_t year,
                                                                                      size_t age 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Calculates catch in numbers at age for each fleet for a given year and age, then adds the value to the expected catch in numbers at age for each fleet.

                                                                                      +
                                                                                      Parameters
                                                                                      + + + + +
                                                                                      i_age_yeardimension folded index for age and year
                                                                                      yearthe year of expected catch composition is being calculated for
                                                                                      agethe age composition is being calculated for
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ CalculateCatchWeightAA()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + +
                                                                                      void fims_popdy::Population< Type >::CalculateCatchWeightAA (size_t year,
                                                                                      size_t age 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Calculates expected catch weight at age for each fleet for a given year and age.

                                                                                      +
                                                                                      Parameters
                                                                                      + + + +
                                                                                      yearthe year of expected catch weight at age
                                                                                      agethe age of expected catch weight at age
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ CalculateIndex()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      void fims_popdy::Population< Type >::CalculateIndex (size_t i_age_year,
                                                                                      size_t year,
                                                                                      size_t age 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Adds to the expected population indices by fleet.

                                                                                      +
                                                                                      Parameters
                                                                                      + + + + +
                                                                                      i_age_yeardimension folded index for age and year
                                                                                      yearthe year of the population index
                                                                                      agethe age of the index that is added into population index
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ CalculateInitialNumbersAA()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + +
                                                                                      void fims_popdy::Population< Type >::CalculateInitialNumbersAA (size_t i_age_year,
                                                                                      size_t a 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Calculates initial numbers at age for index and age.

                                                                                      +

                                                                                      life history calculations

                                                                                      +
                                                                                      Parameters
                                                                                      + + + +
                                                                                      i_age_yeardimension folded index for age and year
                                                                                      aage index
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ CalculateMaturityAA()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + +
                                                                                      void fims_popdy::Population< Type >::CalculateMaturityAA (size_t i_age_year,
                                                                                      size_t age 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Calculates expected proportion of individuals mature at a selected ageage.

                                                                                      +
                                                                                      Parameters
                                                                                      + + + +
                                                                                      i_age_yeardimension folded index for age and year
                                                                                      agethe age of maturity
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ CalculateMortality()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      void fims_popdy::Population< Type >::CalculateMortality (size_t i_age_year,
                                                                                      size_t year,
                                                                                      size_t age 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Calculates total mortality at an index, year, and age.

                                                                                      +
                                                                                      Parameters
                                                                                      + + + + +
                                                                                      i_age_yeardimension folded index for age and year
                                                                                      yearyear index
                                                                                      ageage index
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ CalculateNumbersAA()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      void fims_popdy::Population< Type >::CalculateNumbersAA (size_t i_age_year,
                                                                                      size_t i_agem1_yearm1,
                                                                                      size_t age 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Calculates numbers at age at year and age specific indices.

                                                                                      +
                                                                                      Parameters
                                                                                      + + + + +
                                                                                      i_age_yeardimension folded index for age and year
                                                                                      i_agem1_yearm1dimension folded index for age-1 and year-1
                                                                                      ageage index
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ CalculateRecruitment()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + +
                                                                                      void fims_popdy::Population< Type >::CalculateRecruitment (size_t i_age_year,
                                                                                      size_t year 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Calculates expected recruitment for a given year.

                                                                                      +
                                                                                      Parameters
                                                                                      + + + +
                                                                                      i_age_yeardimension folded index for age and year
                                                                                      yearthe year recruitment is being calculated for
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ CalculateSBPR0()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + +
                                                                                      Type fims_popdy::Population< Type >::CalculateSBPR0 ()
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Calculates equilibrium spawning biomass per recruit.

                                                                                      +
                                                                                      Returns
                                                                                      Type
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ CalculateSpawningBiomass()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      void fims_popdy::Population< Type >::CalculateSpawningBiomass (size_t i_age_year,
                                                                                      size_t year,
                                                                                      size_t age 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Calculates spawning biomass.

                                                                                      +
                                                                                      Parameters
                                                                                      + + + + +
                                                                                      i_age_yeardimension folded index for age and year
                                                                                      yearthe year spawning biomass is being aggregated for
                                                                                      agethe age who's biomass is being added into total spawning biomass
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ CalculateUnfishedBiomass()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      void fims_popdy::Population< Type >::CalculateUnfishedBiomass (size_t i_age_year,
                                                                                      size_t year,
                                                                                      size_t age 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Adds to existing yearly unfished biomass estimates the biomass for a specified year and age.

                                                                                      +
                                                                                      Parameters
                                                                                      + + + + +
                                                                                      i_age_yeardimension folded index for age and year
                                                                                      yearthe year of unfished biomass to add
                                                                                      agethe age of unfished biomass to add
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ CalculateUnfishedNumbersAA()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      void fims_popdy::Population< Type >::CalculateUnfishedNumbersAA (size_t i_age_year,
                                                                                      size_t i_agem1_yearm1,
                                                                                      size_t age 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Calculates unfished numbers at age at year and age specific indices.

                                                                                      +
                                                                                      Parameters
                                                                                      + + + + +
                                                                                      i_age_yeardimension folded index for age and year
                                                                                      i_agem1_yearm1dimension folded index for age-1 and year-1
                                                                                      ageage index
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ CalculateUnfishedSpawningBiomass()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      void fims_popdy::Population< Type >::CalculateUnfishedSpawningBiomass (size_t i_age_year,
                                                                                      size_t year,
                                                                                      size_t age 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Adds to existing yearly unfished spawning biomass estimates the biomass for a specified year and age.

                                                                                      +
                                                                                      Parameters
                                                                                      + + + + +
                                                                                      i_age_yeardimension folded index for age and year
                                                                                      yearthe year of unfished spawning biomass to add
                                                                                      agethe age of unfished spawning biomass to add
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ Initialize()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      void fims_popdy::Population< Type >::Initialize (int nyears,
                                                                                      int nseasons,
                                                                                      int nages 
                                                                                      )
                                                                                      +                                                                                       		+inline
                                                                                      +
                                                                                      + +

                                                                                      Initialize values. Called once at the start of model run.

                                                                                      +
                                                                                      Parameters
                                                                                      + + + + +
                                                                                      nyearsnumber of years in the population
                                                                                      nseasonsnumber of seasons in the population
                                                                                      nagesnumber of ages in the population
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      +

                                                                                      Member Data Documentation

                                                                                      + +

                                                                                      ◆ ages

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<double> fims_popdy::Population< Type >::ages
                                                                                      +
                                                                                      +

                                                                                      vector of the ages for referencing

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ biomass

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Population< Type >::biomass
                                                                                      +
                                                                                      +

                                                                                      Derived quantity: total population biomass in each year

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ expected_catch

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Population< Type >::expected_catch
                                                                                      +
                                                                                      +

                                                                                      Expected values: Catch

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ expected_numbers_at_age

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Population< Type >::expected_numbers_at_age
                                                                                      +
                                                                                      +

                                                                                      Expected values: Numbers at age (thousands?? millions??)

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ expected_recruitment

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Population< Type >::expected_recruitment
                                                                                      +
                                                                                      +

                                                                                      Expected recruitment

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ fleet_id

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      int fims_popdy::Population< Type >::fleet_id = -999
                                                                                      +
                                                                                      +

                                                                                      id of fleet model object

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ fleets

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<std::shared_ptr<Fleet<Type> > > fims_popdy::Population< Type >::fleets
                                                                                      +
                                                                                      +

                                                                                      shared pointer to fleet module

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ growth

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::shared_ptr<GrowthBase<Type> > fims_popdy::Population< Type >::growth
                                                                                      +
                                                                                      +

                                                                                      shared pointer to growth module

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ growth_id

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      int fims_popdy::Population< Type >::growth_id = -999
                                                                                      +
                                                                                      +

                                                                                      id of growth model object

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ id_g

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + + +
                                                                                      + + + + +
                                                                                      uint32_t fims_popdy::Population< Type >::id_g = 0
                                                                                      +                                                                                       		+static
                                                                                      +
                                                                                      +

                                                                                      reference id for population object

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ log_init_naa

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Population< Type >::log_init_naa
                                                                                      +
                                                                                      +

                                                                                      estimated parameter: log numbers at age

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ log_M

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      ParameterVector fims_popdy::Population< Type >::log_M
                                                                                      +
                                                                                      +

                                                                                      estimated parameter: log Natural Mortality

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ M

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Population< Type >::M
                                                                                      +
                                                                                      +

                                                                                      transformed parameter: Natural Mortality

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ maturity

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::shared_ptr<MaturityBase<Type> > fims_popdy::Population< Type >::maturity
                                                                                      +
                                                                                      +

                                                                                      shared pointer to maturity module

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ maturity_id

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      int fims_popdy::Population< Type >::maturity_id = -999
                                                                                      +
                                                                                      +

                                                                                      id of maturity model object

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ mortality_F

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      ParameterVector fims_popdy::Population< Type >::mortality_F
                                                                                      +
                                                                                      +

                                                                                      vector of fishing mortality summed across fleet by year and age

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ mortality_Z

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Population< Type >::mortality_Z
                                                                                      +
                                                                                      +

                                                                                      vector of total mortality by year and age

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ nages

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      size_t fims_popdy::Population< Type >::nages
                                                                                      +
                                                                                      +

                                                                                      total number of ages in the population

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ nfleets

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      size_t fims_popdy::Population< Type >::nfleets
                                                                                      +
                                                                                      +

                                                                                      total number of fleets in the fishery

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ nseasons

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      size_t fims_popdy::Population< Type >::nseasons
                                                                                      +
                                                                                      +

                                                                                      total number of seasons in the fishery

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ numbers_at_age

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Population< Type >::numbers_at_age
                                                                                      +
                                                                                      +

                                                                                      Derived quantity: population expected numbers at age in each year

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ nyears

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      size_t fims_popdy::Population< Type >::nyears
                                                                                      +
                                                                                      +

                                                                                      total number of years in the fishery

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ proportion_female

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      const Type fims_popdy::Population< Type >::proportion_female
                                                                                      +
                                                                                      +Initial value:
                                                                                      =
                                                                                      +
                                                                                      0.5
                                                                                      +

                                                                                      Sex proportion fixed at 50/50 for M1

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ proportion_mature_at_age

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Population< Type >::proportion_mature_at_age
                                                                                      +
                                                                                      +

                                                                                      Derived quantity: Proportion matura at age

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ recruitment

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::shared_ptr<RecruitmentBase<Type> > fims_popdy::Population< Type >::recruitment
                                                                                      +
                                                                                      +

                                                                                      shared pointer to recruitment module

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ recruitment_id

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      int fims_popdy::Population< Type >::recruitment_id = -999
                                                                                      +
                                                                                      + +

                                                                                      recruitment

                                                                                      +

                                                                                      id of recruitment model object

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ spawning_biomass

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Population< Type >::spawning_biomass
                                                                                      +
                                                                                      +

                                                                                      Derived quantity: Spawning_biomass

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ unfished_biomass

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Population< Type >::unfished_biomass
                                                                                      +
                                                                                      +

                                                                                      Derived quanity biomass assuming unfished

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ unfished_numbers_at_age

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Population< Type >::unfished_numbers_at_age
                                                                                      +
                                                                                      +

                                                                                      Derived quantity: population expected unfished numbers at age in each year

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ unfished_spawning_biomass

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Population< Type >::unfished_spawning_biomass
                                                                                      +
                                                                                      +

                                                                                      Derived quanity Spawning biomass assuming unfished

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ weight_at_age

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<Type> fims_popdy::Population< Type >::weight_at_age
                                                                                      +
                                                                                      +

                                                                                      Derived quantity: expected weight at age

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ years

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      std::vector<double> fims_popdy::Population< Type >::years
                                                                                      +
                                                                                      +

                                                                                      vector of years for referencing

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      The documentation for this struct was generated from the following file: +
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
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                                                                                      fims_popdy::RecruitmentBase< Type > Member List
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      This is the complete list of members for fims_popdy::RecruitmentBase< Type >, including all inherited members.

                                                                                      + + + + + + + + + + + + + + + + + + + +
                                                                                      constrain_deviationsfims_popdy::RecruitmentBase< Type >
                                                                                      estimate_recruit_deviationsfims_popdy::RecruitmentBase< Type >
                                                                                      evaluate(const Type &spawners, const Type &ssbzero)=0fims_popdy::RecruitmentBase< Type >pure virtual
                                                                                      evaluate_nll()fims_popdy::RecruitmentBase< Type >inlinevirtual
                                                                                      fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      GetId() constfims_model_object::FIMSObject< Type >inline
                                                                                      idfims_model_object::FIMSObject< Type >
                                                                                      id_gfims_popdy::RecruitmentBase< Type >static
                                                                                      log_rzerofims_popdy::RecruitmentBase< Type >
                                                                                      log_sigma_recruitfims_popdy::RecruitmentBase< Type >
                                                                                      parametersfims_model_object::FIMSObject< Type >
                                                                                      Prepare()fims_popdy::RecruitmentBase< Type >inline
                                                                                      PrepareConstrainedDeviations()fims_popdy::RecruitmentBase< Type >inline
                                                                                      random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      recruit_deviationsfims_popdy::RecruitmentBase< Type >
                                                                                      RecruitmentBase()fims_popdy::RecruitmentBase< Type >inline
                                                                                      ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                                      ~RecruitmentBase() (defined in fims_popdy::RecruitmentBase< Type >)fims_popdy::RecruitmentBase< Type >inlinevirtual
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
                                                                                      + + diff --git a/docs/structfims__popdy_1_1RecruitmentBase.html b/docs/structfims__popdy_1_1RecruitmentBase.html new file mode 100644 index 0000000..ac9d86c --- /dev/null +++ b/docs/structfims__popdy_1_1RecruitmentBase.html @@ -0,0 +1,366 @@ + + + + + + + +FIMS: fims_popdy::RecruitmentBase< Type > Struct Template Reference + + + + + + + + + + + +
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                                                                                      +
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                                                                                      fims_popdy::RecruitmentBase< Type > Struct Template Referenceabstract
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      Base class for all recruitment functors. + More...

                                                                                      + +

                                                                                      #include <recruitment_base.hpp>

                                                                                      +
                                                                                      +Inheritance diagram for fims_popdy::RecruitmentBase< Type >:
                                                                                      +
                                                                                      +
                                                                                      + + +fims_model_object::FIMSObject< Type > +fims_popdy::SRBevertonHolt< Type > + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + +

                                                                                      +Public Member Functions

                                                                                      + RecruitmentBase ()
                                                                                       Constructor.
                                                                                       
                                                                                      +void Prepare ()
                                                                                       Prepares the recruitment deviations vector.
                                                                                       
                                                                                      virtual const Type evaluate (const Type &spawners, const Type &ssbzero)=0
                                                                                       Calculates the expected recruitment for a given spawning input. More...
                                                                                       
                                                                                      virtual const Type evaluate_nll ()
                                                                                       Calculates the negative log likelihood of recruitment deviations. More...
                                                                                       
                                                                                      +void PrepareConstrainedDeviations ()
                                                                                       Prepare constrained recruitment deviations. Based on ADMB sum-to-zero constraint implementation. We still need to adde 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.
                                                                                       
                                                                                      + + + + + + + + + + + + + + + + + + + + +

                                                                                      +Public Attributes

                                                                                      fims::ModelTraits< Type >::ParameterVector recruit_deviations
                                                                                       
                                                                                      bool constrain_deviations = false
                                                                                       
                                                                                      Type log_sigma_recruit
                                                                                       
                                                                                      Type log_rzero
                                                                                       
                                                                                      bool estimate_recruit_deviations
                                                                                       
                                                                                      - 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
                                                                                      + + +
                                                                                      TypeThe type of the recruitment functor.
                                                                                      +
                                                                                      +
                                                                                      +

                                                                                      Member Function Documentation

                                                                                      + +

                                                                                      ◆ evaluate()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + +
                                                                                      virtual const Type fims_popdy::RecruitmentBase< Type >::evaluate (const Type & spawners,
                                                                                      const Type & ssbzero 
                                                                                      )
                                                                                      +                                                                                       		+pure virtual
                                                                                      +
                                                                                      + +

                                                                                      Calculates the expected recruitment for a given spawning input.

                                                                                      +
                                                                                      Parameters
                                                                                      + + + +
                                                                                      spawnersA measure for spawning output.
                                                                                      ssbzeroA measure for spawning output in unfished population.
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      Implemented in fims_popdy::SRBevertonHolt< Type >.

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ evaluate_nll()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + +
                                                                                      virtual const Type fims_popdy::RecruitmentBase< Type >::evaluate_nll ()
                                                                                      +                                                                                       		+inlinevirtual
                                                                                      +
                                                                                      + +

                                                                                      Calculates the negative log likelihood of recruitment deviations.

                                                                                      +

                                                                                      < The negative log likelihood value

                                                                                      + +
                                                                                      +
                                                                                      +

                                                                                      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_recruit_deviations

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      bool fims_popdy::RecruitmentBase< Type >::estimate_recruit_deviations
                                                                                      +
                                                                                      +Initial value:
                                                                                      =
                                                                                      +
                                                                                      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_rzero

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      Type fims_popdy::RecruitmentBase< Type >::log_rzero
                                                                                      +
                                                                                      +

                                                                                      Log of unexploited recruitment.

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ log_sigma_recruit

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      Type fims_popdy::RecruitmentBase< Type >::log_sigma_recruit
                                                                                      +
                                                                                      +

                                                                                      Log standard deviation of log recruitment deviations

                                                                                      + +
                                                                                      +
                                                                                      + +

                                                                                      ◆ recruit_deviations

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<class Type >
                                                                                      + + + + +
                                                                                      fims::ModelTraits<Type>::ParameterVector fims_popdy::RecruitmentBase< Type >::recruit_deviations
                                                                                      +
                                                                                      +

                                                                                      A vector of recruitment deviations

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      The documentation for this struct was generated from the following file: +
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
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                                                                                      fims_popdy::SRBevertonHolt< Type > Member List
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      This is the complete list of members for fims_popdy::SRBevertonHolt< Type >, including all inherited members.

                                                                                      + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      constrain_deviationsfims_popdy::RecruitmentBase< Type >
                                                                                      estimate_recruit_deviationsfims_popdy::RecruitmentBase< Type >
                                                                                      evaluate(const Type &spawners, const Type &phi_0)fims_popdy::SRBevertonHolt< Type >inlinevirtual
                                                                                      evaluate_nll()fims_popdy::RecruitmentBase< Type >inlinevirtual
                                                                                      fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      GetId() constfims_model_object::FIMSObject< Type >inline
                                                                                      idfims_model_object::FIMSObject< Type >
                                                                                      id_gfims_popdy::RecruitmentBase< Type >static
                                                                                      log_rzerofims_popdy::RecruitmentBase< Type >
                                                                                      log_sigma_recruitfims_popdy::RecruitmentBase< Type >
                                                                                      logit_steepfims_popdy::SRBevertonHolt< Type >
                                                                                      parametersfims_model_object::FIMSObject< Type >
                                                                                      Prepare()fims_popdy::RecruitmentBase< Type >inline
                                                                                      PrepareConstrainedDeviations()fims_popdy::RecruitmentBase< Type >inline
                                                                                      random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      recruit_deviationsfims_popdy::RecruitmentBase< Type >
                                                                                      RecruitmentBase()fims_popdy::RecruitmentBase< Type >inline
                                                                                      SRBevertonHolt() (defined in fims_popdy::SRBevertonHolt< Type >)fims_popdy::SRBevertonHolt< Type >inline
                                                                                      ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                                      ~RecruitmentBase() (defined in fims_popdy::RecruitmentBase< Type >)fims_popdy::RecruitmentBase< Type >inlinevirtual
                                                                                      ~SRBevertonHolt() (defined in fims_popdy::SRBevertonHolt< Type >)fims_popdy::SRBevertonHolt< Type >inlinevirtual
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
                                                                                      + + diff --git a/docs/structfims__popdy_1_1SRBevertonHolt.html b/docs/structfims__popdy_1_1SRBevertonHolt.html new file mode 100644 index 0000000..c8820fc --- /dev/null +++ b/docs/structfims__popdy_1_1SRBevertonHolt.html @@ -0,0 +1,246 @@ + + + + + + + +FIMS: fims_popdy::SRBevertonHolt< Type > Struct Template Reference + + + + + + + + + + + +
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                                                                                      FIMS +
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                                                                                      +Public Member Functions | +Public Attributes | +List of all members
                                                                                      +
                                                                                      +
                                                                                      fims_popdy::SRBevertonHolt< Type > Struct Template Reference
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      BevertonHolt class that returns the Beverton Holt SR from fims_math. + More...

                                                                                      + +

                                                                                      #include <sr_beverton_holt.hpp>

                                                                                      +
                                                                                      +Inheritance diagram for fims_popdy::SRBevertonHolt< Type >:
                                                                                      +
                                                                                      +
                                                                                      + + +fims_popdy::RecruitmentBase< Type > +fims_model_object::FIMSObject< Type > + +
                                                                                      + + + + + + + + + + + + + + + + + + + + + + +

                                                                                      +Public Member Functions

                                                                                      virtual const Type evaluate (const Type &spawners, const Type &phi_0)
                                                                                       Beverton Holt implementation of the stock recruitment function. More...
                                                                                       
                                                                                      - Public Member Functions inherited from fims_popdy::RecruitmentBase< Type >
                                                                                      + RecruitmentBase ()
                                                                                       Constructor.
                                                                                       
                                                                                      +void Prepare ()
                                                                                       Prepares the recruitment deviations vector.
                                                                                       
                                                                                      virtual const Type evaluate_nll ()
                                                                                       Calculates the negative log likelihood of recruitment deviations. More...
                                                                                       
                                                                                      +void PrepareConstrainedDeviations ()
                                                                                       Prepare constrained recruitment deviations. Based on ADMB sum-to-zero constraint implementation. We still need to adde 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.
                                                                                       
                                                                                      + + + + + + + + + + + + + + + + + + + + + + + +

                                                                                      +Public Attributes

                                                                                      Type logit_steep
                                                                                       
                                                                                      - Public Attributes inherited from fims_popdy::RecruitmentBase< Type >
                                                                                      fims::ModelTraits< Type >::ParameterVector recruit_deviations
                                                                                       
                                                                                      bool constrain_deviations = false
                                                                                       
                                                                                      Type log_sigma_recruit
                                                                                       
                                                                                      Type log_rzero
                                                                                       
                                                                                      bool estimate_recruit_deviations
                                                                                       
                                                                                      - 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
                                                                                       
                                                                                      + + + + +

                                                                                      +Additional Inherited Members

                                                                                      - Static Public Attributes inherited from fims_popdy::RecruitmentBase< Type >
                                                                                      static uint32_t id_g = 0
                                                                                       
                                                                                      +

                                                                                      Detailed Description

                                                                                      +

                                                                                      template<typename Type>
                                                                                      +struct fims_popdy::SRBevertonHolt< Type >

                                                                                      + +

                                                                                      BevertonHolt class that returns the Beverton Holt SR from fims_math.

                                                                                      +
                                                                                      Parameters
                                                                                      + + +
                                                                                      logit_steepRecruitment relative to unfished recruitment at 20% of unfished spawning biomass. Should be a value between 0.2 and 1.0.
                                                                                      +
                                                                                      +
                                                                                      +

                                                                                      Member Function Documentation

                                                                                      + +

                                                                                      ◆ evaluate()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + + + + + + + + + + + +
                                                                                      virtual const Type fims_popdy::SRBevertonHolt< Type >::evaluate (const Type & spawners,
                                                                                      const Type & phi_0 
                                                                                      )
                                                                                      +                                                                                       		+inlinevirtual
                                                                                      +
                                                                                      + +

                                                                                      Beverton Holt implementation of the stock recruitment function.

                                                                                      +

                                                                                      The Beverton Holt stock recruitment implementation: \( \frac{0.8 R_{0} h S_{t-1}}{0.2 R_{0} \phi_{0} (1 - h) + S_{t-1} (h - 0.2)} \)

                                                                                      +
                                                                                      Parameters
                                                                                      + + + +
                                                                                      spawnersA measure of spawning output.
                                                                                      phi_0Number of spawners per recruit of an unfished population
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      Implements fims_popdy::RecruitmentBase< Type >.

                                                                                      + +
                                                                                      +
                                                                                      +

                                                                                      Member Data Documentation

                                                                                      + +

                                                                                      ◆ logit_steep

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + +
                                                                                      Type fims_popdy::SRBevertonHolt< Type >::logit_steep
                                                                                      +
                                                                                      +

                                                                                      Transformed value of recruitment relative to unfished recruitment at 20% of unfished spawning biomass.

                                                                                      + +
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                                                                                      The documentation for this struct was generated from the following file: +
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                                                                                      +Generated by doxygen 1.9.1 +
                                                                                      + + diff --git a/docs/structfims__popdy_1_1SRBevertonHolt.png b/docs/structfims__popdy_1_1SRBevertonHolt.png new file mode 100644 index 0000000000000000000000000000000000000000..64797658bfaeef45910c9430c8b1f25f2df90243 GIT binary patch literal 1307 zcmeAS@N?(olHy`uVBq!ia0vp^AAq=ngBeJ^`!$URNJ#|vgt-3y{~ySF@#br3|Dg#$ z78oBmaDcV*jy#adQ4-`A%m7pb0#{Fk7%?!gtnzem45?szJNIqTYXu(G>&J~N|GV$& zOm?WbX>l?)YQbaUJO>V4p-=JGN@LxHR;%xyKyel*>GAi3g*_9@|HDyBgj9dju_dCabDBjhT=A zUAdXxn-#O~1Pi@?#`b5&_WL(-th5gV#`(*-9@zbI--?8(sXuo97e2-!(7)^Ci|K2< z?Zu;YCe`vxwhrW%pX+usaLyzSi>QfFX$LZW6gPa@=bEtlNW_tH3-)`;nJ(R~dhE3-Fmbu47hL_OL_ZG#&na_eAh`%r3w3yYm`^!@69IJ!e_6#D(RPZrS$){&kZc+DsGq$zq}T()q!UE8nY1B5fJ@+6vpYONt-6ti|Y&weZTv zMe^wfSo=N|-g=kUyy0o-jE5ygYae;d+;!8*b?>By&#Yru`}pm5uiQFmUs=2Chu`Hp zc6z%ThV9;x`zkQJ=l!2+hYtspFZ-(ZcKe&x6zTtOJv-Y<_p(^{#cyoDZ~jG4?FE*pR>dV23;NzR!KG zHZmXHTw!;|aJ#KdTT+{F!;*qG ze5Ox|A1o=95lKsm$clQH=f3nhPt2(eg<&tAIDFYMrR2739vh$R?;T5`-*3>Le*VtG zXL@r3T9bOY&R(6}eRs?IC9Th6t=MnW{|@`_HJxq6s)FWw|5}*$to*$GPiVq*L;lA7 zr+-I2n8s5-^ZS1W=0AnL2@Ug18yTyvJucp>bK0oyA7k6r1a-dm-nzh&jKR~@&t;uc GLK6U)fq7{F literal 0 HcmV?d00001 diff --git a/docs/structfims__popdy_1_1SelectivityBase-members.html b/docs/structfims__popdy_1_1SelectivityBase-members.html new file mode 100644 index 0000000..5bbe638 --- /dev/null +++ b/docs/structfims__popdy_1_1SelectivityBase-members.html @@ -0,0 +1,98 @@ + + + + + + + +FIMS: Member List + + + + + + + + + + + +
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                                                                                      FIMS +
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                                                                                      fims_popdy::SelectivityBase< Type > Member List
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      This is the complete list of members for fims_popdy::SelectivityBase< Type >, including all inherited members.

                                                                                      + + + + + + + + + + + +
                                                                                      evaluate(const Type &x)=0fims_popdy::SelectivityBase< Type >pure virtual
                                                                                      fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      GetId() constfims_model_object::FIMSObject< Type >inline
                                                                                      idfims_model_object::FIMSObject< Type >
                                                                                      id_gfims_popdy::SelectivityBase< Type >static
                                                                                      parametersfims_model_object::FIMSObject< Type >
                                                                                      random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                                      SelectivityBase()fims_popdy::SelectivityBase< Type >inline
                                                                                      ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                                      ~SelectivityBase() (defined in fims_popdy::SelectivityBase< Type >)fims_popdy::SelectivityBase< Type >inlinevirtual
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
                                                                                      + + diff --git a/docs/structfims__popdy_1_1SelectivityBase.html b/docs/structfims__popdy_1_1SelectivityBase.html new file mode 100644 index 0000000..ae8bd65 --- /dev/null +++ b/docs/structfims__popdy_1_1SelectivityBase.html @@ -0,0 +1,217 @@ + + + + + + + +FIMS: fims_popdy::SelectivityBase< Type > Struct Template Reference + + + + + + + + + + + +
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                                                                                      FIMS +
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                                                                                      +Public Member Functions | +Static Public Attributes | +List of all members
                                                                                      +
                                                                                      +
                                                                                      fims_popdy::SelectivityBase< Type > Struct Template Referenceabstract
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      Base class for all selectivity functors. + More...

                                                                                      + +

                                                                                      #include <selectivity_base.hpp>

                                                                                      +
                                                                                      +Inheritance diagram for fims_popdy::SelectivityBase< Type >:
                                                                                      +
                                                                                      +
                                                                                      + + +fims_model_object::FIMSObject< Type > +fims_popdy::DoubleLogisticSelectivity< Type > +fims_popdy::LogisticSelectivity< Type > + +
                                                                                      + + + + + + + + + + + + +

                                                                                      +Public Member Functions

                                                                                      + SelectivityBase ()
                                                                                       Constructor.
                                                                                       
                                                                                      virtual const Type evaluate (const Type &x)=0
                                                                                       Calculates the selectivity. More...
                                                                                       
                                                                                      - 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.
                                                                                       
                                                                                      + + + +

                                                                                      +Static Public Attributes

                                                                                      static uint32_t id_g = 0
                                                                                       
                                                                                      + + + + + + + + + + +

                                                                                      +Additional Inherited Members

                                                                                      - 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
                                                                                       
                                                                                      +

                                                                                      Detailed Description

                                                                                      +

                                                                                      template<typename Type>
                                                                                      +struct fims_popdy::SelectivityBase< Type >

                                                                                      + +

                                                                                      Base class for all selectivity functors.

                                                                                      +
                                                                                      Template Parameters
                                                                                      + + +
                                                                                      TypeThe type of the selectivity functor.
                                                                                      +
                                                                                      +
                                                                                      +

                                                                                      Member Function Documentation

                                                                                      + +

                                                                                      ◆ evaluate()

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + + + + + +
                                                                                      virtual const Type fims_popdy::SelectivityBase< Type >::evaluate (const Type & x)
                                                                                      +                                                                                       		+pure virtual
                                                                                      +
                                                                                      + +

                                                                                      Calculates the selectivity.

                                                                                      +
                                                                                      Parameters
                                                                                      + + +
                                                                                      xThe independent variable in the logistic function (e.g., age or size in selectivity).
                                                                                      +
                                                                                      +
                                                                                      + +

                                                                                      Implemented in fims_popdy::LogisticSelectivity< Type >, and fims_popdy::DoubleLogisticSelectivity< Type >.

                                                                                      + +
                                                                                      +
                                                                                      +

                                                                                      Member Data Documentation

                                                                                      + +

                                                                                      ◆ id_g

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +template<typename Type >
                                                                                      + + + + + +
                                                                                      + + + + +
                                                                                      uint32_t fims_popdy::SelectivityBase< Type >::id_g = 0
                                                                                      +                                                                                       		+static
                                                                                      +
                                                                                      +

                                                                                      The ID of the instance of the SelectivityBase class

                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      The documentation for this struct was generated from the following file: +
                                                                                      + +
                                                                                      +Generated by doxygen 1.9.1 +
                                                                                      + + diff --git a/docs/structfims__popdy_1_1SelectivityBase.png b/docs/structfims__popdy_1_1SelectivityBase.png new file mode 100644 index 0000000000000000000000000000000000000000..6105380aa6c51cbd5bb5c977f01d28a83ff7ed48 GIT binary patch literal 2185 zcmcImX;c$g76yU~5Tscm*dS}d7Qn(NNV5cNPznNKKp8=nj5bIsA`q8m3u(5YUCW@UnjqGJ@WFR*|esbDVl6_Vxoh|Ws*SG7%s=a ziqu}Ye4GT;k__V%l<*H{q@k7KK!{9;aR#IJb2*o(fLx0b^Q6PlL~s&66tJ5aAuN>3 z(iQt$FO45HCxnJa2mf

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                                                                                      32 #define FIMS_POPULATION_DYNAMICS_POPULATION_SUBPOPULATION_HPP
                                                                                      33 
                                                                                      -
                                                                                      34 namespace fims {
                                                                                      +
                                                                                      34 namespace fims_popdy {
                                                                                      35 
                                                                                      -
                                                                                      40 template <typename T>
                                                                                      -
                                                                                      41 class Subpopulation {};
                                                                                      +
                                                                                      40 template <typename Type>
                                                                                      +
                                                                                      41 class Subpopulation {};
                                                                                      42 
                                                                                      43 } // namespace fims
                                                                                      44 
                                                                                      45 #endif /* FIMS_POPULATION_DYNAMICS_POPULATION_SUBPOPULATION_HPP */
                                                                                      -
                                                                                      fims::Subpopulation
                                                                                      Definition: subpopulation.hpp:41
                                                                                      +
                                                                                      fims_popdy::Subpopulation
                                                                                      Definition: subpopulation.hpp:41
                                                                                      diff --git a/docs/tmb__distributions_8hpp_source.html b/docs/tmb__distributions_8hpp_source.html index 10b7a8c..cf27ac4 100644 --- a/docs/tmb__distributions_8hpp_source.html +++ b/docs/tmb__distributions_8hpp_source.html @@ -84,44 +84,44 @@
                                                                                      13 
                                                                                      14 #include "distributions_base.hpp"
                                                                                      15 
                                                                                      -
                                                                                      16 namespace fims {
                                                                                      +
                                                                                      16 namespace fims_distributions {
                                                                                      17 
                                                                                      -
                                                                                      21 template <typename T>
                                                                                      -
                                                                                      22 struct Dnorm : public DistributionsBase<T> {
                                                                                      -
                                                                                      23  T x;
                                                                                      -
                                                                                      24  T mean;
                                                                                      -
                                                                                      25  T sd;
                                                                                      -
                                                                                      28  Dnorm() : DistributionsBase<T>() {}
                                                                                      +
                                                                                      21 template <typename Type>
                                                                                      +
                                                                                      22 struct Dnorm : public DistributionsBase<Type> {
                                                                                      +
                                                                                      23  Type x;
                                                                                      +
                                                                                      24  Type mean;
                                                                                      +
                                                                                      25  Type sd;
                                                                                      +
                                                                                      28  Dnorm() : DistributionsBase<Type>() {}
                                                                                      29 
                                                                                      30  virtual ~Dnorm() {}
                                                                                      31 
                                                                                      -
                                                                                      39  virtual const T evaluate(const bool& do_log) {
                                                                                      +
                                                                                      39  virtual const Type evaluate(const bool& do_log) {
                                                                                      40  return dnorm(x, mean, sd, do_log);
                                                                                      41  }
                                                                                      42 };
                                                                                      43 
                                                                                      -
                                                                                      47 template <typename T>
                                                                                      -
                                                                                      48 struct Dmultinom : public DistributionsBase<T> {
                                                                                      -
                                                                                      50  using Vector = typename fims::ModelTraits<T>::EigenVector;
                                                                                      +
                                                                                      47 template <typename Type>
                                                                                      +
                                                                                      48 struct Dmultinom : public DistributionsBase<Type> {
                                                                                      +
                                                                                      50  using Vector = typename fims::ModelTraits<Type>::EigenVector;
                                                                                      51  Vector x;
                                                                                      52  Vector p;
                                                                                      -
                                                                                      55  Dmultinom() : DistributionsBase<T>() {}
                                                                                      +
                                                                                      55  Dmultinom() : DistributionsBase<Type>() {}
                                                                                      56 
                                                                                      -
                                                                                      66  virtual const T evaluate(const bool& do_log) {
                                                                                      +
                                                                                      66  virtual const Type evaluate(const bool& do_log) {
                                                                                      67  return dmultinom(x, p, do_log);
                                                                                      68  }
                                                                                      69 };
                                                                                      70 
                                                                                      -
                                                                                      75 template <typename T>
                                                                                      -
                                                                                      76 struct Dlnorm : public DistributionsBase<T> {
                                                                                      -
                                                                                      77  T x;
                                                                                      -
                                                                                      78  T meanlog;
                                                                                      -
                                                                                      79  T sdlog;
                                                                                      -
                                                                                      81  Dlnorm() : DistributionsBase<T>() {}
                                                                                      +
                                                                                      75 template <typename Type>
                                                                                      +
                                                                                      76 struct Dlnorm : public DistributionsBase<Type> {
                                                                                      +
                                                                                      77  Type x;
                                                                                      +
                                                                                      78  Type meanlog;
                                                                                      +
                                                                                      79  Type sdlog;
                                                                                      +
                                                                                      81  Dlnorm() : DistributionsBase<Type>() {}
                                                                                      82 
                                                                                      -
                                                                                      92  virtual const T evaluate(const bool& do_log) {
                                                                                      -
                                                                                      93  T logx = log(x);
                                                                                      -
                                                                                      94  T nll;
                                                                                      +
                                                                                      92  virtual const Type evaluate(const bool& do_log) {
                                                                                      +
                                                                                      93  Type logx = log(x);
                                                                                      +
                                                                                      94  Type nll;
                                                                                      95 
                                                                                      96  nll = dnorm(logx, meanlog, sdlog, true) - logx;
                                                                                      97 
                                                                                      @@ -132,7 +132,7 @@
                                                                                      102  }
                                                                                      103  }
                                                                                      104 };
                                                                                      -
                                                                                      105 } // namespace fims
                                                                                      +
                                                                                      105 } // namespace fims_distributions
                                                                                      106 
                                                                                      107 #endif
                                                                                      108