Model< FP > Class Template Reference

CPP API: mio::oseirmetapop::Model< FP > Class Template Reference

CPP API

The Model holds the Parameters and the initial Populations for every region and defines the ordinary differential equations. More...

#include <model.h>

Inheritance diagram for mio::oseirmetapop::Model< FP >:

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Collaboration diagram for mio::oseirmetapop::Model< FP >:

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Public Member Functions
void	get_flows (Eigen::Ref< const Eigen::VectorX< FP >> pop, Eigen::Ref< const Eigen::VectorX< FP >> y, FP t, Eigen::Ref< Eigen::VectorX< FP >> flows) const override
	Compute the values of the flows between compartments at a given time. More...

IOResult< ScalarType >	get_reproduction_number (size_t t_idx, const mio::TimeSeries< ScalarType > &y)
	Computes the reproduction number at a given index time of the Model output obtained by the Simulation. More...

Eigen::VectorXd	get_reproduction_numbers (const mio::TimeSeries< ScalarType > &y)
	Computes the reproduction number for all time points of the Model output obtained by the Simulation. More...

	Model (int num_regions, int num_agegroups)
	Create a Model with the given number of Regions and AgeGroups. More...

template<class IOContext >
void	serialize (IOContext &io) const
	serialize this. More...

void	set_commuting_strengths ()
	Set the CommutingStrengths matrix without data. More...

void	set_commuting_strengths (const Eigen::MatrixXd &commuting_strengths)
	Set the CommutingStrengths matrix and update the PopulationAfterCommuting. More...

Public Member Functions inherited from mio::FlowModel< ScalarType, InfectionState, mio::Populations< ScalarType, mio::regions::Region, AgeGroup, InfectionState >, Parameters< ScalarType >, Flows >
	FlowModel (Args... args)
	Default constructor, forwarding args to Base constructor. More...

void	get_derivatives (Eigen::Ref< const Eigen::VectorX< ScalarType >> flows, Eigen::Ref< Eigen::VectorX< ScalarType >> dydt) const
	Compute the right-hand-side of the ODE dydt = f(y, t) from flow values. More...

void	get_derivatives (Eigen::Ref< const Eigen::VectorX< ScalarType >> pop, Eigen::Ref< const Eigen::VectorX< ScalarType >> y, ScalarType t, Eigen::Ref< Eigen::VectorX< ScalarType >> dydt) const final
	Compute the right-hand-side f(y, t) of the ODE and store it in dydt. More...

constexpr size_t	get_flat_flow_index () const
	A flat index into an array of flows (as computed by get_flows), if the only used category in Pop is Comp. More...

size_t	get_flat_flow_index (const FlowIndex &indices) const
	A flat index into an array of flows (as computed by get_flows), given the indices of each category. More...

virtual void	get_flows (Eigen::Ref< const Eigen::VectorX< ScalarType >>, Eigen::Ref< const Eigen::VectorX< ScalarType >>, ScalarType, Eigen::Ref< Eigen::VectorX< ScalarType >>) const=0

Eigen::VectorX< ScalarType >	get_initial_flows () const
	Initial values for flows. More...

Public Member Functions inherited from mio::CompartmentalModel< FP, Comp, Pop, Params >
bool	apply_constraints ()
	Checks whether the model satisfies all constraints. More...

bool	check_constraints () const
	Checks that the model satisfies all constraints (e.g. More...

	CompartmentalModel (CompartmentalModel &&)=default

	CompartmentalModel (const CompartmentalModel &)=default

	CompartmentalModel (Populations const &po, ParameterSet const &pa)
	CompartmentalModel default constructor. More...

void	eval_right_hand_side (Eigen::Ref< const Eigen::VectorX< FP >> pop, Eigen::Ref< const Eigen::VectorX< FP >> y, FP t, Eigen::Ref< Eigen::VectorX< FP >> dydt) const
	This function evaluates the right-hand-side f of the ODE dydt = f(y, t). More...

virtual void	get_derivatives (Eigen::Ref< const Eigen::VectorX< FP >>, Eigen::Ref< const Eigen::VectorX< FP >>, FP, Eigen::Ref< Eigen::VectorX< FP >>) const

Eigen::VectorX< FP >	get_initial_values () const
	Get the initial conditions for the ODE dydt = f(y, t). More...

CompartmentalModel &	operator= (CompartmentalModel &&)=default

CompartmentalModel &	operator= (const CompartmentalModel &)=default

virtual	~CompartmentalModel ()=default

Static Public Member Functions
template<class IOContext >
static IOResult< Model >	deserialize (IOContext &io)
	deserialize an object of this class. More...

Private Types
using	Base = FlowModel< FP, InfectionState, mio::Populations< FP, mio::regions::Region, AgeGroup, InfectionState >, Parameters< FP >, Flows >

Additional Inherited Members
Public Types inherited from mio::FlowModel< ScalarType, InfectionState, mio::Populations< ScalarType, mio::regions::Region, AgeGroup, InfectionState >, Parameters< ScalarType >, Flows >
using	Base = CompartmentalModel< ScalarType, InfectionState, mio::Populations< ScalarType, mio::regions::Region, AgeGroup, InfectionState >, Parameters< ScalarType > >

Public Types inherited from mio::CompartmentalModel< FP, Comp, Pop, Params >
using	Compartments = Comp

using	ParameterSet = Params

using	Populations = Pop

Public Attributes inherited from mio::CompartmentalModel< FP, Comp, Pop, Params >
ParameterSet	parameters {}

Populations	populations {}

Detailed Description

template<typename FP = ScalarType>
class mio::oseirmetapop::Model< FP >

The Model holds the Parameters and the initial Populations for every region and defines the ordinary differential equations.

Member Typedef Documentation

◆ Base

template<typename FP = ScalarType>

using mio::oseirmetapop::Model< FP >::Base = FlowModel<FP, InfectionState, mio::Populations<FP, mio::regions::Region, AgeGroup, InfectionState>, Parameters<FP>, Flows>

private

Constructor & Destructor Documentation

◆ Model()

template<typename FP = ScalarType>

mio::oseirmetapop::Model< FP >::Model	(	int	num_regions,
		int	num_agegroups
	)

inline

Create a Model with the given number of Regions and AgeGroups.

Parameters

[in]	num_regions	The number of Regions.
[in]	num_agegroups	The number of AgeGroups.

Member Function Documentation

◆ deserialize()

template<typename FP = ScalarType>

template<class IOContext >

static IOResult<Model> mio::oseirmetapop::Model< FP >::deserialize ( IOContext & io )

inlinestatic

deserialize an object of this class.

See also: mio::deserialize

◆ get_flows()

template<typename FP = ScalarType>

void mio::oseirmetapop::Model< FP >::get_flows	(	Eigen::Ref< const Eigen::VectorX< FP >>	pop,
		Eigen::Ref< const Eigen::VectorX< FP >>	y,
		FP	t,
		Eigen::Ref< Eigen::VectorX< FP >>	flows
	)		const

inlineoverride

Compute the values of the flows between compartments at a given time.

Parameters

[in]	pop	The current population by #InfectionState, AgeGroup and Region.
[in]	y	The current population by #InfectionState, AgeGroup and Region.
[in]	t	The current time.
[in,out]	flows	The computed flows between compartments.

◆ get_reproduction_number()

template<typename FP = ScalarType>

IOResult<ScalarType> mio::oseirmetapop::Model< FP >::get_reproduction_number	(	size_t	t_idx,
		const mio::TimeSeries< ScalarType > &	y
	)

inline

Computes the reproduction number at a given index time of the Model output obtained by the Simulation.

Parameters

[in]	t_idx	The index time at which the reproduction number is computed.
[in]	y	The TimeSeries obtained from the Model Simulation.

Returns: The computed reproduction number at the provided index time.

◆ get_reproduction_numbers()

template<typename FP = ScalarType>

Eigen::VectorXd mio::oseirmetapop::Model< FP >::get_reproduction_numbers ( const mio::TimeSeries< ScalarType > & y )

inline

Computes the reproduction number for all time points of the Model output obtained by the Simulation.

Parameters

[in] y The TimeSeries obtained from the Model Simulation.

Returns: Vector containing all reproduction numbers

◆ serialize()

template<typename FP = ScalarType>

template<class IOContext >

void mio::oseirmetapop::Model< FP >::serialize ( IOContext & io ) const

inline

serialize this.

See also: mio::serialize

◆ set_commuting_strengths() [1/2]

template<typename FP = ScalarType>

void mio::oseirmetapop::Model< FP >::set_commuting_strengths ( )

inline

Set the CommutingStrengths matrix without data.

This function sets the CommutingStrengths matrix to the identity matrix, which corresponds to no commuting between Regions. This prevents division by zero but does not produce meaningful results.

◆ set_commuting_strengths() [2/2]

template<typename FP = ScalarType>

void mio::oseirmetapop::Model< FP >::set_commuting_strengths ( const Eigen::MatrixXd & commuting_strengths )

inline

Set the CommutingStrengths matrix and update the PopulationAfterCommuting.

Parameters

[in] commuting_strengths The matrix containing the fractions of the commuting population between Regions.

Model&lt; FP &gt; Class Template Reference

Public Member Functions

Static Public Member Functions

Private Types

Additional Inherited Members

Detailed Description

template<typename FP = ScalarType> class mio::oseirmetapop::Model< FP >

Member Typedef Documentation

◆ Base

Constructor & Destructor Documentation

◆ Model()

Member Function Documentation

◆ deserialize()

◆ get_flows()

◆ get_reproduction_number()

◆ get_reproduction_numbers()

◆ serialize()

◆ set_commuting_strengths() [1/2]

◆ set_commuting_strengths() [2/2]

Model< FP > Class Template Reference

template<typename FP = ScalarType>
class mio::oseirmetapop::Model< FP >