Model< FP, LctStates > Class Template Reference

CPP API: mio::lsecir2d::Model< FP, LctStates > Class Template Reference

CPP API

Class that defines an LCT-SECIR-2-DISEASE model. More...

#include <model.h>

Inheritance diagram for mio::lsecir2d::Model< FP, LctStates >:

Collaboration diagram for mio::lsecir2d::Model< FP, LctStates >:

Public Types
using	Base = CompartmentalModel< FP, InfectionState, LctPopulations< FP, LctStates... >, Parameters< FP > >

using	LctStatesGroups = TypeList< LctStates... >

Public Types inherited from mio::CompartmentalModel< FP, InfectionState, LctPopulations< FP, LctStates... >, Parameters< FP > >
using	Compartments = InfectionState

using	ParameterSet = Parameters< FP >

using	Populations = LctPopulations< FP, LctStates... >

Public Member Functions
TimeSeries< FP >	calculate_compartments (const TimeSeries< FP > &subcompartments_ts) const
	Cumulates a simulation result with subcompartments to produce a result that divides the population only into the infection states defined in InfectionState. More...

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

void	get_derivatives (Eigen::Ref< const Eigen::VectorX< FP >> pop, Eigen::Ref< const Eigen::VectorX< FP >> y, FP t, Eigen::Ref< Eigen::VectorX< FP >> dydt) const override
	Evaluates the right-hand-side f of the ODE dydt = f(y, t). More...

	Model ()
	Default constructor. More...

	Model (const Populations &pop, const ParameterSet &params)
	Constructor using Populations and ParameterSet. More...

Public Member Functions inherited from mio::CompartmentalModel< FP, InfectionState, LctPopulations< FP, LctStates... >, Parameters< FP > >
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...

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 Attributes
static constexpr size_t	num_groups = sizeof...(LctStates)

Private Member Functions
template<size_t Group = 0>
bool	check_constraints_impl () const
	Checks whether LctState of a group satisfies all constraints. More...

template<size_t Group = 0>
void	compress_vector (const Eigen::VectorX< FP > &subcompartments, Eigen::VectorX< FP > &compartments) const
	Converts a vector with subcompartments in a vector without subcompartments by summing up subcompartment values. More...

template<size_t Group = 0>
void	get_derivatives_impl (Eigen::Ref< const Eigen::VectorX< FP >> pop, Eigen::Ref< const Eigen::VectorX< FP >> y, FP t, Eigen::Ref< Eigen::VectorX< FP >> dydt) const
	Evaluates the right-hand-side f of the ODE dydt = f(y, t) recursively for each group. More...

template<size_t Group1, size_t Group2 = 0>
void	interact (Eigen::Ref< const Eigen::VectorX< FP >> pop, Eigen::Ref< const Eigen::VectorX< FP >> y, FP t, Eigen::Ref< Eigen::VectorX< FP >> dydt, double part_a, double part_b, int relevant_disease) const
	Calculates flows that are caused by people becoming infected (outflow from compartment S, Ra or Rb) for Group1. More...

Additional Inherited Members
Public Attributes inherited from mio::CompartmentalModel< FP, InfectionState, LctPopulations< FP, LctStates... >, Parameters< FP > >
ParameterSet	parameters

Populations	populations

Detailed Description

template<typename FP, class... LctStates>
class mio::lsecir2d::Model< FP, LctStates >

Class that defines an LCT-SECIR-2-DISEASE model.

Template Parameters

LctStates The LCT2D model can work with any number of LctStates, where each LctState corresponds to a group, e.g. one AgeGroup. The purpose of the LctStates is to define the number of subcompartments for each InfectionState. If you do not want to divide the population into groups, just use one LctState. If you want to divide the population according to more than one category, e.g. sex and age, you have to specify one LctState for each pair of groups, e.g. for (female, A00-A04), (female, A05-A14) etc. This is because the number of subcompartments can be different for each group. Therefore, the number of LctStates also determines the number of groups.

Member Typedef Documentation

◆ Base

template<typename FP , class... LctStates>

using mio::lsecir2d::Model< FP, LctStates >::Base = CompartmentalModel<FP, InfectionState, LctPopulations<FP, LctStates...>, Parameters<FP> >

◆ LctStatesGroups

template<typename FP , class... LctStates>

using mio::lsecir2d::Model< FP, LctStates >::LctStatesGroups = TypeList<LctStates...>

Constructor & Destructor Documentation

◆ Model() [1/2]

template<typename FP , class... LctStates>

mio::lsecir2d::Model< FP, LctStates >::Model ( )

inline

Default constructor.

◆ Model() [2/2]

template<typename FP , class... LctStates>

mio::lsecir2d::Model< FP, LctStates >::Model	(	const Populations &	pop,
		const ParameterSet &	params
	)

inline

Constructor using Populations and ParameterSet.

Parameters

[in]	pop	An instance of the Populations class.
[in]	params	Parameters used to be used in the simulation.

Member Function Documentation

◆ calculate_compartments()

template<typename FP , class... LctStates>

TimeSeries<FP> mio::lsecir2d::Model< FP, LctStates >::calculate_compartments ( const TimeSeries< FP > & subcompartments_ts ) const

inline

Cumulates a simulation result with subcompartments to produce a result that divides the population only into the infection states defined in InfectionState.

If the model is used for simulation, we will get a result in form of a TimeSeries with infection states divided in subcompartments. The function calculates a TimeSeries without subcompartments from another TimeSeries with subcompartments. This is done by summing up the numbers in the subcompartments.

Parameters

[in] subcompartments_ts Result of a simulation with the model.

Returns: Result of the simulation divided in infection states without subcompartments. Returns TimeSeries with values -1 if calculation is not possible.

◆ check_constraints()

template<typename FP , class... LctStates>

bool mio::lsecir2d::Model< FP, LctStates >::check_constraints ( ) const

inline

Checks that the model satisfies all constraints (e.g.

parameter or population constraints).

Returns: Returns true if one or more constraints are not satisfied, false otherwise.

◆ check_constraints_impl()

template<typename FP , class... LctStates>

template<size_t Group = 0>

bool mio::lsecir2d::Model< FP, LctStates >::check_constraints_impl ( ) const

inlineprivate

Checks whether LctState of a group satisfies all constraints.

Recursively, it checks that all groups satisfy the constraints.

Template Parameters

group The group for which the constraints should be checked.

Returns: Returns true if one or more constraints are not satisfied, false otherwise.

◆ compress_vector()

template<typename FP , class... LctStates>

template<size_t Group = 0>

void mio::lsecir2d::Model< FP, LctStates >::compress_vector	(	const Eigen::VectorX< FP > &	subcompartments,
		Eigen::VectorX< FP > &	compartments
	)		const

inlineprivate

Converts a vector with subcompartments in a vector without subcompartments by summing up subcompartment values.

This is done recursively for each group which corresponds to a slice of the vector.

Template Parameters

group The group specifying the slice of the vector being considered.

Parameters

[in]	subcompartments	The vector that should be converted.
[out]	compartments	Reference to the vector where the output is stored.

◆ get_derivatives()

template<typename FP , class... LctStates>

void mio::lsecir2d::Model< FP, LctStates >::get_derivatives	(	Eigen::Ref< const Eigen::VectorX< FP >>	pop,
		Eigen::Ref< const Eigen::VectorX< FP >>	y,
		FP	t,
		Eigen::Ref< Eigen::VectorX< FP >>	dydt
	)		const

inlineoverridevirtual

Evaluates the right-hand-side f of the ODE dydt = f(y, t).

The LCT-SECIR-2-DISEASE model is defined through ordinary differential equations of the form dydt = f(y, t). y is a vector containing the number of individuals for each (sub-) compartment. This function evaluates the right-hand-side f of the ODE and can be used in an ODE solver.

Parameters

[in]	pop	The current state of the population in the geographic unit we are considering.
[in]	y	The current state of the model (or a subpopulation) as a flat array.
[in]	t	The current time.
[out]	dydt	A reference to the calculated output.

Reimplemented from mio::CompartmentalModel< FP, InfectionState, LctPopulations< FP, LctStates... >, Parameters< FP > >.

◆ get_derivatives_impl()

template<typename FP , class... LctStates>

template<size_t Group = 0>

void mio::lsecir2d::Model< FP, LctStates >::get_derivatives_impl	(	Eigen::Ref< const Eigen::VectorX< FP >>	pop,
		Eigen::Ref< const Eigen::VectorX< FP >>	y,
		FP	t,
		Eigen::Ref< Eigen::VectorX< FP >>	dydt
	)		const

inlineprivate

Evaluates the right-hand-side f of the ODE dydt = f(y, t) recursively for each group.

See also the function get_derivative. For each group, one slice of the output vector is calculated.

Template Parameters

group The group specifying the slice of the vector being considered.

Parameters

[in]	pop	The current state of the population in the geographic unit we are considering.
[in]	y	The current state of the model (or a subpopulation) as a flat array.
[in]	t	The current time.
[out]	dydt	A reference to the calculated output.

◆ interact()

template<typename FP , class... LctStates>

template<size_t Group1, size_t Group2 = 0>

void mio::lsecir2d::Model< FP, LctStates >::interact	(	Eigen::Ref< const Eigen::VectorX< FP >>	pop,
		Eigen::Ref< const Eigen::VectorX< FP >>	y,
		FP	t,
		Eigen::Ref< Eigen::VectorX< FP >>	dydt,
		double *	part_a,
		double *	part_b,
		int	relevant_disease
	)		const

inlineprivate

Calculates flows that are caused by people becoming infected (outflow from compartment S, Ra or Rb) for Group1.

This is done recursively by calculating the interaction terms with each group.

Template Parameters

Group1	The group for which the derivative of the compartment should be calculated.
Group2	The group that Group1 interacts with.

Parameters

[in]	pop	The current state of the population in the geographic unit we are considering.
[in]	y	The current state of the model (or a subpopulation) as a flat array.
[in]	t	The current time.
[out]	dydt	A reference to the calculated output. The flow from Susceptible needs to be split into 2 parts for Exposed_1a and Exposed_1b:
[out]	part_a	Reference to amount of flow caused by people infected with disease a.
[out]	part_b	Reference to amount of flow caused by people infected with disease b.
[in]	relevant_disease	Index for which infected people cause the outflow (0 = a, 1 = b, 2 = a and b).

Member Data Documentation

◆ num_groups

template<typename FP , class... LctStates>

constexpr size_t mio::lsecir2d::Model< FP, LctStates >::num_groups = sizeof...(LctStates)

staticconstexpr

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

Public Types

Public Member Functions

Static Public Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

template<typename FP, class... LctStates> class mio::lsecir2d::Model< FP, LctStates >

Member Typedef Documentation

◆ Base

◆ LctStatesGroups

Constructor & Destructor Documentation

◆ Model() [1/2]

◆ Model() [2/2]

Member Function Documentation

◆ calculate_compartments()

◆ check_constraints()

◆ check_constraints_impl()

◆ compress_vector()

◆ get_derivatives()

◆ get_derivatives_impl()

◆ interact()

Member Data Documentation

◆ num_groups

Model< FP, LctStates > Class Template Reference

template<typename FP, class... LctStates>
class mio::lsecir2d::Model< FP, LctStates >