mio::glsecir::Model< FP, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical > Class Template Reference

Class that defines an GLCT-SECIR model. More...

#include <model.h>

Inheritance diagram for mio::glsecir::Model< FP, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical >:

Collaboration diagram for mio::glsecir::Model< FP, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical >:

Public Types
using	Base = CompartmentalModel< FP, LctState, mio::Populations< FP, LctState >, Parameters< FP > >
using	LctState = LctInfectionState< FP, InfectionState, 1, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical, 1, 1 >
	This class specifies the number of subcompartments. More...
using	ParameterSet = Params
using	Populations = Pop
Public Types inherited from mio::CompartmentalModel< FP, LctInfectionState< FP, InfectionState, 1, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical, 1, 1 >, mio::Populations< FP, LctInfectionState< FP, InfectionState, 1, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical, 1, 1 > >, Parameters< FP > >
using	Compartments = LctInfectionState< FP, InfectionState, 1, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical, 1, 1 >
using	ParameterSet = Parameters< FP >
using	Populations = mio::Populations< FP, LctInfectionState< FP, InfectionState, 1, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical, 1, 1 > >

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 GLCT dydt = f(y, t). More...
	Model ()
	Default constructor. More...
Public Member Functions inherited from mio::CompartmentalModel< FP, LctInfectionState< FP, InfectionState, 1, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical, 1, 1 >, mio::Populations< FP, LctInfectionState< FP, InfectionState, 1, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical, 1, 1 > >, 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

Additional Inherited Members
Public Attributes inherited from mio::CompartmentalModel< FP, LctInfectionState< FP, InfectionState, 1, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical, 1, 1 >, mio::Populations< FP, LctInfectionState< FP, InfectionState, 1, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical, 1, 1 > >, Parameters< FP > >
ParameterSet	parameters
Populations	populations

Detailed Description

template<typename FP, size_t NumExposed, size_t NumInfectedNoSymptoms, size_t NumInfectedSymptoms, size_t NumInfectedSevere, size_t NumInfectedCritical>
class mio::glsecir::Model< FP, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical >

Class that defines an GLCT-SECIR model.

Template Parameters

NumExposed	The number of subcompartments used for the Exposed compartment.
NumInfectedNoSymptoms	The number of subcompartments used for the InfectedNoSymptoms compartment.
NumInfectedSymptoms	The number of subcompartments used for the InfectedSymptoms compartment.
NumInfectedSevere	The number of subcompartments used for the InfectedSevere compartment.
NumInfectedCritical	The number of subcompartments used for the InfectedCritical compartment.

Member Typedef Documentation

Base

template<typename FP , size_t NumExposed, size_t NumInfectedNoSymptoms, size_t NumInfectedSymptoms, size_t NumInfectedSevere, size_t NumInfectedCritical>

using mio::glsecir::Model< FP, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical >::Base = CompartmentalModel<FP, LctState, mio::Populations<FP, LctState>, Parameters<FP> >

LctState

template<typename FP , size_t NumExposed, size_t NumInfectedNoSymptoms, size_t NumInfectedSymptoms, size_t NumInfectedSevere, size_t NumInfectedCritical>

using mio::glsecir::Model< FP, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical >::LctState = LctInfectionState<FP, InfectionState, 1, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical, 1, 1>

This class specifies the number of subcompartments.

ParameterSet

template<typename FP , size_t NumExposed, size_t NumInfectedNoSymptoms, size_t NumInfectedSymptoms, size_t NumInfectedSevere, size_t NumInfectedCritical>

using mio::CompartmentalModel< FP, Comp, Pop, Params >::ParameterSet = Params

Populations

template<typename FP , size_t NumExposed, size_t NumInfectedNoSymptoms, size_t NumInfectedSymptoms, size_t NumInfectedSevere, size_t NumInfectedCritical>

using mio::CompartmentalModel< FP, Comp, Pop, Params >::Populations = Pop

Constructor & Destructor Documentation

Model()

template<typename FP , size_t NumExposed, size_t NumInfectedNoSymptoms, size_t NumInfectedSymptoms, size_t NumInfectedSevere, size_t NumInfectedCritical>

mio::glsecir::Model< FP, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical >::Model ( )

inline

Default constructor.

Member Function Documentation

calculate_compartments()

template<typename FP , size_t NumExposed, size_t NumInfectedNoSymptoms, size_t NumInfectedSymptoms, size_t NumInfectedSevere, size_t NumInfectedCritical>

TimeSeries<FP> mio::glsecir::Model< FP, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical >::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 corresponding 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 , size_t NumExposed, size_t NumInfectedNoSymptoms, size_t NumInfectedSymptoms, size_t NumInfectedSevere, size_t NumInfectedCritical>

bool mio::glsecir::Model< FP, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical >::check_constraints ( ) const

inline

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

parameter or population constraints), and logs an error if constraints are not satisfied.

Returns

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

get_derivatives()

template<typename FP , size_t NumExposed, size_t NumInfectedNoSymptoms, size_t NumInfectedSymptoms, size_t NumInfectedSevere, size_t NumInfectedCritical>

void mio::glsecir::Model< FP, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical >::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 GLCT dydt = f(y, t).

The GLCT-SECIR model is defined through ordinary differential equations of the form dydt = f(y, t). y is a vector containing 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, LctInfectionState< FP, InfectionState, 1, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical, 1, 1 >, mio::Populations< FP, LctInfectionState< FP, InfectionState, 1, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical, 1, 1 > >, Parameters< FP > >.