mio::CompartmentalModel< FP, Comp, Pop, Params > Struct Template Reference

CompartmentalModel is a template for a compartmental model for an array of initial populations and a parameter set. More...

#include <compartmental_model.h>

Inheritance diagram for mio::CompartmentalModel< FP, Comp, Pop, Params >:

Public Types
using	Compartments = Comp
using	ParameterSet = Params
using	Populations = Pop

Public Member Functions
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

Public Attributes
ParameterSet	parameters {}
Populations	populations {}

Detailed Description

template<typename FP, class Comp, class Pop, class Params>
struct mio::CompartmentalModel< FP, Comp, Pop, Params >

CompartmentalModel is a template for a compartmental model for an array of initial populations and a parameter set.

Template Parameters

FP	A floating point type, e.g., double.

The Populations must be a concrete class derived from the Populations template, i.e. a multi-dimensional array of compartment populations where each dimension corresponds to a category.

The ParameterSet must be a concrete class derived form the ParameterSet template, i.e. a compile-time map of parameters used by the model. These can be referenced when defining the flows between compartments and they can be used for parameter studies.

Member Typedef Documentation

Compartments

template<typename FP , class Comp , class Pop , class Params >

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

ParameterSet

template<typename FP , class Comp , class Pop , class Params >

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

Populations

template<typename FP , class Comp , class Pop , class Params >

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

Constructor & Destructor Documentation

CompartmentalModel() [1/3]

template<typename FP , class Comp , class Pop , class Params >

mio::CompartmentalModel< FP, Comp, Pop, Params >::CompartmentalModel ( Populations const &  po, ParameterSet const &  pa  )

inline

CompartmentalModel default constructor.

CompartmentalModel() [2/3]

template<typename FP , class Comp , class Pop , class Params >

mio::CompartmentalModel< FP, Comp, Pop, Params >::CompartmentalModel ( const CompartmentalModel< FP, Comp, Pop, Params > &  )

default

CompartmentalModel() [3/3]

template<typename FP , class Comp , class Pop , class Params >

mio::CompartmentalModel< FP, Comp, Pop, Params >::CompartmentalModel ( CompartmentalModel< FP, Comp, Pop, Params > &&  )

default

~CompartmentalModel()

template<typename FP , class Comp , class Pop , class Params >

virtual mio::CompartmentalModel< FP, Comp, Pop, Params >::~CompartmentalModel ( )

virtualdefault

Member Function Documentation

apply_constraints()

template<typename FP , class Comp , class Pop , class Params >

bool mio::CompartmentalModel< FP, Comp, Pop, Params >::apply_constraints ( )

inline

Checks whether the model satisfies all constraints.

If not, it changes values to suffice their constraints.

Attention: This function should be used with care. It can not and will not set model parameters and compartments to meaningful values. In most cases it is preferable to use check_constraints, and correct values manually before proceeding with the simulation. The main usage for apply_constraints is in automated tests using random values for initialization.

Returns

Returns true if one or more constraints were corrected, false otherwise.

check_constraints()

template<typename FP , class Comp , class Pop , class Params >

bool mio::CompartmentalModel< FP, Comp, Pop, Params >::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.

eval_right_hand_side()

template<typename FP , class Comp , class Pop , class Params >

void mio::CompartmentalModel< FP, Comp, Pop, Params >::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

inline

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

The heart of the compartmental model is a first order ODE dydt = f(y,t), where y is a flat representation of all the compartmental populations at time t. This function evaluates the right-hand-side f of the ODE from the intercompartmental flows. It can be used in an ODE solver.

The distinction between pop and y is only for the case of mobility. If we have mobility, we want to evaluate the evolution of infection states for a small group of travellers (y) while they are in any population (pop). It is important that pop > y always applies.

If we consider a simulation without mobility, the function is called with model.eval_right_hand_side(y, y, t, dydt).

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.

get_derivatives()

template<typename FP , class Comp , class Pop , class Params >

virtual void mio::CompartmentalModel< FP, Comp, Pop, Params >::get_derivatives ( Eigen::Ref< const Eigen::VectorX< FP >>  , Eigen::Ref< const Eigen::VectorX< FP >>  , FP  , Eigen::Ref< Eigen::VectorX< FP >>    ) const

inlinevirtual

Reimplemented in mio::oseair::Model< FP >, mio::osir::Model< FP >, mio::lsecir2d::Model< FP, LctStates >, mio::lsecir::Model< FP, LctStates >, mio::glsecir::Model< FP, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms, NumInfectedSevere, NumInfectedCritical >, mio::FlowModel< FP, Comp, Pop, Params, Flows >, mio::FlowModel< FP, InfectionState, Populations< FP, AgeGroup, InfectionState >, Parameters< FP >, Flows >, and mio::FlowModel< FP, InfectionState, mio::Populations< FP, AgeGroup, InfectionState >, Parameters< FP >, Flows >.

get_initial_values()

template<typename FP , class Comp , class Pop , class Params >

Eigen::VectorX<FP> mio::CompartmentalModel< FP, Comp, Pop, Params >::get_initial_values ( ) const

inline

Get the initial conditions for the ODE dydt = f(y, t).

See eval_right_hand_side for more detail.

Returns

Current value of model populations as a flat vector.

operator=() [1/2]

template<typename FP , class Comp , class Pop , class Params >

CompartmentalModel& mio::CompartmentalModel< FP, Comp, Pop, Params >::operator= ( CompartmentalModel< FP, Comp, Pop, Params > &&  )

default

operator=() [2/2]

template<typename FP , class Comp , class Pop , class Params >

CompartmentalModel& mio::CompartmentalModel< FP, Comp, Pop, Params >::operator= ( const CompartmentalModel< FP, Comp, Pop, Params > &  )

default

Member Data Documentation

parameters

template<typename FP , class Comp , class Pop , class Params >

ParameterSet mio::CompartmentalModel< FP, Comp, Pop, Params >::parameters {}

populations

template<typename FP , class Comp , class Pop , class Params >

Populations mio::CompartmentalModel< FP, Comp, Pop, Params >::populations {}