mio::oseir::Model< FP > Class Template Reference

#include <model.h>

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

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

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
IOResult< FP >	get_reproduction_number (FP t_value, const mio::TimeSeries< FP > &y)
	Computes the reproduction number at a given time point of the Model output obtained by the Simulation. More...
IOResult< FP >	get_reproduction_number (size_t t_idx, const mio::TimeSeries< FP > &y)
	Computes the reproduction number at a given index time of the Model output obtained by the Simulation. More...
Eigen::VectorX< FP >	get_reproduction_numbers (const mio::TimeSeries< FP > &y)
	Computes the reproduction number for all time points of the Model output obtained by the Simulation. More...
	Model (const Populations &pop, const ParameterSet &params)
	Model (int num_agegroups)
template<class IOContext >
void	serialize (IOContext &io) const
	serialize this. More...
Public Member Functions inherited from mio::FlowModel< FP, InfectionState, mio::Populations< FP, AgeGroup, InfectionState >, Parameters< FP >, Flows >
	FlowModel (Args... args)
	Default constructor, forwarding args to Base constructor. More...
void	get_derivatives (Eigen::Ref< const Eigen::VectorX< FP >> flows, Eigen::Ref< Eigen::VectorX< FP >> 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< FP >> pop, Eigen::Ref< const Eigen::VectorX< FP >> y, FP t, Eigen::Ref< Eigen::VectorX< FP >> 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...
Eigen::VectorX< FP >	get_initial_flows () const
	Initial values for flows. More...
Public Member Functions inherited from mio::CompartmentalModel< FP, InfectionState, mio::Populations< FP, AgeGroup, InfectionState >, 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 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, AgeGroup, InfectionState >, Parameters< FP >, Flows >

Additional Inherited Members
Public Types inherited from mio::FlowModel< FP, InfectionState, mio::Populations< FP, AgeGroup, InfectionState >, Parameters< FP >, Flows >
using	Base = CompartmentalModel< FP, InfectionState, mio::Populations< FP, AgeGroup, InfectionState >, Parameters< FP > >
Public Types inherited from mio::CompartmentalModel< FP, InfectionState, mio::Populations< FP, AgeGroup, InfectionState >, Parameters< FP > >
using	Compartments = InfectionState
using	ParameterSet = Parameters< FP >
using	Populations = mio::Populations< FP, AgeGroup, InfectionState >
Public Attributes inherited from mio::CompartmentalModel< FP, InfectionState, mio::Populations< FP, AgeGroup, InfectionState >, Parameters< FP > >
ParameterSet	parameters
Populations	populations

Member Typedef Documentation

Base

template<typename FP >

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

private

Constructor & Destructor Documentation

Model() [1/2]

template<typename FP >

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

inline

Model() [2/2]

template<typename FP >

mio::oseir::Model< FP >::Model ( int  num_agegroups )

inline

Member Function Documentation

deserialize()

template<typename FP >

template<class IOContext >

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

inlinestatic

deserialize an object of this class.

See also

mio::deserialize

get_flows()

template<typename FP >

void mio::oseir::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

inlineoverridevirtual

Implements mio::FlowModel< FP, InfectionState, mio::Populations< FP, AgeGroup, InfectionState >, Parameters< FP >, Flows >.

get_reproduction_number() [1/2]

template<typename FP >

IOResult<FP> mio::oseir::Model< FP >::get_reproduction_number ( FP  t_value, const mio::TimeSeries< FP > &  y  )

inline

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

If the particular time point is not inside the output, a linearly interpolated value is returned.

Parameters

t_value	The time point at which the reproduction number is computed.
y	The TimeSeries obtained from the Model Simulation.

Returns

The computed reproduction number at the provided time point, potentially using linear interpolation.

get_reproduction_number() [2/2]

template<typename FP >

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

inline

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

Parameters

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

Returns

The computed reproduction number at the provided index time.

get_reproduction_numbers()

template<typename FP >

Eigen::VectorX<FP> mio::oseir::Model< FP >::get_reproduction_numbers ( const mio::TimeSeries< FP > &  y )

inline

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

Parameters

y	The TimeSeries obtained from the Model Simulation.

Returns

vector containing all reproduction numbers

serialize()

template<typename FP >

template<class IOContext >

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

inline

serialize this.

See also

mio::serialize