mio::lsecir::Initializer< FP, Model > Class Template Reference

Class that can be used to compute an initialization vector out of flows for an LCT Model with division in groups. More...

#include <initializer_flows.h>

Collaboration diagram for mio::lsecir::Initializer< FP, Model >:

Public Types
using	LctStatesGroups = typename Model::LctStatesGroups

Public Member Functions
bool	compute_initialization_vector (Eigen::VectorX< FP > const &total_population, Eigen::VectorX< FP > const &deaths, Eigen::VectorX< FP > const &total_confirmed_cases)
	Core function of Initializer. More...
	Initializer (TimeSeries< FP > &&flows, Model &model)
	Constructs a new Initializer object. More...
void	set_tol_for_support_max (FP new_tol)
	Setter for the tolerance used to calculate the maximum support of ErlangDensitys. More...

Private Member Functions
bool	check_constraints () const
	Checks constraints of the Initializer including checks for the model. More...
template<InfectionState State, size_t Group>
bool	compute_compartment (Eigen::VectorX< FP > &init, Eigen::Index idx_incoming_flow, FP transition_rate) const
	Computes a slice of the initial value vector for each subcompartment of one InfectionState for a specified group. More...
template<size_t Group = 0>
bool	compute_initialization_vector_impl (Eigen::VectorX< FP > &init, Eigen::VectorX< FP > const &total_population, Eigen::VectorX< FP > const &deaths, Eigen::VectorX< FP > const &total_confirmed_cases)
	Implementation of the calculation of the initial value vector slice that corresponds to a specified group. More...

Private Attributes
FP	m_dt {}
	Step size of the times in m_flows and time step for the approximation of the integral. More...
TimeSeries< FP >	m_flows
	TimeSeries with the flows which are used to calculate the initial vector. More...
Model &	m_model
	The LCT-SECIR model for which the initialization should be performed. More...
FP	m_tol {1e-10}
	Tolerance used to calculate the maximum support of the ErlangDensitys. More...

Detailed Description

template<typename FP, typename Model>
class mio::lsecir::Initializer< FP, Model >

Class that can be used to compute an initialization vector out of flows for an LCT Model with division in groups.

The initialization method is based on the fact that the LCT model is a special case of an IDE model with special choices of stay time distributions (so-called Erlang distributions). Accordingly, the method for calculating initial values for the compartments from given flows/transitions is taken from the IDE-SECIR model. We cannot use the functionality of the IDE model directly, as we have to calculate a division into sub-compartments and not only the sizes of the compartments. See also the IDE-SECIR model for the general method and for a better understanding of flows/transitions.

Template Parameters

Model

is expected to be an LCT-SECIR model defined in models/lct_secir/model.h.

Member Typedef Documentation

LctStatesGroups

template<typename FP , typename Model >

using mio::lsecir::Initializer< FP, Model >::LctStatesGroups = typename Model::LctStatesGroups

Constructor & Destructor Documentation

Initializer()

template<typename FP , typename Model >

mio::lsecir::Initializer< FP, Model >::Initializer ( TimeSeries< FP > &&  flows, Model &  model  )

inline

Constructs a new Initializer object.

Parameters

[in]	flows	Initializing TimeSeries with flows fitting to these defined in InfectionTransition. For each group of m_model, InfectionTransition::Count entries are required. Timesteps should be equidistant and the values should be non-negative. The time history has to be long enough so that it is possible to calculate the initial vector. The length of the required time history depends on the Erlang densities used to compute the initial vector.
[in,out]	model	The LCT-SECIR model for which the initialization should be performed.

Member Function Documentation

check_constraints()

template<typename FP , typename Model >

bool mio::lsecir::Initializer< FP, Model >::check_constraints ( ) const

inlineprivate

Checks constraints of the Initializer including checks for the model.

Returns

Returns true if one (or more) constraint(s) are not satisfied, otherwise false.

compute_compartment()

template<typename FP , typename Model >

template<InfectionState State, size_t Group>

bool mio::lsecir::Initializer< FP, Model >::compute_compartment ( Eigen::VectorX< FP > &  init, Eigen::Index  idx_incoming_flow, FP  transition_rate  ) const

inlineprivate

Computes a slice of the initial value vector for each subcompartment of one InfectionState for a specified group.

Template Parameters

Group	The group for which the corresponding slice of the initial value vector is calculated.
State	The InfectionState for which the corresponding slice of the initial value vector is calculated

Parameters

[out]	init	The initial value vector under consideration.
[in]	idx_incoming_flow	Index of the flow which is relevant for the calculation, so the flow to the InfectionState.
[in]	transition_rate	Specifies the transition rate of the InfectionState. 'This is equal to 1 / (expected time in the InfectionState).

Returns

Returns true if one (or more) constraint(s) of the computed slice of the initial value vector are not satisfied, otherwise false.

compute_initialization_vector()

template<typename FP , typename Model >

bool mio::lsecir::Initializer< FP, Model >::compute_initialization_vector ( Eigen::VectorX< FP > const &  total_population, Eigen::VectorX< FP > const &  deaths, Eigen::VectorX< FP > const &  total_confirmed_cases  )

inline

Core function of Initializer.

Computes a vector that can be used for the initialization of an LCT model stratified by groups with the number of persons for each subcompartment for each group. The initial value vector is updated in the model.

Parameters

[in]	total_population	The total size of the considered population.
[in]	deaths	Number of deceased people from the disease at time 0.
[in]	total_confirmed_cases	Total number of confirmed cases at time 0.

Returns

Returns true if one (or more) constraint(s) of the model, the initial flows or the computed initial value vector are not satisfied, otherwise false.

compute_initialization_vector_impl()

template<typename FP , typename Model >

template<size_t Group = 0>

bool mio::lsecir::Initializer< FP, Model >::compute_initialization_vector_impl ( Eigen::VectorX< FP > &  init, Eigen::VectorX< FP > const &  total_population, Eigen::VectorX< FP > const &  deaths, Eigen::VectorX< FP > const &  total_confirmed_cases  )

inlineprivate

Implementation of the calculation of the initial value vector slice that corresponds to a specified group.

Computes a vector that can be used for the initialization of an LCT model stratified by groups with the number of persons for each subcompartment. The groups are calculated recursively.

Template Parameters

Group

The group for which the corresponding slice of the initial value vector is calculated.

Parameters

[out]	init	The initial value vector under consideration.
[in]	total_population	The total size of the considered population.
[in]	deaths	Number of deceased people from the disease at time 0.
[in]	total_confirmed_cases	Total number of confirmed cases at time 0.

Returns

Returns true if one (or more) constraint(s) of the computed initial value vector are not satisfied, otherwise false.

set_tol_for_support_max()

template<typename FP , typename Model >

void mio::lsecir::Initializer< FP, Model >::set_tol_for_support_max ( FP  new_tol )

inline

Setter for the tolerance used to calculate the maximum support of ErlangDensitys.

Parameters

[in]

new_tol

New tolerance.

Member Data Documentation

m_dt

template<typename FP , typename Model >

FP mio::lsecir::Initializer< FP, Model >::m_dt {}

private

Step size of the times in m_flows and time step for the approximation of the integral.

m_flows

template<typename FP , typename Model >

TimeSeries<FP> mio::lsecir::Initializer< FP, Model >::m_flows

private

TimeSeries with the flows which are used to calculate the initial vector.

m_model

template<typename FP , typename Model >

Model& mio::lsecir::Initializer< FP, Model >::m_model

private

The LCT-SECIR model for which the initialization should be performed.

m_tol

template<typename FP , typename Model >

FP mio::lsecir::Initializer< FP, Model >::m_tol {1e-10}

private

Tolerance used to calculate the maximum support of the ErlangDensitys.