mio::isecir Namespace Reference

Classes
struct	ContactPatterns
	The contact patterns within the society are modelled using an UncertainContactMatrix. More...
class	Model
class	Parameters
	Parameters of an age-resolved SECIR/SECIHURD model. More...
struct	RelativeTransmissionNoSymptoms
	The relative InfectedNoSymptoms infectability. More...
struct	RiskOfInfectionFromSymptomatic
	The risk of infection from symptomatic cases in the SECIR model. More...
struct	Seasonality
	The seasonality parameter k in the IDE-SECIR model. More...
class	Simulation
	run the simulation in discrete steps and report results. More...
struct	StartDay
	Sets the day in a year at which a simulation with an IDE-SECIR model is started. More...
struct	TransitionDistributions
	Transition distribution for each transition in InfectionTransition. More...
struct	TransitionProbabilities
	Defines the probability for each possible transition to take this flow/transition. More...
struct	TransmissionProbabilityOnContact
	Probability of getting infected from a contact. More...

Typedefs
using	ParametersBase = ParameterSet< TransitionDistributions, TransitionProbabilities, ContactPatterns, TransmissionProbabilityOnContact, RelativeTransmissionNoSymptoms, RiskOfInfectionFromSymptomatic, StartDay, Seasonality >

Enumerations
enum class	InfectionState {   Susceptible = 0 , Exposed = 1 , InfectedNoSymptoms = 2 , InfectedSymptoms = 3 ,   InfectedSevere = 4 , InfectedCritical = 5 , Recovered = 6 , Dead = 7 ,   Count = 8 }
	The #InfectionState enum describes the possible categories for the infectious state of persons. More...
enum class	InfectionTransition {   SusceptibleToExposed = 0 , ExposedToInfectedNoSymptoms = 1 , InfectedNoSymptomsToInfectedSymptoms = 2 , InfectedNoSymptomsToRecovered = 3 ,   InfectedSymptomsToInfectedSevere = 4 , InfectedSymptomsToRecovered = 5 , InfectedSevereToInfectedCritical = 6 , InfectedSevereToRecovered = 7 ,   InfectedCriticalToDead = 8 , InfectedCriticalToRecovered = 9 , Count = 10 }
	The #InfectionTransition enum describes the possible transitions of the infectious state of persons. More...

Functions
template<typename EntryType >
IOResult< void >	set_initial_flows (Model &model, const ScalarType dt, const std::vector< EntryType > rki_data, const Date date, const CustomIndexArray< ScalarType, AgeGroup > scale_confirmed_cases)
TimeSeries< ScalarType >	simulate (ScalarType tmax, ScalarType dt, Model const &model)
	Run a Simulation of an IDE-SECIR model. More...

Variables
static constexpr size_t	InfectionTransitionsCount = 10
static const std::array< std::pair< InfectionState, InfectionState >, InfectionTransitionsCount >	InfectionTransitionsMap

Typedef Documentation

ParametersBase

using mio::isecir::ParametersBase = typedef ParameterSet<TransitionDistributions, TransitionProbabilities, ContactPatterns, TransmissionProbabilityOnContact, RelativeTransmissionNoSymptoms, RiskOfInfectionFromSymptomatic, StartDay, Seasonality>

Enumeration Type Documentation

InfectionState

enum mio::isecir::InfectionState

strong

The InfectionState enum describes the possible categories for the infectious state of persons.

Enumerator
Susceptible
Exposed
InfectedNoSymptoms
InfectedSymptoms
InfectedSevere
InfectedCritical
Recovered
Dead
Count

InfectionTransition

enum mio::isecir::InfectionTransition

strong

The InfectionTransition enum describes the possible transitions of the infectious state of persons.

Enumerator
SusceptibleToExposed
ExposedToInfectedNoSymptoms
InfectedNoSymptomsToInfectedSymptoms
InfectedNoSymptomsToRecovered
InfectedSymptomsToInfectedSevere
InfectedSymptomsToRecovered
InfectedSevereToInfectedCritical
InfectedSevereToRecovered
InfectedCriticalToDead
InfectedCriticalToRecovered
Count

Function Documentation

set_initial_flows()

template<typename EntryType >

IOResult<void> mio::isecir::set_initial_flows	(	Model &	model,
		const ScalarType	dt,
		const std::vector< EntryType >	rki_data,
		const Date	date,
		const CustomIndexArray< ScalarType, AgeGroup >	scale_confirmed_cases
	)

simulate()

TimeSeries< ScalarType > mio::isecir::simulate	(	ScalarType	tmax,
		ScalarType	dt,
		Model const &	model
	)

Run a Simulation of an IDE-SECIR model.

Parameters

[in]	tmax	End time.
[in]	dt	Initial step size of integration.
[in]	model	An instance of an IDE-SECIR model.

Returns

A TimeSeries to represent the final simulation result.

Variable Documentation

InfectionTransitionsCount

constexpr size_t mio::isecir::InfectionTransitionsCount = 10

staticconstexpr

InfectionTransitionsMap

const std::array<std::pair<InfectionState, InfectionState>, InfectionTransitionsCount> mio::isecir::InfectionTransitionsMap

static

Initial value:

=
    {std::make_pair(InfectionState::Susceptible, InfectionState::Exposed),
     std::make_pair(InfectionState::Exposed, InfectionState::InfectedNoSymptoms),
     std::make_pair(InfectionState::InfectedNoSymptoms, InfectionState::InfectedSymptoms),
     std::make_pair(InfectionState::InfectedNoSymptoms, InfectionState::Recovered),
     std::make_pair(InfectionState::InfectedSymptoms, InfectionState::InfectedSevere),
     std::make_pair(InfectionState::InfectedSymptoms, InfectionState::Recovered),
     std::make_pair(InfectionState::InfectedSevere, InfectionState::InfectedCritical),
     std::make_pair(InfectionState::InfectedSevere, InfectionState::Recovered),
     std::make_pair(InfectionState::InfectedCritical, InfectionState::Dead),
     std::make_pair(InfectionState::InfectedCritical, InfectionState::Recovered)}