osecirvvs Namespace Reference

CPP API: mio::osecirvvs Namespace Reference

CPP API

Classes
struct	ContactPatterns
	the contact patterns within the society are modelled using an UncertainContactMatrix More...

struct	CriticalPerSevere
	the percentage of ICU patients per hospitalized patients in the SECIR model More...

struct	DailyFullVaccinations
	Total number of full vaccinations up to the given day. More...

struct	DailyPartialVaccinations
	Total number of first vaccinations up to the given day. More...

struct	DaysUntilEffectiveImprovedImmunity
	Time in days until second vaccine dose takes full effect. More...

struct	DaysUntilEffectivePartialImmunity
	Time in days until first vaccine dose takes full effect. More...

struct	DeathsPerCritical
	the percentage of dead patients per ICU patients in the SECIR model More...

struct	DynamicNPIsImplementationDelay
	The delay with which DynamicNPIs are implemented and enforced after exceedance of threshold. More...

struct	DynamicNPIsInfectedSymptoms
	the NPIs that are enforced if certain infection thresholds are exceeded. More...

struct	ICUCapacity
	the icu capacity in the SECIR model More...

struct	InfectiousnessNewVariant
	Represents the relative infectiousness of a new variant. More...

struct	MaxRiskOfInfectionFromSymptomatic
	risk of infection from symptomatic cases increases as test and trace capacity is exceeded. More...

class	Model

class	Parameters
	Parameters of an age-resolved SECIR/SECIHURD model with paths for partial and improved immunity through vaccination. More...

struct	RecoveredPerInfectedNoSymptoms
	the percentage of asymptomatic cases in the SECIR model More...

struct	ReducExposedImprovedImmunity
	Factor to reduce infection risk for persons with improved immunity. More...

struct	ReducExposedPartialImmunity
	Factor to reduce infection risk for persons with partial immunity. More...

struct	ReducInfectedSevereCriticalDeadImprovedImmunity
	Factor to reduce risk of hospitalization for persons with improved immunity. More...

struct	ReducInfectedSevereCriticalDeadPartialImmunity
	Factor to reduce risk of hospitalization for persons with partial immunity. More...

struct	ReducInfectedSymptomsImprovedImmunity
	Factor to reduce risk of developing symptoms for persons with improved immunity. More...

struct	ReducInfectedSymptomsPartialImmunity
	Factor to reduce risk of developing symptoms for persons with partial immunity. More...

struct	ReducTimeInfectedMild
	Factor to reduce infectious time of persons with partial or improved immunity. 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 in the SECIR model the seasonality is given as (1+k*sin()) where the sine curve is below one in summer and above one in winter More...

struct	SeverePerInfectedSymptoms
	the percentage of hospitalized patients per infected patients in the SECIR model More...

class	Simulation
	specialization of compartment model simulation for the SECIRVVS model. More...

struct	StartDay
	the start day in the SECIRVVS model The start day defines in which season the simulation can be started If the start day is 180 and simulation takes place from t0=0 to tmax=100 the days 180 to 280 of the year are simulated More...

struct	StartDayNewVariant
	the start day of a new variant in the SECIRVVS model The start day of the new variant defines in which day of the simulation the new variant is introduced. More...

struct	TestAndTraceCapacity
	capacity to test and trace contacts of infected for quarantine per day. More...

struct	TestAndTraceCapacityMaxRiskNoSymptoms
	Multiplier for the test and trace capacity to determine when it is considered overloaded from cases without symptoms. More...

struct	TestAndTraceCapacityMaxRiskSymptoms
	Multiplier for the test and trace capacity to determine when it is considered overloaded by symptomatic cases. More...

struct	TimeExposed
	the (mean) latent time in day unit More...

struct	TimeInfectedCritical
	the time people are treated by ICU before returning home in the SECIR model in day unit More...

struct	TimeInfectedNoSymptoms
	the (mean) time in day unit for asymptomatic cases that are infected but have not yet developed symptoms. More...

struct	TimeInfectedSevere
	the time people are 'simply' hospitalized before returning home in the SECIR model in day unit More...

struct	TimeInfectedSymptoms
	the infectious time for symptomatic cases that are infected but who do not need to be hospitalized in the SECIR model in day unit More...

struct	TransmissionProbabilityOnContact
	probability of getting infected from a contact More...

struct	VaccinationGap
	Time in days between first and second vaccine dose. More...

Typedefs
using	Flows = TypeList< Flow< InfectionState::SusceptibleNaive, InfectionState::ExposedNaive >, Flow< InfectionState::ExposedNaive, InfectionState::InfectedNoSymptomsNaive >, Flow< InfectionState::InfectedNoSymptomsNaive, InfectionState::InfectedSymptomsNaive >, Flow< InfectionState::InfectedNoSymptomsNaive, InfectionState::SusceptibleImprovedImmunity >, Flow< InfectionState::InfectedNoSymptomsNaiveConfirmed, InfectionState::InfectedSymptomsNaiveConfirmed >, Flow< InfectionState::InfectedNoSymptomsNaiveConfirmed, InfectionState::SusceptibleImprovedImmunity >, Flow< InfectionState::InfectedSymptomsNaive, InfectionState::InfectedSevereNaive >, Flow< InfectionState::InfectedSymptomsNaive, InfectionState::SusceptibleImprovedImmunity >, Flow< InfectionState::InfectedSymptomsNaiveConfirmed, InfectionState::InfectedSevereNaive >, Flow< InfectionState::InfectedSymptomsNaiveConfirmed, InfectionState::SusceptibleImprovedImmunity >, Flow< InfectionState::InfectedSevereNaive, InfectionState::InfectedCriticalNaive >, Flow< InfectionState::InfectedSevereNaive, InfectionState::SusceptibleImprovedImmunity >, Flow< InfectionState::InfectedSevereNaive, InfectionState::DeadNaive >, Flow< InfectionState::InfectedCriticalNaive, InfectionState::DeadNaive >, Flow< InfectionState::InfectedCriticalNaive, InfectionState::SusceptibleImprovedImmunity >, Flow< InfectionState::SusceptiblePartialImmunity, InfectionState::ExposedPartialImmunity >, Flow< InfectionState::ExposedPartialImmunity, InfectionState::InfectedNoSymptomsPartialImmunity >, Flow< InfectionState::InfectedNoSymptomsPartialImmunity, InfectionState::InfectedSymptomsPartialImmunity >, Flow< InfectionState::InfectedNoSymptomsPartialImmunity, InfectionState::SusceptibleImprovedImmunity >, Flow< InfectionState::InfectedNoSymptomsPartialImmunityConfirmed, InfectionState::InfectedSymptomsPartialImmunityConfirmed >, Flow< InfectionState::InfectedNoSymptomsPartialImmunityConfirmed, InfectionState::SusceptibleImprovedImmunity >, Flow< InfectionState::InfectedSymptomsPartialImmunity, InfectionState::InfectedSeverePartialImmunity >, Flow< InfectionState::InfectedSymptomsPartialImmunity, InfectionState::SusceptibleImprovedImmunity >, Flow< InfectionState::InfectedSymptomsPartialImmunityConfirmed, InfectionState::InfectedSeverePartialImmunity >, Flow< InfectionState::InfectedSymptomsPartialImmunityConfirmed, InfectionState::SusceptibleImprovedImmunity >, Flow< InfectionState::InfectedSeverePartialImmunity, InfectionState::InfectedCriticalPartialImmunity >, Flow< InfectionState::InfectedSeverePartialImmunity, InfectionState::SusceptibleImprovedImmunity >, Flow< InfectionState::InfectedSeverePartialImmunity, InfectionState::DeadPartialImmunity >, Flow< InfectionState::InfectedCriticalPartialImmunity, InfectionState::DeadPartialImmunity >, Flow< InfectionState::InfectedCriticalPartialImmunity, InfectionState::SusceptibleImprovedImmunity >, Flow< InfectionState::SusceptibleImprovedImmunity, InfectionState::ExposedImprovedImmunity >, Flow< InfectionState::ExposedImprovedImmunity, InfectionState::InfectedNoSymptomsImprovedImmunity >, Flow< InfectionState::InfectedNoSymptomsImprovedImmunity, InfectionState::InfectedSymptomsImprovedImmunity >, Flow< InfectionState::InfectedNoSymptomsImprovedImmunity, InfectionState::SusceptibleImprovedImmunity >, Flow< InfectionState::InfectedNoSymptomsImprovedImmunityConfirmed, InfectionState::InfectedSymptomsImprovedImmunityConfirmed >, Flow< InfectionState::InfectedNoSymptomsImprovedImmunityConfirmed, InfectionState::SusceptibleImprovedImmunity >, Flow< InfectionState::InfectedSymptomsImprovedImmunity, InfectionState::InfectedSevereImprovedImmunity >, Flow< InfectionState::InfectedSymptomsImprovedImmunity, InfectionState::SusceptibleImprovedImmunity >, Flow< InfectionState::InfectedSymptomsImprovedImmunityConfirmed, InfectionState::InfectedSevereImprovedImmunity >, Flow< InfectionState::InfectedSymptomsImprovedImmunityConfirmed, InfectionState::SusceptibleImprovedImmunity >, Flow< InfectionState::InfectedSevereImprovedImmunity, InfectionState::InfectedCriticalImprovedImmunity >, Flow< InfectionState::InfectedSevereImprovedImmunity, InfectionState::SusceptibleImprovedImmunity >, Flow< InfectionState::InfectedSevereImprovedImmunity, InfectionState::DeadImprovedImmunity >, Flow< InfectionState::InfectedCriticalImprovedImmunity, InfectionState::DeadImprovedImmunity >, Flow< InfectionState::InfectedCriticalImprovedImmunity, InfectionState::SusceptibleImprovedImmunity > >

template<typename FP >
using	ParametersBase = ParameterSet< StartDay< FP >, Seasonality< FP >, ICUCapacity< FP >, TestAndTraceCapacity< FP >, TestAndTraceCapacityMaxRiskNoSymptoms< FP >, TestAndTraceCapacityMaxRiskSymptoms< FP >, ContactPatterns< FP >, DynamicNPIsImplementationDelay< FP >, DynamicNPIsInfectedSymptoms< FP >, TimeExposed< FP >, TimeInfectedNoSymptoms< FP >, TimeInfectedSymptoms< FP >, TimeInfectedSevere< FP >, TimeInfectedCritical< FP >, TransmissionProbabilityOnContact< FP >, RelativeTransmissionNoSymptoms< FP >, RecoveredPerInfectedNoSymptoms< FP >, RiskOfInfectionFromSymptomatic< FP >, MaxRiskOfInfectionFromSymptomatic< FP >, SeverePerInfectedSymptoms< FP >, CriticalPerSevere< FP >, DeathsPerCritical< FP >, VaccinationGap< FP >, DaysUntilEffectivePartialImmunity< FP >, DaysUntilEffectiveImprovedImmunity< FP >, DailyFullVaccinations< FP >, DailyPartialVaccinations< FP >, ReducExposedPartialImmunity< FP >, ReducExposedImprovedImmunity< FP >, ReducInfectedSymptomsPartialImmunity< FP >, ReducInfectedSymptomsImprovedImmunity< FP >, ReducInfectedSevereCriticalDeadPartialImmunity< FP >, ReducInfectedSevereCriticalDeadImprovedImmunity< FP >, ReducTimeInfectedMild< FP >, InfectiousnessNewVariant< FP >, StartDayNewVariant< FP > >

Enumerations
enum class	InfectionState { SusceptibleNaive = 0 , SusceptiblePartialImmunity , ExposedNaive , ExposedPartialImmunity , ExposedImprovedImmunity , InfectedNoSymptomsNaive , InfectedNoSymptomsPartialImmunity , InfectedNoSymptomsImprovedImmunity , InfectedNoSymptomsNaiveConfirmed , InfectedNoSymptomsPartialImmunityConfirmed , InfectedNoSymptomsImprovedImmunityConfirmed , InfectedSymptomsNaive , InfectedSymptomsPartialImmunity , InfectedSymptomsImprovedImmunity , InfectedSymptomsNaiveConfirmed , InfectedSymptomsPartialImmunityConfirmed , InfectedSymptomsImprovedImmunityConfirmed , InfectedSevereNaive , InfectedSeverePartialImmunity , InfectedSevereImprovedImmunity , InfectedCriticalNaive , InfectedCriticalPartialImmunity , InfectedCriticalImprovedImmunity , SusceptibleImprovedImmunity , DeadNaive , DeadPartialImmunity , DeadImprovedImmunity , Count }
	The InfectionState enum describes the possible categories for the infectious state of persons. More...

Functions
template<typename FP >
Graph< Model< FP >, MobilityParameters< FP > >	draw_sample (Graph< Model< FP >, MobilityParameters< FP >> &graph)
	Draws samples for each model node in a graph. More...

template<typename FP >
void	draw_sample (Model< FP > &model)
	Draws a sample from Model parameter distributions and stores sample values as Parameters parameter values (cf. More...

template<typename FP >
void	draw_sample_demographics (Model< FP > &model)
	draws a sample from the specified distributions for all parameters related to the demographics, e.g. More...

template<typename FP >
void	draw_sample_infection (Model< FP > &model)
	draws a sample from the specified distributions for all parameters related to the infection. More...

template<class Model >
std::vector< Model >	ensemble_params_percentile (const std::vector< std::vector< Model >> &ensemble_params, double p)
	computes the p percentile of the parameters for each node. More...

template<typename FP , class Base = mio::Simulation<FP, Model<FP>>>
FP	get_infections_relative (const Simulation< FP, Base > &model, FP t, const Eigen::Ref< const Eigen::VectorX< FP >> &y)
	get percentage of infections per total population. More...

template<typename FP , class Base = mio::Simulation<FP, Model<FP>>>
auto	get_mobility_factors (const Simulation< Base > &sim, FP, const Eigen::Ref< const Eigen::VectorX< FP >> &y)
	Get mobility factors. More...

template<typename FP >
auto	simulate (FP t0, FP tmax, FP dt, const Model< FP > &model, std::unique_ptr< OdeIntegratorCore< FP >> &&integrator_core=nullptr)
	Specialization of simulate for SECIRVVS models using Simulation. More...

template<typename FP >
auto	simulate_flows (FP t0, FP tmax, FP dt, const Model< FP > &model, std::unique_ptr< OdeIntegratorCore< FP >> &&integrator_core=nullptr)
	Specialization of simulate for SECIRVVS models using the FlowSimulation. More...

template<typename FP , class Base = mio::Simulation<FP, Model<FP>>>
auto	test_commuters (Simulation< FP, Base > &sim, Eigen::Ref< Eigen::VectorX< FP >> mobile_population, FP time)

Typedef Documentation

◆ Flows

◆ ParametersBase

template<typename FP >

using mio::osecirvvs::ParametersBase = typedef ParameterSet< StartDay<FP>, Seasonality<FP>, ICUCapacity<FP>, TestAndTraceCapacity<FP>, TestAndTraceCapacityMaxRiskNoSymptoms<FP>, TestAndTraceCapacityMaxRiskSymptoms<FP>, ContactPatterns<FP>, DynamicNPIsImplementationDelay<FP>, DynamicNPIsInfectedSymptoms<FP>, TimeExposed<FP>, TimeInfectedNoSymptoms<FP>, TimeInfectedSymptoms<FP>, TimeInfectedSevere<FP>, TimeInfectedCritical<FP>, TransmissionProbabilityOnContact<FP>, RelativeTransmissionNoSymptoms<FP>, RecoveredPerInfectedNoSymptoms<FP>, RiskOfInfectionFromSymptomatic<FP>, MaxRiskOfInfectionFromSymptomatic<FP>, SeverePerInfectedSymptoms<FP>, CriticalPerSevere<FP>, DeathsPerCritical<FP>, VaccinationGap<FP>, DaysUntilEffectivePartialImmunity<FP>, DaysUntilEffectiveImprovedImmunity<FP>, DailyFullVaccinations<FP>, DailyPartialVaccinations<FP>, ReducExposedPartialImmunity<FP>, ReducExposedImprovedImmunity<FP>, ReducInfectedSymptomsPartialImmunity<FP>, ReducInfectedSymptomsImprovedImmunity<FP>, ReducInfectedSevereCriticalDeadPartialImmunity<FP>, ReducInfectedSevereCriticalDeadImprovedImmunity<FP>, ReducTimeInfectedMild<FP>, InfectiousnessNewVariant<FP>, StartDayNewVariant<FP> >

Enumeration Type Documentation

◆ InfectionState

enum mio::osecirvvs::InfectionState

strong

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

Enum is usable as an index, e.g. in CustomIndexArray. Suffix Naive means no immunity through vaccination or infection. Suffix PartialImmunity means vaccinated once. Suffix ImprovedImmunity means vaccinated twice or recovered from infection. Suffix Confirmed means infection has been confirmed by a test, e.g. during commute.

Enumerator
SusceptibleNaive
SusceptiblePartialImmunity
ExposedNaive
ExposedPartialImmunity
ExposedImprovedImmunity
InfectedNoSymptomsNaive
InfectedNoSymptomsPartialImmunity
InfectedNoSymptomsImprovedImmunity
InfectedNoSymptomsNaiveConfirmed
InfectedNoSymptomsPartialImmunityConfirmed
InfectedNoSymptomsImprovedImmunityConfirmed
InfectedSymptomsNaive
InfectedSymptomsPartialImmunity
InfectedSymptomsImprovedImmunity
InfectedSymptomsNaiveConfirmed
InfectedSymptomsPartialImmunityConfirmed
InfectedSymptomsImprovedImmunityConfirmed
InfectedSevereNaive
InfectedSeverePartialImmunity
InfectedSevereImprovedImmunity
InfectedCriticalNaive
InfectedCriticalPartialImmunity
InfectedCriticalImprovedImmunity
SusceptibleImprovedImmunity
DeadNaive
DeadPartialImmunity
DeadImprovedImmunity
Count

Function Documentation

◆ draw_sample() [1/2]

template<typename FP >

Graph<Model<FP>, MobilityParameters<FP> > mio::osecirvvs::draw_sample ( Graph< Model< FP >, MobilityParameters< FP >> & graph )

Draws samples for each model node in a graph.

Some parameters are shared between nodes and only sampled once.

Template Parameters

FP	floating point type, e.g., double

Parameters

graph Graph to be sampled.

Returns: Graph with nodes and edges from the input graph sampled.

CHANGENOTE: Make sure to set the parameter InfectiousnessNewVariant. This function used to take a bool variant_high, setting InfectiousnessNewVariant to 1.6 if true, 1.4 otherwise, for all age groups.

◆ draw_sample() [2/2]

template<typename FP >

void mio::osecirvvs::draw_sample ( Model< FP > & model )

Draws a sample from Model parameter distributions and stores sample values as Parameters parameter values (cf.

UncertainValue and Parameters classes)

Template Parameters

FP	floating point type, e.g., double

Parameters

[in,out] model Model including contact patterns for alle age groups

◆ draw_sample_demographics()

template<typename FP >

void mio::osecirvvs::draw_sample_demographics ( Model< FP > & model )

draws a sample from the specified distributions for all parameters related to the demographics, e.g.

population.

Template Parameters

FP	floating point type, e.g., double

Parameters

[in,out] model Model including contact patterns for alle age groups

◆ draw_sample_infection()

template<typename FP >

void mio::osecirvvs::draw_sample_infection ( Model< FP > & model )

draws a sample from the specified distributions for all parameters related to the infection.

Template Parameters

FP	floating point type, e.g., double

Parameters

[in,out] model Model including contact patterns for alle age groups

◆ ensemble_params_percentile()

template<class Model >

std::vector<Model> mio::osecirvvs::ensemble_params_percentile	(	const std::vector< std::vector< Model >> &	ensemble_params,
		double	p
	)

computes the p percentile of the parameters for each node.

Parameters

ensemble_result	graph of multiple simulation runs
p	percentile value in open interval (0, 1)

Returns: p percentile of the parameters over all runs

◆ get_infections_relative()

template<typename FP , class Base = mio::Simulation<FP, Model<FP>>>

FP mio::osecirvvs::get_infections_relative	(	const Simulation< FP, Base > &	model,
		FP	t,
		const Eigen::Ref< const Eigen::VectorX< FP >> &	y
	)

get percentage of infections per total population.

Parameters

model	the compartment model with initial values.
t	current simulation time.
y	current value of compartments.

Template Parameters

Base	simulation type that uses a secir compartment model. see Simulation.

◆ get_mobility_factors()

template<typename FP , class Base = mio::Simulation<FP, Model<FP>>>

auto mio::osecirvvs::get_mobility_factors	(	const Simulation< Base > &	sim,
		FP	,
		const Eigen::Ref< const Eigen::VectorX< FP >> &	y
	)

Get mobility factors.

Used by mobility graph simulation. Like infection risk, mobility of infected individuals is reduced if they are well isolated.

Parameters

model	the compartment model with initial values.
t	current simulation time.
y	current value of compartments.

Returns: vector expression, same size as y, with mobility factors per compartment.

Template Parameters

Base	simulation type that uses a secir compartment model. see Simulation.

◆ simulate()

template<typename FP >

auto mio::osecirvvs::simulate	(	FP	t0,
		FP	tmax,
		FP	dt,
		const Model< FP > &	model,
		std::unique_ptr< OdeIntegratorCore< FP >> &&	integrator_core = `nullptr`
	)

inline

Specialization of simulate for SECIRVVS models using Simulation.

Template Parameters

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

Parameters

[in]	t0	start time.
[in]	tmax	end time.
[in]	dt	time step.
[in]	model	SECIRVVS model to simulate.
[in]	integrator_core	optional IntegratorCore, uses rk45 if nullptr.

Returns: Returns the result of the simulation.

◆ simulate_flows()

template<typename FP >

auto mio::osecirvvs::simulate_flows	(	FP	t0,
		FP	tmax,
		FP	dt,
		const Model< FP > &	model,
		std::unique_ptr< OdeIntegratorCore< FP >> &&	integrator_core = `nullptr`
	)

inline

Specialization of simulate for SECIRVVS models using the FlowSimulation.

Template Parameters

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

Parameters

[in]	t0	start time.
[in]	tmax	end time.
[in]	dt	time step.
[in]	model	SECIRVVS model to simulate.
[in]	integrator_core	optional IntegratorCore, uses rk45 if nullptr.

Returns: Returns the result of the Flowsimulation.

◆ test_commuters()

template<typename FP , class Base = mio::Simulation<FP, Model<FP>>>

auto mio::osecirvvs::test_commuters	(	Simulation< FP, Base > &	sim,
		Eigen::Ref< Eigen::VectorX< FP >>	mobile_population,
		FP	time
	)

osecirvvs Namespace Reference

Classes

Typedefs

Enumerations

Functions

Typedef Documentation

◆ Flows

◆ ParametersBase

Enumeration Type Documentation

◆ InfectionState

Function Documentation

◆ draw_sample() [1/2]

◆ draw_sample() [2/2]

◆ draw_sample_demographics()

◆ draw_sample_infection()

◆ ensemble_params_percentile()

◆ get_infections_relative()

◆ get_mobility_factors()

◆ simulate()

◆ simulate_flows()

◆ test_commuters()