osecir Namespace Reference

CPP API: mio::osecir 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	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	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. More...

struct	RecoveredPerInfectedNoSymptoms
	the percentage of asymptomatic cases in the SECIR 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 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 secir models. More...

struct	StartDay
	the start day in the SECIR 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	TestAndTraceCapacity
	capacity to test and trace contacts of infected for quarantine per day. More...

struct	TestAndTraceCapacityMaxRisk
	Multiplier for the test and trace capacity to determine when it is considered overloaded. 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 infectious 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 hsopitalized in the SECIR model in day unit More...

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

Typedefs
using	Flows = TypeList< Flow< InfectionState::Susceptible, InfectionState::Exposed >, Flow< InfectionState::Exposed, InfectionState::InfectedNoSymptoms >, Flow< InfectionState::InfectedNoSymptoms, InfectionState::InfectedSymptoms >, Flow< InfectionState::InfectedNoSymptoms, InfectionState::Recovered >, Flow< InfectionState::InfectedNoSymptomsConfirmed, InfectionState::InfectedSymptomsConfirmed >, Flow< InfectionState::InfectedNoSymptomsConfirmed, InfectionState::Recovered >, Flow< InfectionState::InfectedSymptoms, InfectionState::InfectedSevere >, Flow< InfectionState::InfectedSymptoms, InfectionState::Recovered >, Flow< InfectionState::InfectedSymptomsConfirmed, InfectionState::InfectedSevere >, Flow< InfectionState::InfectedSymptomsConfirmed, InfectionState::Recovered >, Flow< InfectionState::InfectedSevere, InfectionState::InfectedCritical >, Flow< InfectionState::InfectedSevere, InfectionState::Recovered >, Flow< InfectionState::InfectedSevere, InfectionState::Dead >, Flow< InfectionState::InfectedCritical, InfectionState::Dead >, Flow< InfectionState::InfectedCritical, InfectionState::Recovered > >

template<typename FP >
using	ParametersBase = ParameterSet< StartDay< FP >, Seasonality< FP >, ICUCapacity< FP >, TestAndTraceCapacity< FP >, TestAndTraceCapacityMaxRisk< 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 > >

Enumerations
enum class	InfectionState { Susceptible = 0 , Exposed , InfectedNoSymptoms , InfectedNoSymptomsConfirmed , InfectedSymptoms , InfectedSymptomsConfirmed , InfectedSevere , InfectedCritical , Recovered , Dead , 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)

template<typename FP >
void	draw_sample (Model< FP > &model)
	Draws a sample from Model parameter distributions and stores sample values as SecirParams 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<typename FP , class Model >
std::vector< Model >	ensemble_params_percentile (const std::vector< std::vector< Model >> &ensemble_params, FP 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< FP, Base > &sim, FP, const Eigen::Ref< const Eigen::VectorX< FP >> &y)
	Get mobility factors. More...

template<typename FP , class Base >
IOResult< FP >	get_reproduction_number (FP t_value, const Simulation< FP, Base > &sim)
	Computes the reproduction number at a given time point of the Simulation. More...

template<typename FP , class Base >
IOResult< FP >	get_reproduction_number (size_t t_idx, const Simulation< FP, Base > &sim)
	Computes the reproduction number at a given index time of the Model output obtained by the Simulation. More...

template<typename FP , class Base >
Eigen::VectorX< FP >	get_reproduction_numbers (const Simulation< FP, Base > &sim)
	Computes the reproduction number for all time points of the Model output obtained by the Simulation. More...

template<typename FP >
void	set_params_distributions_normal (Model< FP > &model, FP t0, FP tmax, FP dev_rel)
	Sets alls SecirParams parameters normally distributed, using the current value and a given standard deviation. 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 SECIR 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 SECIR 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::osecir::ParametersBase = typedef ParameterSet<StartDay<FP>, Seasonality<FP>, ICUCapacity<FP>, TestAndTraceCapacity<FP>, TestAndTraceCapacityMaxRisk<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> >

Enumeration Type Documentation

◆ InfectionState

enum mio::osecir::InfectionState

strong

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

Enumerator
Susceptible
Exposed
InfectedNoSymptoms
InfectedNoSymptomsConfirmed
InfectedSymptoms
InfectedSymptomsConfirmed
InfectedSevere
InfectedCritical
Recovered
Dead
Count

Function Documentation

◆ draw_sample() [1/2]

template<typename FP >

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

◆ draw_sample() [2/2]

template<typename FP >

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

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

UncertainValue and SecirParams classes).

Parameters

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

◆ draw_sample_demographics()

template<typename FP >

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

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

population.

Parameters

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

◆ draw_sample_infection()

template<typename FP >

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

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

Parameters

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

◆ ensemble_params_percentile()

template<typename FP , class Model >

std::vector<Model> mio::osecir::ensemble_params_percentile	(	const std::vector< std::vector< Model >> &	ensemble_params,
		FP	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::osecir::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

FP	floating point type, e.g., double.
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::osecir::get_mobility_factors	(	const Simulation< FP, 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

FP	floating point type, e.g., double.
Base	simulation type that uses a secir compartment model; see Simulation.

◆ get_reproduction_number() [1/2]

template<typename FP , class Base >

IOResult<FP> mio::osecir::get_reproduction_number	(	FP	t_value,
		const Simulation< FP, Base > &	sim
	)

Computes the reproduction number at a given time point of the Simulation.

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

Parameters

t_value	The time point at which the reproduction number should be computed.
sim	The Model Simulation.

Template Parameters

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

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

◆ get_reproduction_number() [2/2]

template<typename FP , class Base >

IOResult<FP> mio::osecir::get_reproduction_number	(	size_t	t_idx,
		const Simulation< FP, Base > &	sim
	)

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.
sim	The simulation holding the SECIR model

Template Parameters

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

Returns: The computed reproduction number at the provided index time.

◆ get_reproduction_numbers()

template<typename FP , class Base >

Eigen::VectorX<FP> mio::osecir::get_reproduction_numbers ( const Simulation< FP, Base > & sim )

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

Parameters

sim	The Model Simulation.

Template Parameters

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

Returns: Eigen::Vector containing all reproduction numbers

◆ set_params_distributions_normal()

template<typename FP >

void mio::osecir::set_params_distributions_normal	(	Model< FP > &	model,
		FP	t0,
		FP	tmax,
		FP	dev_rel
	)

Sets alls SecirParams parameters normally distributed, using the current value and a given standard deviation.

Parameters

[in,out]	params	SecirParams including contact patterns for alle age groups
[in]	t0	start time
[in]	tmax	end time
[in]	dev_rel	maximum relative deviation from particular value(s) given in params

◆ simulate()

template<typename FP >

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

inline

Specialization of simulate for SECIR 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	SECIR 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::osecir::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 SECIR 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	SECIR 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::osecir::test_commuters	(	Simulation< FP, Base > &	sim,
		Eigen::Ref< Eigen::VectorX< FP >>	mobile_population,
		FP	time
	)

osecir 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()

◆ get_reproduction_number() [1/2]

◆ get_reproduction_number() [2/2]

◆ get_reproduction_numbers()

◆ set_params_distributions_normal()

◆ simulate()

◆ simulate_flows()

◆ test_commuters()