mio::smm::Simulation< FP, Comp, Status, Region > Class Template Reference

A specialized Simulation for mio::smm::Model. More...

#include <simulation.h>

Public Types
using	Model = smm::Model< FP, Comp, Status, Region >

Public Member Functions
Eigen::Ref< Eigen::VectorX< FP > >	advance (FP tmax)
	Advance simulation to tmax. More...
Model &	get_model ()
const Model &	get_model () const
	Returns the model used in the simulation. More...
TimeSeries< FP > &	get_result ()
	Returns the final simulation result. More...
const TimeSeries< FP > &	get_result () const
	Simulation (Model const &model, FP t0=0., FP dt=1.)
	Set up the simulation for a Stochastic Metapopulation Model. More...

Private Member Functions
constexpr const smm::AdoptionRates< FP, Status, Region >::Type &	adoption_rates ()
	Returns the model's adoption rates. More...
size_t	determine_next_event ()
	Get next event i.e. More...
constexpr const smm::TransitionRates< FP, Status, Region >::Type &	transition_rates ()
	Returns the model's transition rates. More...
void	update_current_rates_and_waiting_times ()
	Calculate current values for m_current_rates and m_waiting_times. More...

Private Attributes
std::vector< FP >	m_current_rates
	Current values of both types of rates i.e. adoption and transition rates. More...
FP	m_dt
	Initial step size. More...
std::vector< FP >	m_internal_time
	Internal times of all poisson processes (aka T_k). More...
std::unique_ptr< Model >	m_model
	Pointer to the model used in the simulation. More...
mio::TimeSeries< FP >	m_result
	Result time series. More...
std::vector< FP >	m_tp_next_event
	Internal time points of next event i after m_internal[i] (aka P_k). More...
std::vector< FP >	m_waiting_times
	External times between m_internal_time and m_tp_next_event. More...

Detailed Description

template<typename FP, class Comp, class Status = Comp, class Region = mio::regions::Region>
class mio::smm::Simulation< FP, Comp, Status, Region >

A specialized Simulation for mio::smm::Model.

Template Parameters

regions	The number of regions.
Status	An infection state enum.

Member Typedef Documentation

Model

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

using mio::smm::Simulation< FP, Comp, Status, Region >::Model = smm::Model<FP, Comp, Status, Region>

Constructor & Destructor Documentation

Simulation()

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

mio::smm::Simulation< FP, Comp, Status, Region >::Simulation ( Model const &  model, FP  t0 = 0., FP  dt = 1.  )

inline

Set up the simulation for a Stochastic Metapopulation Model.

Parameters

[in]	model	An instance of mio::smm::Model.
[in]	t0	Start time.
[in]	dt	Initial Step size.

Member Function Documentation

adoption_rates()

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

constexpr const smm::AdoptionRates<FP, Status, Region>::Type& mio::smm::Simulation< FP, Comp, Status, Region >::adoption_rates ( )

inlineconstexprprivate

Returns the model's adoption rates.

advance()

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

Eigen::Ref<Eigen::VectorX<FP> > mio::smm::Simulation< FP, Comp, Status, Region >::advance ( FP  tmax )

inline

Advance simulation to tmax.

This function performs a Gillespie algorithm.

Parameters

tmax	Next stopping point of simulation.

determine_next_event()

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

size_t mio::smm::Simulation< FP, Comp, Status, Region >::determine_next_event ( )

inlineprivate

Get next event i.e.

event with the smallest waiting time.

get_model() [1/2]

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

Model& mio::smm::Simulation< FP, Comp, Status, Region >::get_model ( )

inline

get_model() [2/2]

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

const Model& mio::smm::Simulation< FP, Comp, Status, Region >::get_model ( ) const

inline

Returns the model used in the simulation.

get_result() [1/2]

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

TimeSeries<FP>& mio::smm::Simulation< FP, Comp, Status, Region >::get_result ( )

inline

Returns the final simulation result.

Returns

A TimeSeries to represent the final simulation result.

get_result() [2/2]

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

const TimeSeries<FP>& mio::smm::Simulation< FP, Comp, Status, Region >::get_result ( ) const

inline

transition_rates()

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

constexpr const smm::TransitionRates<FP, Status, Region>::Type& mio::smm::Simulation< FP, Comp, Status, Region >::transition_rates ( )

inlineconstexprprivate

Returns the model's transition rates.

update_current_rates_and_waiting_times()

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

void mio::smm::Simulation< FP, Comp, Status, Region >::update_current_rates_and_waiting_times ( )

inlineprivate

Calculate current values for m_current_rates and m_waiting_times.

Member Data Documentation

m_current_rates

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

std::vector<FP> mio::smm::Simulation< FP, Comp, Status, Region >::m_current_rates

private

Current values of both types of rates i.e. adoption and transition rates.

m_dt

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

FP mio::smm::Simulation< FP, Comp, Status, Region >::m_dt

private

Initial step size.

m_internal_time

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

std::vector<FP> mio::smm::Simulation< FP, Comp, Status, Region >::m_internal_time

private

Internal times of all poisson processes (aka T_k).

m_model

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

std::unique_ptr<Model> mio::smm::Simulation< FP, Comp, Status, Region >::m_model

private

Pointer to the model used in the simulation.

m_result

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

mio::TimeSeries<FP> mio::smm::Simulation< FP, Comp, Status, Region >::m_result

private

Result time series.

m_tp_next_event

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

std::vector<FP> mio::smm::Simulation< FP, Comp, Status, Region >::m_tp_next_event

private

Internal time points of next event i after m_internal[i] (aka P_k).

m_waiting_times

template<typename FP , class Comp , class Status = Comp, class Region = mio::regions::Region>

std::vector<FP> mio::smm::Simulation< FP, Comp, Status, Region >::m_waiting_times

private

External times between m_internal_time and m_tp_next_event.