SWEEPS

Sweeps implements classes which manage infection propagation mechanisms. Class sweeps through the population to decide infection transmission.

Overview:

• SweepInterface

• HouseholdSweep

• SpatialSweep

• PlaceSweep

• BasicHostProgressionSweep

• HostProgressionSweep

• NewInfectionSweep

• RandomSeedSweep

SWEEPS

class SweepInterface

Interface class for sweeps Sweeps can have population bound, and then operate upon the bound populations each timestep.

Subclassed by epiabm::BasicHostProgressionSweep, epiabm::HostProgressionSweep, epiabm::HouseholdSweep, epiabm::NewInfectionSweep, epiabm::PlaceSweep, epiabm::RandomSeedSweep, epiabm::SpatialSweep

Public Functions

SweepInterface()

SweepInterface(SimulationConfigPtr cfg)

virtual ~SweepInterface() = default

void bind_population(PopulationPtr population)

Bind Population Attach population to the sweep.

Parameters:

population –

inline virtual void operator()(const unsigned short)

Apply sweep Act on the population. Called by Simulation class each iteration timestep.

inline virtual bool cellCallback(const unsigned short, Cell*)

Callback to apply sweep to each cell.

Parameters:

• timestep – Current Timestep

• cell – Cell to act on

Returns:

true Returns true to continue and callback on next cell

Returns:

false Terminate Callbacks

class HouseholdSweep : public epiabm::SweepInterface

Spread Infection within Households Process each infected person and try to infect all susceptibles in their household. People to be newly infected get queued in their cell’s people queue.

Public Functions

HouseholdSweep(SimulationConfigPtr cfg)

~HouseholdSweep() = default

virtual void operator()(const unsigned short timestep) override

Perform Household Sweep.

Parameters:

timestep –

virtual bool cellCallback(const unsigned short timestep, Cell *cell) override

Cell callback Process each infectious person in the cell.

Parameters:

• timestep –

• cell –

Returns:

true

Returns:

false

bool cellInfectiousCallback(const unsigned short timestep, Cell *cell, Person *infectious)

Infectious person callback Process each Infectious person by finding their household and attempting to transmit to each houshold member.

Parameters:

• timestep –

• cell –

• infector –

Returns:

true

Returns:

false

class SpatialSweep : public epiabm::SweepInterface

Spread Infection between cells (spatial infection) Process each infected person and try to infect all susceptibles in their household. People to be newly infected get queued in their cell’s people queue.

Public Functions

SpatialSweep(SimulationConfigPtr cfg)

~SpatialSweep() = default

virtual void operator()(const unsigned short timestep) override

Perform Spatial Sweep.

Parameters:

timestep –

virtual bool cellCallback(const unsigned short timestep, Cell *cell) override

Cell callback Determine number of infections.

Parameters:

• timestep –

• cell –

Returns:

true

Returns:

false

bool cellInfectiousCallback(const unsigned short timestep, Cell *cell, Person *infectious)

class PlaceSweep : public epiabm::SweepInterface

Spread Infection within Places Process each infected person and try to infect all susceptibles in their place. People to be newly infected get queued in their cell’s people queue.

Public Functions

PlaceSweep(SimulationConfigPtr cfg)

~PlaceSweep() = default

virtual void operator()(const unsigned short timestep) override

Perform Place Sweep.

Parameters:

timestep –

virtual bool cellCallback(const unsigned short timestep, Cell *cell) override

Cell callback Process each infectious person in the cell.

Parameters:

• timestep –

• infectorCell –

Returns:

true

Returns:

false

bool cellInfectiousCallback(const unsigned short timestep, Cell *infectorCell, Person *infector)

Infectious person callback Process each Infectious person by finding their household and attempting to transmit to each houshold member.

Parameters:

• timestep –

• infectorCell –

• infector –

Returns:

true

Returns:

false

class BasicHostProgressionSweep : public epiabm::SweepInterface

Replication of Covid-sim’s host progression sweep without Severity Checks Person’s time to next state. If the time is past, choose next state and update person. Also decides duration to remain in next state.

Public Functions

BasicHostProgressionSweep(SimulationConfigPtr cfg)

Construct a new Basic Host Progression Sweep:: Basic Host Progression Sweep object.

Parameters:

cfg – Simulation configuration

~BasicHostProgressionSweep()

Destroy the Basic Host Progression Sweep:: Basic Host Progression Sweep object.

virtual void operator()(const unsigned short timestep) override

Perform Host Progression Sweep.

Parameters:

timestep –

virtual bool cellCallback(const unsigned short timestep, Cell *cell) override

Cell callback Process Infectious. Process Exposed.

Parameters:

• timestep –

• cell –

Returns:

true

Returns:

false

bool cellExposedCallback(const unsigned short timestep, Cell *cell, Person *person)

Exposed Person Callback Check if time to transition. If should transition, move person from Exposed to next status (always InfectAsymp in this basic class) Set time to remain in this state. Also update the cell of status for fast looping through subsets of people.

Parameters:

• timestep –

• cell –

• person –

Returns:

true

Returns:

false

bool cellInfectiousCallback(const unsigned short timestep, Cell *cell, Person *person)

Infectious person callback In this class infectious person’s status is always InfectAsymp Check if time to transition has passed. If should transition, decide person’s next state. (In this basic class, this is always Dead or Recovered) Update person’s state. (Since always Dead or Recovered, no next state time) Update cell of state change.

Parameters:

• timestep –

• cell –

• person –

Returns:

true

Returns:

false

class HostProgressionSweep : public epiabm::SweepInterface

Public Functions

HostProgressionSweep(SimulationConfigPtr cfg)

~HostProgressionSweep() = default

virtual void operator()(const unsigned short timestep) override

Perform Host Progression Sweep.

Parameters:

timestep –

virtual bool cellCallback(const unsigned short timestep, Cell *cell) override

Callback to apply sweep to each cell.

Parameters:

• timestep – Current Timestep

• cell – Cell to act on

Returns:

true Returns true to continue and callback on next cell

Returns:

false Terminate Callbacks

bool cellExposedCallback(const unsigned short timestep, Cell *cell, Person *person)

bool cellInfectiousCallback(const unsigned short timestep, Cell *cell, Person *person)

class NewInfectionSweep : public epiabm::SweepInterface

Process New Infections Processes the people queued into each cell, and changes their status from Susceptible to Exposed. This sweep should be called after each of the infection spreading sweeps, which queue people to be infected. Dequeus people as they are moved to exposed. Also marks people as exposed in the Cell for fast looping through subsets.

Public Functions

NewInfectionSweep(SimulationConfigPtr cfg)

~NewInfectionSweep() = default

virtual void operator()(const unsigned short timestep) override

Perform New Infection Processing Sweep.

Parameters:

timestep –

virtual bool cellCallback(const unsigned short timestep, Cell *cell) override

Callback for each cell For each cell, process each person in the queue.

Parameters:

• timestep –

• cell –

Returns:

true

Returns:

false

void cellPersonQueueCallback(unsigned short timestep, Cell *cell, size_t personIndex)

Callback for each person in a cell’s queue Process the people queued to be infected. Change status to Exposed, set the next transition time and mark the person as Exposed in the cell for fast looping through subsets of people.

Parameters:

• timestep –

• cell –

• personIndex –

class RandomSeedSweep : public epiabm::SweepInterface

Public Functions

RandomSeedSweep(SimulationConfigPtr simulationConfig, int per_n_people)

Construct a new Random Seed Sweep object One in every per_n_people is updated to infectious.

Parameters:

infection_rate –

~RandomSeedSweep() = default

virtual void operator()(const unsigned short timestep) override

Sweep through population and infect people.

Parameters:

timestep –

virtual bool cellCallback(const unsigned short timestep, Cell *cell) override

Callback to apply sweep to each cell.

Parameters:

• timestep – Current Timestep

• cell – Cell to act on

Returns:

true Returns true to continue and callback on next cell

Returns:

false Terminate Callbacks

bool cellPersonCallback(unsigned short timestep, Cell *cell, Person *person)