june.simulator_box¶
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exception
june.simulator_box.
SimulatorError
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__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
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with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
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args
¶
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class
june.simulator_box.
SimulatorBox
(world: june.world.World, interaction: june.interaction.interaction.Interaction, timer, activity_manager, infection_selector: june.infection.infection_selector.InfectionSelector = None, infection_seed: Optional[InfectionSeed] = None, checkpoint_dates: List[datetime.date] = None, record: Record = None, checkpoint_path: str = None)¶ Class to run an epidemic spread simulation on a box. It is basically a wrapper around the Simualtor class, disabling the options that are not available in box mode, like moving ill people to households.
- world:
instance of World class
- interaction:
instance of Interaction class
- infection:
instance of Infection class
- activity_to_groups:
mapping between an activity and its corresponding groups
- time_config:
dictionary with temporal configuration to set up the simulation
- min_age_home_alone:
minimum age of a child to be left alone at home when ill
- policies:
policies to be implemented at different time steps
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ActivityManager
¶ alias of
june.activity.activity_manager_box.ActivityManagerBox
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__init__
(world: june.world.World, interaction: june.interaction.interaction.Interaction, timer, activity_manager, infection_selector: june.infection.infection_selector.InfectionSelector = None, infection_seed: Optional[InfectionSeed] = None, checkpoint_dates: List[datetime.date] = None, record: Record = None, checkpoint_path: str = None)¶ Class to run an epidemic spread simulation on a box. It is basically a wrapper around the Simualtor class, disabling the options that are not available in box mode, like moving ill people to households.
- world:
instance of World class
- interaction:
instance of Interaction class
- infection:
instance of Infection class
- activity_to_groups:
mapping between an activity and its corresponding groups
- time_config:
dictionary with temporal configuration to set up the simulation
- min_age_home_alone:
minimum age of a child to be left alone at home when ill
- policies:
policies to be implemented at different time steps
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bury_the_dead
(world: june.world.World, person: june.demography.person.Person)¶ When someone dies, send them to cemetery. ZOMBIE ALERT!!
time person:
person to send to cemetery
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static
check_inputs
(time_config: dict)¶ Check that the iput time configuration is correct, i.e., activities are among allowed activities and days have 24 hours.
- time_config:
dictionary with time steps configuration
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clear_world
()¶ Removes everyone from all possible groups, and sets everyone’s busy attribute to False.
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do_timestep
()¶ Perform a time step in the simulation
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classmethod
from_checkpoint
(world: june.world.World, checkpoint_path: str, interaction: june.interaction.interaction.Interaction, infection_selector=None, policies: Optional[june.policy.policy.Policies] = None, infection_seed: Optional[june.infection_seed.infection_seed.InfectionSeed] = None, leisure: Optional[june.groups.leisure.leisure.Leisure] = None, travel: Optional[june.groups.travel.travel.Travel] = None, config_filename: str = PosixPath('/home/sadie/JUNE/configs/config_example.yaml'), record: Optional[Record] = None)¶
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classmethod
from_file
(world: june.world.World, interaction: june.interaction.interaction.Interaction, infection_selector=None, policies: Optional[june.policy.policy.Policies] = None, infection_seed: Optional[june.infection_seed.infection_seed.InfectionSeed] = None, leisure: Optional[june.groups.leisure.leisure.Leisure] = None, travel: Optional[june.groups.travel.travel.Travel] = None, config_filename: str = PosixPath('/home/sadie/JUNE/configs/config_example.yaml'), checkpoint_path: str = None, record: Optional[Record] = None) → Simulator¶ Load config for simulator from world.yaml
leisure infection_seed policies interaction world config_filename
The path to the world yaml configuration
- comment
A brief description of the purpose of the run(s)
A Simulator
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infect_people
(infected_ids, people_from_abroad_dict)¶ Given a list of infected ids, it initialises an infection object for them and sets it to person.infection. For the people who do not live in this domain a dictionary with their ids and domains is prepared to be sent through MPI.
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recover
(person: june.demography.person.Person)¶ When someone recovers, erase the health information they carry and change their susceptibility.
- person:
person to recover
- time:
time (in days), at which the person recovers
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run
()¶ Run simulation with n_seed initial infections
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save_checkpoint
(saving_date)¶
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tell_domains_to_infect
(infect_in_domains)¶ Sends information about the people who got infected in this domain to the other domains.
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update_health_status
(time: float, duration: float)¶ Update symptoms and health status of infected people. Send them to hospital if necessary, or bury them if they have died.
- time:
time now
- duration:
duration of time step