june.infection_seed.infection_seed.InfectionSeed¶
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class
june.infection_seed.infection_seed.
InfectionSeed
(world: World, infection_selector: june.infection.infection_selector.InfectionSelector, seed_strength: float = 1.0, age_profile: Optional[dict] = None, daily_super_area_cases: Optional[pandas.core.frame.DataFrame] = None) Class that generates the seed for the infection.
- world:
world to infect
- infection_selector:
selector to generate infections
- seed_strength:
float that controls the strength of the seed
- age_profile:
dictionary with weight on age groups. Example: age_profile = {‘0-20’: 0., ‘21-50’:1, ‘51-100’:0.} would only infect people aged between 21 and 50
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__init__
(world: World, infection_selector: june.infection.infection_selector.InfectionSelector, seed_strength: float = 1.0, age_profile: Optional[dict] = None, daily_super_area_cases: Optional[pandas.core.frame.DataFrame] = None) Class that generates the seed for the infection.
- world:
world to infect
- infection_selector:
selector to generate infections
- seed_strength:
float that controls the strength of the seed
- age_profile:
dictionary with weight on age groups. Example: age_profile = {‘0-20’: 0., ‘21-50’:1, ‘51-100’:0.} would only infect people aged between 21 and 50
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get_people_from_age_group
(susceptible_ids: List[int], n_people: int, age_group: str) → List[int] Get
`n_people`
in a given`age_group`
from the list of susceptible_ids- susceptible_ids:
list of ids of susceptible people to select from
- n_people:
number of people to select
- age_group:
age limits to select from (Example: ‘18-25’)
ids of people in age group
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infect_super_areas
(n_cases_per_super_area: pandas.core.frame.DataFrame, record: Optional[Record] = None) Infect super areas with numer of cases given by data frame
- n_cases_per_super_area:
data frame containig the number of cases per super area
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select_susceptiles_by_age
(susceptible_ids: List[int], n_cases: int) → List[int] Select cases according to an age profile
- susceptible_ids:
list of ids of susceptible people to select from
- n_cases:
number of cases
- choices:
ids of people to infect, following the age profile given
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unleash_virus
(population: Population, n_cases: int, mpi_rank: int = 0, mpi_comm: Optional[MPI.COMM_WORLD] = None, mpi_size: Optional[int] = None, box_mode=False, record: Optional[Record] = None) Infects
`n_cases`
people in`population`
- population:
population to infect
- n_cases:
number of initial cases
- mpi_rank:
rank of the process
- mpi_comm:
mpi comm_world to enable communication between different processes
- mpi_size:
number of processes
- box_mode:
whether to run on box mode
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unleash_virus_per_day
(date: datetime, record: Optional[Record] = None) Infect super areas at a given
`date`
- date:
datetime object