june.interaction.interaction.Interaction¶
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class
june.interaction.interaction.
Interaction
(alpha_physical: float, beta: Dict[str, float], contact_matrices: dict, susceptibilities_by_age: Dict[str, int] = None, population: june.demography.demography.Population = None) Class to handle interaction in groups.
- alpha_physical
Scaling factor for physical contacts, an alpha_physical factor of 1, means that physical contacts count as much as non-physical contacts.
- beta
dictionary mapping the group specs with their contact intensities
- contact_matrices
dictionary mapping the group specs with their contact matrices
- susceptibilities_by_age
dictionary mapping age ranges to their susceptibility. Example: susceptibilities_by_age = {“0-13” : 0.5, “13-99” : 0.5} note that the right limit of the range is not included.
- population
list of people to have the susceptibilities changed.
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__init__
(alpha_physical: float, beta: Dict[str, float], contact_matrices: dict, susceptibilities_by_age: Dict[str, int] = None, population: june.demography.demography.Population = None) Initialize self. See help(type(self)) for accurate signature.
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adapt_contacts_to_schools
(input_contact_matrix, xi, age_min, age_max, physical=False)
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classmethod
from_file
(config_filename: str = PosixPath('/home/sadie/JUNE/configs/defaults/interaction/interaction.yaml'), population: june.demography.demography.Population = None) → june.interaction.interaction.Interaction
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process_contact_matrices
(groups: List[str], input_contact_matrices: dict)
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process_school_matrices
(input_contact_matrices, age_min=0, age_max=20)
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set_population_susceptibilities
(susceptibilities_by_age: dict, population: june.demography.demography.Population) Changes the population susceptibility to the disease.
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time_step_for_group
(delta_time: float, group: june.interaction.interactive_group.InteractiveGroup)
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time_step_for_subgroup
(subgroup_transmission_probabilities, susceptible_ids, susceptibilities, infector_subgroups, infector_subgroup_sizes, contact_matrix, beta, delta_time, subgroup_idx, school_years) → List[int]