june.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]¶
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june.interaction.interaction.
_get_contacts_in_school
(contact_matrix, school_years, susceptibles_idx, infecters_idx)¶
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june.interaction.interaction.
_subgroup_to_subgroup_transmission
(contact_matrix, subgroup_transmission_probabilities, subgroup_size, susceptibles_idx, infecters_idx, school_years=None) → float¶
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june.interaction.interaction.
_translate_school_subgroup
(idx, school_years)¶
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june.interaction.interaction.
compute_effective_transmission
(subgroup_transmission_probabilities: numpy.array, susceptibles_group_idx: numpy.array, infector_subgroups: tuple, infector_subgroup_sizes: numpy.array, contact_matrix: numpy.array, delta_time: float, beta: float, school_years: numpy.array)¶ Computes the effective transmission probability of all the infected people in the group, that is, the sum of all infection probabilities divided by the number of infected people.
subgroup_transmission_probabilities : transmission probabilities per subgroup.
susceptibles_group_idx : indices of suceptible people
infector_subgroup_sizes : subgroup sizes where the infected people are.
contact_matrix : contact matrix of the group
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june.interaction.interaction.
get_contact_matrix
(alpha, contacts, physical)¶ Computes the contact matrix used in the interaction, which boosts the physical contacts by a factor.
alpha : relative weight of physical contacts respect to the normal ones.
(1 = same as normal). - contacts : contact matrix - physical : proportion of physical contacts.
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june.interaction.interaction.
infect_susceptibles
(effective_transmission, susceptible_ids, suscetibilities)¶
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june.interaction.interaction.
random
() → x in the interval [0, 1).¶