Index

_

__call__() (pyEpiabm.intervention.AbstractIntervention method) (pyEpiabm.intervention.CaseIsolation method) (pyEpiabm.intervention.DiseaseTesting method) (pyEpiabm.intervention.HouseholdQuarantine method) (pyEpiabm.intervention.PlaceClosure method) (pyEpiabm.intervention.SocialDistancing method) (pyEpiabm.intervention.TravelIsolation method) (pyEpiabm.intervention.Vaccination method) (pyEpiabm.sweep.AbstractSweep method) (pyEpiabm.sweep.HostProgressionSweep method) (pyEpiabm.sweep.HouseholdSweep method) (pyEpiabm.sweep.InitialDemographicsSweep method) (pyEpiabm.sweep.InitialHouseholdSweep method) (pyEpiabm.sweep.InitialInfectedSweep method) (pyEpiabm.sweep.InitialisePlaceSweep method) (pyEpiabm.sweep.InitialVaccineQueue method) (pyEpiabm.sweep.InterventionSweep method) (pyEpiabm.sweep.PlaceSweep method) (pyEpiabm.sweep.QueueSweep method) (pyEpiabm.sweep.SpatialSweep method) (pyEpiabm.sweep.TravelSweep method) (pyEpiabm.sweep.UpdatePlaceSweep method) (pyEpiabm.utility.AntibodyMultiplier method) (pyEpiabm.utility.RateMultiplier method)

__del__() (pyEpiabm.output._CsvDictWriter method) (pyEpiabm.output._CsvWriter method) __init__() (pyEpiabm.intervention.AbstractIntervention method) (pyEpiabm.intervention.CaseIsolation method) (pyEpiabm.intervention.DiseaseTesting method) (pyEpiabm.intervention.HouseholdQuarantine method) (pyEpiabm.intervention.PlaceClosure method) (pyEpiabm.intervention.SocialDistancing method) (pyEpiabm.intervention.TravelIsolation method) (pyEpiabm.intervention.Vaccination method) (pyEpiabm.output._CsvDictWriter method) (pyEpiabm.output._CsvWriter method) (pyEpiabm.output.AbstractReporter method) (pyEpiabm.output.AgeStratifiedNewCasesWriter method) (pyEpiabm.output.NewCasesWriter method) _CompartmentCounter (class in pyEpiabm) _CsvDictWriter (class in pyEpiabm.output) _CsvWriter (class in pyEpiabm.output)

A

AbstractIntervention (class in pyEpiabm.intervention) AbstractPopulationFactory (class in pyEpiabm.routine) AbstractReporter (class in pyEpiabm.output) AbstractSweep (class in pyEpiabm.sweep) add_cells() (pyEpiabm.Population method) add_household() (pyEpiabm.Microcell method) add_households() (pyEpiabm.routine.FilePopulationFactory static method) (pyEpiabm.routine.ToyPopulationFactory static method) add_microcells() (pyEpiabm.Cell method) add_people() (pyEpiabm.Microcell method) add_person() (pyEpiabm.Household method) (pyEpiabm.Microcell method) (pyEpiabm.Place method)

add_place() (pyEpiabm.Microcell method) (pyEpiabm.Person method) add_places() (pyEpiabm.routine.ToyPopulationFactory static method) add_susceptible_person() (pyEpiabm.Household method) AgeStratifiedNewCasesWriter (class in pyEpiabm.output) AntibodyMultiplier (class in pyEpiabm.utility) assign_cell_locations() (pyEpiabm.routine.ToyPopulationFactory static method) assign_microcell_and_household() (pyEpiabm.sweep.TravelSweep method) assign_priority_group() (pyEpiabm.sweep.InitialVaccineQueue method) asympt_uninf_testing_queue() (pyEpiabm.sweep.HostProgressionSweep method)

B

bind_population() (pyEpiabm.sweep.AbstractSweep method) (pyEpiabm.sweep.InterventionSweep method) (pyEpiabm.sweep.SpatialSweep method)

C

calc_number_of_children() (pyEpiabm.sweep.InitialHouseholdSweep method) CaseIsolation (class in pyEpiabm.intervention) Cell (class in pyEpiabm) cell_inf() (pyEpiabm.property.SpatialInfection static method) check_leaving_individuals() (pyEpiabm.sweep.TravelSweep method) clear_counter() (pyEpiabm._CompartmentCounter method) compress() (pyEpiabm.output._CsvDictWriter method) compress_csv() (pyEpiabm.routine.Simulation method)

configure() (pyEpiabm.routine.Simulation method) covid_sim_rand() (pyEpiabm.utility.RandomMethods method) create_age_weights() (pyEpiabm.sweep.InitialisePlaceSweep method) create_empty_state_transition_matrix() (pyEpiabm.sweep.StateTransitionMatrix static method) create_introduced_individuals() (pyEpiabm.sweep.TravelSweep method) create_state_transition_matrix() (pyEpiabm.sweep.StateTransitionMatrix method) create_transition_time_matrix() (pyEpiabm.sweep.TransitionTimeMatrix method) create_waning_transition_matrix() (pyEpiabm.sweep.StateTransitionMatrix method)

D

DiseaseTesting (class in pyEpiabm.intervention) dist() (pyEpiabm.utility.DistanceFunctions static method) dist_euclid() (pyEpiabm.utility.DistanceFunctions static method)

dist_periodic() (pyEpiabm.utility.DistanceFunctions static method) DistanceFunctions (class in pyEpiabm.utility) do_infection_event() (pyEpiabm.sweep.SpatialSweep method) do_testing() (pyEpiabm.intervention.DiseaseTesting method)

E

empty_place() (pyEpiabm.Place method) enqueue_LFT_testing() (pyEpiabm.Cell method)

enqueue_PCR_testing() (pyEpiabm.Cell method) enqueue_person() (pyEpiabm.Cell method) enqueue_vaccine() (pyEpiabm.Population method)

F

FilePopulationFactory (class in pyEpiabm.routine) find_cell() (pyEpiabm.routine.FilePopulationFactory static method)

find_infectees() (pyEpiabm.sweep.SpatialSweep method) find_infectees_Covidsim() (pyEpiabm.sweep.SpatialSweep method) find_nearby_cells() (pyEpiabm.Cell method)

G

get_group_index() (pyEpiabm.Place method)

H

HostProgressionSweep (class in pyEpiabm.sweep) Household (class in pyEpiabm) household_allocation() (pyEpiabm.sweep.InitialHouseholdSweep method) household_foi() (pyEpiabm.property.HouseholdInfection static method)

household_inf() (pyEpiabm.property.HouseholdInfection static method) household_susc() (pyEpiabm.property.HouseholdInfection static method) HouseholdInfection (class in pyEpiabm.property) HouseholdQuarantine (class in pyEpiabm.intervention) HouseholdSweep (class in pyEpiabm.sweep)

I

icdf_choose_exp() (pyEpiabm.utility.InverseCdf method) icdf_choose_noexp() (pyEpiabm.utility.InverseCdf method) identifier (pyEpiabm._CompartmentCounter property) increment_num_times_infected() (pyEpiabm.Person method) increment_secondary_infections() (pyEpiabm.Person method) InfectionStatus (class in pyEpiabm.property) InitialDemographicsSweep (class in pyEpiabm.sweep) InitialHouseholdSweep (class in pyEpiabm.sweep) InitialInfectedSweep (class in pyEpiabm.sweep)

InitialisePlaceSweep (class in pyEpiabm.sweep) InitialVaccineQueue (class in pyEpiabm.sweep) instance() (pyEpiabm.Parameters static method) InterventionSweep (class in pyEpiabm.sweep) InverseCdf (class in pyEpiabm.utility) is_active() (pyEpiabm.intervention.AbstractIntervention method) is_infectious() (pyEpiabm.Person method) is_place_closed() (pyEpiabm.Person method) is_susceptible() (pyEpiabm.Person method) is_symptomatic() (pyEpiabm.Person method)

L

log_exceptions() (in module pyEpiabm.utility)

M

make_pop() (pyEpiabm.routine.FilePopulationFactory static method) (pyEpiabm.routine.ToyPopulationFactory static method) Microcell (class in pyEpiabm)

minimum_between_cells() (pyEpiabm.utility.DistanceFunctions method) module pyEpiabm

N

NewCasesWriter (class in pyEpiabm.output) notify_person_status_change() (pyEpiabm.Cell method) (pyEpiabm.Microcell method)

number_infectious() (pyEpiabm.Cell method)

O

one_person_household_age() (pyEpiabm.sweep.InitialHouseholdSweep method)

P

Parameters (class in pyEpiabm) Person (class in pyEpiabm) person_inf() (pyEpiabm.property.PersonalInfection static method) person_selection_method() (pyEpiabm.intervention.CaseIsolation method) (pyEpiabm.intervention.TravelIsolation method) person_susc() (pyEpiabm.property.PersonalInfection static method) PersonalInfection (class in pyEpiabm.property) Place (class in pyEpiabm) place_foi() (pyEpiabm.property.PlaceInfection static method) place_inf() (pyEpiabm.property.PlaceInfection static method)

place_susc() (pyEpiabm.property.PlaceInfection static method) PlaceClosure (class in pyEpiabm.intervention) PlaceInfection (class in pyEpiabm.property) PlaceSweep (class in pyEpiabm.sweep) PlaceType (class in pyEpiabm.property) Population (class in pyEpiabm) print_population() (pyEpiabm.routine.FilePopulationFactory static method) py2c_convert_population() (in module pyEpiabm.py2c) pyEpiabm module

Q

QueueSweep (class in pyEpiabm.sweep)

R

RandomMethods (class in pyEpiabm.utility) RateMultiplier (class in pyEpiabm.utility) remove_age_dependence() (pyEpiabm.sweep.StateTransitionMatrix method) remove_household() (pyEpiabm.Household method) remove_leaving_individuals() (pyEpiabm.sweep.TravelSweep method) remove_person() (pyEpiabm.Person method) (pyEpiabm.Place method)

remove_place() (pyEpiabm.Person method) remove_susceptible_person() (pyEpiabm.Household method) report() (pyEpiabm._CompartmentCounter method) retrieve() (pyEpiabm._CompartmentCounter method) run_sweeps() (pyEpiabm.routine.Simulation method)

S

set_exposure_period() (pyEpiabm.Person method) set_file() (pyEpiabm.Parameters static method) set_id() (pyEpiabm.Cell method) (pyEpiabm.Household method) (pyEpiabm.Microcell method) (pyEpiabm.Person method) set_infectiousness() (pyEpiabm.Place method) (pyEpiabm.sweep.HostProgressionSweep static method) set_infector_latent_period() (pyEpiabm.Person method) set_latent_period() (pyEpiabm.Person method) set_location() (pyEpiabm.Cell method) (pyEpiabm.Microcell method) set_random_age() (pyEpiabm.Person method) set_random_seed() (pyEpiabm.routine.Simulation static method)

set_susceptibility() (pyEpiabm.Place method) set_time_of_recovery() (pyEpiabm.Person method) Simulation (class in pyEpiabm.routine) SocialDistancing (class in pyEpiabm.intervention) spatial_foi() (pyEpiabm.property.SpatialInfection static method) spatial_inf() (pyEpiabm.property.SpatialInfection static method) spatial_susc() (pyEpiabm.property.SpatialInfection static method) SpatialInfection (class in pyEpiabm.property) SpatialKernel (class in pyEpiabm.utility) SpatialSweep (class in pyEpiabm.sweep) StateTransitionMatrix (class in pyEpiabm.sweep) store_generation_time() (pyEpiabm.Person method) store_infection_periods() (pyEpiabm.sweep.AbstractSweep static method) store_serial_interval() (pyEpiabm.Person method) sympt_testing_queue() (pyEpiabm.sweep.HostProgressionSweep method)

T

three_or_more_person_household_ages() (pyEpiabm.sweep.InitialHouseholdSweep method) total_people() (pyEpiabm.Population method) ToyPopulationFactory (class in pyEpiabm.routine) TransitionTimeMatrix (class in pyEpiabm.sweep) TravelIsolation (class in pyEpiabm.intervention) TravelSweep (class in pyEpiabm.sweep) turn_off() (pyEpiabm.intervention.AbstractIntervention method) (pyEpiabm.intervention.CaseIsolation method) (pyEpiabm.intervention.DiseaseTesting method) (pyEpiabm.intervention.HouseholdQuarantine method) (pyEpiabm.intervention.PlaceClosure method) (pyEpiabm.intervention.SocialDistancing method) (pyEpiabm.intervention.TravelIsolation method) (pyEpiabm.intervention.Vaccination method)

two_person_household_ages() (pyEpiabm.sweep.InitialHouseholdSweep method)

U

update_age_group() (pyEpiabm.Person method) update_next_infection_status() (pyEpiabm.sweep.HostProgressionSweep method) update_place_group() (pyEpiabm.sweep.UpdatePlaceSweep method) update_probability() (pyEpiabm.sweep.StateTransitionMatrix method)

update_status() (pyEpiabm.Person method) update_time_status_change() (pyEpiabm.sweep.HostProgressionSweep method) update_transition_time_with_float() (pyEpiabm.sweep.TransitionTimeMatrix method) update_transition_time_with_icdf() (pyEpiabm.sweep.TransitionTimeMatrix method) UpdatePlaceSweep (class in pyEpiabm.sweep)

V

vaccinate() (pyEpiabm.Person method)

Vaccination (class in pyEpiabm.intervention)

W

weighting() (pyEpiabm.utility.SpatialKernel static method) write() (pyEpiabm.output._CsvDictWriter method) (pyEpiabm.output._CsvWriter method) (pyEpiabm.output.AbstractReporter method) (pyEpiabm.output.AgeStratifiedNewCasesWriter method) (pyEpiabm.output.NewCasesWriter method)

write_to_file() (pyEpiabm.routine.Simulation method) write_to_generation_time_file() (pyEpiabm.routine.Simulation method) write_to_ih_file() (pyEpiabm.routine.Simulation method) write_to_Rt_file() (pyEpiabm.routine.Simulation method) write_to_serial_interval_file() (pyEpiabm.routine.Simulation method)