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Parameters

get_parameters()
Establish the list of model parameters

Variables

create_variables()
Generate a list of the model variables
generate_initial_age_classes()
Generates a vector of the age classes of all individuals in the population
generate_initial_disease_states()
Generate a vector of the initial disease states of all individuals in the population
generate_initial_households()
Generates a vector of households for all individuals in the population
generate_initial_households_bootstrap()
Generates a vector of households for all individuals in the population
generate_initial_leisure()
Generate a list of leisure settings that each individual visits
generate_initial_schools()
Generate a vector of school assignments for all individuals in the population
generate_initial_schools_bootstrap()
Generate a vector of school assignments for all individuals in the population
generate_initial_workplaces()
Gets workplace assignments for all individuals in the population

Processes

create_EI_process()
Create process governing exposed to infectious disease state transition
create_IR_process()
Create process governing infectious to recovered disease state transition
create_RS_process()
Create process governing recovered (and immune) back to susceptible disease state transition
create_SE_process()
Create process governing susceptible to exposed disease state transition
create_external_source_process()
Create process governing exposed to infectious disease state transition
create_processes()
Define and create all model processes

Events

create_events()
Generate a list of model events with listeners

Model

run_simulation()
Run the simulation
run_simulations_from_table()
Run helios simulations using table of parameter values

Sampling

sample_log_normal()
Sample variables from an log-normal distribution with fixed sum
sample_negbinom()
Sample variables from a negative binomial distribution with fixed sum
sample_offset_truncated_power_distribution()
Sample variables from an offset truncated power distribution with fixed sum

Data

baseline_household_demographics_uk
Data from ONS 2011 on baseline household demographics from Hinch et al.
baseline_household_demographics_usa
Data from RTI Synthetic population of USA containing information on household size and age distribution. Selected for the county of San Francisco.
schools_uk
Data on English schools from the 2022/2023 School Census
schools_usa
Data on US schools from 2019/2020 from the National Center for Education Statistics

Intervention

generate_far_uvc_switches()
Update model parameters with far UVC switches
generate_setting_far_uvc_switches()
Generate far UVC switches for particular setting
set_uvc()
Update model parameters with far UVC settings

Riskiness

generate_setting_specific_riskinesses()
generate_setting_specific_riskinesses
set_setting_specific_riskiness()
set_setting_specific_riskiness

Miscellaneous

generate_betas()
generate_betas
get_setting_size()
get_setting_size