Package index • helios

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_external_source_process(): Create process governing exposed to infectious disease state transition

create_IR_process(): Create process governing infectious to recovered disease state transition

create_processes(): Define and create all model processes

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

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_joint_far_uvc_switches(): Generate joint 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