Function reference • safir2

Variables

Age

Functions to help make age variables.

create_age_variables(): Create age variables

create_continuous_age_variable(): Continuous age variable

create_discrete_age_variable(): Discrete age variable

identify_ages_to_adjust(): Identify ages to adjust

swap_ages(): Swap values that have been identified

Compartments

Functions to help make the compartmental state variables.

create_variables(): Create age & compartment variables

create_compartment_variables(): Create compartmental state variables

get_state_vector(): Get vector of states from parameters

Events

Events are used to simulate disease progression.

create_events(): Create disease progression events

attach_event_listeners(): Attach listeners to events

create_event_scheduler_listener(): A listener to schedule future events

create_state_update_listener(): A listener to update state

Immunity

Function which help model NAT (neutralizing antibody titres) and their relationship to protection against infection, severe disease, and onward infectiousness.

make_get_NAT(): Make function to calculate population NAT

make_get_ve_severe(): Make function to calculate efficacy against severe disease

ve_infection_functional_form(): Function for efficacy against infection

Utilities

Parameters

Utilities to help get potentially time-varying parameters during simulation runs. Most return functions that are called within safir2.

make_get_age_probabilities(): Get age-structured transition probabilities at current timestep

make_get_contact_matrix(): Get contact matrix at current timestep

make_get_vector(): Get vector or scalar parameter at current timestep

Distributions

Utilities which help draw random variates.

make_rexp(): Make exponential waiting time distribution

make_rerlang(): Make Erlang waiting time distribution

Setup

Utilities useful for initializing the model.

add_named_listener(): Add named listener to an event

get_asymptomatic(): Function to add asymptomatic information

get_population(): Get population from SQUIRE model

get_squire_parameters(): Get parameters from squire model

interp_input_par(): Interpolate input parameters

interpolate_rt(): Produce piecewise linear Rt

Other

safir2: safir2: squire and friends individual rewrite rewrite

iso3c_ages: Median ages for countries