Function reference • safir

All functions
`allocate_treatment()`	Allocate treatment
`assign_doses()`	Assign doses to eligible persons based on available supply (multi-dose, no types)
`attach_event_listeners()`	Attach listeners to events
`attach_event_listeners_independent_nat()`	Attach event listeners for modeling independent infection-derived NAT
`attach_event_listeners_natural_immunity()`	Attach event listeners for natural immunity events
`attach_event_listeners_nimue()`	Attach listeners to events (nimue vaccine model)
`attach_event_listeners_vaccination()`	Attach event listeners for vaccination events (multi-dose, no types)
`attach_hosp_listeners()`	Attach listeners to track hospitalization and ICU incidence
`attach_tracking_listener_age_incidence()`	Attach listener to track age-stratified incidence
`attach_tracking_listener_incidence()`	Attach listener to track incidence
`categorical_count_renderer_process_daily()`	Render categories every day
`compartments_age_render_process_daily()`	Render categories by age every day
`create_age_incidence_tracking_listener()`	Create listener to track age-stratified incidence
`create_age_variables()`	Create age variables
`create_continuous_age_variable()`	Continuous age variable
`create_discrete_age_variable()`	Discrete age variable
`create_event_scheduler_listener()`	A listener to schedule future events
`create_events()`	Create events
`create_events_nimue()`	Append vaccination events (nimue vaccine model)
`create_events_vaccination()`	Append vaccination events
`create_exposure_scheduler_listener_nimue()`	Modelling the progression to either IMild, ICase, IAsymp (nimue vaccine model)
`create_exposure_scheduler_listener_vaccine()`	Modelling the progression to either IMild, ICase, IAsymp (vaccine model, multi-dose, no types)
`create_hosp_renderers()`	Create list of renderer objects to track hospitalization and ICU incidence
`create_hospital_scheduler_listener()`	Create listener function to schedule events upon hospitilisation
`create_hospital_scheduler_listener_cpp()`	Create C++ listener function to schedule events upon hospitilisation
`create_hospital_scheduler_listener_cpp_internal()`	Internal C++ function factory for scheduling events upon hospitilisation
`create_incidence_tracking_listener()`	Create listener to track incidence
`create_independent_nat_variables()`	Create independent infection-derived NAT variables
`create_natural_immunity_variables()`	Create natural immunity variables
`create_state_update_listener()`	A listener to update state
`create_state_variables()`	Define model states
`create_v0_to_v1v2_listener_nimue()`	Create listener for initial vaccination (nimue vaccine model)
`create_v1v2_to_v3v4_listener_nimue()`	Create listener for start of vaccine protection (nimue vaccine model)
`create_v3v4_to_v5_listener_nimue()`	Create listener for decay of vaccine protection (nimue vaccine model)
`create_vaccination_dose_listener()`	Create listener for vaccination dose (multi-dose, no types)
`create_vaccine_variables()`	Create vaccination variables (multi-dose, no types)
`create_vaccine_variables_nimue()`	Create vaccination variables (nimue vaccine model)
`create_variables()`	Create age & state variables
`cross_tab_compartments_age()`	Cross tabulate compartments and age
`cross_tab_doses_age()`	Cross tabulate doses and age
`cross_tab_margins()`	Cross tabulate two vectors with given margins
`dose_age_render_process_daily()`	Render doses by age every day
`get_asymptomatic()`	Function to add asymptomatic information
`get_contact_matrix_cpp()`	Get contact matrix
`get_current_coverage()`	Get people who either have this dose or are scheduled for it
`get_current_eligible_from_coverage()`	Get persons who are eligible for this dose
`get_parameters()`	Get parameters from squire model
`get_parameters_nimue()`	Get parameters for safir (nimue vaccine model)
`get_population()`	Get population from SQUIRE model
`get_proportion_vaccinated_nimue()`	Get proportion of an age group that is vaccinated (nimue vaccine model)
`get_state_vector()`	Get vector of states from parameters
`get_time_since_last_dose()`	Calculate the time elapsed in days since each person's last dose
`get_time_since_last_dose_or_infection()`	Calculate the time elapsed in days since each person's last dose or infection
`get_time_since_last_infection()`	Calculate the time elapsed in days since each person's last infection
`get_vaccination_priority_stage()`	Get prioritisation step for a specific dosing phase
`get_vaccine_ab_titre_parameters()`	Get vaccine efficacy and Ab titre parameters
`get_vector_cpp()`	Get a value from a vector
`identify_ages_to_adjust()`	Identify ages to adjust
`independent_ab_titre_process()`	Update NAT for seperate vaccine and infection-derived NAT
`infection_process()`	Infection process (squire transmission model)
`infection_process_cpp()`	C++ infection process (squire transmission model)
`infection_process_cpp_internal()`	C++ infection process (squire transmission model)
`infection_process_nimue()`	Infection process (nimue vaccine model)
`infection_process_nimue_cpp()`	C++ infection process (nimue vaccine model)
`infection_process_nimue_cpp_internal()`	C++ infection process (nimue vaccine model)
`infection_process_vaccine()`	Infection process for vaccine model (multi-dose, no types)
`infection_process_vaccine_cpp()`	C++ infection process for vaccine model (multi-dose, no types)
`infection_process_vaccine_cpp_internal()`	C++ infection process for vaccine model (multi-dose, no types)
`initialize_vaccine_variables()`	Initialize vaccination variables (multi-dose, no types)
`integer_count_render_process()`	Render integer variables
`integer_count_render_process_daily()`	Render integer variables every day
`interp_input_par()`	Interpolate input parameters
`interpolate_rt()`	Produce piecewise linear Rt
`iso3c_ages`	Median ages for countries
`make_calculate_nat()`	Make function to calculate population NAT
`make_immune_parameters()`	Attach parameters dealing with immune (NAT) dynamics to parameter list
`make_independent_vaccine_infection_nat_parameters()`	Attach parameters for modeling seperate vaccine and infection derived NAT
`make_rerlang()`	Make Erlang waiting time distribution
`make_rexp()`	Make discretized exponential waiting time distribution
`make_vaccine_parameters()`	Combine and verify vaccine parameters
`matrix_2vec_mult_cpp()`	Multiply a matrix by a integer vector and a double vector
`matrix_vec_mult_cpp()`	Multiply a matrix by a integer vector
`mult_2matrix_rowsum()`	Element-wise multiply two matrices and take row sums
`natural_immunity_ab_titre_process()`	Process that updates the antibody (Ab) titre each time step for model vaccine model with natural immunity
`process_hosp_renderers()`	Process rendering output of hospitalization and ICU incidence
`safir` `safir-package`	safir: squire and friends individual rewrite
`schedule_dose_vaccine()`	Schedule some individuals for a vaccination dose
`schedule_outcome()`	Schedule outcome
`setup_events()`	Schedule events for individuals at initialisation
`setup_events_nimue()`	Schedule events for individuals at initialisation (nimue vaccine model)
`simulation_loop_safir()`	Simulation loop for safir models
`swap_ages()`	Swap values that have been identified
`tab_bins()`	Tabulate a vector of observations
`tab_bins_weighted()`	Tabulate a weighted vector of observations
`target_pop()`	Target persons in each age group to vaccinate (multi-dose, no types)
`update_vaccine_variables()`	Update vaccine variables
`vaccination_process()`	Vaccination distribution process (multiple doses, no types)
`vaccination_process_nimue()`	Vaccination process (nimue vaccine model)
`vaccination_process_nimue_cpp()`	C++ vaccination process (nimue vaccine model)
`vaccination_process_nimue_cpp_internal()`	C++ infection process (nimue vaccine model)
`vaccine_ab_titre_process()`	Process that updates the antibody (Ab) titre each time step
`vaccine_efficacy_infection()`	Compute vaccine efficacy against infection from Ab titre
`vaccine_efficacy_infection_cpp()`	Compute vaccine efficacy against infection from Ab titre (C++)
`vaccine_efficacy_severe()`	Compute vaccine efficacy against severe disease from Ab titre
`vaccine_efficacy_severe_cpp()`	Compute vaccine efficacy against severe disease from Ab titre (C++)
`vaccine_efficacy_transmission()`	Compute vaccine efficacy against onward transmission from Ab titre
`vaccine_efficacy_transmission_cpp()`	Compute vaccine efficacy against onward transmission from Ab titre (C++)
`variant_fold_reduction_vector()`	Make vector of variant fold reduction in natural antibody titre values

Reference

All functions