| allocate_treatment | Allocate treatment |
| assign_doses | Assign doses to eligible persons based on available supply... |
| attach_event_listeners | Attach listeners to events |
| attach_event_listeners_independent_nat | Attach event listeners for modeling independent... |
| 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... |
| 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_events | Create events |
| create_event_scheduler_listener | A listener to schedule future 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... |
| create_exposure_scheduler_listener_vaccine | Modelling the progression to either IMild, ICase, IAsymp... |
| create_hospital_scheduler_listener | Create listener function to schedule events upon... |
| create_hospital_scheduler_listener_cpp | Create C++ listener function to schedule events upon... |
| create_hospital_scheduler_listener_cpp_internal | Internal C++ function factory for scheduling events upon... |
| create_hosp_renderers | Create list of renderer objects to track hospitalization and... |
| 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... |
| create_v3v4_to_v5_listener_nimue | Create listener for decay of vaccine protection (nimue... |
| 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... |
| 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... |
| get_time_since_last_dose_or_infection | Calculate the time elapsed in days since each person's last... |
| get_time_since_last_infection | Calculate the time elapsed in days since each person's last... |
| 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... |
| infection_process_vaccine_cpp_internal | C++ infection process for vaccine model (multi-dose, no... |
| 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... |
| make_independent_vaccine_infection_nat_parameters | Attach parameters for modeling seperate vaccine and infection... |
| 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... |
| process_hosp_renderers | Process rendering output of hospitalization and ICU incidence |
| safir | 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... |
| 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... |
| 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... |
| 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... |
| vaccine_efficacy_transmission | Compute vaccine efficacy against onward transmission from Ab... |
| vaccine_efficacy_transmission_cpp | Compute vaccine efficacy against onward transmission from Ab... |
| variant_fold_reduction_vector | Make vector of variant fold reduction in natural antibody... |
