Files in mrc-ide/safir

Individual-Based Model of COVID Transmission

R/RcppExports.R R/assertions.R R/data.R R/distribution_vaccines.R R/efficacy_nat.R R/events.R R/events_exposure.R R/events_exposure_nimue.R R/events_exposure_vaccine.R R/events_hospital.R R/events_nat.R R/events_vaccination.R R/events_vaccination_nimue.R R/initialize_events.R R/initialize_events_nimue.R R/parameters.R R/parameters_nat.R R/parameters_nimue.R R/parameters_vaccine.R R/process_infection.R R/process_infection_nimue.R R/process_infection_vaccine.R R/process_nat.R R/process_vaccination.R R/process_vaccination_nimue.R R/render-hosp.R R/render.R R/safir.R R/simulation_loop_safir.R R/utils.R R/variables.R R/variables_nat.R R/variables_states.R R/variables_vaccines.R README.md inst/devnotes.md inst/test_scripts/debug.R inst/test_scripts/sim_GBR.R inst/test_scripts/sim_GBR_1core.R inst/test_scripts/sim_nimue.R inst/test_scripts/sim_vaccine_2dose_notypes_model.R inst/test_scripts/sim_vaccine_2dose_notypes_model_vax_effective.R inst/test_scripts/sim_vaccine_2dose_notypes_model_vax_ineffective.R inst/test_scripts/sim_vaccine_3dose_notypes_model.R inst/test_scripts/sim_vaccine_differential_nat.R inst/test_scripts/sim_vaccine_naturalimmunity.R man/allocate_treatment.Rd man/assign_doses.Rd man/attach_event_listeners.Rd man/attach_event_listeners_independent_nat.Rd man/attach_event_listeners_natural_immunity.Rd man/attach_event_listeners_nimue.Rd man/attach_event_listeners_vaccination.Rd man/attach_hosp_listeners.Rd man/attach_tracking_listener_age_incidence.Rd man/attach_tracking_listener_incidence.Rd man/categorical_count_renderer_process_daily.Rd man/compartments_age_render_process_daily.Rd man/create_age_incidence_tracking_listener.Rd man/create_age_variables.Rd man/create_continuous_age_variable.Rd man/create_discrete_age_variable.Rd man/create_event_scheduler_listener.Rd man/create_events.Rd man/create_events_nimue.Rd man/create_events_vaccination.Rd man/create_exposure_scheduler_listener_nimue.Rd man/create_exposure_scheduler_listener_vaccine.Rd man/create_hosp_renderers.Rd man/create_hospital_scheduler_listener.Rd man/create_hospital_scheduler_listener_cpp.Rd man/create_hospital_scheduler_listener_cpp_internal.Rd man/create_incidence_tracking_listener.Rd man/create_independent_nat_variables.Rd man/create_natural_immunity_variables.Rd man/create_state_update_listener.Rd man/create_state_variables.Rd man/create_v0_to_v1v2_listener_nimue.Rd man/create_v1v2_to_v3v4_listener_nimue.Rd man/create_v3v4_to_v5_listener_nimue.Rd man/create_vaccination_dose_listener.Rd man/create_vaccine_variables.Rd man/create_vaccine_variables_nimue.Rd man/create_variables.Rd man/cross_tab_compartments_age.Rd man/cross_tab_doses_age.Rd man/cross_tab_margins.Rd man/dose_age_render_process_daily.Rd man/get_asymptomatic.Rd man/get_contact_matrix_cpp.Rd man/get_current_coverage.Rd man/get_current_eligible_from_coverage.Rd man/get_parameters.Rd man/get_parameters_nimue.Rd man/get_population.Rd man/get_proportion_vaccinated_nimue.Rd man/get_state_vector.Rd man/get_time_since_last_dose.Rd man/get_time_since_last_dose_or_infection.Rd man/get_time_since_last_infection.Rd man/get_vaccination_priority_stage.Rd man/get_vaccine_ab_titre_parameters.Rd man/get_vector_cpp.Rd man/identify_ages_to_adjust.Rd man/independent_ab_titre_process.Rd man/infection_process.Rd man/infection_process_cpp.Rd man/infection_process_cpp_internal.Rd man/infection_process_nimue.Rd man/infection_process_nimue_cpp.Rd man/infection_process_nimue_cpp_internal.Rd man/infection_process_vaccine.Rd man/infection_process_vaccine_cpp.Rd man/infection_process_vaccine_cpp_internal.Rd man/initialize_vaccine_variables.Rd man/integer_count_render_process.Rd man/integer_count_render_process_daily.Rd man/interp_input_par.Rd man/interpolate_rt.Rd man/iso3c_ages.Rd man/make_calculate_nat.Rd man/make_immune_parameters.Rd man/make_independent_vaccine_infection_nat_parameters.Rd man/make_rerlang.Rd man/make_rexp.Rd man/make_vaccine_parameters.Rd man/matrix_2vec_mult_cpp.Rd man/matrix_vec_mult_cpp.Rd man/mult_2matrix_rowsum.Rd man/natural_immunity_ab_titre_process.Rd man/process_hosp_renderers.Rd man/safir.Rd man/schedule_dose_vaccine.Rd man/schedule_outcome.Rd man/setup_events.Rd man/setup_events_nimue.Rd man/simulation_loop_safir.Rd man/swap_ages.Rd man/tab_bins.Rd man/tab_bins_weighted.Rd man/target_pop.Rd man/update_vaccine_variables.Rd man/vaccination_process.Rd man/vaccination_process_nimue.Rd man/vaccination_process_nimue_cpp.Rd man/vaccination_process_nimue_cpp_internal.Rd man/vaccine_ab_titre_process.Rd man/vaccine_efficacy_infection.Rd man/vaccine_efficacy_infection_cpp.Rd man/vaccine_efficacy_severe.Rd man/vaccine_efficacy_severe_cpp.Rd man/vaccine_efficacy_transmission.Rd man/vaccine_efficacy_transmission_cpp.Rd man/variant_fold_reduction_vector.Rd tests/testthat.R tests/testthat/helper-integration.R tests/testthat/helper-test-nat-decay.R tests/testthat/helper-test-vaccination-distribution.R tests/testthat/helper-test-vaccination-phase.R tests/testthat/helper-test-vaccination-process.R tests/testthat/helper-test-vfr.R tests/testthat/test-assertions.R tests/testthat/test-contact_matrices.R tests/testthat/test-differential-vaxx-infection-nat.R tests/testthat/test-efficacy-naturalimmunity.R tests/testthat/test-efficacy-vaccination.R tests/testthat/test-events_hospitalization.R tests/testthat/test-hospitalisation.R tests/testthat/test-nat-decay.R tests/testthat/test-parameters.R tests/testthat/test-processes-nimue.R tests/testthat/test-processes-squire.R tests/testthat/test-processes-vaccination-onwardtransmission.R tests/testthat/test-processes-vaccination.R tests/testthat/test-render.R tests/testthat/test-utils-cpp.R tests/testthat/test-utils.R tests/testthat/test-vaccination-distribution.R tests/testthat/test-vaccination-phase.R tests/testthat/test-vaccination-process.R tests/testthat/test-variables.R tests/testthat/test-vfr.R vignettes/antibody_efficacy.Rmd vignettes/compare_nimue.Rmd vignettes/compare_squire.Rmd vignettes/differential_nat.Rmd vignettes/natural_immunity.Rmd vignettes/vaccine_notypes.Rmd