Files in mrc-ide/spimalot

Support for 'sircovid'

R/aaa.R R/check.R R/combined.R R/combined_spim.R R/control.R R/data.R R/fit.R R/fit_process.R R/fit_process_restart.R R/fit_restart.R R/mtp.R R/new_simulation.R R/parameters.R R/pars.R R/plot_combined.R R/plot_combined_forest.R R/plot_fit.R R/plot_multivariant.R R/plot_util.R R/restart.R R/simulate.R R/simulate_plots.R R/simulate_tools.R R/tools.R R/transform.R R/util.R R/util_assert.R R/vaccination.R README.md man/spim_add_forecast.Rd man/spim_add_par.Rd man/spim_beta_mult_schools.Rd man/spim_beta_mult_seasonality.Rd man/spim_calc_seasonality.Rd man/spim_calculate_doses.Rd man/spim_check_model_type.Rd man/spim_check_region.Rd man/spim_check_sircovid_model.Rd man/spim_combined_load.Rd man/spim_combined_load_multiregion.Rd man/spim_control.Rd man/spim_control_cores.Rd man/spim_data.Rd man/spim_extract_alos.Rd man/spim_extract_variants_rt.Rd man/spim_fit_pars_load.Rd man/spim_fit_process.Rd man/spim_fit_run.Rd man/spim_mtp_age_vaccine_outputs.Rd man/spim_mtp_population.Rd man/spim_mtp_summary_to_template.Rd man/spim_multivariant_rt_plot.Rd man/spim_pars_check_beta_date.Rd man/spim_pars_pmcmc_load.Rd man/spim_pars_pmcmc_save.Rd man/spim_particle_filter.Rd man/spim_plot_Rt.Rd man/spim_plot_alos.Rd man/spim_plot_check_doses.Rd man/spim_plot_check_rt.Rd man/spim_plot_check_state.Rd man/spim_plot_check_state_by_age.Rd man/spim_plot_check_total_doses.Rd man/spim_plot_check_uptake.Rd man/spim_plot_cumulative_attack_rate.Rd man/spim_plot_daily_infections.Rd man/spim_plot_effective_susceptible.Rd man/spim_plot_fit.Rd man/spim_plot_forest.Rd man/spim_plot_ifr_t.Rd man/spim_plot_incidence.Rd man/spim_plot_infection_status.Rd man/spim_plot_infections_per_strain.Rd man/spim_plot_log_traj_by_age.Rd man/spim_plot_ons.Rd man/spim_plot_pillar2_cases.Rd man/spim_plot_pillar2_positivity.Rd man/spim_plot_prop_susceptible.Rd man/spim_plot_react.Rd man/spim_plot_rt_dist.Rd man/spim_plot_seasonality.Rd man/spim_plot_seeding_date.Rd man/spim_plot_serology.Rd man/spim_plot_trajectories.Rd man/spim_plot_trajectories_by_age.Rd man/spim_plot_vaccine_figures.Rd man/spim_plot_vaccine_status.Rd man/spim_plot_variant.Rd man/spim_plot_voc_proportion.Rd man/spim_plot_voc_range.Rd man/spim_population.Rd man/spim_prepare_aggregated_data.Rd man/spim_prop_infected.Rd man/spim_region_name.Rd man/spim_rejuvenatoR.Rd man/spim_restart_initial.Rd man/spim_restart_initial_state.Rd man/spim_restart_join_parent.Rd man/spim_restart_pars.Rd man/spim_rrq_controller.Rd man/spim_scenario_cols.Rd man/spim_simulate_add_all_deaths.Rd man/spim_simulate_add_diagnoses_admitted.Rd man/spim_simulate_add_trajectory_incidence.Rd man/spim_simulate_args.Rd man/spim_simulate_combine_trajectories.Rd man/spim_simulate_complete_doses.Rd man/spim_simulate_control.Rd man/spim_simulate_control_output.Rd man/spim_simulate_create_summary.Rd man/spim_simulate_local.Rd man/spim_simulate_parameter_grid.Rd man/spim_simulate_prepare.Rd man/spim_simulate_process_output.Rd man/spim_simulate_remove_dates_to.Rd man/spim_simulate_reset_cumulative_states.Rd man/spim_simulate_rrq.Rd man/spim_simulate_set_beta_step.Rd man/spim_simulate_simplify_rt.Rd man/spim_simulate_tidy_states.Rd man/spim_simulation_predictors.Rd man/spim_simulation_shaps.Rd man/spim_summary.Rd man/spim_vaccination_data.Rd man/tidy_state_one.Rd tests/testthat.R tests/testthat/helper-spimalot.R tests/testthat/test-check.R tests/testthat/test-control.R tests/testthat/test-pars.R tests/testthat/test-plot-util.R tests/testthat/test-restart.R tests/testthat/test-simulation-new.R tests/testthat/test-tools.R tests/testthat/test-util-assert.R tests/testthat/test-util.R