Man pages for mrc-ide/spimalot
Support for 'sircovid'
| spim_add_forecast | Add forecasts to combined fit object |
| spim_add_par | Add parameter |
| spim_beta_mult_schools | Calculate multiplicative beta for schools |
| spim_beta_mult_seasonality | Calculate multiplicative beta due to seasonality |
| spim_calc_seasonality | Seasonality |
| spim_calculate_doses | Calculate doses given out from simulation |
| spim_check_model_type | Check a model type |
| spim_check_region | Validate and expand regions |
| spim_check_sircovid_model | Check a model type |
| spim_combined_load | Load combined fits |
| spim_combined_load_multiregion | Load multiregion fits as a combined fit object |
| spim_control | High-level control |
| spim_control_cores | Return the number of cores |
| spim_data | Organise input data |
| spim_extract_alos | Extract average length of hospital stay |
| spim_extract_variants_rt | Extract multivariant Rt |
| spim_fit_pars_load | Load parameters |
| spim_fit_process | Process a fit for 'lancelot' model |
| spim_fit_run | Run fit |
| spim_mtp_age_vaccine_outputs | MTP simulation outputs by age and vaccination class |
| spim_mtp_population | Generate MTP population from combined |
| spim_mtp_summary_to_template | Port MTP outcomes to template |
| spim_multivariant_rt_plot | Create multivariant Rt plot |
| spim_pars_check_beta_date | Validate vector of beta dates |
| spim_pars_pmcmc_load | Load a set of parameters for the pmcmc |
| spim_pars_pmcmc_save | Write out parameters |
| spim_particle_filter | Construct a particle filter |
| spim_plot_alos | Plot average length of stay over time |
| spim_plot_check_doses | Check doses given out from simulation |
| spim_plot_check_rt | Check Rt from simulation |
| spim_plot_check_state | Check states from simulation |
| spim_plot_check_state_by_age | Check states by age from simulation |
| spim_plot_check_total_doses | Check total doses given out from simulation |
| spim_plot_check_uptake | Check dose uptake from simulation |
| spim_plot_cumulative_attack_rate | Plot cumulative attack rate |
| spim_plot_daily_infections | Check daily infections from simulation |
| spim_plot_effective_susceptible | Plot effective susceptibles |
| spim_plot_fit | Plots for fit |
| spim_plot_forest | Forest plot |
| spim_plot_ifr_t | Plot IFR over time |
| spim_plot_incidence | Plot incidence |
| spim_plot_infections_per_strain | Plot infections per strain |
| spim_plot_infection_status | Plot infection status |
| spim_plot_log_traj_by_age | Plot log trajectories by age |
| spim_plot_ons | Plot ONS |
| spim_plot_pillar2_cases | Plot Pillar 2 cases |
| spim_plot_pillar2_positivity | Plot Pillar 2 positivity |
| spim_plot_prop_susceptible | Plot proportion susceptible |
| spim_plot_react | Plot REACT |
| spim_plot_Rt | Plot Rt |
| spim_plot_rt_dist | Plot Rt distribution |
| spim_plot_seasonality | Plot seasonality over time |
| spim_plot_seeding_date | Create plot for estimated seeding date |
| spim_plot_serology | Plot serology |
| spim_plot_trajectories | Plot trajectories |
| spim_plot_trajectories_by_age | Plot trajectories by age |
| spim_plot_vaccine_figures | Create plot for vaccine paper figure 1 |
| spim_plot_vaccine_status | Plot vaccine status |
| spim_plot_variant | Plot variant |
| spim_plot_voc_proportion | Create plot for VOC proportion |
| spim_plot_voc_range | Plot relative strain transmissibility ranges |
| spim_population | Get population from combined |
| spim_prepare_aggregated_data | Prepare aggregated data for plotting |
| spim_prop_infected | Get proportion infected from combined |
| spim_region_name | Convert region names |
| spim_rejuvenatoR | Find daily little r values from big R |
| spim_restart_initial | Create restart initial conditions |
| spim_restart_initial_state | Load restart data |
| spim_restart_join_parent | Join parent and restart fits |
| spim_restart_pars | Create restart parameters |
| spim_rrq_controller | Find rrq controller |
| spim_scenario_cols | Return accessible scenario colours |
| spim_simulate_add_all_deaths | Combine all death trajectories |
| spim_simulate_add_diagnoses_admitted | Combine diagnoses and admitted trajectories |
| spim_simulate_add_trajectory_incidence | Calculate incidence trajectories for a simulated object |
| spim_simulate_args | Create simulation parameters |
| spim_simulate_combine_trajectories | Combine regional simulated trajectories |
| spim_simulate_complete_doses | Calculate final doses date |
| spim_simulate_control | Create control parameters |
| spim_simulate_control_output | Create output control for simulations |
| spim_simulate_create_summary | Summarise simulations over particles |
| spim_simulate_local | Run simulations locally |
| spim_simulate_parameter_grid | Prepare parameter update list |
| spim_simulate_prepare | Prepare for simulation |
| spim_simulate_process_output | Process simulation output |
| spim_simulate_remove_dates_to | Remove simulations up to given date |
| spim_simulate_reset_cumulative_states | Reset cumulative states to zero at start of simulation |
| spim_simulate_rrq | Run simulations with rrq |
| spim_simulate_set_beta_step | Add beta_step into control |
| spim_simulate_simplify_rt | Simplify simulation object by moving Rt in with trajectories |
| spim_simulate_tidy_states | Create tidy (long) dataframe of simulated results |
| spim_simulation_predictors | Return predictive simulation variables |
| spim_simulation_shaps | Calculate SHAPs over predicted states |
| spim_summary | Create summaries |
| spim_vaccination_data | Prepare vaccination data |
| tidy_state_one | Create tidy (long) dataframe of simulated results |
