mrc-ide/spimalot
Support for 'sircovid'

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384
Source code
39
Man pages
96
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mrc-ide/spimalot: Support for 'sircovid'
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API

API for mrc-ide/spimalot
Support for 'sircovid'

Global functions
`$<-.immutable` Source code
`%||%` Source code
`[<-.immutable` Source code
`[[<-.immutable` Source code
abind1 Source code
abind_quiet Source code
add_alpha Source code
assert_character Source code
assert_date_string Source code
assert_file_exists Source code
assert_has_names Source code
assert_increasing Source code
assert_integer Source code
assert_is Source code
assert_length Source code
assert_logical Source code
assert_names_setequal Source code
assert_nonmissing Source code
assert_numeric Source code
assert_scalar Source code
assert_scalar_character Source code
assert_scalar_logical Source code
assert_scalar_numeric Source code
assert_scalar_positive_integer Source code
assert_setequal Source code
assert_unique Source code
calc_weighted_protected Source code
calculate_cases Source code
calculate_cases_region Source code
calculate_intrinsic_severity Source code
calculate_intrinsic_severity_region Source code
calculate_lancelot_Rt Source code
calculate_lancelot_Rt_region Source code
calculate_n_protected Source code
calculate_negatives Source code
calculate_negatives_region Source code
calculate_vaccination Source code
check_region Source code
ci_bands Source code
combine_demography Source code
combine_variant_rt Source code
combined_aggregate_data Source code
combined_aggregate_demography Source code
combined_aggregate_intrinsic_severity Source code
combined_aggregate_prop_protected Source code
combined_aggregate_rt Source code
combined_aggregate_samples Source code
combined_aggregate_severity Source code
combined_aggregate_variant_rt Source code
combined_calculate_variant_r0 Source code
combined_intrinsic_severity Source code
combined_severity Source code
combined_severity_1 Source code
combined_switch_levels Source code
create_simulate_object Source code
create_summary_state Source code
data_frame Source code
deaths_filter_time Source code
extract_age_class_outputs Source code
extract_age_class_state Source code
extract_demography Source code
extract_demography_region Source code
extract_severity Source code
extract_severity_region Source code
fit_prior Source code
fit_process_restart Source code
fit_process_restart_priors Source code
gelman_diagnostic Source code
get_deaths_admissions_by_vacc_class Source code
get_names Source code
get_r_vaccinated Source code
get_vaccine_protection Source code
immutable_error Source code
last Source code
list_transpose Source code
load_transform Source code
make_prior Source code
match_value Source code
mean_ci Source code
mix_cols Source code
move_strain_compartments Source code
mtp_template_common Source code
nlayers Source code
plot_ci_bar Source code
proportion_fill Source code
quantile_digest Source code
read_csv Source code
reduce_trajectories Source code
reorder_beta Source code
reorder_intrinsic_severity Source code
reorder_sample_full Source code
reorder_variant_rt Source code
rt_filter_time Source code
seq_rows Source code
set_names Source code
setup_future_betas Source code
simulate_args_names Source code
simulate_args_validate Source code
simulate_calculate_vaccination Source code
simulate_extract_age_class_state Source code
simulate_index Source code
simulate_one_pars_vaccination Source code
simulate_prepare_drop_regions Source code
simulate_prepare_inflate_strain Source code
simulate_prepare_inflate_vacc_classes Source code
simulate_prepare_upgrade Source code
simulate_rt Source code
simulate_seed_parameters Source code
simulate_validate_args1 Source code
simulation_central_analysis Source code
spim_add_forecast Man page Source code
spim_add_forecast_region Source code
spim_add_par Man page Source code
spim_add_par_beta Man page Source code
spim_beta_mult_schools Man page Source code
spim_beta_mult_seasonality Man page Source code
spim_calc_seasonality Man page Source code
spim_calculate_doses Man page Source code
spim_check_model_type Man page Source code
spim_check_region Man page Source code
spim_check_sircovid_model Man page Source code
spim_colours Source code
spim_combined_load Man page Source code
spim_combined_load_multiregion Man page Source code
spim_combined_onward Source code
spim_combined_onward_simulate Source code
spim_control Man page Source code
spim_control_cores Man page Source code
spim_control_parallel Source code
spim_data Man page Source code
spim_data_serology Source code
spim_data_single Source code
spim_extract_alos Man page Source code
spim_extract_variants_rt Man page Source code
spim_fit_parameters Source code
spim_fit_pars_load Man page Source code
spim_fit_pars_load_nested Source code
spim_fit_pars_load_single Source code
spim_fit_process Man page Source code
spim_fit_run Man page Source code
spim_lancelot_data_rtm Source code
spim_lancelot_transform Source code
spim_mtp_age_vaccine_outputs Man page Source code
spim_mtp_population Man page Source code
spim_mtp_summary_to_template Man page Source code
spim_multivariant_rt_plot Man page Source code
spim_pars_check_beta_date Man page Source code
spim_pars_info_nested Source code
spim_pars_info_single Source code
spim_pars_mcmc_nested Source code
spim_pars_mcmc_single Source code
spim_pars_pmcmc_load Man page Source code
spim_pars_pmcmc_save Man page Source code
spim_pars_prior_nested Source code
spim_pars_prior_single Source code
spim_pars_proposal_nested Source code
spim_pars_proposal_single Source code
spim_particle_filter Man page Source code
spim_plot_Rt Man page Source code
spim_plot_Rt_region Source code
spim_plot_alos Man page Source code
spim_plot_alos_region Source code
spim_plot_check_doses Man page Source code
spim_plot_check_rt Man page Source code
spim_plot_check_state Man page Source code
spim_plot_check_state_by_age Man page Source code
spim_plot_check_total_doses Man page Source code
spim_plot_check_uptake Man page Source code
spim_plot_cumulative_attack_rate Man page Source code
spim_plot_cumulative_attack_rate_region Source code
spim_plot_daily_infections Man page Source code
spim_plot_effective_susceptible Man page Source code
spim_plot_effective_susceptible_region Source code
spim_plot_fit_forecasts Man page Source code
spim_plot_fit_posteriors Man page Source code
spim_plot_fit_traces Man page Source code
spim_plot_fit_traces_separate Man page Source code
spim_plot_forest Man page Source code
spim_plot_ifr_t Man page Source code
spim_plot_ifr_t_region Source code
spim_plot_incidence Man page Source code
spim_plot_incidence_region Source code
spim_plot_infection_status Man page Source code
spim_plot_infection_status_region Source code
spim_plot_infections_per_strain Man page Source code
spim_plot_infections_per_strain_region Source code
spim_plot_log_traj_by_age Man page Source code
spim_plot_log_traj_by_age_region Source code
spim_plot_log_traj_by_age_region1 Source code
spim_plot_ons Man page Source code
spim_plot_ons_region Source code
spim_plot_pillar2_cases Man page Source code
spim_plot_pillar2_cases_region Source code
spim_plot_pillar2_positivity Man page Source code
spim_plot_pillar2_positivity_region Source code
spim_plot_prop_susceptible Man page Source code
spim_plot_prop_susceptible_region Source code
spim_plot_react Man page Source code
spim_plot_react_region Source code
spim_plot_rt_dist Man page Source code
spim_plot_seasonality Man page Source code
spim_plot_seeding_date Man page Source code
spim_plot_serology Man page Source code
spim_plot_serology_region Source code
spim_plot_trajectories Man page Source code
spim_plot_trajectories_by_age Man page Source code
spim_plot_trajectories_region Source code
spim_plot_trajectories_region1 Source code
spim_plot_vaccine_figures Man page Source code
spim_plot_vaccine_status Man page Source code
spim_plot_vaccine_status_region Source code
spim_plot_variant Man page Source code
spim_plot_variant_region Source code
spim_plot_variant_transmission Source code
spim_plot_voc_proportion Man page Source code
spim_plot_voc_range Man page Source code
spim_pmcmc_predict Source code
spim_population Man page Source code
spim_prepare_aggregated_data Man page Source code
spim_prop_infected Man page Source code
spim_region_name Man page Source code
spim_rejuvenatoR Man page Source code
spim_restart_initial Man page Source code
spim_restart_initial_state Man page Source code
spim_restart_join_parent Man page Source code
spim_restart_pars Man page Source code
spim_rrq_controller Man page Source code
spim_scenario_cols Man page Source code
spim_simulate Source code
spim_simulate_add_all_deaths Man page Source code
spim_simulate_add_diagnoses_admitted Man page Source code
spim_simulate_add_trajectory_incidence Man page Source code
spim_simulate_args Man page Source code
spim_simulate_combine_trajectories Man page Source code
spim_simulate_complete_doses Man page Source code
spim_simulate_control Man page Source code
spim_simulate_control_output Man page Source code
spim_simulate_create_summary Man page Source code
spim_simulate_local Man page Source code
spim_simulate_one Source code
spim_simulate_parameter_grid Man page Source code
spim_simulate_prepare Man page Source code
spim_simulate_process_output Man page Source code
spim_simulate_remove_dates_to Man page Source code
spim_simulate_reset_cumulative_states Man page Source code
spim_simulate_rrq Man page Source code
spim_simulate_set_beta_step Man page Source code
spim_simulate_simplify_rt Man page Source code
spim_simulate_tidy_states Man page Source code
spim_simulation_predictors Man page Source code
spim_simulation_shaps Man page Source code
spim_summary_nowcast Man page Source code
spim_summary_quantiles Source code
spim_summary_region_forecast Source code
spim_summary_region_forecast_trajectory Source code
spim_summary_region_growth_rate Source code
spim_summary_region_incidence Source code
spim_summary_region_prevalence Source code
spim_summary_region_rt Source code
spim_summary_time_series Man page Source code
spim_summary_write Man page Source code
spim_template Source code
spim_vaccination_data Man page Source code
spimalot_file Source code
squote Source code
str_collapse Source code
summarise_intrinsic_severity Source code
summarise_states Source code
summarise_states_region Source code
summary_quantile_range Source code
tidy_state_one Man page Source code
trajectories_filter_time Source code
validate_rt_future Source code
validate_rt_schools_schedule Source code
validate_simulate_parameters Source code
validate_strain_seed_rate Source code
validate_strain_severity_modifier Source code
validate_vaccine_doses Source code
validate_vaccine_efficacy Source code
vlapply Source code
vnapply Source code
write_csv Source code
mrc-ide/spimalot documentation built on Oct. 15, 2024, 12:15 p.m.

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