API for EpiNow2
Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters
| Global functions | |
|---|---|
| +.dist_spec | Man page |
| .print.dist_spec | Source code |
| Distributions | Man page |
| EpiNow2 | Man page |
| EpiNow2-package | Man page |
| Fixed | Man page Source code |
| Gamma | Man page Source code |
| LogNormal | Man page Source code |
| NonParametric | Man page Source code |
| Normal | Man page Source code |
| R_to_growth | Man page Source code |
| `+.dist_spec` | Source code |
| add_day_of_week | Man page |
| adjust_infection_to_report | Man page Source code |
| allocate_delays | Man page Source code |
| allocate_empty | Man page Source code |
| apply_default_cdf_cutoff | Man page Source code |
| apply_tolerance | Man page Source code |
| backcalc_opts | Man page Source code |
| bootstrapped_dist_fit | Man page Source code |
| bound_dist | Man page Source code |
| c.dist_spec | Man page Source code |
| calc_CrI | Man page |
| calc_CrIs | Man page |
| calc_summary_measures | Man page |
| calc_summary_stats | Man page |
| check_generation_time | Man page Source code |
| check_na_setting_against_data | Man page Source code |
| check_reports_valid | Man page Source code |
| check_sparse_pmf_tail | Man page Source code |
| check_stan_delay | Man page Source code |
| clean_nowcasts | Man page Source code |
| clean_regions | Man page Source code |
| collapse | Man page Source code |
| collapse.dist_spec | Man page Source code |
| collapse.multi_dist_spec | Source code |
| construct_output | Man page |
| convert_to_logmean | Man page |
| convert_to_logsd | Man page |
| convert_to_natural | Man page Source code |
| convolve_and_scale | Man page |
| copy_results_to_latest | Man page |
| create_backcalc_data | Man page |
| create_clean_reported_cases | Man page Source code |
| create_complete_cases | Man page |
| create_delay_inits | Man page |
| create_future_rt | Man page |
| create_gp_data | Man page |
| create_initial_conditions | Man page |
| create_obs_model | Man page |
| create_rt_data | Man page |
| create_shifted_cases | Man page |
| create_stan_args | Man page |
| create_stan_data | Man page |
| create_stan_delays | Man page |
| delay_opts | Man page Source code |
| discrete_pmf | Man page Source code |
| discretise | Man page Source code |
| discretise.dist_spec | Man page Source code |
| discretise.multi_dist_spec | Source code |
| discretize | Man page |
| dist_fit | Man page Source code |
| dist_skel | Man page Source code |
| dist_spec | Man page Source code |
| doubling_time | Source code |
| epinow | Man page Source code |
| epinow2_cmdstan_model | Man page Source code |
| epinow2_rstan_model | Man page Source code |
| epinow2_stan_model | Man page Source code |
| estimate_delay | Man page Source code |
| estimate_infections | Man page Source code |
| estimate_secondary | Man page Source code |
| estimate_truncation | Man page Source code |
| estimates_by_report_date | Man page Source code |
| example_confirmed | Man page |
| example_generation_time | Man page |
| example_incubation_period | Man page |
| example_reporting_delay | Man page |
| example_truncated | Man page |
| expose_stan_fns | Man page Source code |
| extract_CrIs | Man page |
| extract_inits | Man page |
| extract_parameter | Man page Source code |
| extract_parameter_samples | Man page |
| extract_params | Man page Source code |
| extract_samples | Man page |
| extract_single_dist | Man page Source code |
| extract_stan_param | Man page |
| extract_static_parameter | Man page |
| filter_opts | Man page Source code |
| fit_model | Man page Source code |
| fit_model_approximate | Man page Source code |
| fit_model_with_nuts | Man page Source code |
| fix_dist | Man page Source code |
| fix_parameters | Man page Source code |
| fix_parameters.dist_spec | Man page Source code |
| fix_parameters.multi_dist_spec | Source code |
| forecast_infections | Man page Source code |
| forecast_secondary | Man page |
| format_fit | Man page |
| gamma_dist_def | Man page Source code |
| generation_time_opts | Man page |
| generation_times | Man page |
| get_dist | Man page Source code |
| get_distribution | Man page Source code |
| get_element | Man page Source code |
| get_generation_time | Man page Source code |
| get_incubation_period | Man page Source code |
| get_parameters | Man page Source code |
| get_pmf | Man page Source code |
| get_raw_result | Man page Source code |
| get_regional_results | Man page Source code |
| get_regions | Man page Source code |
| get_regions_with_most_reports | Man page Source code |
| get_seeding_time | Man page |
| gp_opts | Man page Source code |
| growth_to_R | Man page Source code |
| gt_opts | Man page Source code |
| incubation_periods | Man page |
| init_cumulative_fit | Man page Source code |
| is_constrained | Man page Source code |
| is_constrained.dist_spec | Man page Source code |
| is_constrained.multi_dist_spec | Source code |
| lapply_func | Man page |
| lognorm_dist_def | Man page Source code |
| lower_bounds | Man page Source code |
| make_conf | Man page Source code |
| map_prob_change | Man page Source code |
| match_output_arguments | Man page Source code |
| max.dist_spec | Man page Source code |
| max.multi_dist_spec | Source code |
| mean.dist_spec | Man page Source code |
| mean.multi_dist_spec | Source code |
| natural_params | Man page Source code |
| ndist | Man page Source code |
| new_dist_spec | Man page Source code |
| obs_opts | Man page Source code |
| opts_list | Man page Source code |
| plot | Man page |
| plot.dist_spec | Man page Source code |
| plot.epinow | Man page |
| plot.estimate_infections | Man page |
| plot.estimate_secondary | Man page Source code |
| plot.estimate_truncation | Man page |
| plot_CrIs | Man page Source code |
| plot_estimates | Man page Source code |
| plot_summary | Man page |
| print.dist_spec | Man page Source code |
| process_region | Man page |
| process_regions | Man page |
| regional_epinow | Man page Source code |
| regional_runtimes | Man page |
| regional_summary | Man page |
| report_cases | Man page Source code |
| report_plots | Man page Source code |
| report_summary | Man page Source code |
| rstan_opts | Man page Source code |
| rstan_sampling_opts | Man page Source code |
| rstan_vb_opts | Man page Source code |
| rt_opts | Man page Source code |
| run_region | Man page |
| sample_approx_dist | Man page Source code |
| save_estimate_infections | Man page Source code |
| save_input | Man page Source code |
| sd | Man page Source code |
| sd.default | Source code |
| sd.dist_spec | Man page Source code |
| sd.multi_dist_spec | Source code |
| secondary_opts | Man page Source code |
| set_dt_single_thread | Man page |
| setup_default_logging | Man page Source code |
| setup_dt | Man page Source code |
| setup_future | Man page Source code |
| setup_logging | Man page Source code |
| setup_target_folder | Man page Source code |
| simulate_infections | Man page Source code |
| simulate_secondary | Man page Source code |
| stan_laplace_opts | Man page Source code |
| stan_opts | Man page Source code |
| stan_pathfinder_opts | Man page Source code |
| stan_sampling_opts | Man page Source code |
| stan_vb_opts | Man page Source code |
| summarise_key_measures | Man page |
| summarise_results | Man page Source code |
| summary | Man page |
| summary.epinow | Man page |
| summary.estimate_infections | Man page |
| test_data_complete | Man page Source code |
| trunc_opts | Man page Source code |
| update_horizon | Man page Source code |
| update_secondary_args | Man page Source code |
