API for EpiNow2
Estimate and Forecast Real-Time Infection Dynamics
| Global functions | |
|---|---|
| !=.dist_spec | Man page |
| $.epinow | Man page |
| $.estimate_infections | Man page |
| $.estimate_secondary | Man page |
| +.dist_spec | Man page |
| .build_forecast_sample | Source code |
| .extract_to_dist_spec | Man page Source code |
| .get_dist_id | Man page Source code |
| .get_param_names | Man page Source code |
| .prepare_linelist_data | Man page Source code |
| .print.dist_spec | Source code |
| ==.dist_spec | Man page |
| Dirichlet | Man page Source code |
| Distributions | Man page |
| EpiNow2 | Man page |
| EpiNow2-package | Man page |
| Exp | Man page Source code |
| Fixed | Man page Source code |
| Gamma | Man page Source code |
| LogNormal | Man page Source code |
| NonParametric | Man page Source code |
| Normal | Man page Source code |
| R_to_growth | Man page Source code |
| Weibull | Man page Source code |
| [[.epinow | Man page |
| [[.estimate_infections | Man page |
| [[.estimate_secondary | Man page |
| `!=.dist_spec` | Source code |
| `$.epinow` | Source code |
| `$.estimate_infections` | Source code |
| `+.dist_spec` | Source code |
| `==.dist_spec` | Source code |
| `[[.epinow` | Source code |
| `[[.estimate_infections` | Source code |
| add_breakpoints | Man page |
| add_day_of_week | Man page |
| add_horizon | 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_zero_threshold | Man page |
| as_forecast_sample | Man page |
| as_forecast_sample.epinow | Man page Source code |
| as_forecast_sample.estimate_infections | Man page Source code |
| as_forecast_sample.estimate_truncation | Man page Source code |
| as_forecast_sample.forecast_secondary | Man page Source code |
| backcalc_opts | Man page Source code |
| bootstrapped_dist_fit | Man page Source code |
| bound_dist | Man page Source code |
| build_np_est_data | 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_reports_valid | Man page Source code |
| check_simulation_input | Man page Source code |
| check_sparse_pmf_tail | Man page Source code |
| check_stan_delay | Man page Source code |
| check_truncation_length | Man page Source code |
| check_truncation_obs_opts | 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 |
| combine_tv_and_static_params | Man page 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 Source code |
| create_delay_inits | Man page Source code |
| create_future_rt | Man page Source code |
| create_gp_data | Man page Source code |
| create_infection_summary | Man page Source code |
| create_initial_conditions | Man page Source code |
| create_obs_model | Man page Source code |
| create_rt_data | Man page Source code |
| create_sampling_log_message | Man page Source code |
| create_shifted_cases | Man page Source code |
| create_stan_args | Man page Source code |
| create_stan_data | Man page Source code |
| create_stan_delays | Man page Source code |
| create_stan_params | Man page Source code |
| 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_id_to_name | 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 |
| epinow_compat_extract | Source code |
| estimate_delay | Man page Source code |
| estimate_dist | Man page Source code |
| estimate_infections | Man page Source code |
| estimate_secondary | Man page Source code |
| estimate_truncation | Man page |
| 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_delay_params | Man page |
| extract_delays | Man page |
| extract_inits | Man page |
| extract_latent_state | Man page Source code |
| extract_parameters | Man page |
| extract_params | Man page Source code |
| extract_samples | Man page |
| extract_scalar_params | Man page |
| extract_single_dist | Man page Source code |
| extract_stan_param | Man page |
| fill_missing | Man page Source code |
| filter_leading_zeros | 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_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_opts | Man page Source code |
| forecast_secondary | Man page |
| format_fit | Man page Source code |
| format_quantile_predictions | Man page |
| format_sample_predictions | Man page |
| format_samples_with_dates | Man page Source code |
| format_simulation_output | Man page Source code |
| generation_time_opts | Man page |
| get_accumulate | Man page Source code |
| get_distribution | Man page Source code |
| get_element | Man page Source code |
| get_parameters | Man page Source code |
| get_parameters.dist_spec | Man page Source code |
| get_parameters.epinowfit | Man page |
| get_parameters.estimate_dist | Man page |
| get_pmf | Man page Source code |
| get_predictions | Man page |
| get_predictions.estimate_infections | Man page |
| get_predictions.estimate_secondary | Man page |
| get_predictions.estimate_truncation | Man page |
| get_predictions.forecast_infections | Man page |
| get_predictions.forecast_secondary | Man page |
| 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_samples | Man page |
| get_samples.epinow | Man page |
| get_samples.estimate_infections | Man page |
| get_samples.estimate_secondary | Man page |
| get_samples.estimate_truncation | Man page |
| get_samples.forecast_infections | Man page |
| get_samples.forecast_secondary | Man page |
| get_seeding_time | Man page |
| gp_opts | Man page Source code |
| growth_to_R | Man page Source code |
| gt_opts | 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 |
| lower_bounds | Man page Source code |
| make_conf | Man page Source code |
| make_init_priors | Man page |
| make_param | Man page |
| 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 |
| merge_trunc_pred_obs | Man page |
| natural_params | Man page Source code |
| ndist | Man page Source code |
| new_dist_spec | Man page Source code |
| nonparametric_pmf_data | Man page Source code |
| obs_opts | Man page Source code |
| opts_list | Man page Source code |
| pack_init_prior | Man page |
| pad_reported_cases | Man page |
| plot.dist_spec | Man page Source code |
| plot.estimate_infections | Man page |
| plot.estimate_secondary | Man page Source code |
| plot.estimate_truncation | Man page |
| plot.forecast_infections | Man page |
| plot.forecast_secondary | Man page |
| plot_CrIs | Man page Source code |
| plot_estimates | Man page Source code |
| plot_summary | Man page |
| posterior_to_normal | Man page |
| prepare_truncation_obs | Man page Source code |
| print.dist_spec | Man page Source code |
| print.epinowfit | Man page |
| process_region | Man page |
| process_regions | Man page |
| rdirichlet | Man page Source code |
| reconstruct_delay | Man page |
| reconstruct_nonparametric | Man page |
| reconstruct_parametric | Man page |
| regional_epinow | Man page Source code |
| regional_runtimes | Man page |
| regional_summary | Man page |
| report_plots | Man page Source code |
| report_summary | Man page Source code |
| rt_opts | Man page Source code |
| run_region | Man page |
| 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 |
| select_plots | Man page |
| 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 |
| stable_convolve | Man page |
| 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_dist | Man page |
| summary.estimate_infections | Man page |
| summary.estimate_secondary | Man page |
| summary.estimate_truncation | Man page |
| summary.forecast_infections | Man page |
| trunc_opts | Man page Source code |
| update_horizon | Man page Source code |
| update_secondary_args | Man page Source code |
