Man pages for epiforecasts/EpiNow
Estimate Realtime Case Counts and Time-varying Epidemiological Parameters
| add_dates | Add Dates from Daata |
| adjust_for_truncation | Adjust Case Counts for Truncation |
| adjust_infection_to_report | Adjust from Case Counts by Infection Date to Date of Report |
| clean_nowcasts | Clean Nowcasts for a Supplied Date |
| country_map | Generate a country map for a single variable. |
| covid_generation_times | Covid Generation Time Estimates |
| covid_generation_times_summary | Covid Generation Time Estimates - Summary |
| covid_incubation_period | Covid Incubation Period |
| covid_serial_intervals | Covid Generation Serial Intervals |
| dist_fit | Fit an integer adjusted exponential or gamma distribution |
| dist_skel | Distribution Skeleton |
| epi_measures_pipeline | Estimate time-varying measures and forecast |
| estimate_doubling_time | Estimate the doubling time |
| estimate_little_r | Estimate r |
| estimate_R0 | Estimate the time varying R0 - using EpiEstim |
| estimate_r_in_window | Estimate r in a set time window |
| estimate_time_varying_r | Estimate time varying r |
| gamma_dist_def | Generate a Gamma Distribution Definition Based on Parameter... |
| generate_pseudo_linelist | Generate a sample linelist from the observed linelist and... |
| get_dist_def | Get a Parameters that Define a Discrete Distribution |
| get_local_import_case_counts | Combine total and imported case counts |
| get_regions | Get Folders with Nowcast Results |
| get_timeseries | Get Timeseries from EpiNow |
| global_map | Generate a global map for a single variable. |
| growth_to_R | Convert Growth Rates to Reproduction numbers. |
| linelist_from_case_counts | Sample a linelist from case counts and a reporting delay... |
| load_nowcast_result | Load nowcast results |
| lognorm_dist_def | Generate a Log Normal Distribution Definition Based on... |
| make_conf | Format Credible Intervals |
| map_prob_change | Categorise the Probability of Change for Rt |
| nowcast_pipeline | Impute Cases Date of Infection |
| plot_confidence | Plot a Time Series with Confidence. |
| plot_forecast | Add a Forecast to a Plot |
| plot_grid | Plot a Grid of Plots |
| plot_pipeline | Plot Pipeline Results |
| plot_summary | Plot a Summary of the Latest Results |
| pull_max_var | Extract a the Maximum Value of a Variable Based on a Filter |
| rbinom_size | Draw with an offset from a negative binomial distribution |
| regional_rt_pipeline | Regional Realtime Pipeline |
| regional_summary | Generate Regional Summary Output |
| report_cases | Report case counts by date of report |
| report_littler | Report Rate of Growth Estimates |
| report_nowcast | Report Case Nowcast Estimates |
| report_reff | Report Effective Reproduction Number Estimates |
| report_summary | Provide Summary Statistics on an Rt Pipeline |
| R_to_growth | Convert Reproduction Numbers to Growth Rates |
| rt_pipeline | Real-time Pipeline |
| sample_approx_dist | Approximate Sampling a Distribution using Counts |
| sample_delay | Sample Onset Dates for Cases missing them |
| simulate_cases | Simulate Cases by Date of Infection, Onset and Report |
| split_linelist_by_day | Convert a linelist into a nested 'data.table" of linelists by... |
| summarise_cast | Summarise a nowcast |
| summarise_results | Summarise Realtime Results |
| summarise_to_csv | Summarise rt and cases as a csv |
| theme_map | Custom Map Theme |
