Man pages for epiforecasts/forecast.vocs
Forecast Case and Sequence Notifications using Variant of Concern Strain Dynamics
| add_forecast_dates | Add the forecast dates to a plot |
| bp_launch_shinystan | Launch shinystan |
| check_dataframe | Check a data.frame |
| check_observations | Check observations are in the correct format |
| check_param | Check a parameter is the correct type and length |
| check_quantiles | Check Quantiles Required are Present |
| convert_to_stanfit | Convert to stanfit object |
| define_scenarios | Define data availability scenarios |
| extract_draws | Extract posterior draws |
| extract_forecast_dates | Extract forecast dates |
| filter_by_availability | Filter data based on availability and forecast date |
| forecast | Forecast using branching processes at a target date |
| forecast_across_dates | Forecast across multiple dates |
| forecast_across_scenarios | Forecast across multiple scenarios and dates |
| forecast_n_strain | Forecast for a single model and summarise |
| forecast.vocs-package | forecast.vocs: Forecast Case and Sequence Notifications using... |
| fv_as_data_list | Format data for use with stan |
| fv_dow_period | Calculate the day of the week periodicity |
| fv_example | Load a package example |
| fv_extract_forecast | Extract forecasts from a summarised posterior |
| fv_inits | Set up initial conditions for model |
| fv_model | Load and compile a strain model |
| fv_posterior | Summarise the posterior |
| fv_sample | Fit a brancing process strain model |
| fv_score_forecast | Evaluate forecasts using proper scoring rules |
| fv_tidy_posterior | Summarise the posterior tidily |
| generate_obs | Generate Simulated Observations |
| generate_obs_scenario | Define observed data for a scenario |
| germany_covid19_delta_obs | Test positive COVID-19 cases and sequences in Germany |
| latest_obs | Filter for latest observations of all types |
| link_dates_with_posterior | Link dates by time for posterior parameter estimates |
| link_obs_with_posterior | Link posterior estimates with observed data |
| piecewise_steps | Calculate piecewise steps |
| plot_cases | Plot the posterior prediction for cases |
| plot_default | Default posterior plot |
| plot.fv_forecast | Plot method for forecast |
| plot.fv_posterior | Plot method for fv_tidy_posterior |
| plot_growth | Plot the posterior prediction for the growth rate |
| plot_pairs | Pairs plot of parameters of interest and fitting diagnostics |
| plot_posterior | Plot posterior predictions |
| plot_rt | Plot the posterior prediction for the reproduction number |
| plot_theme | Add the default plot theme |
| plot_voc_advantage | Plot the posterior prediction for the transmission advantage... |
| plot_voc_frac | Plot the population posterior prediction for the fraction of... |
| print.fv_posterior | Print method for fv_tidy_posterior |
| quantiles_to_long | Convert summarised quantiles from wide to long format |
| sample_sequences | Sample Sequence Observation Model |
| save_plots | Save plots by name |
| summary.fv_forecast | Summary method for forecast |
| summary.fv_posterior | Summary method for fv_tidy_posterior |
| unnest_posterior | Unnest posterior estimates from a forecast data.frame |
| update_obs_availability | Update observations based on availability |
| update_voc_label | Label the Variant of Concern |
