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| epidemia-package | Flexible Epidemic Modeling with epidemia |
| all_obs_types | Get a list of all observation types used in a model |
| all_obs_types.epimodel | Plotting the posterior linear predictor for R or ascertainment rates |
| as.array.epimodel | Extract posterior samples |
| as.data.frame.epimodel | Extract posterior samples |
| as.matrix.epimodel | Extract posterior samples |
| EnglandNewCases | Covid-19 Case Counts for England |
| epidemia | Flexible Epidemic Modeling with epidemia |
| epiinf | Model Latent Infections |
| epim | Fit a Bayesian epidemiological model with epidemia |
| epimodel-objects | Fitted Epidemiological Model Objects |
| epiobs | Define Observational Models |
| epirt | Model Reproduction Rates |
| EuropeCovid | Covid-19 data for European countries |
| EuropeCovid2 | Covid-19 data for European countries |
| evaluate_forecast | Posterior model evaluations |
| formula.epimodel | Formula method for epimodel objects |
| get_samps | Retrieve final states from sampled Markov chains |
| get_x | Extract X or Z from an epimodel object |
| get_z | Extract X or Z from an epimodel object |
| hexp | A hierarchical model for seeded infections |
| model.frame.epimodel | model.frame method for epimodel objects. Please see 'model.frame' for more details. |
| ngrps.mixed | Returns the levels for each grouping factor in the fitted object |
| pairs.epimodel | Pairs method for epimodel objects |
| plot.epimodel | Plot method for epimodel objects |
| plot_coverage | Plot coverage probability of posterior credible intervals |
| plot_infections | Plot latent infections |
| plot_infections.epimodel | Plot latent infections |
| plot_infectious | Plot total infectiousness over time. |
| plot_infectious.epimodel | Plot total infectiousness over time. |
| plot_linpred | Plotting the posterior linear predictor for R or ascertainment rates |
| plot_linpred.epimodel | Plotting the posterior linear predictor for R or ascertainment rates |
| plot_metrics | Plot CRPS, Median/Mean Absolute Error |
| plot_obs | Plot posterior predictive distributions |
| plot_obs.epimodel | Plot posterior predictive distributions |
| plot_rt | Plot time-varying reproduction rates |
| plot_rt.epimodel | Plot time-varying reproduction rates |
| posterior_coverage | Coverage of posterior credible intervals |
| posterior_infections | Generic function for getting posterior draws of daily infections over time |
| posterior_infections.epimodel | Generic function for getting posterior draws of daily infections over time |
| posterior_infectious | Generic function for getting posterior draws of total infectiousness over time |
| posterior_infectious.epimodel | Generic function for getting posterior draws of total infectiousness over time |
| posterior_latent | Generic function for getting posterior draws of a specified latent sequence |
| posterior_latent.epimodel | Generic function for getting posterior draws of a specified latent sequence |
| posterior_linpred | Gives the posterior linear predictor for the reproduction numbers Will be extended for observations in future versions |
| posterior_metrics | CRPS, Mean Absolute Error, Median Absolute Error |
| posterior_predict.epimodel | Draws samples from the posterior predictive distribution of the observations |
| posterior_rt | Generic function for getting posterior draws of the time-varying reproduction rates |
| posterior_rt.epimodel | Generic function for getting posterior draws of the time-varying reproduction rates |
| posterior_sample_size | Get posterior sample size from a fitted model |
| posterior_sample_size.epimodel | Plotting the posterior linear predictor for R or ascertainment rates |
| print.epimodel | Print fitted model details |
| print.prior_summary.epimodel | Print method for 'prior_summary.epimodel' objects |
| print.prior_summary_reg.epimodel | Print method for 'prior_summary_reg.epimodel' objects |
| print.summary.epimodel | Summary method for epimodel objects |
| prior_summary.epimodel | Returns a summary of the prior distributions used |
| rw | Adds random walks with independent Gaussian steps to the parameterization of the time-varying reproduction number. |
| scaled_logit | Represents a 'scaled' logit link |
| shifted_gamma | A shifted gamma prior |
| spaghetti_infections | Plot latent infections |
| spaghetti_obs | Plot posterior predictive distributions |
| spaghetti_rt | Plot time-varying reproduction rates |
| summary.epimodel | Summary method for epimodel objects |
| terms.epimodel | Terms method for epimodel objects |
| terms_rw | Finds random walk terms in a formula object |