Man pages for ImperialCollegeLondon/epidemia
Modeling of Epidemics using Hierarchical Bayesian Models
| all_obs_types | Get a list of all observation types used in a model |
| as.matrix.epimodel | Extract posterior samples |
| EnglandNewCases | Covid-19 Case Counts for England |
| epidemia-package | 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 |
| hexp | A hierarchical model for seeded infections |
| model.frame.epimodel | model.frame method for epimodel objects. Please see... |
| ngrps.mixed | Returns the levels for each grouping factor in the fitted... |
| pairs.epimodel | Pairs method for epimodel objects |
| plot_coverage | Plot coverage probability of posterior credible intervals |
| plot.epimodel | Plot method for epimodel objects |
| plot_infections | Plot latent infections |
| plot_infectious | Plot total infectiousness over time. |
| plot_linpred | Plotting the posterior linear predictor for R or... |
| plot_metrics | Plot CRPS, Median/Mean Absolute Error |
| plot_obs | Plot posterior predictive distributions |
| plot_rt | Plot time-varying reproduction rates |
| posterior_coverage | Coverage of posterior credible intervals |
| posterior_infections | Generic function for getting posterior draws of daily... |
| posterior_infectious | Generic function for getting posterior draws of total... |
| posterior_latent | Generic function for getting posterior draws of a specified... |
| posterior_linpred | Gives the posterior linear predictor for the reproduction... |
| posterior_metrics | CRPS, Mean Absolute Error, Median Absolute Error |
| posterior_predict.epimodel | Draws samples from the posterior predictive distribution of... |
| posterior_rt | Generic function for getting posterior draws of the... |
| posterior_sample_size | Get posterior sample size from a fitted model |
| 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 |
| prior_summary.epimodel | Returns a summary of the prior distributions used |
| reexports | Objects exported from other packages |
| rw | Adds random walks with independent Gaussian steps to the... |
| scaled_logit | Represents a 'scaled' logit link |
| shifted_gamma | A shifted gamma prior |
| summary.epimodel | Summary method for epimodel objects |
| terms.epimodel | Terms method for epimodel objects |
| terms_rw | Finds random walk terms in a formula object |
