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 |