# Modeling of Epidemics using Hierarchical Bayesian Models

## Documentation for package ‘epidemia’ version 1.0.0

- DESCRIPTION file.

## Help Pages

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