Function reference • epidemia

All functions
`EnglandNewCases`	Covid-19 Case Counts for England
`EuropeCovid`	Covid-19 data for European countries
`EuropeCovid2`	Covid-19 data for European countries
`all_obs_types()`	Get a list of all observation types used in a model
`as.matrix(<epimodel>)` `as.array(<epimodel>)` `as.data.frame(<epimodel>)`	Extract posterior samples
`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
`evaluate_forecast()`	Posterior model evaluations
`formula(<epimodel>)`	Formula method for epimodel objects
`get_samps()`	Retrieve final states from sampled Markov chains
`get_x()` `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()` `spaghetti_infections()`	Plot latent infections
`plot_infectious()`	Plot total infectiousness over time.
`posterior_sample_size(<epimodel>)` `all_obs_types(<epimodel>)` `plot_linpred()`	Plotting the posterior linear predictor for R or ascertainment rates
`plot_metrics()`	Plot CRPS, Median/Mean Absolute Error
`plot_obs()` `spaghetti_obs()`	Plot posterior predictive distributions
`plot_rt()` `spaghetti_rt()`	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_infectious()`	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_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_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
`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
`summary(<epimodel>)` `print(<summary.epimodel>)`	Summary method for epimodel objects
`terms(<epimodel>)`	Terms method for epimodel objects
`terms_rw()`	Finds random walk terms in a formula object

Reference

All functions