All functions

EuropeCovid

Covid-19 data for European countries

EuropeCovid2

Covid-19 data for European countries

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

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_infectious()

Plot total infectiousness over time.

plot_linpred()

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_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

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