Modeling of Epidemics using Hierarchical Bayesian Models

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Documentation for package ‘epidemia’ version 1.0.0

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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