R: Bayesian Inference and Model Selection for Stochastic Epidemics

# Bayesian Inference and Model Selection for Stochastic Epidemics

## Documentation for package ‘Bernadette’ version 1.1.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

Bernadette-package | Bayesian inference and model selection for stochastic epidemics
age_distribution | Country-specific age distribution
age_specific_cusum_infection_counts | Age distribution of cumulative reported infections for Greece
age_specific_infection_counts | Age distribution of new reported infections for Greece
age_specific_mortality_counts | Age distribution of new reported deaths for Greece
aggregate_age_distribution | Aggregate the age distribution matrix
aggregate_contact_matrix | Aggregate a contact matrix
aggregate_ifr_react | Aggregate the Infection Fatality Ratio
Bernadette | Bayesian inference and model selection for stochastic epidemics
cauchy | Prior distributions and options
contact_matrices | Contact matrices per country
contact_matrix | Country-specific contact matrix
countries_un | Names of countries with an available age distribution
country_contact_matrices | Names of countries for which a contact matrix is available
exponential | Prior distributions and options
gamma | Prior distributions and options
itd_distribution | Distribution of the time between infection and death
normal | Prior distributions and options
plot_age_distribution | Bar plot of the age distribution
plot_contact_matrix | Contact matrix heatmap
plot_posterior_cm | Plot the posterior contact matrix
plot_posterior_infections | Plot the posterior distribution of the infection counts
plot_posterior_mortality | Plot the posterior distribution of the mortality counts
plot_posterior_rt | Plot the estimated effective reproduction number trajectory
plot_posterior_transmrate | Plot the estimated age-specific transmission rate
posterior_infections | Summarize the posterior distribution of the infection counts
posterior_mortality | Summarize the posterior distribution of the mortality counts
posterior_rt | Estimate the effective reproduction number with the next generation matrix approach
posterior_transmrate | Estimate the age-specific transmission rate
priors | Prior distributions and options
stan_igbm | Bayesian diffusion-driven multi-type epidemic models via Stan
stan_igbm.fit | Bayesian diffusion-driven multi-type epidemic models via Stan
student_t | Prior distributions and options
summary.stanigbm | Summary of stanigbm posterior output