Bayesian Inference and Model Selection for Stochastic Epidemics

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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