Bayesian Inference and Model Selection for Stochastic Epidemics


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Documentation for package ‘Bernadette’ version 1.1.5

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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