Learn R Programming

Bernadette (version 1.1.6)

Bayesian Inference and Model Selection for Stochastic Epidemics

Description

Bayesian analysis for stochastic extensions of non-linear dynamic systems using advanced computational algorithms. Described in Bouranis, L., Demiris, N., Kalogeropoulos, K., and Ntzoufras, I. (2022) .

Copy Link

Version

Install

install.packages('Bernadette')

Monthly Downloads

440

Version

1.1.6

License

GPL (>= 3)

Maintainer

Lampros Bouranis

Last Published

February 28th, 2025

Functions in Bernadette (1.1.6)

plot_posterior_cm

Plot the posterior contact matrix
plot_posterior_transmrate

Plot the estimated age-specific transmission rate
plot_contact_matrix

Contact matrix heatmap
plot_posterior_rt

Plot the estimated effective reproduction number trajectory
itd_distribution

Distribution of the time between infection and death
country_contact_matrices

Names of countries for which a contact matrix is available
plot_posterior_infections

Plot the posterior distribution of the infection counts
plot_age_distribution

Bar plot of the age distribution
countries_un

Names of countries with an available age distribution
plot_posterior_mortality

Plot the posterior distribution of the mortality counts
priors

Prior distributions and options
posterior_transmrate

Estimate the age-specific transmission rate
posterior_infections

Summarize the posterior distribution of the infection counts
stan_igbm

Bayesian diffusion-driven multi-type epidemic models via Stan
posterior_mortality

Summarize the posterior distribution of the mortality counts
posterior_rt

Estimate the effective reproduction number with the next generation matrix approach
summary.stanigbm

Summary of stanigbm posterior output
age_specific_cusum_infection_counts

Age distribution of cumulative reported infections for Greece
age_distribution

Country-specific age distribution
contact_matrices

Contact matrices per country
contact_matrix

Country-specific contact matrix
Bernadette-package

Bayesian inference and model selection for stochastic epidemics
aggregate_ifr_react

Aggregate the Infection Fatality Ratio
aggregate_contact_matrix

Aggregate a contact matrix
aggregate_age_distribution

Aggregate the age distribution matrix
age_specific_mortality_counts

Age distribution of new reported deaths for Greece
age_specific_infection_counts

Age distribution of new reported infections for Greece