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Package: Bernadette 1.1.6

Lampros Bouranis

Bernadette: Bayesian Inference and Model Selection for Stochastic Epidemics

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) <doi:10.48550/arXiv.2211.15229>.

Authors:Lampros Bouranis [aut, cre, cph], European Union [fnd]

Bernadette_1.1.6.tar.gz
Bernadette_1.1.6.zip(r-4.7-x86_64)Bernadette_1.1.6.zip(r-4.7-arm64)Bernadette_1.1.6.zip(r-4.6-x86_64)Bernadette_1.1.6.zip(r-4.6-arm64)
Bernadette_1.1.6.tar.gz(r-4.7-arm64)Bernadette_1.1.6.tar.gz(r-4.7-x86_64)Bernadette_1.1.6.tar.gz(r-4.6-arm64)Bernadette_1.1.6.tar.gz(r-4.6-x86_64)
Bernadette_1.1.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
Bernadette/json (API)

# Install 'Bernadette' in R:

install.packages('Bernadette', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bernadette-eu/bernadette/issues

Uses libs:

onetbb– Parallelism library for C++
c++– GNU Standard C++ Library v3

Datasets:

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
contact_matrices - Contact matrices per country

On CRAN:

onetbb cpp

2.00 score 6 scripts 356 downloads 26 exports 48 dependencies

Last updated from:1cf37e2ba5. Checks:10 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	OK	220
linux-devel-x86_64	OK	271
source / vignettes	OK	352
linux-release-arm64	OK	224
linux-release-x86_64	OK	228
windows-devel-arm64	OK	317
windows-devel-x86_64	OK	284
windows-release-arm64	OK	334
windows-release-x86_64	OK	236
wasm-release	OK	191

Exports:age_distribution aggregate_age_distribution aggregate_contact_matrix aggregate_ifr_react cauchy contact_matrix countries_un country_contact_matrices exponential gamma itd_distribution normal plot_age_distribution plot_contact_matrix plot_posterior_cm plot_posterior_infections plot_posterior_mortality plot_posterior_rt plot_posterior_transmrate posterior_infections posterior_mortality posterior_rt posterior_transmrate stan_igbm stan_igbm.fit student_t

Dependencies:abind backports BH callr checkmate cli cpp11 desc distributional farver generics ggplot2 glue gridExtra gtable inline isoband labeling lifecycle loo magrittr matrixStats numDeriv otel pillar pkgbuild pkgconfig posterior processx ps QuickJSR R6 RColorBrewer Rcpp RcppEigen RcppParallel rlang rstan rstantools S7 scales StanHeaders tensorA tibble utf8 vctrs viridisLite withr

Bernadette

Rendered fromBernadette.Rmdusingknitr::rmarkdown

Last update: 2023-05-18
Started: 2023-05-18

Citation

Readme and manuals

Help Manual

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

Package: Bernadette 1.1.6

Bernadette: Bayesian Inference and Model Selection for Stochastic Epidemics

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)