epidemia: Modeling of Epidemics using Hierarchical Bayesian Models

Flexibly specify and fit Bayesian statistical models for epidemics. 'epidemia' leverages Rs formula interface so that users can parameterize reproduction numbers and ascertainment rates in terms of predictors. Infections are propagated over time using self-exciting point processes. Multiple regions can be modeled simultaneously with multilevel models. The models and framework behind the package are described in Bhatt et al. (2021) <arXiv:2012.00394>. The design of the package has been inspired by, and has borrowed from, 'rstanarm' (Goodrich et al., 2020) <https://mc-stan.org/rstanarm/>. 'rstan' (Stan Development Team, 2020) <https://mc-stan.org/> is used as the back end for fitting models.

Version: 1.0.0
Depends: R (≥ 3.5.0)
Imports: dplyr (≥ 0.8.5), methods, Rcpp (≥ 0.12.0), rstan (≥ 2.18.1), rstantools (≥ 2.0.0), magrittr, rstanarm, lme4, ggplot2, Matrix, scales, Rdpack, stats, zoo, tidyr, rlang, bayesplot, hrbrthemes
LinkingTo: BH (≥ 1.66.0), Rcpp (≥ 0.12.0), RcppEigen (≥ 0.3.3.3.0), rstan (≥ 2.18.1), StanHeaders (≥ 2.18.0)
Suggests: testthat, knitr, gridExtra, bookdown, EpiEstim, lubridate, kableExtra, extrafont
Published: 2021-10-25
Author: James Scott ORCID iD [aut, cre], Axel Gandy ORCID iD [aut], Swapnil Mishra ORCID iD [aut], Juliette Unwin ORCID iD [aut], Seth Flaxman ORCID iD [aut], Samir Bhatt ORCID iD [aut], Jonathan Ish-Horowicz ORCID iD [ctb], Leon Wu [ctb], Ben Goodrich [ctb], Jonah Gabry [ctb], Trustees of Columbia University [cph] (R/helpers.R), Paul-Christian Burkner [cph] (R/misc.R), Triad Sou [cph] (R/geom_stepribbon.R), Kengo Nagashima [cph] (R/geom_stepribbon.R)
Maintainer: James Scott <james.scott15 at imperial.ac.uk>
License: GPL-3
URL: https://github.com/ImperialCollegeLondon/epidemia/
NeedsCompilation: yes
SystemRequirements: GNU make
Citation: epidemia citation info
Materials: README NEWS
CRAN checks: epidemia results

Documentation:

Reference manual: epidemia.pdf

Downloads:

Package source: epidemia_1.0.0.tar.gz
Windows binaries: r-devel: not available, r-devel-UCRT: epidemia_1.0.0.zip, r-release: not available, r-oldrel: not available
macOS binaries: r-release (arm64): not available, r-release (x86_64): not available, r-oldrel: not available

Linking:

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