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  [aut,
cre],
Axel Gandy [aut],
Swapnil Mishra
[aut],
Juliette Unwin
[aut],
Seth Flaxman
[aut],
Samir Bhatt [aut],
Jonathan Ish-Horowicz
[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 |