CRAN/E | epidemia

epidemia

Modeling of Epidemics using Hierarchical Bayesian Models

Installation

About

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) . The design of the package has been inspired by, and has borrowed from, 'rstanarm' (Goodrich et al., 2020) . 'rstan' (Stan Development Team, 2020) is used as the back end for fitting models.

Citation epidemia citation info
github.com/ImperialCollegeLondon/epidemia/
System requirements GNU make

Key Metrics

Version 1.0.0
R ≥ 3.5.0
Published 2021-10-25 908 days ago
Needs compilation? yes
License GPL-3
CRAN checks epidemia results

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Maintainer

Maintainer

James Scott

james.scott15@imperial.ac.uk

Authors

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)

Material

README
NEWS
Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

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

Suggests

testthat
knitr
gridExtra
bookdown
EpiEstim
lubridate
kableExtra
extrafont

LinkingTo

BH ≥ 1.66.0
Rcpp ≥ 0.12.0
RcppEigen ≥ 0.3.3.3.0
rstan ≥ 2.18.1
StanHeaders ≥ 2.18.0