This package was removed from CRAN on 2022-10-26. Its history is shown below.

Reason: issues were not corrected in time

Details below reflect version 1.0.0, its last release before removal.

epidemia

1.0.0

Modeling of Epidemics using Hierarchical Bayesian Models

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by James Scott1 releasesCRAN page ↗GitHub ↗

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.

Install

R (source archive)pak (dev)Ubuntu (r2u)

url <- "https://cran.r-project.org/src/contrib/Archive/epidemia/epidemia_1.0.0.tar.gz"
pkgFile <- "epidemia_1.0.0.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.0.0) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ImperialCollegeLondon/epidemia")

Development version from ImperialCollegeLondon/epidemia. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-epidemia

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 0.22

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Documentation

READMEYes · 156 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 33%
Documented parameters: 95%
Return-value docs: 97%
References docs: 13%

Downloads

epidemia Releases R versions

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Also on320 r2u

Dependencies

Declared dependencies

28 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (18)

dplyrmethodsRcpp rstan (>= 2.18.1)rstantools magrittr rstanarm lme4 ggplot2Matrixscales Rdpackstatszoo tidyr rlang bayesplot hrbrthemes

LinkingTo (5)

BH Rcpp RcppEigen rstan StanHeaders

Suggests (8)

testthat knitr gridExtra bookdown EpiEstim lubridate kableExtra extrafont

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (14)

Maintainer (1)

James Scott

Author, Maintainer

Authors (6)

Author, Maintainer

Author

Author

Author

Author

Author

Contributors (4)

Jonathan Ish-Horowicz

Contributor

Leon Wu

Contributor

Ben Goodrich

Contributor

Jonah Gabry

Contributor

Trustees of Columbia University

Paul-Christian Burkner

Triad Sou

Kengo Nagashima

Package Timeline

1 release. R releases are shown for context.

R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2022-10-26
issues were not corrected in time
R
R 4.2.0 released · 2022-04-22
1.0.0
2021-10-25
R
R 4.1.0 released · 2021-05-18

Package metadata

Total releases: 1
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 22 KB / 3 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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