R Observatory: Metrics for EpiEstim version 2.2-5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

EpiEstim

2.2-5

Estimate Time Varying Reproduction Numbers from Epidemic Curves

7packages depend

29.3Kdownloads / year

41.4%test coverage

13/13checks pass

Overview

About

Maintained by Anne CoriFirst published 2012-06-079 releasesCRAN page ↗GitHub ↗

Tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence as described in Cori et al. (2013) doi:10.1093/aje/kwt133 and Wallinga and Teunis (2004) doi:10.1093/aje/kwh255.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("EpiEstim", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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

Development version from mrc-ide/EpiEstim. 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-epiestim

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-EpiEstim

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-EpiEstim

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 4.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.19

41.4%

Coverage · measured lines

100%

Documentation · exports

11

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 56 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 65%
Documented parameters: 94%
Return-value docs: 73%
References docs: 46%

Downloads

29.3K

CRAN downloads in the past year

Rank #2,823 · ~80/day · ~2.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.6K30 days

5.2K90 days

29.3K1 year

Compare downloads with other packages →

Also on152 r2u4 autocran31 c2d4u

Repository

GitHub ↗ mrc-ide/epiestim

104Stars

40Forks

54Open issues

7Open PRs

5Releases

866Commits

19Contributors

866 commits · Last activity 2026-07-29 · 0% stars, 30d

Stars over time

2025-07-10 · 992026-07-07 · 104

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/mrc-ide/epiestim on 2026-08-16.

Continuous integration (1)

GitHub Actions

Lint, format, editor (2)

lintrRStudio project

Coverage (1)

Codecov

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (11)

coarseDataToolsstatsgraphicsreshape2 ggplot2 gridExtra fitdistrplus coda incidence scalesgrDevices

LinkingTo (0)

none

Suggests (6)

testthatutilsvdiffr covr knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

7direct

0indirect

EpiLPS ViroReportR covid19india earlyR ern EpiNova projections

Code & Tests

Datasets

People & History

People (14)

Maintainer (1)

Anne Cori

Author, Maintainer

Authors (1)

Anne Cori

Author, Maintainer

Contributors (13)

Simon Cauchemez

Contributor · added in 2.2-1

Elisabeth Dahlqwist

Contributor · added in 2.2-1

P. Alex Demarsh

Contributor · added in 2.2-1

Neil M. Ferguson

Contributor · added in 2.2-1

Christophe Fraser

Contributor · added in 2.2-1

Thibaut Jombart

Contributor · added in 2.2-1

Zhian N. Kamvar

Contributor · added in 2.2-1

Justin Lessler

Contributor · added in 2.2-1

Show 5 more contributors

Shikun Li

Contributor · added in 2.2-1

Jonathan A. Polonsky

Contributor · added in 2.2-1

Jake Stockwin

Contributor · added in 2.2-1

Robin Thompson

Contributor · added in 2.2-1

Rolina van Gaalen

Contributor · added in 2.2-1

Package Timeline

9 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
2.2-5Latest
2025-06-27 · current release · diff ↗
2.2-4.1
2025-06-23 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
2.2-4
2021-01-07 · diff ↗
2.2-3
2020-05-29 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.2-1
2019-07-08 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03

Show 8 earlier events

R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
1.1-2
2013-03-08 · diff ↗
1.1-1
2013-03-01 · diff ↗
1.1-0
2013-02-19 · diff ↗
1.0-0
2012-06-07
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2012-06-07
Total releases: 9 / 14 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10
Bundled data: 4.5 KB / 8 files
Download size: 585 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("EpiEstim")

Format

Cori, A., Cauchemez, S., Dahlqwist, E., Demarsh, P. A., Ferguson, N. M., Fraser, C., Jombart, T., Kamvar, Z. N., Lessler, J., Li, S., Polonsky, J. A., Stockwin, J., Thompson, R., & van Gaalen, R. (2025). EpiEstim: Estimate Time Varying Reproduction Numbers from Epidemic Curves (Version 2.2-5) [Computer software]. https://doi.org/10.32614/CRAN.package.EpiEstim

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for EpiEstim version 2.2-5 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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