EpiEstim

2.2-5

Estimate Time Varying Reproduction Numbers from Epidemic Curves

7packages depend

27.9Kdownloads / 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: 5.1 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.19

41.4%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

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

27.9K

CRAN downloads in the past year

Rank #3,295 · ~77/day · ~2.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.4K30 days

3.8K90 days

27.9K1 year

Compare downloads with other packages →

Also on134 r2u15 autocran31 c2d4u

Repository

GitHub ↗ mrc-ide/epiestim

104Stars

40Forks

54Open issues

7Open PRs

5Releases

860Commits

19Contributors

860 commits · Last activity 2026-07-20 · 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 2026-07-19.

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

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

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