R Observatory: Metrics for EpiEstim version 2.2-5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

EpiEstim

2.2-5Package record

Estimate Time Varying Reproduction Numbers from Epidemic Curves

4packages dependsuggested by 2

23.4Kdownloads / year

41.4%test coverage

13/13flavors OK

Overview

About

Maintained by Anne CoriCRAN page ↗GitHub ↗Issues ↗

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

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

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.2-5

READMEYes · 56 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · does not mention 2.2-5Citation fileNo

Help pages: 24
Examples that run: 65%13 run in a plain check · 7 never run
Exported functions with examples: 73%
Documented parameters: 94%
Return-value docs: 73%
Help pages citing references: 46%

Vignettes (1)

EpiEstim demonstration HTML

How these are measured

Downloads

23.4K

CRAN downloads in the past year

Rank #2,211 · ~64/day · ~2K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.4K30 days

7.9K90 days

23.4K1 year

Compare downloads with other packages →

Also on165 r2u3 autocran89 c2d4u

How downloads are counted

Repository

mrc-ide/epiestim ↗Organization: mrc-ide

106Stars

40Forks

55Open issues

11Open PRs

5Releases

866Commits

19Commit identities

866 commits · Last activity 2026-07-20 · +1% stars, 30d · Default branch at 3.0.0, ahead of CRAN 2.2-5 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 87%
Median days to close, 50 most recently updated closed issues: 423
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-10-18 · 1002026-10-25 · 106

How these are measured

PracticesBeta

11 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/mrc-ide/epiestim on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (2)

Contributing guidePR template

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-07-20 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 1 practice

Lint, format, editor (3)

lintrLint workflowRStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2026-01-29
Pull request: opened by its own account

How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing EpiEstim adds 34 packages (16 with compiled code, 35 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, fitdistrplus 2.4 MB.

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

4direct

0indirect

Imports 4

Suggested by 2

Depends, Imports or LinkingTo, most downloaded first

EpiLPS ern covid19india ViroReportR

Suggests, most downloaded first

projections EpiNova

How these are counted

Code & Tests

Datasets

People & History

People (14)

Anne Cori

Author, Maintainer since 1.0-0 (2012)

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 contributorsHide 5 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

Releases (9)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.2-5Latest
record
2025-06-27 · current release · diff ↗
2.2-4.1
record
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
record
2021-01-07 · diff ↗
2.2-3
record
2020-05-29 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.2-1
record
2019-07-08 · diff ↗ ·
removed 1 export
pattern:.

added 15 exports
DiscrSI, EstimateR, OverallInfectivity, WT, check_cdt_samples_convergence, coarse2estim, discr_si, estimate_R, estimate_R_plots, init_mcmc_params, make_config, make_mcmc_control, overall_infectivity, sample_posterior_R, wallinga_teunis
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 eventsHide 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
record
2013-03-08 · diff ↗
1.1-1
record
2013-03-01 · diff ↗
1.1-0
record
2013-02-19 · diff ↗
1.0-0
record
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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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