R Observatory: Metrics for EpiNow2 version 1.9.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

EpiNow2

1.9.0

Estimate and Forecast Real-Time Infection Dynamics

0packages depend

12Kdownloads / year

70.0%test coverage

13/13checks pass

Overview

About

Maintained by Sebastian FunkFirst published 2020-09-0116 releasesCRAN page ↗GitHub ↗

Estimates the time-varying reproduction number, rate of spread, and doubling time using a renewal equation approach combined with Bayesian inference via Stan. Supports Gaussian process and random walk priors for modelling changes in transmission over time. Accounts for delays between infection and observation (incubation period, reporting delays), right-truncation in recent data, day-of-week effects, and observation overdispersion. Can estimate relationships between primary and secondary outcomes (e.g., cases to hospitalisations or deaths) and forecast both. Runs across multiple regions in parallel. Based on Abbott et al. (2020) doi:10.12688/wellcomeopenres.16006.1 and Gostic et al. (2020) doi:10.1101/2020.06.18.20134858.

Install

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

install.packages("EpiNow2", 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("epiforecasts/EpiNow2")

Development version from epiforecasts/EpiNow2. 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-epinow2

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-EpiNow2

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-EpiNow2

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

Health

CRAN checks

13OK

Slowest check: 32.6 min · r-oldrel-windows-x86_64

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
OK2026-07-29
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-27
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 5 earlier snapshots

NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-18
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-03-17
11 OK · 2 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

Documentation signals are not tracked yet for this package.

Downloads

12K

CRAN downloads in the past year

Rank #3,846 · ~33/day · ~996/mo

EpiNow2 Releases R versions

Daily download trend is not available in this view yet.

63030 days

2.3K90 days

12K1 year

Compare downloads with other packages →

Also on522 r2u16 autocran13 c2d4u

Repository

GitHub ↗ epiforecasts/epinow2

141Stars

40Forks

65Open issues

10Open PRs

20Releases

1,912Commits

35Contributors

backcalculationreproduction-numberopen-sourcerstatscovid-19stangaussian-processes

1,912 commits · Last activity 2026-08-17 · +0.7% stars, 30d

Repository practices

Upstream repositoryBeta

12 development-tooling and community-health practices detected across 9 families in the upstream repository

Checks run against github.com/epiforecasts/epinow2 on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Research and citation (1)

CITATION.cff

Automation and maintenance (2)

Dependabotpre-commit

Lint, format, editor (2)

lintrRStudio project

Coverage (1)

Codecov

Governance and community (2)

Issue templatesPR template

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

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: claude on 2025-11-05

claude

Most recent: claude on 2025-11-05

Evidence

claude: on 2025-11-05 · evidence A, B, D · sole bot-author seen

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

36 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (22)

checkmate cli data.table futile.logger (>= 1.4)ggplot2 lifecycle lubridatemethodspatchwork posterior primarycensored purrr R.utils Rcpp (>= 0.12.0)rlang rstan rstantools (>= 2.2.0)runner scalesstatstruncnormutils

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.26.0)

Suggests (11)

cmdstanr future future.apply knitr parallelly progressr rmarkdown scoringutils spelling testthat withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (21)

Maintainer (1)

Sebastian Funk

Author, Maintainer

Authors (10)

Sebastian Funk

Author, Maintainer

Sam Abbott

Author · added in 1.3.4

James M. Azam

Author · added in 1.4.0

Hamada S. Badr

Author · added in 1.2.1

Michael DeWitt

Author · added in 1.2.1

Author

Author

Author

Author · added in 1.8.0

Katharine Sherratt

Author

Contributors (11)

Nikos Bosse

Contributor

Lloyd Chapman

Contributor · added in 1.3.4

Peter Ellis

Contributor

Adam Howes

Contributor · added in 1.8.0

Andrew Johnson

Contributor · added in 1.4.0

Kaitlyn Johnson

Contributor · added in 1.6.0

Sophie Meakin

Contributor

Paul Mee

Contributor

Show 3 more contributors

Pietro Monticone

Contributor · added in 1.3.4

James Munday

Contributor

Robin Thompson

Contributor

Listed in earlier versions (2)

EpiForecasts

no longer listed · 1.1.0 to 1.7.1

Sam

no longer listed · 1.2.1 to 1.3.2

Package Timeline

16 releases. R releases are shown for context.

1.9.0Latest
2026-06-17 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.8.0
2026-02-05 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.7.1
2025-02-20 · diff ↗
1.7.0
2025-02-05 · diff ↗
1.6.1
2024-10-31 · diff ↗
1.6.0
2024-10-02 · diff ↗
1.5.2
2024-05-17 · diff ↗
1.5.1
2024-05-14 · diff ↗
1.5.0
2024-05-10 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.4.0
2023-09-26 · diff ↗
1.3.5
2023-04-27 · diff ↗
unarchivedReturned to CRAN
2023-04-27
R
R 4.3.0 released · 2023-04-21

Show 11 earlier events

archivedRemoved from CRAN
2023-03-02
issues were not corrected in time
1.3.4
2023-02-12 · diff ↗
unarchivedReturned to CRAN
2023-02-12
archivedRemoved from CRAN
2022-10-19
issues were not corrected in time
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.3.2
2020-12-14 · diff ↗
1.3.1
2020-11-22 · diff ↗
1.2.1
2020-10-20 · diff ↗
1.1.0
2020-09-01
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-09-01
Total releases: 16 / 6 yrs
License: MIT + file LICENSE OSI
Download size: 6.6 MB
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("EpiNow2")

The authors publish a CITATION.cff, so they have said how they want this cited. Run citation() and use what it gives you.

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 EpiNow2 version 1.9.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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