CRAN requires the check problems on this package to be fixed before 2026-08-31 or it will be archived.

earlyR

0.0.5

Estimation of Transmissibility in the Early Stages of a Disease Outbreak

0packages depend

6Kdownloads / year

91.3%test coverage

0/13checks pass

Overview

About

Maintained by Thibaut JombartFirst published 2017-12-062 releasesCRAN page ↗GitHub ↗

Implements a simple, likelihood-based estimation of the reproduction number (R0) using a branching process with a Poisson likelihood. This model requires knowledge of the serial interval distribution, and dates of symptom onsets. Infectiousness is determined by weighting R0 by the probability mass function of the serial interval on the corresponding day. It is a simplified version of the model introduced by Cori et al. (2013) doi:10.1093/aje/kwt133.

Install

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

install.packages("earlyR", 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("reconhub/earlyR")

Development version from reconhub/earlyR. 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-earlyr

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-earlyR

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

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

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 2.2 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.99

91.3%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 50%
References docs: 0%

Downloads

CRAN downloads in the past year

Rank #12,325 · ~16/day · ~499/mo

Releases R versions

Daily download trend is not available in this view yet.

28930 days

82890 days

6K1 year

Compare downloads with other packages →

Also on95 r2u42 c2d4u

Repository

GitHub ↗ reconhub/earlyr

9Stars

3Forks

11Open issues

0Open PRs

1Releases

77Commits

4Contributors

77 commits · Last activity 2020-10-27

Stars over time

2024-04-01 · 92026-07-07 · 9

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/reconhub/earlyr on 2026-07-26.

Continuous integration (3)

GitHub ActionsTravis CIAppVeyor

Docs source (1)

README.Rmd

Lint, format, editor (1)

lintr

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.3.0

Imports (5)

statsdistcrete EpiEstim epitrix ggplot2

LinkingTo (0)

none

Suggests (8)

testthat vdiffr roxygen2 incidence knitr rmarkdown projections covr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (6)

Maintainer (1)

Thibaut Jombart

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author · added in 0.0.5

Contributors (2)

Zhian N. Kamvar

Contributor · added in 0.0.5

Tim Taylor

Contributor · added in 0.0.5

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
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
0.0.5Latest
2020-10-27 · current release · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.0.1
2017-12-06
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-12-06
Total releases: 2 / 9 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.3.0
Download size: 323 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Epidemiology

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