R Observatory: Metrics for R0 version 1.3-1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

R0

1.3-1

Estimation of R0 and Real-Time Reproduction Number from Epidemics

0packages depend

6.2Kdownloads / year

59.7%test coverage

0/13flavors OK

Overview

About

Maintained by Thomas ObadiaCRAN page ↗GitHub ↗

Estimation of reproduction numbers for disease outbreak, based on incidence data. The R0 package implements several documented methods. It is therefore possible to compare estimations according to the methods used. Depending on the methods requested by user, basic reproduction number (commonly denoted as R0) or real-time reproduction number (referred to as R(t)) is computed, along with a 95% Confidence Interval. Plotting outputs will give different graphs depending on the methods requested : basic reproductive number estimations will only show the epidemic curve (collected data) and an adjusted model, whereas real-time methods will also show the R(t) variations throughout the outbreak time period. Sensitivity analysis tools are also provided, and allow for investigating effects of varying Generation Time distribution or time window on estimates.

Install

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

install.packages("R0", 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("tobadia/R0")

Development version from tobadia/R0. 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-r0

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-R0

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-R0

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

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) est.R0.ML.Rd:98: Lost braces
    98 | Supplementary Material S1 from \doi{10.1186/1472-6947-12-147}{Obadia et al., 2012}.
       |                                                              ^
checkRd: (-1) plot.R0.R.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from one estimation method.
       |                                                      ^
checkRd: (-1) plot.R0.sR.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from an
       |                                                      ^

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Thomas Obadia <thomas.obadia@pasteur.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Pierre-Yves",
                      family = "Boelle",
                      role = "aut"),
               person(given = "Thomas",
                      family = "Obadia",
                      role = c("aut", "cre"),
                      email = "thomas.obadia@pasteur.fr"))
as necessary.

CRAN check page ↗

Slowest check: 1.6 min · r-release-windows-x86_64

Status changes

NOTE13 NOTE2026-09-08
ERROR12 NOTE, 1 ERROR2026-09-07
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3-1

README· In the repository, left out of the releaseVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 44 (29 internal)
Examples that run: 100%12 run in a plain check
Exported functions with examples: 67%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 23%

Also includes 1 demo script (run with demo())

How these are measured

Downloads

6.2K

CRAN downloads in the past year

Rank #5,320 · ~17/day · ~517/mo

Releases R versions

Daily download trend is not available in this view yet.

54430 days

1.5K90 days

6.2K1 year

Compare downloads with other packages →

Also on81 r2u6 autocran315 bioconda84 c2d4u

How downloads are counted

Repository

tobadia/r0 ↗Account: tobadia

5Stars

4Forks

4Open issues

4Open PRs

0Releases

73Commits

4Commit identities

73 commits · Last activity 2025-02-25 · 0% stars, 30d · The default branch showed an older version (1.3-0) than CRAN on 2026-10-11

Responsiveness

How these are sampled

PRs merged (all time): 83%
Median days to close, 50 most recently updated closed issues: 7
Median days to close, 50 most recently updated closed PRs: 74

Stars over time

2024-06-04 · 42026-07-07 · 5

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/tobadia/r0 on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Lint, format, editor (1)

lintr

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

Installing R0 adds no packages beyond those that come with R.

Depends (1)

R >= 2.13.0

Imports (1)

MASS

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (2)

Pierre-Yves Boelle

Thomas Obadia

Maintainer since 1.1 (2012)

Releases (12)

Pick two releases to compare their code metrics.

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
1.3-1Latest
record
2023-09-26 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2022-09-05
1.2-10
record
2022-09-05 · diff ↗ ·
added 1 export
inspect.data
archivedRemoved from CRAN
2022-06-10
check problems were not corrected despite reminders
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
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
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
1.2-6
record
2015-05-21 · diff ↗

Show 13 earlier eventsHide 13 earlier events

R
R 3.2.0 released · 2015-04-16
1.2-5
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2014-11-25 · diff ↗
R
R 3.1.0 released · 2014-04-10
1.2-4
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2013-12-13 · diff ↗
1.2-3
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2013-10-07 · diff ↗
1.2-2
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2013-09-02 · diff ↗
1.2-1
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2013-07-09 · diff ↗
R
R 3.0.0 released · 2013-04-03
1.2-0
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2012-11-22 · diff ↗
1.1-3
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2012-09-26 · diff ↗
1.1-2
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2012-08-10 · diff ↗
1.1
record
2012-07-27
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2012-07-27
Total releases: 12 / 14 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.13.0
Bundled data: 1.1 KB / 3 files
Download size: 73 KB

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("R0")

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 R0 version 1.3-1 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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