R Observatory: Metrics for Rnaught version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Rnaught

0.1.0Package record

Estimate the Basic Reproduction Number (R0)

0packages depend

1.9Kdownloads / year

72.9%test coverage

13/13flavors OK

Overview

About

Maintained by Naeem ModelCRAN page ↗GitHub ↗Website ↗Issues ↗

A collection of methods for estimating the basic reproduction number (R0) of infectious diseases. Features a web application to interface with the estimators. Uses the models from: Fisman et al. (2013) DOI:10.1371/journal.pone.0083622, Bettencourt and Ribeiro (2008) DOI:10.1371/journal.pone.0002185, and White and Pagano (2008) DOI:10.1002/sim.3136. Includes datasets for Canadian national and provincial COVID-19 case counts provided by Berry et al. (2021) DOI:10.1038/s41597-021-00955-2.

Changes in 0.1.0

Initial CRAN submission.

From NEWS.md in the release

Install

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

install.packages("Rnaught", 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("MI2YorkU/Rnaught")

Development version from MI2YorkU/Rnaught. 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-rnaught

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-Rnaught

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-Rnaught

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: 1.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-10
WARNING12 OK, 1 WARNING2026-05-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMEYes · 274 wordsVignettesYes · 3 · dynamicNEWSYes · 67% structured · mentions 0.1.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 8 (1 internal)includes a package overview page
Examples that run: 100%4 run in a plain check
Exported functions with examples: 80%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 50%

Vignettes (3)

How these are measured

Downloads

1.9K

CRAN downloads in the past year

Rank #22,777 · ~5/day · ~158/mo

Releases R versions

Daily download trend is not available in this view yet.

22530 days

58190 days

1.9K1 year

Compare downloads with other packages →

Also on54 r2u

How downloads are counted

Repository

mi2yorku/rnaught ↗Organization: MI2YorkU

1Stars

1Forks

0Open issues

0Open PRs

1Releases

134Commits

4Commit identities

basic-reproduction-numbercompartmental-modelsinfectious-disease-modelsinfectious-diseasesrr0shiny

License file reads as AGPL-3.0 · 134 commits · Last activity 2025-11-06 · 0% stars, 30d · Default branch at 0.1.0.9000, ahead of CRAN 0.1.0 (checked 2026-10-22)

Responsiveness

not measured

Stars over time

2025-10-06 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/mi2yorku/rnaught on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-11-06 · The repository has a site deploy workflow

pkgdown site last built 2025-11-06

Research and citation (1)

CITATION.cff

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

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

Depends (1)

R >= 2.10

Imports (2)

statsutils

LinkingTo (0)

none

Suggests (7)

knitr rmarkdown shiny bslib DT plotly testthat (>= 3.0.0)

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 (6)

Naeem Model

Sawitree Boonpatcharanon

Author, Copyright holder

Jane Heffernan

Author, Copyright holder

Hanna Jankowski

Author, Copyright holder

Tatiana Krikella

Author, Copyright holder

Kseniia Lipikhin

Contributor, Copyright holder

Releases (1)

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
record
2025-09-02 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-09-02
Total releases: 1 / 1 yrs
License: AGPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 63 KB / 2 files
Download size: 280 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Rnaught")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

The repository also keeps a CITATION.cff.

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 Rnaught version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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