R Observatory: Metrics for superspreading version 0.4.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

superspreading

0.4.0

Understand Individual-Level Variation in Infectious Disease Transmission

0packages depend

2.4Kdownloads / year

94.6%test coverage

13/13checks pass

Overview

About

Maintained by Joshua W. LambertFirst published 2025-01-272 releasesCRAN page ↗GitHub ↗

Estimate and understand individual-level variation in transmission. Implements density and cumulative compound Poisson discrete distribution functions (Kremer et al. (2021) doi:10.1038/s41598-021-93578-x), as well as functions to calculate infectious disease outbreak statistics given epidemiological parameters on individual-level transmission; including the probability of an outbreak becoming an epidemic/extinct (Kucharski et al. (2020) doi:10.1016/S1473-3099(20)30144-4), or the cluster size statistics, e.g. what proportion of cases cause X\% of transmission (Lloyd-Smith et al. (2005) doi:10.1038/nature04153).

Install

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

install.packages("superspreading", 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("epiverse-trace/superspreading")

Development version from epiverse-trace/superspreading. 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-superspreading

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-superspreading

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-superspreading

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

Health

CRAN checks

13OK

Slowest check: 6.1 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.96

94.6%

Coverage · measured lines

100%

Documentation · exports

3

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-30
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-23
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,039 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 28%

Downloads

2.4K

CRAN downloads in the past year

Rank #14,945 · ~6/day · ~197/mo

Releases R versions

Daily download trend is not available in this view yet.

17830 days

71390 days

2.4K1 year

Compare downloads with other packages →

Also on125 r2u29 autocran

Repository

GitHub ↗ epiverse-trace/superspreading

5Stars

2Forks

5Open issues

3Open PRs

4Releases

511Commits

7Contributors

rr-packageepidemiologyepiversedisease-transmission

511 commits · Last activity 2026-07-01

Stars over time

2025-06-18 · 52026-07-07 · 5

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/epiverse-trace/superspreading on 2026-08-23.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Research and citation (1)

CITATION.cff

Show all practices

Automation and maintenance (1)

Dependabot

Lint, format, editor (2)

lintrRStudio project

Coverage (1)

Codecov

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (3)

checkmate rlangstats

LinkingTo (0)

none

Suggests (11)

dplyr epiparameter fitdistrplus ggplot2 ggtext knitr purrr rmarkdown scales spelling testthat (>= 3.0.0)

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (8)

Maintainer (1)

Joshua W. Lambert

Author, Maintainer, Copyright holder

Authors (3)

Joshua W. Lambert

Author, Maintainer, Copyright holder

Dillon C. Adam

Author

Adam Kucharski

Author, Copyright holder

Contributors (2)

James M. Azam

Reviewer, Contributor

Sebastian Funk

Contributor, Copyright holder

Copyright holders (3)

Joshua W. Lambert

Author, Maintainer, Copyright holder

Adam Kucharski

Author, Copyright holder

Sebastian Funk

Contributor, Copyright holder

Reviewers (4)

James M. Azam

Reviewer, Contributor

Hugo Gruson

Reviewer

Pratik Gupte

Reviewer

Chris Hartgerink

Reviewer

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
0.4.0Latest
2025-07-15 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.3.0
2025-01-27
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-01-27
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Download size: 901 KB
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("superspreading")

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 superspreading version 0.4.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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