superspreading: Understand Individual-Level Variation in Infectious Disease Transmission

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>).

Version: 0.4.0
Imports: checkmate, rlang, stats
Suggests: dplyr, epiparameter (≥ 0.4.0), fitdistrplus, ggplot2, ggtext, knitr, purrr, rmarkdown, scales, spelling, testthat (≥ 3.0.0)
Published: 2025-07-15
DOI: 10.32614/CRAN.package.superspreading
Author: Joshua W. Lambert ORCID iD [aut, cre, cph], Adam Kucharski ORCID iD [aut, cph], Dillon C. Adam ORCID iD [aut], Sebastian Funk ORCID iD [ctb, cph] (.chain_sim uses code from bpmodels::chain_sim), Pratik Gupte ORCID iD [rev], Hugo Gruson ORCID iD [rev], James M. Azam ORCID iD [rev, ctb], Chris Hartgerink ORCID iD [rev]
Maintainer: Joshua W. Lambert <joshua.lambert at lshtm.ac.uk>
BugReports: https://github.com/epiverse-trace/superspreading/issues
License: MIT + file LICENSE
URL: https://github.com/epiverse-trace/superspreading, https://epiverse-trace.github.io/superspreading/
NeedsCompilation: no
Language: en-GB
Materials: README, NEWS
In views: Epidemiology
CRAN checks: superspreading results

Documentation:

Reference manual: superspreading.html , superspreading.pdf
Vignettes: Design Principles for {superspreading} (source, R code)
Pathogen evolution in the emergence of infectious disease outbreaks (source, R code)
Epidemic Risk (source, R code)
Estimate individual-level transmission (source, R code)
Outbreaks in heterogeneous networks (source, R code)
Methods for calculating the proportion of transmission (source, R code)
Getting started with {superspreading} (source, R code)

Downloads:

Package source: superspreading_0.4.0.tar.gz
Windows binaries: r-devel: superspreading_0.4.0.zip, r-release: superspreading_0.4.0.zip, r-oldrel: superspreading_0.4.0.zip
macOS binaries: r-release (arm64): superspreading_0.4.0.tgz, r-oldrel (arm64): superspreading_0.4.0.tgz, r-release (x86_64): superspreading_0.4.0.tgz, r-oldrel (x86_64): superspreading_0.4.0.tgz
Old sources: superspreading archive

Linking:

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