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:	0.3.0
Imports:	checkmate, rlang, stats
Suggests:	dplyr, epiparameter (≥ 0.4.0), fitdistrplus, ggplot2, ggtext, knitr, purrr, rmarkdown, scales, spelling, testthat (≥ 3.0.0)
Published:	2025-01-27
DOI:	10.32614/CRAN.package.superspreading
Author:	Joshua W. Lambert [aut, cre, cph], Adam Kucharski [aut, cph], Dillon C. Adam [aut], Sebastian Funk [ctb, cph] (.chain_sim uses code from bpmodels::chain_sim), Pratik Gupte [rev], Hugo Gruson [rev], James M. Azam [rev, ctb], Chris Hartgerink [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.pdf
Vignettes:	Design Principles for {superspreading} (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_0.3.0.tar.gz
Windows binaries:	r-devel: superspreading_0.3.0.zip, r-release: superspreading_0.3.0.zip, r-oldrel: superspreading_0.3.0.zip
macOS binaries:	r-devel (arm64): superspreading_0.3.0.tgz, r-release (arm64): superspreading_0.3.0.tgz, r-oldrel (arm64): superspreading_0.3.0.tgz, r-devel (x86_64): superspreading_0.3.0.tgz, r-release (x86_64): superspreading_0.3.0.tgz, r-oldrel (x86_64): superspreading_0.3.0.tgz

Linking:

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