Package: superspreading 0.4.0.9000

Joshua W. Lambert

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>).

Authors:Joshua W. Lambert [aut, cre, cph], Adam Kucharski [aut, cph], Dillon C. Adam [aut], Sebastian Funk [ctb, cph], Pratik Gupte [rev], Hugo Gruson [rev], James M. Azam [rev, ctb], Chris Hartgerink [rev], London School of Hygiene and Tropical Medicine, LSHTM [cph]

superspreading_0.4.0.9000.tar.gz
superspreading_0.4.0.9000.zip(r-4.7)superspreading_0.4.0.9000.zip(r-4.6)superspreading_0.4.0.9000.zip(r-4.5)
superspreading_0.4.0.9000.tgz(r-4.6-any)superspreading_0.4.0.9000.tgz(r-4.5-any)
superspreading_0.4.0.9000.tar.gz(r-4.7-any)superspreading_0.4.0.9000.tar.gz(r-4.6-any)
superspreading_0.4.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
superspreading/json (API)

# Install 'superspreading' in R:
install.packages('superspreading', repos = c('https://epiverse-trace.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/epiverse-trace/superspreading/issues

Pkgdown/docs site:https://epiverse-trace.github.io

On CRAN:

Conda:

disease-transmissionepidemiologyepiverse

7.18 score 5 stars 31 scripts 197 downloads 12 exports 3 dependencies

Last updated from:e76d7b4101. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK175
source / vignettesOK214
linux-release-x86_64OK165
macos-release-arm64OK148
macos-oldrel-arm64OK157
windows-develOK128
windows-releaseOK116
windows-oldrelOK154
wasm-releaseOK130

Exports:calc_network_Rdpoislnormdpoisweibullic_tblppoislnormppoisweibullprobability_containprobability_emergenceprobability_epidemicprobability_extinctproportion_cluster_sizeproportion_transmission

Dependencies:backportscheckmaterlang

Estimate individual-level transmission
Transmission data | Superspreading using alternative distributions | References
Rendered fromestimate_individual_level_transmission.Rmdusingknitr::rmarkdown

Last update: 2025-07-16
Started: 2023-05-26

Epidemic Risk
plot probability of epidemic across dispersion | plot probability of epidemic across introductions | plot probability of extinction across R for multiple k | Controls on transmission | plot probability of epidemic across introductions for multiple k
Rendered fromepidemic_risk.Rmdusingknitr::rmarkdown

Last update: 2025-07-15
Started: 2023-06-13

Design Principles for {superspreading}
Scope | Output | Design decisions | Dependencies | Contribute
Rendered fromdesign-principles.Rmdusingknitr::rmarkdown

Last update: 2025-07-15
Started: 2023-12-14

Getting started with {superspreading}
Definition | Probability of epidemic | Empirical superspreading | References
Rendered fromsuperspreading.Rmdusingknitr::rmarkdown

Last update: 2025-07-15
Started: 2023-05-18

Outbreaks in heterogeneous networks
Rendered fromheterogeneous_network_outbreaks.Rmdusingknitr::rmarkdown

Last update: 2025-07-15
Started: 2024-01-09

Pathogen evolution in the emergence of infectious disease outbreaks
Rendered fromemergence.Rmdusingknitr::rmarkdown

Last update: 2025-07-15
Started: 2025-07-11

Methods for calculating the proportion of transmission
Definitions | Exploring each method
Rendered fromproportion_transmission.Rmdusingknitr::rmarkdown

Last update: 2025-07-11
Started: 2024-09-27