outbreaker2

MaRDI QIDQ1352408swMATHCRANFDO

Authors Finlay Campbell, Thibaut Jombart, Rich Fitzjohn

Last update 17 December 2025

Copyright license MIT license, File License

Software version identifier 1.1.3, PACKAGES.rds, 1.0-0, 1.0.1, 1.1.0, 1.1.1, 1.1.2, 1.1.4

Official website https://cran.r-project.org/web/packages/outbreaker2/index.html

Source code repository https://github.com/cran/outbreaker2

Description

Bayesian reconstruction of disease outbreaks using epidemiological and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C and Ferguson N. 2014. <doi:10.1371/journal.pcbi.1003457>. Campbell, F, Cori A, Ferguson N, Jombart T. 2019. <doi:10.1371/journal.pcbi.1006930>.

Cites work

• Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data
• Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

Cited in

(4)

• o2geosocial
• InfectionTrees
• RcppAlgos
• Branching Process Models to Identify Risk Factors for Infectious Disease Transmission

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