outbreaker2: Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

Jombart, T

; Campbell, F and Fitzjohn, R (2018). outbreaker2: Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data. [Dataset]. The Comprehensive R Archive Network. https://CRAN.R-project.org/package=outbreaker2

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outbreaker2 is a Bayesian framework for integrating epidemiological and genetic data to reconstruct transmission trees of densely sampled outbreaks. It re-implements, generalises and replaces the model of outbreaker, and uses a modular approach which enables fine customisation of priors, likelihoods and parameter movements.

Keywords

Outbreak reconstruction; Transmission tree reconstruction

Item Type	Dataset
Resource Type	Resource Type Resource Description Software R script
Capture method	Other
Date	30 November 2018
Language(s) of written materials	English
Creator(s)	Jombart, T ; Campbell, F and Fitzjohn, R
LSHTM Faculty/Department	Faculty of Epidemiology and Population Health > Dept of Infectious Disease Epidemiology (-2023)
Participating Institutions	London School of Hygiene & Tropical Medicine, London, United Kingdom
Funders	Project Funder Grant Number Funder URI UNSPECIFIED Wellcome Trust UNSPECIFIED UNSPECIFIED UNSPECIFIED Medical Research Council UNSPECIFIED UNSPECIFIED UNSPECIFIED National Institute for Health Research (NIHR) UNSPECIFIED UNSPECIFIED
Date Deposited	18 Dec 2018 10:55
Last Modified	19 Mar 2026 11:10
Publisher	The Comprehensive R Archive Network