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
; 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
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 |
| Date Deposited | 18 Dec 2018 10:55 |
| Last Modified | 19 Mar 2026 11:10 |
| Publisher | The Comprehensive R Archive Network |
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