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

Jombart, TORCID logo, 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

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