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outbreaker2: a modular platform for outbreak reconstruction.

Finlay Campbell1, Xavier Didelot1, Rich Fitzjohn1

  • 1MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK.

BMC Bioinformatics
|October 23, 2018
PubMed
Summary
This summary is machine-generated.

outbreaker2 is a new R package for reconstructing infectious disease transmission chains. It offers a flexible, modular platform for custom outbreak models, enhancing customisability and interoperability for researchers.

Keywords:
BayesianChainEpidemicsGenomicsLikelihoodMCMCSoftwareTransmissionTree

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Area of Science:

  • Epidemiology
  • Computational Biology
  • Bioinformatics

Background:

  • Reconstructing infectious disease transmission chains is crucial for public health policy.
  • Existing methods for transmission reconstruction lack customisability and interoperability.
  • Current tools often require users to develop their own algorithms.

Purpose of the Study:

  • To present outbreaker2, a flexible R package for infectious disease outbreak reconstruction.
  • To provide a modular platform for users to specify custom transmission models.
  • To demonstrate the integration of diverse evolutionary models within a unified framework.

Main Methods:

  • Development of outbreaker2 as an R package.
  • Implementation of a modular framework for custom model specification.
  • Integration of the TransPhylo within-host evolutionary model as a proof of concept.

Main Results:

  • outbreaker2 offers a flexible and extensible framework for outbreak reconstruction.
  • The package successfully integrates distinct evolutionary models, such as TransPhylo.
  • Custom models can be incorporated with minimal user effort.

Conclusions:

  • outbreaker2 serves as a valuable foundation for future outbreak analysis tools.
  • The package promotes customisability and interoperability in transmission reconstruction.
  • outbreaker2 contributes to the growing ecosystem of R tools for outbreak analysis.