EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering

• Ciara Judge ,

  Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing

  * E-mail: ciara.judge@lshtm.ac.uk (CJ); oliver.brady@lshtm.ac.uk (OB); sahill@rvc.ac.uk (SH)

  Affiliations Department of Infectious Disease Epidemiology and Dynamics, Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, United Kingdom, Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom, Department of Pathobiology and Population Sciences, Royal Veterinary College, United Kingdom

  https://orcid.org/0000-0001-7923-9898

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• Timothy Vaughan,

  Roles Conceptualization, Investigation, Methodology, Writing – review & editing

  Affiliations Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland

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• Timothy Russell,

  Roles Conceptualization

  Affiliations Department of Infectious Disease Epidemiology and Dynamics, Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, United Kingdom, Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom

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• Sam Abbott,

  Roles Conceptualization, Methodology, Writing – review & editing

  Affiliations Department of Infectious Disease Epidemiology and Dynamics, Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, United Kingdom, Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom

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• Louis du Plessis,

  Roles Conceptualization, Data curation, Methodology, Resources, Writing – review & editing

  Affiliations Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland

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• Tanja Stadler,

  Roles Conceptualization, Writing – review & editing

  Affiliations Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland

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• Oliver Brady ,

  Roles Conceptualization, Investigation, Methodology, Resources, Supervision, Writing – review & editing

  * E-mail: ciara.judge@lshtm.ac.uk (CJ); oliver.brady@lshtm.ac.uk (OB); sahill@rvc.ac.uk (SH)

  Affiliations Department of Infectious Disease Epidemiology and Dynamics, Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, United Kingdom, Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom

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• Sarah Hill

  Roles Conceptualization, Data curation, Investigation, Methodology, Project administration, Resources, Supervision, Writing – review & editing

  * E-mail: ciara.judge@lshtm.ac.uk (CJ); oliver.brady@lshtm.ac.uk (OB); sahill@rvc.ac.uk (SH)

  Affiliation Department of Pathobiology and Population Sciences, Royal Veterinary College, United Kingdom

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