Epiflows: An R package for risk assessment of travel-related spread of disease [version 2; peer review: 2 approved]

Paula Moraga; Ilaria Dorigatti; Zhian N. Kamvar; Pawel Piatkowski; Salla E. Toikkanen; VP Nagraj; Christl A. Donnelly; Thibaut Jombart

doi:10.12688/f1000research.16032.3

Epiflows: An R package for risk assessment of travel-related spread of disease [version 2; peer review: 2 approved]

Paula Moraga, Ilaria Dorigatti, Zhian N. Kamvar, Pawel Piatkowski, Salla E. Toikkanen, VP Nagraj, Christl A. Donnelly, Thibaut Jombart

Department of Mathematical Sciences

Research output: Contribution to journal › Article › peer-review

9 Citations (SciVal)

Abstract

As international travel increases worldwide, new surveillance tools are needed to help identify locations where diseases are most likely to be spread and prevention measures need to be implemented. In this paper we present epiflows, an R package for risk assessment of travel-related spread of disease. epiflows produces estimates of the expected number of symptomatic and/or asymptomatic infections that could be introduced to other locations from the source of infection. Estimates (average and confidence intervals) of the number of infections introduced elsewhere are obtained by integrating data on the cumulative number of cases reported, population movement, length of stay and information on the distributions of the incubation and infectious periods of the disease. The package also provides tools for geocoding and visualization. We illustrate the use of epiflows by assessing the risk of travel-related spread of yellow fever cases in Southeast Brazil in December 2016 to May 2017.

Original language	English
Article number	1374
Pages (from-to)	1-20
Number of pages	20
Journal	F1000 Research
Volume	7
Early online date	31 Aug 2018
DOIs	https://doi.org/10.12688/f1000research.16032.3
Publication status	Published - 12 Sept 2019

Bibliographical note

Funding Information:
ID acknowledges research funding from the Imperial College Junior Research Fellowship. ID, CAD and TJ thank the UK Medical Research Council for Centre funding. TJ is funded by the National Institute for Health Research Health Protection Research Unit (NIHRHPRU) in Modelling Methodology at Imperial College London in partnership with Public Health England (PHE). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Publisher Copyright:
© 2019 Moraga P et al.

Keywords

Disease surveillance
Epidemics
Infectious
Outbreaks
R,RECON

ASJC Scopus subject areas

General Biochemistry,Genetics and Molecular Biology
General Immunology and Microbiology
Pharmacology, Toxicology and Pharmaceutics(all)

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.12688/f1000research.16032.3Licence: CC BY

Cite this

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title = "Epiflows: An R package for risk assessment of travel-related spread of disease [version 2; peer review: 2 approved]",

abstract = "As international travel increases worldwide, new surveillance tools are needed to help identify locations where diseases are most likely to be spread and prevention measures need to be implemented. In this paper we present epiflows, an R package for risk assessment of travel-related spread of disease. epiflows produces estimates of the expected number of symptomatic and/or asymptomatic infections that could be introduced to other locations from the source of infection. Estimates (average and confidence intervals) of the number of infections introduced elsewhere are obtained by integrating data on the cumulative number of cases reported, population movement, length of stay and information on the distributions of the incubation and infectious periods of the disease. The package also provides tools for geocoding and visualization. We illustrate the use of epiflows by assessing the risk of travel-related spread of yellow fever cases in Southeast Brazil in December 2016 to May 2017.",

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note = "Funding Information: ID acknowledges research funding from the Imperial College Junior Research Fellowship. ID, CAD and TJ thank the UK Medical Research Council for Centre funding. TJ is funded by the National Institute for Health Research Health Protection Research Unit (NIHRHPRU) in Modelling Methodology at Imperial College London in partnership with Public Health England (PHE). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: {\textcopyright} 2019 Moraga P et al.",

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Epiflows: An R package for risk assessment of travel-related spread of disease [version 2; peer review: 2 approved]

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

UN SDGs

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