Epiflows

an R package for risk assessment of travel-related spread of disease

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

Research output: Contribution to journalArticle

2 Citations (Scopus)

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 languageEnglish
Article number1374
Pages (from-to)1-20
Number of pages20
JournalF1000 Research
Volume7
Early online date31 Aug 2018
DOIs
Publication statusPublished - 12 Sep 2019

Keywords

  • Disease surveillance
  • Epidemics
  • Infectious
  • Outbreaks
  • R,RECON

ASJC Scopus subject areas

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

Cite this

Moraga, P., Dorigatti, I., Kamvar, Z. N., Piatkowski, P., Toikkanen, S. E., Nagraj, VP., ... Jombart, T. (2019). Epiflows: an R package for risk assessment of travel-related spread of disease. F1000 Research, 7, 1-20. [1374]. https://doi.org/10.12688/f1000research.16032.3

Epiflows : an R package for risk assessment of travel-related spread of disease. / Moraga, Paula; Dorigatti, Ilaria; Kamvar, Zhian N.; Piatkowski, Pawel; Toikkanen, Salla E.; Nagraj, VP; Donnelly, Christl A.; Jombart, Thibaut.

In: F1000 Research, Vol. 7, 1374, 12.09.2019, p. 1-20.

Research output: Contribution to journalArticle

Moraga, P, Dorigatti, I, Kamvar, ZN, Piatkowski, P, Toikkanen, SE, Nagraj, VP, Donnelly, CA & Jombart, T 2019, 'Epiflows: an R package for risk assessment of travel-related spread of disease', F1000 Research, vol. 7, 1374, pp. 1-20. https://doi.org/10.12688/f1000research.16032.3
Moraga P, Dorigatti I, Kamvar ZN, Piatkowski P, Toikkanen SE, Nagraj VP et al. Epiflows: an R package for risk assessment of travel-related spread of disease. F1000 Research. 2019 Sep 12;7:1-20. 1374. https://doi.org/10.12688/f1000research.16032.3
Moraga, Paula ; Dorigatti, Ilaria ; Kamvar, Zhian N. ; Piatkowski, Pawel ; Toikkanen, Salla E. ; Nagraj, VP ; Donnelly, Christl A. ; Jombart, Thibaut. / Epiflows : an R package for risk assessment of travel-related spread of disease. In: F1000 Research. 2019 ; Vol. 7. pp. 1-20.
@article{f48d738a9cd34dcfb62a0899077b3e9c,
title = "Epiflows: an R package for risk assessment of travel-related spread of disease",
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.",
keywords = "Disease surveillance, Epidemics, Infectious, Outbreaks, R,RECON",
author = "Paula Moraga and Ilaria Dorigatti and Kamvar, {Zhian N.} and Pawel Piatkowski and Toikkanen, {Salla E.} and VP Nagraj and Donnelly, {Christl A.} and Thibaut Jombart",
year = "2019",
month = "9",
day = "12",
doi = "10.12688/f1000research.16032.3",
language = "English",
volume = "7",
pages = "1--20",
journal = "F1000 Research",
issn = "2046-1402",
publisher = "F1000 Research Ltd.",

}

TY - JOUR

T1 - Epiflows

T2 - an R package for risk assessment of travel-related spread of disease

AU - Moraga, Paula

AU - Dorigatti, Ilaria

AU - Kamvar, Zhian N.

AU - Piatkowski, Pawel

AU - Toikkanen, Salla E.

AU - Nagraj, VP

AU - Donnelly, Christl A.

AU - Jombart, Thibaut

PY - 2019/9/12

Y1 - 2019/9/12

N2 - 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.

AB - 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.

KW - Disease surveillance

KW - Epidemics

KW - Infectious

KW - Outbreaks

KW - R,RECON

UR - http://www.scopus.com/inward/record.url?scp=85072912705&partnerID=8YFLogxK

U2 - 10.12688/f1000research.16032.3

DO - 10.12688/f1000research.16032.3

M3 - Article

VL - 7

SP - 1

EP - 20

JO - F1000 Research

JF - F1000 Research

SN - 2046-1402

M1 - 1374

ER -