Epidemic curves made easy using the R package incidence [version 1; referees: awaiting peer review]
File(s)
Published version
Author(s)
Kamvar, Zhian
Cai, Jun
Pulliam, Juliet RC
Schumacher, Jakob
Jombart, Thibaut
Type
Journal Article
Abstract
The epidemiological curve (epicurve) is one of the simplest yet most useful tools used by field epidemiologists, modellers, and decision makers for assessing the dynamics of infectious disease epidemics. Here, we present the free, open-source package incidence for the R programming language, which allows users to easily compute, handle, and visualise epicurves from unaggregated linelist data. This package was built in accordance with the development guidelines of the R Epidemics Consortium (RECON), which aim to ensure robustness and reliability through extensive automated testing, documentation, and good coding practices. As such, it fills an important gap in the toolbox for outbreak analytics using the R software, and provides a solid building block for further developments in infectious disease modelling. incidence is available from https://www.repidemicsconsortium.org/incidence.
Date Issued
2019-01-31
Date Acceptance
2019-01-25
Citation
F1000Research, 8
ISSN
2046-1402
Publisher
F1000 Research Ltd
Journal / Book Title
F1000Research
Volume
8
Copyright Statement
© 2019 Kamvar ZN et al. This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Sponsor
Medical Research Council (MRC)
National Institute for Health Research
Medical Research Council (MRC)
Grant Number
MR/K010174/1B
HPRU-2012-10080
MR/R015600/1
Publication Status
Published online
Date Publish Online
2019-01-31