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https://github.com/mrc-ide/epiestim
A tool to estimate time varying instantaneous reproduction number during epidemics
https://github.com/mrc-ide/epiestim
Last synced: 4 days ago
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A tool to estimate time varying instantaneous reproduction number during epidemics
- Host: GitHub
- URL: https://github.com/mrc-ide/epiestim
- Owner: mrc-ide
- Created: 2015-11-06T13:09:56.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2024-08-30T08:53:49.000Z (4 months ago)
- Last Synced: 2024-12-24T07:52:56.869Z (8 days ago)
- Language: R
- Homepage: https://mrc-ide.github.io/EpiEstim
- Size: 17.4 MB
- Stars: 95
- Watchers: 16
- Forks: 39
- Open Issues: 48
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# EpiEstim
[](https://github.com/mrc-ide/EpiEstim/actions)
[](https://codecov.io/gh/annecori/EpiEstim?branch=master)
[](https://doi.org/10.5281/zenodo.3871387)
EpiEstim is a tool to estimate the time-varying instantaneous reproduction number during epidemics.
To install the latest version, use:
```r
install.packages('EpiEstim', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))
```
### Vignettes
Please see https://mrc-ide.github.io/EpiEstim/ for vignettes with worked examples,
FAQs and details about how EpiEstim can be used alongside some other R packages
in an outbreak analysis workflow.
### Cite our papers
Anne Cori, Neil M. Ferguson, Christophe Fraser, Simon Cauchemez, [A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics](https://doi.org/10.1093/aje/kwt133), American Journal of Epidemiology, Volume 178, Issue 9, 1 November 2013, Pages 1505–1512.
```console
@article{Cori2013,
author={Cori, A and Ferguson, NM and Fraser, C and Cauchemez, S},
year={2013},
title={{A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics}},
journal={Am. J. Epidemiol.},
doi={10.1093/aje/kwt133},
}
```
Thompson RN, Stockwin JE, van Gaalen RD, Polonsky JA, Kamvar ZN, Demarsh PA, et al. [Improved inference of time-varying reproduction numbers during infectious disease outbreaks](https://doi.org/10.1016/j.epidem.2019.100356), Epidemics, Volume 29, 1 December 2019, 100356.
Nash RK, Nouvellet P, Cori A. [Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges](https://doi.org/10.1371/journal.pdig.0000052), PLOS Digital Health, Volume 1, Issue 6, 27 June 2022, e0000052.
Bhatia S, Wardle J, Nash RK, Nouvellet P, Cori A. [Extending EpiEstim to estimate the transmission advantage of pathogen variants in real-time: SARS-CoV-2 as a case-study](https://doi.org/10.1016/j.epidem.2023.100692), Epidemics, 21 June 2023, 100692.
Nash RK, Cori A, Nouvellet P. [Estimating the epidemic reproduction number from temporally aggregated incidence data: a statistical modelling approach and software tool](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011439), PLOS Computational Biology, Volume 19, Issue 8, 28 August 2023, e1011439.
Brizzi A, O'Driscoll M, Dorigatti I., [Refining Reproduction Number Estimates to Account for Unobserved Generations of Infection in Emerging Epidemics](https://doi.org/10.1093/cid/ciac138), Clinical Infectious Diseases, Volume 75, Issue 1, 1 July 2022, Pages e114–e121.
### Citing this code resource
We kindly request that you cite this codebase as follows (BibTeX format):
```console
@misc{Cori2022,
author={Cori, A and Kamvar, ZN and Stockwin, J and Jombart, T and Dahlqwist, E and FitzJohn, R and Thompson, R and Nash, RK and Wardle, J and Bhatia, S},
year={2022},
title={{EpiEstim v2.2-4: A tool to estimate time varying instantaneous reproduction number during epidemics}},
publisher={GitHub},
journal={GitHub repository},
howpublished = {\url{https://github.com/mrc-ide/EpiEstim}},
}
```