https://github.com/avallecam/epiestim

A tool to estimate time varying instantaneous reproduction number during epidemics

https://github.com/avallecam/epiestim

Repository

A tool to estimate time varying instantaneous reproduction number during epidemics

https://github.com/avallecam/EpiEstim/blob/master/

# EpiEstim


[![R build status](https://github.com/mrc-ide/EpiEstim/workflows/R-CMD-check/badge.svg)](https://github.com/mrc-ide/EpiEstim/actions)
[![Codecov test coverage](https://codecov.io/gh/annecori/EpiEstim/branch/master/graph/badge.svg)](https://codecov.io/gh/annecori/EpiEstim?branch=master)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3871387.svg)](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
devtools::install_github("mrc-ide/EpiEstim", build_vignettes = TRUE)
```

## Vignettes
The following vignettes provide worked examples, FAQs and details about how EpiEstim can be used alongside some other R packages in an outbreak analysis workflow.

```r
vignette("short_demo", package = "EpiEstim")
vignette("full_EpiEstim_vignette", package = "EpiEstim")
```

To apply EpiEstim to temporally aggregated incidence data (e.g. weekly), please see:

```r
vignette("EpiEstim_aggregated_data", package = "EpiEstim")
```

To estimate the transmission advantage of pathogen variants or strains in real-time, please see the pre-print by Bhatia et al (https://www.medrxiv.org/content/10.1101/2021.11.26.21266899v1) and the vignette below:

```r
vignette("MV_EpiEstim_vignette", package="EpiEstim")   
```

To find out more about alternative software that may be more suitable for your specific data or analysis, please see below:

```r
vignette("alternative_software", package = "EpiEstim")
```

## 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 15051512. 

> @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. [A generic method and software to estimate the transmission advantage of pathogen variants in real-time : SARS-CoV-2 as a case-study](https://www.medrxiv.org/content/10.1101/2021.11.26.21266899v1), medRxiv pre-print.

Nash RK, Cori A, Nouvellet P. Estimating the epidemic reproduction number from temporally aggregated incidence data: a statistical modelling approach and software tool. (medRxiv pre-print)


## Citing this code resource
We kindly request that you cite this codebase as follows (BibTeX format):

> @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}},  
}

Owner

GitHub Events