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README.md with clearer citation info including DOI
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rebeccanash committed Apr 30, 2021
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* New vignette

# EpiEstim 2.2-3

* This release is also available at https://zenodo.org/record/3871387 which is the source of the DOI for this codebase; for v2.2-3 that is doi:10.5281/zenodo.3871387. Also added as a link to the top-right of the landing page. Don't forget to update in the next release!
## FIXED
* Fixed bugs in draw_one_set_of_ancestries resulting from incorrect lengths and an undefined variable (issue #92) (#93, @jstockwin)
* Fixed incorrect quantiles (issue #88) (#89, @jstockwin)
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27 changes: 21 additions & 6 deletions README.md
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<!-- badges: start -->
[![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.3333654.svg)](https://doi.org/10.5281/zenodo.3333654)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3871387.svg)](https://doi.org/10.5281/zenodo.3871387)
<!-- badges: end -->

A tool to estimate time varying instantaneous reproduction number during epidemics
A tool to estimate time varying instantaneous reproduction number during epidemics. It is described in the following paper:

This tool is described in the following paper:
> @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},
}

A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics
Anne Cori, Neil M. Ferguson, Christophe Fraser and Simon Cauchemez
American Journal of Epidemiology 2013.
## Citing this code resource
We kindly request that you cite this codebase as follows (BibTeX format):

> @misc{Cori2021,
author={Cori, A and Kamvar, ZN and Stockwin, J and Jombart, T and Dahlqwist, E and FitzJohn, R and Thompson, R},
year={2021},
title={{EpiEstim v2.2-3: A tool to estimate time varying instantaneous reproduction number during epidemics}},
publisher={GitHub},
journal={GitHub repository},
howpublished = {\url{https://github.com/mrc-ide/EpiEstim}},
commit={c18949d93fe4dcc384cbcae7567a788622efc781},
}

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