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README for USA-Paper code release
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s-mishra authored Oct 8, 2020
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Expand Up @@ -6,6 +6,17 @@ Code for modelling estimated deaths and infections for COVID-19 from ["Estimatin

If you are looking for the individual based model used in Imperial's [Report 9, Ferguson, Laydon, Nedjati-Gilani et al](https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-9-impact-of-npis-on-covid-19/), please look [here](https://github.com/mrc-ide/covid-sim).

## Version 10 Release [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4059564.svg)](https://doi.org/10.5281/zenodo.4059564)

This is the release related to our usa-paper (soon to be out) and [medRxiv paper](https://www.medrxiv.org/content/10.1101/2020.07.13.20152355v2?rss=1%22), where we use mobility data to estimate situation in all states of the USA. All other code is still the same.

To run this code you can directly run the base-usa.r file or from command line after seting the current directory as the repository directory run the following command `Rscript base-usa-cases.r`

The code should be run in full mode to obtain credible results. Not running a full run to estimate anything is not recommended and discouraged. Only a full run should be used to get results.

The instructions for European, Italy, Brazil, USA, Nature, IFR, USA age-specific code are the same as earlier (Look at version 3, version 4, version 5, version 6, version 7, version 8, and version 9). This release is specific to [ usa-paper (soon to be out) and [medRxiv paper](https://www.medrxiv.org/content/10.1101/2020.07.13.20152355v2?rss=1%22).

This release has been checked on macOS Catalina version 10.15.6/7 and Ubuntu version 18.04.2.

## Version 9 Release [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4059564.svg)](https://doi.org/10.5281/zenodo.4059564)

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