first commit

.gitignore

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+.ipynb_checkpoints/*
+Sant_Eufemia/.ipynb_checkpoints/*
+*/.Rhistory

DataGIS/README.md

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+This folder contains a GIS shape file for the city of Venice, divided by parish.

README.md

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+# Death in Venice: A Digital Reconstruction of a Large Plague Outbreak During 1630-1631
+
+Paper: https://www.medrxiv.org/content/10.1101/2020.03.11.20034116v1.
+
+## Contents
+
+* The main dataset: [dataset](./dataset) folder.
+* Exploratory analysis on main dataset: [space\_time\_exploration](space_time_exploration.ipynb) notebook.
+* Deterministic modeling: [models\_of\_plague\_epid](TO_BE_CLEANED_models_of_plague_epid.ipynb) notebook.
+* Stochastic modeling: [epid\_simulations](epid_simulations.ipynb) notebook.
+* Analysis of the **Sant'Eufemia** parish dataset: [Sant_Eufemia](./Sant_Eufemia) folder.
+
+## Cite as 
+
+_Lazzari, G., Colavizza, G., Bortoluzzi, F., Drago, D., Erboso, A., Zugno, F., ... & Salathe, M. (2020). Death in Venice: A Digital Reconstruction of a Large Plague Outbreak During 1630-1631. medRxiv._
+
+or
+
+```
+@article{lazzari2020death,
+  title={Death in Venice: A Digital Reconstruction of a Large Plague Outbreak During 1630-1631},
+  author={Lazzari, Gianrocco and Colavizza, Giovanni and Bortoluzzi, Fabio and Drago, Davide and Erboso, Andrea and Zugno, Francesca and Kaplan, Frederic and Salathe, Marcel},
+  journal={medRxiv},
+  year={2020},
+  publisher={Cold Spring Harbor Laboratory Press}
+}
+```

Sant_Eufemia/README.md

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+Analysis are contained in the [Sant_Eufemia](./Sant_Eufemia.ipynb) notebook
+
+In this folder there is the exploration of the Sant'Eufemia dataset, and in particular the code for fig **2b**, **SI2** and **SI3** from the paper