Lessons from SARS-CoV-2 in India: A data-driven framework for pandemic resilience

Maxwell Salvatore, Soumik Purkayastha, Lakshmi Ganapathi, Rupam Bhattacharyya, Ritoban Kundu, Lauren Zimmermann, Debashree Ray, Aditi Hazra, Michael Kleinsasser, Sunil Solomon, Ramnath Subbaraman, Bhramar Mukherjee

Materials

This repository contains scripts used to perform the analyses and generate the figures presented in the above-titled manuscript.

• The figure/ folder contains subfolders corresponding to each figure. Each subfolder contains an R script that generates and saves the figure in its respective folder. These folders may also contain additional files/scripts that are needed to recreate the image. The scripts in these folder may also source scripts in the model/ folder

• The model/ folder contains the eSAIR model scripts (e.g.,, tvt.wi.eSAIR.R) that are used to generate the results. It also contains a toy example that runs the model script (toy_run.R). It also contains some data files that are used to specify conditions in the model, like the intervention effect schedules (pi_schedule_extended.csv).

• The model/seir/ folder contain the scripts to run the modified SEIR model in our paper. The scripts with the prefix Run_* are scripts that run the model scripts. We also provide SEIRfansy scripts in model/seirfansy_f=0, which was modified for our SEIR model.

• The model/seir_results/ folder contains the model results in ./results/ and the data for plotting in ./plot_data/.

• The tables/ folder contains subfolders for each table from which the model results were extracted from model results.

• The old versions/ folder contains scripts from previous submissions and revisions.