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This repo contains all code needed to generate the outputs and figures for the variant tracker manuscript

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The Pandemic Prevention Institute Global COVID-19 Variant Tracker

Downloading the latest data

The latest version of this data is available for download as a zip file.

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About the data
The zip file contains the latest data on:

Data Data File
(Click to download)
Data Dictionary (Click to download)
Global variant fitness advantage posterior distributions multicountry_mu_distrib.csv codebook
Country-specific variant fitness advantages summary stats fitness_advantages_summary.csv codebook
Country-specific summary stats, corresponding variant prevalence estimates, and inferred variant cases in the past 90 days variant_dynamics_summary_data.csv codebook
Country-specific draws from the posterior on variant prevalence estimates and corresponding data in the past 90 days variant_dynamics_full_distribution_data.csv codebook
7d average of cases per 100k over the past 90 days in each country total_cases.csv codebook
US state-specific summary stats, corresponding variant prevalence estimates, and inferred variant cases in the past 90 days US_variant_dynamics_summary_data.csv codebook
US 7d average of cases per 100k over the past 90 days in each state US_state_total_cases.csv codebook

Codebooks
Codebooks describing each dataset are available as CSV files in the codebooks folder.

Contact
Please email kjohnson@rockfound.org or zsusswein@rockfound.org to access time-stamped historical datasets of these estimates or for any questions/issues regarding this data.

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This repo contains all code needed to generate the outputs and figures for the variant tracker manuscript

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