Covmuller

Covmuller is an R-package designed for analysis of SARS-CoV-2 sequencing metadata deposited on GISAID.

Features

Covmuller currently supports the following features:

• Read and preprocess metadata file downloaded from GISAID: Vignette
• Plot variant prevalence: Vignette
• Fit multinomial models to variant prevalence data:
  • India
  • USA
  • Canada
  • UK
  • Australia
  • SouthAfrica
• Estimate totals prevalence of variants by projecting case prevalence data on multinomila fits:
  • India
  • New York state
  • New York City
  • South Africa
  • United Kingdom
  • USA