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: