STAVE is an R package with three basic functionalities:
- Stores aggregate genetic data (i.e. numerator and denominator) in variant string format. This is a convenient format when dealing with amino acid level data, as is common for drug resistance markers. It can handle single codons as well as multi-locus haplotypes.
- Links genetic data to a specific point in space and time. This avoids any issues with country or admin names changing or being spelled differently.
- Calculates prevalence from the encoded data. This is not as simple as it sounds, for example the variant of interest may be a subset of an encoded haplotype, or there may be mixed (heterozygous) calls in the data.
All documentation, including installation instructions and tutorials, can be found on the STAVE website.
See the tagged versions for the latest release, and please refer to a
specific tag when installing (i.e. @v2.0.4) to avoid issues with
backward incompatibility.