https://github.com/mrc-ide/stave

Spatial-temporal aggregate variant encoding
https://github.com/mrc-ide/stave

Last synced: 10 days ago
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Spatial-temporal aggregate variant encoding

• Host: GitHub
• URL: https://github.com/mrc-ide/stave
• Owner: mrc-ide
• License: other
• Created: 2024-09-17T12:03:34.000Z (4 months ago)
• Default Branch: main
• Last Pushed: 2024-12-17T14:23:49.000Z (17 days ago)
• Last Synced: 2024-12-17T15:28:51.218Z (17 days ago)
• Language: R
• Size: 266 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE

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README

        
---

output: github_document

---

```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```

# STAVE

[![master checks](https://github.com/mrc-ide/STAVE/workflows/checks_main/badge.svg)](https://github.com/mrc-ide/STAVE/actions)

[![develop checks](https://github.com/mrc-ide/STAVE/workflows/checks_develop/badge.svg)](https://github.com/mrc-ide/STAVE/actions)

[![Codecov test coverage](https://codecov.io/gh/mrc-ide/STAVE/branch/main/graph/badge.svg)](https://app.codecov.io/gh/mrc-ide/STAVE?branch=main)

STAVE is an R package designed for storing and managing **aggregate

spatial-temporal genetic data**. By “aggregate” we mean that data consist solely

of counts (numerator and denominator). By “spatial-temporal” we mean that

each observation is tied to a specific geographic location (latitude and

longitude), and a precise collection time (a single day).

The primary goals of STAVE are:

1. To provide a flexible data structure that can accommodate genetic data with varying levels of detail.

2. To standardize data through a tightly defined format.

3. To facilitate prevalence calculation from aggregate counts.

All documentation, including installation instructions and tutorials, are on [the STAVE website](https://mrc-ide.github.io/STAVE/).

# Version History

The current version of the software is 1.0.0, released 16 Oct 2024.