o2ools/README.Rmd at main · CyGei/o2ools · GitHub

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---
output: github_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

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# o2ools <a href="https://cygei.github.io/o2ools/"><img src="man/figures/logo.png" alt="o2ools website" align="right" height="242"/></a>

Tools to process the results of [`outbreaker2`](https://github.com/reconhub/outbreaker2).

## Installation

Install the package from [CRAN](https://cran.r-project.org/web/packages/o2ools/index.html):

```{r, eval=FALSE}
install.packages("o2ools")
library(o2ools)
```

Or the development version from GitHub:

```{r, eval=FALSE}
devtools::install_github("cygei/o2ools")
```

## Information

The inference of transmission chains from genomic, epidemiological and contact data is central to outbreak investigations. [`outbreaker2`](https://github.com/reconhub/outbreaker2) and other popular models use Bayesian inference to reconstruct who infected whom. However, the results of these models are difficult to interpret and visualise.
`o2ools` provides tools to analyse and visualise the results of `outbreaker2`. To get started, check the package [vignette](https://cygei.github.io/o2ools/articles/o2ools.html).