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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# linktree <a href="https://cygei.github.io/linktree/"><img src="man/figures/logo.png" alt="linktree website" align="right" height="242"/></a>
<!-- badges: start -->
[](https://CRAN.R-project.org/package=linktree)
[](https://CRAN.R-project.org/package=linktree)
[](https://www.codefactor.io/repository/github/cygei/linktree)
[](https://github.com/CyGei/linktree/actions/workflows/R-CMD-check.yaml)
<!-- badges: end -->
`linktree` is a novel framework that estimates ***group transmission assortativity*** from transmission trees.
## Installation
You can install `linktree` from CRAN:
``` r
install.packages("linktree")
```
## Definition
Group transmission assortativity quantifies the extent to which individuals transmit within their own group compared to others. The methodology is described in our [paper](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0313037), and briefly discussed on [YouTube](https://www.youtube.com/watch?v=Ib5dBunDPN0).
The $\gamma$ coefficient ranges from 0 to $\infty$. It describes the excess propability of transmitting within your own group versus other groups. See `get_gamma()`.
We can rescale $\gamma$ to the $\delta$ coefficient, which ranges from -1 to 1 using `get_delta()`.
## Documentation
`linktree` requires that you have transmission chain data (*i.e.* who infected whom) and group membership for each individual in the transmission chain.
For more information, check the dedicated [vignette](https://cygei.github.io/linktree/articles/linktree.html).