README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  echo = TRUE, 
  warning = FALSE, 
  message = FALSE, 
  dpi=400,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%",
  fig.align = "center"
)
```


<div style="display: flex; align-items: center;">
  <h1 style="margin-right: 20px;">linktree</h1>
  <img src="man/figures/hexsticker.png" width="150">
</div>

<!-- badges: start -->

[![R-CMD-check](https://github.com/CyGei/linktree/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/CyGei/linktree/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/CyGei/linktree/graph/badge.svg)](https://app.codecov.io/gh/CyGei/linktree)
<!-- badges: end -->

`linktree` is a novel framework that leverages transmission chain data to estimate ***group transmission assortativity***; this 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).

## Installation

```{r}
# install.packages("devtools")
# devtools::install_github("CyGei/linktree")
library(linktree)
```

## Documentation

For more information, check the deticated webiste: [linktree](https://cygei.github.io/linktree/)