
# The ‘avotrex’ R package

[![CRAN
Downloads](http://cranlogs.r-pkg.org/badges/grand-total/avotrex)](https://cran.r-project.org/package=avotrex)
[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/avotrex)](https://cran.r-project.org/package=avotrex)
[![License: GPL
v3](https://img.shields.io/badge/License-GPLv3-yellow.svg)](https://www.gnu.org/licenses/gpl-3.0)
[![CircleCI](https://circleci.com/gh/joe-wayman/avotrex/tree/main.svg?style=svg)](https://app.circleci.com/pipelines/github/joe-wayman/avotrex?branch=main)
[![Codecov test
coverage](https://codecov.io/gh/joe-wayman/avotrex/branch/main/graph/badge.svg)](https://app.codecov.io/gh/joe-wayman/avotrex?branch=main)

Repository for the avotrex R package.

The avotrex package provides functionality to graft extinct avian
species, present in the AvoTrex dataset, to existing BirdTree backbone
trees.

Note that the package imports and loads in the ‘ape’ R package in its
entirety, as this provides access to its full range of classes and
functions.

As this is version 1.3.0 of the package, it is possible that there are
some bugs in places. Please report any issues to us via GitHub.

Please see the accompanying paper (Sayol et al., in review) and package
vignette for more detailed information regarding use of the package.

Sayol, F., J. P. Wayman, P. Dufour, and et al. 2024. “AVOTREX: A Global
Dataset of Extinct Birds and Their Traits.” Journal Article. In Review.

## Installation

You can install the released version of avotrex from CRAN and the
development version from GitHub.

## Example usage

library(avotrex)

data(BirdTree_trees) \# Load in the example trees  
data(BirdTree_tax) \# Load extant BirdTree taxonomy  
data(AvotrexPhylo) \# Load in the extinct grafting database and
instructions

trees \<- AvoPhylo(ctrees = Trees, avotrex = AvotrexPhylo, PER = 0.2,
PER_FIXED = 0.75, mindist = 0.1, ord = FALSE, tax = tax, Ntree = 1,
n.cores = 1, cluster.ips = NULL)
