A Global Dataset of Anthropogenic Extinct Birds and their Traits: Phylogeny Builder

Grafts the extinct bird species from the 'Avotrex' database (Sayol et al., in review) on to the 'BirdTree' phylogenies < https://birdtree.org>, using a set of different commands.

The ‘avotrex’ R package

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)