Skip to content

joe-wayman/avotrex

Repository files navigation

The ‘avotrex’ R package

CRAN Downloads CRAN_Status_Badge License: GPL v3 CircleCI Codecov test coverage

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 1.3.1 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)

About

Repository for R package Avotrex.

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published