treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data

TR Number

Date

2021-11-26

Journal Title

Journal ISSN

Volume Title

Publisher

PeerJ

Abstract

The number of terminals in phylogenetic trees has significantly increased over the last decade. This trend reflects recent advances in next-generation sequencing, accessibility of public data repositories, and the increased use of phylogenies in many fields. Despite R being central to the analysis of phylogenetic data, manipulation of phylogenetic comparative datasets remains slow, complex, and poorly reproducible. Here, we describe the first R package extending the functionality and syntax of data.table to explicitly deal with phylogenetic comparative datasets. treedata.table significantly increases speed and reproducibility during the data manipulation steps involved in the phylogenetic comparative workflow in R. The latest release of treedata.table is currently available through CRAN (https://cran.r-project.org/web/packages/treedata.table/). Additional documentation can be accessed through rOpenSci (https://ropensci.github.io/treedata.table/).

Description

Keywords

data.table, Evolution, Phylogenetics, Phylogenetic comparative analyses, R package

Citation

Román Palacios C, Wright A, Uyeda J. 2021. treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data. PeerJ 9:e12450 https://doi.org/10.7717/peerj.12450