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

PeerJ

article

Cristian Román Palacios¹  April Wright⁵  Josef Uyeda⁶ 

[1] Department of Atmospheric and Oceanic Sciences;Department of Earth, Planetary, and Space Sciences, Institute of the Environment and Sustainability;Center for Diverse Leadership in Science, University of California;School of Information, University of Arizona;Biology Department, Southeastern Louisiana University;Department of Biological Sciences, Virginia Polytechnic Institute and State University

关键词: Data.table;    Evolution;    Phylogenetics;    Phylogenetic comparative analyses;    R Package;   

DOI  :  10.7717/peerj.12450

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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/).

【 授权许可】

CC BY