treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data
| dc.contributor.author | Román Palacios, Cristian | en |
| dc.contributor.author | Wright, April | en |
| dc.contributor.author | Uyeda, Josef C. | en |
| dc.date.accessioned | 2021-11-29T16:04:39Z | en |
| dc.date.available | 2021-11-29T16:04:39Z | en |
| dc.date.issued | 2021-11-26 | en |
| dc.description.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/). | en |
| dc.description.sponsorship | This package was partially developed during the “Nantucket phylogeny developeR workshop”, organized by Liam J. Revell (NSF DBI-1759940). April Wright was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P2O GM103424-18. Josef Uyeda was funded on NSF DEB-1208912 to Luke Harmon in creating treeplyr, which served as a precursor for this project and code. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. | en |
| dc.description.version | Published version | en |
| dc.format.mimetype | application/pdf | en |
| dc.identifier.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 | en |
| dc.identifier.doi | https://doi.org/10.7717/peerj.12450 | en |
| dc.identifier.uri | http://hdl.handle.net/10919/106772 | en |
| dc.identifier.volume | 9 | en |
| dc.language.iso | en | en |
| dc.publisher | PeerJ | en |
| dc.rights | Creative Commons Attribution 4.0 International | en |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | en |
| dc.subject | data.table | en |
| dc.subject | Evolution | en |
| dc.subject | Phylogenetics | en |
| dc.subject | Phylogenetic comparative analyses | en |
| dc.subject | R package | en |
| dc.title | treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data | en |
| dc.title.serial | PeerJ | en |
| dc.type | Article - Refereed | en |
| dc.type.dcmitype | Text | en |