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

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 o...

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Autores principales:	Cristian Román Palacios, April Wright, Josef Uyeda
Formato:	article
Lenguaje:	EN
Publicado:	PeerJ Inc. 2021
Materias:	Data.table Evolution Phylogenetics Phylogenetic comparative analyses R Package Medicine R
Acceso en línea:	https://doaj.org/article/1bd79dbac9e3433787b7c09cd9667897
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id	oai:doaj.org-article:1bd79dbac9e3433787b7c09cd9667897
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spelling	oai:doaj.org-article:1bd79dbac9e3433787b7c09cd96678972021-11-28T15:05:14Z treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data10.7717/peerj.124502167-8359https://doaj.org/article/1bd79dbac9e3433787b7c09cd96678972021-11-01T00:00:00Zhttps://peerj.com/articles/12450.pdfhttps://peerj.com/articles/12450/https://doaj.org/toc/2167-8359The 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/).Cristian Román PalaciosApril WrightJosef UyedaPeerJ Inc.articleData.tableEvolutionPhylogeneticsPhylogenetic comparative analysesR PackageMedicineRENPeerJ, Vol 9, p e12450 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Data.table Evolution Phylogenetics Phylogenetic comparative analyses R Package Medicine R
spellingShingle	Data.table Evolution Phylogenetics Phylogenetic comparative analyses R Package Medicine R Cristian Román Palacios April Wright Josef Uyeda treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data
description	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/).
format	article
author	Cristian Román Palacios April Wright Josef Uyeda
author_facet	Cristian Román Palacios April Wright Josef Uyeda
author_sort	Cristian Román Palacios
title	treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data
title_short	treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data
title_full	treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data
title_fullStr	treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data
title_full_unstemmed	treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data
title_sort	treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data
publisher	PeerJ Inc.
publishDate	2021
url	https://doaj.org/article/1bd79dbac9e3433787b7c09cd9667897
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treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data

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