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

Area of Science:

• Computational Biology
• Bioinformatics
• Evolutionary Biology

Background:

• The number of terminals in phylogenetic trees has rapidly increased due to advances in next-generation sequencing and data accessibility.
• Phylogenetic trees are increasingly utilized across diverse scientific fields.
• Current R-based manipulation of phylogenetic comparative datasets is often slow, complex, and lacks reproducibility.

Purpose of the Study:

• To introduce the first R package designed to streamline the manipulation of phylogenetic comparative datasets.
• To enhance the speed and reproducibility of phylogenetic comparative data workflows in R.
• To extend the functionality and syntax of the data.table package for phylogenetic data.

Main Methods:

• Development of the treedata.table R package.
• Integration of data.table syntax and functionality for phylogenetic datasets.
• Testing and validation within the R environment for phylogenetic comparative analyses.

Main Results:

• The treedata.table package significantly improves the speed of data manipulation for phylogenetic comparative datasets.
• It enhances the reproducibility of the data manipulation steps in phylogenetic comparative workflows.
• The package provides an efficient and user-friendly interface for handling large phylogenetic datasets in R.

Conclusions:

• treedata.table offers a substantial improvement for researchers working with phylogenetic comparative data in R.
• The package addresses key limitations in speed, complexity, and reproducibility of data manipulation.
• It is available via CRAN and supported by rOpenSci documentation.