Kruse, P. M.; Ring, C. L.

This paper presents the treecompareR package for R, which provides tools for reproducible visualizations of data through the use of taxonomies. The package builds on developments from ggplot2 and ggtree to provide visualizations tailored for use with taxonomic classification data. Additionally, it provides tools that leverage developments in network analysis to compare data sets. While designed specifically for chemical classification objectives using ClassyFire (http://classyfire.wishartlab.com/), treecompareR also provides tools for use with more general taxonomies. treecompareR is available from GitHub at https://github.com/USEPA/treecompareR.