phytools 2.0: An updated R ecosystem for phylogenetic comparative methods (and other things)
This paper describes the updated features and functionalities of the 'phytools' R package, a widely used tool for phylogenetic comparative methods. It provides multiple example workflows illustrating the use of 'phytools' for analyzing discrete and continuous character evolution, diversification rates, and visualizing phylogenetic data, including stochastic character mapping, ancestral state reconstruction, and lineage-through-time plots.
2023.03.08.531791.full.pdf