phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things)

🤖 Plain-English Summary

Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution, diversification dynamics, biogeography, community ecology, and a wide range of other phenomena or processes. As of the time of writing, phytools included functionality for fitting models of trait evolution, for reconstructing ancestral states, for studying diversification on trees, and for visualizing phylogenies, comparativ...

🔑 Key Findings

• Over the past ten years or so, the phytools R package has grown to become an important research tool for phylogenetic comparative analysis.
• phytools is a diverse contributed R library now consisting of hundreds of different functions covering a variety of methods and purposes in phylogenetic biology.
• As of the time of writing, phytools included functionality for fitting models of trait evolution, for reconstructing ancestral states, for studying diversification on trees, and for visualizing phylogenies, comparative data, and fitted models, as well numerous other tasks related to phylogenetic biology.

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