phytools 2.0: A Phylogenetic Toolkit for R (Hold the Groundbreaking Science)

Overview

Paper Summary › Explain Like I'm Five › Conflicts of Interest › Identified Limitations › Rating Explanation › Good to know › Topic Hierarchy › File Information ›

Paper Summary

Paperzilla title

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.

Explain Like I'm Five

Scientists updated a special computer program that helps them figure out how different animals and plants are related, and how they got their unique features over many, many years.

Possible Conflicts of Interest

The author is the developer and maintainer of the 'phytools' package, which could create a potential bias in the presentation and evaluation of its features. However, this is transparently disclosed and is inherent in software-focused publications.

Identified Limitations

Lack of novel research or hypothesis testing

The paper focuses primarily on describing and illustrating the functionality of the 'phytools' R package, rather than presenting novel research findings or testing specific hypotheses. While software papers can be valuable, this one reads more like an extended tutorial or manual.

Limited generalizability and real-world application

The reliance on pre-packaged datasets and limited real-world application examples makes it difficult to assess the generalizability and practical utility of the methods presented. More diverse and complex datasets would strengthen the paper's impact.

Excessive number of examples without a unifying theme

While the visualizations are well-presented, the sheer number of examples without a clear unifying theme can feel overwhelming and detract from the paper's overall coherence. A more focused approach would enhance readability and impact.

Rating Explanation

The paper provides a comprehensive overview of 'phytools' functionality and workflows, which is useful for users of the package. However, the lack of novel scientific findings and the heavy reliance on examples limits its broader scientific impact. The author's conflict of interest as the package developer is noted, but does not significantly detract from the paper's value as a software description.

Good to know

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Topic Hierarchy

Domain: Physical Sciences

Field: Earth and Planetary Sciences

Subfield: Paleontology

File Information

Original Title: phytools 2.0: An updated R ecosystem for phylogenetic comparative methods (and other things)

Uploaded: July 14, 2025 at 11:03 AM

Privacy: Public