Orangutan: an R package for analyzing and visualizing phenotypic data in the context of ecology and systematics

Abstract

Aim Phenotypic characters have long been central to species diagnosis and delimitation and remain indispensable even in the age of genomics. However, phenotypic datasets are often complex— spanning dozens of traits of varying types and units, with correlated variables and unbalanced sampling—posing challenges for robust, reproducible analysis. Existing software solutions are fragmented, usually requiring labor-intensive workflows across multiple tools and manual steps, which undermines reproducibility and hinders comparisons across studies. To address these methodological and practical challenges, I introduce Orangutan, an R package designed to provide a flexible, easy-to-implement framework for comparing groups using mensural and meristic data. Innovation Orangutan provides a flexible and efficient framework for analyzing mensural and meristic data, supporting a full suite of statistical and visualization tools optimized for species delimitation and population comparisons. The package streamlines the identification of diagnostic, non-overlapping traits between species, while enabling rigorous assessment of both individual and multivariate trait differences. Core features include optional allometric correction to remove size effects, automated selection of appropriate univariate tests with post hoc comparisons, and integrated multivariate analyses. All outputs, including summary statistics and annotated publication-ready figures, are generated with minimal coding, ensuring accessibility and standardization. Main Conclusions Empirical validation with real-world datasets—including animal and plant species— demonstrates that Orangutan robustly identifies diagnostic traits, reveals both subtle and clear group differences, and achieves high classification accuracy with phenotypic data alone. By automating and unifying key analytical steps, Orangutan promotes reproducibility, transparency, and efficiency in phenotypic research. This package empowers researchers in taxonomy, ecology, and evolutionary biology to adopt quantitative best practices for species delimitation, facilitating comparative studies and advancing methodological standards in morphological data analysis. Orangutan is freely available with comprehensive documentation to support widespread adoption.

Plant phenotyping relevance

植物を含む形態形質データの解析・可視化を標準化するRパッケージの開発論文であり、植物種データでの検証も行っているため、表現型解析手法が中心です。

Code and data availability

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