TraitTrainR: Accelerating Large-scale Simulation Under Models of Continuous Trait Evolution

Overview

Journal Bioinform Adv

Publisher Oxford University Press

Specialty Biology

Date 2025 Jan 6

PMID 39758830

Authors

Jenniffer Roa Lozano

Mataya Duncan

Duane D McKenna

Todd A Castoe

Michael DeGiorgio

Richard Adams

Affiliations

Soon will be listed here.

Abstract

Motivation: The scale and scope of comparative trait data are expanding at unprecedented rates, and recent advances in evolutionary modeling and simulation sometimes struggle to match this pace. Well-organized and flexible applications for conducting large-scale simulations of evolution hold promise in this context for understanding models and more so our ability to confidently estimate them with real trait data sampled from nature.

Results: We introduce , an R package designed to facilitate efficient, large-scale simulations under complex models of continuous trait evolution. employs several output formats, supports popular trait data transformations, accommodates multi-trait evolution, and exhibits flexibility in defining input parameter space and model stacking. Moreover, permits measurement error, allowing for investigation of its potential impacts on evolutionary inference. We envision a wealth of applications of , and we demonstrate one such example by examining the problem of evolutionary model selection in three empirical phylogenetic case studies. Collectively, these demonstrations of applying to explore problems in model selection underscores its utility and broader promise for addressing key questions, including those related to experimental design and statistical power, in comparative biology.

Availability And Implementation: is developed in R 4.4.0 and is freely available at https://github.com/radamsRHA/TraitTrainR/, which includes detailed documentation, quick-start guides, and a step-by-step tutorial.

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