: Agent‐Based Model of Complex Life Cycle Evolution—R Tools
Source: PubMed Central Open Access, NCBI / U.S. National Library of Medicine
ABSTRACT Agent‐based models (ABMs) are increasingly used to study eco‐evolutionary dynamics in organisms with complex life cycles, but downstream analysis of model output remains a bottleneck. Simulations can generate millions of records across individuals, time points, and replicates, often spread across many files and requiring extensive custom preprocessing before biological interpretation is possible. We present ACERT (Agent‐based model of Complex life cycle Evolution—R Tools), an open‐source R package that provides an integrated workflow for importing, cleaning, analyzing, and visualizing ABM outputs tailored to systems with complex life cycles. ACERT reads individual‐level records for mobile agents, called “turtles” in NetLogo terminology, patch‐level environment data, and allelic mutation files; standardizes these streams into analysis‐ready structures; and links directly to established population‐genetic inference methods. The package supports phenotype and demographic summaries, spatial and landscape diagnostics, migration and replicate similarity assessment, population‐genetic diversity and differentiation statistics, and exploratory microevolutionary tools including major‐allele trajectory tracking and selection‐screening workflows. ACERT also includes functions for generating synthetic example datasets and building reproducible reports. By consolidating domain‐specific preprocessing and analysis steps into a single, coherent package, ACERT reduces the technical ov
Abstract
ABSTRACT Agent‐based models (ABMs) are increasingly used to study eco‐evolutionary dynamics in organisms with complex life cycles, but downstream analysis of model output remains a bottleneck. Simulations can generate millions of records across individuals, time points, and replicates, often spread across many files and requiring extensive custom preprocessing before biological interpretation is possible. We present ACERT (Agent‐based model of Complex life cycle Evolution—R Tools), an open‐source R package that provides an integrated workflow for importing, cleaning, analyzing, and visualizing ABM outputs tailored to systems with complex life cycles. ACERT reads individual‐level records for mobile agents, called “turtles” in NetLogo terminology, patch‐level environment data, and allelic mutation files; standardizes these streams into analysis‐ready structures; and links directly to established population‐genetic inference methods. The package supports phenotype and demographic summaries, spatial and landscape diagnostics, migration and replicate similarity assessment, population‐genetic diversity and differentiation statistics, and exploratory microevolutionary tools including major‐allele trajectory tracking and selection‐screening workflows. ACERT also includes functions for generating synthetic example datasets and building reproducible reports. By consolidating domain‐specific preprocessing and analysis steps into a single, coherent package, ACERT reduces the technical overhead associated with simulation‐based inference and improves reproducibility. ACERT is an open‐source R package that closes the gap between raw agent‐based model output and biological interpretation for systems with complex life cycles. It provides a single, coherent pipeline for data preprocessing, population‐genetic analysis, spatial diagnostics, and replicate quality control, eliminating the custom scripting bottleneck that limits reproducibility in simulation‐based eco‐evolutionary research. graphical