The nlrx r package: A next‐generation framework for reproducible NetLogo model analyses

Abstract

1.Agent-based models find wide application in all fields of science where large scale patterns emerge from properties of individuals. Due to increasing capacities of computing resources it was possible to improve the level of detail and structural realism of next-generation models in recent years. However, this is at the expense of increased model complexity, which requires more efficient tools for model exploration, analysis and documentation that enable reproducibility, repeatability and parallelisation. NetLogo is a widely used environment for agent-based model development, but it does not provide sufficient built-in tools for extensive model exploration, such as sensitivity analyses. One tool for controlling NetLogo externally is the R-package RNetLogo. However, this package is not suited for efficient, reproducible research as it has stability and resource allocation issues, is not straightforward to be setup and used on high performance computing clusters and does not provide utilities, such as storing and exchanging metadata, in an easy way. 2.We present the R-package nlrx, which overcomes stability and resource allocation issues by running NetLogo simulations via dynamically created XML experiment files. Class objects make setting up experiments more convenient and helper functions provide many parameter exploration approaches, such as Latin Hypercube designs, Sobol sensitivity analyses or optimization approaches. Output is automatically collected in user-friendly formats and can be post-processed with provided utility functions. nlrx enables reproducibility by storing all relevant information and simulation output of experiments in one R object which can conveniently be archived and shared. 3.We provide a detailed description of the nlrx package functions and the overall workflow. We also present a use case scenario using a NetLogo model, for which we performed a sensitivity analysis and a genetic algorithm optimization. 4.The nlrx package is the first framework for documentation and application of reproducible NetLogo simulation model analysis.