aae.pop: Flexible population dynamics simulations in R

This is a Preprint and has not been peer reviewed. This is version 2 of this Preprint. You must log in to post a comment. There are no comments or no comments have been made public for this article. This is a Preprint and has not been peer reviewed. This is version 2 of this Preprint. Add a Comment You must log in to post a comment. Comments There are no comments or no comments have been made public for this article. 1. Matrix population models (MPMs) are commonly used to address fundamental ecological questions and guide real-world management decisions. Several open-source software packages support the fundamental analysis of MPMs, but few options exist to simulate from models that include realistic ecological complexity, such as density dependence, covariate effects, and interspecific interactions. 2. The aae.pop R package is a plug-and-play tool to simulate from MPMs. Originally developed for applications in aquatic ecology (“aae”), the package enables simulations of population dynamics incorporating a range of processes, such as external environmental forcing, density dependence, interspecific interactions, and harvest or release of individuals. 3. aae.pop provides a general framework for simulating from MPMs. This framework is described here, and illustrated with two case studies on freshwater fish populations in south-eastern Australia. 4. Models developed in aae.pop are easily shared, fully reproducible, and updateable. These features mean that aae.pop can support transparent and defensible applications of MPMs. Given its explicit focus on applications, aae.pop complements existing R packages for the analysis of MPMs. https://doi.org/10.32942/X2P08V Applied Mathematics, Ecology and Evolutionary Biology conservation biology, population viability analysis, software, R, population dynamics, matrix population model Published: 2026-04-30 06:30 Last Updated: 2026-05-02 12:00 CC BY Attribution 4.0 International Conflict of interest statement: None Data and Code Availability Statement: The aae.pop R package is publicly available on CRAN (DOI: 10.32614/CRAN.package.aae.pop). Code to recreate the analyses and examples presented in the preprint is available at Zenodo (DOI: 10.5281/zenodo.19901285). Language: English