This repository is the main documentation of the AED aquatic ecosystem modelling library, developed in R bookdown.

View the latest version here: https://aquaticecodynamics.github.io/aed-science/

AED is an open-source scientific modelling library written in Fortran for simulating aquatic ecosystems.

This aed-science repository is the home of the Modelling Aquatic Eco-Dynamics: overview of the AED modular simulation platform online book, which describes the technical (scientific and operational) details of AED and is referred to as "The AED manual". This book summarises the mathematical basis for AED's balance equations and interactions among modules. In addition, we provide a summary of parameter values for lake, river, and estuary ecosystems from a range of applications.

The AED modelling code-base is an open-source community-driven library of model components for simulation of Aquatic Ecosystem Dynamics. The model has been developed by researchers at The University of Western Australia, with active developers also from industry, government, and the broader research community. The code of the AED library consists of numerous modules that are designed as individual model ‘components’ that can be configured to facilitate custom aquatic ecosystem conceptualisations – either simple or complex. Users select water quality and ecosystem variables they wish to simulate and then are able to customize connections and dependencies with other modules, thereby constructing relevant interactions and feedbacks that may be occurring within an aquatic ecosystem. Consequently, AED is easily tailored to specific water quality problems or aquatic ecosystem investigations.

The code also allows for easy customisation at an algorithm level of how model components operate (e.g., photosynthesis functions, sorption algorithms etc.). In general, model components consider the cycling of oxygen, carbon, nitrogen, and phosphorus, and are able to simulate organisms including different functional groups of phytoplankton and zooplankton, and also organic matter. Modules to support simulation of water column and sediment geochemistry, e.g., coupled kinetic equilibria interactions, are also included.

The model can be used in a wide range of spatial contexts – including with 0D, 1D, 2D and 3D models that are able to simulate the aquatic environment (termed 'host' models). AED has been applied to many diverse aquatic environments across the globe, and this book provides assistance to users in getting started, or advanced users looking to customise their simulation.

Please cite this edited book and the AED model in scientific publications as:

Hipsey, M.R., (ed.). 2022. Modelling Aquatic Eco-Dynamics: Overview of the AED modular simulation platform. Zenodo. https://doi.org/10.5281/zenodo.6516222.

If you would like to cite an individual chapter of this book (not the AED model), please use this format (example given for Chapter 4):

Hipsey, M.R. and P. Huang, 2022. Chapter 4: Dissolved oxygen. In: Hipsey, M.R. (ed.) Modelling Aquatic Eco-Dynamics: Overview of the AED modular simulation platform. Zenodo. https://doi.org/10.5281/zenodo.6516222.

You may be a new user seeking to understand how to get started working with AED, or you may be interested in tailoring a module to your research or management application. As the AED modules evolve, through incremental improvements or wholesale changes, experts working on these changes can ensure the latest information is available to the community by continuously updating and improving the model's documentation.

This documentation uses bookdown, which makes editing a book as easy as editing a wiki, provided you have a GitHub account (sign-up at github.com). Once logged-in to GitHub, click on the 'edit me' icon highlighted with a red ellipse in the image below.

This will take you to an editable version of the R Markdown source file that generated the page you're on:

To raise an issue about the model or book's content (e.g. code not running) or make a feature request, check-out the issue tracker.

Readers may also use the hypothes.is utility on the right margin of the book to add personal annotations and public comments on the book content.

Maintainers and contributors must follow this repository’s CODE OF CONDUCT.

The AED project is largely a voluntary effort supported by numerous researchers working on scientific grants. If you find AED useful, please support it by:

• Telling people about it
• Join our Slack channel: general-lake-model.slack.com
• Communicating about the model in digital media, e.g. via the "AEDmodel" hashtag on Twitter
• Citing the book, as described above
• Contributing to this book via GitHub or the AED model more broadly via Github