Microxanox: An R package for simulating an aquatic MICRobial ecosystem that can occupy OXic or ANOXic states

Abstract

Microxanox is an R package to simulate a three functional group ecosystem (cyanobacteria, phototrophic sulfur bacteria, and sulfate-reducing bacteria) with four chemical substrates (phosphorus, oxygen, reduced sulfur, and oxidized sulfur) using a set of ordinary differential equations. Simulations can be run individually or over a parameter range. The model can be implemented with different numbers of species per functional group. The package is constructed in such a way that the results contain the input parameter used, so that a saved results can be loaded again and the simulation be repeated. Furthermore, the package framework and code should serve as a useful starting point for making simulation models of other types of ecosystems.

Keywords

• Reproducibility
• Regime shift
• Final state
• Ordinary differential equations