Dynamic Energy Budget theory meets individual-based modelling: a generic and accessible implementation

Authored by Volker Grimm, Tjalling Jager, Benjamin T Martin, Elke I Zimmer

Date Published: 2012

DOI: 10.1111/j.2041-210x.2011.00168.x

Sponsors: European Union

Platforms: NetLogo

Model Documentation: ODD Pseudocode Mathematical description

Model Code URLs: http://cream-itn.eu/creamwp/wp-content/uploads/DEB_IBM-model-v2.txt

Abstract

1. Dynamic Energy Budget (DEB) theory was designed to understand the dynamics of biological systems from cells to populations and ecosystems via a mass balance approach of individuals. However, most work so far has focused on the level of the individual. To encourage further use of DEB theory in a population context, we developed DEB-IBM, a generic individual-based model (IBM) that is based on DEB theory. 2. The generic IBM is implemented as a computer program using NetLogo, a free software platformthat is accessible to biologists with little programming background. The IBMuses DEB to represent assimilation, maintenance, growth and reproduction of individuals. The model description follows the overview, design and details ( ODD) protocol, a generic format for describing IBMs, and thereby provides a novel and accessible introduction to DEB theory and how it works in a population context. 3. Dynamic Energy Budget- individual- based model can be used to explore properties of both individual life- history traits and population dynamics, which emerge from the set of DEB parameters of a species, and their interaction with environmental variables such as food density. Furthermore, DEB- IBM can be adapted to address specific research questions, for example by including spatial effects. A user manual explains how this can be done. 4. Dynamic Energy Budget- individual- based model is designed to both facilitate use and testing DEB theory in a population context and to advance individual- based modelling by basing the representation of individuals on well- tested physiological principles.

Tags

ecology growth Platforms Protocol Life Consequences Matrix population-models Daphnia