Opening the black box—Development, testing and documentation of a mechanistically rich agent-based model

摘要

Although increasingly widely used in biology, complex adaptive simulation models such as agent-based models have been criticised for being difficult to communicate and test. This study demonstrates the application of pattern-oriented model testing, and a novel documentation procedure to present a detailed agent-based model of the European brown hare, a species in widespread decline in Europe. The model was built based on available literature data, using multiple field data patterns from an island hare population study to guide model development. A general and widely applicable approach to the pattern-oriented protocol for testing and developing ecological models of this kind was defined together with the development of the ODdox documentation protocol, a combination of the current ODD protocol for describing agent-based models and source-code documentation. The result is a detailed and yet accessible description of the processes included in the model. Application of the model to a comprehensive historical data set supported the hypothesis that interference competition is the primary population regulating factor in the absence of mammal predators in the brown hare, and that the effect works through reduced fecundity. With a clearly defined testing protocol and documentation, this in silico modelling approach has clear advantages for applications requiring integration of many factors, especially when spatio-temporal variability is important. Providing multi-facetted output which can be compared to real-world data allows the formulation and testing of varied hypotheses in ways not tractable to experimentation. In the case of the brown hare the results provide a new insight into population regulation and the causes of the declines.