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Simulation models that describe autonomous individual organisms (individual based models, IBM) or agents (agent-based models, ABM) have become a widely used tool, not only in ecology, but also in many other disciplines dealing with complex systems made up of autonomous entities. However, there is no standard protocol for describing such simulation models, which can make them difficult to understand and to duplicate. This paper presents a proposed standard protocol, ODD, for describing IBMs and ABMs, developed and tested by 28 modellers who cover a wide range of fields within ecology. This protocol consists of three blocks (Overview, Design concepts, and Details), which are subdivided into seven elements: Purpose, State variables and scales, Process overview and scheduling, Design concepts, Initialization, Input, and Submodels. We explain which aspects of a model should be described in each element, and we present an example to illustrate the protocol in use. In addition, 19 examples are available in an Online Appendix. We consider ODD as a first step for establishing a more detailed common format of the description of IBMs and ABMs. Once initiated, the protocol will hopefully evolve as it becomes used by a sufficiently large proportion of modellers. (c) 2006 Elsevier B.V. All rights reserved.
Individual-based models (IBMs) are increasingly used to link the dynamics of individuals to higher levels of biological organization. Still, many IBMs are data hungry, species specific, and time-consuming to develop and analyze. Many of these issues would be resolved by using general theories of individual dynamics as the basis for IBMs. While such theories have frequently been examined at the individual level, few cross-level tests exist that also try to predict population dynamics. Here we performed a cross-level test of dynamic energy budget (DEB) theory by parameterizing an individual-based model using individual-level data of the water flea, Daphnia magna, and comparing the emerging population dynamics to independent data from population experiments. We found that DEB theory successfully predicted population growth rates and peak densities but failed to capture the decline phase. Further assumptions on food-dependent mortality of juveniles were needed to capture the population dynamics after the initial population peak. The resulting model then predicted, without further calibration, characteristic switches between small-and large-amplitude cycles, which have been observed for Daphnia. We conclude that cross-level tests help detect gaps in current individual-level theories and ultimately will lead to theory development and the establishment of a generic basis for individual-based models and ecology.
The distribution of poikilotherms is determined by the thermal structure of the marine environment that they are exposed to. Recent research has indicated that changes in migration phenology of beluga whales in the Arctic are triggered by changes in the thermal structure of the marine environment in their summering area. If sea temperatures reflect the spatial distribution of food resources, then changes in the thermal regime will affect how homogeneous or clumped food is distributed. We explore, by individual-based modelling, the hypothesis that changes in migration phenology are not necessarily or exclusively triggered by changes in food abundance, but also by changes in the spatial aggregation of food. We found that the level of food aggregation can significantly affect the relationship between the timing of the start of migration to the winter grounds and the total prey capture of individuals. Our approach strongly indicates that changes in the spatial distribution of food resources should be considered for understanding and quantitatively predicting changes in the phenology of animal migration.
Pattern-oriented modelling as a novel way to verify and validate functional-structural plant models
(2018)
Background and Aims Functional-structural plant (FSP) models have been widely used to understand the complex interactions between plant architecture and underlying developmental mechanisms. However, to obtain evidence that a model captures these mechanisms correctly, a clear distinction must be made between model outputs used for calibration and thus verification, and outputs used for validation. In pattern-oriented modelling (POM), multiple verification patterns are used as filters for rejecting unrealistic model structures and parameter combinations, while a second, independent set of patterns is used for validation. Key Results After calibration, our model simultaneously reproduced multiple observed architectural patterns. The model then successfully predicted, without further calibration, the validation patterns. The model supports the hypothesis that carbon allocation can be modelled as being dependent on current organ biomass and sink strength of each organ type, and also predicted the observed developmental timing of the leaf sink-source transition stage.
Intraspecific trait variation (ITV) is thought to play a significant role in community assembly, but the magnitude and direction of its influence are not well understood. Although it may be critical to better explain population persistence, species interactions, and therefore biodiversity patterns, manipulating ITV in experiments is challenging. We therefore incorporated ITV into a trait‐ and individual‐based model of grassland community assembly by adding variation to the plants’ functional traits, which then drive life‐history tradeoffs. Varying the amount of ITV in the simulation, we examine its influence on pairwise‐coexistence and then on the species diversity in communities of different initial sizes. We find that ITV increases the ability of the weakest species to invade most, but that this effect does not scale to the community level, where the primary effect of ITV is to increase the persistence and abundance of the competitively‐average species. Diversity of the initial community is also of critical importance in determining ITV's efficacy; above a threshold of interspecific diversity, ITV does not increase diversity further. For communities below this threshold, ITV mainly helps to increase diversity in those communities that would otherwise be low‐diversity. These findings suggest that ITV actively maintains diversity by helping the species on the margins of persistence, but mostly in habitats of relatively low alpha and beta diversity.
Ecosystems respond in various ways to disturbances. Quantifying ecological stability therefore requires inspecting multiple stability properties, such as resistance, recovery, persistence and invariability. Correlations among these properties can reduce the dimensionality of stability, simplifying the study of environmental effects on ecosystems. A key question is how the kind of disturbance affects these correlations. We here investigated the effect of three disturbance types (random, species-specific, local) applied at four intensity levels, on the dimensionality of stability at the population and community level. We used previously parameterized models that represent five natural communities, varying in species richness and the number of trophic levels. We found that disturbance type but not intensity affected the dimensionality of stability and only at the population level. The dimensionality of stability also varied greatly among species and communities. Therefore, studying stability cannot be simplified to using a single metric and multi-dimensional assessments are still to be recommended.