Handbook of Ecological Modelling and Informatics

Chapter 1: Introduction: sub-disciplines of ecology and the history of ecological modeling - History of the ecological sub-disciplines The development of ecological modeling Chapter 2: Overview of the model types available for ecological modeling - Issues in model development Increasing number of model types Characteristics of the model types available today Applicability of the model types Chapter 3: Ecological informatics: current scope and feature areas - Introduction Feature areas Future directions Chapter 4: Model making - Modelling procedure Institutionalized modeling When to apply IMM? Chapter 5: Ecopath with Ecosim: linking fisheries and ecology - Why ecosystem modeling in fisheries? The Ecopath with Ecosim (EwE) modeling approach EwE modules and applications EwE applications Getting hold of the EwE software Exercise: trawling cultivates the ocean bottom for squid Chapter 6: Surface modelling of population distribution - Introduction YUE-SMPD An application of YUE-SMPD Discussion Chapter 7: Individual-based models - Introduction Properties of individuals Model construction Case study 1: flocking behaviour Case study 2: population dispersal hapter 8: A fuzzy approach to ecological modelling and data analysis - Imprecision, uncertainty and heterogeneity of environmental data Fuzzy sets and fuzzy logic in ecological applications Fuzzy classification: a fuzzy clustering approach Fuzzy modelling Final remarks Chapter 9: Ecological informatics by means of neural, evolutionary and object-oriented computation - Introduction Artificial neural networks Conclusions Chapter 10: Hybridisation of process-based ecosystem models with evolutionary algorithms: multi-objective optimisation of process and parameter representations of the lake simulation library SALMO-OO - Introduction Evolutionary algorithm for the optimisation of process representations and parameters Optimisation of process representations in SALMO-OO by means of EA Case study of parameter optimisation in SALMO-OO Conclusions and future work Chapter 11: Biogeochemical models - The characteristics of biogeochemical models The application of biogeochemical models Biogeochemical models Model of sub-surface wetland Chapter 12: Stochastic population dynamic models as probability networks - Introduction Methods Example models and their applications Availability of models and software Chapter 13: Structurally dynamic models - Introduction: why structurally dynamic models? Ecosystem characteristics Structurally dynamic models Development of SDM for Darwin's finches Model of the ectoparasite-bird interactions Chapter 14: Ecotoxicological models - Introduction: characteristics of ecotoxicological models Classification of ecotoxicological models The application of parameter estimation methods in ecotoxicological modelling Biogeochemical and ecotoxicological models: tylosine Chapter 15: Behavioral methods in ecotoxicology - Why behavioral methods in ecotoxicology? Monitoring at the individual level Modeling the gene-individual-population relationships Chapter 16: Cellular automata - Introduction to cellular automata Development and application of EcoC A Development and application of LYC Discussion Chapter 17: Rule-based ecological model - Introduction to rule-based technique Rule-based modelling of algal biomass in Dutch coastal waters Integrated numerical and rule-based technique Discussion User guide for FuzzHab Chapter 18: Network calculations II: a user's manual for EcoNet - Introduction How to create an EcoNet model How to run an EcoNet model Simulation and analysis results Study of an EcoNet model Chapter 19: Mediating conceptual knowledge using qualitative reasoning - Introduction Background and principles Garp3: QR workbench Examples of QR models Assignments Evaluating QR models Conclusion and discussion Chapter 20: Models of flow pattern and mass distribution - Introduction Mohid overview Finite volumes Boundaries Hydrodynamic model Transport models Numerical modelling of water properties Mohid's results Conclusions Chapter 21: Applications of data mining in ecological modelling - Introduction Data mining Applications Conclusions