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Predicting how many animals will be where: How to build, calibrate and evaluate individual-based models

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  • van der Vaart, Elske
  • Johnston, Alice S.A.
  • Sibly, Richard M.

Abstract

Individual-based models (IBMs) can simulate the actions of individual animals as they interact with one another and the landscape in which they live. When used in spatially-explicit landscapes IBMs can show how populations change over time in response to management actions. For instance, IBMs are being used to design strategies of conservation and of the exploitation of fisheries, and for assessing the effects on populations of major construction projects and of novel agricultural chemicals. In such real world contexts, it becomes especially important to build IBMs in a principled fashion, and to approach calibration and evaluation systematically. We argue that insights from physiological and behavioural ecology offer a recipe for building realistic models, and that Approximate Bayesian Computation (ABC) is a promising technique for the calibration and evaluation of IBMs.

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  • van der Vaart, Elske & Johnston, Alice S.A. & Sibly, Richard M., 2016. "Predicting how many animals will be where: How to build, calibrate and evaluate individual-based models," Ecological Modelling, Elsevier, vol. 326(C), pages 113-123.
  • Handle: RePEc:eee:ecomod:v:326:y:2016:i:c:p:113-123
    DOI: 10.1016/j.ecolmodel.2015.08.012
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    References listed on IDEAS

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    1. Nabe-Nielsen, Jacob & Sibly, Richard M. & Tougaard, Jakob & Teilmann, Jonas & Sveegaard, Signe, 2014. "Effects of noise and by-catch on a Danish harbour porpoise population," Ecological Modelling, Elsevier, vol. 272(C), pages 242-251.
    2. van der Vaart, Elske & Beaumont, Mark A. & Johnston, Alice S.A. & Sibly, Richard M., 2015. "Calibration and evaluation of individual-based models using Approximate Bayesian Computation," Ecological Modelling, Elsevier, vol. 312(C), pages 182-190.
    3. Jan C. Thiele & Winfried Kurth & Volker Grimm, 2014. "Facilitating Parameter Estimation and Sensitivity Analysis of Agent-Based Models: A Cookbook Using NetLogo and 'R'," Journal of Artificial Societies and Social Simulation, Journal of Artificial Societies and Social Simulation, vol. 17(3), pages 1-11.
    4. Kułakowska, K.A. & Kułakowski, T.M. & Inglis, I.R. & Smith, G.C. & Haynes, P.J. & Prosser, P. & Thorbek, P. & Sibly, R.M., 2014. "Using an individual-based model to select among alternative foraging strategies of woodpigeons: Data support a memory-based model with a flocking mechanism," Ecological Modelling, Elsevier, vol. 280(C), pages 89-101.
    5. Liu, Chun & Sibly, Richard M. & Grimm, Volker & Thorbek, Pernille, 2013. "Linking pesticide exposure and spatial dynamics: An individual-based model of wood mouse (Apodemus sylvaticus) populations in agricultural landscapes," Ecological Modelling, Elsevier, vol. 248(C), pages 92-102.
    6. Johnston, A.S.A. & Hodson, M.E. & Thorbek, P. & Alvarez, T. & Sibly, R.M., 2014. "An energy budget agent-based model of earthworm populations and its application to study the effects of pesticides," Ecological Modelling, Elsevier, vol. 280(C), pages 5-17.
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    Cited by:

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    2. Clark, Matt & Andrews, Jeffrey & Kolarik, Nicholas & Omar, Mbarouk Mussa & Hillis, Vicken, 2024. "Causal attribution of agricultural expansion in a small island system using approximate Bayesian computation," Land Use Policy, Elsevier, vol. 137(C).
    3. Grimm, Volker & Berger, Uta, 2016. "Structural realism, emergence, and predictions in next-generation ecological modelling: Synthesis from a special issue," Ecological Modelling, Elsevier, vol. 326(C), pages 177-187.
    4. de Jager, Monique & Hengeveld, Geerten M. & Mooij, Wolf M. & Slooten, Elisabeth, 2019. "Modelling the spatial dynamics of Maui dolphins using individual-based models," Ecological Modelling, Elsevier, vol. 402(C), pages 59-65.
    5. Boyd, Robin & Roy, Shovonlal & Sibly, Richard & Thorpe, Robert & Hyder, Kieran, 2018. "A general approach to incorporating spatial and temporal variation in individual-based models of fish populations with application to Atlantic mackerel," Ecological Modelling, Elsevier, vol. 382(C), pages 9-17.

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