Individual‒Based Models
10 Mar 2008-pp 228-248
About: The article was published on 2008-03-10. It has received 54 citations till now.
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TL;DR: Approximate Bayesian Computing and Pattern-Oriented Modelling are discussed, their potential for integrating stochastic simulation models into a unified framework for statistical modelling is demonstrated, and principles and advantages of these methods are discussed.
Abstract: Statistical models are the traditional choice to test scientific theories when observations, processes or boundary conditions are subject to stochasticity Many important systems in ecology and biology, however, are difficult to capture with statistical models Stochastic simulation models offer an alternative, but they were hitherto associated with a major disadvantage: their likelihood functions can usually not be calculated explicitly, and thus it is difficult to couple them to well-established statistical theory such as maximum likelihood and Bayesian statistics A number of new methods, among them Approximate Bayesian Computing and Pattern-Oriented Modelling, bypass this limitation These methods share three main principles: aggregation of simulated and observed data via summary statistics, likelihood approximation based on the summary statistics, and efficient sampling We discuss principles as well as advantages and caveats of these methods, and demonstrate their potential for integrating stochastic simulation models into a unified framework for statistical modelling
335 citations
TL;DR: This approach expands, simplifies and unifies the analysis of laboratory data parameterizing the thermal responses of insects in particular and poikilotherms in general, and makes possible the development of process-based phenology models that are based on optimal use of available information.
300 citations
TL;DR: In this article, the authors present Markov chain methods for computing the mean and variance of the lifetime number of visits to any transient state, the Mean and Variability of longevity, the net reproductive rate R0, and the cohort generation time.
Abstract: Demography is the study of the population consequences of the fates of individuals. Individuals are differentiated on the basis of age or, in general, life cycle stages. The movement of an individual through its life cycle is a random process, and although the eventual destination (death) is certain, the pathways taken to that destination are stochastic and will differ even between identical individuals; this is individual stochasticity. A stage-classified demographic model contains implicit age-specific information, which can be analyzed using Markov chain methods. The living stages in the life cycles are transient states in an absorbing Markov chain; death is an absorbing state. This paper presents Markov chain methods for computing the mean and variance of the lifetime number of visits to any transient state, the mean and variance of longevity, the net reproductive rate R0, and the cohort generation time. It presents the matrix calculus methods needed to calculate the sensitivity and elasticity of all these indices to any life history parameters. These sensitivities have many uses, including calculation of selection gradients. It is shown that the use of R0 as a measure of fitness or an invasion exponent gives erroneous results except when R0 � l� 1. The Markov chain approach is then generalized to variable environments (deterministic environmental sequences, periodic environments, iid random environments, Markovian environments). Variable environments are analyzed using the vec-permutation method to create a model that classifies individuals jointly by the stage and environmental condition. Throughout, examples are presented using the North Atlantic right whale (Eubaleana glacialis) and an endangered prairie plant (Lomatium bradshawii ) in a stochastic fire environment.
153 citations
TL;DR: This work postulates, based on a 15-year time series of nation-wide, spatially referenced catch and effort data, that the establishment of the Goukamma MPA benefited the adjacent fishery for roman, a South African endemic seabream.
Abstract: Potential fishery benefits of Marine Protected Areas are widely acknowledged, yet their impact on fishery dynamics remains poorly understood. Here the authors provide evidence that Marine Protected Areas can rapidly increase catch rates in adjacent areas, without measurable disadvantages for fishers.
152 citations
TL;DR: Knowledge of physiological ecology is used to identify major issues confronting the modeller and to make recommendations about how energy budgets for use in ABMs should be constructed.
Abstract: Summary
1. Agent-based models (ABMs) are widely used to predict how populations respond to changing environments. As the availability of food varies in space and time, individuals should have their own energy budgets, but there is no consensus as to how these should be modelled. Here, we use knowledge of physiological ecology to identify major issues confronting the modeller and to make recommendations about how energy budgets for use in ABMs should be constructed.
2. Our proposal is that modelled animals forage as necessary to supply their energy needs for maintenance, growth and reproduction. If there is sufficient energy intake, an animal allocates the energy obtained in the order: maintenance, growth, reproduction, energy storage, until its energy stores reach an optimal level. If there is a shortfall, the priorities for maintenance and growth/reproduction remain the same until reserves fall to a critical threshold below which all are allocated to maintenance. Rates of ingestion and allocation depend on body mass and temperature. We make suggestions for how each of these processes should be modelled mathematically.
3. Mortality rates vary with body mass and temperature according to known relationships, and these can be used to obtain estimates of background mortality rate.
4. If parameter values cannot be obtained directly, then values may provisionally be obtained by parameter borrowing, pattern-oriented modelling, artificial evolution or from allometric equations.
5. The development of ABMs incorporating individual energy budgets is essential for realistic modelling of populations affected by food availability. Such ABMs are already being used to guide conservation planning of nature reserves and shell fisheries, to assess environmental impacts of building proposals including wind farms and highways and to assess the effects on nontarget organisms of chemicals for the control of agricultural pests.
Keywords: bioenergetics; energy budget; individual-based models; population dynamics.
128 citations
References
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TL;DR: Back-propagation repeatedly adjusts the weights of the connections in the network so as to minimize a measure of the difference between the actual output vector of the net and the desired output vector, which helps to represent important features of the task domain.
Abstract: We describe a new learning procedure, back-propagation, for networks of neurone-like units. The procedure repeatedly adjusts the weights of the connections in the network so as to minimize a measure of the difference between the actual output vector of the net and the desired output vector. As a result of the weight adjustments, internal ‘hidden’ units which are not part of the input or output come to represent important features of the task domain, and the regularities in the task are captured by the interactions of these units. The ability to create useful new features distinguishes back-propagation from earlier, simpler methods such as the perceptron-convergence procedure1.
23,814 citations
01 Aug 1987
TL;DR: In this article, an approach based on simulation as an alternative to scripting the paths of each bird individually is explored, with the simulated birds being the particles and the aggregate motion of the simulated flock is created by a distributed behavioral model much like that at work in a natural flock; the birds choose their own course.
Abstract: The aggregate motion of a flock of birds, a herd of land animals, or a school of fish is a beautiful and familiar part of the natural world. But this type of complex motion is rarely seen in computer animation. This paper explores an approach based on simulation as an alternative to scripting the paths of each bird individually. The simulated flock is an elaboration of a particle systems, with the simulated birds being the particles. The aggregate motion of the simulated flock is created by a distributed behavioral model much like that at work in a natural flock; the birds choose their own course. Each simulated bird is implemented as an independent actor that navigates according to its local perception of the dynamic environment, the laws of simulated physics that rule its motion, and a set of behaviors programmed into it by the "animator." The aggregate motion of the simulated flock is the result of the dense interaction of the relatively simple behaviors of the individual simulated birds.
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TL;DR: The second volume in a series on terrestrial and marine comparisons focusing on the temporal complement of the earlier spatial analysis of patchiness and pattern was published by Levin et al..
Abstract: This book is the second of two volumes in a series on terrestrial and marine comparisons, focusing on the temporal complement of the earlier spatial analysis of patchiness and pattern (Levin et al. 1993). The issue of the relationships among pattern, scale, and patchiness has been framed forcefully in John Steele’s writings of two decades (e.g., Steele 1978). There is no pattern without an observational frame. In the words of Nietzsche, “There are no facts… only interpretations.”
5,833 citations
TL;DR: This paper will develop a model for the use of a “patchy habitat” by an optimal predator and depresses the availability of food to itself so that the amount of food gained for time spent in a patch of type i is hi(T), where the function rises to an asymptote.
4,772 citations
TL;DR: In this article, the Dickcissel sex ratio is employed as an indirect index of suitability and a sex ratio index was found to be correlated positively with density, consistent with the hypothesis that territorial behavior in males of this species limits their density.
Abstract: This example is provided so that non-theorists may see actual applications of the theory previously described. The Dickcissel sex ratio is employed as an indirect index of suitability. A sex ratio index was found to be correlated positively with density. This is consistent with the hypothesis that territorial behavior in the males of this species limits their density. This study provides a valid example of how the problem can be approached and offers a first step in the eventual identification of the role of territorial behavior in the habitat distribution of a common species.
4,210 citations