Home About us Contact
|
Home About us Contact | ||
|
|
||
Modelling Framework (modelling + framework)
Selected AbstractsSynthesis of pattern and process in biodiversity conservation assessment: a flexible whole-landscape modelling frameworkDIVERSITY AND DISTRIBUTIONS, Issue 3 2010Simon Ferrier Abstract Aim, To describe a general modelling framework for integrating multiple pattern- and process-related factors into biodiversity conservation assessments across whole landscapes. Location, New South Wales (Australia), and world-wide. Methods, The framework allows for a rich array of alternatives to the target-based model traditionally underpinning systematic conservation planning and consists of three broad modelling components. The first component models the future state (condition) of habitat across a landscape as a function of present state, current and projected pressures acting on this state, and any proposed, or implemented, management interventions. The second component uses this spatially explicit prediction of future habitat state to model the level of persistence expected for each of a set of surrogate biodiversity entities. The third component then integrates these individual expectations to estimate the overall level of persistence expected for biodiversity as a whole. Results, Options are explored for tailoring implementation of the framework to suit planning processes varying markedly in purpose, and in availability of data, time, funding and expertise. The framework allows considerable flexibility in the nature of employed biodiversity surrogates (species-level, discrete or continuous community-level) and spatial data structures (polygonal planning units, or fine-scaled raster), the level of sophistication with which each of the three modelling components is implemented (from simple target-based assessment to complex process-based modelling approaches), and the forms of higher-level analysis supported (e.g. optimal plan development, priority mapping, interactive scenario evaluation). Main conclusions, The described framework provides a logical, and highly flexible, foundation for integrating disparate pattern- and process-related factors into conservation assessments in dynamic, multiple-use landscapes. [source] Modelling species distributions in Britain: a hierarchical integration of climate and land-cover dataECOGRAPHY, Issue 3 2004Richard G. Pearson A modelling framework for studying the combined effects of climate and land-cover changes on the distribution of species is presented. The model integrates land-cover data into a correlative bioclimatic model in a scale-dependent hierarchical manner, whereby Artificial Neural Networks are used to characterise species' climatic requirements at the European scale and land-cover requirements at the British scale. The model has been tested against an alternative non-hierarchical approach and has been applied to four plant species in Britain: Rhynchospora alba, Erica tetralix, Salix herbacea and Geranium sylvaticum. Predictive performance has been evaluated using Cohen's Kappa statistic and the area under the Receiver Operating Characteristic curve, and a novel approach to identifying thresholds of occurrence which utilises three levels of confidence has been applied. Results demonstrate reasonable to good predictive performance for each species, with the main patterns of distribution simulated at both 10 km and 1 km resolutions. The incorporation of land-cover data was found to significantly improve purely climate-driven predictions for R. alba and E. tetralix, enabling regions with suitable climate but unsuitable land-cover to be identified. The study thus provides an insight into the roles of climate and land-cover as determinants of species' distributions and it is demonstrated that the modelling approach presented can provide a useful framework for making predictions of distributions under scenarios of changing climate and land-cover type. The paper confirms the potential utility of multi-scale approaches for understanding environmental limitations to species' distributions, and demonstrates that the search for environmental correlates with species' distributions must be addressed at an appropriate spatial scale. Our study contributes to the mounting evidence that hierarchical schemes are characteristic of ecological systems. [source] Computational modelling of amino acid transfer interactions in the placentaEXPERIMENTAL PHYSIOLOGY, Issue 7 2010B. G. Sengers Amino acid transfer from mother to fetus via the placenta plays a critical role in normal development, and restricted transfer is associated with fetal growth restriction. Placental amino acid transfer involves the interaction of 15 or more transporters and 20 amino acids. This complexity means that knowing which transporters are present is not sufficient to predict how they operate together as a system. Therefore, in order to investigate how placental amino acid transfer occurs as a system, an integrated mathematical/computational modelling framework was developed to represent the simultaneous transport of multiple amino acids. The approach was based on a compartmental model, in which separate maternal, syncytiotrophoblast and fetal volumes were distinguished, and transporters were modelled on the maternal- and fetal-facing membranes of the syncytiotrophoblast using Michaelis,Menten-type kinetics. The model was tested in comparison with placental perfusion experiments studying serine,alanine exchange and found to correspond well. The results demonstrated how the different transporters can work together as an integrated system and allowed their relative importance to be assessed. Placental,fetal serine exchange was found to be most sensitive to basal membrane transporter characteristics, but a range of secondary, less intuitive effects were also revealed. While this work only addressed a relatively simple three amino acid system, it demonstrates the feasibility of the approach and could be extended to incorporate additional experimental parameters. Ultimately, this approach will allow physiological simulations of amino acid transfer. This will enhance our understanding of these complex systems and placental function in health and disease. [source] Enabling regional management in a changing climate through Bayesian meta-analysis of a large-scale disturbanceGLOBAL ECOLOGY, Issue 3 2010M Aaron MacNeil ABSTRACT Aim, Quantifying and predicting change in large ecosystems is an important research objective for applied ecologists as human disturbance effects become increasingly evident at regional and global scales. However, studies used to make inferences about large-scale change are frequently of uneven quality and few in number, having been undertaken to study local, rather than global, change. Our aim is to improve the quality of inferences that can be made in meta-analyses of large-scale disturbance by integrating studies of varying quality in a unified modelling framework that is informative for both local and regional management. Innovation, Here we improve conventionally structured meta-analysis methods by including imputation of unknown study variances and the use of Bayesian factor potentials. The approach is a coherent framework for integrating data of varying quality across multiple studies while facilitating belief statements about the uncertainty in parameter estimates and the probable outcome of future events. The approach is applied to a regional meta-analysis of the effects of loss of coral cover on species richness and the abundance of coral-dependent fishes in the western Indian Ocean (WIO) before and after a mass bleaching event in 1998. Main conclusions, Our Bayesian approach to meta-analysis provided greater precision of parameter estimates than conventional weighted linear regression meta-analytical techniques, allowing us to integrate all available data from 66 available study locations in the WIO across multiple scales. The approach thereby: (1) estimated uncertainty in site-level estimates of change, (2) provided a regional estimate for future change at any given site in the WIO, and (3) provided a probabilistic belief framework for future management of reef resources at both local and regional scales. [source] Predicting the impacts of climate change on the distribution of species: are bioclimate envelope models useful?GLOBAL ECOLOGY, Issue 5 2003Richard G. Pearson ABSTRACT Modelling strategies for predicting the potential impacts of climate change on the natural distribution of species have often focused on the characterization of a species' bioclimate envelope. A number of recent critiques have questioned the validity of this approach by pointing to the many factors other than climate that play an important part in determining species distributions and the dynamics of distribution changes. Such factors include biotic interactions, evolutionary change and dispersal ability. This paper reviews and evaluates criticisms of bioclimate envelope models and discusses the implications of these criticisms for the different modelling strategies employed. It is proposed that, although the complexity of the natural system presents fundamental limits to predictive modelling, the bioclimate envelope approach can provide a useful first approximation as to the potentially dramatic impact of climate change on biodiversity. However, it is stressed that the spatial scale at which these models are applied is of fundamental importance, and that model results should not be interpreted without due consideration of the limitations involved. A hierarchical modelling framework is proposed through which some of these limitations can be addressed within a broader, scale-dependent context. [source] A modular approach to addressing model design, scale, and parameter estimation issues in distributed hydrological modellingHYDROLOGICAL PROCESSES, Issue 2 2002G. H. Leavesley Abstract A modular approach to model design and construction provides a flexible framework in which to focus the multidisciplinary research and operational efforts needed to facilitate the development, selection, and application of the most robust distributed modelling methods. A variety of modular approaches have been developed, but with little consideration for compatibility among systems and concepts. Several systems are proprietary, limiting any user interaction. The US Geological Survey modular modelling system (MMS) is a modular modelling framework that uses an open source software approach to enable all members of the scientific community to address collaboratively the many complex issues associated with the design, development, and application of distributed hydrological and environmental models. Implementation of a common modular concept is not a trivial task. However, it brings the resources of a larger community to bear on the problems of distributed modelling, provides a framework in which to compare alternative modelling approaches objectively, and provides a means of sharing the latest modelling advances. The concepts and components of the MMS are described and an example application of the MMS, in a decision-support system context, is presented to demonstrate current system capabilities. Copyright © 2002 John Wiley & Sons, Ltd. [source] A method for representing boundaries in discrete element modelling,part I: Geometry and contact detectionINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 12 2001M. Kremmer Abstract The discrete element method for analysis of the dynamic behaviour of discontinuous media is well established. However, its application to engineering problems is still limited to simplified representations of structural boundaries and their kinematics. In this paper a method is developed for representing three-dimensional boundaries of arbitrary geometry and for modelling the interaction between boundary objects and particles within the discrete element modelling framework. The approach, which we term the finite wall method, uses planar triangular elements to approximate the boundary surface topology. Any number of wall elements can be used to model the shape of the structure. A contact detection scheme is presented for boundary surfaces and spheres based on a series of vector projections to reduce the problem dimensionally. The algorithm employs spatial sporting to obtain the set of potential contacts between spheres and wall elements prior to contact resolution. In a further stage, all possible contact conditions including contact with surfaces, edges and corners are explicitly determined. Part I of this two-part series of papers describes the finite wall method for representation of surface geometry and fully elaborates the method for detecting and resolving contact between boundary wall elements and spheres. In Part II the finite wall method is extended to apply kinematics to linearly independent boundary objects using combinations of translational and rotational motion. An approach is developed for coupling the DEM with the FEM for the purpose of optimising the design of structures which are dynamically interacting with particulate media. Copyright © 2001 John Wiley & Sons, Ltd. [source] A modularized framework for solving an economic,environmental power generation mix problemINTERNATIONAL JOURNAL OF ENERGY RESEARCH, Issue 9 2004Haoxiang Xia Abstract This paper presents a modularized simulation modelling framework for evaluating the impacts on economic cost and CO2 emissions resulting from the introduction of a solid oxide fuel cell (SOFC) system into the existing mix of centralized power generation technologies in Japan. The framework is comprised of three parts: a dual-objective linear programming model that solves the generation best-mix problem for the existing power generation technologies; a nonlinear SOFC system model in which the economic cost and CO2 emissions by the SOFC system can be calculated; and the Queuing Multi-Objective Optimizer (QMOO), a multi-objective evolutionary algorithm (MOEA) developed at the EPFL in Switzerland as the overall optimizer of the combined power supply system. Thus, the framework integrates an evolutionary algorithm that is more suitable for handling nonlinearities with a calculus-based method that is more efficient in solving linear programming problems. Simulation experiments show that the framework is successful in solving the stated problem. Moreover, the three components of the modularized framework can be interconnected through a platform-independent model integration environment. As a result, the framework is flexible and scalable, and can potentially be modified and/or integrated with other models to study more complex problems. Copyright © 2004 John Wiley & Sons, Ltd. [source] Reciprocal phenotypic plasticity can lead to stable predator,prey interactionJOURNAL OF ANIMAL ECOLOGY, Issue 6 2009Akihiko Mougi Summary 1.,Inducible defences of prey and inducible offences of predators are prevalent strategies in trophic interactions with temporal variation. Due to the inducible properties of the functional traits themselves, which drive the dynamic predator,prey relationship on an ecological time-scale, predator and prey may reciprocally interact through their inducible traits (i.e. reciprocal phenotypic plasticity). 2.,Although overwhelming evidence of the stabilizing effect of inducible traits in either species on community dynamics forcefully suggests a critical ecological role for reciprocal plasticity in predator,prey population dynamics, our understanding of its ecological consequences is very limited. 3.,Within a mathematical modelling framework, we investigated how reciprocal plasticity influences the stability of predator,prey systems. 4.,By assuming two types of phenotypic shift, a density-dependent shift and an adaptive phenotypic shift, we examined two interaction scenarios with reciprocal plasticity: (i) an arms-race-like relationship, in which the defensive prey phenotype is more protective against both predator phenotypes (i.e. normal and offensive) than the normal prey phenotype, and the offensive predator is a more efficient consumer, preying upon both prey phenotypes (i.e. normal and defensive), than the normal predator and (ii) a matching response-like relationship, in which the offensive predator consumes more defensive prey and fewer normal prey than the normal predator. 5.,Results of both phenotypic shift models consistently suggest that given the used set of parameter values, the arms-race-like reciprocal plasticity scenario has the largest stability area, when compared with the other scenarios. In particular, higher stability is achieved when the prey exhibits a high-performance inducible defence. Furthermore, this stabilization is so strong that the destabilizing effects of enrichment may be eliminated, even though the higher flexibility of plasticity does not always stabilize a system. 6.,Recent empirical studies support our model predictions. Clear-cut examples of reciprocal phenotypic plasticity show an arms-race-like relationship in which prey species exhibit induced high-performance defences. We may need to re-examine reported predator,prey interactions in which predator or prey exhibits inducible plasticity to determine whether arms-race-like reciprocal plasticity is a general ecological phenomenon. [source] The anatomy of predator,prey dynamics in a changing climateJOURNAL OF ANIMAL ECOLOGY, Issue 6 2007CHRISTOPHER C. WILMERS Summary 1Humans are increasingly influencing global climate and regional predator assemblages, yet a mechanistic understanding of how climate and predation interact to affect fluctuations in prey populations is currently lacking. 2Here we develop a modelling framework to explore the effects of different predation strategies on the response of age-structured prey populations to a changing climate. 3We show that predation acts in opposition to temporal correlation in climatic conditions to suppress prey population fluctuations. 4Ambush predators such as lions are shown to be more effective at suppressing fluctuations in their prey than cursorial predators such as wolves, which chase down prey over long distances, because they are more effective predators on prime-aged adults. 5We model climate as a Markov process and explore the consequences of future changes in climatic autocorrelation for population dynamics. We show that the presence of healthy predator populations will be particularly important in dampening prey population fluctuations if temporal correlation in climatic conditions increases in the future. [source] Hierarchical spatial models for predicting pygmy rabbit distribution and relative abundanceJOURNAL OF APPLIED ECOLOGY, Issue 2 2010Tammy L. Wilson Summary 1.,Conservationists routinely use species distribution models to plan conservation, restoration and development actions, while ecologists use them to infer process from pattern. These models tend to work well for common or easily observable species, but are of limited utility for rare and cryptic species. This may be because honest accounting of known observation bias and spatial autocorrelation are rarely included, thereby limiting statistical inference of resulting distribution maps. 2.,We specified and implemented a spatially explicit Bayesian hierarchical model for a cryptic mammal species (pygmy rabbit Brachylagus idahoensis). Our approach used two levels of indirect sign that are naturally hierarchical (burrows and faecal pellets) to build a model that allows for inference on regression coefficients as well as spatially explicit model parameters. We also produced maps of rabbit distribution (occupied burrows) and relative abundance (number of burrows expected to be occupied by pygmy rabbits). The model demonstrated statistically rigorous spatial prediction by including spatial autocorrelation and measurement uncertainty. 3.,We demonstrated flexibility of our modelling framework by depicting probabilistic distribution predictions using different assumptions of pygmy rabbit habitat requirements. 4.,Spatial representations of the variance of posterior predictive distributions were obtained to evaluate heterogeneity in model fit across the spatial domain. Leave-one-out cross-validation was conducted to evaluate the overall model fit. 5.,Synthesis and applications. Our method draws on the strengths of previous work, thereby bridging and extending two active areas of ecological research: species distribution models and multi-state occupancy modelling. Our framework can be extended to encompass both larger extents and other species for which direct estimation of abundance is difficult. [source] Food-dependent individual growth and population dynamics in fishes,JOURNAL OF FISH BIOLOGY, Issue 2006L. Persson It is long since well established that growth and development in fish individuals are heavily dependent on food intake. Yet, this dependence of individual development on food levels has only to a limited extent been taken into consideration when studying fish population and community processes. Using the modelling framework of physiologically structured population models and empirical data for a number of species configurations, how different size-dependent processes may affect fish population dynamics and community structures are reviewed. Considering competitive interactions, cohort interactions will often give rise to cohort cycles driven by an inequality in competitive abilities between differently sized individuals. The addition of cannibalism may dampen these cycles, the extent to which is dependent on life-history characteristics of the cannibals. The circumstance that individuals change their trophic position over their life cycle as a result of an increase in size gives rise to life history omnivory. In such omnivorous systems, food-dependent growth demotes the potential for predatory and prey fishes to coexist. In tritrophic food chains, food-dependent growth in the intermediate consumer may lead to the presence of bistability including sensitivity to catastrophic behaviour. These results shed new light on the drastic decreases observed in the stocks of many marine fish top predators including their inability to recover after fishing moratoria, and on the suggested presence of alternative states in freshwater fish communities. [source] Statistical analyses of freeway traffic flowsJOURNAL OF FORECASTING, Issue 1 2002Claudia Tebaldi Abstract This paper concerns the exploration of statistical models for the analysis of observational freeway flow data, and the development of empirical models to capture and predict short-term changes in traffic flow characteristics on sequences of links in a partially detectorized freeway network. A first set of analyses explores regression models for minute-by-minute traffic flows, taking into account time of day, day of the week, and recent upstream detector-based flows. Day- and link-specific random effects are used in a hierarchical statistical modelling framework. A second set of analyses captures day-specific idiosyncrasies in traffic patterns by including parameters that may vary throughout the day. Model fit and short-term predictions of flows are thus improved significantly. A third set of analyses includes recent downstream flows as additional predictors. These further improvements, though marginal in most cases, can be quite radically useful in cases of very marked breakdown of freeway flows on some links. These three modelling stages are described and developed in analyses of observational flow data from a set of links on Interstate Highway 5 (I-5) near Seattle. Copyright © 2002 John Wiley & Sons, Ltd. [source] A family of measures to evaluate scale reliability in a longitudinal settingJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES A (STATISTICS IN SOCIETY), Issue 1 2009Annouschka Laenen Summary., The concept of reliability denotes one of the most important psychometric properties of a measurement scale. Reliability refers to the capacity of the scale to discriminate between subjects in a given population. In classical test theory, it is often estimated by using the intraclass correlation coefficient based on two replicate measurements. However, the modelling framework that is used in this theory is often too narrow when applied in practical situations. Generalizability theory has extended reliability theory to a much broader framework but is confronted with some limitations when applied in a longitudinal setting. We explore how the definition of reliability can be generalized to a setting where subjects are measured repeatedly over time. On the basis of four defining properties for the concept of reliability, we propose a family of reliability measures which circumscribes the area in which reliability measures should be sought. It is shown how different members assess different aspects of the problem and that the reliability of the instrument can depend on the way that it is used. The methodology is motivated by and illustrated on data from a clinical study on schizophrenia. On the basis of this study, we estimate and compare the reliabilities of two different rating scales to evaluate the severity of the disorder. [source] Hierarchical related regression for combining aggregate and individual data in studies of socio-economic disease risk factorsJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES A (STATISTICS IN SOCIETY), Issue 1 2008Christopher Jackson Summary., To obtain information about the contribution of individual and area level factors to population health, it is desirable to use both data collected on areas, such as censuses, and on individuals, e.g. survey and cohort data. Recently developed models allow us to carry out simultaneous regressions on related data at the individual and aggregate levels. These can reduce ,ecological bias' that is caused by confounding, model misspecification or lack of information and increase power compared with analysing the data sets singly. We use these methods in an application investigating individual and area level sociodemographic predictors of the risk of hospital admissions for heart and circulatory disease in London. We discuss the practical issues that are encountered in this kind of data synthesis and demonstrate that this modelling framework is sufficiently flexible to incorporate a wide range of sources of data and to answer substantive questions. Our analysis shows that the variations that are observed are mainly attributable to individual level factors rather than the contextual effect of deprivation. [source] A hierarchical modelling framework for identifying unusual performance in health care providersJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES A (STATISTICS IN SOCIETY), Issue 4 2007David I. Ohlssen Summary. A wide variety of statistical methods have been proposed for detecting unusual performance in cross-sectional data on health care providers. We attempt to create a unified framework for comparing these methods, focusing on a clear distinction between estimation and hypothesis testing approaches, with the corresponding distinction between detecting ,extreme' and ,divergent' performance. When assuming a random-effects model the random-effects distribution forms the null hypothesis, and there appears little point in testing whether individual effects are greater or less than average. The hypothesis testing approach uses p -values as summaries and brings with it the standard problems of multiple testing, whether Bayesian or classical inference is adopted. A null random-effects formulation allows us to answer appropriate questions of the type: ,is a particular provider worse than we would expect the true worst provider (but still part of the null distribution) to be'? We outline a broad three-stage strategy of exploratory detection of unusual providers, detailed modelling robust to potential outliers and confirmation of unusual performance, illustrated by using two detailed examples. The concepts are most easily handled within a Bayesian analytic framework using Markov chain Monte Carlo methods, but the basic ideas should be generally applicable. [source] Using Difference-Based Methods for Inference in Regression with Fractionally Integrated ProcessesJOURNAL OF TIME SERIES ANALYSIS, Issue 6 2007Wen-Jen Tsay Abstract., This paper suggests a difference-based method for inference in the regression model involving fractionally integrated processes. Under suitable regularity conditions, our method can effectively deal with the inference problems associated with the regression model consisting of nonstationary, stationary and intermediate memory regressors, simultaneously. Although the difference-based method provides a very flexible modelling framework for empirical studies, the implementation of this method is extremely easy, because it completely avoids the difficult problems of choosing a kernel function, a bandwidth parameter, or an autoregressive lag length for the long-run variance estimation. The asymptotic local power of our method is investigated with a sequence of local data-generating processes (DGP) in what Davidson and MacKinnon [Canadian Journal of Economics. (1985) Vol. 18, pp. 38,57] call ,regression direction'. The simulation results indicate that the size control of our method is excellent even when the sample size is only 100, and the pattern of power performance is highly consistent with the theoretical finding from the asymptotic local power analysis conducted in this paper. [source] Critical habitat during the transition from maternal provisioning in freshwater fish, with emphasis on Atlantic salmon (Salmo salar) and brown trout (Salmo trutta)JOURNAL OF ZOOLOGY, Issue 4 2006J. D. Armstrong Abstract In freshwater fish, the transition from dependence on maternal yolk reserves to independent foraging can be an early critical period, with survival during this stage having a strong influence on population abundance and cohort strength. Information concerning Atlantic salmon Salmo salar and brown trout Salmo trutta as model species is reviewed to show how population dynamics are influenced by habitat use during the transitional stage and illustrate the role of maternal provisioning along with density-dependent and -independent factors. The allocation of resources in yolk and timing and position of spawning strongly influence the biotic and abiotic environments of juveniles and their subsequent performance. Vulnerability to predators, adverse environmental conditions and restricted conditions over which they can successfully forage result in specific habitat requirements for newly independent juveniles. The availability of slow-flowing habitats at stream margins during the first month of independence is crucial. Alteration of natural flow regimes and physical habitat structure, associated with a wide range of anthropogenic influences, can have significant deleterious effects on the availability of critical juvenile habitat. A model combining habitat structure and the relationship between density-dependent and -independent mortality is presented to explore the range of conditions under which the transitional period would have a strong influence on population abundance. This model provides a framework for establishing thresholds or optima for habitat availability that will favour sufficient recruitment out of the transitional stage. Using the modelling framework, managers can make informed decisions on the utility and cost effectiveness of fisheries and habitat management activities designed to increase juvenile survival during the transition to independence. A range of management options is outlined for improving habitat quality and increasing juvenile survival during the transitional period, including restoration of structural complexity, provision of suitable flow regimes, and tailoring stocking and reintroduction strategies to mimic natural dynamics. [source] Revisiting the Impact of Union Structures on Wages: Integrating Different Dimensions of CentralizationLABOUR, Issue 4 2003Nicole GürtzgenArticle first published online: 26 NOV 200 In particular, two dimensions along which centralization may occur, namely the professional and firm line, are integrated into one modelling framework. It will be shown that, when taking into account different centralization dimensions, wage outcomes of different bargaining regimes cannot simply be ranked according to the degree of bargaining centralization. The argument will be that negotiated wages rather depend on the technical relationship between different groups of labour and goods as well as upon the dimension along which centralization takes place. [source] Seascape genetics along a steep cline: using genetic patterns to test predictions of marine larval dispersalMOLECULAR ECOLOGY, Issue 17 2010HEATHER M. GALINDO Abstract Coupled biological and physical oceanographic models are powerful tools for studying connectivity among marine populations because they simulate the movement of larvae based on ocean currents and larval characteristics. However, while the models themselves have been parameterized and verified with physical empirical data, the simulated patterns of connectivity have rarely been compared to field observations. We demonstrate a framework for testing biological-physical oceanographic models by using them to generate simulated spatial genetic patterns through a simple population genetic model, and then testing these predictions with empirical genetic data. Both agreement and mismatches between predicted and observed genetic patterns can provide insights into mechanisms influencing larval connectivity in the coastal ocean. We use a high-resolution ROMS-CoSINE biological-physical model for Monterey Bay, California specifically modified to simulate dispersal of the acorn barnacle, Balanus glandula. Predicted spatial genetic patterns generated from both seasonal and annual connectivity matrices did not match an observed genetic cline in this species at either a mitochondrial or nuclear gene. However, information from this mismatch generated hypotheses testable with our modelling framework that including natural selection, larval input from a southern direction and/or increased nearshore larval retention might provide a better fit between predicted and observed patterns. Indeed, moderate selection and a range of combined larval retention and southern input values dramatically improve the fit between simulated and observed spatial genetic patterns. Our results suggest that integrating population genetic models with coupled biological-physical oceanographic models can provide new insights and a new means of verifying model predictions. [source] Quantifying the impact of above- and belowground higher trophic levels on plant and herbivore performance by modeling1OIKOS, Issue 7 2009Katrin M. Meyer Growing empirical evidence suggests that aboveground and belowground multitrophic communities interact. However, investigations that comprehensively explore the impacts of above- and belowground third and higher trophic level organisms on plant and herbivore performance are thus far lacking. We tested the hypotheses that above- and belowground higher trophic level organisms as well as decomposers affect plant and herbivore performance and that these effects cross the soil,surface boundary. We used a well-validated simulation model that is individual-based for aboveground trophic levels such as shoot herbivores, parasitoids, and hyperparasitoids while considering belowground herbivores and their antagonists at the population level. We simulated greenhouse experiments by removing trophic levels and decomposers from the simulations in a factorial design. Decomposers and above- and belowground third trophic levels affected plant and herbivore mortality, root biomass, and to a lesser extent shoot biomass. We also tested the effect of gradual modifications of the interactions between different trophic level organisms with a sensitivity analysis. Shoot and root biomass were highly sensitive to the impact of the fourth trophic level. We found effects that cross the soil surface, such as aboveground herbivores and parasitoids affecting root biomass and belowground herbivores influencing aboveground herbivore mortality. We conclude that higher trophic level organisms and decomposers can strongly influence plant and herbivore performance. We propose that our modelling framework can be used in future applications to quantitatively explore the possible outcomes of complex above- and belowground multitrophic interactions under a range of environmental conditions and species compositions. [source] Generalising the Hit Rates Test for Racial Bias in Law Enforcement, With an Application to Vehicle Searches in Wichita,THE ECONOMIC JOURNAL, Issue 515 2006Nicola Persico This article considers the use of outcomes-based tests for detecting racial bias in the context of police searches of motor vehicles. We characterise the police and motorist decision problems in a game theoretic framework, where police encounter motorists and decide whether to search them and motorists decide whether to carry contraband. Our modelling framework generalises that of Knowles et al. (2001). We apply the tests to data on police searches of motor vehicles gathered by the Wichita police department. The empirical findings are consistent with the notion that police in Wichita choose their search strategies to maximise successful searches. [source] On the Specification and Estimation of the Production Function for Cognitive Achievement*THE ECONOMIC JOURNAL, Issue 485 2003Petra E. Todd This paper considers methods for modelling the production function for cognitive achievement in a way that captures theoretical notions that child development is a cumulative process depending on the history of family and school inputs and on innate ability. It develops a general modelling framework that accommodates many of the estimating equations used in the literatures. It considers different ways of addressing data limitations, and it makes precise the identifying assumptions needed to justify alternative approaches. Commonly used specifications are shown to place restrictive assumptions on the production technology. Ways of testing modelling assumptions and of relaxing them are discussed. [source] FOAM, a new simple benthic degradative module for the LAMP3D model: an application to a Mediterranean fish farmAQUACULTURE RESEARCH, Issue 11 2008Patrizia De Gaetano Abstract The modelling framework already introduced by Doglioli, Magaldi, Vezzulli and Tucci to predict the potential impact of a marine fish farm is improved following different directions, namely (1) real historic current-metre data are used to force the simulations, (2) settling velocity values specifically targeting Mediterranean fish species are used, and (3) a new benthic degradative module, the Finite Organic Accumulation Module, is added to the modelling framework. The Finite Organic Accumulation Module uses the output of the other functional units of the modelling framework to calculate the organic load on the seabed. The Finite Organic Accumulation Module considers the natural capability of the seafloor in absorbing part of the organic load. Different remineralization rates reflect the sediment stress level according to the work of Findlay and Watling. Organic degradation for both uneaten feed and faeces is evaluated by changing the release modality (continuous and periodical) and by varying the settling velocities. It is found that the maximum impact on the benthic community is observed either for quickly sinking uneaten feed released twice a day, or for less intense near-bottom current conditions. If both the above-mentioned scenarios coexist, a high stress level is established in the sediment. The model also suggests that the use of self-feeders in cages can reduce farm impacts significantly. These results show how the new and more complete modelling framework presented here is able to improve the objectivity in the decision-making processes and how it may be successfully used for planning and monitoring purposes. [source] Lumped dynamic model for a bistable genetic regulatory circuit within a variable-volume whole-cell modelling frameworkASIA-PACIFIC JOURNAL OF CHEMICAL ENGINEERING, Issue 6 2009Gheorghe Maria Abstract Genetic regulatory circuits (GRCs) including switches, oscillators, signal amplifiers or filters, and signalling circuits are responsible for the control of cell metabolism. Modelling such complex GRCs is a difficult task due to high complexity of the the process (partly known) and the structural, functional and temporal hierarchical organisation of the cell system. Modular lumped representation, grouping some reactions/components and including different types of variables, is a promising alternative allowing individual module characterisation and elaboration of extended simulation platforms for representing the GRC dynamic properties and designing new cell functions. Such models allow to in-silico design modified micro-organisms with desirable properties for practical applications in bioprocess engineering and biotechnology. In the present work, the analysis of a designed bistable switch formed by two gene expression modules is performed in a variable-volume and whole-cell modelling framework, by mimicking the Escherichia coli cell growth. The advantages but also limitations of such a new approach are investigated, by using a Hill-type kinetics combined with few elementary steps, with the aim of better representing the adjustable levels of key intermediates tuning the GRC regulatory properties in terms of stability strength, species connectivity, responsiveness, and regulatory efficiency under stationary and dynamic perturbations. Copyright © 2009 Curtin University of Technology and John Wiley & Sons, Ltd. [source] | ||||||||||||||||||||||