A generic individual-based spatially explicit model as a novel tool for investigating insect-plant interactions: A case study of the behavioural ecology of frugivorous Tephritidae

Computational modelling of mechanisms underlying processes in the real world can be of great value in understanding complex biological behaviours. Uptake in general biology and ecology has been rapid. However, it often requires specific data sets that are overly costly in time and resources to collect. The aim of the current study was to test whether a generic behavioural ecology model constructed using published data could give realistic outputs for individual species. An individual-based model was developed using the Pattern-Oriented Modelling (POM) strategy and protocol, based on behavioural rules associated with insect movement choices. Frugivorous Tephritidae (fruit flies) were chosen because of economic significance in global agriculture and the multiple published data sets available for a range of species. The Queensland fruit fly (Qfly), Bactrocera tryoni, was identified as a suitable individual species for testing. Plant canopies with modified architecture were used to run predictive simulations. A field study was then conducted to validate our model predictions on how plant architecture affects fruit flies’ behaviours. Characteristics of plant architecture such as different shapes, e.g., closed-canopy and vase-shaped, affected fly movement patterns and time spent on host fruit. The number of visits to host fruit also differed between the edge and centre in closed-canopy plants. Compared to plant architecture, host fruit has less contribution to effects on flies’ movement patterns. The results from this model, combined with our field study and published empirical data suggest that placing fly traps in the upper canopy at the edge should work best. Such a modelling approach allows rapid testing of ideas about organismal interactions with environmental substrates in silico rather than in vivo, to generate new perspectives. Using published data provides a saving in time and resources. Adjustments for specific questions can be achieved by refinement of parameters based on targeted experiments.

Spatially-explicit modelling of grassland classes - an improved method of integrating a climate-based classification model with interpolated climate surfaces

Spatially-explicit modelling of grassland classes is important to site-specific planning for improving grassland and environmental management over large areas. In this study, a climate-based grassland classification model, the Comprehensive and Sequential Classification System (CSCS) was integrated with spatially interpolated climate data to classify grassland in Gansu province, China. The study area is characterized by complex topographic features imposed by plateaus, high mountains, basins and deserts. To improve the quality of the interpolated climate data and the quality of the spatial classification over this complex topography, three linear regression methods, namely an analytic method based on multiple regression and residues (AMMRR), a modification of the AMMRR method through adding the effect of slope and aspect to the interpolation analysis (M-AMMRR) and a method which replaces the IDW approach for residue interpolation in M-AMMRR with an ordinary kriging approach (I-AMMRR), for interpolating climate variables were evaluated. The interpolation outcomes from the best interpolation method were then used in the CSCS model to classify the grassland in the study area. Climate variables interpolated included the annual cumulative temperature and annual total precipitation. The results indicated that the AMMRR and M-AMMRR methods generated acceptable climate surfaces but the best model fit and cross validation result were achieved by the I-AMMRR method. Twenty-six grassland classes were classified for the study area. The four grassland vegetation classes that covered more than half of the total study area were "cool temperate-arid temperate zonal semi-desert", "cool temperate-humid forest steppe and deciduous broad-leaved forest", "temperate-extra-arid temperate zonal desert", and "frigid per-humid rain tundra and alpine meadow". The vegetation classification map generated in this study provides spatial information on the locations and extents of the different grassland classes. This information can be used to facilitate government agencies' decision-making in land-use planning and environmental management, and for vegetation and biodiversity conservation. The information can also be used to assist land managers in the estimation of safe carrying capacities which will help to prevent overgrazing and land degradation.

Spatially explicit structural equation modeling

Structural equation modeling (SEM) is a powerful statistical approach for the testing of networks of direct and indirect theoretical causal relationships in complex data sets with intercorrelated dependent and independent variables. SEM is commonly applied in ecology, but the spatial information commonly found in ecological data remains difficult to model in a SEM framework. Here we propose a simple method for spatially explicit SEM (SE-SEM) based on the analysis of variance/covariance matrices calculated across a range of lag distances. This method provides readily interpretable plots of the change in path coefficients across scale and can be implemented using any standard SEM software package. We demonstrate the application of this method using three studies examining the relationships between environmental factors, plant community structure, nitrogen fixation, and plant competition. By design, these data sets had a spatial component, but were previously analyzed using standard SEM models. Using these data sets, we demonstrate the application of SE-SEM to regularly spaced, irregularly spaced, and ad hoc spatial sampling designs and discuss the increased inferential capability of this approach compared with standard SEM. We provide an R package, sesem, to easily implement spatial structural equation modeling.

The Long-Term Irrelevance of Trust in Outsourcing Decisions for New Technologies: Insights from an Agent-Based Model

Significant empirical data from the fields of management and business strategy suggest that it is a good idea for a company to make in-house the components and processes underpinning a new technology. Other evidence suggests exactly the opposite, saying that firms would be better off buying components and processes from outside suppliers. One possible explanation for this lack of convergence is that earlier research in this area has overlooked two important aspects of the problem: reputation and trust. To gain insight into how these variables may impact make-buy decisions throughout the innovation process, the Sporas algorithm for measuring reputation was added to an existing agent-based model of how firms interact with each other throughout the development of new technologies. The model�s results suggest that reputation and trust do not play a significant role in the long-term fortunes of an individual firm as it contends with technological change in the marketplace. Accordingly, this model serves as a cue for management researchers to investigate more thoroughly the temporal limitations and contingencies that determine how the trust between firms may affect the R&D process.

Agent-based model of passenger flows in airport terminals

Passenger flow studies in airport terminals have shown consistent statistical relationships between airport spatial layout and pedestrian movement, facilitating prediction of movement from terminal designs. However, these studies are done at an aggregate level and do not incorporate how individual passengers make decisions at a microscopic level. Therefore, they do not explain the formation of complex movement flows. In addition, existing models mostly focus on standard airport processing procedures such as immigration and security, but seldom consider discretionary activities of passengers, and thus are not able to truly describe the full range of passenger flows within airport terminals. As the route-choice decision-making of passengers involves many uncertain factors within the airport terminals, the mechanisms to fulfill the capacity of managing the route-choice have proven difficult to acquire and quantify. Could the study of cognitive factors of passengers (i.e. human mental preferences of deciding which on-airport facility to use) be useful to tackle these issues? Assuming the movement in virtual simulated environments can be analogous to movement in real environments, passenger behaviour dynamics can be similar to those generated in virtual experiments. Three levels of dynamics have been devised for motion control: the localised field, tactical level, and strategic level. A localised field refers to basic motion capabilities, such as walking speed, direction and avoidance of obstacles. The other two fields represent cognitive route-choice decision-making. This research views passenger flow problems via a "bottom-up approach", regarding individual passengers as independent intelligent agents who can behave autonomously and are able to interact with others and the ambient environment. In this regard, passenger flow formation becomes an emergent phenomenon of large numbers of passengers interacting with others. In the thesis, first, the passenger flow in airport terminals was investigated. Discretionary activities of passengers were integrated with standard processing procedures in the research. The localised field for passenger motion dynamics was constructed by a devised force-based model. Next, advanced traits of passengers (such as their desire to shop, their comfort with technology and their willingness to ask for assistance) were formulated to facilitate tactical route-choice decision-making. The traits consist of quantified measures of mental preferences of passengers when they travel through airport terminals. Each category of the traits indicates a decision which passengers may take. They were inferred through a Bayesian network model by analysing the probabilities based on currently available data. Route-choice decision-making was finalised by calculating corresponding utility results based on those probabilities observed. Three sorts of simulation outcomes were generated: namely, queuing length before checkpoints, average dwell time of passengers at service facilities, and instantaneous space utilisation. Queuing length reflects the number of passengers who are in a queue. Long queues no doubt cause significant delay in processing procedures. The dwell time of each passenger agent at the service facilities were recorded. The overall dwell time of passenger agents at typical facility areas were analysed so as to demonstrate portions of utilisation in the temporal aspect. For the spatial aspect, the number of passenger agents who were dwelling within specific terminal areas can be used to estimate service rates. All outcomes demonstrated specific results by typical simulated passenger flows. They directly reflect terminal capacity. The simulation results strongly suggest that integrating discretionary activities of passengers makes the passenger flows more intuitive, observing probabilities of mental preferences by inferring advanced traits make up an approach capable of carrying out tactical route-choice decision-making. On the whole, the research studied passenger flows in airport terminals by an agent-based model, which investigated individual characteristics of passengers and their impact on psychological route-choice decisions of passengers. Finally, intuitive passenger flows in airport terminals were able to be realised in simulation.

A comparison of spatially explicit landscape representation methods and their relationship to stream condition

1. Biodiversity, water quality and ecosystem processes in streams are known to be influenced by the terrestrial landscape over a range of spatial and temporal scales. Lumped attributes (i.e. per cent land use) are often used to characterise the condition of the catchment; however, they are not spatially explicit and do not account for the disproportionate influence of land located near the stream or connected by overland flow. 2. We compared seven landscape representation metrics to determine whether accounting for the spatial proximity and hydrological effects of land use can be used to account for additional variability in indicators of stream ecosystem health. The landscape metrics included the following: a lumped metric, four inverse-distance-weighted (IDW) metrics based on distance to the stream or survey site and two modified IDW metrics that also accounted for the level of hydrologic activity (HA-IDW). Ecosystem health data were obtained from the Ecological Health Monitoring Programme in Southeast Queensland, Australia and included measures of fish, invertebrates, physicochemistry and nutrients collected during two seasons over 4 years. Linear models were fitted to the stream indicators and landscape metrics, by season, and compared using an information-theoretic approach. 3. Although no single metric was most suitable for modelling all stream indicators, lumped metrics rarely performed as well as other metric types. Metrics based on proximity to the stream (IDW and HA-IDW) were more suitable for modelling fish indicators, while the HA-IDW metric based on proximity to the survey site generally outperformed others for invertebrates, irrespective of season. There was consistent support for metrics based on proximity to the survey site (IDW or HA-IDW) for all physicochemical indicators during the dry season, while a HA-IDW metric based on proximity to the stream was suitable for five of the six physicochemical indicators in the post-wet season. Only one nutrient indicator was tested and results showed that catchment area had a significant effect on the relationship between land use metrics and algal stable isotope ratios in both seasons. 4. Spatially explicit methods of landscape representation can clearly improve the predictive ability of many empirical models currently used to study the relationship between landscape, habitat and stream condition. A comparison of different metrics may provide clues about causal pathways and mechanistic processes behind correlative relationships and could be used to target restoration efforts strategically.

Analysis of passenger group behaviour and its impact on passenger flow using an agent-based model

Group interaction within crowds is a common phenomenon and has great influence on pedestrian behaviour. This paper investigates the impact of passenger group dynamics using an agent-based simulation method for the outbound passenger process at airports. Unlike most passenger-flow models that treat passengers as individual agents, the proposed model additionally incorporates their group dynamics as well. The simulation compares passenger behaviour at airport processes and discretionary services under different group formations. Results from experiments (both qualitative and quantitative) show that incorporating group attributes, in particular, the interactions with fellow travellers and wavers can have significant influence on passengers activity preference as well as the performance and utilisation of services in airport terminals. The model also provides a convenient way to investigate the effectiveness of airport space design and service allocations, which can contribute to positive passenger experiences. The model was created using AnyLogic software and its parameters were initialised using recent research data published in the literature.

Maximising the manufacturer performance value through lean initiatives using cost based model

Numerous tools and techniques have been developed to eliminate or reduce waste and carry out lean concepts in the manufacturing environment. However, appropriate lean tools need to be selected and implemented in order to fulfil the manufacturer needs within their budgetary constraints. As a result, it is important to identify manufacturer needs and implement only those tools, which contribute maximum benefit to their needs. In this research a mathematical model is proposed for maximising the perceived value of manufacturer needs and developed a step-by-step methodology to select best performance metrics along with appropriate lean strategies within the budgetary constraints. With the help of a case study, the proposed model and method have been demonstrated.

Models of collective cell behaviour with crowding effects : comparing lattice-based and lattice-free approaches

Individual-based models describing the migration and proliferation of a population of cells frequently restrict the cells to a predefined lattice. An implicit assumption of this type of lattice based model is that a proliferative population will always eventually fill the lattice. Here we develop a new lattice-free individual-based model that incorporates cell-to-cell crowding effects. We also derive approximate mean-field descriptions for the lattice-free model in two special cases motivated by commonly used experimental setups. Lattice-free simulation results are compared to these mean-field descriptions and to a corresponding lattice-based model. Data from a proliferation experiment is used to estimate the parameters for the new model, including the cell proliferation rate, showing that the model fits the data well. An important aspect of the lattice-free model is that the confluent cell density is not predefined, as with lattice-based models, but an emergent model property. As a consequence of the more realistic, irregular configuration of cells in the lattice-free model, the population growth rate is much slower at high cell densities and the population cannot reach the same confluent density as an equivalent lattice-based model.

Relative entropy rate based model selection for linear hybrid system filters of uncertain nonlinear systems

Hybrid system representations have been exploited in a number of challenging modelling situations, including situations where the original nonlinear dynamics are too complex (or too imprecisely known) to be directly filtered. Unfortunately, the question of how to best design suitable hybrid system models has not yet been fully addressed, particularly in the situations involving model uncertainty. This paper proposes a novel joint state-measurement relative entropy rate based approach for design of hybrid system filters in the presence of (parameterised) model uncertainty. We also present a design approach suitable for suboptimal hybrid system filters. The benefits of our proposed approaches are illustrated through design examples and simulation studies.

Morphology-based model for predicting osteocyte-like cell line (MLO-Y4) growth process

This work has led to the development of empirical mathematical models to quantitatively predicate the changes of morphology in osteocyte-like cell lines (MLO-Y4) in culture. MLO-Y4 cells were cultured at low density and the changes in morphology recorded over 11 hours. Cell area and three dimensional shape features including aspect ratio, circularity and solidity were then determined using widely accepted image analysis software (ImageJTM). Based on the data obtained from the imaging analysis, mathematical models were developed using the non-linear regression method. The developed mathematical models accurately predict the morphology of MLO-Y4 cells for different culture times and can, therefore, be used as a reference model for analyzing MLO-Y4 cell morphology changes within various biological/mechanical studies, as necessary.