An overview of APSIM, a model designed for farming systems simulation

The Agricultural Production Systems Simulator (APSIM) is a modular modelling framework that has been developed by the Agricultural Production Systems Research Unit in Australia. APSIM was developed to simulate biophysical process in farming systems, in particular where there is interest in the economic and ecological outcomes of management practice in the face of climatic risk. The paper outlines APSIM's structure and provides details of the concepts behind the different plant, soil and management modules. These modules include a diverse range of crops, pastures and trees, soil processes including water balance, N and P transformations, soil pH, erosion and a full range of management controls. Reports of APSIM testing in a diverse range of systems and environments are summarised. An example of model performance in a long-term cropping systems trial is provided. APSIM has been used in a broad range of applications, including support for on-farm decision making, farming systems design for production or resource management objectives, assessment of the value of seasonal climate forecasting, analysis of supply chain issues in agribusiness activities, development of waste management guidelines, risk assessment for government policy making and as a guide to research and education activity. An extensive citation list for these model testing and application studies is provided. Crown Copyright (C) 2002 Published by Elsevier Science B.V. All rights reserved.

Modelling High-Dimensional Data by Mixtures of Factor Analyzers

We focus on mixtures of factor analyzers from the perspective of a method for model-based density estimation from high-dimensional data, and hence for the clustering of such data. This approach enables a normal mixture model to be fitted to a sample of n data points of dimension p, where p is large relative to n. The number of free parameters is controlled through the dimension of the latent factor space. By working in this reduced space, it allows a model for each component-covariance matrix with complexity lying between that of the isotropic and full covariance structure models. We shall illustrate the use of mixtures of factor analyzers in a practical example that considers the clustering of cell lines on the basis of gene expressions from microarray experiments. (C) 2002 Elsevier Science B.V. All rights reserved.

Fitting genetic models to twin data with binary and ordered categorical responses: A comparison of structural equation modelling and Bayesian hierarchical models

We compare Bayesian methodology utilizing free-ware BUGS (Bayesian Inference Using Gibbs Sampling) with the traditional structural equation modelling approach based on another free-ware package, Mx. Dichotomous and ordinal (three category) twin data were simulated according to different additive genetic and common environment models for phenotypic variation. Practical issues are discussed in using Gibbs sampling as implemented by BUGS to fit subject-specific Bayesian generalized linear models, where the components of variation may be estimated directly. The simulation study (based on 2000 twin pairs) indicated that there is a consistent advantage in using the Bayesian method to detect a correct model under certain specifications of additive genetics and common environmental effects. For binary data, both methods had difficulty in detecting the correct model when the additive genetic effect was low (between 10 and 20%) or of moderate range (between 20 and 40%). Furthermore, neither method could adequately detect a correct model that included a modest common environmental effect (20%) even when the additive genetic effect was large (50%). Power was significantly improved with ordinal data for most scenarios, except for the case of low heritability under a true ACE model. We illustrate and compare both methods using data from 1239 twin pairs over the age of 50 years, who were registered with the Australian National Health and Medical Research Council Twin Registry (ATR) and presented symptoms associated with osteoarthritis occurring in joints of the hand.

A note on quasi-stationary distributions of birth-death processes and the SIS logistic epidemic

For Markov processes on the positive integers with the origin as an absorbing state, Ferrari, Kesten, Martinez and Picco studied the existence of quasi-stationary and limiting conditional distributions by characterizing quasi-stationary distributions as fixed points of a transformation Phi on the space of probability distributions on {1, 2,.. }. In the case of a birth-death process, the components of Phi(nu) can be written down explicitly for any given distribution nu. Using this explicit representation, we will show that Phi preserves likelihood ratio ordering between distributions. A conjecture of Kryscio and Lefevre concerning the quasi-stationary distribution of the SIS logistic epidemic follows as a corollary.

Conceptual modelling and ontology: Possibilities and pitfalls

Conceptual modelling is an activity undertaken during information systems development work to build a representation of selected semantics about some real-world domain. Ontological theories have been developed to account for the structure and behavior of the real world in general. In this paper, I discuss why ontological theories can be used to inform conceptual modelling research, practice, and pedagogy. I provide examples from my research to illustrate how a particular ontological theory has enabled me to improve my understanding of certain conceptual modelling practices and grammars. I describe, also, how some colleagues and I have used this theory to generate several counter-intuitive, sometimes surprising predictions about widely advocated conceptual modelling practices - predictions that subsequently were supported in empirical research we undertook. Finally, I discuss several possibilities and pitfalls I perceived to be associated with our using ontological theories to underpin research on conceptual modelling.

Conspicuous males suffer higher predation risk: visual modelling and experimental evidence from lizards

Colour pattern variation is a striking and widespread phenomenon. Differential predation risk between individuals is often invoked to explain colour variation, but empirical support for this hypothesis is equivocal. We investigated differential conspicuousness and predation risk in two species of Australian rock dragons, Ctenophorus decresii and C. vadnappa. To humans, the coloration of males of these species varies between 'bright' and 'dull'. Visual modelling based on objective colour measurements and the spectral sensitivities of avian visual pigments showed that dragon colour variants are differentially conspicuous to the visual system of avian predators when viewed against the natural background. We conducted field experiments to test for differential predation risk, using plaster models of 'bright' and 'dull' males. 'Bright' models were attacked significantly more often than 'dull' models suggesting that differential conspicuousness translates to differential predation risk in the wild. We also examined the influence of natural geographical range on predation risk. Results from 22 localities suggest that predation rates vary according to whether predators are familiar with the prey species. This study is among the first to demonstrate both differential conspicuousness and differential predation risk in the wild using an experimental protocol. (C) 2003 Published by Elsevier Ltd on behalf of The Association for the Study of Animal Behaviour.

Indirect evidence of density-dependent population regulation in Aponomma hydrosauri (Acari : Ixodidae), an ectoparasite of reptiles

The extent to which density-dependent processes regulate natural populations is the subject of an ongoing debate. We contribute evidence to this debate showing that density-dependent processes influence the population dynamics of the ectoparasite Aponomma hydrosauri (Acari: Ixodidae), a tick species that infests reptiles in Australia. The first piece of evidence comes from an unusually long-term dataset on the distribution of ticks among individual hosts. If density-dependent processes are influencing either host mortality or vital rates of the parasite population, and those distributions can be approximated with negative binomial distributions, then general host-parasite models predict that the aggregation coefficient of the parasite distribution will increase with the average intensity of infections. We fit negative binomial distributions to the frequency distributions of ticks on hosts, and find that the estimated aggregation coefficient k increases with increasing average tick density. This pattern indirectly implies that one or more vital rates of the tick population must be changing with increasing tick density, because mortality rates of the tick's main host, the sleepy lizard, Tiliqua rugosa, are unaffected by changes in tick burdens. Our second piece of evidence is a re-analysis of experimental data on the attachment success of individual ticks to lizard hosts using generalized linear modelling. The probability of successful engorgement decreases with increasing numbers of ticks attached to a host. This is direct evidence of a density-dependent process that could lead to an increase in the aggregation coefficient of tick distributions described earlier. The population-scale increase in the aggregation coefficient is indirect evidence of a density-dependent process or processes sufficiently strong to produce a population-wide pattern, and thus also likely to influence population regulation. The direct observation of a density-dependent process is evidence of at least part of the responsible mechanism.

Applying discrete element modelling to vertical and horizontal shaft impact crushers

The PFC3D (particle flow code) that models the movement and interaction of particles by the DEM techniques was employed to simulate the particle movement and to calculate the velocity and energy distribution of collision in two types of impact crusher: the Canica vertical shaft crusher and the BJD horizontal shaft swing hammer mill. The distribution of collision energies was then converted into a product size distribution for a particular ore type using JKMRC impact breakage test data. Experimental data of the Canica VSI crusher treating quarry and the BJD hammer mill treating coal were used to verify the DEM simulation results. Upon the DEM procedures being validated, a detailed simulation study was conducted to investigate the effects of the machine design and operational conditions on velocity and energy distributions of collision inside the milling chamber and on the particle breakage behaviour. (C) 2003 Elsevier Ltd. All rights reserved.

The rheology of flotation froths

A literature review has highlighted the need to measure flotation froth rheology in order to fully characterise the role of the froth in the flotation process. The initial investigation using a coaxial cylinder viscometer for froth rheology measurement led to the development of a new device employing a vane measuring head. The modified rheometer was used in industrial scale flotation tests at Mt. Isa Copper Concentrator. The measured froth rheograms show a non-Newtonian nature for the flotation froths (pseudoplastic flow). The evidence of the non-Newtonian flow has questioned the validity of application of the Laplace equation in froth motion modelling as used by a number of researchers, since the assumption of irrotational flow is violated. Correlations between the froth rheology and the froth retention time, water hold-up in the froth and concentrate grades have been found. These correlations are independent of air flow rate (test data at various air flow rates fall on one similar trend line). This implies that froth rheology may be used as a lumped parameter for other operating variables in flotation modelling and scale up. (C) 2003 Elsevier Science B.V. All rights reserved.

Modelling the size of the crushed zone around a blasthole

A new model to predict the extent of crushing around a blasthole is presented. The model is based on the back-analysis of a comprehensive experimental program that included the direct measurement of the zone of crushing from 92 blasting tests on concrete blocks using two commercial explosives. The concrete blocks varied from low, medium to high strength and measured 1.5 in in length, 1.0 m in width and 1.1 m in height. A dimensionless parameter called the crushing zone index (CZI) is introduced. This index measures the crushing potential of a charged blasthole and is a function of the borehole pressure, the unconfined compressive strength of the rock material, dynamic Young's modulus and Poisson's ratio. It is shown that the radius of crushing is a function of the CZI and the blasthole radius. A good correlation between the new model and measured results was obtained. A number of previously proposed models could not approximate the conditions measured in the experimental work and there are noted discrepancies between the different approaches reviewed, particularly for smaller diameter holes and low strength rock conditions. The new model has been verified with full scale tests reported in the literature. Results from this validation and model evaluations show its applicability to production blasting. (C) 2003 Elsevier Science Ltd. All rights reserved.

A mathematical model of concentrate solids content for the wet drum magnetic separator

Low concentrate density from wet drum magnetic separators in dense medium circuits can cause operating difficulties due to inability to obtain the required circulating medium density and, indirectly, high medium solids losses. The literature is almost silent on the processes controlling concentrate density. However, the common name for the region through which concentrate is discharged-the squeeze pan gap-implies that some extrusion process is thought to be at work. There is no model of magnetics recovery in a wet drum magnetic separator, which includes as inputs all significant machine and operating variables. A series of trials, in both factorial experiments and in single variable experiments, was done using a purpose built rig which featured a small industrial scale (700 mm lip length, 900 turn diameter) wet drum magnetic separator. A substantial data set of 191 trials was generated in this work. The results of the factorial experiments were used to identify the variables having a significant effect on magnetics recovery. It is proposed, based both on the experimental observations of the present work and on observations reported in the literature, that the process controlling magnetic separator concentrate density is one of drainage. Such a process should be able to be defined by an initial moisture, a drainage rate and a drainage time, the latter being defined by the volumetric flowrate and the volume within the drainage zone. The magnetics can be characterised by an experimentally derived ultimate drainage moisture. A model based on these concepts and containing adjustable parameters was developed. This model was then fitted to a randomly chosen 80% of the data, and validated by application to the remaining 20%. The model is shown to be a good fit to data over concentrate solids content values from 40% solids to 80% solids and for both magnetite and ferrosilicon feeds. (C) 2003 Elsevier Science B.V. All rights reserved.

Discrete element modelling of power draw of tumbling mills

The power required to operate large mills is typically 5-10 MW. Hence, optimisation of power consumption will have a significant impact on overall economic performance and environmental impact. Power draw modelling results using the discrete element code PFC3D have been compared with results derived from the widely used empirical Model of Morrell. This is achieved by calculating the power draw for a range of operating conditions for constant mill size and fill factor using two modelling approaches. fThe discrete element modelling results show that, apart from density, selection of the appropriate material damping ratio is critical for the accuracy of modelling of the mill power draw. The relative insensitivity of the power draw to the material stiffness allows selection of moderate stiffness values, which result in acceptable computation time. The results obtained confirm that modelling of the power draw for a vertical slice of the mill, of thickness 20% of the mill length, is a reliable substitute for modelling the full mill. The power draw predictions from PFC3D show good agreement with those obtained using the empirical model. Due to its inherent flexibility, power draw modelling using PFC3D appears to be a viable and attractive alternative to empirical models where necessary code and computer power are available.