Hierarchical models for 2D presence/absence data having ambiguous zeroes: With a biogeographical case study on dingo behaviour

This dissertation is primarily an applied statistical modelling investigation, motivated by a case study comprising real data and real questions. Theoretical questions on modelling and computation of normalization constants arose from pursuit of these data analytic questions. The essence of the thesis can be described as follows. Consider binary data observed on a two-dimensional lattice. A common problem with such data is the ambiguity of zeroes recorded. These may represent zero response given some threshold (presence) or that the threshold has not been triggered (absence). Suppose that the researcher wishes to estimate the effects of covariates on the binary responses, whilst taking into account underlying spatial variation, which is itself of some interest. This situation arises in many contexts and the dingo, cypress and toad case studies described in the motivation chapter are examples of this. Two main approaches to modelling and inference are investigated in this thesis. The first is frequentist and based on generalized linear models, with spatial variation modelled by using a block structure or by smoothing the residuals spatially. The EM algorithm can be used to obtain point estimates, coupled with bootstrapping or asymptotic MLE estimates for standard errors. The second approach is Bayesian and based on a three- or four-tier hierarchical model, comprising a logistic regression with covariates for the data layer, a binary Markov Random field (MRF) for the underlying spatial process, and suitable priors for parameters in these main models. The three-parameter autologistic model is a particular MRF of interest. Markov chain Monte Carlo (MCMC) methods comprising hybrid Metropolis/Gibbs samplers is suitable for computation in this situation. Model performance can be gauged by MCMC diagnostics. Model choice can be assessed by incorporating another tier in the modelling hierarchy. This requires evaluation of a normalization constant, a notoriously difficult problem. Difficulty with estimating the normalization constant for the MRF can be overcome by using a path integral approach, although this is a highly computationally intensive method. Different methods of estimating ratios of normalization constants (N Cs) are investigated, including importance sampling Monte Carlo (ISMC), dependent Monte Carlo based on MCMC simulations (MCMC), and reverse logistic regression (RLR). I develop an idea present though not fully developed in the literature, and propose the Integrated mean canonical statistic (IMCS) method for estimating log NC ratios for binary MRFs. The IMCS method falls within the framework of the newly identified path sampling methods of Gelman & Meng (1998) and outperforms ISMC, MCMC and RLR. It also does not rely on simplifying assumptions, such as ignoring spatio-temporal dependence in the process. A thorough investigation is made of the application of IMCS to the three-parameter Autologistic model. This work introduces background computations required for the full implementation of the four-tier model in Chapter 7. Two different extensions of the three-tier model to a four-tier version are investigated. The first extension incorporates temporal dependence in the underlying spatio-temporal process. The second extensions allows the successes and failures in the data layer to depend on time. The MCMC computational method is extended to incorporate the extra layer. A major contribution of the thesis is the development of a fully Bayesian approach to inference for these hierarchical models for the first time. Note: The author of this thesis has agreed to make it open access but invites people downloading the thesis to send her an email via the 'Contact Author' function.

A novel winding structure in planar inductors to decrease the overall capacitive couplings

This paper presents a new method for winding configuration in planar magnetic elements with more than two layers. It has been proven by 3D Finite Element method and mathematical modeling that this suggested configuration results in reduction of the equivalent capacitive coupling in the planar inductor

Controller structure and design of firing angle controllers for (unit connected) HVDC systems

This paper investigates the control of a HVDC link, fed from an AC source through a controlled rectifier and feeding an AC line through a controlled inverter. The overall objective is to maintain maximum possible link voltage at the inverter while regulating the link current. In this paper the practical feedback design issues are investigated with a view of obtaining simple, robust designs that are easy to evaluate for safety and operability. The investigations are applicable to back-to-back links used for frequency decoupling and to long DC lines. The design issues discussed include: (i) a review of overall system dynamics to establish the time scale of different feedback loops and to highlight feedback design issues; (ii) the concept of using the inverter firing angle control to regulate link current when the rectifier firing angle controller saturates; and (iii) the design issues for the individual controllers including robust design for varying line conditions and the trade-off between controller complexity and the reduction of nonlinearity and disturbance effects

Collaborative research to develop a specialist, post-graduate competency-based education curriculum and continuing professional development structure for health librarians in Australia

Through a grant received from the Australian Library and Information Association (ALIA), members of Health Libraries Australia (HLA) are collaborating with a researcher/educator to conduct a twelve month research project with the goal of developing an educational framework for the Australian health librarianship workforce of the future. The collaboration comprises the principal researcher and a representative group of practitioners from different sectors of the health industry who are affiliated with ALIA in various committees, advisory groups and roles. The research has two main aims: to determine the future skills requirements for the health librarian workforce in Australia; and to develop a structured, modular education framework for specialist post-graduate qualifications together with a structure for ongoing continuing professional development. The paper highlights some of the major trends in the health sector and some of the main environmental influences that may act as drivers for change for health librarianship as a profession, and particularly for educating the future workforce. The research methodology is outlined and the main results are described; the findings are discussed with regard to their implications for the development of a structured, competency-based education framework.

Implementing a Pattern and Structure Mathematics Awareness Program (PASMAP) in kindergarten

This paper provides an interim report of a large empirical evaluation study in progress. An intervention was implemented to evaluate the effectiveness of the Pattern and Structure Mathematical Awareness Program (PASMAP) on Kindergarten students’ mathematical development. Four large schools (two from Sydney and two from Brisbane), 16 teachers and their 316 students participated in the first phase of a 2-year longitudinal study. Eight of 16 classes implemented the PASMAP program over three school terms. This paper provides an overview of key aspects of the intervention, and preliminary analysis of the impact of PASMAP on students’ representation, abstraction and generalisation of mathematical ideas.

Household type and structure, time-use pattern, and trip-chaining behavior

In order to examine time allocation patterns within household-level trip-chaining, simultaneous doubly-censored Tobit models are applied to model time-use behavior within the context of household activity participation. Using the entire sample and a sub-sample of worker households from Tucson's Household Travel Survey, two sets of models are developed to better understand the phenomena of trip-chaining behavior among five types of households: single non-worker households, single worker households, couple non-worker households, couple one-worker households, and couple two-worker households. Durations of out-of-home subsistence, maintenance, and discretionary activities within trip chains are examined. Factors found to be associated with trip-chaining behavior include intra-household interactions with the household types and their structure and household head attributes.

Network structure, knowledge governance, and firm performance : evidence from innovation networks and SMEs in the UK

It is increasingly understood that learning and thus innovation often occurs via highly interactive, iterative, network-based processes. Simultaneously, economic development policy is increasingly focused on small and medium-sized enterprises (SMEs) as a means of generating growth, creating a clear research issue in terms of the roles and interactions of government policy, universities, and other sources of knowledge, SMEs, and the creation and dissemination of innovation. This paper analyses the contribution of a range of actors in an SME innovation creation and dissemination framework, reviewing the role of various institutions therein, exploring the contribution of cross-locality networks, and identifying the mechanisms required to operationalise such a framework. Bivariate and multivariate (regression) techniques are employed to investigate both innovation and growth outcomes in relation to these structures; data are derived from the survey responses of over 450 SMEs in the UK. Results are complex and dependent upon the nature of institutions involved, the type of knowledge sought, and the spatial level of the linkages in place but overall highlight the value of cross-locality networks, network governance structures, and certain spillover effects from universities. In general, we find less support for the factors predicting SME growth outcomes than is the case for innovation. Finally, we outline an agenda for further research in the area.

Geographical information systems : an effective planning and decision-making platform for community health coalitions in Australia

The development of locally-based healthcare initiatives, such as community health coalitions that focus on capacity building programs and multi-faceted responses to long-term health problems, have become an increasingly important part of the public health landscape. As a result of their complexity and the level of investment, it has become necessary to develop innovative ways to help manage these new healthcare approaches. Geographical Information Systems (GIS) have been suggested as one of the innovative approaches that will allow community health coalitions to better manage and plan their activities. The focus of this paper is to provide a commentary on the use of GIS as a tool for community coalitions and discuss some of the potential benefits and issues surrounding the development of these tools.

Ownership structure and business evaluation practices in family SMEs : evidence from empirical research in Italy

This paper presents early results from a pilot project which aims to investigate the relationship between proprietary structure of small and medium- sized Italian family firms and their owners’ orientation towards a “business evaluation process”. Evidence from many studies point out the importance of family business in a worldwide economic environment: in Italy 93% of the businesses are represented by family firms; 98% of them have less than 50 employees (Italian Association of Family Firms, 2004) so we judged family SMEs as a relevant field of investigation. In this study we assume a broad definition of family business as “a firm whose control (50% of shares or voting rights) is closely held by the members of the same family” (Corbetta,1995). “Business evaluation process” is intended here both as “continuous evaluation process” (which is the expression of a well developed managerial attitude) or as an “immediate valuation” (i.e. in the case of new shareholder’s entrance, share exchange among siblings, etc). We set two hypotheses to be tested in this paper: the first is “quantitative” and aims to verify whether the number of owners (independent variable) in a family firm is positively correlated to the business evaluation process. If a family firm is led by only one subject, it is more likely that personal values, culture and feelings may affect his choices more than “purely economic opportunities”; so there is less concern about monitoring economic performance or about the economic value of the firm. As the shareholders’ number increases, economic aspects in managing the firm grow in importance over the personal values and "value orientation" acquires a central role. The second hypothesis investigates if and to what extent the presence of “non- family members” among the owners affects their orientation to the business evaluation process. The “Cramer’s V” test has been used to test the hypotheses; both were not confirmed from these early results; next steps will lead to make an inferential analysis on a representative sample of the population.

Examination of the latent structure of the psychological sense of school membership scale

Despite its widespread use, there has been limited examination of the underlying factor structure of the Psychological Sense of School Membership (PSSM) scale. The current study examined the psychometric properties of the PSSM to refine its utility for researchers and practitioners using a sample of 504 Australian high school students. Results from exploratory and confirmatory factor analyses indicated that the PSSM is a multidimensional instrument. Factor analysis procedures identified three factors representing related aspects of students’ perceptions of their school membership: caring relationships, acceptance, and rejection

Genetic resources in wild and cultured stocks of the Asian mud crab, Scylla paramamosain

The mud crab (Scylla spp.) aquaculture industry has expanded rapidly in recent years in many countries in the Indo - West Pacific (IWP) region as an alternative to marine shrimp culture because of significant disease outbreaks and associated failures of many shrimp culture industries in the region. Currently, practices used to produce and manage breeding crabs in hatcheries may compromise levels of genetic diversity, ultimately compromising growth rates, disease resistance and stock productivity. Therefore, to avoid “genetic pollution” and its harmful effects and to promote further development of mud crab aquaculture and fisheries in a sustainable way, a greater understanding of the genetic attributes of wild and cultured mud crab stocks is required. Application of these results can provide benefits for managing wild and cultured Asian mud crab populations for multiple purposes including for commercial production, recreation and conservation and to increase profitability and sustainability of newly emerging crab culture industries. Phylogeographic patterns and the genetic structure of Asian mud crab populations across the IWP were assessed to determine if they were concordant with those of other widespread taxa possessing pelagic larvae of relatively long duration. A 597 bp fragment of the mitochondrial DNA COI gene was amplified and screened for variation in a total of 297 individuals of S. paramamosain from six sampling sites across the species’ natural geographical distribution in the IWP and 36 unique haplotypes were identified. Haplotype diversities per site ranged from 0.516 to 0.879. Nucleotide diversity estimates among haplotypes were 0.11% – 0.48%. Maximum divergence observed among S. paramamosain samples was 1.533% and samples formed essentially a single monophyletic group as no obvious clades were related to geographical location of sites. A weak positive relationship was observed however, between genetic distance and geographical distance among sites. Microsatellite markers were then used to assess contemporary gene flow and population structure in Asian mud crab populations sampled across their natural distribution in the IWP. Eight microsatellite loci were screened in sampled S. paramamosain populations and all showed high allelic diversity at all loci in sampled populations. In total, 344 individuals were analysed, and 304 microsatellite alleles were found across the 8 loci. The mean number of alleles per locus at each site ranged from 20.75 to 28.25. Mean allelic richness per site varied from 17.2 to 18.9. All sites showed high levels of heterozygosity as average expected heterozygosities for all loci ranged from 0.917 – 0.953 while mean observed heterozygosity ranged from 0.916 – 0.959. Allele diversities were similar at all sites and across all loci. The results did not show any evidence for major differences in allele frequencies among sites and patterns of allele frequencies were very similar in all populations across all loci. Estimates of population differentiation (FST) were relatively low and most probably largely reflect intra – individual variation for very highly variable loci. Results from nDNA analysis showed evidence for only very limited population genetic structure among sampled S. paramamosain, and a positive and significant association for genetic and geographical distance among sample sites. Microsatellite markers were then employed to determine if adequate levels of genetic diversity has been captured in crab hatcheries for the breeding cycle. The results showed that all microsatellite loci were polymorphic in hatchery samples. Culture populations were in general, highly genetically depauperate, compared with comparable wild populations, with only 3 to 8 alleles recorded for the same loci set per population. In contrast, very high numbers of alleles per locus were found in reference wild S. paramamosain populations, which ranged from 18 to 46 alleles per locus per population. In general, this translates into a 3 to 10 fold decline in mean allelic richness per locus in all culture stocks compared with wild reference counterparts. Furthermore, most loci in all cultured S. paramamosain samples showed departures from HWE equilibrium. Allele frequencies were very different in culture samples from that present in comparable wild reference samples and this in particular, was reflected in a large decline in allele diversity per locus. The pattern observed was best explained by significant impacts of breeding practices employed in hatcheries rather than natural differentiation among wild populations used as the source of brood stock. Recognition of current problems and management strategies for the species both for the medium and long-term development of the new culture industry are discussed. The priority research to be undertaken over the medium term for S. paramamosain should be to close the life cycle fully to allow individuals to be bred on demand and their offspring equalised to control broodstock reproductive contributions. Establishing a broodstock register and pedigree mating system will be required before any selection program is implemented. This will ensure that sufficient genetic variation will be available to allow genetic gains to be sustainably achieved in a future stock improvement program. A fundamental starting point to improve hatchery practices will be to encourage farmers and hatchery managers to spawn more females in their hatcheries as it will increase background genetic diversity in culture stocks. Combining crablet cohorts from multiple hatcheries into a single cohort for supply to farmers or rotation of breeding females regularly in hatcheries will help to address immediate genetic diversity problems in culture stocks. Application of these results can provide benefits for managing wild and cultured Asian mud crab populations more efficiently. Over the long-term, application of data on genetic diversity in wild and cultured stocks of Asian mud crab will contribute to development of sustainable and productive culture industries in Vietnam and other countries in the IWP and can contribute towards conservation of wild genetic resources.

Application of acoustic emission technology in monitoring structure integrity of bridges

Bridges are an important part of a nation’s infrastructure and reliable monitoring methods are necessary to ensure their safety and efficiency. Most bridges in use today were built decades ago and are now subjected to changes in load patterns that can cause localized distress, which can result in bridge failure if not corrected. Early detection of damage helps in prolonging lives of bridges and preventing catastrophic failures. This paper briefly reviews the various technologies currently used in health monitoring of bridge structures and in particular discusses the application and challenges of acoustic emission (AE) technology. Some of the results from laboratory experiments on a bridge model are also presented. The main objectives of these experiments are source localisation and assessment. The findings of the study can be expected to enhance the knowledge of acoustic emission process and thereby aid in the development of an effective bridge structure diagnostics system.

Semantic oscillations : encoding context and structure in complex valued holographic vectors

In computational linguistics, information retrieval and applied cognition, words and concepts are often represented as vectors in high dimensional spaces computed from a corpus of text. These high dimensional spaces are often referred to as Semantic Spaces. We describe a novel and efficient approach to computing these semantic spaces via the use of complex valued vector representations. We report on the practical implementation of the proposed method and some associated experiments. We also briefly discuss how the proposed system relates to previous theoretical work in Information Retrieval and Quantum Mechanics and how the notions of probability, logic and geometry are integrated within a single Hilbert space representation. In this sense the proposed system has more general application and gives rise to a variety of opportunities for future research.

Influence of historical landscapes, drainage evolution and ecological traits on patterns of genetic diversity in Southeast Asian freshwater snakehead fishes

Snakehead fishes in the family Channidae are obligate freshwater fishes represented by two extant genera, the African Parachannna and the Asian Channa. These species prefer still or slow flowing water bodies, where they are top predators that exercise high levels of parental care, have the ability to breathe air, can tolerate poor water quality, and interestingly, can aestivate or traverse terrestrial habitat in response to seasonal changes in freshwater habitat availability. These attributes suggest that snakehead fishes may possess high dispersal potential, irrespective of the terrestrial barriers that would otherwise constrain the distribution of most freshwater fishes. A number of biogeographical hypotheses have been developed to account for the modern distributions of snakehead fishes across two continents, including ancient vicariance during Gondwanan break-up, or recent colonisation tracking the formation of suitable climatic conditions. Taxonomic uncertainty also surrounds some members of the Channa genus, as geographical distributions for some taxa across southern and Southeast (SE) Asia are very large, and in one case is highly disjunct. The current study adopted a molecular genetics approach to gain an understanding of the evolution of this group of fishes, and in particular how the phylogeography of two Asian species may have been influenced by contemporary versus historical levels of dispersal and vicariance. First, a molecular phylogeny was constructed based on multiple DNA loci and calibrated with fossil evidence to provide a dated chronology of divergence events among extant species, and also within species with widespread geographical distributions. The data provide strong evidence that trans-continental distribution of the Channidae arose as a result of dispersal out of Asia and into Africa in the mid–Eocene. Among Asian Channa, deep divergence among lineages indicates that the Oligocene-Miocene boundary was a time of significant species radiation, potentially associated with historical changes in climate and drainage geomorphology. Mid-Miocene divergence among lineages suggests that a taxonomic revision is warranted for two taxa. Deep intra-specific divergence (~8Mya) was also detected between C. striata lineages that occur sympatrically in the Mekong River Basin. The study then examined the phylogeography and population structure of two major taxa, Channa striata (the chevron snakehead) and the C. micropeltes (the giant snakehead), across SE Asia. Species specific microsatellite loci were developed and used in addition to a mitochondrial DNA marker (Cyt b) to screen neutral genetic variation within and among wild populations. C. striata individuals were sampled across SE Asia (n=988), with the major focus being the Mekong Basin, which is the largest drainage basin in the region. The distributions of two divergent lineages were identified and admixture analysis showed that where they co-occur they are interbreeding, indicating that after long periods of evolution in isolation, divergence has not resulted in reproductive isolation. One lineage is predominantly confined to upland areas of northern Lao PDR to the north of the Khorat Plateau, while the other, which is more closely related to individuals from southern India, has a widespread distribution across mainland SE Asian and Sumatra. The phylogeographical pattern recovered is associated with past river networks, and high diversity and divergence among all populations sampled reveal that contemporary dispersal is very low for this taxon, even where populations occur in contiguous freshwater habitats. C. micropeltes (n=280) were also sampled from across the Mekong River Basin, focusing on the lower basin where it constitutes an important wild fishery resource. In comparison with C. striata, allelic diversity and genetic divergence among populations were extremely low, suggesting very recent colonisation of the greater Mekong region. Populations were significantly structured into at least three discrete populations in the lower Mekong. Results of this study have implications for establishing effective conservation plans for managing both species, that represent economically important wild fishery resources for the region. For C. micropeltes, it is likely that a single fisheries stock in the Tonle Sap Great Lake is being exploited by multiple fisheries operations, and future management initiatives for this species in this region will need to account for this. For C. striata, conservation of natural levels of genetic variation will require management initiatives designed to promote population persistence at very localised spatial scales, as the high level of population structuring uncovered for this species indicates that significant unique diversity is present at this fine spatial scale.