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.

Swept frequency biompedance analysis for the determination of body water compartments

Bioelectrical impedance analysis, (BIA), is a method of body composition analysis first investigated in 1962 which has recently received much attention by a number of research groups. The reasons for this recent interest are its advantages, (viz: inexpensive, non-invasive and portable) and also the increasing interest in the diagnostic value of body composition analysis. The concept utilised by BIA to predict body water volumes is the proportional relationship for a simple cylindrical conductor, (volume oc length2/resistance), which allows the volume to be predicted from the measured resistance and length. Most of the research to date has measured the body's resistance to the passage of a 50· kHz AC current to predict total body water, (TBW). Several research groups have investigated the application of AC currents at lower frequencies, (eg 5 kHz), to predict extracellular water, (ECW). However all research to date using BIA to predict body water volumes has used the impedance measured at a discrete frequency or frequencies. This thesis investigates the variation of impedance and phase of biological systems over a range of frequencies and describes the development of a swept frequency bioimpedance meter which measures impedance and phase at 496 frequencies ranging from 4 kHz to 1 MHz. The impedance of any biological system varies with the frequency of the applied current. The graph of reactance vs resistance yields a circular arc with the resistance decreasing with increasing frequency and reactance increasing from zero to a maximum then decreasing to zero. Computer programs were written to analyse the measured impedance spectrum and determine the impedance, Zc, at the characteristic frequency, (the frequency at which the reactance is a maximum). The fitted locus of the measured data was extrapolated to determine the resistance, Ro, at zero frequency; a value that cannot be measured directly using surface electrodes. The explanation of the theoretical basis for selecting these impedance values (Zc and Ro), to predict TBW and ECW is presented. Studies were conducted on a group of normal healthy animals, (n=42), in which TBW and ECW were determined by the gold standard of isotope dilution. The prediction quotients L2/Zc and L2/Ro, (L=length), yielded standard errors of 4.2% and 3.2% respectively, and were found to be significantly better than previously reported, empirically determined prediction quotients derived from measurements at a single frequency. The prediction equations established in this group of normal healthy animals were applied to a group of animals with abnormally low fluid levels, (n=20), and also to a group with an abnormal balance of extra-cellular to intracellular fluids, (n=20). In both cases the equations using L2/Zc and L2/Ro accurately and precisely predicted TBW and ECW. This demonstrated that the technique developed using multiple frequency bioelectrical impedance analysis, (MFBIA), can accurately predict both TBW and ECW in both normal and abnormal animals, (with standard errors of the estimate of 6% and 3% for TBW and ECW respectively). Isotope dilution techniques were used to determine TBW and ECW in a group of 60 healthy human subjects, (male. and female, aged between 18 and 45). Whole body impedance measurements were recorded on each subject using the MFBIA technique and the correlations between body water volumes, (TBW and ECW), and heighe/impedance, (for all measured frequencies), were compared. The prediction quotients H2/Zc and H2/Ro, (H=height), again yielded the highest correlation with TBW and ECW respectively with corresponding standard errors of 5.2% and 10%. The values of the correlation coefficients obtained in this study were very similar to those recently reported by others. It was also observed that in healthy human subjects the impedance measured at virtually any frequency yielded correlations not significantly different from those obtained from the MFBIA quotients. This phenomenon has been reported by other research groups and emphasises the need to validate the technique by investigating its application in one or more groups with abnormalities in fluid levels. The clinical application of MFBIA was trialled and its capability of detecting lymphoedema, (an excess of extracellular fluid), was investigated. The MFBIA technique was demonstrated to be significantly more sensitive, (P<.05), in detecting lymphoedema than the current technique of circumferential measurements. MFBIA was also shown to provide valuable information describing the changes in the quantity of muscle mass of the patient during the course of the treatment. The determination of body composition, (viz TBW and ECW), by MFBIA has been shown to be a significant improvement on previous bioelectrical impedance techniques. The merit of the MFBIA technique is evidenced in its accurate, precise and valid application in animal groups with a wide variation in body fluid volumes and balances. The multiple frequency bioelectrical impedance analysis technique developed in this study provides accurate and precise estimates of body composition, (viz TBW and ECW), regardless of the individual's state of health.

Obstacle-free range determination for rail track maintenance vehicles

Maintenance trains travel in convoy. In Australia, only the first train of the convoy pays attention to the track sig- nalization (the other convoy vehicles simply follow the preceding vehicle). Because of human errors, collisions can happen between the maintenance vehicles. Although an anti-collision system based on a laser distance meter is already in operation, the existing system has a limited range due to the curvature of the tracks. In this paper, we introduce an anti-collision system based on vision. The two main ideas are, (1) to warp the camera image into an image where the rails are parallel through a projective transform, and (2) to track the two rail curves simultaneously by evaluating small parallel segments. The performance of the system is demonstrated on an image dataset.

Web searching and Σ2 queries

In the terminology of Logic programming, current search engines answer Sigma1 queries (formulas of the form where is a boolean combination of attributes). Such a query is determined by a particular sequence of keywords input by a user. In order to give more control to users, search engines will have to tackle more expressive queries, namely, Sigma2 queries (formulas of the form ). The purpose of the talk is to examine which directions could be explored in order to move towards more expressive languages, more powerful search engines, and the benefits that users should expect.

A GIS framework for streamlining the Nature Refuge Gazettal process

Nature Refuges encompass the second largest extent of protected area estate in Queensland. Major problems exist in the data capture, map presentation, data quality and integrity of these boundaries. The spatial accuracies/inaccuracies of the Nature Refuge administrative boundaries directly influence the ability to preserve valuable ecosystems by challenging negative environmental impacts on these properties. This research work is about supporting the Nature Refuge Programs efforts to secure Queensland’s natural and cultural values on private land by utilising GIS and its advanced functionalities. The research design organizes and enters Queensland’s Nature Refuge boundaries into a spatial environment. Survey quality data collection techniques such as the Global Positioning Systems (GPS) are investigated to capture Nature Refuge boundary information. Using the concepts of map communication GIS Cartography is utilised for the protected area plan design. New spatial datasets are generated facilitating the effectiveness of investigative data analysis. The geodatabase model developed by this study adds rich GIS behaviour providing the capability to store, query, and manipulate geographic information. It provides the ability to leverage data relationships and enforces topological integrity creating savings in customization and productivity. The final phase of the research design incorporates the advanced functions of ArcGIS. These functions facilitate building spatial system models. The geodatabase and process models developed by this research can be easily modified and the data relating to mining can be replaced by other negative environmental impacts affecting the Nature Refuges. Results of the research are presented as graphs and maps providing visual evidence supporting the usefulness of GIS as means for capturing, visualising and enhancing spatial quality and integrity of Nature Refuge boundaries.

Real-time performance modelling of a sustained attention to response task

Vigilance declines when exposed to highly predictable and uneventful tasks. Monotonous tasks provide little cognitive and motor stimulation and contribute to human errors. This paper aims to model and detect vigilance decline in real time through participant’s reaction times during a monotonous task. A lab-based experiment adapting the Sustained Attention to Response Task (SART) is conducted to quantify the effect of monotony on overall performance. Then relevant parameters are used to build a model detecting hypovigilance throughout the experiment. The accuracy of different mathematical models are compared to detect in real-time – minute by minute - the lapses in vigilance during the task. We show that monotonous tasks can lead to an average decline in performance of 45%. Furthermore, vigilance modelling enables to detect vigilance decline through reaction times with an accuracy of 72% and a 29% false alarm rate. Bayesian models are identified as a better model to detect lapses in vigilance as compared to Neural Networks and Generalised Linear Mixed Models. This modelling could be used as a framework to detect vigilance decline of any human performing monotonous tasks.

Expert elicitation and its interface with technology : a review with a view to designing Elicitator

Expert knowledge is valuable in many modelling endeavours, particularly where data is not extensive or sufficiently robust. In Bayesian statistics, expert opinion may be formulated as informative priors, to provide an honest reflection of the current state of knowledge, before updating this with new information. Technology is increasingly being exploited to help support the process of eliciting such information. This paper reviews the benefits that have been gained from utilizing technology in this way. These benefits can be structured within a six-step elicitation design framework proposed recently (Low Choy et al., 2009). We assume that the purpose of elicitation is to formulate a Bayesian statistical prior, either to provide a standalone expert-defined model, or for updating new data within a Bayesian analysis. We also assume that the model has been pre-specified before selecting the software. In this case, technology has the most to offer to: targeting what experts know (E2), eliciting and encoding expert opinions (E4), whilst enhancing accuracy (E5), and providing an effective and efficient protocol (E6). Benefits include: -providing an environment with familiar nuances (to make the expert comfortable) where experts can explore their knowledge from various perspectives (E2); -automating tedious or repetitive tasks, thereby minimizing calculation errors, as well as encouraging interaction between elicitors and experts (E5); -cognitive gains by educating users, enabling instant feedback (E2, E4-E5), and providing alternative methods of communicating assessments and feedback information, since experts think and learn differently; and -ensuring a repeatable and transparent protocol is used (E6).

Who's at risk: Answerability and the critical possibilities of classroom discourse

Our aim in this article is twofold. First, we challenge the essentialized notion of adolescents and young people as perpetually driven to resist the authority of adults. At the same time, we disrupt linguistic conceptions of adolescent discourse, along with the discourse of youth at risk, by analyzing a transcript of classroom discourse that reflects an exchange between a highly regarded and well liked preservice teacher and his students. This representative transcript highlights the preservice teacher's ability to query, without a concomitant ability to listen, respond, and build a classroom dialogue with his students; what we call here a Socratic monologue. Second, we link the notions of dialogue and responsiveness to Bakhtin's concept of answerability, emphasizing the joint construction of classroom discourse as an ethically answerable relation between teacher and students.

A secure framework and related protocols for ubiquitous access to electronic health records using Java sim cards

Ubiquitous access to patient medical records is an important aspect of caring for patient safety. Unavailability of sufficient medical information at the point-ofcare could possibly lead to a fatality. The U.S. Institute of Medicine has reported that between 44,000 and 98,000 people die each year due to medical errors, such as incorrect medication dosages, due to poor legibility in manual records, or delays in consolidating needed information to discern the proper intervention. In this research we propose employing emergent technologies such as Java SIM Cards (JSC), Smart Phones (SP), Next Generation Networks (NGN), Near Field Communications (NFC), Public Key Infrastructure (PKI), and Biometric Identification to develop a secure framework and related protocols for ubiquitous access to Electronic Health Records (EHR). A partial EHR contained within a JSC can be used at the point-of-care in order to help quick diagnosis of a patient’s problems. The full EHR can be accessed from an Electronic Health Records Centre (EHRC) when time and network availability permit. Moreover, this framework and related protocols enable patients to give their explicit consent to a doctor to access their personal medical data, by using their Smart Phone, when the doctor needs to see or update the patient’s medical information during an examination. Also our proposed solution would give the power to patients to modify the Access Control List (ACL) related to their EHRs and view their EHRs through their Smart Phone. Currently, very limited research has been done on using JSCs and similar technologies as a portable repository of EHRs or on the specific security issues that are likely to arise when JSCs are used with ubiquitous access to EHRs. Previous research is concerned with using Medicare cards, a kind of Smart Card, as a repository of medical information at the patient point-of-care. However, this imposes some limitations on the patient’s emergency medical care, including the inability to detect the patient’s location, to call and send information to an emergency room automatically, and to interact with the patient in order to get consent. The aim of our framework and related protocols is to overcome these limitations by taking advantage of the SIM card and the technologies mentioned above. Briefly, our framework and related protocols will offer the full benefits of accessing an up-to-date, precise, and comprehensive medical history of a patient, whilst its mobility will provide ubiquitous access to medical and patient information everywhere it is needed. The objective of our framework and related protocols is to automate interactions between patients, healthcare providers and insurance organisations, increase patient safety, improve quality of care, and reduce the costs.

RatSLAM : a hippocampal model for simultaneous localization and mapping

The work presents a new approach to the problem of simultaneous localization and mapping - SLAM - inspired by computational models of the hippocampus of rodents. The rodent hippocampus has been extensively studied with respect to navigation tasks, and displays many of the properties of a desirable SLAM solution. RatSLAM is an implementation of a hippocampal model that can perform SLAM in real time on a real robot. It uses a competitive attractor network to integrate odometric information with landmark sensing to form a consistent representation of the environment. Experimental results show that RatSLAM can operate with ambiguous landmark information and recover from both minor and major path integration errors.

Conducting statistical tests of hypotheses : five common misconceptions found in transportation research

Most statistical methods use hypothesis testing. Analysis of variance, regression, discrete choice models, contingency tables, and other analysis methods commonly used in transportation research share hypothesis testing as the means of making inferences about the population of interest. Despite the fact that hypothesis testing has been a cornerstone of empirical research for many years, various aspects of hypothesis tests commonly are incorrectly applied, misinterpreted, and ignored—by novices and expert researchers alike. On initial glance, hypothesis testing appears straightforward: develop the null and alternative hypotheses, compute the test statistic to compare to a standard distribution, estimate the probability of rejecting the null hypothesis, and then make claims about the importance of the finding. This is an oversimplification of the process of hypothesis testing. Hypothesis testing as applied in empirical research is examined here. The reader is assumed to have a basic knowledge of the role of hypothesis testing in various statistical methods. Through the use of an example, the mechanics of hypothesis testing is first reviewed. Then, five precautions surrounding the use and interpretation of hypothesis tests are developed; examples of each are provided to demonstrate how errors are made, and solutions are identified so similar errors can be avoided. Remedies are provided for common errors, and conclusions are drawn on how to use the results of this paper to improve the conduct of empirical research in transportation.

Quantifying N2O and CO2 emissions from subtropical pasture

Greenhouse gas emissions from a well established, unfertilized tropical grass-legume pasture were monitored over two consecutive years using high resolution automatic sampling. Nitrous oxide emissions were highest during the summer months and were highly episodic, related more to the size and distribution of rain events than WFPS alone. Mean annual emissions were significantly higher during 2008 (5.7 ± 1.0 g N2O-N/ha/day) than 2007 (3.9 ± 0.4 and g N2O-N/ha/day) despite receiving nearly 500 mm less rain. Mean CO2 (28.2 ± 1.5 kg CO2 C/ha/day) was not significantly different (P < 0.01) between measurement years, emissions being highly dependent on temperature. A negative correlation between CO2 and WFPS at >70% indicated a threshold for soil conditions favouring denitrification. The use of automatic chambers for high resolution greenhouse gas sampling can greatly reduce emission estimation errors associated with temperature and WFPS changes.

Systematic variations in polymer gel dosimeter calibration due to container influence and deviations from water equivalence

There are a number of gel dosimeter calibration methods in contemporary usage. The present study is a detailed Monte Carlo investigation into the accuracy of several calibration techniques. Results show that for most arrangements the dose to gel accurately reflects the dose to water, with the most accurate method involving the use of a large diameter flask of gel into which multiple small fields of varying dose are directed. The least accurate method was found to be that of a long test tube in a water phantom, coaxial with the beam. The large flask method is also the most straightforward and least likely to introduce errors during setup, though, to its detriment, the volume of gel required is much more than other methods.