Application of bag sampling technique for particle size distribution measurements

Bag sampling techniques can be used to temporarily store an aerosol and therefore provide sufficient time to utilize sensitive but slow instrumental techniques for recording detailed particle size distributions. Laboratory based assessment of the method were conducted to examine size dependant deposition loss coefficients for aerosols held in VelostatTM bags conforming to a horizontal cylindrical geometry. Deposition losses of NaCl particles in the range of 10 nm to 160 nm were analysed in relation to the bag size, storage time, and sampling flow rate. Results of this study suggest that the bag sampling method is most useful for moderately short sampling periods of about 5 minutes.

Addressing issues in sparseness, ecological bias and formulation of the adjacency matrix in Bayesian spatio-temporal analysis of disease counts

The main objective of this PhD was to further develop Bayesian spatio-temporal models (specifically the Conditional Autoregressive (CAR) class of models), for the analysis of sparse disease outcomes such as birth defects. The motivation for the thesis arose from problems encountered when analyzing a large birth defect registry in New South Wales. The specific components and related research objectives of the thesis were developed from gaps in the literature on current formulations of the CAR model, and health service planning requirements. Data from a large probabilistically-linked database from 1990 to 2004, consisting of fields from two separate registries: the Birth Defect Registry (BDR) and Midwives Data Collection (MDC) were used in the analyses in this thesis. The main objective was split into smaller goals. The first goal was to determine how the specification of the neighbourhood weight matrix will affect the smoothing properties of the CAR model, and this is the focus of chapter 6. Secondly, I hoped to evaluate the usefulness of incorporating a zero-inflated Poisson (ZIP) component as well as a shared-component model in terms of modeling a sparse outcome, and this is carried out in chapter 7. The third goal was to identify optimal sampling and sample size schemes designed to select individual level data for a hybrid ecological spatial model, and this is done in chapter 8. Finally, I wanted to put together the earlier improvements to the CAR model, and along with demographic projections, provide forecasts for birth defects at the SLA level. Chapter 9 describes how this is done. For the first objective, I examined a series of neighbourhood weight matrices, and showed how smoothing the relative risk estimates according to similarity by an important covariate (i.e. maternal age) helped improve the model’s ability to recover the underlying risk, as compared to the traditional adjacency (specifically the Queen) method of applying weights. Next, to address the sparseness and excess zeros commonly encountered in the analysis of rare outcomes such as birth defects, I compared a few models, including an extension of the usual Poisson model to encompass excess zeros in the data. This was achieved via a mixture model, which also encompassed the shared component model to improve on the estimation of sparse counts through borrowing strength across a shared component (e.g. latent risk factor/s) with the referent outcome (caesarean section was used in this example). Using the Deviance Information Criteria (DIC), I showed how the proposed model performed better than the usual models, but only when both outcomes shared a strong spatial correlation. The next objective involved identifying the optimal sampling and sample size strategy for incorporating individual-level data with areal covariates in a hybrid study design. I performed extensive simulation studies, evaluating thirteen different sampling schemes along with variations in sample size. This was done in the context of an ecological regression model that incorporated spatial correlation in the outcomes, as well as accommodating both individual and areal measures of covariates. Using the Average Mean Squared Error (AMSE), I showed how a simple random sample of 20% of the SLAs, followed by selecting all cases in the SLAs chosen, along with an equal number of controls, provided the lowest AMSE. The final objective involved combining the improved spatio-temporal CAR model with population (i.e. women) forecasts, to provide 30-year annual estimates of birth defects at the Statistical Local Area (SLA) level in New South Wales, Australia. The projections were illustrated using sixteen different SLAs, representing the various areal measures of socio-economic status and remoteness. A sensitivity analysis of the assumptions used in the projection was also undertaken. By the end of the thesis, I will show how challenges in the spatial analysis of rare diseases such as birth defects can be addressed, by specifically formulating the neighbourhood weight matrix to smooth according to a key covariate (i.e. maternal age), incorporating a ZIP component to model excess zeros in outcomes and borrowing strength from a referent outcome (i.e. caesarean counts). An efficient strategy to sample individual-level data and sample size considerations for rare disease will also be presented. Finally, projections in birth defect categories at the SLA level will be made.

Electronic telephone directory listings : preferred sampling frame for a population-based study of childhood cancer in Australia

PURPOSE: We report our telephone-based system for selecting community control series appropriate for a complete Australia-wide series of Ewing's sarcoma cases. METHODS: We used electronic directory random sampling to select age-matched controls. The sampling has all listed telephone numbers on an up-dated CD-Rom. RESULTS: 95% of 2245 telephone numbers selected were successfully contacted. The mean number of attempts needed was 1.94, 58% answering at the first attempt. On average, we needed 4.5 contacts per control selected. Calls were more likely to be successful (reach a respondent) when made in the evening (except Saturdays). The overall response rate among contacted telephone numbers was 92.8%. Participation rates among female and male respondents were practically the same. The exclusion of unlisted numbers (13.5% of connected households) and unconnected households (3.7%) led to potential selection bias. However, restricting the case series to listed cases only, plus having external information on the direction of potential bias allow meaningful interpretation of our data. CONCLUSION: Sampling from an electronic directory is convenient, economical and simple, and gives a very good yield of eligible subjects compared to other methods.

Optimal mission path planning (MPP) for an air sampling unmanned aerial system

This paper presents advanced optimization techniques for Mission Path Planning (MPP) of a UAS fitted with a spore trap to detect and monitor spores and plant pathogens. The UAV MPP aims to optimise the mission path planning search and monitoring of spores and plant pathogens that may allow the agricultural sector to be more competitive and more reliable. The UAV will be fitted with an air sampling or spore trap to detect and monitor spores and plant pathogens in remote areas not accessible to current stationary monitor methods. The optimal paths are computed using a Multi-Objective Evolutionary Algorithms (MOEAs). Two types of multi-objective optimisers are compared; the MOEA Non-dominated Sorting Genetic Algorithms II (NSGA-II) and Hybrid Game are implemented to produce a set of optimal collision-free trajectories in three-dimensional environment. The trajectories on a three-dimension terrain, which are generated off-line, are collision-free and are represented by using Bézier spline curves from start position to target and then target to start position or different position with altitude constraints. The efficiency of the two optimization methods is compared in terms of computational cost and design quality. Numerical results show the benefits of coupling a Hybrid-Game strategy to a MOEA for MPP tasks. The reduction of numerical cost is an important point as the faster the algorithm converges the better the algorithms is for an off-line design and for future on-line decisions of the UAV.

Bayesian hybrid algorithms and models : implementation and associated issues

This thesis addresses computational challenges arising from Bayesian analysis of complex real-world problems. Many of the models and algorithms designed for such analysis are ‘hybrid’ in nature, in that they are a composition of components for which their individual properties may be easily described but the performance of the model or algorithm as a whole is less well understood. The aim of this research project is to after a better understanding of the performance of hybrid models and algorithms. The goal of this thesis is to analyse the computational aspects of hybrid models and hybrid algorithms in the Bayesian context. The first objective of the research focuses on computational aspects of hybrid models, notably a continuous finite mixture of t-distributions. In the mixture model, an inference of interest is the number of components, as this may relate to both the quality of model fit to data and the computational workload. The analysis of t-mixtures using Markov chain Monte Carlo (MCMC) is described and the model is compared to the Normal case based on the goodness of fit. Through simulation studies, it is demonstrated that the t-mixture model can be more flexible and more parsimonious in terms of number of components, particularly for skewed and heavytailed data. The study also reveals important computational issues associated with the use of t-mixtures, which have not been adequately considered in the literature. The second objective of the research focuses on computational aspects of hybrid algorithms for Bayesian analysis. Two approaches will be considered: a formal comparison of the performance of a range of hybrid algorithms and a theoretical investigation of the performance of one of these algorithms in high dimensions. For the first approach, the delayed rejection algorithm, the pinball sampler, the Metropolis adjusted Langevin algorithm, and the hybrid version of the population Monte Carlo (PMC) algorithm are selected as a set of examples of hybrid algorithms. Statistical literature shows how statistical efficiency is often the only criteria for an efficient algorithm. In this thesis the algorithms are also considered and compared from a more practical perspective. This extends to the study of how individual algorithms contribute to the overall efficiency of hybrid algorithms, and highlights weaknesses that may be introduced by the combination process of these components in a single algorithm. The second approach to considering computational aspects of hybrid algorithms involves an investigation of the performance of the PMC in high dimensions. It is well known that as a model becomes more complex, computation may become increasingly difficult in real time. In particular the importance sampling based algorithms, including the PMC, are known to be unstable in high dimensions. This thesis examines the PMC algorithm in a simplified setting, a single step of the general sampling, and explores a fundamental problem that occurs in applying importance sampling to a high-dimensional problem. The precision of the computed estimate from the simplified setting is measured by the asymptotic variance of the estimate under conditions on the importance function. Additionally, the exponential growth of the asymptotic variance with the dimension is demonstrated and we illustrates that the optimal covariance matrix for the importance function can be estimated in a special case.

Incorporating uncertainty in environmental models informed by imagery

In this thesis, the issue of incorporating uncertainty for environmental modelling informed by imagery is explored by considering uncertainty in deterministic modelling, measurement uncertainty and uncertainty in image composition. Incorporating uncertainty in deterministic modelling is extended for use with imagery using the Bayesian melding approach. In the application presented, slope steepness is shown to be the main contributor to total uncertainty in the Revised Universal Soil Loss Equation. A spatial sampling procedure is also proposed to assist in implementing Bayesian melding given the increased data size with models informed by imagery. Measurement error models are another approach to incorporating uncertainty when data is informed by imagery. These models for measurement uncertainty, considered in a Bayesian conditional independence framework, are applied to ecological data generated from imagery. The models are shown to be appropriate and useful in certain situations. Measurement uncertainty is also considered in the context of change detection when two images are not co-registered. An approach for detecting change in two successive images is proposed that is not affected by registration. The procedure uses the Kolmogorov-Smirnov test on homogeneous segments of an image to detect change, with the homogeneous segments determined using a Bayesian mixture model of pixel values. Using the mixture model to segment an image also allows for uncertainty in the composition of an image. This thesis concludes by comparing several different Bayesian image segmentation approaches that allow for uncertainty regarding the allocation of pixels to different ground components. Each segmentation approach is applied to a data set of chlorophyll values and shown to have different benefits and drawbacks depending on the aims of the analysis.

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.

Development and validation of a novel approach to work sampling : a study of nurse practitioner work patterns

Objectives: This methodological paper reports on the development and validation of a work sampling instrument and data collection processes to conduct a national study of nurse practitioners’ work patterns. ---------- Design: Published work sampling instruments provided the basis for development and validation of a tool for use in a national study of nurse practitioner work activities across diverse contextual and clinical service models. Steps taken in the approach included design of a nurse practitioner-specific data collection tool and development of an innovative web-based program to train and establish inter rater reliability of a team of data collectors who were geographically dispersed across metropolitan, rural and remote health care settings. ---------- Setting: The study is part of a large funded study into nurse practitioner service. The Australian Nurse Practitioner Study is a national study phased over three years and was designed to provide essential information for Australian health service planners, regulators and consumer groups on the profile, process and outcome of nurse practitioner service. ---------- Results: The outcome if this phase of the study is empirically tested instruments, process and training materials for use in an international context by investigators interested in conducting a national study of nurse practitioner work practices. ---------- Conclusion: Development and preparation of a new approach to describing nurse practitioner practices using work sampling methods provides the groundwork for international collaboration in evaluation of nurse practitioner service.

The work of nurse practitioners : a national work sampling study

Aim: This paper is a report of a study of variations in the pattern of nurse practitioner work in a range of service fields and geographical locations, across direct patient care, indirect patient care and service-related activities. Background. The nurse practitioner role has been implemented internationally as a service reform model to improve the access and timeliness of health care. There is a substantial body of research into the nurse practitioner role and service outcomes, but scant information on the pattern of nurse practitioner work and how this is influenced by different service models. --------- Methods: We used work sampling methods. Data were collected between July 2008 and January 2009. Observations were recorded from a random sample of 30 nurse practitioners at 10-minute intervals in 2-hour blocks randomly generated to cover two weeks of work time from a sampling frame of six weeks. --------- Results: A total of 12,189 individual observations were conducted with nurse practitioners across Australia. Thirty individual activities were identified as describing nurse practitioner work, and these were distributed across three categories. Direct care accounted for 36.1% of how nurse practitioners spend their time, indirect care accounted for 32.2% and service-related activities made up 31.9%. --------- Conclusion. These findings provide useful baseline data for evaluation of nurse practitioner positions and the service effect of these positions. However, the study also raises questions about the best use of nurse practitioner time and the influences of barriers to and facilitators of this model of service innovation.

On the nature of over-dispersion in motor vehicle crash prediction models

Statistical modeling of traffic crashes has been of interest to researchers for decades. Over the most recent decade many crash models have accounted for extra-variation in crash counts—variation over and above that accounted for by the Poisson density. The extra-variation – or dispersion – is theorized to capture unaccounted for variation in crashes across sites. The majority of studies have assumed fixed dispersion parameters in over-dispersed crash models—tantamount to assuming that unaccounted for variation is proportional to the expected crash count. Miaou and Lord [Miaou, S.P., Lord, D., 2003. Modeling traffic crash-flow relationships for intersections: dispersion parameter, functional form, and Bayes versus empirical Bayes methods. Transport. Res. Rec. 1840, 31–40] challenged the fixed dispersion parameter assumption, and examined various dispersion parameter relationships when modeling urban signalized intersection accidents in Toronto. They suggested that further work is needed to determine the appropriateness of the findings for rural as well as other intersection types, to corroborate their findings, and to explore alternative dispersion functions. This study builds upon the work of Miaou and Lord, with exploration of additional dispersion functions, the use of an independent data set, and presents an opportunity to corroborate their findings. Data from Georgia are used in this study. A Bayesian modeling approach with non-informative priors is adopted, using sampling-based estimation via Markov Chain Monte Carlo (MCMC) and the Gibbs sampler. A total of eight model specifications were developed; four of them employed traffic flows as explanatory factors in mean structure while the remainder of them included geometric factors in addition to major and minor road traffic flows. The models were compared and contrasted using the significance of coefficients, standard deviance, chi-square goodness-of-fit, and deviance information criteria (DIC) statistics. The findings indicate that the modeling of the dispersion parameter, which essentially explains the extra-variance structure, depends greatly on how the mean structure is modeled. In the presence of a well-defined mean function, the extra-variance structure generally becomes insignificant, i.e. the variance structure is a simple function of the mean. It appears that extra-variation is a function of covariates when the mean structure (expected crash count) is poorly specified and suffers from omitted variables. In contrast, when sufficient explanatory variables are used to model the mean (expected crash count), extra-Poisson variation is not significantly related to these variables. If these results are generalizable, they suggest that model specification may be improved by testing extra-variation functions for significance. They also suggest that known influences of expected crash counts are likely to be different than factors that might help to explain unaccounted for variation in crashes across sites

Incorporating parameter uncertainty into quantitative microbial risk assessment (QMRA)

Modern statistical models and computational methods can now incorporate uncertainty of the parameters used in Quantitative Microbial Risk Assessments (QMRA). Many QMRAs use Monte Carlo methods, but work from fixed estimates for means, variances and other parameters. We illustrate the ease of estimating all parameters contemporaneously with the risk assessment, incorporating all the parameter uncertainty arising from the experiments from which these parameters are estimated. A Bayesian approach is adopted, using Markov Chain Monte Carlo Gibbs sampling (MCMC) via the freely available software, WinBUGS. The method and its ease of implementation are illustrated by a case study that involves incorporating three disparate datasets into an MCMC framework. The probabilities of infection when the uncertainty associated with parameter estimation is incorporated into a QMRA are shown to be considerably more variable over various dose ranges than the analogous probabilities obtained when constants from the literature are simply ‘plugged’ in as is done in most QMRAs. Neglecting these sources of uncertainty may lead to erroneous decisions for public health and risk management.

Persistent ocean monitoring with underwater gliders : adapting sampling resolution

Ocean processes are dynamic, complex, and occur on multiple spatial and temporal scales. To obtain a synoptic view of such processes, ocean scientists collect data over long time periods. Historically, measurements were continually provided by fixed sensors, e.g., moorings, or gathered from ships. Recently, an increase in the utilization of autonomous underwater vehicles has enabled a more dynamic data acquisition approach. However, we still do not utilize the full capabilities of these vehicles. Here we present algorithms that produce persistent monitoring missions for underwater vehicles by balancing path following accuracy and sampling resolution for a given region of interest, which addresses a pressing need among ocean scientists to efficiently and effectively collect high-value data. More specifically, this paper proposes a path planning algorithm and a speed control algorithm for underwater gliders, which together give informative trajectories for the glider to persistently monitor a patch of ocean. We optimize a cost function that blends two competing factors: maximize the information value along the path, while minimizing deviation from the planned path due to ocean currents. Speed is controlled along the planned path by adjusting the pitch angle of the underwater glider, so that higher resolution samples are collected in areas of higher information value. The resulting paths are closed circuits that can be repeatedly traversed to collect long-term ocean data in dynamic environments. The algorithms were tested during sea trials on an underwater glider operating off the coast of southern California, as well as in Monterey Bay, California. The experimental results show significant improvements in data resolution and path reliability compared to previously executed sampling paths used in the respective regions.

Spatially stratified sampling using auxiliary information for geostatistical mapping

This paper presents a method of spatial sampling based on stratification by Local Moran’s I i calculated using auxiliary information. The sampling technique is compared to other design-based approaches including simple random sampling, systematic sampling on a regular grid, conditional Latin Hypercube sampling and stratified sampling based on auxiliary information, and is illustrated using two different spatial data sets. Each of the samples for the two data sets is interpolated using regression kriging to form a geostatistical map for their respective areas. The proposed technique is shown to be competitive in reproducing specific areas of interest with high accuracy.