New Insights into History Matching via Sequential Monte Carlo

The aim of the history matching method is to locate non-implausible regions of the parameter space of complex deterministic or stochastic models by matching model outputs with data. It does this via a series of waves where at each wave an emulator is fitted to a small number of training samples. An implausibility measure is defined which takes into account the closeness of simulated and observed outputs as well as emulator uncertainty. As the waves progress, the emulator becomes more accurate so that training samples are more concentrated on promising regions of the space and poorer parts of the space are rejected with more confidence. Whilst history matching has proved to be useful, existing implementations are not fully automated and some ad-hoc choices are made during the process, which involves user intervention and is time consuming. This occurs especially when the non-implausible region becomes small and it is difficult to sample this space uniformly to generate new training points. In this article we develop a sequential Monte Carlo (SMC) algorithm for implementation which is semi-automated. Our novel SMC approach reveals that the history matching method yields a non-implausible distribution that can be multi-modal, highly irregular and very difficult to sample uniformly. Our SMC approach offers a much more reliable sampling of the non-implausible space, which requires additional computation compared to other approaches used in the literature

Geostatistical based optimization of groundwater monitoring well network design

Monitoring groundwater quality in economically important and other aquifers is carried out regularly as part of regulatory processes for water and other resource development. Many water quality parameters are measured as part of baseline monitoring around mining and onshore gas resource development regions to develop improved understanding of the hydrogeological system as well as to inform managerial decisions to assess and manage contamination risks and health hazards. Water quality distribution in an aquifer is most often inferred from point measurements from limited number of bores drilled at arbitrary locations. Estimating the distribution of water quality parameters in the aquifer based on these point measurements is often a challenging task and results in high uncertainty in the estimates due to limited data availability. Minimizing uncertainty can be achieved by drilling more bores to collect water quality data and several approaches are available to identify optimal bore hole locations to minimize estimation uncertainty. However, optimization of borehole locations is difficult when multiple water quality parameters are of interest and have different spatial distributions in the aquifer. In this study we use geostatistical kriging to interpolate a large number of groundwater quality parameters. Then we integrate these predicted values and use the Differential Evolution algorithm to determine optimal locations for bores that would simultaneously reduce spatial prediction uncertainty of all parameters. The method is applied for designing a groundwater monitoring network in the Namoi region of Australia for monitoring groundwater quality in an economically important aquifer of the Great Artesian Basin. Optimal locations for 10 new monitoring bores are identified using this approach

A semiautomatic method for history matching using sequential Monte Carlo

The aim of the history matching method is to locate nonimplausible regions of the parameter space of complex deterministic or stochastic models by matching model outputs with data. It does this via a series of waves where at each wave an emulator is fitted to a small number of training samples. An implausibility measure is defined which takes into account the closeness of simulated and observed outputs as well as emulator uncertainty. As the waves progress, the emulator becomes more accurate so that training samples are more concentrated on promising regions of the space and poorer parts of the space are rejected with more confidence. While history matching has proved to be useful, existing implementations are not fully automated, and some ad hoc choices are made during the process, which involves user intervention and is time consuming. This occurs especially when the nonimplausible region becomes small and it is difficult to sample this space uniformly to generate new training points. In this article we develop a sequential Monte Carlo (SMC) algorithm for implementing history matching that is semiautomated. Our novel SMC approach reveals that the history matching method yields a nonimplausible region that can be multimodal, highly irregular, and very difficult to sample uniformly. Our SMC approach offers a much more reliable sampling of the nonimplausible space, which requires additional computation compared to other approaches used in the literature.</p

Urban landscape features influence the movement and distribution of the Australian container-inhabiting mosquito vectors Aedes aegypti (Diptera: Culicidae) and Aedes notoscriptus (Diptera: Culicidae)

Urban landscape features play an important role in the distribution and population spread of mosquito vectors. Furthermore, current insecticide and novel rear-and-release strategies for urban mosquito management rarely consider the spatial structure of the landscape when applying control practices. Here, we undertake a mark-recapture experiment to examine how urban features influence the movement and distribution of Australian container-inhabiting Aedes vectors. We pay attention to the role of semipermanent water storage containers, called rainwater tanks, and the influence of movement barriers, such as roads, on the spread and distribution of vector populations. Results suggest that Aedes aegypti (Linnaeus) (Diptera: Culicidae) were more likely to be captured around rainwater tanks, and that released males travel throughout residential blocks but do not cross roads. Conversely, female Aedes notoscriptus (Skuse) (Diptera: Culicidae) movement was uninhibited by roads and rainwater tanks did not influence female distribution or oviposition behavior. Using an isotropic Gaussian kernel framework, we show that vector movement is likely to be greater when applying a temporal effect, than when estimated by traditional methods. We conclude that a greater understanding on the role of urban features on vector movement will be important in the new age of rear-and-release mosquito control strategies, particularly those where estimations of movement are important for ensuring efficacy of application

Development of a Multiplexed Bead-Based Suspension Array for the Detection and Discrimination of Pospiviroid Plant Pathogens

Efficient and reliable diagnostic tools for the routine indexing and certification of clean propagating material are essential for the management of pospiviroid diseases in horticultural crops. This study describes the development of a true multiplexed diagnostic method for the detection and identification of all nine currently recognized pospiviroid species in one assay using Luminex bead-based suspension array technology. In addition, a new data-driven, statistical method is presented for establishing thresholds for positivity for individual assays within multiplexed arrays. When applied to the multiplexed array data generated in this study, the new method was shown to have better control of false positives and false negative results than two other commonly used approaches for setting thresholds. The 11-plex Luminex MagPlex-TAG pospiviroid array described here has a unique hierarchical assay design, incorporating a near-universal assay in addition to nine species-specific assays, and a co-amplified plant internal control assay for quality assurance purposes. All assays of the multiplexed array were shown to be 100% specific, sensitive and reproducible. The multiplexed array described herein is robust, easy to use, displays unambiguous results and has strong potential for use in routine pospiviroid indexing to improve disease management strategies

Spatio-temporal assimilation of modelled catchment loads with monitoring data in the Great Barrier Reef

Soil erosion and sediment transport into waterways and the ocean can adversely affect water clarity, leading to the deterioration of marine ecosystems such as the iconic Great Barrier Reef (GBR) in Australia. Quantifying a sediment load and its associated uncertainty is an important task in delineating how changes in management practices can contribute to improvements in water quality, and therefore continued sustainability of the GBR. However, monitoring data are spatially (and often temporally) sparse, making load estimation complicated, particularly when there are lengthy periods between sampling or during peak flow periods of major events when samples cannot be safely taken.\ud \ud We develop a spatio-temporal statistical model that is mechanistically motivated by a process-based deterministic model called Dynamic SedNet. The model is developed within a Bayesian hierarchical modelling framework that uses dimension reduction to accommodate seasonal and spatial patterns to assimilate monitored sediment concentration and flow data with output from Dynamic SedNet. The approach is applied in the Upper Burdekin catchment in Queensland, Australia, where we obtain daily estimates of sediment concentrations, stream discharge volumes and sediment loads at 411 spatial locations across 20 years. Our approach provides a method for assimilating both monitoring data and modelled output, providing a statistically rigorous method for quantifying uncertainty through space and time that was previously unavailable through process-based models

Mark-release-recapture of male Aedes aegypti (Diptera: Culicidae): Use of rhodamine B to estimate movement, mating and population parameters in preparation for an incompatible male program.

Rapid advances in biological and digital support systems are revolutionizing the population control of invasive disease vectors such as Aedes aegypti. Methods such as the sterile and incompatible insect techniques (SIT/IIT) rely on modified males to seek out and successfully mate with females, and in doing so outcompete the wild male population for mates. Currently, these interventions most frequently infer mating success through area-wide population surveillance and estimates of mating competitiveness are rare. Furthermore, little is known about male Ae. aegypti behaviour and biology in field settings. In preparation for a large, community scale IIT program, we undertook a series of mark- release-recapture experiments using rhodamine B to mark male Ae. aegypti sperm and measure mating interactions with females. We also developed a Spatial and Temporally Evolving Isotropic Kernel (STEIK) framework to assist researchers to estimate the movement of individuals through space and time. Results showed that ~40% of wild females captured daily were unmated, suggesting interventions will need to release males multiple times per week to be effective at suppressing Ae. aegypti populations. Males moved rapidly through the landscape, particularly when released during the night. Although males moved further than what is typically observed in females of the species, survival was considerably lower. These unique insights improve our understanding of mating interactions in wild Ae. aegypti populations and lay the foundation for robust suppression strategies in the future

Predictions of the number of isolates of each pospiviroid species that will be detected using universal and species-specific assays of the Luminex MagPlex-TAG pospiviroid array.

<p>Predictions of the number of isolates of each pospiviroid species that will be detected using universal and species-specific assays of the Luminex MagPlex-TAG pospiviroid array.</p

Results of the blind testing of single and mixed infections of pospiviroids in plant samples, showing a comparison of three separate methods for setting thresholds for positivity.

<p>Results of the blind testing of single and mixed infections of pospiviroids in plant samples, showing a comparison of three separate methods for setting thresholds for positivity.</p

Percentages of false positive and false negative results for Luminex MagPlex-TAG pospiviroid array data when analyzed using three different methods for setting thresholds for positivity.

<p>Percentages of false positive and false negative results for Luminex MagPlex-TAG pospiviroid array data when analyzed using three different methods for setting thresholds for positivity.</p