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    Optimising the use of new data streams for making epidemiological inferences in veterinary epidemiology : a thesis presented in partial fulfilment of the requirements for the degree of PhD in Veterinary Epidemiology at Massey University, Manawatu, New Zealand
    (Massey University, 2018) Hidano, Arata
    Many ‘big data’ streams have recently become available in animal health disciplines. While these data may be able to provide valuable epidemiological information, researchers are at risk of making erroneous inferences if limitations in these data are overlooked. This thesis focused on understanding the better use of two data streams—livestock movement records and genetic sequence data. The first study analysed national dairy cattle movement data in New Zealand to explore whether regionalisation of the country based on bovine tuberculosis risk influenced trade decisions. The results suggested that the observed livestock movement patterns could be explained by the majority of, but not all, farmers avoiding purchasing cattle from high disease risk areas. The second study took an alternative approach—qualitative interviews—to understanding farmers’ livestock purchasing practices. This study suggested that farmers are not necessarily concerned with disease status of source farms and that it may be the reliance on stock agents to facilitate trade that creates the observed livestock movement patterns in New Zealand. The findings from this study also implied that various demographic and production characteristics of animals may influence farmers’ livestock selling practices, which were quantitatively verified in the third study analysing livestock movement data and animal production data. These studies not only showed that analyses based solely on ‘big data’ can be misleading but also provided useful information necessary to predict future livestock movement patterns. The final study evaluated the performance of various genetic sequence sampling strategies in making phylodynamic inferences. We showed that using all available genetic samples can be not only computationally expensive, but also may lead to erroneous inferences. The results also suggested that strategies for sampling genetic sequences for phylodynamic analyses may need to be tailored based on epidemiological characteristics of each epidemic.
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    An investigation into the effects of database use on the organisation of student knowledge : a thesis presented in partial fulfilment of the requirements of the degree of Master of Philosophy in education, Education Department, Massey University
    (Massey University, 1989) Anderson, Bill
    A knowledge based view of expertise points to the importance of well structured domain specific knowledge in developing expertise in a particular field. This study reports on the way in which a computer based data management system appears to influence student organisation of declarative knowledge of a domain towards more expert-like cognitive structures. A class of Intermediate School students was divided into two groups. Groups had equal access to computers in terms of time, but one group used a word processor during the class program while students in the other group used a database to assist them in their classwork. For both groups, classroom practice stressed the importance of working in an environment that emphasised use of metacognitive strategies. It was hypothesised that the database group would show significant improvement in terms of the number of chunks, and the depth, of cognitive structure inferred, relative to the word processing group, as a result of their increased ability to discover relationships and trends in the data through datafile manipulation. Cognitive structures were inferred using two techniques. The main technique (Ordered Tree Technique) inferred cognitive structures from each student's ordering of a set of concepts relating to the class unit of work. Analysis of pre- and post-unit structures inferred from this technique indicates that the database group did in fact develop significantly more expert-like cognitive structures than the word processing group. A second technique (Concept Structuring Analysis Technique), used only post-unit, provides converging evidence that supports this finding. Results are discussed in terms of the type of restructuring that has occurred, the context in which the results arose, and the validity of depth and chunking as variables relevant to education. It is suggested that further research could focus on explicit knowledge representation by students as a way of helping those students develop their expertise in particular knowledge domains.
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    Measuring, defining, and valuing change: A database on development indicators for policy-makers, activists, and researchers
    (Institute of Development Studies, Massey University, 2013) Prinsen, Gerard; Purcell, Gisela
    The use of indicators in international development has increased exponentially since the 1990s. Composite and proxy indicators are used to measure a wide range of concepts but their shortcomings have been widely critiqued. Through a review of over 300 documents, this paper gives a brief history of the rise of “indicatorology” and then summarizes the key challenges in three categories: technical/operational, political/strategic and epistemological/conceptual. Technical challenges faced by development practitioners revolve around the over-simplification of complex issues and the conflation of the goals with indicators. Political challenges involve the inherent power of indicators and the implications they have for policy making. Epistemological challenges question how to balance scientific rigor with local knowledge in the creation and use of indicators. A database of all publications used in this research is being made accessible to development practitioners and researchers via Massey University – watch this space!
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    Compressing DNA sequence databases with coil
    (BioMed Central, 2008-05-20) White, W. Timothy J.; Hendy, Michael D.
    Background: Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results: We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion: coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.
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    Expressibility of higher-order logics on relational databases : proper hierarchies : a dissertation presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Information Systems at Massey University, Wellington, New Zealand
    (Massey University, 2008) Ferrarotti, Flavio Antonio
    We investigate the expressive power of different fragments of higher-order logics over finite relational structures (or equivalently, relational databases) with special emphasis in higher-order logics of order greater than or equal three. Our main results concern the study of the effect on the expressive power of higher-order logics, of simultaneously bounding the arity of the higher-order variables and the alternation of quantifiers.