Bayesian Modelling of Direct and Indirect Effects of Marine Reserves on Fishes : A thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Statistics at Massey University, Albany, New Zealand.

This thesis reviews and develops modern advanced statistical methodology for sampling and modelling count data from marine ecological studies, with specific applications to quantifying potential direct and indirect effects of marine reserves on fishes in north eastern New Zealand. Counts of snapper (Pagrus auratus: Sparidae) from baited underwater video surveys from an unbalanced, multi-year, hierarchical sampling programme were analysed using a Bayesian Generalised Linear Mixed Model (GLMM) approach, which allowed the integer counts to be explicitly modelled while incorporating multiple fixed and random effects. Overdispersion was modelled using a zero-inflated negative-binomial error distribution. A parsimonious method for zero inflation was developed, where the mean of the count distribution is explicitly linked to the probability of an excess zero. Comparisons of variance components identified marine reserve status as the greatest source of variation in counts of snapper above the legal size limit. Relative densities inside reserves were, on average, 13-times greater than outside reserves. Small benthic reef fishes inside and outside the same three reserves were surveyed to evaluate evidence for potential indirect effects of marine reserves via restored populations of fishery-targeted predators such as snapper. Sites for sampling were obtained randomly from populations of interest using spatial data and geo-referencing tools in R—a rarely used approach that is recommended here more generally to improve field-based ecological surveys. Resultant multispecies count data were analysed with multivariate GLMMs implemented in the R package MCMCglmm, based on a multivariate Poisson lognormal error distribution. Posterior distributions for hypothesised effects of interest were calculated directly for each species. While reserves did not appear to affect densities of small fishes, reserve-habitat interactions indicated that some endemic species of triplefin (Tripterygiidae) had different associations with small-scale habitat gradients inside vs outside reserves. These patterns were consistent with a behavioural risk effect, where small fishes may be more strongly attracted to refuge habitats to avoid predators inside vs outside reserves. The approaches developed and implemented in this thesis respond to some of the major current statistical and logistic challenges inherent in the analysis of counts of organisms. This work provides useful exemplar pathways for rigorous study design, modelling and inference in ecological systems

Dispatch From Flipping A Record

“Dispatch From Flipping A Record is a flash creative non-fiction piece written in first person. It opens with me holding a vinyl record between my two hands, poised to flip it over, but not rushing through this liminal moment. I ruminate on the intentionality of this space between songs. Next, I cast my gaze down onto the tracks carved in wax and compare them to a poem I am drafting back on my desk. The former is fixed and finished. The latter is rough and fluid. I draw hope for my poem that it too can have space to step into. The piece is separated into paragraphs and comes in just under 500 words

Take A Moment

The poems, essays, and flash pieces in this creative collection, Take A Moment, engage with the promise of being present. We currently live in a time in which so many people simultaneously busy themselves with noise and distractions while also wishing they could step away from it all and experience the world around them

A matrix perturbation view of the small world phenomenon

We use techniques from applied matrix analysis to study small world cutoff in a Markov chain. Our model consists of a periodic random walk plus uniform jumps. This has a direct interpretation as a teleporting random walk, of the type used by search engines to locate web pages, on a simple ring network. More loosely, the model may be regarded as an analogue of the original small world network of Watts and Strogatz [Nature, 393 (1998), pp. 440-442]. We measure the small world property by expressing the mean hitting time, averaged over all states, in terms of the expected number of shortcuts per random walk. This average mean hitting time is equivalent to the expected number of steps between a pair of states chosen uniformly at random. The analysis involves nonstandard matrix perturbation theory and the results come with rigorous and sharp asymptotic error estimates. Although developed in a different context, the resulting cutoff diagram agrees closely with that arising from the mean-field network theory of Newman, Moore, and Watts [Phys. Rev. Lett., 84 (2000), pp. 3201-3204]

The Evolution of Obstruction: Mike Mansfield and Multiple Tracks

A core question in analyzing political institutions is how these institutions themselves change. This thesis seeks to understand how the institutional procedure change of multiple tracks affects the functioning of the filibuster in the U.S. Senate. The data utilized are Washington Post discussions of the filibuster before and after the implementation of multiple tracks. Descriptive statistics, analyses of mean differences, and OLS regression are utilized to test how this change altered the functioning of the filibuster in the Senate. Ultimately, this thesis finds that the implementation of multiple tracks does not affect the functioning of the filibuster, but does alter the duties of the majority leader within the chamber in relation to managing filibusters. This finding is linked to classical and contemporary examples of the filibuster to illustrate how the role of the majority leader changes in practice

Wall rock geochemistry of the Chester Vein, Sunshine Mine, Kellogg, Idaho

The Chester vein has been the major source of ore from the Sunshine mine, largest single producer of silver in the world. 425 samples of quartzite and argillite wall rocks were collected in 13 traverses across this vein on the 4400, 4600, and 4800 mining levels. These samples were analyzed for aluminum, magnesium, calcium, sodium, potassium, manganese, iron, lead, copper, and zinc by atomic absorption spectroscopy, and for silicon and sulfur by x-ray emission spectroscopy. Element distribution plots, linear correlation coefficient matrices, varimax factor analysis, and cluster analysis were employed to determine the geochemical processes that occurred in the wall rock. Examination of element distributions established that large scale leaching of calcium occurred concurrently with a stage of bleaching in the wall rock. Subsequent to this bleaching process, carbonatization (sideritization) of the wall rock, which occurred during siderite emplacement in the vein, resulted in aureoles of iron, manganese, magnesium, and calcium in the wall rock near the vein. These aureoles were shown to increase the exploration target by a factor of about 10. An inverse relationship was statistically established between sericite, represented by aluminum and potassium, and siderite, represented by iron and manganese, in the wall rock. The cause of this relationship was not determinable. It is recommended that a mineralogical study supercede this study to resolve this problem. The technique of cluster analysis was modified in order to permit meaningful geochemical interpretations. The modified technique provided the same results as factor analysis, but offered the advantage of an easily understood graphical representation of results --Abstract, page ii

The background concentrations of copper, lead, and zinc in streams of the New Lead Belt , Missouri

This study was initiated to determine the background concentrations of copper, lead, and zinc in the streams of the Viburnum Trend or New Lead Belt of southeast Missouri. Analytical methods were developed for atomic adsorption spectroscopy. These methods initially consisted of coextraction of cooper, lead, and zinc using the APDC/MIBK system, and finally of extraction of copper by APDC/MIBK and direct analysis of lead and zinc using the newly developed Sampling Boat technique. The data obtained from these analyses were arranged in histograms and critically analyzed. The background concentrations were established to be 4-6 ppb for all three elements. Methods are presented for identifying both short term and long term contamination by using the data distributions. Short term contamination of a factor of 2-3 was determined to occur on the Bee Fork below the St. Joseph Lead Company\u27s Fletcher Mine. The data distributions were not useful for geochemical prospecting under the studied geological conditions. It is recommended that future studies be initiated in order to establish the degree of long term contamination introduced by the industrialization of this beautiful area --Abstract, page ii

Life after Covid-19: start planning now

COVID-19 has exposed Britain’s failure to plan for both a pandemic and a growing elderly population, write Nicholas Barr and Howard Glennerster (LSE). Splitting the budget for care between hospitals, social care and GPs has given each an incentive to pass on costs to each other, rather than trying to prevent problems developing in the first place