Spatial analysis of notified dengue fever infections

This study aimed to investigate the spatial clustering and dynamic dispersion of dengue incidence in Queensland, Australia. We used Moran’s I statistic to assess the spatial autocorrelation of reported dengue cases. Spatial empirical Bayes smoothing estimates were used to display the spatial distribution of dengue in postal areas throughout Queensland. Local indicators of spatial association (LISA) maps and logistic regression models were used to identify spatial clusters and examine the spatio-temporal patterns of the spread of dengue. The results indicate that the spatial distribution of dengue was clustered during each of the three periods of 1993–1996, 1997–2000 and 2001–2004. The high-incidence clusters of dengue were primarily concentrated in the north of Queensland and low-incidence clusters occurred in the south-east of Queensland. The study concludes that the geographical range of notified dengue cases has significantly expanded in Queensland over recent years.

Spatial incidence of dengue infections in Queensland, Australia - reply

This study aimed to investigate the spatial clustering and dynamic dispersion of dengue incidence in Queensland, Australia. We used Moran's I statistic to assess the spatial autocorrelation of reported dengue cases. Spatial empirical Bayes smoothing estimates were used to display the spatial distribution of dengue in postal areas throughout Queensland. Local indicators of spatial association (LISA) maps and logistic regression models were used to identify spatial clusters and examine the spatio-temporal patterns of the spread of dengue. The results indicate that the spatial distribution of dengue was clustered during each of the three periods of 1993–1996, 1997–2000 and 2001–2004. The high-incidence clusters of dengue were primarily concentrated in the north of Queensland and low-incidence clusters occurred in the south-east of Queensland. The study concludes that the geographical range of notified dengue cases has significantly expanded in Queensland over recent years.

Spatial analysis of notified cryptosporidiosis infections in Brisbane, Australia

Purpose: This study explored the spatial distribution of notified cryptosporidiosis cases and identified major socioeconomic factors associated with the transmission of cryptosporidiosis in Brisbane, Australia. Methods: We obtained the computerized data sets on the notified cryptosporidiosis cases and their key socioeconomic factors by statistical local area (SLA) in Brisbane for the period of 1996 to 2004 from the Queensland Department of Health and Australian Bureau of Statistics, respectively. We used spatial empirical Bayes rates smoothing to estimate the spatial distribution of cryptosporidiosis cases. A spatial classification and regression tree (CART) model was developed to explore the relationship between socioeconomic factors and the incidence rates of cryptosporidiosis. Results: Spatial empirical Bayes analysis reveals that the cryptosporidiosis infections were primarily concentrated in the northwest and southeast of Brisbane. A spatial CART model shows that the relative risk for cryptosporidiosis transmission was 2.4 when the value of the social economic index for areas (SEIFA) was over 1028 and the proportion of residents with low educational attainment in an SLA exceeded 8.8%. Conclusions: There was remarkable variation in spatial distribution of cryptosporidiosis infections in Brisbane. Spatial pattern of cryptosporidiosis seems to be associated with SEIFA and the proportion of residents with low education attainment.

Empirical Bayes method in the study of traffic safety via heterogeneous negative multinomial model

In the study of traffic safety, expected crash frequencies across sites are generally estimated via the negative binomial model, assuming time invariant safety. Since the time invariant safety assumption may be invalid, Hauer (1997) proposed a modified empirical Bayes (EB) method. Despite the modification, no attempts have been made to examine the generalisable form of the marginal distribution resulting from the modified EB framework. Because the hyper-parameters needed to apply the modified EB method are not readily available, an assessment is lacking on how accurately the modified EB method estimates safety in the presence of the time variant safety and regression-to-the-mean (RTM) effects. This study derives the closed form marginal distribution, and reveals that the marginal distribution in the modified EB method is equivalent to the negative multinomial (NM) distribution, which is essentially the same as the likelihood function used in the random effects Poisson model. As a result, this study shows that the gamma posterior distribution from the multivariate Poisson-gamma mixture can be estimated using the NM model or the random effects Poisson model. This study also shows that the estimation errors from the modified EB method are systematically smaller than those from the comparison group method by simultaneously accounting for the RTM and time variant safety effects. Hence, the modified EB method via the NM model is a generalisable method for estimating safety in the presence of the time variant safety and the RTM effects.

Using the empirical Bayes method to estimate and evaluate bycatch rates of seabirds from individual fishing vessels

Minimizing bycatch of seabirds is a major goal of the U.S. National Marine Fisheries Service. In Alaska waters, the bycatch (i.e., inadvertent catches) of seabirds has been an incidental result of demersal groundfish longline fishery operations. Notably, the endangered short-tailed albatross (Phoebastria albatrus) has been taken in this groundfish fishery. Bycatch rates of seabirds from individual vessels may be of particular interest because vessels with high bycatch rates may not be functioning effectively with seabird avoidance gears, and there may be a need for suggestions on how to use these avoidance gears more effectively. Therefore, bycatch estimates are usually made on an individual vessel basis and then summed to obtain the total estimate for the entire fleet.

Bayes and empirical-Bayes multiplicity adjustment in the variable-selection problem

This paper studies the multiplicity-correction effect of standard Bayesian variable-selection priors in linear regression. Our first goal is to clarify when, and how, multiplicity correction happens automatically in Bayesian analysis, and to distinguish this correction from the Bayesian Ockham's-razor effect. Our second goal is to contrast empirical-Bayes and fully Bayesian approaches to variable selection through examples, theoretical results and simulations. Considerable differences between the two approaches are found. In particular, we prove a theorem that characterizes a surprising aymptotic discrepancy between fully Bayes and empirical Bayes. This discrepancy arises from a different source than the failure to account for hyperparameter uncertainty in the empirical-Bayes estimate. Indeed, even at the extreme, when the empirical-Bayes estimate converges asymptotically to the true variable-inclusion probability, the potential for a serious difference remains. © Institute of Mathematical Statistics, 2010.

Empirical Bayes self-test quiz

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Development of safety performance functions for empirical Bayes estimation of crash reduction factors

Crash reduction factors (CRFs) are used to estimate the potential number of traffic crashes expected to be prevented from investment in safety improvement projects. The method used to develop CRFs in Florida has been based on the commonly used before-and-after approach. This approach suffers from a widely recognized problem known as regression-to-the-mean (RTM). The Empirical Bayes (EB) method has been introduced as a means to addressing the RTM problem. This method requires the information from both the treatment and reference sites in order to predict the expected number of crashes had the safety improvement projects at the treatment sites not been implemented. The information from the reference sites is estimated from a safety performance function (SPF), which is a mathematical relationship that links crashes to traffic exposure. The objective of this dissertation was to develop the SPFs for different functional classes of the Florida State Highway System. Crash data from years 2001 through 2003 along with traffic and geometric data were used in the SPF model development. SPFs for both rural and urban roadway categories were developed. The modeling data used were based on one-mile segments that contain homogeneous traffic and geometric conditions within each segment. Segments involving intersections were excluded. The scatter plots of data show that the relationships between crashes and traffic exposure are nonlinear, that crashes increase with traffic exposure in an increasing rate. Four regression models, namely, Poisson (PRM), Negative Binomial (NBRM), zero-inflated Poisson (ZIP), and zero-inflated Negative Binomial (ZINB), were fitted to the one-mile segment records for individual roadway categories. The best model was selected for each category based on a combination of the Likelihood Ratio test, the Vuong statistical test, and the Akaike's Information Criterion (AIC). The NBRM model was found to be appropriate for only one category and the ZINB model was found to be more appropriate for six other categories. The overall results show that the Negative Binomial distribution model generally provides a better fit for the data than the Poisson distribution model. In addition, the ZINB model was found to give the best fit when the count data exhibit excess zeros and over-dispersion for most of the roadway categories. While model validation shows that most data points fall within the 95% prediction intervals of the models developed, the Pearson goodness-of-fit measure does not show statistical significance. This is expected as traffic volume is only one of the many factors contributing to the overall crash experience, and that the SPFs are to be applied in conjunction with Accident Modification Factors (AMFs) to further account for the safety impacts of major geometric features before arriving at the final crash prediction. However, with improved traffic and crash data quality, the crash prediction power of SPF models may be further improved.

Geographical and temporal distribution of human giardiasis in Ontario, Canada

Affiliation: Pascal Michel : Département de pathologie et microbiologie, Faculté de médecine vétérinaire, Université de Montréal

Empirical evaluation of alternative approaches in identifying crash hot spots

This study proposes a framework of a model-based hot spot identification method by applying full Bayes (FB) technique. In comparison with the state-of-the-art approach [i.e., empirical Bayes method (EB)], the advantage of the FB method is the capability to seamlessly integrate prior information and all available data into posterior distributions on which various ranking criteria could be based. With intersection crash data collected in Singapore, an empirical analysis was conducted to evaluate the following six approaches for hot spot identification: (a) naive ranking using raw crash data, (b) standard EB ranking, (c) FB ranking using a Poisson-gamma model, (d) FB ranking using a Poisson-lognormal model, (e) FB ranking using a hierarchical Poisson model, and (f) FB ranking using a hierarchical Poisson (AR-1) model. The results show that (a) when using the expected crash rate-related decision parameters, all model-based approaches perform significantly better in safety ranking than does the naive ranking method, and (b) the FB approach using hierarchical models significantly outperforms the standard EB approach in correctly identifying hazardous sites.

A review of the spatial economics of non-timber forest product extraction: implications for policy

Patterns of forest cover and forest degradation determine the size and types of ecosystem services forests provide. Particularly in low-income countries, nontimber forest product (NTFP) extraction by rural people, which provides important resources and income to the rural poor, contributes to the level and pattern of forest degradation. Although recent policy, particularly in Africa, emphasizes forest degradation, relatively little research describes the spatial aspects of NTFP collection that lead to spatial degradation patterns. This paper reviews both the spatial empirical work on NTFP extraction and related forest degradation patterns, and spatial models of behavior of rural people who extract NTFPs from forest. Despite the impact of rural people's behavior on resulting quantities and patterns of forest resources, spatial–temporal models/patterns rarely inform park siting and sizing decisions, econometric assessments of park effectiveness, development projects to support conservation, or REDD protocols. Using the literature review as a lens, we discuss the models' implications for these policies with particular emphasis on effective conservation spending and leakage.

Multiple Testing With an Empirical Alternative Hypothesis

An optimal multiple testing procedure is identified for linear hypotheses under the general linear model, maximizing the expected number of false null hypotheses rejected at any significance level. The optimal procedure depends on the unknown data-generating distribution, but can be consistently estimated. Drawing information together across many hypotheses, the estimated optimal procedure provides an empirical alternative hypothesis by adapting to underlying patterns of departure from the null. Proposed multiple testing procedures based on the empirical alternative are evaluated through simulations and an application to gene expression microarray data. Compared to a standard multiple testing procedure, it is not unusual for use of an empirical alternative hypothesis to increase by 50% or more the number of true positives identified at a given significance level.

Agglomeration and firm-level productivity : a Bayesian spatial approach

This paper estimates the impact of industrial agglomeration on firm-level productivity in Chinese manufacturing sectors. To account for spatial autocorrelation across regions, we formulate a hierarchical spatial model at the firm level and develop a Bayesian estimation algorithm. A Bayesian instrumental-variables approach is used to address endogeneity bias of agglomeration. Robust to these potential biases, we find that agglomeration of the same industry (i.e. localization) has a productivity-boosting effect, but agglomeration of urban population (i.e. urbanization) has no such effects. Additionally, the localization effects increase with educational levels of employees and the share of intermediate inputs in gross output. These results may suggest that agglomeration externalities occur through knowledge spillovers and input sharing among firms producing similar manufactures.

Space-Time Smoothing Models for Surveillance and Complex Survey Data

Thesis (Ph.D.)--University of Washington, 2016-06

Feasibility of "subjective" engineering assessments of road safety improvements : Bayesian analysis development

Regional safety program managers face a daunting challenge in the attempt to reduce deaths, injuries, and economic losses that result from motor vehicle crashes. This difficult mission is complicated by the combination of a large perceived need, small budget, and uncertainty about how effective each proposed countermeasure would be if implemented. A manager can turn to the research record for insight, but the measured effect of a single countermeasure often varies widely from study to study and across jurisdictions. The challenge of converting widespread and conflicting research results into a regionally meaningful conclusion can be addressed by incorporating "subjective" information into a Bayesian analysis framework. Engineering evaluations of crashes provide the subjective input on countermeasure effectiveness in the proposed Bayesian analysis framework. Empirical Bayes approaches are widely used in before-and-after studies and "hot-spot" identification; however, in these cases, the prior information was typically obtained from the data (empirically), not subjective sources. The power and advantages of Bayesian methods for assessing countermeasure effectiveness are presented. Also, an engineering evaluation approach developed at the Georgia Institute of Technology is described. Results are presented from an experiment conducted to assess the repeatability and objectivity of subjective engineering evaluations. In particular, the focus is on the importance, methodology, and feasibility of the subjective engineering evaluation for assessing countermeasures.