JAGS model specification for spatiotemporal epidemiological modelling.

Bayesian inference in modelling infectious diseases using Bayesian inference using Gibbs Sampling (BUGS) is notable in the last two decades in parallel with the advancements in computing and model development. The ability of BUGS to easily implement the Markov chain Monte Carlo (MCMC) method brought Bayesian analysis to the mainstream of infectious disease modelling. However, with the existing software that runs MCMC to make Bayesian inferences, it is challenging, especially in terms of computational complexity, when infectious disease models become more complex with spatial and temporal components, in addition to the increasing number of parameters and large datasets. This study investigates two alternative subscripting strategies for creating models in Just Another Gibbs Sampler (JAGS) environment and their performance in terms of run times. Our results are useful for practitioners to ensure the efficiency and timely implementation of Bayesian spatiotemporal infectious disease modelling.

Bayesian estimation of the effect of health inequality in disease detection.

BACKGROUND: Measuring health inequality is essential to ensure that everyone has equal accessibility to health care. Studies in the past have continuously presented and showed areas or groups of people affected by various inequality in accessing the health resources and services to help improve this matter. Alongside, disease prevention is as important to minimise the disease burden and improve health and quality of life. These aspects are interlinked and greatly contributes to one's health. METHOD: In this study, the Gini coefficient and Lorenz curve are used to give an indication of the overall health inequality. The impact of this inequality in granular level is demonstrated using Bayesian estimation for disease detection. The Bayesian estimation used a two-component modelling approach that separates the case detection process and incidence rate using a mixed Poisson distribution while capturing underlying spatio-temporal characteristics. Bayesian model averaging is used in conjunction with the two-component modelling approach to improve the accuracy of estimates by incorporating many candidate models into the analysis instead of using fixed component models. This method is applied to an infectious disease, influenza, in Victoria, Australia between 2013 and 2016 and the corresponding primary health care of the state. RESULT: There is a relatively equal distribution of health resources and services pertaining to general practitioners (GP) and GP clinics in Victoria, Australia. Roughly 80 percent of the population shares 70 percent of the number of GPs and GP clinics. The Bayesian estimation with model averaging revealed that access difficulty to health services impacts both case detection probability and incidence rate. Minimal differences are recorded in the observed and estimated incidence of influenza cases considering social deprivation factors. In most years, areas in Victoria's southwest and eastern parts have potential under-reported cases consistent with their relatively lower number of GP or GP clinics. CONCLUSION: The Bayesian model estimated a slight discrepancy between the estimated incidence and the observed cases of influenza in Victoria, Australia in 2013-2016 period. This is consistent with the relatively equal health resources and services in the state. This finding is beneficial in determining areas with potential under-reported cases and under-served health care. The proposed approach in this study provides insight into the impact of health inequality in disease detection without requiring costly and time-extensive surveys and relying mainly on the data at hand. Furthermore, the application of Bayesian model averaging provided a flexible modelling framework that allows covariates to move between case detection and incidence models.

Bayesian approaches to the weighted kappa-like inter-rater agreement measures.

Inter-rater agreement measures are used to estimate the degree of agreement between two or more assessors. When the agreement table is ordinal, different weight functions that incorporate row and column scores are used along with the agreement measures. The selection of row and column scores is effectual on the estimated degree of agreement. The weighted measures are prone to the anomalies frequently seen in agreement tables such as unbalanced table structures or grey zones due to the assessment behaviour of the raters. In this study, Bayesian approaches for the estimation of inter-rater agreement measures are proposed. The Bayesian approaches make it possible to include prior information on the assessment behaviour of the raters in the analysis and impose order restrictions on the row and column scores. In this way, we improve the accuracy of the agreement measures and mitigate the impact of the anomalies in the estimation of the strength of agreement between the raters. The elicitation of prior distributions is described theoretically and practically for the Bayesian estimation of five agreement measures with three different weights using an agreement table having two grey zones. A Monte Carlo simulation study is conducted to assess the classification accuracy of the Bayesian and classical approaches for the considered agreement measures for a given level of agreement. Recommendations for the selection of the highest performing agreement measure and weight combination are made in the breakdown of the table structure and sample size.

The impact of grey zones on the accuracy of agreement measures for ordinal tables.

BACKGROUND: In an inter-rater agreement study, if two raters tend to rate considering different aspects of the subject of interest or have different experience levels, a grey zone occurs among the levels of a square contingency table showing the inter-rater agreement. These grey zones distort the degree of agreement between raters and negatively impact the decisions based on the inter-rater agreement tables. In this sense, it is important to know how the existence of a grey zone impacts the inter-rater agreement coefficients to choose the most reliable agreement coefficient against the grey zones to reach out with more reliable decisions. METHODS: In this article, we propose two approaches to create grey zones in simulations setting and conduct an extensive Monte Carlo simulation study to figure out the impact of having grey zones on the weighted inter-rater agreement measures for ordinal tables over a comprehensive simulation space. RESULTS: The weighted inter-rater agreement coefficients are not reliable against the existence of grey zones. Increasing sample size and the number of categories in the agreement table decreases the accuracy of weighted inter-rater agreement measures when there is a grey zone. When the degree of agreement between the raters is high, the agreement measures are not significantly impacted by the existence of grey zones. However, if there is a medium to low degree of inter-rater agreement, all the weighted coefficients are more or less impacted. CONCLUSIONS: It is observed in this study that the existence of grey zones has a significant negative impact on the accuracy of agreement measures especially for a low degree of true agreement and high sample and tables sizes. In general, Gwet's AC2 and Brennan-Prediger's κ with quadratic or ordinal weights are reliable against the grey zones.

Transmission network reconstruction for foot-and-mouth disease outbreaks incorporating farm-level covariates.

Transmission network modelling to infer 'who infected whom' in infectious disease outbreaks is a highly active area of research. Outbreaks of foot-and-mouth disease have been a key focus of transmission network models that integrate genomic and epidemiological data. The aim of this study was to extend Lau's systematic Bayesian inference framework to incorporate additional parameters representing predominant species and numbers of animals held on a farm. Lau's Bayesian Markov chain Monte Carlo algorithm was reformulated, verified and pseudo-validated on 100 simulated outbreaks populated with demographic data Japan and Australia. The modified model was then implemented on genomic and epidemiological data from the 2010 outbreak of foot-and-mouth disease in Japan, and outputs compared to those from the SCOTTI model implemented in BEAST2. The modified model achieved improvements in overall accuracy when tested on the simulated outbreaks. When implemented on the actual outbreak data from Japan, infected farms that held predominantly pigs were estimated to have five times the transmissibility of infected cattle farms and be 49% less susceptible. The farm-level incubation period was 1 day shorter than the latent period, the timing of the seeding of the outbreak in Japan was inferred, as were key linkages between clusters and features of farms involved in widespread dissemination of this outbreak. To improve accessibility the modified model has been implemented as the R package 'BORIS' for use in future outbreaks.

Impact of increasing temperature anomalies and carbon dioxide emissions on wheat production.

Climate change is one of the serious issues humankind is currently facing. It impacts almost all the processes in nature and threatens the existence of species and biodiversity; hence, the whole process of the food cycle. To mitigate the influence of climate change on vital processes in nature, we need to understand the pattern and magnitude of the relationship between climate change and impacted processes in nature. In this article, we explore the impact of climate change on wheat production in terms of short and long-run relationships between world wheat production, carbon dioxide emissions, and surface temperature anomalies. We present new information on the nexus between climate change and wheat production using autoregressive distributed lag (ARDL) models and ARDL bounds test of cointegration. We observe a significant cointegration relationship among world wheat production, carbon dioxide emissions, and surface temperature anomalies series. Lagged short-run impacts of temperature anomalies and carbon dioxide emissions are found significant. The long-run impact of both series on world wheat production is significant with a high correction speed to any instability between wheat production and the proxies of climate change.

Incorporation of expert knowledge in the statistical detection of diagnosis related group misclassification.

BACKGROUND: In activity based funding systems, the misclassification of inpatient episode Diagnostic Related Groups (DRGs) can have significant impacts on the revenue of health care providers. Weakly informative Bayesian models can be used to estimate an episode's probability of DRG misclassification. METHODS: This study proposes a new, Hybrid prior approach which utilises guesses that are elicited from a clinical coding auditor, switching to non-informative priors where this information is inadequate. This model's ability to detect DRG revision is compared to benchmark weakly informative Bayesian models and maximum likelihood estimates. RESULTS: Based on repeated 5-fold cross-validation, classification performance was greatest for the Hybrid prior model, which achieved best classification accuracy in 14 out of 20 trials, significantly outperforming benchmark models. CONCLUSIONS: The incorporation of elicited expert guesses via a Hybrid prior produced a significant improvement in DRG error detection; hence, it has the ability to enhance the efficiency of clinical coding audits when put into practice at a health care provider.

Bayesian logistic regression approaches to predict incorrect DRG assignment.

Episodes of care involving similar diagnoses and treatments and requiring similar levels of resource utilisation are grouped to the same Diagnosis-Related Group (DRG). In jurisdictions which implement DRG based payment systems, DRGs are a major determinant of funding for inpatient care. Hence, service providers often dedicate auditing staff to the task of checking that episodes have been coded to the correct DRG. The use of statistical models to estimate an episode's probability of DRG error can significantly improve the efficiency of clinical coding audits. This study implements Bayesian logistic regression models with weakly informative prior distributions to estimate the likelihood that episodes require a DRG revision, comparing these models with each other and to classical maximum likelihood estimates. All Bayesian approaches had more stable model parameters than maximum likelihood. The best performing Bayesian model improved overall classification per- formance by 6% compared to maximum likelihood, with a 34% gain compared to random classification, respectively. We found that the original DRG, coder and the day of coding all have a significant effect on the likelihood of DRG error. Use of Bayesian approaches has improved model parameter stability and classification accuracy. This method has already lead to improved audit efficiency in an operational capacity.

Power comparisons for group sequential tests with nonparametric statistics in case of nonproportional hazards.

In clinical trials, it is important to set up a design to reach a decision on effectiveness of a drug in treating a disease with the loss of the minimum number of patients. Group sequential designs are very beneficial on this point. However, the proportional hazards assumption must hold to work under a group sequential design properly. A trial running under a group sequential design covers a long time period; therefore, assuming that hazards remain proportional over a long time period is somewhat unrealistic. We should examine and figure out the impact of nonproportional hazards over the hypothesis tests conducted under a group sequential design to set up more reliable designs and decide which test to use in which conditions. In this article, powers of group sequential tests with nonparametric statistics are evaluated under nonproportional hazards by a Monte Carlo simulation study. The simulation study covers different nonproportional hazards scenarios, censoring rates, survival distributions, sample sizes, and tied observations. With this study, we intend to be helpful for clinical trial designers to set up a more reliable group sequential design.

Quality of life among Turkish immigrants in Sweden.

OBJECTIVES: To assess quality of life among Turkish immigrants in Sweden by using the WHOQOL-100 scale and to evaluate the domains' contribution to explain the variance in the quality of life of the immigrants. Our hypothesis was QOL among Turkish immigrants in Sweden are better than Turkish people who are living in their home country. MATERIAL AND METHODS: This study was performed in the districts of Stockholm where Turkish immigrants have mostly settled. With the help and guidance of the Turkish Association, a sample of 520 participants was selected. We collected the demographic data by printed questionnaires, and to measure the quality of life, we used the WHOQOL-100 scale Turkish version. For analysis, we used the SPSS V.13.0 and R package programs, variance analyses, and Bayesian regression. RESULTS: The quality of life among the sample of Turkish immigrants was found to be moderate, but higher than the sample of the Turkish population. The quality of life of male immigrants was found to be higher than for females. Swedish-born Turks had better quality of life perceptions. CONCLUSION: Turkish immigrants' quality of life perceptions were better than those of the Turkish sample. The best scores were received from the third generation. The first generation and female immigrants need attention in order to receive higher quality of life perceptions.