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Cancer incidence numbers are routinely recorded by national or regional population-based cancer registries (PBCRs). However, in most southern European countries, the local PBCRs cover only a fraction of the country. Therefore, national cancer incidence can be only obtained through estimation methods. In this paper, we predict incidence rates in areas without cancer registry using multivariate spatial models modelling jointly cancer incidence and mortality. To evaluate the proposal, we use cancer incidence and mortality data from all the German states. We also conduct a simulation study by mimicking the real case of Spain considering different scenarios depending on the similarity of spatial patterns between incidence and mortality, the levels of lethality, and varying the amount of incidence data available. The new proposal provides good interval estimates in regions without PBCRs and reduces the relative error in estimating national incidence compared to one of the most widely used methodologies. [ABSTRACT FROM AUTHOR]

The need for rigorous and timely health and demographic summaries has provided the impetus for an explosion in geographic studies in low- and middle-income countries. Many of these studies present fine-scale pixel-level maps in an attempt to answer the needs of the current era of precision public health. However, even though household surveys with a two-stage cluster design stratified by region and urbanicity are a major source of data, cavalier approaches are taken to acknowledging the survey design. We investigate the extent to which accounting for the sample design affects the predictive performance at the aggregate level of interest for health policy decisions. We consider various commonly used models and introduce a new Bayesian cluster-level model with a discrete spatial smoothing prior. The investigation is performed through a simulation study in which realistic sampling frames are created for Kenya, based on the population and demographic information, with a survey design that mimics a Demographic Health Survey (DHS). We find that including stratification and cluster-level random effects can improve predictive performance. Spatially smoothed direct (weighted) estimates and area-level models accounting for stratification were robust to the underlying population and survey design. Continuous spatial models showed some promise in the presence of fine-scale variation; however, these models require the most "hand holding." Subsequently, we examine how the models perform on real data, estimating the prevalence of secondary education for women aged 20–29 and neonatal mortality rates, using data from the 2014 Kenya DHS. [ABSTRACT FROM AUTHOR]

To account for measurement error (ME) in explanatory variables, Bayesian approaches provide a flexible framework, as expert knowledge can be incorporated in the prior distributions. Recently, integrated nested Laplace approximations have been proven to be a computationally convenient alternative to sampling approaches for Bayesian inference in latent Gaussian models. We show how the most common approaches to adjust for ME, the classical and the Berkson ME, fit into this framework. This is achieved through a reformulation with augmented pseudo-observations and a suitable extension of the latent Gaussian field. Two specific classes are described, which allow for a particularly simple implementation using integrated nested Laplace approximations. We present three applications within the framework of generalized linear (mixed) models with ME. To illustrate the practical feasibility, R code is provided in on-line supplementary material. [ABSTRACT FROM AUTHOR]

Summary. Suicide has become one of the leading causes of death of Swiss males aged between 15 and 44 years, whose age-standardized rates are about three times higher than those for females. We compared age-stratified suicide rates of Swiss men and women aged 15-79 years and analysed gender-specific differences from 1950 to 2007. Furthermore, we explored whether changes in measures of family integration can explain changes in suicide trends. The use of multivariate age-period-cohort models avoids age aggregation and allows the exploration of heterogeneous time trends across age, period and birth cohort. In addition, explanatory variables can be included. We found strong gender-specific differences in suicide mortality. Although the same risk factors may act on age and overdispersion, there was no significant correlation between gender-specific cohort effects. Family integration had an effect on Swiss suicide risk but only partially explained the underlying trends over time. [ABSTRACT FROM AUTHOR]

Spatiotemporal disease mapping models have been used extensively to describe the pattern of surveillance data. They are usually formulated in a hierarchical Bayesian framework and posterior marginals are not available in closed form. Hence, the standard method for parameter estimation is Markov chain Monte Carlo algorithms. A new method for approximate Bayesian inference in latent Gaussian models using integrated nested Laplace approximations has recently been proposed as an alternative. This approach promises very precise results in short computational time. The aim of the paper is to show how integrated nested Laplace approximations can be used as an inferential tool for a variety of spatiotemporal models for the analysis of reported cases of bovine viral diarrhoea in cattle from Switzerland. Conclusions concerning the problem of under-reporting in the data are drawn via a multilevel modelling strategy. Furthermore, a comparison with Markov chain Monte Carlo methods with regard to the accuracy of the parameter estimates and the usability of both approaches in practice is conducted. Approaches to model choice using integrated nested Laplace approximations are also presented. [ABSTRACT FROM AUTHOR]

Age–period–cohort (APC) models are frequently used to analyze mortality or morbidity rates stratified by age group and period. For the case in which rates are given in different strata, multivariate APC models have been considered only recently. Such models share a set of parameters, for example, the age effects, while the other parameters may vary across strata. We show that differences of strata-specific effects are identifiable. We then propose a Bayesian approach based on smoothing priors to estimate multivariate APC models. This provides an alternative to maximum likelihood (ML) estimates of relative risk in the case of equal intervals and gives useful results even in the case of unequal intervals, where ML estimates have severe artifacts. This is illustrated with data on female mortality in Denmark and Norway and data on chronic obstructive pulmonary disease mortality of males in England and Wales, stratified by 3 different areas: Greater London, conurbations excluding Greater London, and nonconurbation areas. [ABSTRACT FROM PUBLISHER]

We extend an Fst-based Bayesian hierarchical model, implemented via Markov chain Monte Carlo, for the detection of loci that might be subject to positive selection. This model divides the Fst-influencing factors into locus-specific effects, population-specific effects, and effects that are specific for the locus in combination with the population. We introduce a Bayesian auxiliary variable for each locus effect to automatically select nonneutral locus effects. As a by-product, the efficiency of the original approach is improved by using a reparameterization of the model. The statistical power of the extended algorithm is assessed with simulated data sets from a Wright-Fisher model with migration. We find that the inclusion of model selection suggests a clear improvement in discrimination as measured by the area under the receiver operating characteristic (ROC) curve. Additionally, we illustrate and discuss the quality of the newly developed method on the basis of an allozyme data set of the fruit fly Drosophila melanogaster and a sequence data set of the wild tomato Solanum chilense. For data sets with small sample sizes, high mutation rates, and/or long sequences, however, methods based on nucleotide statistics should be preferred. [ABSTRACT FROM AUTHOR]

We propose a novel Bayesian approach that robustifies genomic modeling by leveraging expert knowledge (EK) through prior distributions. The central component is the hierarchical decomposition of phenotypic variation into additive and nonadditive genetic variation, which leads to an intuitive model parameterization that can be visualized as a tree. The edges of the tree represent ratios of variances, for example broad-sense heritability, which are quantities for which EK is natural to exist. Penalized complexity priors are defined for all edges of the tree in a bottom-up procedure that respects the model structure and incorporates EK through all levels. We investigate models with different sources of variation and compare the performance of different priors implementing varying amounts of EK in the context of plant breeding. A simulation study shows that the proposed priors implementing EK improve the robustness of genomic modeling and the selection of the genetically best individuals in a breeding program. We observe this improvement in both variety selection on genetic values and parent selection on additive values; the variety selection benefited the most. In a real case study, EK increases phenotype prediction accuracy for cases in which the standard maximum likelihood approach did not find optimal estimates for the variance components. Finally, we discuss the importance of EK priors for genomic modeling and breeding, and point to future research areas of easy-to-use and parsimonious priors in genomic modeling. [ABSTRACT FROM AUTHOR]