Bayesian survival analysis with INLA.

This tutorial shows how various Bayesian survival models can be fitted using the integrated nested Laplace approximation in a clear, legible, and comprehensible manner using the INLA and INLAjoint R-packages. Such models include accelerated failure time, proportional hazards, mixture cure, competing risks, multi-state, frailty, and joint models of longitudinal and survival data, originally presented in the article "Bayesian survival analysis with BUGS." In addition, we illustrate the implementation of a new joint model for a longitudinal semicontinuous marker, recurrent events, and a terminal event.

Non-stationary Bayesian spatial model for disease mapping based on sub-regions.

This paper aims to extend the Besag model, a widely used Bayesian spatial model in disease mapping, to a non-stationary spatial model for irregular lattice-type data. The goal is to improve the model's ability to capture complex spatial dependence patterns and increase interpretability. The proposed model uses multiple precision parameters, accounting for different intensities of spatial dependence in different sub-regions.

Joint quantile disease mapping with application to malaria and G6PD deficiency.

Statistical analysis based on quantile methods is more comprehensive, flexible and less sensitive to outliers when compared to mean methods. Joint disease mapping is useful for inferring correlation between different diseases. Most studies investigate this link through multiple correlated mean regressions.

Sex differences in mortality among children, adolescents, and young people aged 0-24 years: a systematic assessment of national, regional, and global trends from 1990 to 2021.

Background: Differences in mortality exist between sexes because of biological, genetic, and social factors. Sex differentials are well documented in children younger than 5 years but have not been systematically examined for ages 5-24 years. We aimed to estimate the sex ratio of mortality from birth to age 24 years and reconstruct trends in sex-specific mortality between 1990 and 2021 for 200 countries, major regions, and the world.

Fast and flexible inference for joint models of multivariate longitudinal and survival data using integrated nested Laplace approximations.

Modeling longitudinal and survival data jointly offers many advantages such as addressing measurement error and missing data in the longitudinal processes, understanding and quantifying the association between the longitudinal markers and the survival events, and predicting the risk of events based on the longitudinal markers. A joint model involves multiple submodels (one for each longitudinal/survival outcome) usually linked together through correlated or shared random effects. Their estimation is computationally expensive (particularly due to a multidimensional integration of the likelihood over the random effects distribution) so that inference methods become rapidly intractable, and restricts applications of joint models to a small number of longitudinal markers and/or random effects.

Bayesian estimation of two-part joint models for a longitudinal semicontinuous biomarker and a terminal event with INLA: Interests for cancer clinical trial evaluation.

Two-part joint models for a longitudinal semicontinuous biomarker and a terminal event have been recently introduced based on frequentist estimation. The biomarker distribution is decomposed into a probability of positive value and the expected value among positive values. Shared random effects can represent the association structure between the biomarker and the terminal event.

Variance partitioning in spatio-temporal disease mapping models.

Bayesian disease mapping, yet if undeniably useful to describe variation in risk over time and space, comes with the hurdle of prior elicitation on hard-to-interpret random effect precision parameters. We introduce a reparametrized version of the popular spatio-temporal interaction models, based on Kronecker product intrinsic Gaussian Markov random fields, that we name the variance partitioning model. The variance partitioning model includes a mixing parameter that balances the contribution of the main and interaction effects to the total (generalized) variance and enhances interpretability.

Sensitivity and identification quantification by a relative latent model complexity perturbation in Bayesian meta-analysis.

In recent years, Bayesian meta-analysis expressed by a normal-normal hierarchical model (NNHM) has been widely used for combining evidence from multiple studies. Data provided for the NNHM are frequently based on a small number of studies and on uncertain within-study standard deviation values. Despite the widespread use of Bayesian NNHM, it has always been unclear to what extent the posterior inference is impacted by the heterogeneity prior (sensitivity ) and by the uncertainty in the within-study standard deviation values (identification ).

Combined effects of hydrometeorological hazards and urbanisation on dengue risk in Brazil: a spatiotemporal modelling study.

Background: Temperature and rainfall patterns are known to influence seasonal patterns of dengue transmission. However, the effect of severe drought and extremely wet conditions on the timing and intensity of dengue epidemics is poorly understood. In this study, we aimed to quantify the non-linear and delayed effects of extreme hydrometeorological hazards on dengue risk by level of urbanisation in Brazil using a spatiotemporal model.

A Bayesian spatiotemporal statistical analysis of out-of-hospital cardiac arrests.

We propose a Bayesian spatiotemporal statistical model for predicting out-of-hospital cardiac arrests (OHCAs). Risk maps for Ticino, adjusted for demographic covariates, are built for explaining and forecasting the spatial distribution of OHCAs and their temporal dynamics. The occurrence intensity of the OHCA event in each area of interest, and the cardiac risk-based clustering of municipalities are efficiently estimated, through a statistical model that decomposes OHCA intensity into overall intensity, demographic fixed effects, spatially structured and unstructured random effects, time polynomial dependence, and spatiotemporal random effect.

Discrete versus continuous domain models for disease mapping.

The main goal of disease mapping is to estimate disease risk and identify high-risk areas. Such analyses are hampered by the limited geographical resolution of the available data. Typically the available data are counts per spatial unit and the common approach is the Besag-York-Mollié (BYM) model.

A note on intrinsic conditional autoregressive models for disconnected graphs.

In this note we discuss (Gaussian) intrinsic conditional autoregressive (CAR) models for disconnected graphs, with the aim of providing practical guidelines for how these models should be defined, scaled and implemented. We show how these suggestions can be implemented in two examples, on disease mapping.

Estimating multilevel regional variation in excess mortality of cancer patients using integrated nested Laplace approximation.

Models of excess mortality with random effects were used to estimate regional variation in relative or net survival of cancer patients. Statistical inference for these models based on the Markov chain Monte Carlo (MCMC) methods is computationally intensive and, therefore, not feasible for routine analyses of cancer register data. This study assessed the performance of the integrated nested Laplace approximation (INLA) in monitoring regional variation in cancer survival.

Bayesian bivariate meta-analysis of diagnostic test studies with interpretable priors.

In a bivariate meta-analysis, the number of diagnostic studies involved is often very low so that frequentist methods may result in problems. Using Bayesian inference is particularly attractive as informative priors that add a small amount of information can stabilise the analysis without overwhelming the data. However, Bayesian analysis is often computationally demanding and the selection of the prior for the covariance matrix of the bivariate structure is crucial with little data.

An intuitive Bayesian spatial model for disease mapping that accounts for scaling.

In recent years, disease mapping studies have become a routine application within geographical epidemiology and are typically analysed within a Bayesian hierarchical model formulation. A variety of model formulations for the latent level have been proposed but all come with inherent issues. In the classical BYM (Besag, York and Mollié) model, the spatially structured component cannot be seen independently from the unstructured component.

Bayesian penalized spline models for the analysis of spatio-temporal count data.

In recent years, the availability of infectious disease counts in time and space has increased, and consequently, there has been renewed interest in model formulation for such data. In this paper, we describe a model that was motivated by the need to analyze hand, foot, and mouth disease surveillance data in China. The data are aggregated by geographical areas and by week, with the aims of the analysis being to gain insight into the space-time dynamics and to make short-term predictions, which will aid in the implementation of public health campaigns in those areas with a large predicted disease burden.

A Bayesian approach to estimate the biomass of anchovies off the coast of Perú.

The Northern Humboldt Current System (NHCS) is the world's most productive ecosystem in terms of fish. In particular, the Peruvian anchovy (Engraulis ringens) is the major prey of the main top predators, like seabirds, fish, humans, and other mammals. In this context, it is important to understand the dynamics of the anchovy distribution to preserve it as well as to exploit its economic capacities.

Spatial and spatio-temporal models with R-INLA.

During the last three decades, Bayesian methods have developed greatly in the field of epidemiology. Their main challenge focusses around computation, but the advent of Markov Chain Monte Carlo methods (MCMC) and in particular of the WinBUGS software has opened the doors of Bayesian modelling to the wide research community. However model complexity and database dimension still remain a constraint.

Spatial and spatio-temporal models with R-INLA.

During the last three decades, Bayesian methods have developed greatly in the field of epidemiology. Their main challenge focusses around computation, but the advent of Markov Chain Monte Carlo methods (MCMC) and in particular of the WinBUGS software has opened the doors of Bayesian modelling to the wide research community. However model complexity and database dimension still remain a constraint.

Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors.

Next generation sequencing is quickly replacing microarrays as a technique to probe different molecular levels of the cell, such as DNA or RNA. The technology provides higher resolution, while reducing bias. RNA sequencing results in counts of RNA strands.

Log Gaussian Cox processes and spatially aggregated disease incidence data.

This article presents a methodology for modeling aggregated disease incidence data with the spatially continuous log-Gaussian Cox process. Statistical models for spatially aggregated disease incidence data usually assign the same relative risk to all individuals in the same reporting region (census areas or postal regions). A further assumption that the relative risks in two regions are independent given their neighbor's risks (the Markov assumption) makes the commonly used Besag-York-Mollié model computationally simple.

Assessing the impact of a movement network on the spatiotemporal spread of infectious diseases.

Linking information on a movement network with space-time data on disease incidence is one of the key challenges in infectious disease epidemiology. In this article, we propose and compare two statistical frameworks for this purpose, namely, parameter-driven (PD) and observation-driven (OD) models. Bayesian inference in PD models is done using integrated nested Laplace approximations, while OD models can be easily fitted with existing software using maximum likelihood.

Bayesian inference for generalized linear mixed models.

Generalized linear mixed models (GLMMs) continue to grow in popularity due to their ability to directly acknowledge multiple levels of dependency and model different data types. For small sample sizes especially, likelihood-based inference can be unreliable with variance components being particularly difficult to estimate. A Bayesian approach is appealing but has been hampered by the lack of a fast implementation, and the difficulty in specifying prior distributions with variance components again being particularly problematic.

New Doppler-based imaging method in echocardiography with applications in blood/tissue segmentation.

A parametric model for the ultrasound signals from blood and tissue is developed and a new imaging method, knowledge-based imaging, is defined. This method utilizes the likelihood ratio function to classify blood and tissue signals. The method separates blood and tissue signals by the difference in movement patterns in addition to the difference in powers.

New echocardiographic imaging method based on the bandwidth of the ultrasound Doppler signal with applications in blood/tissue segmentation in the left ventricle.

A new imaging method, Bandwidth Imaging, which is related to the bandwidth of the ultrasound Doppler signal is proposed as a classification function for blood and tissue signal in transthoracial echocardiography in the left ventricle. An in vivo experiment is presented, where the apparent error rate of Bandwidth Imaging is compared with the apparent error rate of Second-Harmonic Imaging on 15 healthy men. The apparent error rates are calculated from the 16 myocardial wall segments defined in [M.