Virgilio Gómez Rubio

University of Castilla-La Mancha · Departamento de Matemáticas

Gestational diabetes mellitus (GDM) is a major pregnancy complication affecting approximately 14.0% of pregnancies around the world. Air pollution exposure, particularly exposure to PM2.5, has become a major environmental issue affecting health, especially for vulnerable pregnant women. Associations between PM2.5 exposure and adverse birth outcomes...

Bayesian methods and software for spatial data analysis are generally now well established in the scientific community. Despite the wide application of spatial models, the analysis of multivariate spatial data using R-INLA has not been widely described in the existing literature. Therefore, the main objective of this article is to demonstrate that...

Calvo, GabrielArmero, CarmenGómez-Rubio, VirgilioMazzinari, GuidoLaparoscopy is a surgical procedure carried out in the abdomen or pelvis through small incisions with the help of a camera to view the organs in the abdomen or permit small-scale surgery. This technique needs the abdomen to be insufflated with carbon dioxide (CO2) to obtain a working...

Conventional DNA analysis techniques can hardly detect DNA damage in ruminant spermatozoa due to high DNA compaction in these cells. Furthermore, these techniques cannot discriminate whether the damage is due to oxidative stress. The main purpose of this study was to evaluate the efficacy of two techniques for determining DNA damage in ovine sperm...

To predict the health effects of accidental or therapeutic radiation exposure, one must estimate the radiation dose that person received. A well-known ionising radiation biomarker, phosphorylated γ-H2AX protein, is used to evaluate cell damage and is thus suitable for the dose estimation process. In this paper, we present new Bayesian methods that,...

Disentangling the relative importance of different biodiversity drivers (i.e., climate, edaphic, historical factors, or human impact) to predict plant species richness at the local scale is one of the most important challenges in ecology. Biodiversity modelling is a key tool for the integration of these drivers and the predictions generated are ess...

To predict the health effects of accidental or therapeutic radiation exposure, one must estimate the radiation dose that person received. A well-known ionising radiation biomarker, phosphorylated gamma-H2AX protein, is used to evaluate cell damage and is thus suitable for the dose estimation process. In this paper, we present new Bayesian methods t...

Double hierarchical generalized linear models (DHGLM) are a family of models that are flexible enough as to model hierarchically the mean and scale parameters. In a Bayesian framework, fitting highly parameterized hierarchical models is challenging when this problem is addressed using typical Markov chain Monte Carlo (MCMC) methods due to the poten...

The integrated nested Laplace approximation (INLA) is a deterministic approach to Bayesian inference on latent Gaussian models (LGMs) and focuses on fast and accurate approximation of posterior marginals for the parameters in the models. Recently, methods have been developed to extend this class of models to those that can be expressed as condition...

The impact of the COVID-19 pandemic on excess mortality from all causes in 2020 varied across and within European countries. Using data for 2015–2019, we applied Bayesian spatio-temporal models to quantify the expected weekly deaths at the regional level had the pandemic not occurred in England, Greece, Italy, Spain, and Switzerland. With around 30...

Double hierarchical generalized linear models (DHGLM) are a family of models that are flexible enough as to model hierarchically the mean and scale parameters. In a Bayesian framework, fitting highly parameterized hierarchical models is challenging when this problem is addressed using typical Markov chain Monte Carlo (MCMC) methods due to the poten...

COVID-19 related deaths underestimate the pandemic burden on mortality because they suffer from completeness and accuracy issues. Excess mortality is a popular alternative, as it compares observed with expected deaths based on the assumption that the pandemic did not occur. Expected deaths had the pandemic not occurred depend on population trends,...

COVID-19 related deaths underestimate the pandemic burden on mortality because they suffer from completeness and accuracy issues. Excess mortality is a popular alternative, as it compares observed with expected deaths based on the assumption that the pandemic did not occur. Expected deaths had the pandemic not occurred depend on population trends,...

In this summary we introduce the papers published in the special issue on Bayesian statistics. This special issue comprises 20 papers on Bayesian statistics and Bayesian inference on different topics such as general packages for hierarchical linear model fitting, survival models, clinical trials, missing values, time series, hypothesis testing, pri...

The impact of the COVID-19 pandemic on excess mortality from all causes in 2020 varied across and within European countries. Using data for 2015-2019, we applied Bayesian spatio-temporal models to quantify the expected weekly deaths at the regional level had the pandemic not occurred in England, Greece, Italy, Spain, and Switzerland. With around 30...

Laparoscopy is an operation carried out in the abdomen or pelvis through small incisions with external visual control by a camera. This technique needs the abdomen to be insufflated with carbon dioxide to obtain a working space for surgical instruments' manipulation. Identifying the critical point at which insufflation should be limited is crucial...

The INLAMSM package for the R programming language provides a collection of multivariate spatial models for lattice data that can be used with the INLA package for Bayesian inference. The multivariate spatial models implemented include different structures to model the spatial variation of the variables and the between-variables variability. In thi...

Survival analysis is one of the most important fields of statistics in medicine and biological sciences. In addition, the computational advances in the last decades have favored the use of Bayesian methods in this context, providing a flexible and powerful alternative to the traditional frequentist approach. The objective of this article is to summ...

The analysis of population-wide datasets can provide insight on the health status of large populations so that public health officials can make data-driven decisions. The analysis of such datasets often requires highly parameterized models with different types of fixed and random effects to account for risk factors, spatial and temporal variations,...

The Integrated Nested Laplace Approximation (INLA) is a deterministic approach to Bayesian inference on latent Gaussian models (LGMs) and focuses on fast and accurate approximation of posterior marginals for the parameters in the models. Recently, methods have been developed to extend this class of models to those that can be expressed as condition...

The analysis of population-wide datasets can provide insight on the health status of large populations so that public health officials can make data-driven decisions. The analysis of such datasets often requires highly parameterized models with different types of fixed and randoms effects to account for risk factors, spatial and temporal variations...

We present a novel approach for analysing multivariate case‐control georeferenced data in a Bayesian disease mapping context using stochastic partial differential equations (SPDEs) and the integrated nested Laplace approximation (INLA) for model fitting. In particular, we propose smooth terms based on SPDE models to estimate the underlying spatial...

Zhou and Hanson; Zhou and Hanson; Zhou and Hanson ( 2015 , Nonparametric Bayesian Inference in Biostatistics, pages 215–46. Cham: Springer; 2018, Journal of the American Statistical Association, 113, 571–81; 2020, spBayesSurv: Bayesian Modeling and Analysis of Spatially Correlated Survival Data. R package version 1.1.4) and Zhou et al. (2020, Journ...

Rock art paintings present high sensitivity to light, and an exhaustive evaluation of the potential color degradation effects is essential for further conservation and preservation actions on these rock art systems. Microfading spectrometry (MFS) is a technique that provides time series of stochastic observations that represent color fading over ti...

Sensor noise sources cause differences in the signal recorded across pixels in a single image and across multiple images. This study presents a Bayesian approach to decomposing and characterising the sensor noise sources involved in imaging with digital cameras. A Bayesian probabilistic model based on the (theoretical) model for noise sources in im...

Vitamin E is considered a powerful biological antioxidant; however, its characteristics such as high hydrophobicity and low stability limit its application. We propose to use nanotechnology as an innovative tool in spermatology, formulating nanoemulsions (NE) that accommodate vitamin E, protecting it from oxidation and promoting its release into th...

Survival analysis is one of the most important fields of statistics in medicine and the biological sciences. In addition, the computational advances in the last decades have favoured the use of Bayesian methods in this context, providing a flexible and powerful alternative to the traditional frequentist approach. The objective of this paper is to s...

The integrated nested Laplace approximation (INLA) for Bayesian inference is an efficient approach to estimate the posterior marginal distributions of the parameters and latent effects of Bayesian hierarchical models that can be expressed as latent Gaussian Markov random fields (GMRF). The representation as a GMRF allows the associated software R-I...

Sensor noise sources cause differences in the signal recorded across pixels in a single image and across multiple images. This paper presents a Bayesian approach to decomposing and characterizing the sensor noise sources involved in imaging with digital cameras. A Bayesian probabilistic model based on the (theoretical) model for noise sources in im...

'Bayesian inference with INLA' describes the integrated nested Laplace approximation (INLA) method and its associated R package R-INLA to fit a wide range of models. Printed copies of the book are available from https://www.crcpress.com/Bayesian-inference-with-INLA/Gomez-Rubio/p/book/9781138039872 . A free Gitbook version of the book is availabl...

In this paper we recast the problem of missing values in the covariates of a regression model as a latent Gaussian Markov random field (GMRF) model in a fully Bayesian framework. Our proposed approach is based on the definition of the covariate imputation sub-model as a latent effect with a GMRF structure. We show how this formulation works for con...

The integrated nested Laplace approximation (INLA) for Bayesian inference is an efficient approach to estimate the posterior marginal distributions of the parameters and latent effects of Bayesian hierarchical models that can be expressed as latent Gaussian Markov random fields (GMRF). The representation as a GMRF allows the associated software R-I...

Microfading Spectrometry (MFS) is a method for assessing light sensitivity color (spectral) variations of cultural heritage objects. Each measured point on the surface gives rise to a time-series of stochastic observations that represents color fading over time. Color degradation is expected to be non-decreasing as a function of time and stabilize...

Cure models in survival analysis deal with populations in which a part of the individuals cannot experience the event of interest. Mixture cure models consider the target population as a mixture of susceptible and non-susceptible individuals. The statistical analysis of these models focuses on examining the probability of cure (incidence model) and...

The INLAMSM package for the R programming language provides a collection of multivariate spatial models for lattice data that can be used with package INLA for Bayesian inference. The multivariate spatial models include different structures to model the spatial variation of the variables and the between-variables variability. In this way, fitting m...

Ecological niche models are powerful tools in ecology. Factors operating at different spatial scales are known to jointly influence species distributions, but their integration in meaningful and reliable niche models is still methodologically complex and requires further research and validation. Here, we compare six different hierarchical niche mod...

Aim Long‐distance dispersal research in plants has long been dominated by the assumption that an association between plant diaspore adaptations and related transport vectors (standard dispersal) determines the success of colonization. However, the role of diaspore adaptations in a biogeographic context is being increasingly questioned, as evidence...

Methods: We used connectivity models for prevailing wind and ocean currents based on satellite data to explore the correspondence between connectivity and species distribution patterns. Using a randomization test to eliminate the effect of wind and current directionality, we evaluated whether the proportion of species that is more connected than ra...

Aim: Long‐distance dispersal research in plants has long been dominated by the assumption that an association between plant diaspore adaptations and related transport vectors (standard dispersal) determines the success of colonization. However, the role of diaspore adaptations in a biogeographic context is being increasingly questioned, as evidence...

In air pollution studies a key issue concerns the change of support: pollutant concentrations are continuous phenomena in space but their measurements are typically available at a finite number of point-referenced monitoring stations or result from numerical models. When linking exposure to health outcomes, the latter are usually available at admin...

We present a novel approach for the analysis of multivariate case-control georeferenced data using Bayesian inference in the context of disease mapping, where the spatial distribution of different types of cancers is analyzed. Extending other methodology in point pattern analysis, we propose a log-Gaussian Cox process for point pattern of cases and...

Book on spatial and spatio-temporal modeling with SPDEs and INLA. R code and free Gitbook version here: http://www.r-inla.org/spde-book .

The Integrated Nested Laplace Approximation (INLA) has established itself as a widely used method for approximate inference on Bayesian hierarchical models which can be represented as a latent Gaussian model (LGM). INLA is based on producing an accurate approximation to the posterior marginal distributions of the parameters in the model and some ot...

Cure models in survival analysis deal with populations in which a part of the individuals cannot experience the event of interest. Mixture cure models consider the target population as a mixture of susceptible and non-susceptible individuals. The statistical analysis of these models focuses on examining the probability of cure (incidence model) and...

Book review of 'Generalized Additive Models: An Introduction with R', 2nd 2d.

In this paper, we present a novel approach to fitting mixture models based on estimating first the posterior distribution of the auxiliary variables that assign each observation to a group in the mixture. The posterior distributions of the remainder of the parameters in the mixture is obtained by averaging over their conditional posterior marginals...

Background High prevalence of functional limitations has been previously observed in nursing homes. Disability may depend not only on the characteristics of the residents but also on the facility characteristics. The aims of this study were: 1, to describe the prevalence of functional disability in older people living in Spanish nursing homes; and...

Multilevel models including individual or/and institutional variables. (TIFF)

Ranked point estimates of the institutional total effect together with an interval that covers plus/minus one standard error. (TIFF)

Average Barthel Index of the residents for each residence plus a horizontal line with the global average Barthel Index. (TIFF)

Flow diagram of included/excluded participants and data collection. (TIFF)

Integrated Nested Laplace Approximation provides a fast and effective method for marginal inference on Bayesian hierarchical models. This methodology has been implemented in the R-INLA package which permits INLA to be used from within R statistical software. Although INLA is implemented as a general methodology, its use in practice is limited to th...

The detection of regions with unusually high risk plays an important role in disease mapping and the analysis of public health data. In particular, the detection of groups of areas (i.e., clusters) where the risk is significantly high is often conducted by Public Health authorities. Many methods have been proposed for the detection of these disease...

In this paper we propose a novel Bayesian hierarchical spatio-temporal model for the joint analysis of several diseases. Our model allows for specific and joint spatial and temporal variation, so that different effects can be disentangled. Our proposal extends other spatio-temporal models in a number of ways. First of all, it allows areas to show s...

The Integrated Nested Laplace Approximation (INLA) is a convenient way to obtain approximations to the posterior marginals for parameters in Bayesian hierarchical models when the latent effects can be expressed as a Gaussian Markov Random Field (GMRF). In addition, its implementation in the R-INLA package for the R statistical software provides an...

We propose a framework fast method for detecting clusters of disease based on generalized spatial scan statistics set in the context of Bayesian Hierarchical Models. The approach models clusters of disease as dummy variables as part of a Generalized Linear Model using advanced estimation procedures based on Laplace approximations. We discuss both t...

It remains hotly debated whether latitudinal diversity gradients are common across taxonomic groups and whether a single mechanism can explain such gradients. Investigating species richness (SR) patterns of European land plants, we determine whether SR increases with decreasing latitude, as predicted by theory, and whether the assembly mechanisms d...

The new slm latent model for estimating spatial econometrics models using INLA has recently been introduced. It will be described briefly and its use will be demonstrated in the accompanying poster.

Air pollution epidemiological studies suggest that elevated exposure to fine particulate matter (PM2.5) is associated with higher prevalence of term low birth weight (TLBW). Previous studies have generally assumed the exposure-response of PM2.5 on TLBW to be the same throughout a large geographical area. Health effects related to PM2.5 exposures, h...