arXiv subjects

Stephen Jun Villejo

Publications and source records attributed to Stephen Jun Villejo.

6 recordsLinked to original sources

arXiv2026

A spatio-temporal block aggregation model for latent log Gaussian outcomes: application on modelling wastewater virus concentration in Wales

Wastewater-based epidemiology has emerged as a valuable tool for monitoring community-level infectious disease dynamics, providing population-wide signals that complement clinical surveillance. However, wastewater measurements are often observed as aggregated values over irregular spatial units. This work develops an approach to link an underlying spatially continuous processes and an aggregated outcome. We propose a spatio-temporal model for latent log-Gaussian outcomes that provides a coherent framework for inference and prediction, allowing the process to be integrated over arbitrary spatial configurations. This framework can also be used for subsequent analyses, such as linking wastewater signal to health outcomes at administrative areas. We use a Bayesian framework for inference via the linearised integrated nested Laplace approximation (INLA) approach. We apply the proposed methodology to model SARS-CoV-2 N1 gene copies in wastewater across 47 catchment areas in Wales from the beginning of August 2022 to the end of July 2023. The results demonstrate that the model captures spatial and temporal patterns and has good predictive performance. Results also show that estimated viral gene copies are strongly linked to positivity rates from COVID-19 PCR tests at the local authority level. Our findings highlight the importance of explicitly modelling block aggregation when analysing wastewater surveillance data. The proposed framework provides a flexible and principled approach for integrating environmental surveillance data into public health monitoring systems.

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arXiv2026

Spatially continuous modelling of aggregated outcome data

This work develops a block aggregation approach to spatial estimation and prediction when the response is observed at a coarse spatial scale, for example as counts of events in administrative areas, or blocks, while covariates are available at a finer spatial resolution, typically as raster images. Our approach specifies a linear predictor at the finer resolution as a combination of covariate effects and a latent, spatially continuous Gaussian process. This linear predictor then determines the distribution of the response through an inverse link function and spatial integration. We use a simulation study to evaluate the performance of the proposed approach in comparison to two industry standard approaches: a traditional geostatistical model that associates each response with the centroid of its block; and a Markov random field (MRF) approach that aggregates covariate data to block-level. As expected, the differences in performance among the three approaches are small with respect to block-level prediction. The rationale for, and advantage of, the block aggregation approach lies in its delivery of reliable inferences at whatever spatial resolution is required in a particular application. We describe two applications: a linear Gaussian sampling model of wastewater virus concentrations in England, using population density as covariate; and log-linear Poisson model of cardiovascular hospitalisations in England using socio-demographic variables at fine-scale administrative units as covariates.

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arXiv2025

Linking climate and dengue in the Philippines using a two-stage Bayesian spatio-temporal model

Dengue is an infectious disease which poses significant socioeconomic and disease burden in many tropical and subtropical regions of the world. This work aims to provide additional insight into the association between dengue and climate in the Philippines. We employ a two-stage modelling framework: the first stage fits climate models, while the second stage fits a health model that uses the climate predictions from the first stage as inputs. We postulate a Bayesian spatio-temporal model and use the integrated nested Laplace approximation (INLA) approach for inference. To account for the uncertainty in the climate models, we perform posterior sampling and then perform Bayesian model averaging to compute the final posterior estimates of second-stage model parameters. The results indicate that temperature is positively associated with dengue, although extremely hot conditions tend to have a negative effect. Moreover, the relationship between rainfall and dengue varies in space. In areas with uniform amounts of rainfall all year round, rainfall is negatively associated with dengue. In contrast, in regions with pronounced dry and wet season, rainfall shows a positive association with dengue. Finally, there remains unexplained structured variation in space and time after accounting for the impact of climate variables and other covariates.

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arXiv2025

Validating uncertainty propagation approaches for two-stage Bayesian spatial models using simulation-based calibration

This work tackles the problem of uncertainty propagation in two-stage Bayesian models, with a focus on spatial applications. A two-stage modeling framework has the advantage of being more computationally efficient than a fully Bayesian approach when the first-stage model is already complex in itself, and avoids the potential problem of unwanted feedback effects. Two ways of doing two-stage modeling are the crude plug-in method and the posterior sampling method. The former ignores the uncertainty in the first-stage model, while the latter can be computationally expensive. This paper validates the two aforementioned approaches and proposes a new approach to do uncertainty propagation, which we call the $\mathbf{Q}$ uncertainty method, implemented using the Integrated Nested Laplace Approximation (INLA). We validate the different approaches using the simulation-based calibration method, which tests the self-consistency property of Bayesian models. Results show that the crude plug-in method underestimates the true posterior uncertainty in the second-stage model parameters, while the resampling approach and the proposed method are correct. We illustrate the approaches in a real life data application which aims to link relative humidity and Dengue cases in the Philippines for August 2018.

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arXiv2025

A Data Fusion Model for Meteorological Data using the INLA-SPDE method

This work aims to combine two primary meteorological data sources in the Philippines: data from a sparse network of weather stations and outcomes of a numerical weather prediction model. To this end, we propose a data fusion model which is primarily motivated by the problem of sparsity in the observational data and the use of a numerical prediction model as an additional data source in order to obtain better predictions for the variables of interest. The proposed data fusion model assumes that the different data sources are error-prone realizations of a common latent process. The outcomes from the weather stations follow the classical error model while the outcomes of the numerical weather prediction model involves a constant multiplicative bias parameter and an additive bias which is spatially-structured and time-varying. We use a Bayesian model averaging approach with the integrated nested Laplace approximation (INLA) for doing inference. The proposed data fusion model outperforms the stations-only model and the regression calibration approach, when assessed using leave-group-out cross-validation (LGOCV). We assess the benefits of data fusion and evaluate the accuracy of predictions and parameter estimation through a simulation study. The results show that the proposed data fusion model generally gives better predictions compared to the stations-only approach especially with sparse observational data.

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arXiv2022

Data Fusion in a Two-stage Spatio-Temporal Model using the INLA-SPDE Approach

This paper proposes a two-stage estimation approach for a spatial misalignment scenario that is motivated by the epidemiological problem of linking pollutant exposures and health outcomes. We use the integrated nested Laplace approximation method to estimate the parameters of a two-stage spatio-temporal model; the first stage models the exposures while the second stage links the health outcomes to exposures. The first stage is based on the Bayesian melding model, which assumes a common latent field for the geostatistical monitors data and a high-resolution data such as satellite data. The second stage fits a GLMM using the spatial averages of the estimated latent field, and additional spatial and temporal random effects. Uncertainty from the first stage is accounted for by simulating repeatedly from the posterior predictive distribution of the latent field. A simulation study was carried out to assess the impact of the sparsity of the data on the monitors, number of time points, and the specification of the priors in terms of the biases, RMSEs, and coverage probabilities of the parameters and the block-level exposure estimates. The results show that the parameters are generally estimated correctly but there is difficulty in estimating the latent field parameters. The method works very well in estimating block-level exposures and the effect of exposures on the health outcomes, which is the primary parameter of interest for spatial epidemiologists and health policy makers, even with the use of non-informative priors.

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