arXiv subjects

Peter Diggle

Publications and source records attributed to Peter Diggle.

9 recordsLinked to original sources

arXiv2026

Comment on: "The Two Cultures of Prevalence Mapping: Small Area Estimation and Model-Based Geostatistics"

Small Area Estimation (SAE) and Model-Based Geostatistics (MBG) provide complementary approaches to prevalence mapping, with their relative advantages depending on the inferential goals and characteristics of the available data. We argue that a fuller comparison should consider model interpretability, the role of epidemiologically motivated covariates, inferential objectives beyond area-level prediction, integration of data from different spatial partitions and surveys, and task-specific model validation. In particular, we question whether survey design variables should routinely be included in MBG models when their effects may instead be mediated by measurable environmental and socio-economic risk factors. We further argue that simulation-based validation, tailored to the operational objectives of prevalence mapping, can provide a more informative assessment of model performance than conventional cross-validation alone.

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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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arXiv2024

Highly Multivariate Large-scale Spatial Stochastic Processes -- A Cross-Markov Random Field Approach

Key challenges in the analysis of highly multivariate large-scale spatial stochastic processes, where both the number of components (p) and spatial locations (n) can be large, include achieving maximal sparsity in the joint precision matrix, ensuring efficient computational cost for its generation, accommodating asymmetric cross-covariance in the joint covariance matrix, and delivering scientific interpretability. We propose a cross-MRF model class, consisting of a mixed spatial graphical model framework and cross-MRF theory, to collectively address these challenges in one unified framework across two modelling stages. The first stage exploits scientifically informed conditional independence (CI) among p component fields and allows for a step-wise parallel generation of joint covariance and precision matrix, enabling a simultaneous accommodation of asymmetric cross-covariance in joint covariance matrix and sparsity in joint precision matrix. The second stage extends the first-stage CI to doubly CI among both p and n and unearths the cross-MRF via an extended Hammersley-Clifford theorem for multivariate spatial stochastic processes. This results in the sparsest possible representation of the joint precision matrix and ensures its lowest generation complexity. We demonstrate with 1D simulated comparative studies and 2D real-world data.

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arXiv2022

A large-scale and PCR-referenced vocal audio dataset for COVID-19

The UK COVID-19 Vocal Audio Dataset is designed for the training and evaluation of machine learning models that classify SARS-CoV-2 infection status or associated respiratory symptoms using vocal audio. The UK Health Security Agency recruited voluntary participants through the national Test and Trace programme and the REACT-1 survey in England from March 2021 to March 2022, during dominant transmission of the Alpha and Delta SARS-CoV-2 variants and some Omicron variant sublineages. Audio recordings of volitional coughs, exhalations, and speech were collected in the 'Speak up to help beat coronavirus' digital survey alongside demographic, self-reported symptom and respiratory condition data, and linked to SARS-CoV-2 test results. The UK COVID-19 Vocal Audio Dataset represents the largest collection of SARS-CoV-2 PCR-referenced audio recordings to date. PCR results were linked to 70,794 of 72,999 participants and 24,155 of 25,776 positive cases. Respiratory symptoms were reported by 45.62% of participants. This dataset has additional potential uses for bioacoustics research, with 11.30% participants reporting asthma, and 27.20% with linked influenza PCR test results.

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arXiv2022

Audio-based AI classifiers show no evidence of improved COVID-19 screening over simple symptoms checkers

Recent work has reported that AI classifiers trained on audio recordings can accurately predict severe acute respiratory syndrome coronavirus 2 (SARSCoV2) infection status. Here, we undertake a large scale study of audio-based deep learning classifiers, as part of the UK governments pandemic response. We collect and analyse a dataset of audio recordings from 67,842 individuals with linked metadata, including reverse transcription polymerase chain reaction (PCR) test outcomes, of whom 23,514 tested positive for SARS CoV 2. Subjects were recruited via the UK governments National Health Service Test-and-Trace programme and the REal-time Assessment of Community Transmission (REACT) randomised surveillance survey. In an unadjusted analysis of our dataset AI classifiers predict SARS-CoV-2 infection status with high accuracy (Receiver Operating Characteristic Area Under the Curve (ROCAUC) 0.846 [0.838, 0.854]) consistent with the findings of previous studies. However, after matching on measured confounders, such as age, gender, and self reported symptoms, our classifiers performance is much weaker (ROC-AUC 0.619 [0.594, 0.644]). Upon quantifying the utility of audio based classifiers in practical settings, we find them to be outperformed by simple predictive scores based on user reported symptoms.

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arXiv2021

The $\mathcal{F}$-family of covariance functions: A Mat\'ern analogue for modeling random fields on spheres

The Mat{\'e}rn family of isotropic covariance functions has been central to the theoretical development and application of statistical models for geospatial data. For global data defined over the whole sphere representing planet Earth, the natural distance between any two locations is the great circle distance. In this setting, the Mat{\'e}rn family of covariance functions has a restriction on the smoothness parameter, making it an unappealing choice to model smooth data. Finding a suitable analogue for modelling data on the sphere is still an open problem. This paper proposes a new family of isotropic covariance functions for random fields defined over the sphere. The proposed family has a parameter that indexes the mean square differentiability of the corresponding Gaussian field, and allows for any admissible range of fractal dimension. Our simulation study mimics the fixed domain asymptotic setting, which is the most natural regime for sampling on a closed and bounded set. As expected, our results support the analogous results (under the same asymptotic scheme) for planar processes that not all parameters can be estimated consistently. We apply the proposed model to a dataset of precipitable water content over a large portion of the Earth, and show that the model gives more precise predictions of the underlying process at unsampled locations than does the Mat{\'e}rn model using chordal distances.

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arXiv2019

A Spatially Discrete Approximation to Log-Gaussian Cox Processes for Modelling Aggregated Disease Count Data

In this paper, we develop a computationally efficient discrete approximation to log-Gaussian Cox process (LGCP) models for the analysis of spatially aggregated disease count data. Our approach overcomes an inherent limitation of spatial models based on Markov structures, namely that each such model is tied to a specific partition of the study area, and allows for spatially continuous prediction. We compare the predictive performance of our modelling approach with LGCP through a simulation study and an application to primary biliary cirrhosis incidence data in Newcastle-Upon-Tyne, UK. Our results suggest that when disease risk is assumed to be a spatially continuous process, the proposed approximation to LGCP provides reliable estimates of disease risk both on spatially continuous and aggregated scales. The proposed methodology is implemented in the open-source R package SDALGCP.

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arXiv2018

A Geostatistical Framework for Combining Spatially Referenced Disease Prevalence Data from Multiple Diagnostics

Multiple diagnostic tests are often used due to limited resources or because they provide complementary information on the epidemiology of a disease under investigation. Existing statistical methods to combine prevalence data from multiple diagnostics ignore the potential over-dispersion induced by the spatial correlations in the data. To address this issue, we develop a geostatistical framework that allows for joint modelling of data from multiple diagnostics by considering two main classes of inferential problems: (1) to predict prevalence for a gold-standard diagnostic using low-cost and potentially biased alternative tests; (2) to carry out joint prediction of prevalence from multiple tests. We apply the proposed framework to two case studies: mapping Loa loa prevalence in Central and West Africa, using miscroscopy and a questionnaire-based test called RAPLOA; mapping Plasmodium falciparum malaria prevalence in the highlands of Western Kenya using polymerase chain reaction and a rapid diagnostic test. We also develop a Monte Carlo procedure based on the variogram in order to identify parsimonious geostatistical models that are compatible with the data. Our study highlights (i) the importance of accounting for diagnostic-specific residual spatial variation and (ii) the benefits accrued from joint geostatistical modelling so as to deliver more reliable and precise inferences on disease prevalence.

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