Ben Swallow
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View article: Advances in approximate Bayesian inference for models in epidemiology
Advances in approximate Bayesian inference for models in epidemiology Open
Bayesian inference methods are useful in infectious diseases modeling due to their capability to propagate uncertainty, manage sparse data, incorporate latent structures, and address high-dimensional parameter spaces. However, parameter in…
View article: Gaussian process modelling of infectious diseases using the Greta software package and GPUs
Gaussian process modelling of infectious diseases using the Greta software package and GPUs Open
Gaussian process are a widely-used statistical tool for conducting non-parametric inference in applied sciences, with many computational packages available to fit to data and predict future observations. We study the use of the Greta softw…
View article: Effect of caesarean birth on perinatal mortality for singleton breech presentation in spontaneous preterm labour—A target trial emulation using Scottish health record data
Effect of caesarean birth on perinatal mortality for singleton breech presentation in spontaneous preterm labour—A target trial emulation using Scottish health record data Open
Background The effects of mode of birth for women in preterm breech labour could not be successfully determined in randomised trials. We aimed to explore the effect of caesarean birth on perinatal mortality for women in spontaneous-onset p…
View article: Effect of caesarean birth on perinatal mortality for singleton breech presentation in spontaneous preterm labour – a target trial emulation using Scottish health record data.
Effect of caesarean birth on perinatal mortality for singleton breech presentation in spontaneous preterm labour – a target trial emulation using Scottish health record data. Open
Background The effects of mode of birth for women in preterm breech labour could not be successfully determined in randomised trials. We aimed to explore the effect of caesarean birth on perinatal mortality for women in spontaneous-onset p…
View article: Advances in Approximate Bayesian Inference for Models in Epidemiology
Advances in Approximate Bayesian Inference for Models in Epidemiology Open
Bayesian inference methods are useful in infectious diseases modeling due to their capability to propagate uncertainty, manage sparse data, incorporate latent structures, and address high-dimensional parameter spaces. However, parameter in…
View article: Gaussian process modelling of infectious diseases using the Greta software package and GPUs
Gaussian process modelling of infectious diseases using the Greta software package and GPUs Open
Gaussian process are a widely-used statistical tool for conducting non-parametric inference in applied sciences, with many computational packages available to fit to data and predict future observations. We study the use of the Greta softw…
View article: Target Trial Emulation: Impact of C-Section on Birth Outcomes for Spontaneous Preterm Breech Presentations
Target Trial Emulation: Impact of C-Section on Birth Outcomes for Spontaneous Preterm Breech Presentations Open
Breech presentation is a risk factor for poor birth outcomes. Guidance for safest mode of delivery in breech presenting full term pregnancies is available but there is a lack of evidence on the optimal mode of delivery in breech presenting…
View article: Quantifying transmissibility and dispersion of SARS-CoV-2 variants and subvariants of concern in England
Quantifying transmissibility and dispersion of SARS-CoV-2 variants and subvariants of concern in England Open
The SARS-CoV-2 pandemic was characterised by continual emergence of variants. For improved future pandemic preparedness it is important to understand whether each successive variant has been more infectious and more widely spread. In this …
View article: A Novel Approximate Bayesian Inference Method for Compartmental Models in Epidemiology using Stan
A Novel Approximate Bayesian Inference Method for Compartmental Models in Epidemiology using Stan Open
Mechanistic compartmental models are widely used in epidemiology to study the dynamics of infectious disease transmission. These models have significantly contributed to designing and evaluating effective control strategies during pandemic…
View article: Selecting the most informative positive and negative controls for self-controlled case series (SCCS): Rationale, approach, and lessons from studies investigating the safety of COVID-19 vaccines
Selecting the most informative positive and negative controls for self-controlled case series (SCCS): Rationale, approach, and lessons from studies investigating the safety of COVID-19 vaccines Open
Peer reviewed
View article: Irruptions of crossbills <i>Loxia</i> spp. in northern Europe – patterns and correlations with seed production by key and non‐key conifers
Irruptions of crossbills <i>Loxia</i> spp. in northern Europe – patterns and correlations with seed production by key and non‐key conifers Open
Irruptions by boreal seed‐eating and frugivorous birds are assumed to be driven by the production of seeds and fruits, crops of which are highly variable between years. Using data from Sweden, we tested whether irruptions of Common Crossbi…
View article: Risk of winter hospitalisation and death from acute respiratory infections in Scotland: national retrospective cohort study
Risk of winter hospitalisation and death from acute respiratory infections in Scotland: national retrospective cohort study Open
Objectives We undertook a national analysis to characterise and identify risk factors for acute respiratory infections (ARIs) resulting in hospitalisation during the winter period in Scotland. Design A population-based retrospective cohort…
View article: Caveats in reporting of national vaccine uptake
Caveats in reporting of national vaccine uptake Open
EAVE II is supported by the Medical Research Council (MR/R008345/1) with the support of BREATHE – The Health Data Research Hub for Respiratory Health [MC_PC_19004], which is funded through the UK Research and Innovation Industrial Strategy…
View article: A Bayesian multivariate extreme value mixture model
A Bayesian multivariate extreme value mixture model Open
Impact assessment of natural hazards requires the consideration of both extreme and non-extreme events. Extensive research has been conducted on the joint modeling of bulk and tail in univariate settings; however, the corresponding body of…
View article: Bayesian Inference for Stochastic Oscillatory Systems Using the Phase-Corrected Linear Noise Approximation
Bayesian Inference for Stochastic Oscillatory Systems Using the Phase-Corrected Linear Noise Approximation Open
Funding: BS acknowledges funding from BBSRC grant BB/K003097/1 and the Edinburgh Mathematical Society.
View article: Ben Swallow's contribution to the Discussion of ‘Martingale Posterior Distributions’ by Fong, Holmes and Walker
Ben Swallow's contribution to the Discussion of ‘Martingale Posterior Distributions’ by Fong, Holmes and Walker Open
Comment on Fong, Holmes & Walker, 2022.
View article: Association between antibody responses post-vaccination and severe COVID-19 outcomes: national population-based cohort study in Scotland
Association between antibody responses post-vaccination and severe COVID-19 outcomes: national population-based cohort study in Scotland Open
Several population-level studies have described individual clinical risk factors associated with suboptimal antibody responses following COVID-19 vaccination, but none have examined multimorbidity. Others have shown that suboptimal post-va…
View article: Data fusion in a two-stage spatio-temporal model using the INLA-SPDE approach
Data fusion in a two-stage spatio-temporal model using the INLA-SPDE approach Open
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 integrated nested Laplace approximation met…
View article: PCP-Ed: Parallel coordinate plots for ensemble data
PCP-Ed: Parallel coordinate plots for ensemble data Open
Funding: This research was funded in part by EPSRC Grant EPSRC EP/S01-0238/2. We would also like to thank the Ministry of Education of the Turkish Republic for their financial support.
View article: Tracking the national and regional COVID-19 epidemic status in the UK using weighted principal component analysis
Tracking the national and regional COVID-19 epidemic status in the UK using weighted principal component analysis Open
One of the difficulties in monitoring an ongoing pandemic is deciding on the metric that best describes its status when multiple intercorrelated measurements are available. Having a single measure, such as the effective reproduction number…
View article: Visualization for epidemiological modelling: challenges, solutions, reflections and recommendations
Visualization for epidemiological modelling: challenges, solutions, reflections and recommendations Open
We report on an ongoing collaboration between epidemiological modellers and visualization researchers by documenting and reflecting upon knowledge constructs—a series of ideas, approaches and methods taken from existing visualization resea…
View article: Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions
Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions Open
The English SARS-CoV-2 epidemic has been affected by the emergence of new viral variants such as B.1.177, Alpha and Delta, and changing restrictions. We used statistical models and the agent-based model Covasim, in June 2021, to estimate B…
View article: Data Fusion in a Two-stage Spatio-Temporal Model using the INLA-SPDE Approach
Data Fusion in a Two-stage Spatio-Temporal Model using the INLA-SPDE Approach Open
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…