arXiv subjects

Edwin van Leeuwen

Publications and source records attributed to Edwin van Leeuwen.

3 recordsLinked to original sources

arXiv2024

Evaluating Forecasts with scoringutils in R

Evaluating forecasts is essential to understand and improve forecasting and make forecasts useful to decision makers. A variety of R packages provide a broad variety of scoring rules, visualisations and diagnostic tools. One particular challenge, which scoringutils aims to address, is handling the complexity of evaluating and comparing forecasts from several forecasters across multiple dimensions such as time, space, and different types of targets. scoringutils extends the existing landscape by offering a convenient and flexible data.table-based framework for evaluating and comparing probabilistic forecasts (forecasts represented by a full predictive distribution). Notably, scoringutils is the first package to offer extensive support for probabilistic forecasts in the form of predictive quantiles, a format that is currently used by several infectious disease Forecast Hubs. The package is easily extendable, meaning that users can supply their own scoring rules or extend existing classes to handle new types of forecasts. scoringutils provides broad functionality to check the data and diagnose issues, to visualise forecasts and missing data, to transform data before scoring, to handle missing forecasts, to aggregate scores, and to visualise the results of the evaluation. The paper presents the package and its core functionality and illustrates common workflows using example data of forecasts for COVID-19 cases and deaths submitted to the European COVID-19 Forecast Hub.

stat.ME↗

arXiv2024

Real-time modelling of the SARS-CoV-2 pandemic in England 2020-2023: a challenging data integration

A central pillar of the UK's response to the SARS-CoV-2 pandemic was the provision of up-to-the moment nowcasts and short term projections to monitor current trends in transmission and associated healthcare burden. Here we present a detailed deconstruction of one of the 'real-time' models that was key contributor to this response, focussing on the model adaptations required over three pandemic years characterised by the imposition of lockdowns, mass vaccination campaigns and the emergence of new pandemic strains. The Bayesian model integrates an array of surveillance and other data sources including a novel approach to incorporating prevalence estimates from an unprecedented large-scale household survey. We present a full range of estimates of the epidemic history and the changing severity of the infection, quantify the impact of the vaccination programme and deconstruct contributing factors to the reproduction number. We further investigate the sensitivity of model-derived insights to the availability and timeliness of prevalence data, identifying its importance to the production of robust estimates.

stat.AP↗

arXiv2019

Contemporary statistical inference for infectious disease models using Stan

This paper is concerned with the application of recent statistical advances to inference of infectious disease dynamics. We describe the fitting of a class of epidemic models using Hamiltonian Monte Carlo and Variational Inference as implemented in the freely available Stan software. We apply the two methods to real data from outbreaks as well as routinely collected observations. Our results suggest that both inference methods are computationally feasible in this context, and show a trade-off between statistical efficiency versus computational speed. The latter appears particularly relevant for real-time applications.

stat.AP↗