60 research outputs found

    Bayesian imputation of COVID-19 positive test counts for nowcasting under reporting lag

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    Obtaining up to date information on the number of UK COVID-19 regional infections is hampered by the reporting lag in positive test results for people with COVID-19 symptoms. In the UK, for "Pillar 2" swab tests for those showing symptoms, it can take up to five days for results to be collated. We make use of the stability of the under reporting process over time to motivate a statistical temporal model that infers the final total count given the partial count information as it arrives. We adopt a Bayesian approach that provides for subjective priors on parameters and a hierarchical structure for an underlying latent intensity process for the infection counts. This results in a smoothed time-series representation now-casting the expected number of daily counts of positive tests with uncertainty bands that can be used to aid decision making. Inference is performed using sequential Monte Carlo

    Bayesian imputation of COVID-19 positive test counts for nowcasting under reporting lag

    Get PDF
    Obtaining up to date information on the number of UK COVID-19 regional infections is hampered by the reporting lag in positive test results for people with COVID-19 symptoms. In the UK, for ‘Pillar 2’ swab tests for those showing symptoms, it can take up to five days for results to be collated. We make use of the stability of the under reporting process over time to motivate a statistical temporal model that infers the final total count given the partial count information as it arrives. We adopt a Bayesian approach that provides for subjective priors on parameters and a hierarchical structure for an underlying latent intensity process for the infection counts. This results in a smoothed time-series representation nowcasting the expected number of daily counts of positive tests with uncertainty bands that can be used to aid decision making. Inference is performed using sequential Monte Carlo

    The thin(ning) green line? Investigating changes in Kenya's seagrass coverage

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    Knowledge of seagrass distribution is limited to a few well-studied sites and poor where resourcesare scant (e.g. Africa), hence global estimates of seagrass carbon storage are inaccurate. Here, we analysed freely available Sentinel-2 and Landsat imagery to quantify contemporary coverage and change in seagrass between 1986 and 2016 on Kenya’s coast. Using field surveys and independent estimates of historical seagrass, we estimate total cover of Kenya’s seagrass to be 317.1 ± 27.2 km226 , following losses of 0.85% yr-1 since 1986. Losses increased from 0.29% yr-1 in 2000 to 1.59% yr-1 in 2016, releasing up to 2.17 Tg carbon since 1986. Anecdotal evidence suggests fishing pressure is an important cause of loss and is likely to intensify in the near future. If these results are representative for Africa, global estimates of seagrass extent and loss need reconsidering

    Sequential quasi-Monte Carlo: Introduction for Non-Experts, Dimension Reduction, Application to Partly Observed Diffusion Processes

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    SMC (Sequential Monte Carlo) is a class of Monte Carlo algorithms for filtering and related sequential problems. Gerber and Chopin (2015) introduced SQMC (Sequential quasi-Monte Carlo), a QMC version of SMC. This paper has two objectives: (a) to introduce Sequential Monte Carlo to the QMC community, whose members are usually less familiar with state-space models and particle filtering; (b) to extend SQMC to the filtering of continuous-time state-space models, where the latent process is a diffusion. A recurring point in the paper will be the notion of dimension reduction, that is how to implement SQMC in such a way that it provides good performance despite the high dimension of the problem.Comment: To be published in the proceedings of MCMQMC 201
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