Stan being used to study and fight coronavirus

Publicity
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The source and corrected draft and a small case study explaining how to code Andrew’s and my model in Stan is available in our diagnostic-testing repo on GitHub.

Every statistical model is an error model in some sense. Specifically, our model lets you perform inference using a hierarchical meta-analysis of the sensitivity and specificity at a specific existing site or at a newly created test site.

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Code for published paper

that is to some (unclear) extent being used by the model relied upon by Dallas County health officials

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Has anyone tried Fractional differential equations on STAN for modeling diseases?

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The EpiNow2 R package uses Stan. It’s being used for national and subnational R/growth rate estimates which themselves have been used in a number of publications, e.g. Li et al. (2020), Davies et al. (2021), and others.

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Stan has also been used for nowcasts and projections of COVID-19 in the UK , to estimate epidemiological parameters from repeated cross-sectional prevalence studies, to perform nowcasting of censored case counts, and to estimate transmission advantage and generation intervals of new variants.

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The extensive supplement to Jones et al. (2021) is also built on Stan.

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Sharing my 2 main COVID-19 papers, using STAN.

  1. To my knowledge the best estimates of age-stratified COVID-19 severity, estimated through a literature meta-analysis. STAN was instrumental to put together information sources with widely different uncertainties https://link.springer.com/article/10.1186/s12879-022-07262-0 Open code and data here: GitHub - dherrera1911/estimate_covid_severity

  2. A meta-analysis of time-varying sensitivity in COVID-19 serological assays that can serve as a guide to correct for this source of bias in the literature. https://www.medrxiv.org/content/10.1101/2022.09.08.22279731v1 Code and data here: GitHub - dherrera1911/seroreversion_metaanalysis

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Thanks!

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Here’s our preprint, currently under review:

Bayesian analysis of diffusion-driven multi-type epidemic models with application to COVID-19

The Bernadette R package [CRAN link] accompanies the work.

Lampros