Model calibration, nowcasting, and operational prediction of the COVID-19 pandemic

  1. J. D. Annan
  2. J. C. Hargreaves

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Abstract

We present a simple operational nowcasting/forecasting scheme based on a joint state/parameter estimate of the COVID-19 epidemic at national or regional scale, performed by assimilating the time series of reported daily death numbers into a simple SEIR model. This system generates estimates of the current reproductive rate, R t , together with predictions of future daily deaths and clearly outperforms a number of alternative forecasting systems that have been presented recently. Our current (14th April 2020) estimates for R t are, respectively, UK 0.49 (0.0 – 1.02), Spain 0.55 (0.33 – 0.77), Italy 0.90 (0.74 – 1.06) and France 0.67 (0.40 – 0.94) (mean and 95% credible intervals). Thus, we believe that the epidemics have been successfully suppressed in each of these countries, with high probability. Our approach is trivial to set up for any region and generates results in a few minutes on a laptop. We believe it would be straightforward to set up equivalent frameworks using more complex and realistic models, and hope that some experts in the field of epidemiological modelling will consider investigating this approach further.

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    SciScore for 10.1101/2020.04.14.20065227: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    This data set did not include the earliest deaths and these were added by hand based on the Wikipedia page: https://en.wikipedia.org/wiki/2019-20_coronavirus_pandemic_in_mainland_China.
    Wikipedia
    suggested: (Wikipedia, RRID:SCR_004897)

    Results from OddPub: Thank you for sharing your code.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

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  2. Version published to 10.1101/2020.04.14.20065227v2 on medRxiv
  3. Version published to 10.1101/2020.04.14.20065227v1 on medRxiv