The incidence-based dynamic reproduction index: accurate determination, diagnostic sensitivity, and predictive power
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Abstract
Two methods of calculating the reproduction index from daily new infection data are considered, one by using the generation time t G as a shift ( R G ), and an incidence-based method directly derived from the differential equation system of an SIR epidemic dynamics model ( R I ). While the former is shown to have few in common with the true reproduction index, we find that the latter provides a sensitive detection device for intervention effects and other events affecting the epidemic, making it well-suited for diagnostic purposes in policy making. Furthermore, we introduce a similar quantity, , which can be calculated directly from R G . It shows largely the same behaviour as R I , with less fine structure. However, it is accurate in particular in the vicinity of R = 1, where accuracy is important for the corrrect prediction of epidemic dynamics. We introduce an entirely new, self-consistent method to derive, from both quantities, an improved which is both accurate and contains the details of the epidemic spreading dynamics. Hence we obtain R accurately from data on daily new infections (incidence) alone. Moreover, by using R I instead of R G in plots of R versus incidence, orbital trajectories of epidemic waves become visible in a particularly insightful way, demonstrating that the widespread use of only incidence as a diagniostic tool is clearly inappropriate.
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SciScore for 10.1101/2022.04.11.22273599: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
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:…
SciScore for 10.1101/2022.04.11.22273599: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
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.
Results from scite Reference Check: We found no unreliable references.
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