1. SciScore for 10.1101/2021.11.24.21266401: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: Thank you for sharing your code and data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    24 Our study comes with limitations, most importantly the potential for misclassification of the direction of transmission, the lack of inclusion of waning vaccine protection and the diversity of vaccines lineages and age groups in the dataset. To minimise the potential for misclassification we restrict the main analyses to only those putative transmission pairs where the there was no evidence against direct transmission based on phylogenetic distance (which was available for 63% of all putative transmission pairs) and where symptom onset in the contact did not pre-date that of the index case by more than 2 days. If residual misclassification between infector and infected remained this would re-attribute infection protection to transmission protection and vice versa. We also did not include waning of vaccine protection in our analyses26In the analysed dataset the longest reported time since vaccine receipt was 169 days. While some individuals in the analysis have since become eligible for booster vaccination over concerns of waning protection some of this potential effect will have been absorbed in our model in the age structuring because of the strong correlation between age and timing of vaccine eligibility as per vaccine roll-out strategy in the UK. Lastly, data collection spanned a period of multiple months during which Delta became the dominant strain in circulation in the UK and included participants vaccinated with two different vaccine products; thus requiring sub-str...

    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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

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