1. SciScore for 10.1101/2021.11.23.21266574: (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

    Software and Algorithms
    Linkage to health records and occupational databases: Using the Common Healthcare Identifier (CHI) held on all Scottish health records these individuals were linked to the population register, the national vaccination database, registers of teachers and health care workers, the list of those designated as clinically extremely vulnerable (eligible for shielding), the ECOSS database of test results, a database of hospitalisations (RAPID) that is updated daily, dispensed prescriptions in primary care and death registrations as described elsewhere [4–7].
    Common Healthcare
    suggested: None

    Results from OddPub: Thank you for sharing your code.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Statement of principal findings: Strengths and limitations: Strengths of this study are the large cohort of test-positive individuals based on ascertainment of all detected infections in the population, the comprehensive linkage to electronic health records, and the ability to examine associations with occupation. Although reinfections with new strains were not confirmed by sequencing, the 90-day interval should be enough to exclude persistent infection except in the immunosuppressed. Restriction to those with definite previous infection – at least two positive tests or Ct < 30 – excludes those who tested positive only once before September 2020, when the Lighthouse labs began reporting Ct values. Stratification by calendar time should eliminate almost all confounding by Alpha and Delta variants, as it took only a few weeks for each of these variants to replace pre-existing strains in Scotland. The main limitation is that without regular scheduled testing, estimates of association with detected reinfection are subject to ascertainment bias. Because testing rates are lower in unvaccinated than in vaccinated individuals in this cohort, the efficacy of vaccination is likely to be underestimated by a model with calendar timescale. We have attempted to overcome this by comparing two alternative models: a conventional Cox regression with calendar timescale, and a Cox regression with tests as timescale to adjust for differential testing rates. The model with tests as timescale is eq...

    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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