Assessing COVID-19 risk, vulnerability and infection prevalence in communities

  1. Amin Kiaghadi
  2. Hanadi S. Rifai
  3. Winston Liaw

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Abstract

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  1. Version published to 10.1371/journal.pone.0241166
  2. ScreenIT

    SciScore for 10.1101/2020.05.03.20089839: (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
    ArcMap was used to extract the coordinates of both origins (centroids) and destinations (medical facilities), and the minimum travel time in minutes was then recorded for each tract in Microsoft Excel.
    Microsoft Excel
    suggested: (Microsoft Excel, RRID:SCR_016137)
    For ozone, the 8-hour average concentrations were calculated using IBM SPSS (version 26) for all of the available monitoring stations (40) and compared with the 70 ppb standard established by the United States Environmental Protection Agency (EPA).
    SPSS
    suggested: (SPSS, RRID:SCR_002865)
    Interpolation tools in ArcMap were used to convert the median measured concentration for each station to a continuous raster to overcome the spatial sparsity in measurements.
    ArcMap
    suggested: None

    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: We detected the following sentences addressing limitations in the study:
    As mentioned previously, one caveat that places greater uncertainty for Harris County reported rates is the fact that Texas is listed as the 46th state in terms of rates of testing (~542 per 100,000 population as of this writing [47]). Estimating hospitalizations based on age distributions and hospitalization rates reported by CDC [50] resulted in a total of 672 hospitalized patients (S15 Fig) and a rate of 15.37 per 100,000 population over the County (this estimate is also in excess of the reported data for Harris County on a daily basis that is between 7.86 and 9.84 per 100,000 persons (obtained by dividing the current day number of hospitalized patients to the total population, [48]). A worst-case scenario using NYC data leads to 16,200 hospitalizations and a rate of ~366 per 100,000 persons (S16 Fig). As shown in S16 Fig, the highest rate of hospitalization is predicted for the northeast and northwest parts of Harris County, where people have the least access to medical facilities (Fig 3) and are prone to flooding (Fig 5). Fig 8C (based on [51]) and S17 Fig (based on [52]) show the calculated mortality rates in Harris County census tracts. The average mortality rates (ratio of the number of total deaths to the number of confirmed COVID-19 cases) in Harris County, calculated based on the rates from China [51] and Italy [52] were 1.39% and 1.28%, respectively, which are both lower than the current rate of 1.54% in the County. Fig 8D shows the total deaths estimated in indiv...

    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.

    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.

  3. Version published to 10.1101/2020.05.03.20089839v1 on medRxiv