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. 2024 Apr 15:2024:baae028.
doi: 10.1093/database/baae028.

nhanesA: achieving transparency and reproducibility in NHANES research

Laha Ale  1 , Robert Gentleman  2 , Teresa Filshtein Sonmez  3 , Deepayan Sarkar  4 , Christopher Endres  5
Affiliations

nhanesA: achieving transparency and reproducibility in NHANES research

Laha Ale et al. Database (Oxford). .

Abstract

The National Health and Nutrition Examination Survey provides comprehensive data on demographics, sociology, health and nutrition. Conducted in 2-year cycles since 1999, most of its data are publicly accessible, making it pivotal for research areas like studying social determinants of health or tracking trends in health metrics such as obesity or diabetes. Assembling the data and analyzing it presents a number of technical and analytic challenges. This paper introduces the nhanesA R package, which is designed to assist researchers in data retrieval and analysis and to enable the sharing and extension of prior research efforts. We believe that fostering community-driven activity in data reproducibility and sharing of analytic methods will greatly benefit the scientific community and propel scientific advancements. Database URL: https://github.com/cjendres1/nhanes.

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Conflict of interest statement

R.G. consults broadly in the pharmaceutical and biotech industries. He owns shares or options in a number of publicly traded and private companies. T.F.S. owns shares in a publicly traded company.

Figures

Figure 1.
Figure 1.
Number of participants by recorded ethnicity and gender by cycle, excluding the pre-pandemic (2017–March 2020) cycle.
Figure 2.
Figure 2.
Panel (a) shows the raw data, where both gender and ethnicity are encoded as integers. Panel (b) shows the translated data.
Figure 3.
Figure 3.
Questions BPQ_020 and BPQ_030 from table BPQ_D.
Figure 4.
Figure 4.
Workflow for ensuring transparent and reproducible research: (i) authors use Rmarkdown and R files, managed with Git version control for organization and collaboration. The nhanesA package facilitates NHANES access. Git and GitHub facilitate this by archiving and source code control. (ii) Work is committed, pushed and made public on GitHub in the form of Rmarkdown and R files. (iii) Anyone who wants to reproduce the work can fork or clone the repository to reproduce or expand upon the work. External users can access the NHANES database in the same way as the original authors. Contributions or extensions can be integrated via pull requests and subsequent merging.
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References

    1. CDC . National Health and Nutrition Examination Survey. https://www.cdc.gov/nchs/nhanes/index.htm (16 February 2024, date last accessed).
    1. NIH . Library of Medicine at the National Institutes of Health. https://pubmed.ncbi.nlm.nih.gov (22 February 2024, date last accessed).
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