NHANES 1988-2018

The National Health and Nutrition Examination Survey (NHANES) provides data on the health and environmental exposure of the non-institutionalized US population. Such data have considerable potential to understand how the environment and behaviors impact human health. These data are also currently leveraged to answer public health questions such as prevalence of disease. However, these data need to first be processed before new insights can be derived through large-scale analyses. NHANES data are stored across hundreds of files with multiple inconsistencies. Correcting such inconsistencies takes systematic cross examination and considerable efforts but is required for accurately and reproducibly characterizing the associations between the exposome and diseases (e.g., cancer mortality outcomes). Thus, we developed a set of curated and unified datasets and accompanied code by merging 614 separate files and harmonizing unrestricted data across NHANES III (1988-1994) and Continuous (1999-2018), totaling 134,310 participants and 4,740 variables. The variables convey 1) demographic information, 2) dietary consumption, 3) physical examination results, 4) occupation, 5) questionnaire items (e.g., physical activity, general health status, medical conditions), 6) medications, 7) mortality status linked from the National Death Index, 8) survey weights, 9) environmental exposure biomarker measurements, and 10) chemical comments that indicate which measurements are below or above the lower limit of detection. We also provide a data dictionary listing the variables and their descriptions to help researchers browse the data. We also provide R markdown files to show example codes on calculating summary statistics and running regression models to help accelerate high-throughput analysis of the exposome and secular trends on cancer mortality. <strong>csv Data Record:</strong> The curated NHANES datasets and the data dictionaries includes 13 .csv files and 1 excel file. The curated NHANES datasets involves 10 .csv formatted files, one for each module and labeled as the following: 1) mortality, 2) dietary, 3) demographics, 4) response, 5) medications, 6) questionnaire, 7) chemicals, 8) occupation, 9) weights, and 10) comments. The eleventh file is a dictionary that lists the variable name, description, module, category, units, CAS Number, comment use, chemical family, chemical family shortened, number of measurements, and cycles available for all 4,740 variables in NHANES ("dictionary_nhanes.csv"). The 12th csv file contains the harmonized categories for the categorical variables ("dictionary_harmonized_categories.csv"). The 13th file contains the dictionary for descriptors on the drugs codes (“dictionary_drug_codes.csv”). The 14th file is an excel file that contains the cleaning documentation, which records all the inconsistencies for all affected variables to help curate each of the NHANES datasets (“nhanes_inconsistencies_documentation.xlsx”). <strong>R Data Record:</strong> For researchers who want to conduct their analysis in the R programming language, the curated NHANES datasets and the data dictionaries can be downloaded as a .zip file which include an .RData file and an .R file. We provided an .RData file that contains all the aforementioned datasets as R data objects (“w - nhanes_1988_2018.RData”). Also in this .RData file, we make available all R scripts on customized functions that were written to curate the data. We also provide an .R file that shows how we used the customized functions (i.e. our pipeline) to curate the data (“m - nhanes_1988_2018.R”).

美国国家健康与营养检查调查（National Health and Nutrition Examination Survey, NHANES）提供了美国非机构化人群的健康与环境暴露相关数据。这类数据对于解析环境与行为因素如何影响人体健康具有极高的研究价值，目前也被广泛用于解答公共卫生领域的诸多问题，例如疾病患病率相关研究。不过，若要通过大规模分析从中挖掘新的研究结论，首先需要对这些数据进行预处理。

NHANES的数据分散存储于数百个文件中，且存在多处不一致之处。修正这类不一致需要系统性的交叉核查与大量工作，但这是准确且可重复地表征暴露组（exposome）与疾病（例如癌症死亡率结局）之间关联的必要前提。

为此，我们整合了NHANES Ⅲ（1988-1994年）与连续调查周期（1999-2018年）的614个独立文件，对无限制的原始数据进行标准化统一，构建了一套经过整理与标准化的数据集，并配套提供了相关代码。该数据集共涵盖134310名参与者的信息，包含4740个变量。

这些变量涵盖以下10大类：1）人口统计学信息；2）膳食摄入情况；3）体格检查结果；4）职业暴露信息；5）问卷条目（例如体力活动、总体健康状况、既往病史）；6）用药情况；7）关联美国国家死亡索引的死亡状态数据；8）调查权重；9）环境暴露生物标志物检测结果；10）化学物质注释信息，用于标注检测值低于或高于检测下限的情况。

我们还提供了数据字典，列出了所有变量及其详细说明，以帮助研究人员快速浏览数据集。此外，我们提供了R Markdown文件，展示用于计算汇总统计量与构建回归模型的示例代码，以加速暴露组与癌症死亡率长期趋势的高通量分析工作。

<strong>CSV 数据记录：</strong>
整理后的NHANES数据集与数据字典共包含13个CSV文件与1个Excel文件。其中，10个CSV格式文件对应前述10大类数据模块，分别命名为：1）死亡率数据（mortality）、2）膳食数据（dietary）、3）人口统计学数据（demographics）、4）应答数据（response）、5）用药数据（medications）、6）问卷数据（questionnaire）、7）化学物质数据（chemicals）、8）职业暴露数据（occupation）、9）权重数据（weights）、10）注释数据（comments）。
第11个文件为数据字典文件"dictionary_nhanes.csv"，该文件列出了NHANES全部4740个变量的变量名、说明、所属模块、分类、单位、CAS编号（CAS Number）、注释用途、化学物质家族、简化化学物质家族名称、检测次数与可用调查周期。
第12个CSV文件"dictionary_harmonized_categories.csv"包含分类变量的标准化分类体系。
第13个CSV文件"dictionary_drug_codes.csv"为药物代码描述字典。
第14个文件为Excel文件"nhanes_inconsistencies_documentation.xlsx"，其中记录了所有受影响变量的不一致情况，用于辅助各NHANES数据集的整理工作。

<strong>R 数据记录：</strong>
对于希望使用R语言开展分析的研究人员，整理后的NHANES数据集与数据字典可通过ZIP压缩包下载，其中包含一个RData文件与一个R脚本文件。
我们提供了包含前述所有数据集的RData文件"w - nhanes_1988_2018.RData"，该文件中还包含了用于数据整理的自定义R函数脚本。此外，我们还提供了R脚本文件"m - nhanes_1988_2018.R"，用于展示如何使用上述自定义函数（即我们的数据整理流程）完成数据集的整理工作。