nhanes

Python interface to NHANES dataset

What is NHANES?

NHANES is the National Health and Nutrition Examination Survey, which is run by the US Centers for Disease Control. Every year, the study examines a representative sample of about 5000 individuals from across the United States, using a broad range of surveys, physiological measurements, and laboratory tests. These data are useful for many purposes --- the main interest of the developer is to use them in teaching introductory statistics. There is a R package that provides access to the NHANES dataset, and the present package is meant to provide similar access to python users.

NOTE: A number of the variables have been recoded in order to make the data more usable. Before using these data for any serious analysis project, please examine the code and make sure that you understand the potential impact of this recoding on your analyses.

Installing the package

You can install the package using the following command:

pip install nhanes

Currently the dataset gives access to data from the most recent release at the time of development, which is the 2017-2018 data release.

Using the package

The package provides both a selected subset of the data, as well as detailed metadata regarding the selected variables, both stored as pandas data frames. To access the data and metadata, use the following code:

from nhanes.load import load_NHANES_data, load_NHANES_metadata

data_df = load_NHANES_data(year='2017-2018')
metadata_df = load_NHANES_metadata(year='2017-2018')

The row indices in the metadata match the column names in the data:

In [10]: data_df['GeneralHealthCondition']
Out[10]:
SEQN
93703.0           NaN
93704.0           NaN
93705.0          Good
93706.0     Very good
93707.0          Good
              ...
102952.0    Very good
102953.0         Fair
102954.0         Good
102955.0    Very good
102956.0         Good
Name: GeneralHealthCondition, Length: 8366, dtype: object

In [11]: metadata_df.loc['GeneralHealthCondition']
Out[11]:
Variable                                                                   HSD010
Type                                                                      Numeric
Format                                                                        NaN
Informat                                                                      NaN
Label                                                    General health condition
Source                                                                        HSQ
VariableName                                                               HSD010
SASLabel                                                 General health condition
EnglishText                     Next I have some general questions about {your...
Target                           Both males and females 12 YEARS -\n\n\t\t\t15...
VariableNameLong_variable_df                               GeneralHealthCondition
Source_variable_df                                                            HSQ
EnglishInstructions                                                           NaN
HardEdits                                                                     NaN
Recoded                                                                      True
Name: GeneralHealthCondition, dtype: object

Additional information about each variable can be found on the NHANES web site; a helpful function called open_variable_page() is included that will open the relevant page for any particular data source.

Building our own data

A script called make_combined_NHANES_data.py is provided so that you can recreate the data for different releases and using different variable sets.