add daily PM2.5, NO2, and O3 concentrations from Schwartz Model to data

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DeGAUSS example call

If my_address_file_geocoded_schwartz_site_index.csv (output from the schwartz_grid_lookup container) is a file in the current working directory with columns named sitecode, start_date, end_date, and index_date (optional, see below), then

docker run --rm -v "$PWD":/tmp degauss/schwartz:0.5.5 my_address_file_geocoded_schwartz_site_index.csv

will produce my_address_file_geocoded_schwartz_site_index_schwartz.csv with added columns named date, PM25, NO2, O3, and days_from_index_date (if index_date was supplied in the input data).

The output will be in “long” format, meaning there will be a row for every day between the start_date and end_date, defined by the new date column.

Optional index_date

The user may choose to include a column called index_date to be used to anonymize dates. For example, the index date may be the patient’s date of birth. When the index_date column is present in the input data, the output will include all columns as usual, plus a column called days_from_index_date (defined asdate - index_date). The user can then remove the start_date, end_date, and index_date columns from the output (as long as index_date is stored elsewhere) to anonymize the data in terms of date.

Dates and Sitecode formatting

See Excel formatting for DeGAUSS for more information.

geomarker methods

Details on methods can be found at

geomarker data

DeGAUSS details

For detailed documentation on DeGAUSS, including general usage and installation, please see the DeGAUSS homepage.