daymet_chicago

Background

The Daymet weather variables included in this package are daily minimum and maximum temperature at a 1 km x 1 km gridded surface over the area of Cook County, IL for the years 2011 through 2023. This package is specifically for data linkage in the Cook County area between those years and for those variables, and cannot be altered.

Daymet data documentation: https://daac.ornl.gov/DAYMET/guides/Daymet_Daily_V4.html

Note: The Daymet calendar is based on a standard calendar year. All Daymet years, including leap years, have 1–365 days. For leap years, the Daymet data include leap day (February 29) and December 31 is discarded from leap years to maintain a 365-day year.

Using

If my_addresses.csv is a file in the current working directory with the following columns:

• ID column id
• date of the encounter enc_admit_date in YYYY-mm-dd
• start and end date columns start_date and end_date where end_date should match the date of the encounter in YYYY-mm-dd
• subsequent number of addresses per patient address_number
• census tract of patient census_tract
• date of last known address census_tract_date in YYYY-mm-dd
• and coordinate columns named lat and lon

Then the DeGAUSS command:

On Windows/PC:

docker run --rm -v $PWD:/tmp ghcr.io/degauss-org/daymet_chicago:0.1.2 my_addresses.csv

On iOS/Mac or if you want to explicitly define your file path:

docker run --rm -v "/Users/path_to/your/project":/tmp ghcr.io/degauss-org/daymet_chicago:0.1.2 my_addresses.csv

will produce my_addresses_daymet.csv with added columns:

• tmax: maximum temperature
• tmin: minimum temperature

Other columns may be present in the input my_addresses.csv file, and these other columns will be linked in and included in the output my_addresses_daymet.csv file.

Optional Arguments

There are no optional arguments associated with this package. All arguments are pre-coded or inferred from the address file.

Geomarker Methods

Daymet data on a specified date is linked to coordinate data within the my_addresses.csv file by matching on the Daymet 1 km x 1 km raster cell number. The set boundary box is Cook County, IL.

Geomarker Data

• This package takes pre-downloaded environmental data from Daymet as netCDF file(s).
• The R code that links the environmental data to the input coordinates is within entrypoint.R.

DeGAUSS Details

The Daymet_Chicago DeGAUSS package was created by Ben Barrett and Peter Graffy, and is designed for use by the Chicago Area Patient-Centered Outcomes Research Network (CAPriCORN). For detailed documentation on DeGAUSS, including general usage and installation, please see the DeGAUSS homepage.