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Decentralized Geomarker Assessment for Multi-Site Studies
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cole-brokamp use rocker/geospatial as base image
- this also fixes a bug where images would fail due to the tigris
package not being able to load
- i couldn't find the exact problem, but loading the sf package ahead of
time explicitly seemed to avoid the failure, but a warning message still
occurs
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CONTRIBUTING.md
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README.md

DeGAUSS

Decentralized Geomarker Assessment for Multi-Site Studies

Build Status License: GPL v3 status DOI

Questions? Problems? Please file an issue on GitHub and/or see our troubleshooting guide.

About

DeGAUSS is a decentralized method for geocoding and deriving community and individual level environmental characteristics while maintaining the privacy of protected health information. It is a standalone and versatile software application based on containerization. This means that geomarker assessment is reproducible, standardized, and can be computed on at scale. Importantly, DeGAUSS is executable on a local machine -- it does not require extensive computational resources and PHI is never exposed to a third party or the internet, making it ideal for geomarker assessment in a multi-site study. Please see detailed documentation within the wiki:

Currently Available Images

image description version source build
degauss/geocoder batch geocoding
degauss/census_tracts census tract FIPS ID
degauss/dist_to_major_roadway distance to TIGER/Line 2015 S1100 line in meters
degauss/acs_income census tract median household income from 2015 5-year ACS
degauss/geocoder_slim return geocoded text string as JSON
degauss/cchmc_batch_geocoder geocoding, census tract, deprivation index
degauss/crew_census historical census tracts and data built for CREW Docker Repository on Quay

Contributing

Please see CONTRIBUTING.md for guidelines on how to contribute to the development of DeGAUSS. Pull requests for new containers using the DeGAUSS framework are always welcome but early visibility is highly encouraged; we often create containers that are not yet publicly available and would love to still work together. Automated tests for containers are conducted through Travis, see .travis.yml for details.

Citation

If you use this software in a scientific publication, please consider citing one of our publications:

  • Cole Brokamp, Chris Wolfe, Todd Lingren, John Harley, Patrick Ryan. Decentralized and Reproducible Geocoding and Characterization of Community and Environmental Exposures for Multi-Site Studies. Journal of American Medical Informatics Association. 25(3). 309-314. 2018. Download.
  • Cole Brokamp. DeGAUSS: Decentralized Geomarker Assessment for Multi-Site Studies. Journal of Open Source Software. 2018. Download.
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