This repository contains code for Claire Graves' Endocrine Surgery Access project. The project uses surgeon address data as well as population, demographic, and socioeconomic data from the US Census to understand the distribution of endocrine surgeons in relation to the US population. The goal of our collaboration is is to better understand the distribution of endocrine surgery centers in the United States and who has access to these centers. The larger goal of this work is to reduce the barriers for patients to access care requiring an endocrine surgeon.
The research resulting from this collaboration was published in the journal Surgery. We suggest the following citation:
Maeve M Alterio, Michele Tobias, Arthur Koehl, Alexis L Woods, Kiyomi Sun, Michael J Campbell, Claire E Graves. 2023. Who Serves Where: A Geospatial Analysis of Access to Endocrine Surgeons in the United States and Puerto Rico. Surgery, Nov. 2023.
Claire Graves, M.D. - Department of Surgery, University of California Davis
Maeve Alterio - Washington State University Elson S. Floyd College of Medicine
Alexis Woods, M.D. - Department of Surgery, University of California Davis
Kiyomi Sun - Department of Surgery, University of California Davis
Michael Campbell, M.D. - Department of Surgery, University of California Davis
Michele Tobias, PhD - Geospatial Data Specialist
Arthur Koehl - Data Scientist
Alison Wong - Student Employee
Sebastian Lopez - Student Employee
The directory structure for the project is:
LICENSE Currently unvavailable
README.md Project overview document
.gitignore A file listing files to ignore for version control (git) processes
data/ Data sets (files > 1MB go on Google Drive)
|--- geocoded_addresses_2022-06-29_144609.csv Surgeon's office addresses geocoded by Geocodio and by hand using Google Maps; output from combine_geocoding_results.R
|--- isochrones_120_min.rds 120-minute isochrone (access boundary); output from compute_isochrones.R
|--- isochrones_60_min.rds 60-minute isochrone (access boundary); output from compute_isochrones.R
|--- isochrones_90_min.rds 90-minute isochrone (access boundary); output from compute_isochrones.R
|--- tract_population.rds Census tracts containing population calculation for each isochrone; output from access_calculation.R
docs/ Supporting documents - documentation of the process of setting up Valhalla with Docker on the DataLab server
|--- census_variables.csv Variables downloaded in the second stage of this project from the R TidyCensus package
|--- docker_installation.md Instructions for how to set up docker on the DataLab server
|--- valhalla_installation.md Instructions for how to set up Valhalla on the DataLab server
R/ R source code
|--- access_calculation.R Calculates the intersection of the isochrone boundaries and the census tracts, then calculates the population in each polygon created
|--- census_data.R Downloads the census data from the TidyCensus package
|--- combine_geocoding_results.R A script to join the output from Geocodio and the hand geocoding process
|--- compute_isochrones.R Computes the isochrone boundaries using Valhalla
|--- distance_method_demo.R A script used at the beginning of this project to communicate the proposed methods
|--- write_isochrone_to_geopackage.R Combines the data in the isochrone .rds files to make one geopackage for ease of use in QGIS for mapmakingData and supporting documents for this project will be stored in a Google Drive folder on DataLab's account.
The directory stucture for the files on Google Drive is:
data/ Data sets
documentation Documentation for the workflow and methods used in the analysis
literature Published papers related to the work at hand
support_documents/ Project proposal, collaboration agreement, scoping document, etc.
weekly_updates/ Weekly progress reports from the DataLab team
meeting_notes_graves_2022_endocrine_surgery Running meeting notes