Code and data associated with "Reductions in commuting mobility predict geographic differences in SARS-CoV-2 prevalence in New York City"
Stephen M. Kissler, Nishant Kishore, Malavika Prabhu, Dena Goffman, Yaakov Beilin, Ruth Landau, Cynthia Gyamfi-Bannerman, Brian T. Bateman, Jon Snyder, Armin S. Razavi, Daniel Katz, Jonathan Gal, Angela Bianco, Joanne Stone, Daniel Larremore, Caroline O. Buckee, Yonatan H. Grad
Analysis was run using R version 3.6.2 on a 2017 MacBook Pro using an 2.3 GHz Intel Core i5 processor.
figuremaker.R: Main file for reproducing the figures and analysis from the article. Expected runtime: 5 min.
serofunctions2.R: Code for inferring population prevalence given test sensitivity and specificity; see https://github.com/LarremoreLab/covid_serological_sampling and https://larremorelab.github.io/covid19testgroup
borough_zip.csv: Mapping from boroughs to ZIP codes
borough_zip3.csv: Mapping from boroughs to 3-digit ZIP code prefixes
borough_zip3.csv: Mapping from boroughs to 3-digit ZIP code prefixes, separating North and South Queens
nyc_hospital_data.csv: Data from the New York City hospitals
All code is available under the GNU General Public License, version 3, included in this repository under the following terms: This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.