Spatial aggregation choice in the era of digital and administrative surveillance data

This repository provides the data and source code for the following paper: Lee, Elizabeth C., Ali Arab, Vittoria Colizza, and Shweta Bansal. "Spatial aggregation choice in the era of digital and administrative surveillance data." PLOS Digital Health. https://doi.org/10.1371/journal.pdig.0000039

Note: This repository uses git lfs due to a handful of large files. You may need to install this extension on your computer to pull these large files when cloning the repository. See more details here.

Data (R_export/)

Processed weekly time series of influenza-like illness (ILI) intensity from 2001 through 2009. A codebook for the key column names can be found in this folder.

• county scale: R_export/fullIndicAll_periodicReg_irDt_Octfit_span0.4_degree2_analyzeDB_cty.csv
• state scale: R_export/fullIndicAll_periodicReg_irDt_Octfit_span0.4_degree2_analyzeDB_st.csv
• HHS region scale: R_export/fullIndicAll_periodicReg_irDt_Octfit_span0.4_degree2_analyzeDB_reg.csv

Other data in this folder may be required data input files to run the code or analysis outputs generated by the code.

Code (programs/)

Scripts in this folder were used to perform analyses described in this paper or produce figures in the main text or supplementary material (See SM_figures/ folder).

Other Input Files (reference_data/)

Files in this folder may be required input files to run the code. They are county, state, and HHS region coordinates, abbreviations, and shapefiles derived from public sources of information.