Code for models and figures for manuscript entitled: Passive surveillance assesses compliance with COVID-19 behavioral restrictions in a rural US county

Authors: Faust, Lambert, Kochenour, Robinson, Bharti

Data are all from open access sources:

1. Traffic camera still images captured in real-time from PA DOT (e.g. http://www.dot35.state.pa.us/public/Districts/District2/WebCams/CAM02005CCTV9.jpg)
2. SafeGraph mobile phone location data: [https://catalog.safegraph.io/app/browse]. Downloaded on 03/15/21.
3. COVID-19 case reports, Pennsylvania Department of Health (https://data.pa.gov/Health/COVID-19-Aggregate-Cases-Current-Daily-County-Heal/j72v-r42c).Aggregated case data used in this analysis downloaded on December 17, 2020

Code in this repository provides details on workflow for processing raw data and analyzing each dataset:

Traffic analyses:

1. vehicle_counter.py: classification of traffic camera stills
2. vehicle_cleaning.R: cleaning of hourly count data for traffic cameras - namely removing frozen image counts.
3. vehicle_predictions.R: fitting GAMs to observed data and using to predict missing counts.
4. vehicle_viz.R: vizualizations for vehicle data; plots for main text and SI

SafeGraph analyses:

1. safegraph_extract_weekly_visits_and_devices_residing.rb: identifying and extracting dataset for Centre County
2. safegraph_create_centre_county_dataframes.py: converting raw data for Centre County into time series
3. safegraph_cleaning.R: adjusting mobile phone counts to match policy 'weeks' (Friday to Thursday) and normalization
4. safegraph_analysis.R: time series analysis of three years data

COVID-19 case analyses:

1. covid19_cleaning.R: truncating data to counties of interest and time period
2. covid19_analysis.R: visualizing epidemic curves for region and analysis for cross-correlation with movement data

Phase_functions.R: function to assign phase based on year and academic calendar (see SI of manuscript for justification)