Code and data to reproduce "Epidemic time series similarity is related to geographic distance and age structure"

This repository contains code and data to reproduce the analyses from > Dallas, TA, G Foster, R Richards, B Elderd. 2022. Epidemic time series similarity is related to geographic distance and age structure. The code to analyze and reproduce manuscript figures is all contained in the `analysis.Rmd` file, which contains the R code. This code loads the most current epidemic time series data, allowing the analyses to be re-run as more data are added. The main text considers the period between Jan 22, 2020 and May 9, 2022. A copy of these data are provided as `time_series_covid19_confirmed_US.csv` for reproducibility. We rely on a couple of other data sources, including data from the US Census Burueau (`county-pop-data.csv`) and estimates of R0 (`Ives&BozzutoTableS113Oct20.csv`) from > Ives, Anthony R., and Claudio Bozzuto. "Estimating and explaining the spread of COVID-19 at the county level in the USA." Communications biology 4.1 (2021): 1-9.