This repository has all code and data necessary to generate the results reported in Incorporating Testing Volume into Estimation of Effective Reproduction Number Dynamics. All code was written in R or Stan. Each file that produces visualizations has the names of all files used to create that visualization.
Files used to generate simulated outbreak data are located in the simulation scripts folder. Files used to analyze simulated outbreak data are located in the simulation analysis scripts folder. Much of this code was written to run on a computing cluster using the Slurm scheduler. Pre-processed results and code for creating the manuscript figures are stored in the simulation results folder.
Data from the California Open Data Portal used in this study is stored in the data folder. Code for analyzing this data is available in the real data analysis scripts folder. Again, much of this code was written to be run on a computing cluster. Pre-processed results and code for creating the manuscript figures are stored in the real data results folder.