Challenges in Estimating Time-Varying Epidemic Severity Rates from Aggregate Data

This repository contains all code, data, and writing for the paper on bias in estimating time-varying severity rates, such as the case fatality rate (CFR).

Usage

All data and experimental results can be fully reproduced using the provided R scripts.

1. Preprocess real-world data
   Download and preprocess datasets using scripts in Code/Preprocessing.

2. Compute severity rates
   Use scripts in Code/Analysis starting with data_for_* to estimate severity rates, saving results in Data/HFR_estimates.

3. Generate figures
   Create figures using the other scripts in Code/Analysis. These scripts run quickly.