Measuring the unknown: an estimator and simulation study for assessing case reporting during epidemic

Repository for simulations of underreporting method, see preprint here: https://www.biorxiv.org/content/10.1101/2021.02.17.431606v1

Folder structure:

• r: contains r scripts for running the simulations
• r/functions: contains user written functions used for simulations
• outputs: Tables and Figures in the paper
• data: simulated data
• artwork: figure explaining method used in the paper.

Scripts

• 00_packages: This can be run once to install the needed packages.
• 01_simulate_outbreaks.R: Simulates outbreaks of various sizes.
• 02_remove_cases.R: Removes a proporiton of cases from the simulated outbreaks.
• 03_combine_sims.R: Combines all the simulations together.
• 04_create_measures.R: Calculates the performance measures used to evaluate the method under the simulations.
• 05_analyse_sims.R: Create graphs and analysis of the simulations using the performance measures.