swo/epic1

Absenteeism model

This model simulates the transmission of COVID-19 to an employee or their household, transmission within the household, the health outcomes experienced by members of the household, and the effects of those outcomes on the employee's absenteeism.

Getting started

1. Download R
2. Install packages in R: install.packages(c("tidyverse", "lubridate", "zoo"))
3. Ensure the input employee data is in the right place (see below)
4. Run make
5. Interpret the output file results/results.tsv
6. Make adjustments to run_employees.R, such as increasing the number of iterations (n_iter) or the epidemiological parameters (base_pars).

Input data

The scripts expect a file employees.tsv in this folder. This file should be tab-separated, with at least the following 4 columns:

• state: 2-letter abbreviations
• sex: either M or F
• age: an integer between 1 and 100
• n_dependents (number of dependents): a nonnegative integer

White papers

• Paper 1
• Paper 2
• Paper 3

File overview

• model.R: Main modeling functions
• run_employees.R: Runs simulations and stores the results
• analyze.R: Loads stored results and produces plots and tables
• scrape_state_data.R: Script to scrape incidences by state
• compute_risks_by_age.R: Derives certain risk ratios by age
• generate_fake_data.R: Generates fake employee data for debugging
• utils.R: Utility functions shared across scripts
• Makefile: Automated model running using make
• cache/: Stored simulation results
• results/: Output tables