covid-age

This repository contains the C++ code used to run a stochastic SEIR model for COVID-19. Specifically, the model is fitted to Chicago's data for the first year of the pandemic. The model is modified from Northwestern University Malaria Modelling team's early work during the COVID-19 pandemic. The code in this repository is used in the following publication:

• Toh KB, Runge M, Richardson RAK, Hladish TJ and Gerardin J. Design of effective outpatient sentinel surveillance for COVID-19 decision-making: a modeling study. Currently under review in BMC Infectious Disease. Available as a preprint in medRxiv.

General structure

src folder contains the "backbone" of the event driven algorithm and the SEIR model. exp folder contains the individual folder to each "experiment". chicago_yr1 subfolder contains code and parameters to reproduce first year of pandemic in Chicago. 1pop subfolder is used in the main experiment conducted for the sentinel surveillance paper; 2pop subfolder is used to model two partially mixing subpopulations (0 to 39 years old and > 40 years old). 2pop allows us to investigate the behaviour of surveillance indicator when two subpopulations experience different transmission intensity. See covid-age-description.txt for detailed description of the parameters, links to the model diagram and descriptions, and how they are specified in the code.

Usage

Use the Makefile (make all) in src to compile the model, then use Makefile in the individual experiment folder to compile the code specific to the experiment via make model. Then you can do ./model 1234 to run the model with a random number seed of 1234.

Serialization

The functionality to serialize simulation is added on 2023 Aug 3 commit. To use the functionality, download the cereal library and drop the cereal folder into ./src/.

Currently the serialization functionality is reflected in two files, ./src/NUCOVID_cereal.h and ./exp/chicago_yr1/chicago_yr1_cereal.cpp. To run it, you need to change the path in the runsim section of the cpp file to point to your desired folders navigate to ./exp/chicago_yr1/ and make model_cereal. Then type ./model_cereal to see the usage.

Example:

./model_cereal 1234 0 # Run first 100 days of simulation using seed 1234 and serialize
./model_cereal 2134 1 1234 # Pick up from serialize.1234 and run the next 271 days using seed 2134