Covasim is a stochastic COVID-19 agent-based simulator that can be used for COVID-19 (novel coronavirus, SARS-CoV-2) epidemic projections, scenario interventions, etc. It can also be adapted to different contexts (for example, the Diamond Princess cruise ship, cities, countries).

Python >=3.6 (64-bit).

We also recommend, but do not require, using Python virtual environments. For more information, see documentation for venv or Anaconda.

1. Clone a copy of the repository. If you intend to make changes to the code, we recommend that you fork it first.

2. (Optional) Create and activate a virtual environment.

3. Navigate to the root of the repository and install the Covasim Python package using one of the following options:

   • To install with webapp support (recommended):

     python setup.py develop

   • To install as a standalone Python model without webapp support:

     python setup.py develop nowebapp

   • To install Covasim and optional dependencies (be aware this may fail since it relies on private packages), enter:

     python setup.py develop full

   The module should then be importable as import covasim.

There are several examples under the examples directory. Run them using the following syntax:

python examples/simple.py

The example above creates a figure and other examples run Covasim simulations.

All core model code is located in the covasim subfolder; standard usage is import covasim as cv. The other subfolders, cruise_ship and webapp, are also described below.

The model consists of two core classes: the Person class (which contains information on health state), and the Sim class (which contains methods for running, calculating results, plotting, etc.).

The structure of the covasim folder is as follows:

• base.py: The ParsObj class, plus basic methods of the BaseSim class, and associated functions.
• interventions.py: The classes for adding interventions and dynamically modifying parameters.
• parameters.py: Functions for creating the parameters dictionary and populating correct attributes for people.
• people.py: Class for people and functions to create a population of people.
• README.md: Detailed information on the model parameters.
• requirements.py: Check that imports succeeded, and turn off features if they didn't.
• run.py: Functions for running simulations (e.g. parallel runs and scenarios).
• sim.py: The core class defining the model, namely Sim, which initializes the model, runs, and plots.
• utils.py: Numeric utilities, mostly based on Numba, for choosing random numbers (plus other helper functions).
• version.py: Version and version date information.

A version of the Covasim model specifically adapted for modeling the Diamond Princess cruise ship. It uses its own parameters file (parameters.py) and has slight variations to the model (model.py).

For running the interactive web application: please see the README.md in that folder for more information, including information on Docker deployment.

The code in this repository was developed by IDM to support our research in disease transmission and managing epidemics. We’ve made it publicly available under the Creative Commons Attribution-Noncommercial-ShareAlike 4.0 License to provide others with a better understanding of our research and an opportunity to build upon it for their own work. We make no representations that the code works as intended or that we will provide support, address issues that are found, or accept pull requests. You are welcome to create your own fork and modify the code to suit your own modeling needs as contemplated under the Creative Commons Attribution-Noncommercial-ShareAlike 4.0 License.