Package: episimmer
Episimmer : Epidemic Simulation PlatformPowered byHealthBadgeEpisimmer is an Epidemic Simulation Platform that aims to provide Decision and Recommendation Support to help answer your questions related
to policies and restrictions during an epidemic. Using simulation techniques widely applied to other fields, we can help schools and colleges
discover and hone the opportunities and optimizations they could make to their COVID-19 strategy.From the most simple decisions (Which days to be online or offline) to more complex strategies (What restrictions should I put on library use?,
How many times should I test?, Whom do I test?) Episimmer is the tool for the job.The EnvironmentEpisimmer is an agent-based epidemic simulator which allows you to model any kind of disease spreading environment. With the help
of simple text files, you can have your agents and the interaction network setup in no time. Here are some example
of the environments you can create.Completely connected agents at two locationsRandom Graph G(100, 0.1)Star GraphCellular AutomatonMulti-cycle graphThe edges represent connections between the agents and the node colours represent the changing agent disease state.But these are static networks, which aren't truly representing real-world phenomena. Episimmer allows you to have cycling dynamic networks which more closely
align with real-world social networks than static networks.Dynamic NetworkThe Disease ModelEpisimmer also allows easy creation of compartmental disease models. You can be as creative as you like, for example,Complex Model 1 (Taken fromhere)Complex Model 2 (Taken fromhere)Or you could even model a fancy Zombie Apocalypse disease model like thisZombie ApocalypseIntervention PoliciesThere are many kinds of policies that can be implemented in Episimmer by the user and each policy is built to be flexible.
Multiple policies defined by the user can be run in a simulation seamlessly. We have also created templates for the user to test different kinds of examples of policies.Currently, the policies that can be implemented are:Lockdown PolicyTesting PolicyVaccination PolicyContact Tracing PolicyVulnerability DetectionVulnerability Detection refers to finding vulnerabilities in the system that highly affect or are highly affected by
disease spread. A major part of decision support is detecting vulnerabilities in the ecosystem and taking appropriate
actions to control the disease spread.Two kinds of Vulnerability Detection exist in Episimmer -Agent-based Vulnerability DetectionEvent-based Vulnerability DetectionFor more details, check out theofficial documentation.InstallationPrerequisitesEpisimmer requires python 3.7+.Install using pipIf you are using Linux or macOS you can install episimmer from PyPI with pip:pip install episimmerInstall from sourceOr you can install from sourceFirst clone this repository:git clone https://github.com/healthbadge/episimmer.gitThen, to install the package, run the following command inside the episimmer directory:pip install -e .If you do not have pip you can instead use:python setup.py installIf you do not have root access, you should add the--useroption to the above lines.Running ExamplesTo run examples -If you installed episimmer through PyPI, run:episimmer <Path_to_Example>Otherwise, in the repository, run:python episimmer/main.py <Path_to_Example>Command line Argumentspositional arguments:example_path : Pass the path to the data folderoptional arguments:-np or --noplot : Restrict plotting the time plot after simulation. Default = False
-vul or --vuldetect : Run Vulnerability Detection on the data folder based on VD_config.txt. Default = False
-a or --animate : Creates a gif animation of the time plot. Default = False
-s or --stats : Choose to store statistics. Default = False
-viz or --vizdyn : Creates a gif of the simulation environment progressing through the days. Default = FalseTutorialsCheck out Episimmer'sofficial documentationfor a complete tutorial on the simulator. You may also go through these colab notebooks for a more hands-on tutorial on Episimmer:Tutorial 1 - Episimmer BasicsTutorial 2 - The EnvironmentTutorial 3 - Disease ModellingTutorial 4 - Intervention PoliciesTutorial 5 - Vulnerability DetectionUIOur current UI can be found athere. Note that it has minimal functionality as compared to running the codebase directly. Yet it competes with the current state of the art systems with multiple novel features.Episimmer is currently Work in Progress. Check out these point solutions built using the Episimmer codebase.Optimizing LockdownsEfficient Contact tracingYACHT protocolCustom Stochastic Model on a complete graphTesting strategies (Pool testing, Friendship testing)Vaccination with multiple vaccine types