EpidemicRepos

Epi Group

Epiforecasts

MRC Centre for Global Infectious Disease Analysis

COVID-19 Wastewater Epidemiology SARS-CoV-2 | Covid19wbec.org

Institute for Disease Modeling

publications - MOBS Lab

R Epidemics Consortium

Oxford Big Data Institute: Pathogen Dynamics Group

Mac-Theobio

Compartment Models

Python:

uiuc-covid19-modeling/pydemic: a python driver for epidemic modeling and inference

I-Bouros/multi-epi-model-cross-analysis: A collection of multiple epidemiological models used in the modelling of cases observed during the COVID-19 pandemic.

Julia

Include data cleaningberndblasius/Covid19: Wang et al SEIR-like model for 2019/20 Covid-19 outbreak

jtmatamalas/MMCAcovid19.jl: Microscopic Markov Chain Approach to model the spreading of COVID-19

affans/covid-19-lancetid: A clone of Peter Jentsch's covid19 model

uncomfyhalomacro/covid19_mindanao_seir_model: COVID19 SEIR model in Mindanao, Philippines using Julia

schrimpf/CovidSEIR.jl: Bayesian estimation of a SEIR model or Corona Virus

ImperialCollegeLondon/epidemia: epidemia package

Agent based modelling

Julia: RenuSolanki/EasyABM.jl: An easy to use and performant Julia framework for agent based modeling.

BDI-pathogens/OpenABM-Covid19: OpenABM-Covid19: an agent-based model for modelling the spread of SARS-CoV-2 (coronavirus) and control interventions for the Covid-19 epidemic

jangevaare/Pathogen.jl: Simulation, visualization, and inference tools for modelling the spread of infectious diseases with Julia

affans/covid19abm.jl: Agent Based Model for COVID 19 transmission dynamics

thomasvilches/vac_covid_ontario

goodETACE/ace_covid19: An integrated agent-based economic and epidemiological model of the COVID-19 pandemic.

thomasvilches/multiple_strains

IgorDouven/COVID.jl: Julia code for agent-based model of COVID-19 outbreaks and possible intervention strategies

werzum/COVID19-ABM: An Agent-Based model of the COVID-19 spread in Germany

kkmann/cov19sim: agent-based simulation of covid-19 for small populations

Python:

GoodInstituteforDiseaseModeling/covasim: COVID-19 Agent-based Simulator (Covasim): a model for exploring coronavirus dynamics and interventions

petroniocandido/COVID19_AgentBasedSimulation: COVID-ABS: An Agent-Based Model of COVID-19 Epidemic to Simulate Health and Economic Effects of Social Distancing Interventions

BDI-pathogens/OpenABM-Covid19: OpenABM-Covid19: an agent-based model for modelling the spread of SARS-CoV-2 (coronavirus) and control interventions for the Covid-19 epidemic

worldbank/covid19-agent-based-model: This repository contains the Python implementation of the agent-based model used to model the spread of COVID-19.

maplerainresearch/covid19-sim-mesa: COVID-19 infection multi-agent simulation using Mesa framework

Matlab:

Network Model

Julia:

bridgewalker/Fastnet.jl

csimal/NetworkEpidemics.jl: A Small package for simulating epidemic spreading on networks, including a generic Gillespie algorithm and Mean Field Approximations

EdMHill/covid19_uni_network_model

EdMHill/covid19_worker_network_model

social_agent_based_modelling/scripts at 606f5ec1ed51781926b7891f67f87ac4404c7d57 · lquante/social_agent_based_modelling

csimal/temporal-networks

Python:

ryansmcgee/seirsplus: Models of SEIRS epidemic dynamics with extensions, including network-structured populations, testing, contact tracing, and social distancing.

alsnhll/COVID19NetworkSimulations: Public repository for stochastic network simulations of COVID19 dynamics

COVID-IWG/epimargin: networked, stochastic SIRD epidemiological model with Bayesian parameter estimation and policy scenario comparison tools

springer-math/Mathematics-of-Epidemics-on-Networks: Source code accompanying 'Mathematics of Epidemics on Networks' by Kiss, Miller, and Simon http://www.springer.com/us/book/9783319508047 . Documentation for the software package is at https://epidemicsonnetworks.readthedocs.io/en/latest/

simoninireland/epydemic: Epidemic processes on networks in Python

EpiModel/EpiModel-Gallery: Gallery of Network-Based Epidemic Model Templates for EpiModel

Partial Differential Model

Julia:

R-DjidjouDemasse/Age-structured-model-COVID19-Julia-code: Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic by Q. Richard, S. Alizon, M. Choisy, M.T. Sofonea, R. Djidjou-Demasse

Epiforecasting

The Reich Lab at UMass-Amherst

reichlab/covid19-forecast-hub: Projections of COVID-19, in standardized format

Social Contact Matrix

sbfnk/epimixr: Epidemiological analysis using social mixing matrices

R Epidemics Consortium

Rt

ResearchLuxembourg/restimator: Real time estimation of epidemic Effective Reproduction Number for Luxembourg

epiforecasts/covid-rt-estimates: National and subnational estimates of the time-varying reproduction number for Covid-19

Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters • EpiNow2

mrc-ide/EpiEstim: A tool to estimate time varying instantaneous reproduction number during epidemics

lo-hfk/epyestim: Python package to estimate the time-varying effective reproduction number of an epidemic from reported case numbers

davidearn/epigrowthfit: Estimating Epidemic Growth Rates