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individual.jl

Tools to specify and simulate individual based models, using applied category theory

influenza

juliacall

Embed Julia in R

kenya-covid-three-waves

Model supporting "COVID-19 Transmission Dynamics Underlying Epidemic Waves in Kenya"

kenyacovaccines

Vaccine modelling

linelist

R package for handing linelist data

livestock_disease_control_differing_social_perspectives

ltcf-covid

mathepia.jl

Spatial and temporal epidemiology data mining flow tools including data processing and analysis, model setup and simulation, inference and evaluation. Focusing on state-of-the-art methods such as universal differential equations, epidemiology-informed deep learning methods.

mathepiadata.jl

Spatial and temporal data preprocessing and analysis tools including missing value handling, outlier detection, data smoothing, interpolate, time-series analysis, data visualization, and so on. It is part of Mathepia.jl

mathepiainference.jl

Bayesian inference tools. Including state-of-the-art inference methods: HMC family, ABC family, Data assimilation, and so on. Part of Mathepia.jl

mathepiamodels.jl

Epidemic spatial and temporal model setup and simulation. Focusing on state of the art epidemiology models such as universal differential equations, epidemiology-informed deep learning models. Part of Mathepia.jl

mathepiaoptimal.jl

Optimization, optimal control and optimal transport tools for spatial and temporal data mining. Part of Mathepia.jl

mathepideeplearning

Awesome-spatial-temporal-data-mining-packages. Julia and Python resources on spatial and temporal data mining. Mathematical epidemiology as an application. Most about package information. Data Sources Links and Epidemic Repos are also included. Keep updating.

mcmasterpandemic

SEIR+ model

mit-global-covid-modelling-project-1

mmcacovid19.jl

Microscopic Markov Chain Approach to model the spreading of COVID-19

model-runner

Service for running epidemiological models and storing their output

modelinginfectiousdiseases.jl

Julia versions of the programmes from Keeling, M.J. and Rohani, P., *Modeling Infectious Diseases in Humans and Animals*. The code is being developed as a learning exercise. It is not associated with the authors or publishers of the book, and is saved here in 'as is' form.

monkeypox_heavytail

Underlying code for Endo et al. "Heavy-tailed sexual contact networks and the epidemiology of monkeypox outbreak in non-endemic regions, May 2022."

monkeypox_uk

Some code for monkeypox

ncov2019odemodel

COVID-19 ODE model for publication

networkepidemics.jl

A Small package for simulating epidemic spreading on networks, including a generic Gillespie algorithm and Mean Field Approximations

nowcasting_covid19

Bayesian Nowcasting with application to COVID-19 fatalities in Sweden

npt-saliva-testing

COVID 19 NP vs Saliva testing

outbreaker2

Disease outbreak reconstruction from epidemiological and genetic data

pathogen.jl

Simulation, visualization, and inference tools for modelling the spread of infectious diseases with Julia

processing-household-composition-data

The scripts in this repository construct histograms of age-stratified household compositions from census data for use in infectious disease modelling.

rcall.jl

Call R from Julia

reopening_impactsimulator_us_states