A collection of software packages and related resources produced by the Monash Epidemiological Modelling Unit.
Software Packages
Summer
Summer is a package for simple and expressive development of compartmental
timeseries ODE models of infectious diseases.
It uses jax to compile these models to fast optimized code.
Estival
Estival is a Bayesian modelling package for summer, allowing convenient expression of observations/likelihoods/priors.
It includes tight integration with tools like PyMC and nevergrad
Epidemiological applications
Textbook
A summer based textbook of infectious disease modelling
Output validation
Reproduction of the Vynnycky & White models using summer
Publications
A few selected publications using summer:
- Understanding how Victoria, Australia gained control of its second COVID-19 wave. Trauer JM, Lydeamore MJ, Dalton GW, Pilcher D, Meehan MT, McBryde ES, Cheng AC, Sutton B, Ragonnet R. Nature Communications 2021.
- Estimating the long-term effects of mass screening for latent and active tuberculosis in the Marshall Islands. Ragonnet R, Williams BM, Largen A, Nasa J, Jack T, Langinlur MK, Ko E, Rahevar K, Islam T, Denholm JT, Marais BJ, Marks GB, McBryde ES, Trauer JM. International Journal of Epidemiology 2022.
- Understanding COVID-19 dynamics and the effects of interventions in the Philippines: A mathematical modelling study. Caldwell JM, de Lara-Tuprio E, Teng TR, Estuar MRJE, Sarmiento RFR, Abayawardana M, Leong RNF, Gray RT, Wood JG, Le LV, McBryde ES, Ragonnet R, Trauer JM. Lancet Regional Health Western Pacific 2021.
- Sustaining effective COVID-19 control in Malaysia through large-scale vaccination. Jayasundara P, Peariasamy KM, Law KB, Abd Rahim KNK, Lee SW, Ghazali IMM, Abayawardana M, Le LV, Khalaf RKS, Razali K, Le X, Chong ZL, McBryde ES, Meehan MT, Caldwell JM, Ragonnet R, Trauer JM. Epidemics 2021.
See more publications from our team here.