This textbook is maintained by the Epidemiological Modelling Unit
at Monash University's School of Public Health and Preventive Medicine.
The notebooks (or chapters) run over Google's Colab interface,
and are introduced in the first notebook below.
Of course, we encourage users to download these and run them locally
with their preferred environments and interfaces.
requirements_frozen.txt can be pip installed to provide the needed dependencies
Feedback is very welcome, please send comments to [email protected]
Notebook 01 The field of infectious disease modelling and the rationale and scope for this textbook
Notebook 02
The messages we can learn from a basic infectious disease model constructed in summer
Notebook 03 How to think about the "flows" or "transitions" we implement in our models
Notebook 04 How to think about the "parameters" or "rates" of these flows/transitions
Notebook 05 The incubation period, the latent period and chaining compartments in series
Notebook 06 Post-infection immunity and its effects on epidemic dynamics
Notebook 07 Getting numeric solutions for the system
Notebook 08 Model outputs other than the size of an individual compartment
Notebook 09 Frequency-dependent and density-dependent transmission
Notebook 10 The reproduction number
Notebook 11 Cyclical epidemic dynamics
Notebook 12 Heterogeneous mixing introduction
Notebook 13 Frequency-dependent and density-dependent transmission with heterogeneous mixing
Notebook 14 Assortative mixing
Notebook 15 The relationship between mixing matrices and heterogeneity in susceptibility and infectiousness
Notebook 16 Using empiric data on population interactions in our models (introduction)
Notebook 17 Understanding data from contact surveys
Notebook 18 Implementing contact survey data in a model
Notebook 19 Adapting mixing matrices to new contexts
Notebook 20 Model calibration with the Metropolis algorithm