EMU 2023 Agreement for Performance of Work with WHO Western Pacific Regional Office

Notebooks illustrate various epidemiological processes using the summer2 platform.

To run these over Google Colab, follow the links below and the instructions in the first cell.

Colab notebooks links for recapping previously introduced materials

Simple SEIR model

Child susceptibility

Calibration

Heterogeneous mixing

Serial latent compartments

Age-specific infection fatality rate

Multiple strains

Renewal introduction

Local installation

To interact with the code from this repository on your local computer, you would need to undertake the following steps:

• Set up a conda environment
• Install summer with the command pip install summerepi2
• Git clone the repository
• Install jupyter, or use an IDE with integrated notebook support like Visual Studio Code Please familiarise yourself with these tools before setting up your environment.

Other resources

The notebooks listed above provide a brief introduction to participants in our 2023/2024 capacity building program.

Further resources are available through our main homepage. In particular, we draw your attention to:

• Full online documentation of the summer platform
• Our textbook of infectious disease modelling using summer