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 notebook links

1. Simple SEIR model

2. Stratification

3. Calibration

4. Heterogeneous mixing

5. Serial latent compartments

6. Tracking model outputs

7. Multiple strains

8. Post-immunity dynamics

9. Renewal introduction

10. Renewal implementation

11. Tuberculosis

Local installation

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

• Git clone the repository

git clone https://github.com/monash-emu/WPROEpiModellingTraining.git

• Install conda, and set up an environment

conda create -n summertraining python=3.10
conda activate summertraining

• Install the requirements into the active environment (this can take several minutes)

pip install -r requirements.txt

• Use an IDE with integrated notebook support like Visual Studio Code, or install jupyter

Other resources

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

Further resources are available through the Monash EMU homepage. In particular, we draw your attention to:

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

Notes on the manual

The PDF of the training manual is generated from the supplied notebook file using Quarto

quarto render .\WPRO_WHO_Capacity_Training_Manual.ipynb --to pdf --toc