Tutorials
These tutorials will guide you through the main features of Typhoidsim. Each tutorial is interactive and includes executable code examples.
A quick introduction to the Typhoidsim framework.
How to assemble the main ingredients of a simulation.
Modeling the environmental reservoir and pathogen concentration.
Direct contact transmission between agents.
Combining environmental and contact transmission routes.
Adding seasonal modulation to environmental transmission.
Implementing vaccination campaigns to reduce burden.
Interventions: chronic carriers
Detecting and treating chronic typhoid carriers.
Calibrating a Typhoidsim model to data.
You can download these tutorials as Jupyter notebooks to run them locally. Look for the download button at the top of each tutorial.
To run these tutorials locally:
- Clone the Typhoidsim repository
- Install Typhoidsim and its dependencies (
pip install -e .) - Navigate to the
docs/tutorialsdirectory - Convert to Jupyter:
./convert_notebooks(or just open them directly ifjupytextis installed) - Launch Jupyter:
jupyter lab