opentak 0.1.0

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OpenTAK Clustering

OpenTAK is a python package for clustering and visualizing treatment sequences in a cohort. It aims to identify, cluster, and represent the different treatment sequences used, while quantifying the number of patients involved in each of these sequences.

Under the hood, it runs on a Hierarchical Clustering Algorithm.

📖 Documentation: https://heva-io.github.io/opentak/latest/
📝 Blog (methodology + real use cases): https://hevaweb.com/en/articles/tak-r-celebrates-its-4th-anniversary/120

Installation

To get started with the package, run one of the following command:

pip install opentak

or:

poetry add opentak

or:

uv add opentak

Quick Start

Starting from an event log with 3 columns — ID_PATIENT, EVT, and TIMESTAMP (int) — you can easily plot treatment sequences for each patient.
The sequences are automatically ordered and clustered by similarity.

👉 Check out the full documentation for more details.

from opentak import TakBuilder, TakVisualizer
from opentak.generation_cohort_tak import GenerateCohortTAK

NB_PATIENTS = 400
NB_JOURS_END = 370
n_clusters = 3

# Event log generation
evtlog = GenerateCohortTAK(
    nb_patients=NB_PATIENTS, nb_days_end=NB_JOURS_END, random_state=42
)
evtlog.initialisation_dataframe(
    treatment_name="Treatment A",
    dose_mean=int(NB_JOURS_END / 10),
    dose_std=int(NB_JOURS_END / 25),
)
evtlog.add_switch_gaussien("Treatment B")
evtlog = evtlog.add_in_out()
evtlog = evtlog.sort_values(by=["ID_PATIENT", "TIMESTAMP"])

# TAK builder 
tak = TakBuilder(evtlog).build()
tak.fit(n_clusters=n_clusters)

# TAK visualizer
tak_viz = TakVisualizer(tak)
tak_viz.process_visualization()
figplotly = tak_viz.get_plot(add_sep=True, unit_as_months=True, nb_months=2)
figplotly.update_layout(height=500, width=700)
figplotly.show()

You should obtain the following visualization.

You can explore the examples folder to see additional applications on various event logs.

Contributing

Contributions are welcome! To contribute:

1. Fork the repository and create a new branch for your changes.

2. Install the package dependencies using uv.
   First install uv by following the official documentation guide. Then run:

   uv sync --all-groups
   

3. Ensure your code is well-documented and includes relevant tests.

4. Checklist before submitting a pull request:

   • All tests pass with pytest
   • Ruff reports no linting errors when you run:

     uv run ruff format .
     uv run ruff check .
     

   • Mypy reports no type errors when you run:

     uv run mypy opentak
     

5. Open a pull request with a clear description of your changes and reference any related issues when possible.

Acknowledgements

• Big thanks to Marie Laurent for kicking off the idea and building the first version of the package.
• Shout-out to Alexandre Batisse, Martin Prodel, Hugo de Oliveira, and all former contributors from the Heva Data Science team for their feedback, refactoring, and feature enhancements.
• And of course, cheers to all future contributors who will keep pushing this project forward.