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.. _README:

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https://pharmpy.github.io

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Pharmpy is a library and toolkit for pharmacometrics. It can be used as a regular Python package, in R via the pharmr <https://github.com/pharmpy/pharmr>_ package or via its built in command line interface.

Current features:

• A model abstraction as a foundation for higher level operations on models
• Functions for manipulation of models, e.g. changing model components like elimination or absorption
• Reading NONMEM models and results
• Running models and complex workflows (with NONMEM or to some extent nlmixr)

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Getting started

Installation

For installation in R see pharmr <https://github.com/pharmpy/pharmr>_.

Install the latest stable version from PyPI::

pip install pharmpy-core    # or 'pip3 install' if that is your default python3 pip

To be able to use components using machine learning the tflite package is needed. It can be installed using::

pip install --index-url https://google-coral.github.io/py-repo/ tflite_runtime

Python Example

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from pharmpy.modeling import read_model, read_modelfit_results model = read_model("run1.mod") res = read_modelfit_results("run1.mod") res.parameter_estimates THETA_1 0.004696 THETA_2 0.984258 THETA_3 0.158920 OMEGA_1_1 0.029351 OMEGA_2_2 0.027906 SIGMA_1_1 0.013241 Name: ests, dtype: float64 model.parameters name value lower upper fix THETA_1 0.004693 0.00 1000000 False THETA_2 1.009160 0.00 1000000 False THETA_3 0.100000 -0.99 1000000 False OMEGA_1_1 0.030963 0.00 oo False OMEGA_2_2 0.031128 0.00 oo False SIGMA_1_1 0.013086 0.00 oo False

CLI Example

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# Get help
pharmpy -h

# Remove first ID from dataset and save new model using new dataset
pharmpy data filter run1.mod 'ID!=1'

# Extract and print ofvs from multiple model runs
pharmpy results ofv run*.mod

Contact

This is the team behind Pharmpy <https://pharmpy.github.io/latest/contributors.html>_

Please ask a question in an issue or contact one of the maintainers if you have any questions.

Contributing

If you interested in contributing to Pharmpy, you can find more information under Contribute <https://pharmpy.github.io/latest/contribute.html#contribute>_.