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:target: https://github.com/pharmpy/pharmpy/blob/main/LICENSE.LESSER
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:target: https://github.com/pharmpy/pharmpy/actions
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:target: https://www.python.org/downloads/
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.. _README:
|logo|
======
.. |logo| image:: https://github.com/pharmpy/pharmpy/raw/main/docs/Pharmpy_logo.svg
:width: 250
Pharmpy is an open-source software package for pharmacometric modeling. It has functionality ranging from reading and
manipulating model files and datasets to full tools where subsequent results are collected and presented.
Features include:
* A **model abstraction** which splits a model into core components which Pharmpy understands and can manipulate:
parameters, random variables, statements (including ODE system), dataset, and execution steps
* An **abstraction for modelfit results** which splits a parsed results into core components: e.g. OFV, parameter
estimates, relative standard errors (RSEs), residuals, predictions
* **Functions for manipulation of models and datasets** in the modeling-module: e.g. change structural model, add
time-after-dose column, deidentify dataset
* **Tools to aid model development** in the tools-module: execution of models within Python/R scripts, automatic
development of models (e.g. AMD, IIVSearch, RUVSearch), comparison of estimation methods
* Support for **multiple estimation tools**: parse NONMEM models, execute NONMEM, nlmixr2, and rxODE2 models, run all
Pharmpy tools with NONMEM and some with nlmixr2
For more comprehensive information and documentation, see: https://pharmpy.github.io
Pharmpy 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.
Getting started
===============
The sections below are intended as first steps, please check our `website <https://pharmpy.github.io>`_ website for
more comprehensive documentation, such as user guides and API references.
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
Python Example
--------------
.. code-block:: none
>>> from pharmpy.modeling import read_model
>>> from pharmpy.tools import load_example_modelfit_results
>>> model = load_example_model("pheno")
>>> model.parameters
value lower upper fix
POP_CL 0.004693 0.00 ∞ False
POP_VC 1.009160 0.00 ∞ False
COVAPGR 0.100000 -0.99 ∞ False
IIV_CL 0.030963 0.00 ∞ False
IIV_VC 0.031128 0.00 ∞ False
SIGMA 0.013086 0.00 ∞ False
>>> res = load_example_modelfit_results("pheno")
>>> res.parameter_estimates
POP_CL 0.004696
POP_VC 0.984258
COVAPGR 0.158920
IIV_CL 0.029351
IIV_VC 0.027906
SIGMA 0.013241
Name: estimates, dtype: float64
>>>
CLI Example
-----------
.. code-block:: none
# Get help
pharmpy -h
# Remove first ID from dataset and save new model using new dataset
pharmpy data filter run1.mod 'ID!=1'
# Run tool for selecting IIV structure
pharmpy run iivsearch run1.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>`_.
Raw data
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