Welcome to PEtab Select’s documentation!
PEtab Select brings model selection to PEtab. PEtab Select comprises file formats, a Python package and a command line interface.
Model selection is the process of choosing the best model from a set of candidate models. PEtab Select provides a standardized and compact way to specify the candidate model space, implements a number of model selection algorithms and criteria.
Supported model selection algorithms:
brute force
Supported model selection criteria:
(corrected) Akaike Information Criterion (AIC / AICc)
Model calibration is performed outside of PEtab Select. For example, PEtab Select is well-integrated with:
Other model calibration tools can easily be integrated using the provided Python package or command line interface. An example of this is provided for the Python package statsmodels at Model selection with non-SBML models and unsupported calibration tools.
For users, in most cases, model selection is performed entirely via one of the calibration tools, rather than the PEtab Select package directly. Hence, we recommend reading the documentation from your calibration tool on model selection. After model selection, the analysis and visualization methods in the PEtab Select package can be used directly with the results from your calibration tool.
For developers, we provide some examples of how integrate model selection with PEtab Select into unsupported calibration tools via the CLI and Python interfaces of the PEtab Select package.
Installation
The Python 3 package provides both the Python 3 and command-line (CLI) interfaces, and can be installed from PyPI, with:
pip install petab-select