symbolic-compartmental-model
A symbolic package based on SymPy for simulating and fitting Compartmental Models (CMs).
Overview
Symbolic Compartmental Model is a python package for constructing, simulating, and fitting
compartmental models. It is based on the symbolic calculations package sympy but can
also perform numerical calculations.
Current Features
- Defining a CM based on the contributed turnovers (M-matrix) and observed pool sizes
- Optionally include symbolic parameters and set their bounds for later fitting
- Several fitting functions, including single/multiple pools and mass balance constraints (optional)
- Both numerical and symbolic outputs for dynamic parameters: age, residence time, decay rate, etc.
- Plotting of simulated data
Getting started
- To fit a model without installing anything, use the browser app: Fit compartmental models online. It loads your data, fits it, and lets you download the results — everything runs locally in your browser and nothing is uploaded.
- For installing the package in your current python environment, can simply
pip install symbolic-compartmental-model. - The package documentation can be found on ReadTheDocs.
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