Breaking down the ParamEst Class

- 1 min

I have been using the PyDSTool package by Rob Clewley for creating and simulating my models. This neat package allows you to worry about the creation and analysis of the model using a logical workflow rather than struggling with clumsy model definition functions like the ones Matlab’s ode solvers require. The tools for bifurcation analysis are quite sophisticated, providing a programmatic interface to functionality otherwise found easily in XPP. Overall, the Python Dynamical Systems ToolBox is an amazing package for simulation of non-linear systems in python.

I began running into problems when I attepted parameter estimation using PyDSTool’s ParamEst class. Seeking to use the Levenberg-Marquardt Least Squares Fit function LMpest, I tried figuring out the example script pest_test1.py that comes with the example scripts. This post will try and outline my main areas of confusion about this example script. To make it easier to read, I stripped down this script to an even simpler example.

• What really are Model Interfaces?
• Why does ParamEst throw up an error if the variable name in the reference trajectory differs from that in the model?
• Can I extract values during the parameter estimation?

(To be continued..)