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Data2Dynamics / d2d

a modeling environment tailored to parameter estimation in dynamical systems
https://github.com/Data2Dynamics/d2d
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ODE Parameter Estimation #171

Closed iliailmer closed 1 year ago

iliailmer commented 1 year ago

Hi, I had a question about using d2d for estimation of initial conditions and parameters from an ODE system with outputs.

I have a small ODE such as

d/dt(r) = k1 * r - k2 * r * w,
d/dt(w) = k2 * r * w - k3 * w

and the output sample from the following functions

y1 = r+w
y2 = w

How can I convert this model into d2d-accepted format for estimation? Is there a tutorial/example on how to do that? Thanks!

clemenskreutz commented 1 year ago

Our Wiki https://github.com/Data2Dynamics/d2d/wiki provides a lot of documentation and examples.

Model definition is described at this page: https://github.com/Data2Dynamics/d2d/wiki/Setting%20up%20models

Many example models are in the folder "arFramework3/Examples".

A few short hints: Use arCreateProject to get almost empty standard templates for the model definition file and adapt this. You need 2 STATES (use more then one letter, e.g. rState instead of r), parameters for initial conditions are automatically created and two OBSERVABLES. You don't need an INPUTS, all STATES are in one COMPARTMENT.