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Update models with adaptation mechanisms and change tag 'adaptive threshold' to 'adaptation' #3241

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merged 2 commits into from
Jul 31, 2024

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@jessica-mitchell jessica-mitchell commented Jun 27, 2024

This PR updates the model tag for models that use an adaptation mechanism to 'adaptation' after discussions with @ddahmen
The reason is that not all the models have the same adaptation mechanism, and the ones labeled with adaptive threshold (i.e. 'aeif' models) technically do not have an adaptive threshold.
We were also missing tags for several models that have an adaptation mechanism but were not 'aeif' models.

See Read the Docs output here: https://nest-simulator--3241.org.readthedocs.build/en/3241/models/index.html#adaptation

@shimoura agreed to review, thanks!

@jessica-mitchell jessica-mitchell added S: Normal Handle this with default priority T: Maintenance Work to keep up the quality of the code and documentation. I: No breaking change Previously written code will work as before, no one should note anything changing (aside the fix) labels Jun 27, 2024
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The ones included seem right. I noted one that is missing. The "Izhikevich" model can present spike frequency adaptation.

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jessica-mitchell commented Jul 31, 2024

The ones included seem right. I noted one that is missing. The "Izhikevich" model can present spike frequency adaptation.

@shimoura I don't see, however, an obvious parameter that reflects an adaptive mechanism in the model code

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The ones included seem right. I noted one that is missing. The "Izhikevich" model can present spike frequency adaptation.

@shimoura I don't see, however, an obvious parameter that reflects an adaptive mechanism in the model code

The model is similar to aeif category. The main difference is the dependence of membrane voltage with quadratic terms instead of exponential. And the parameters "a", "b", and "d" are in some way similar to the parameters "a" and "b" of aeif models.
In summary, different values of these parameters will give similar behavior as aeif models. The spike frequency adaptation is one of them. Fig. 2 of the main Izhikevich reference shows it.

Obs: I noticed in Izhikevich documentation that du/dt should be dU_m/dt to match the variable names.

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thanks for the explanation, Izhikevich is now added

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Merging with 1 reviewer, since it's documentation related, also discussed in person at NEST meeting, to general approval of concept

@jessica-mitchell jessica-mitchell merged commit 468edda into nest:master Jul 31, 2024
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@jessica-mitchell jessica-mitchell deleted the add-tags branch July 31, 2024 12:33
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I: No breaking change Previously written code will work as before, no one should note anything changing (aside the fix) S: Normal Handle this with default priority T: Maintenance Work to keep up the quality of the code and documentation.
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