I am trying to find parameters for the Lotka-Volterra equations using halfnormal prior for each of the parameter.Here’s the code- with pm.Model() as model: a = pm.HalfNormal('a', 1, transform=None) b = pm.HalfNormal('b', 0.5, transform=None) c = pm.HalfNormal('c', 1.5, transform=None) …

You are right, is not yet in PyMC3, but Agustina and I have plans to continue developing it and adding it to PyMC3 this year.

Due to unavailability of the Simulator in pymc3 ,I am not able to experiment out the model ,but I would be very happy to contribute to it or to some other features if you want to add in the pymc3 module for improving the acceptance ratio /computational efficiency.

@aloctavodia might have an experimental branch that you can test/contribute to

Hi @Adarsh-kumar your help is certainly appreciated. There are some changes in SMC that are now part of PyMC3 but not reflected yet in SMC-ABC, although @agustina may have a newer version I am not aware of. I will talk to Agustina next Monday (she is on vacations now) and we then could coordinate to…

Hi @ Adarsh-kumar . The Lotka-Volterra example should run on the code currently on this branch . It is not merged to pymc3’s master branch yet. I suggest you use this branch for testing.

thanks @agustina, it seems to me your branch has not incorporated the last changes in SMC, right?

@aloctavodia and @agustinaarroyuelo thanks for the response , I will test model on the branch mentioned by @agustinaarroyuelo . I am ready to contribute from Monday , till then i will test the models on some example datasets /known distributions and get my hands on it.

hi @agustinaarroyuelo ,but I am getting the same error message while running the Lotka-Volterra example on the branch you mentioned. Error AttributeError: module ‘pymc3’ has no attribute ‘Simulator’

@aloctavodia @agustinaarroyuelo may you recheck the branch on which I can test the The Lotka-Volterra example and will be able to contribute to the project in the coming time.

AttributeError: module 'pymc3' has no attribute 'Simulator'

Questions

junpenglao February 6, 2019, 8:49am 20

BTW, I gather that you are using scipy function to generate ODE? You might find this interesting as well: Dynamical model in pymc3

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AttributeError: module 'pymc3' has no attribute 'Simulator'

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