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I am simulating a system of ODEs by using parameters taking from the literature. The next step would be to use ABC in order to estimate them (I have experimental data about all the curves of the model).

I tried to implement a very rudimental ABC rejection scheme but probably the model is too complex for this (10 equations and 39 parameters). Therefore I am trying to find a library (Python or R) that can do the job. Unfortunately, there are no examples for such a procedure and I am having some difficulties adapting existing code to my problem (AstroABC, ELFI, etc...). Does anyone have any suggestion?

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  • $\begingroup$ Have you checked on Darren Wilkinson's webpages? $\endgroup$
    – Xi'an
    Commented May 16, 2018 at 21:10

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There are a number of ABC related packages in R or Python - what you're having trouble with in terms of adapting is somewhat unclear.

For example, EasyABC https://cran.r-project.org/web/packages/EasyABC/vignettes/EasyABC.pdf for R or ABC-SysBio in Python https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894518/

It should be noted however that trying to use ABC to fit 39 parameters simultaneously is a tall order. Trying to fit 39 free parameters for an ODE model using any method is honestly a tall order.

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