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datalorax / equatiomatic

Convert models to LaTeX equations
https://datalorax.github.io/equatiomatic/
Creative Commons Attribution 4.0 International
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Suppor for high dimension ODEs? #109

Open AMHGeorgetown opened 3 years ago

AMHGeorgetown commented 3 years ago

Would this be able to pull large ODEs from model objects? In particular, ones used in the MRGsolve package?

datalorax commented 3 years ago

Hi - thanks for your interest. I'm not really sure what you're referring to. Do you mind providing a bit more context and possibly an example of what you're looking for?

mattfidler commented 3 years ago

I think you would have to extract the mrgsolve equations which are not formulas; It is similar to:

https://github.com/datalorax/equatiomatic/issues/52

AMHGeorgetown commented 3 years ago

It appears very similar to #52 - nlmixr uses ODE's (I think) as well. MRG solve uses LSODA ODE solver for Pharmacokinetic applications. In the world of PBPK, it would be very helpful to be able to extract the systems of equations in a "pretty" format for publications.

It sounds like its not general enough to be able to handle this. But this package looks great...why I was so excited!

datalorax commented 3 years ago

Thanks for the comment. I am always open to new ideas for enhancements and new developments, including building something that works generally across these. With that said, however, I know next to nothing about what we're talking about here and would need some more guidance. An example model, and what the output should look like, would be really helpful.

My highest priority is currently implementing mixed effects/multilevel models (e.g., see #107), but I'd be happy to put this on the list of future development priorities. I just need more context/examples to help me understand how it should be implemented.

mattfidler commented 3 years ago

I can give you details for RxODE and nlmixr, but I will wait until they don't require python to run, since it isn't your first priority.

For nlmixr and RxODE models, the ODEs can be extracted as text (w/Leibnetz notation) as well as the mixed effects, but I think you are referring to linear mixed effects models here.

datalorax commented 3 years ago

Yes, I'm currently working on linear mixed effects models via lme4. It's possible some of that code could transfer.

mattfidler commented 3 years ago

I'm hopeful; Thanks for entertaining this.