Open pratikunterwegs opened 6 months ago
Hi @pratikunterwegs
Just checking whether this is the right place for this; I'm trying to demonstrate interop with Julia SciML, and all I need for this is a function that returns either the RHS of the ODE (as odin
can do) or the next step for discrete models. The idea here is that if you can step through a model, you can link different models together more easily. Is it possible to return this information?
Hi @sdwfrost thanks, this seems really interesting!
The deterministic model ODE systems are defined as RHS in the package headers inst/include/model_*.h
- one header per model. They're FunctionObjects suitable for the Boost odeint paradigm, so might work for your use case?
We only have one discrete model for Ebola in R/model_ebola.R
, but the 'next step' function is combined with a loop in model_ebola_internal()
.
Happy to hear any feedback on the model functions for better interoperability/more efficiency! Also, I've got Epidemics.jl
as an unregistered package that mirrors this one, and would be happy to include an interop demo there.
Thanks @pratikunterwegs! I've added an issue to my repo here as it'll take me a little while to get the boilerplate code working.
Thanks for the pointer to Epidemics.jl - I took a quick look. Have you thought about generating ModelingToolkit code rather than low level stuff?
Thanks @sdwfrost - I've seen the repo before - looks interesting!
With Epidemics.jl it's mostly just a way for me to learn and keep engaged with Julia programming; I haven't looked into ModelingToolkit at all before.
This issue proposes that the internal ODE model functions be exposed to the user as 'unsafe' scalar versions of the updated, vectorised model functions, as detailed in #160.
For Rcpp implementations, this would involve exposing
.model_*_cpp()
. R-only implementations may be removed as part of this project (see #162), and if not, would require a thin wrapper accepting only scalars around.ode_model_*()
, whilemodel_*_r()
would be vectorised.This issue is planned to be taken up if a specific need for exposing these internal functions to users becomes evident.