Open samjrrr opened 9 months ago
Sam, Thanks for looking at this, sorry I'm just getting to this now. There is a branch called mu-referencing, we recognized that this would be something that users would need, just haven't gotten it into the master yet. But, we'd be very interested in your solution to this. WRT the templates, those are completely the users responsibility. That said, an example with a general solution to rates and number of compartments for ODEs would be great. So, yes, please fork it, and do a PR, we'll take a look. Mark
Hi Mark, Thanks for the message. Will hopefully have a pull request ready next month.
The other changes with dynamic rate constants and compartment numbers are not just a template convention they also involve modifications to PyDarwin. In both cases the user can enter a variable in the template rather than the actual number of compartments or the correctly numbered rate constant. PyDarwin substitutes these variables for the correctly formatted value expected by NONMEM. We used these dynamic variables to enable the addition of a variable number of transient compartments to our model space.
Thanks Sam, we'll look forward to seeing what you've done. It sounds useful, (although maybe a bit of a deviation from the general purpose architecture) Mark
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From: Sam Richardson @.> Sent: Thursday, March 28, 2024 9:37:49 AM To: certara/pyDarwin @.> Cc: Mark Sale @.>; Comment @.> Subject: Re: [certara/pyDarwin] Updates to the NONMEM adapter (Issue #73)
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Hi Mark, Thanks for the message. Will hopefully have a pull request ready next month.
The other changes with dynamic rate constants and compartment numbers are not just a template convention they also involve modifications to PyDarwin. In both cases the user can enter a variable in the template rather than the actual number of compartments or the correctly numbered rate constant. PyDarwin substitutes these variables for the correctly formatted value expected by NONMEM. We used these dynamic variables to enable the addition of a variable number of transient compartments to our model space.
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Hello,
Thanks for the great library! I've recently been working with PyDarwin and getting some nice results.
We had some challenges when designing model spaces which were overcome using a modified version of the NONMEM adapter.
The features enabled with the NONMEM adapter modifications were:
If you are interested, I would be happy to create a new branch and open a pull request with these modifications. I'll provide a little more detail about the implementation below.
Please let me know what you think. Thanks, Sam
Mu parameters
Dynamic rate constants
Dynamic compartment number
Added NUMBER_COMPARTMENTS as a variable in the template. A user can specify
NCOMP=NUMBER_COMPARTMENTS
without knowing the final number of compartments we used this to add a variable number of transient compartments to the absorption model.Compartment count in template:
Compartment count in model file: