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simulation of concentrations from two compartments

modeling PML

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#1 mjPK

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Posted 28 February 2024 - 03:35 PM

Hi 

 

I have a fitted model that I would like to try alternative dosing schemes. My problem is I have two compartments that I wish to simulate in the same model. My model was made in text mode and I have to obs variables in it. 

 

I am not sure how to get Phoenix to give me data back from both compartments? In the online video and manual they denote C as the calculated concentration from the model but I am not sure what that means for models fit to two sets of data (parent & metabolite etc...)

 

Any help much appreciated. 

 


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#2 mjPK

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Posted 28 February 2024 - 05:22 PM

Also, is there anything special you need to do to run a simulation on PML derived model. I copied my model over and simply switched to simulation and I get a wildly different answer. Should I go in an manually freeze the parameters? 


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#3 Simon Davis

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Posted 28 February 2024 - 05:26 PM

Do ensure you accepted the final estimates before running your simulation.

 

if you forgot to do that then simply map your final model's theta sheet into parameters input in your simulation
(and of course check you've been consistent with dosing units....


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#4 mjPK

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Posted 28 February 2024 - 05:30 PM

I do accept my parameters. I am trying to simulate a simple individual model. I go to parameters and fix everything but I cannot recapture the fit from the previous step let alone simulate a different dose.

 

I have tried adding a table that reflects my variable naming and that did not work either. 



#5 Simon Davis

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Posted 28 February 2024 - 05:31 PM

i'd have to see you project to comment further - you can send to support if confidentiality is an issue.



#6 mjPK

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Posted 28 February 2024 - 05:35 PM

Here is my project file. Anything suggestions would be much appreciated. 

 

Also I need help decoding the dose point line 

 

 

dosepoint(A1, idosevar = A1Dose, infdosevar = A1InfDose, infratevar = A1InfRate)

 

where are idosevar, infdosevar, infratevar defined. It seems the PML code will not allow hard coded values. 

 

 

Attached Files



#7 mjPK

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Posted 28 February 2024 - 06:27 PM

OK I think I found my issue. The standard output plot from fitting does not seem to be responsive to the simulation parameters. If I add a table I do get the number of points I am looking for and the change in dosing. I can plot from the table and work around that. 

 

Weird that the base plot would not reflect the table.... I attached my project file reflecting this.... 

Attached Files


Edited by mjPK, 28 February 2024 - 06:45 PM.


#8 Simon Davis

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Posted 28 February 2024 - 07:07 PM

be sure to read your Warnings tab in your sium object, you need to type CObs;

Fixed effect 'Tmax' is not used and will be frozen
Fixed effect 'k_clog' is not used and will be frozen
Sim Table simtbl01 observations: Cobs is not an observation
 
also I'm not sure you have the right parameters looking at your source fitting model; Nano Plasma plus Turmor NonLinear Alt2
 
i think the problem in your sim is it's not separating out your tumour and plasma concs properly, but I've not looked too deeply into your code yet.

Can you clean up your project so it's all 'up to date' u.e. no red text and then we'll have a bette ridea of what  param estimates you're trying to use for your sim.
 
 

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  • fit_alt2.jpg






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