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Running simulation in command line mode


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#1 vetpharma

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Posted 08 June 2022 - 01:28 PM

Hi,

 

I am trying to run simulations from the command line. My final model (.MDL) is a simple one compartment (following) model. I would like to run a simulation with a different dose level from the command line. so I created a dummy table for simulation as .csv file. Now, the question is how I should change the following script (PML) in the model file below to be able to simulate the new dose by command and receive the sim table as an output? 

 

test(){
cfMicro(A1, Cl / V, first = (Aa = Ka))
dosepoint(Aa)
C = A1 / V
error(CEps = 28.5596588388192)
observe(CObs = C + CEps * sqrt(1 + C^2 * (CMultStdev/sigma())^2))
stparm(Ka = tvKa * exp(nKa))
stparm(V = tvV * exp(nV))
stparm(Cl = tvCl * exp(nCl))
stparm(CMultStdev = tvCMultStdev)
fixef(tvKa = c(, 0.60176277128161, ))
fixef(tvV = c(, 0.0144284881142417, ))
fixef(tvCl = c(, 0.0299291076746268, ))
fixef(tvCMultStdev = c(, 0.458258322029198, ))
ranef(diag(nV, nCl, nKa) = c(1.0100196, 0.92041129, 0.9488175))
}
 
Best
Amir


#2 cradhakr

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Posted 08 June 2022 - 01:55 PM

Hi Amir,

 

I have attached a project file with a sample simulation. Also, there are a few youtube links that could be of use to you.

 

Attached File  Forum_A_sim.phxproj   444.05KB   94 downloads

 

 


 

Hi,

 

I am trying to run simulations from the command line. My final model (.MDL) is a simple one compartment (following) model. I would like to run a simulation with a different dose level from the command line. so I created a dummy table for simulation as .csv file. Now, the question is how I should change the following script (PML) in the model file below to be able to simulate the new dose by command and receive the sim table as an output? 

 

test(){
cfMicro(A1, Cl / V, first = (Aa = Ka))
dosepoint(Aa)
C = A1 / V
error(CEps = 28.5596588388192)
observe(CObs = C + CEps * sqrt(1 + C^2 * (CMultStdev/sigma())^2))
stparm(Ka = tvKa * exp(nKa))
stparm(V = tvV * exp(nV))
stparm(Cl = tvCl * exp(nCl))
stparm(CMultStdev = tvCMultStdev)
fixef(tvKa = c(, 0.60176277128161, ))
fixef(tvV = c(, 0.0144284881142417, ))
fixef(tvCl = c(, 0.0299291076746268, ))
fixef(tvCMultStdev = c(, 0.458258322029198, ))
ranef(diag(nV, nCl, nKa) = c(1.0100196, 0.92041129, 0.9488175))
}
 
Best
Amir

 



#3 cradhakr

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Posted 08 June 2022 - 01:58 PM

http://https://www.y...h?v=daSpOq1mczc

 

http://https://www.y...h?v=4PpZHGAHlsQ

 

 

Hi Amir,

 

I have attached a project file with a sample simulation. Also, there are a few youtube links that could be of use to you. (

)

attachicon.gifForum_A_sim.phxproj

 

 


 

Hi,

 

I am trying to run simulations from the command line. My final model (.MDL) is a simple one compartment (following) model. I would like to run a simulation with a different dose level from the command line. so I created a dummy table for simulation as .csv file. Now, the question is how I should change the following script (PML) in the model file below to be able to simulate the new dose by command and receive the sim table as an output? 

 

test(){
cfMicro(A1, Cl / V, first = (Aa = Ka))
dosepoint(Aa)
C = A1 / V
error(CEps = 28.5596588388192)
observe(CObs = C + CEps * sqrt(1 + C^2 * (CMultStdev/sigma())^2))
stparm(Ka = tvKa * exp(nKa))
stparm(V = tvV * exp(nV))
stparm(Cl = tvCl * exp(nCl))
stparm(CMultStdev = tvCMultStdev)
fixef(tvKa = c(, 0.60176277128161, ))
fixef(tvV = c(, 0.0144284881142417, ))
fixef(tvCl = c(, 0.0299291076746268, ))
fixef(tvCMultStdev = c(, 0.458258322029198, ))
ranef(diag(nV, nCl, nKa) = c(1.0100196, 0.92041129, 0.9488175))
}
 
Best
Amir

 

 

 


Edited by cradhakr, 08 June 2022 - 02:00 PM.


#4 vetpharma

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Posted 21 June 2022 - 10:22 AM

 

Hi Cradhakr, 

 

Thanks for your reply. I think I should elaborate  a bit on my work. I built a popPk for L-dopa. Now, what I am trying to do, is making a platform (such as a website) for physicians to be able to see the simulated PK profile of L-Dopa with different dose levels and various dosing interval. This required that I have four components to be able to run simulations from a command line. which I have them.

Certara Phoenix Assistance

 

I know how to build this website connecting that to the command line to run simulations. 

The only problem that I have is what I should do in the PML code of my .MDL file to be able to run simulations through command line (without needing to open software). 

 

I hope I could express my idea more clearly. 

 

p.s. the youtube links are not accessible. Could you please check their address? 



#5 cradhakr

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Posted 22 June 2022 - 09:38 PM

Hi Cradhakr, 

 

Thanks for your reply. I think I should elaborate  a bit on my work. I built a popPk for L-dopa. Now, what I am trying to do, is making a platform (such as a website) for physicians to be able to see the simulated PK profile of L-Dopa with different dose levels and various dosing interval. This required that I have four components to be able to run simulations from a command line. which I have them.

Certara Phoenix Assistance

 

I know how to build this website connecting that to the command line to run simulations. 

The only problem that I have is what I should do in the PML code of my .MDL file to be able to run simulations through command line (without needing to open software). 

 

I hope I could express my idea more clearly. 

 

p.s. the youtube links are not accessible. Could you please check their address? 

Hi,

 

I have to check with my technical team on this and get back to you.

 

Thanks

Mouli






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