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NONMEM TO NLME transit compartments


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#1 amashehri

amashehri

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Posted 17 September 2020 - 01:47 AM

Hi 

 

I am trying to use differential equations from a NONMEM published model on NLME but I cant figure it out "I am new in modeling". The model is two compartment, first order of absorption with a chain of transit compartment.

 

Please find the attached document.

 

Thanks 

 

 

 

 

 

Attached Files



#2 bwendt@certara.com

bwendt@certara.com

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Posted 22 September 2020 - 09:24 AM

We asked one of our developers to translate the NM-Tran code to PML, here is the code:

 

test(){

# ntr is the structural parameter representing one less than the number of transit stages.

transit(Aa, mtt, ntr, max=50, out=-Aa*Ka)

    deriv(A1 = Ka * Aa - Cl * C - Cl2 * (C - C2))

    deriv(A2 = Cl2 * (C - C2))

   

    dosepoint(Aa)

 

    C = A1 / V

    C2 = A2 / V2

 

    error(CEps = 0.11) # sqrt(0.508876 )

covariate(ASSAY())

covariate(WT)

CRatio = ASSAY == 3? C*Ratio : C

CMultStdev = ASSAY == 3? PROP_ERR_DBS:PROP_ERR_Plasma

    observe(CObs = CRatio + CEps * sqrt(1 + CRatio^2 * (CMultStdev/sigma())^2))

 

    stparm(Ka = tvKa)

    stparm(V = tvV * exp(nV))

    stparm(V2 = tvV2 * exp(nV2) * (WT/70))

    stparm(Cl = tvCl * exp(nCl) * (WT/70)**0.75)

    stparm(Cl2 = tvCl2 * exp(nCl2))

    stparm(mtt = tvmtt * exp(nmtt))

    stparm(ntr = tvntr) # fixed

 

    fixef(tvKa = c(, .55, ))

    fixef(tvV = c(, 89, ))

    fixef(tvV2 = c(, 234, ))

    fixef(tvCl = c(, 7.6, ))

    fixef(tvCl2 = c(, 19, ))

    fixef(tvmtt = c(,1.05, ))

 

    fixef(tvntr(freeze) =c(,6,))

fixef(Ratio = c(, 0.71, ))

# define multiplicative sigmas

# although we cannot code the correlation

fixef(PROP_ERR_Plasma = 0.09) #sqrt(0.00878848 )

fixef(PROP_ERR_DBS = 0.11) # sqrt(0.0124671)

 

    ranef(diag(nV, nCl, nV2, nCl2, nmtt) = c(0.01, 0.064, 0.04, 0.17, 0.36))

}

 

Please try in Phoenix and let us know if you run into issues.

 

Bernd  






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