Re: How to set CMT value for 2-compartment bacterial model
Hi,
Just to expand on this topic a little.
I only use the CMT data item to specify the compartment when AMT is > 0 and the default CMT=1 is not appropriate (or when I need to turn off/turn on a compartment). Otherwise I don't use CMT or set CMT to "." (which NM-TRAN translates to 0 for NONMEM) for all observation records. The CMT data item does not directly affect the prediction of any observation.
When I have different kinds of observations (e.g. parent, metabolite or conc, effect) then I include a DVID data item in the data set to determine which prediction ('Y') should be used. Some people use CMT for this but this can cause problems e.g. if you have only 1 PK compartment and a conc and 2 effects to predict then you cannot use CMT to choose which effect should be used for the prediction.
e.g. here is an example that does not use CMT explicitly (it is 1 by default for AMT>0) but uses DVID to determine the prediction.
$INPUT ID TIME AMT DV DVID
$SUBR ADVAN1
$ERROR
IF (DVID.EQ.1) THEN
Y=CONC + EPS(1)
ENDIF
IF (DVID.EQ.2) THEN
Y=EFFECT1+ EPS(2)
ENDIF
IF (DVID.EQ.3) THEN
Y=EFFECT2+ EPS(3)
ENDIF
Quoted reply history
On 10/01/2012 9:50 a.m., Elisabet Nielsen wrote:
> Dear Sherwin,
>
> Since you have specified IPRED=ATOT (and ATOT=A1+A2), NONMEM is disregarding
> the CMT value you have specified on the observation record when calculating
> IPRED, i.e. you can set CMT to any value.
>
> Best regards,
>
> Elisabet
>
> ----------------------------------------------------------------
> Elisabet Nielsen, PhD
> The Pharmacometrics group
> Department of Pharmaceutical Biosciences
> Uppsala University
>
> -----Original Message-----
> From: [email protected] [mailto:[email protected]] On
> Behalf Of Sherwin K Sy
> Sent: Friday, January 06, 2012 10:59 PM
> To: [email protected]
> Subject: [NMusers] How to set CMT value for 2-compartment bacterial model
>
> Dear NONMEM users,
>
> I want to set-up a bacterial model consisting of susceptible (S) and
> resting phases (R). I use Advan9 in NONMEM for the subroutine. With
> Advan9, one has to declare compartments.
>
> My experimental bacterial counts belong to both S and R (i.e. sum of S
> and R). And the compartments are such that:
>
> CA=(A(3)) ; compartment for drug
>
> DRUG=EMAX*(CA)/(EC50+(CA)) ; relationship for drug using an Emax model
>
> DADT(1)=K1*A(1)-(K2+DRUG)*A(1)-KSR*A(1)
> DADT(2)=KSR*A(1)-K2*A(2)
> DADT(3)=KDEG*A(3)
>
> A1=A(1) ; S
> A2=A(2) ; R
> ATOT=A1+A2 ; N=S+R
> A3=A(3) ; Drug Concentration
>
> IPRED = ATOT
>
> I'm wondering as to how or what to set-up for the compartment value
> CMT in the input file whenever I have bacterial count observations. I
> understand that the CMT for the initial drug concentration will be set
> to 3 since drug belongs to compartment 3.
>
> Thank you in advance for your help.
>
> Best regards,
>
> Sherwin Sy
--
Nick Holford, Professor Clinical Pharmacology
Dept Pharmacology& Clinical Pharmacology, Bldg 505 Room 202D
University of Auckland,85 Park Rd,Private Bag 92019,Auckland,New Zealand
tel:+64(9)923-6730 fax:+64(9)373-7090 mobile:+64(21)46 23 53
email: [email protected]
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford