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
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
