NONMEM Users Network Archive

Hosted by Cognigen

RE: model dynamic data with $DES subroutine

From: Bill Bachman <bachmanw>
Date: Thu, 3 Dec 2009 10:16:18 -0500

I did not fully think this out before my first reply regretfully. you may
also have to define a depot compartment, then dummy dose to the depot and
observations in the second compartment
 
 
$DES
DADT(1)= -KIN*(1-DIS)*A(1)
DADT(2)=KIN*(1-DIS)*A(1)-KOUT*A(2)

you could probably use ADVAN1 TRANS1 for this with F1 instead of DIS without
differential equations. not sure why you coded "1-DIS". you may want to
constrain this factor between 0 and 1.
 
I am sure someone will follow with corrections to my corrections, they
always do. But this should point you in the right direction.


  _____

From: Bill Bachman [mailto:bachmanw
Sent: Thursday, December 03, 2009 9:56 AM
To: 'Jing Nie'; 'nmusers
Subject: RE: [NMusers] model dynamic data with $DES subroutine


Try putting a dummy dose of 1 in the first compartment via your data file
records, eg"
 
ID TIME AMT PDK=DV EVID
1 0 1 0 1
for each individual

  _____

From: owner-nmusers
Behalf Of Jing Nie
Sent: Thursday, December 03, 2009 9:29 AM
To: nmusers
Subject: [NMusers] model dynamic data with $DES subroutine


Dear NMusers,

I have a question I would like your help. The data I have is only the
dynamic data since we didn't give dose to the animal. I am trying to capture
the nature of disease progression. And the PD decrease with time. I have
seen people model only the PD data use $PRED subroutine but they use the
explicit equation.But I want to use a differential equation like dA/dt=
kin(1-dis)-kout*A while A0=kin/kout.

When I ran the control stream, the gradient for most of the parameters are
0. And the only parameter estimation I got is the sigma. The output of Y is
0. I guess it's because I don't have dose to compartment(PDK) but I don't
know how should I fix the problem.
Any suggestion is appreciated!

The control stream I wrote is:

$PROB Demo for turn over PD model
$INPUT ID TIME AMT PDK=DV EVID
$DATA demo.csv IGNORE=#

$ESTIM MAXEVAL=3000 NOABORT PRINT=1
METHOD=COND INTERACTION SIG=5 MSFO=save.msf

$COV MATRIX=S SLOW

$SUBROUTINE ADVAN6 TOL=5

$MODEL
COMP=(PDK)

$PK
KIN=THETA(1)*EXP(ETA(1))
KOUT=THETA(2)
DIS=THETA(3)*EXP(ETA(2))

$DES
DADT(1)=KIN*(1-DIS)-KOUT*A(1)

$ERROR
Y = F + ERR(1)

; Fixed effects
$THETA 174 FIX ; KIN
$THETA 77 FIX ; KOUT
$THETA (0,0.28,1) ; AGE_EFFECT_PDK

; Random effects
$OMEGA 0 FIX; BSVKIN_PDK
$OMEGA 0 FIX; BSVDIS_PDK


$SIGMA 0.1


$TABLE ID TIME PDK Y
NOPRINT ONEHEADER FILE=DEMO.fit



And my data looks like:
#ID TIME AMT PDK EVID
101 4 . 1.49 0
102 4 . 1.58 0
61 8 . 0.57 0
62 8 . 2.03 0
63 8 . 1.58 0
64 8 . 1.52 0
109 12 . 0.71 0
110 12 . 1.18 0
21 12 . 1.25 0



-Jing


 
This e-mail and any files transmitted with it, are intended solely for the
use of the individual or entity to whom they are addressed.?If you have
received this e-mail in error, please reply to this message and let the
sender know.




  _____

Chat with Messenger straight from your Hotmail inbox. Check it out
<http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?o
cid=PID23879::T:WLMTAGL:ON:WL:en-ww:WM_IMHM_4:092009>


  _____

No viruses found in this incoming message
Scanned by iolo AntiVirus 1.5.8.3
http://www.iolo.com <http://www.iolo.com/iav/iavpop3>

Received on Thu Dec 03 2009 - 10:16:18 EST

The NONMEM Users Network is maintained by ICON plc. Requests to subscribe to the network should be sent to: nmusers-request@iconplc.com.

Once subscribed, you may contribute to the discussion by emailing: nmusers@globomaxnm.com.