From: Jurgen Bulitta <*jbulitta*>

Date: Thu, 3 Dec 2009 22:13:59 -0500

Dear Jing,

Please find below a revised control stream:

You needed some code like this to define your initial condition.

IF (A_0FLG.EQ.1) THEN

A_0(1)=KIN/KOUT

ENDIF

This method of initializing a compartment requires either

an observation or a simulated time event at time zero.

Therefore, I added an EVID=2 event into your dataset

(which I sent you off-line).

Alternatively, you can use the dummy dose at time zero method

which Bill proposed. Both methods should work fine.

If you want to describe disease progression, you may also

want to define the inhibitory or stimulatory effect of DIS

in a time-dependent manner. In your original code, DIS

was a constant which multiplied as (1-DIS) on Kin.

Depending if you initialize A(1) at Kin/Kout or at Kin*(1-DIS)/Kout,

DIS may or may not have any effect in the original code.

As a sample code, you might start with this function:

INH = 1.0D0 - DEXP(-DIS*T)

DADT(1)= KIN*INH - KOUT*A(1)

This may or may not be a good function for your data.

So please feel free to try other functions for INH. It is

important that you use T and not TIME in $DES, since

only T is continuous time, whereas TIME is not.

I also changed the headers of your datafile and

added two new columns. Hope this helps.

Best wishes

Juergen

Model code:

$PROB Demo7 for turn over PD model

$INPUT IDD=DROP ID TIME AMT DV EVID MDV

$DATA demo7.csv IGNORE=#

$ESTIM MAXEVAL=100 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)

IF (A_0FLG.EQ.1) THEN

A_0(1)=KIN/KOUT

ENDIF

$DES

INH = 1.0D0 - DEXP(-DIS*T)

DADT(1)= KIN*INH - KOUT*A(1)

$ERROR

Y = A(1) + ERR(1)

; Fixed effects

$THETA 174 ; KIN_PDK

$THETA 77 ; KOUT_PDK

$THETA (0,0.05,1) ; AGE_EFFECT_PDK

; Random effects

$OMEGA 0 FIX; BSVKIN_PDK

$OMEGA 0 FIX; BSVDIS_PDK

$SIGMA 0.1

$TABLE ID TIME Y DV

NOPRINT ONEHEADER FILE=DEMO.fit

#ID_real,ID,TIME,AMT,DV,EVID,MDV,CORT,strain,diet

.,1,0,.,.,2,1,.,CON,N

101,1,4,.,1.495201124,0,0,175.1,CON,N

102,1,4,.,1.5808647,0,0,105.37,CON,N

103,1,4,.,3.179360818,0,0,223.91,CON,N

...

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 dyna=

mic data since we didn't give dose to the animal. I am trying to capture th=

e nature of disease progression. And the PD decrease with time. I have see=

n people model only the PD data use $PRED subroutine but they use the expli=

cit equation.But I want to use a differential equation like dA/dt= k=

in(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 rec=

eived 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://w=

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D23879::T:WLMTAGL:ON:WL:en-ww:WM_IMHM_4:092009>

Received on Thu Dec 03 2009 - 22:13:59 EST

Date: Thu, 3 Dec 2009 22:13:59 -0500

Dear Jing,

Please find below a revised control stream:

You needed some code like this to define your initial condition.

IF (A_0FLG.EQ.1) THEN

A_0(1)=KIN/KOUT

ENDIF

This method of initializing a compartment requires either

an observation or a simulated time event at time zero.

Therefore, I added an EVID=2 event into your dataset

(which I sent you off-line).

Alternatively, you can use the dummy dose at time zero method

which Bill proposed. Both methods should work fine.

If you want to describe disease progression, you may also

want to define the inhibitory or stimulatory effect of DIS

in a time-dependent manner. In your original code, DIS

was a constant which multiplied as (1-DIS) on Kin.

Depending if you initialize A(1) at Kin/Kout or at Kin*(1-DIS)/Kout,

DIS may or may not have any effect in the original code.

As a sample code, you might start with this function:

INH = 1.0D0 - DEXP(-DIS*T)

DADT(1)= KIN*INH - KOUT*A(1)

This may or may not be a good function for your data.

So please feel free to try other functions for INH. It is

important that you use T and not TIME in $DES, since

only T is continuous time, whereas TIME is not.

I also changed the headers of your datafile and

added two new columns. Hope this helps.

Best wishes

Juergen

Model code:

$PROB Demo7 for turn over PD model

$INPUT IDD=DROP ID TIME AMT DV EVID MDV

$DATA demo7.csv IGNORE=#

$ESTIM MAXEVAL=100 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)

IF (A_0FLG.EQ.1) THEN

A_0(1)=KIN/KOUT

ENDIF

$DES

INH = 1.0D0 - DEXP(-DIS*T)

DADT(1)= KIN*INH - KOUT*A(1)

$ERROR

Y = A(1) + ERR(1)

; Fixed effects

$THETA 174 ; KIN_PDK

$THETA 77 ; KOUT_PDK

$THETA (0,0.05,1) ; AGE_EFFECT_PDK

; Random effects

$OMEGA 0 FIX; BSVKIN_PDK

$OMEGA 0 FIX; BSVDIS_PDK

$SIGMA 0.1

$TABLE ID TIME Y DV

NOPRINT ONEHEADER FILE=DEMO.fit

#ID_real,ID,TIME,AMT,DV,EVID,MDV,CORT,strain,diet

.,1,0,.,.,2,1,.,CON,N

101,1,4,.,1.495201124,0,0,175.1,CON,N

102,1,4,.,1.5808647,0,0,105.37,CON,N

103,1,4,.,3.179360818,0,0,223.91,CON,N

...

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 dyna=

mic data since we didn't give dose to the animal. I am trying to capture th=

e nature of disease progression. And the PD decrease with time. I have see=

n people model only the PD data use $PRED subroutine but they use the expli=

cit equation.But I want to use a differential equation like dA/dt= k=

in(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 rec=

eived 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://w=

ww.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?ocid=PI=

D23879::T:WLMTAGL:ON:WL:en-ww:WM_IMHM_4:092009>

Received on Thu Dec 03 2009 - 22:13:59 EST