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RE: how to implement AR residual error model in Nonmem with FOCE INT routine

From: Ludden, Thomas <Thomas.Ludden>
Date: Wed, 6 Jan 2010 16:50:17 -0500

Dear Elodie:
 
Thank you for pointing out the documentation error in the help item. It
will be corrected in the next release.
 
Also, thank you for pointing out the need for using abbreviated code
instead of verbatim code for introducing the THETA used to estimate
correlation when using the SAEM method.
 
Tom

________________________________

From: Elodie Plan [mailto:elodie.plan
Sent: Wednesday, January 06, 2010 3:28 PM
To: Ludden, Thomas; nonmem
Subject: RE: [NMusers] how to implement AR residual error model in
Nonmem with FOCE INT routine



Dear Tom and all,

 

I work with the code provided in the html help for NM7 and it
successfully estimates autocorrelation between observations; I just want
to point out what appeared to be a typo to me: " IF (NEWIND.LE.2) =
I=0
should be " IF (NEWIND.NE.2) I=0, and to share that to my experience
it is required (with the new methods like SAEM) to introduce the THETA
(through a variable name) in the abbreviated code rather than in the
verbatim code.

 

Best regards,

Elodie

 

            Elodie L. Plan, PharmD, MSc,

                            PhD student

********************************************

   The Pharmacometrics Research Group

 

From: owner-nmusers
On Behalf Of Ludden, Thomas
Sent: Wednesday, January 06, 2010 6:57 PM
To: nonmem
Subject: RE: [NMusers] how to implement AR residual error model in
Nonmem with FOCE INT routine

 

If ADVAN13 is used then one must be using NONMEM 7.1.0. NONMEM 7.1.0 is
coded in Fortran 90/95. Try replacing

 

$ERROR

" FIRST

" COMMON /NMPRD5/ C(50,29)

" DIMENSION T(300)

" IF(NEWIND.NE.2) I=0

 

with


$ERROR
" FIRST

" USE SIZES, ONLY: NO
" USE NMPRD_REAL, ONLY: C=>CORRL2

" REAL (KIND=DPSIZE) :: T(NO)

" INTEGER (KIND=ISIZE) :: I,J

" MAIN

" IF(NEWIND.NE.2) I=0

 

The dimension of T should be the same as NO in SIZES.f90.

 

There is a help item available. In the html directory double-click the
file named index.htm (not $index.htm) to open the index for html-help,
select "a" as the first letter of the keyword, and then proceed to the
link for autocorrelation.

 

It is difficult (impossible) to anticipate how individuals will use
verbatim code so any use of verbatim code may be problematic. Only the
simplest examples have been tested using NONMEM 7.1.0, so please proceed
with caution.

 

If you continue to have problems then provide us the control stream and
at least a few individuals from the data set and we will attempt to help
with implementation.

 

Tom

 

ICON Development Solutions

e-mail: thomas.ludden

 

 

 

 

________________________________

From: owner-nmusers
On Behalf Of nonmem
Sent: Wednesday, January 06, 2010 11:29 AM
To: nmusers
Subject: Re: [NMusers] how to implement AR residual error model in
Nonmem with FOCE INT routine

The following code causes errors. I use ADVAN13 to run a PD model.

 

$ERROR
" FIRST
" COMMON /NMPRD5/ C(50,29)
" DIMENSION T(300)
" IF (NEWIND.NE.2) I=0
" IF (CMT==4) THEN
" I=I+1
" T(I)=TIME
" DO 5 J=1,I
" 5 C(J,I) = EXP(-THETA(9)*(TIME-T(J)))
" ENDIF

 

Errors:

 

FIRST
 1
Error: Unclassifiable statement at (1)
fsubs.f90:365.25:

 COMMON /NMPRD5/ C(50,29)
                         1
Error: Unexpected COMMON statement at (1)
fsubs.f90:366.21:

     DIMENSION T(300)
                     1
Error: Unexpected attribute declaration statement at (1)
fsubs.f90:370.22:

  T(I)=EVTREC(NVNT,03)
                      1
Error: Unexpected STATEMENT FUNCTION statement at (1)
fsubs.f90:372.50:

 5 C(J,I) = EXP(-THETA(9)*(EVTREC(NVNT,03)-T(J)))
                                                  1
Error: Unexpected STATEMENT FUNCTION statement at (1)
fsubs.f90:373.4:

 ENDIF
    1
Error: Expecting END DO statement at (1)
fsubs.f90:492.6:

      END
      1
Error: END DO statement expected at (1)
fsubs.f90:493.6:

      SUBROUTINE TOL(NRD)
      1
Error: Unclassifiable statement at (1)
fsubs.f90:494.39:

      USE SIZES, ONLY: DPSIZE,ISIZE
                                       1
Error: Unexpected USE statement at (1)
fsubs.f90:495.25:

      DIMENSION :: NRD(*)
                         1
Error: Unexpected attribute declaration statement at (1)
fsubs.f90:496.32:

      INTEGER(KIND=ISIZE) :: NRD
                                1
Error: Unexpected data declaration statement at (1)
fsubs.f90:497.6:

      NRD(1)=7
      1
Error: Unclassifiable statement at (1)
fsubs.f90:500.6:

      END
      1
Error: END DO statement expected at (1)
fsubs.f90:501.6:

      SUBROUTINE DES (A,P,T,DADT,IR,DA,DP,DT)
      1
Error: Unclassifiable statement at (1)
fsubs.f90:502.17:

      USE NMPRD4P
                 1
Error: Unexpected USE statement at (1)
fsubs.f90:503.39:

      USE SIZES, ONLY: DPSIZE,ISIZE
                                       1
Error: Unexpected USE statement at (1)
fsubs.f90:504.57:

      USE NMPRD_INT, ONLY: MSEC=>ISECDER,MFIRST=>IFRSTDER
                                                         1
Error: Unexpected USE statement at (1)
fsubs.f90:505.33:

      USE PROCM_REAL,ONLY: EVTREC
                                 1
Error: Unexpected USE statement at (1)
fsubs.f90:506.39:

      USE PROCM_INT, ONLY: NVNT=>NEVENT
                                       1
Error: Unexpected USE statement at (1)
fsubs.f90:507.52:

      USE PRMOD_INT, ONLY: ICALL=>ICALLD,IDEFD,IDEFA
                                                    1
Error: Unexpected USE statement at (1)
fsubs.f90:508.78:

   IMPLICIT REAL(KIND=DPSIZE) (A-Z)
 
1
Error: Letter A already has an IMPLICIT type at (1)
fsubs.f90:509.10:

      SAVE
          1
Error: Unexpected attribute declaration statement at (1)
fsubs.f90:510.78:

   INTEGER(KIND=ISIZE) :: IR
 
1
Error: Unexpected data declaration statement at (1)
fsubs.f90:511.20:

      DIMENSION :: A(*),P(*),DADT(*),DA(IR,*),DP(IR,*),DT(*)
                    1
Error: Cannot change attributes of USE-associated symbol amnt at (1)
fsubs.f90:514.6:

      IDEFD(1)= 0
      1
Error: Unclassifiable statement at (1)
Fatal Error: Error count reached limit of 25.
gfortran: Internal error: Aborted (program f951)
Please submit a full bug report.
See <http://gcc.gnu.org/bugs.html <http://gcc.gnu.org/bugs.html> > for
instructions.
gfortran: fsubs.o: No such file or directory
No nonmem execution.

 


----- Original Message -----
From: nonmem
Date: Wednesday, January 6, 2010 10:50 am
Subject: Re: [NMusers] how to implement AR residual error model in
Nonmem with FOCE INT routine
To: nmusers

> Hello Nonmem Users,
>
> Is there a more detailed explanation of the code in
>
>
>
> http://cognigencorp.com/nonmem/nm/97dec172003.html somwhere? I
> try to implement a second-order autoregressive process. If
> C(J,1) is a correlation coefficient, can I use more complex
> equations for C(j,1)? Will this code work if we use ADVAN13 (PD
> model here)?
>
> Thanks!
> Pavel
>
>
>
>
> ----- Original Message -----
> From: "Gastonguay, Marc"
> Date: Tuesday, December 29, 2009 10:09 am
> Subject: Re: [NMusers] how to implement AR residual error model
> in Nonmem with FOCE INT routine
> To: Ethan Wu
> Cc: nmusers
>
> > Hello Ethan,
> > This archived NMusers discussion thread might be useful:
> >
> > http://cognigencorp.com/nonmem/nm/97dec172003.html
> >
> > Marc
> >
> > Marc R. Gastonguay, Ph.D.
> > President & CEO, Metrum Research Group LLC < metrumrg.com >
> > Scientific Director, Metrum Institute < metruminstitute.org >
> > 2 Tunxis Rd, Suite 112, Tariffville, CT 06081 Direct:
> > +1.860.670.0744 Main: +1.860.735.7043 Fax: +1.860.760.6014
> >
> >
> >
> > On Dec 29, 2009, at 9:14 AM, Ethan Wu wrote:
> >
> > > Dear all,
> > > I am fitting a PK/PD model using FOCE INT. I do see a high
> >
> > > correlation between WRES
> > > I wonder could someone help me with implementation of AR
> > residual
> > > error model in NONMEM.
> > > Many thanks! Happy new year to all.
> > >
> > >
> >
> >
>

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Received on Wed Jan 06 2010 - 16:50:17 EST

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