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

From: nonmem
Date: Fri, 08 Jan 2010 16:37:03 +0000 (GMT)

Hello Thomas,

I tried the code as described in your email and in "correlations accross L2 records" help file:

$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
" IF (NEWL2.EQ.1.AND.CMT.EQ.4) THEN
" I=I+1
" T(I)=TIME
" DO 5 J=1,I
" 5 C(J,I) = EXP(-THETA(9)*(TIME-T(J)))
" ENDIF

The following errors occur:

IL1D027J.txt
newline
        1 file(s) copied.
IL1D027J.OUT
FMSG
        1 file(s) copied.
        1 file(s) copied.
fsubs.f90:339.12:
      REAL (EVTREC(NVNT,31)=DPSIZE) :: T(NO)
            1
Error: Assumed size array 'evtrec' at (1) is not permitted in an initialization expressi
fsubs.f90:340.15:
      INTEGER (EVTREC(NVNT,31)=ISIZE) :: I,J
               1
Error: Assumed size array 'evtrec' at (1) is not permitted in an initialization expressi
fsubs.f90:371.22:
  T(I)=EVTREC(NVNT,03)
                      1
Error: Unexpected STATEMENT FUNCTION statement at (1)
fsubs.f90:373.6:
 5 C(J,I) = EXP(-THETA(9)*(EVTREC(NVNT,03)-T(J)))
      1
Warning: Extension: REAL array index at (1)
fsubs.f90:373.8:
 5 C(J,I) = EXP(-THETA(9)*(EVTREC(NVNT,03)-T(J)))
        1
Warning: Extension: REAL array index at (1)
fsubs.f90:372.6:
  DO 5 J=1,I
      1
Warning: Deleted feature: Loop variable at (1) must be integer
fsubs.f90:372.11:
  DO 5 J=1,I
           1
Warning: Deleted feature: End expression in DO loop at (1) must be integer
gfortran: fsubs.o: No such file or directory
No nonmem execution.

Thanks,
Pavel


----- Original Message -----
From: Ludden, Thomas
Date: Wednesday, January 6, 2010 4:50 pm
Subject: RE: [NMusers] how to implement AR residual error model in Nonmem with FOCE INT routine
To: Elodie Plan , nonmem

> 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
> nmusers
> 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
> proceedwith 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
> nmusers
> 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
> > 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 Fri Jan 08 2010 - 11:37:03 EST

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