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

From: Alison Boeckmann <alisonboeckmann>
Date: Wed, 20 Jan 2010 11:17:51 -0800

If indeed the difficulty is caused by having a variable named KIND,
then the character
being applied:

 "
 "

See the help item for verbatim code.


On Fri, 8 Jan 2010 11:57:53 -0500, "Ludden, Thomas"
<Thomas.Ludden
> Dear Pavel,
>
> Do you have a variable in $INPUT named "KIND"? If so, it is causing
> that data item (EVTREC(NVNT,31) to be substituted for KIND in the
> Fortran statements
>
> " REAL (KIND=DPSIZE) :: T(NO)
> " INTEGER (KIND=ISIZE) :: I,J
> .
> If that is not the case, then can you send me your control stream and a
> few individuals from the data file to test?
>
> Thanks,
>
> Tom
>
> ________________________________
>
> From: nonmem
> Sent: Friday, January 08, 2010 11:37 AM
> To: Ludden, Thomas
> Cc: nmusers
> Subject: Re: RE: [NMusers] how to implement AR residual error model in
> Nonmem with FOCE INT routine
>
>
> 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.
> > > > >
> > > > >
> > > >
> > > >
> > >
> >
> > ICON plc made the following annotations.
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--
  Alison Boeckmann
  alisonboeckmann
Received on Wed Jan 20 2010 - 14:17:51 EST

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