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

----- 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. > > > > > > > > > > > > > > > > > >