If indeed the difficulty is caused by having a variable named KIND, then the character @ may be used to prevent the "replacement rule" from being applied:
"@ REAL (KIND=DPSIZE) :: T(NO) "@ INTEGER (KIND=ISIZE) :: I,J See the help item for verbatim code. On Fri, 8 Jan 2010 11:57:53 -0500, "Ludden, Thomas" <thomas.lud...@iconplc.com> said: > 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: non...@optonline.net [mailto:non...@optonline.net] > Sent: Friday, January 08, 2010 11:37 AM > To: Ludden, Thomas > Cc: nmusers@globomaxnm.com > 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 , non...@optonline.net, nmusers@globomaxnm.com > > > 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.p...@farmbio.uu.se] > > Sent: Wednesday, January 06, 2010 3:28 PM > > To: Ludden, Thomas; non...@optonline.net; nmusers@globomaxnm.com > > 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-nmus...@globomaxnm.com [mailto:owner- > > nmus...@globomaxnm.com]on Behalf Of Ludden, Thomas > > Sent: Wednesday, January 06, 2010 6:57 PM > > To: non...@optonline.net; nmusers@globomaxnm.com > > 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.lud...@iconplc.com > > > > > > > > > > > > > > > > > > > > ________________________________ > > > > From: owner-nmus...@globomaxnm.com [mailto:owner- > > nmus...@globomaxnm.com]on Behalf Of non...@optonline.net > > Sent: Wednesday, January 06, 2010 11:29 AM > > To: nmusers@globomaxnm.com > > 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: non...@optonline.net > > 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@globomaxnm.com > > > > > 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@globomaxnm.com > > > > > > > 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. > > ----------------------------------------------------------------- > > ------- > > ------ > > This e-mail transmission may contain confidential or legally > > privilegedinformation > > that is intended only for the individual or entity named in the > > e-mail > > address. If you > > are not the intended recipient, you are hereby notified that any > > disclosure, copying, > > distribution, or reliance upon the contents of this e-mail is strictly > > prohibited. 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If > > you have received this e-mail transmission in error, please > > reply to the sender, so that > > ICON plc can arrange for proper delivery, and then please delete > > the message. > > Thank You, > > ICON plc > > South County Business Park > > Leopardstown > > Dublin 18 > > Ireland > > Registered number: 145835 > > > > > > ICON plc made the following annotations. > ------------------------------------------------------------------------------ > This e-mail transmission may contain confidential or legally privileged > information > that is intended only for the individual or entity named in the e-mail > address. If you > are not the intended recipient, you are hereby notified that any > disclosure, copying, > distribution, or reliance upon the contents of this e-mail is strictly > prohibited. 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