RE: output SE of population PK parameters in Nonmem

Rik, It isn't pretty (but what Fortran is?, wouldn't be Fortran without a GOTO) but this seems to work. The previous wasn't working because I didn't notice that the variables in COMMON /CM12/ are REAL, not the default DOUBLE PRECISION. $INFN " FIRST " INCLUDE 'C:\NMVI\SIZES' " COMMON /CM12/ COVM(LPAR3),COVINM(LPAR3),STHTA(LTH) " 1 ,SEN(LVR,LVR),CORRM(LPAR3) " REAL COVM,COVINM,STHTA,SEN,CORRM " INTEGER I,N,P IF (ICALL.EQ.3) THEN OPEN! (50,FILE='parms') WRITE (50,*) 'THETAS' WRITE (50,*) THETA WRITE (50,*) 'OMEGAS' WRITE (50,*) OMEGA(DIAG) WRITE (50,*) 'MVOF' WRITE (50,*) OBJECT WRITE (50,*) 'SE THETAS' WRITE (50,*) SETHET WRITE (50,*) 'CORR MATRIX EST' " DO 20 I = 1,70 " DO 10 N = 1, I " P = P + 1 " IF(CORRM(P).EQ.0) GOTO 30 " WRITE (50,777) CORRM(P) " 10 CONTINUE " WRITE(50,'(A2)') ' ' " 20 CONTINUE " 30 CONTINUE " 777 FORMAT (' ',F8.6,$) ENDIF Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com 919-846-9185 > -------- Original Message -------- Subject: RE: [NMusers] output SE of population PK parameters in Nonmem From: "Rik Schoemaker" <[EMAIL PROTECTED]> Date: Wed, February 06, 2008 1:23 pm To: < > > [email protected] > > > Dear Alison, I'm not sure I'm the one to suggest you update NMTRAN! It seems there are enough tools out there to either extract the info from the output file or to use a custom written INFN routine instead (for instance if you want more decimals). It's just that I'd been searching the documentation for a 'reserved variable' and couldn't find it... Thanks! Rik -----Original Message----- From: Alison Boeckmann [mailto: > > alisonboeckmann @fastmail.fm > > ] Sent: 06 February 2008 18:15 To: Rik Schoemaker; > > nmusers @globomaxnm.com > > Subject: RE: [NMusers] output SE of population PK parameters in Nonmem Rik, There is no "keyword" at present for these values. Lets call them "reserved variables" rather than "keywords". To make a new reserved variable of this sort, there are three steps. 1) Someone must identify a common in NONMEM that contains the values of interest. The other responders seem to think that CM12 is the one for the correlation matrix of the estimate. Whatever, someone must use verbatim or user-written code to be sure that the commons have the values under the appropriate circumstances. 2) Let me or ICON know about this, with an example of the code that you use to display them. 3) NMTRAN could then be revised to make a reserved variable in the same family as SETHET et. al, and to allow it to be used in WRITE/PRINT statements in a similar manner. An easier and faster approach is to use nmsee to mark the values of interest in the NONMEM output report, and then use grep or findstr to extract them. Nmsee can supply the following -- prefixes (appearing in nmsee output with the prefix option): ti, tu, tl theta initial, upper bound, and lower bound oi, si omega and sigma initial tj, oj, sj theta, omega, sigma from init estimates step gi, gf gradients initial and final pf scaled transformed parameters final mm minimum value of objective function tf, of, sf theta, omega, and sigma final te, oe, se theta, omega, and sigma std errors cx, cr, cv covar, correl, and inv covar matrices of est cy T matrix xx text lines I have been planning to change it to mark the following: xx ETABAR: -0.13E-02 -0.45E-02 -0.25E-01 xx SE: 0.29E-01 0.27E-01 0.21E-01 xx P VAL.: 0.96E+00 0.87E+00 0.24E+00 It is much easier and faster to change nmsee than to change NMTRAN! Steps 1 and 2 are up to the user community. Step 3 is something that could be implemented in a future release of NONMEM. On Wed, 6 Feb 2008 14:30:42 +0100, "Rik Schoemaker" < > > rik.schoemaker @exprimo.com > > > said: > Dear all, > > It's a neat trick and works very well, but can anyone tell me the > keyword (like for instance SETHET below) for exporting the correlation > matrix of the estimates and for the non-parametric estimates: > 'expected value of ETA' and 'Covariance matrix of ETA'.... > > Thanks in advance, > > Rik > > -----Original Message----- From: owner- > > nmusers @globomaxnm.com > > [mailto:owner- > > > nmusers @globomaxnm.com > > ] On Behalf Of GIRARD PASCAL Sent: 01 February > 2008 18:08 To: Jin, Bo; > > nmusers @globomaxnm.com > > Subject: RE : [NMusers] > output SE of population PK parameters in Nonmem > > Hi Jin, > > See in NONMEM help: > ___________________________________________________________________ > | | > | FINALIZATION EXAMPLE ($PRED AND $INFN) | > | ___________________________________________________- > | ______________| > > This example contains abbreviated code which can be inserted in a > $PRED or $INFN block. This code outputs final parameter > estimates, standard errors, minimum value of the objective function, > and condi- tional estimates of etas to various user files. The > return codes from Estimation and Covariance steps (zero for normal > termination) are also output. > > IF (ICALL.EQ.3) THEN DO WHILE(DATA) IF (NEWIND.LE.1) WRITE (50,*) > ETA ENDDO WRITE (51,*) OBJECT WRITE (52,*) THETA WRITE (53,*) > SETHET WRITE (54,*) OMEGA(BLOCK) WRITE (55,*) SEOMEG(BLOCK) WRITE > (56,*) SIGMA(BLOCK) WRITE (57,*) SESIGM(BLOCK) WRITE (58,*) > IERE,IERC ENDIF > > Alternatively, you take advantage of the fact that all those > estimmates are stored in Vectors and matrices of various COMMON: > COMMON /ROCM6/ THETAF(40),OMEGAF(30,30),SIGMAF(30,30) COMMON > /ROCM7/ SETH(40),SEOM(30,30),SESIG(30,30) COMMON /ROCM8/ OBJECT > COMMON /ROCM9/ IERE,IERC COMMON /CM12/ COV(2850) and write your > own INFN subroutine (see INFN help). > > Best regards, > > Pascal Girard, PhD EA 3738, CTO Fac Medecine Lyon-Sud, BP12 69921 > OULLINS Cedex, France > > pascal.girard @adm.univ-lyon1.fr > > Tel +33 (0)4 26 > 23 59 54 / Fax +33 (0)4 26 23 59 76 > > Master Recherche Lyon 1 Santé et Populations, Spécialité PhIT > > > http://master-sante-pop.univ-lyon1.fr/ > > > > >-----Message d'origine----- De : owner- > > nmusers @globomaxnm.com > > [mailto:owner- > > > > nmusers @globomaxnm.com > > ] De la part de Jin, Bo Envoyé : vendredi 1 > >février 2008 17:48 À : > > nmusers @globomaxnm.com > > Objet : [NMusers] > >output SE of population PK parameters in Nonmem > > > >Dear all: I have a question. Is there any way to output the SE or SD > >of a population PK parameter estimate in Nonmem (say typical value of > >Cl) into some files which can be read by SAS or S-Plus etc.? (e.g. > > some excel or TAB files?) > > > >thanks, > > > >- Bo > > > >_____________________________________ > > > >BO JIN Clinical Pharmacology Statistics Merck Research Labs Phone: > >267-305-7876 > > > > > > > >-------------------------------------------------------------------- > >------- > >--- > >Notice: This e-mail message, together with any attachments, contains > >information of Merck & Co., Inc. (One Merck Drive, Whitehouse > >Station, New Jersey, USA 08889), and/or its affiliates (which may be > >known outside the United States as Merck Frosst, Merck Sharp & Dohme > >or MSD and in Japan, as Banyu - direct contact information for > >affiliates is available at > > > > http://www.merck.com/contact/contacts.html > > ) that may be confidential, > >proprietary copyrighted and/or legally privileged. It is intended > >solely for the use of the individual or entity named on this message. > >If you are not the intended recipient, and have received this message > >in error, please notify us immediately by reply e-mail and then > >delete it from your system. > > > >-------------------------------------------------------------------- > >------- > >--- > -- Alison Boeckmann > > alisonboeckmann @fastmail.fm