Re: OMEGA off-diagonal elements parameterized as correlations

Alison, Thanks very much for taking the time to document the history of the CORRELATION option. I hope that a future release of NONMEM might add it back again. It doesnt seem like it would be too much work as it seems like it is only a simple reparameterization of the OMEGA matrix. Nick Alison Boeckmann wrote: > Nick, > > I can only offer you a litle bit of history. > > The CORRELATION option for $OMEGA was supported by NMTRAN and described > in NONMEM VI's help guide during most of its development, from Oct 2000 > till at least May 2005. Several other interesting new options were > described, such as VARIANCE vs. STANDARD. > > It is less easy for me to track the years during which these options > were actually implemented in early versions of NONMEM VI. Presumably > Paolo must have had access to the on-line help that was distributed with > a beta test version. Perhaps some of the former fellows remember. > > By the time Tom Ludden and I were finalizing NONMEM VI 1.0, after Stuart > Beal's death in January 2006, Stuart had deleted these new features from > NONMEM VI. It was not uncommon for Stuart to put an experimental new > feature in NONMEM, and later decide that it was not worth while and > withdraw it. The OMEGA help entry back was restored to what it had been, > and NMTRAN was changed to give an error message saying that this feature > is not available with NONMEM VI, just in case a previous beta tester > might still try to use them. > > The feature was never restored to NONMEM because, basically, no one > asked for it. You might say, how could we ask for something we did not > know about? Good point. It can be put on the list for a future release, > though it is too late for NONMEM VII 1.0. > > On Wed, 08 Jul 2009 17:07:00 +0200, "Nick Holford" > <[email protected]> said: > > > Paolo, > > > > I too was disappointed when NONMEM VI appeared without the $OMEGA > > CORRELATION option. I agree with you that correlations are more > > intuitive and easier to use than covariances. > > > > Unfortunately NONMEM VII beta continues with the same lack of support > > for a CORRELATION option. > > > > AN ERROR WAS FOUND IN THE CONTROL STATEMENTS. > > > > AN ERROR WAS FOUND ON LINE 12 AT THE APPROXIMATE POSITION NOTED: > > $OMEGA BLOCK(3) CORRELATION X 584 THIS > > FEATURE IS NOT PART OF NONMEM VII. > > > > I wonder if someone from the NONMEM development team could explain why > > this feature remains unimplemented? > > > > Nick > > > > Paolo Denti wrote: > > > > > Dear all, I was wondering if it is possible to insert the off- > > > diagonal elements of OMEGA as correlations rather than covariances, > > > because I find it more intuitive. > > > > > > To my greatest happiness, I found the following information in a > > > NONMEM chm help file: > > > > > > ___________________________________________________________________ > > > | | > > > | $OMEGA | > > > | __________________________________- > > > | _______________________________| > > > > > > MEANING: Supplies initial estimates for the NONMEM OMEGA Matrix > > > CONTEXT: NM-TRAN Control Record > > > > > > USAGE: $OMEGA [DIAGONAL(n)|BLOCK(n)|BLOCK(n) SAME|BLOCK SAME] 5 > > > [[value1] [value2] [value3] ... [FIXED]] 5 $OMEGA > > > [DIAGONAL(n)|BLOCK(n)|BLOCK(n,m) L [[value1] [value2] > > > [value3]] ... L [VARIANCE|STANDARD] [COVARIANCE|CORRELATON] > > > L [FIXED] [ALLOFFFIX] [FIRSTFIXED] [PRINCIPAL]] L > > > |BLOCK(n) SAME|BLOCK SAME] L > > > > > > SAMPLE: $OMEGA BLOCK(3) 6. .005 .3 .0002 .006 .4 > > > > > > Reading on in the file, the [COVARIANCE|CORRELATON] sounded (in > > > spite of the incorrect spelling) like the panacea I was looking for. > > > Unfortunately, when I try to compile, I get a message saying that > > > this option is not available in NONMEM VI. :-( Is this sadly only a > > > feature planned for future versions of NONMEM? And if so, does > > > anyone you know of other simple workarounds to use correlations > > > instead of covariances? > > > > > > Thank you in advance, Paolo > > > > -- > > Nick Holford, Professor Clinical Pharmacology Dept Pharmacology & > > Clinical Pharmacology University of Auckland, 85 Park Rd, Private Bag > > 92019, Auckland, New Zealand > > [email protected] tel:+64(9)923-6730 fax:+64(9)373-7090 mobile: > > +33 64 271-6369 (Apr 6-Jul 20 2009) > > http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford -- Nick Holford, Professor Clinical Pharmacology Dept Pharmacology & Clinical Pharmacology University of Auckland, 85 Park Rd, Private Bag 92019, Auckland, New Zealand [email protected] tel:+64(9)923-6730 fax:+64(9)373-7090 mobile: +33 64 271-6369 (Apr 6-Jul 20 2009) http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford