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
