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Re: OMEGA off-diagonal elements parameterized as correlations

From: Nick Holford <n.holford>
Date: Fri, 10 Jul 2009 20:31:04 +0200

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"
> <n.holford
>
>> 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
>> n.holford
>> +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
n.holford
mobile: +33 64 271-6369 (Apr 6-Jul 20 2009)
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford


Received on Fri Jul 10 2009 - 14:31:04 EDT

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