Is it possible to include the off-diagonal correlation of ETAs in the $TABLE
output? If so, how is it done? ETAR12 is not recognized.
I'd like to import into R for summary stats.
Thank you!
Paul
Paul R. Hutson, PharmD, BCOP
Professor (CHS)
UW School of Pharmacy
Director, UW Madison Transdisciplinary Center for Research in Psychoactive
Substances
Associate Member, Paul P. Carbone Comprehensive Cancer Center
T: 608.263.2496
[email protected]
Off diagonals in $TABLE
This should do it:
OM12 = OMEGA(1,2)
$TAB OM12
Quoted reply history
On 12/20/2022 1:55 PM, Paul Hutson wrote:
> Is it possible to include the off-diagonal correlation of ETAs in the $TABLE output? If so, how is it done? ETAR12 is not recognized.
>
> I’d like to import into R for summary stats.
>
> Thank you!
> Paul
>
> Paul R. Hutson, PharmD, BCOP
>
> Professor (CHS)
>
> UW School of Pharmacy
>
> Director, UW Madison Transdisciplinary Center for Research in Psychoactive Substances
>
> Associate Member, Paul P. Carbone Comprehensive Cancer Center
>
> T: 608.263.2496
>
> [email protected]
Hi Paul,
One cannot have a correlation based on a single individual, so there is no such
number that could be output in the TABLE file.
However, if you are interested in the correlation between EBE of etas (across
all subjects in your analysis data) you can just output the etas using TABLE,
then read into R, take one row per subject (assuming this is IIV, no IOV), and
calculate the correlation, e.g. between ETA1 and ETA2.
For most eta diagnostics/processing I would suggest you set any etas that are
exactly zero to NA. Otherwise, you will have misleadingly lower magnitude of
correlation, e.g. because half you the subjects received placebo and have the
eta on Emax as exactly zero. Likewise, one would get higher shrinkage for this
eta if including these subjects with zero eta value, and for most purposes that
is not how I would prefer to use the term shrinkage. But there are exceptions
so I do not mean to start a separate discussion on this - sometimes it may be
useful to include also the zero etas in calculations, graphs, etc.
Or did you mean the uncertainty in the individual EBEs, and the correlation
between these (EBE) estimates? In that case the above is irrelevant, but I do
not think that is what you mean.
Best regards
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
Cell/Mobile: +46 (0)70 514 33 77
[email protected]
www.pharmetheus.com
Phone, Office: +46 (0)18 513 328
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Quoted reply history
> On 20 Dec 2022, at 19:55, Paul Hutson <[email protected]> wrote:
>
> Is it possible to include the off-diagonal correlation of ETAs in the $TABLE
> output? If so, how is it done? ETAR12 is not recognized.
> I’d like to import into R for summary stats.
> Thank you!
> Paul
>
> Paul R. Hutson, PharmD, BCOP
> Professor (CHS)
> UW School of Pharmacy
> Director, UW Madison Transdisciplinary Center for Research in Psychoactive
> Substances
> Associate Member, Paul P. Carbone Comprehensive Cancer Center
> T: 608.263.2496
> [email protected] <mailto:[email protected]>
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Hi,
Not a direct answer to your question but... if you are using a more or less
recent version of NONMEM, correlation information can be extracted from the
.cor file. This file is a standard output for any NONMEM run for which the
covariance is determined upon completion of the run.
Correlation is determined at the population level, so it would be a waste of
disk-space to output (and repeat the same) off-diagonal elements of the
covariance matrix in the record-by-record $TABLE output.
Sebastien Bihorel
Quoted reply history
________________________________
From: [email protected] <[email protected]> on behalf of
Paul Hutson <[email protected]>
Sent: Tuesday, December 20, 2022 1:55 PM
To: [email protected] <[email protected]>
Subject: [External] [NMusers] Off diagonals in $TABLE
EXTERNAL MESSAGE
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Is it possible to include the off-diagonal correlation of ETAs in the $TABLE
output? If so, how is it done? ETAR12 is not recognized.
I’d like to import into R for summary stats.
Thank you!
Paul
Paul R. Hutson, PharmD, BCOP
Professor (CHS)
UW School of Pharmacy
Director, UW Madison Transdisciplinary Center for Research in Psychoactive
Substances
Associate Member, Paul P. Carbone Comprehensive Cancer Center
T: 608.263.2496
[email protected]
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Hi Paul,
If you use Wings for NONMEM the eta correlations are calculated for you and
shown in the smy file.
These off-diagonal covariances and corresponding correlations are a property of
the all the subjects in the study. They are not subject specific so they don’t
really belong in the $TABLE file (unless that is the only way you know to get
input into R).
Best wishes,
Nick
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From: [email protected] <[email protected]> On Behalf Of
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Sent: Wednesday, 21 December 2022 7:56 am
To: [email protected]
Subject: [NMusers] Off diagonals in $TABLE
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Is it possible to include the off-diagonal correlation of ETAs in the $TABLE
output? If so, how is it done? ETAR12 is not recognized.
I’d like to import into R for summary stats.
Thank you!
Paul
Paul R. Hutson, PharmD, BCOP
Professor (CHS)
UW School of Pharmacy
Director, UW Madison Transdisciplinary Center for Research in Psychoactive
Substances
Associate Member, Paul P. Carbone Comprehensive Cancer Center
T: 608.263.2496
[email protected]<mailto:[email protected]>