Nele,
going by the nonmem user manual, part VIII, p 94 ($OMEGA), "If FIXED
appears anywhere among the list of values, the entire block is fixed."
I did not see anyone pointing that out yet.
This does in fact imply that you need to reorder the sequence of random
effects (which can be quite a nu
Hi,
Nick wrote:
"Mats, can you suggest a way to try to correct for the Bayesian shrinkage
problem for obtaining MIXEST?"
As the problem is created by using model estimates for stratification, the
simple answer is not to do it. I can't think of a situation where it would
be useful to stratify bas
Hi,
It is indeed a nuisance to have to renumber all the ETAs if you have a
complex model and you change the sequence of $OMEGA.
You can of course choose to use the awk script which comes with WFN
(http://wfn.sourceforge.net) translate an extended NM-TRAN control
stream, which uses parameter
If you want both CL1 and CL2 to be correlated with F (i.e. allow Omega(CL1,F)
and Omega(CL2,F) to be free in
the objective function optimization),
then I don't think there is any simple reordering of the random effects that
will allow the correlation
between CL1 and CL2 to be fixed to zero - i
Dear all,
There is an undocumented option in NONMEM called Band, allowing to fix at
least one correlation to zero in a block(n).
In the specific case you just have to put zero as initial estimate for Omega
(CL1,CL2).
It should work I used it in the past with NONMEM V!
Hope this helps.
Dear all,
I am fitting a PD response, and the equation goes like this:
total response = baseline+f(placebo response) +f(drug response)
first, I tried full omega block, and model was able to converge, but $COV stop
failed.
To me, this indicates that too many parameters in the model. The structure
Well, the first thing that I would do is look at the magnitude of the
estimates of the etas. I would eliminate those etas that are poorly
estimated (essentially the very large values or those approaching zero).
From: owner-nmus...@globomaxnm.com [mailto:owner-nmu
Dear All
I am not sure if this topic has been covered before or not, but as its
related to the question below, I thought I would bring it up again.
I have to wonder at the appropriateness of including the IIV term for F in
an omega BLOCK structure in the first place? I can certainly unders
also, you will get a lot of responses to ignore whether or not the $COV
step succeeds or fails (especially Nick).
From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com]
On Behalf Of Ethan Wu
Sent: Wednesday, April 15, 2009 11:47 AM
To: nmusers@gl
Ethan,
Do not pay any attention to whether or not the $COV step runs or even if
the run is 'SUCCESSFUL' to conclude anything about your model. Your
opinion is not supported experimentally e.g. see
http://www.mail-archive.com/nmusers@globomaxnm.com/msg00454.html for
discussion and references.
Nick et al. At this risk of starting an discussion that probably has little mileage left in it. First I agree with Nick on covariance - it probably doesn't matter. But, I'd like to point out what may be an error in our logic. We content that we have demonstrated that covariance doesn't matte
some Etas estimated to be around 2 or 3, but since I am fitting a quite noisy
PD data, I think they are actually reasonable
no Etas close to 0
cov% esimated in the range of 10-90%.should those small ones like 10% be taken
out?
From: "Bachman, William"
To:
Nick,
in this case, the model fixed effects parameter estimates do make sense
since the objective of analysis is for simulation, should I still ignore
failing of $COV ?
From: Nick Holford
To: nmusers@globomaxnm.com
Sent: Wednesday, April 15, 2009 12:17:57 PM
In my opinion, I would not remove those in the 10-90% range. I would be
suspect of anything over 100%, even with noisy data, they are being poorly
estimated.
_
From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On
Behalf Of Ethan Wu
Sent: Wednesday, April 15, 200
I think Christian is referring to this feature of NONMEM 5 (from the
NONMEM 5 Supplement guide):
"Changes to NONMEM Inputs
Band Symmetric Matrices
An initial estimate of a diagonal block of ether the OMEGA or
SIGMA matrices may have a band symmetric form, in which case
the final estimate has the s
Mark,
I agree with your logic. In the meantime I will ignore the $COV step (it
rarely happens for me) and wait for some empirical evidence that the
$COV step is of demonstrable value for model building. Perhaps your grid
computing system could take on that challenge by comparing the results
o
Hi,
How can I modify the diagnostic plot output file from pdf to multiple pngs
after running NONR function using MIfuns package developed by Metrum
Institute? I tried exploring the functions in R but each function led to
another function. I am lost on which function exactly defines the device.
Dear Sir/Madam,
I have been a NONMEN user for a year and I have benefited from the discussion,
I really appreciate your effort to set up this forum. At this time, however, I
can't continue my subscription for further discussion any further, and I would
be really thankful if you can unsubscribe
Pavan,
There is no option in NONR that will allow the output of multiple
png's in place of one pdf. We did away with an option like that a
number of versions ago. What you can do is supply your own R script
using the "epilog" argument of NONR. There is a starter epilog script
titled epilogEx.R in
Thanks!
_
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Dear all,
thank you for all your responses, and it seems to me the topic has raised
quite some discussions. Especially the point Diane brought up seemed to be
a very reasonable thought to me, and I will definitely try and see if this
changes anything with respect to model stability, and if I ca
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