Hello,
I'm trying to build a model where I need to have ETAs generated on
separately for the ID and another variable (MACH). What I have is a PD
experiment that was run on several different machines (MACH). Each
machine appears to have a different slope per day and a different
calibration. I still need to keep some ETAs on the ID column, so I
can't just assign MACH=ID.
I've heard that there are ways to do similar to this, but I have been
unable to find examples of how to set etas to key off of different
columns.
Thanks,
Bill
Notice: This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates (which may be known
outside the United States as Merck Frosst, Merck Sharp & Dohme or
MSD and in Japan, as Banyu - direct contact information for affiliates is
available at http://www.merck.com/contact/contacts.html) that may be
confidential, proprietary copyrighted and/or legally privileged. It is
intended solely for the use of the individual or entity named on this
message. If you are not the intended recipient, and have received this
message in error, please notify us immediately by reply e-mail and
then delete it from your system.
More Levels of Random Effects
16 messages
8 people
Latest: Oct 22, 2008
Bill,
Is it really an eta you want, or is this rather solved by different error
models for the different machines?
If still want etas, one way would be to model in the same way as IOV. In the
case of intermachine-variability you would have to assume the variability
between all machines are the same...
Or would you rather assume interindividual variability is different with
different machine, and you then would want one eta for TH(X) for every
machine...? It depends on what you mean by different slope every day,
regarding on what your experiments like, but calibration differences should
perhaps be taken care of by looking into your error model, eta on epsilon
for starters...
Without knowing your structure of data, a short example of IOV-like
variability would be:
MA1=0
MA2=0
IF(MACH=1)MA1=1
IF(MACH=2)MA2=1
;Intermachine variability:
ETAM = MA1*ETA(Y)+MA2*ETA(Z)
PAR= TH(X) *EXP(ETA(X)+ETAM)
$OMEGA
value1
$OMEGA BLOCK(1) value2
$OMEGA BLOCK(1) same
/Johan
_________________________________________
Johan Wallin, M.Sci./Ph.D.-student
Pharmacometrics Group
Div. of Pharmacokinetics and Drug therapy
Uppsala University
_________________________________________
Quoted reply history
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Denney, William S.
Sent: den 15 oktober 2008 14:39
To: [email protected]
Subject: [NMusers] More Levels of Random Effects
Hello,
I'm trying to build a model where I need to have ETAs generated on
separately for the ID and another variable (MACH). What I have is a PD
experiment that was run on several different machines (MACH). Each
machine appears to have a different slope per day and a different
calibration. I still need to keep some ETAs on the ID column, so I
can't just assign MACH=ID.
I've heard that there are ways to do similar to this, but I have been
unable to find examples of how to set etas to key off of different
columns.
Thanks,
Bill
Notice: This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates (which may be known
outside the United States as Merck Frosst, Merck Sharp & Dohme or
MSD and in Japan, as Banyu - direct contact information for affiliates is
available at http://www.merck.com/contact/contacts.html) that may be
confidential, proprietary copyrighted and/or legally privileged. It is
intended solely for the use of the individual or entity named on this
message. If you are not the intended recipient, and have received this
message in error, please notify us immediately by reply e-mail and
then delete it from your system.
Xia,
There is no requirement to use the SAME option. However, it is a
reasonable model for IOV that it has the same variability on each occasion.
If you dont use the SAME option then you just need to estimate an extra
OMEGA parameter for each occasion you dont use SAME. You can test if the
SAME assumption is supported by your data or not by comparing models
with and without SAME.
Nick
PS Your computer clock seems to be more than 2 years out of date. Your
email claimed it was sent in 17 Jan 2006.
Xia Li wrote:
> Dear All,
> Do we have to assume the variability between all occasions are the same when
> we estimate IOV? What will happen if I don't use the 'same' constrain in the
> $OMEGA BLOCK statement? Any input will be appreciated.
>
> Best,
>
> Xia Li
>
Quoted reply history
> -----Original Message-----
> From: owner-nmusers
> Behalf Of Johan Wallin
> Sent: Wednesday, October 15, 2008 9:17 AM
> To: nmusers
> Subject: RE: [NMusers] More Levels of Random Effects
>
> Bill,
> Is it really an eta you want, or is this rather solved by different error
> models for the different machines?
>
> If still want etas, one way would be to model in the same way as IOV. In the
> case of intermachine-variability you would have to assume the variability
> between all machines are the same...
> Or would you rather assume interindividual variability is different with
> different machine, and you then would want one eta for TH(X) for every
> machine...? It depends on what you mean by different slope every day,
> regarding on what your experiments like, but calibration differences should
> perhaps be taken care of by looking into your error model, eta on epsilon
> for starters...
>
> Without knowing your structure of data, a short example of IOV-like
> variability would be:
>
> MA1=0
> MA2=0
> IF(MACH=1)MA1=1
> IF(MACH=2)MA2=1
> ;Intermachine variability:
> ETAM = MA1*ETA(Y)+MA2*ETA(Z)
>
> PAR= TH(X) *EXP(ETA(X)+ETAM)
>
> $OMEGA
> value1
> $OMEGA BLOCK(1) value2
> $OMEGA BLOCK(1) same
>
> /Johan
>
>
>
> _________________________________________
> Johan Wallin, M.Sci./Ph.D.-student
> Pharmacometrics Group
> Div. of Pharmacokinetics and Drug therapy
> Uppsala University
> _________________________________________
>
>
> -----Original Message-----
> From: owner-nmusers
> Behalf Of Denney, William S.
> Sent: den 15 oktober 2008 14:39
> To: nmusers
> Subject: [NMusers] More Levels of Random Effects
>
> Hello,
>
> I'm trying to build a model where I need to have ETAs generated on
> separately for the ID and another variable (MACH). What I have is a PD
> experiment that was run on several different machines (MACH). Each
> machine appears to have a different slope per day and a different
> calibration. I still need to keep some ETAs on the ID column, so I
> can't just assign MACH=ID.
>
> I've heard that there are ways to do similar to this, but I have been
> unable to find examples of how to set etas to key off of different
> columns.
>
> Thanks,
>
> Bill
> Notice: This e-mail message, together with any attachments, contains
> information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
> New Jersey, USA 08889), and/or its affiliates (which may be known
> outside the United States as Merck Frosst, Merck Sharp & Dohme or
> MSD and in Japan, as Banyu - direct contact information for affiliates is
> available at http://www.merck.com/contact/contacts.html) that may be
> confidential, proprietary copyrighted and/or legally privileged. It is
> intended solely for the use of the individual or entity named on this
> message. If you are not the intended recipient, and have received this
> message in error, please notify us immediately by reply e-mail and
> then delete it from your system.
>
>
>
--
Nick Holford, Dept Pharmacology & Clinical Pharmacology
University of Auckland, 85 Park Rd, Private Bag 92019, Auckland, New Zealand
n.holford
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
Hi Xia, Nick
Technically, one can use different variances on different occasions but
then we loose predictive power of the model: we do not know what will be
the variability on the next occasion. One can use occasion-dependent IOV
variance to check for trends (for example, to investigate the time
dependence of the IOV variability, or to check whether the first
occasion (e.g., after the first dose of a long-term study) is for some
reasons different from the others) but the final model should have some
condition that specifies the relations of IOV variances at different
occasion (SAME being the simplest, most reasonable and the most-often
used option).
Thanks
Leonid
--------------------------------------
Leonid Gibiansky, Ph.D.
President, QuantPharm LLC
web: www.quantpharm.com
e-mail: LGibiansky at quantpharm.com
tel: (301) 767 5566
Nick Holford wrote:
> Xia,
>
> There is no requirement to use the SAME option. However, it is a
> reasonable model for IOV that it has the same variability on each occasion.
>
> If you dont use the SAME option then you just need to estimate an extra
> OMEGA parameter for each occasion you dont use SAME. You can test if the
> SAME assumption is supported by your data or not by comparing models
> with and without SAME.
>
> Nick
>
> PS Your computer clock seems to be more than 2 years out of date. Your
> email claimed it was sent in 17 Jan 2006.
>
> Xia Li wrote:
>> Dear All,
>> Do we have to assume the variability between all occasions are the
>> same when
>> we estimate IOV? What will happen if I don't use the 'same' constrain
>> in the
>> $OMEGA BLOCK statement? Any input will be appreciated.
>>
>> Best,
>>
>> Xia Li
>>
>> -----Original Message-----
Quoted reply history
>> From: owner-nmusers
>> [mailto:owner-nmusers
>> Behalf Of Johan Wallin
>> Sent: Wednesday, October 15, 2008 9:17 AM
>> To: nmusers
>> Subject: RE: [NMusers] More Levels of Random Effects
>>
>> Bill,
>> Is it really an eta you want, or is this rather solved by different error
>> models for the different machines?
>>
>> If still want etas, one way would be to model in the same way as IOV.
>> In the
>> case of intermachine-variability you would have to assume the variability
>> between all machines are the same... Or would you rather assume
>> interindividual variability is different with
>> different machine, and you then would want one eta for TH(X) for every
>> machine...? It depends on what you mean by different slope every day,
>> regarding on what your experiments like, but calibration differences
>> should
>> perhaps be taken care of by looking into your error model, eta on epsilon
>> for starters...
>>
>> Without knowing your structure of data, a short example of IOV-like
>> variability would be:
>>
>> MA1=0
>> MA2=0
>> IF(MACH=1)MA1=1
>> IF(MACH=2)MA2=1
>> ;Intermachine variability:
>> ETAM = MA1*ETA(Y)+MA2*ETA(Z)
>>
>> PAR= TH(X) *EXP(ETA(X)+ETAM)
>>
>> $OMEGA value1
>> $OMEGA BLOCK(1) value2
>> $OMEGA BLOCK(1) same
>>
>> /Johan
>>
>>
>> _________________________________________
>> Johan Wallin, M.Sci./Ph.D.-student
>> Pharmacometrics Group
>> Div. of Pharmacokinetics and Drug therapy
>> Uppsala University
>> _________________________________________
>>
>>
>> -----Original Message-----
>> From: owner-nmusers
>> [mailto:owner-nmusers
>> Behalf Of Denney, William S.
>> Sent: den 15 oktober 2008 14:39
>> To: nmusers
>> Subject: [NMusers] More Levels of Random Effects
>>
>> Hello,
>>
>> I'm trying to build a model where I need to have ETAs generated on
>> separately for the ID and another variable (MACH). What I have is a PD
>> experiment that was run on several different machines (MACH). Each
>> machine appears to have a different slope per day and a different
>> calibration. I still need to keep some ETAs on the ID column, so I
>> can't just assign MACH=ID.
>>
>> I've heard that there are ways to do similar to this, but I have been
>> unable to find examples of how to set etas to key off of different
>> columns.
>>
>> Thanks,
>>
>> Bill
>> Notice: This e-mail message, together with any attachments, contains
>> information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
>> New Jersey, USA 08889), and/or its affiliates (which may be known
>> outside the United States as Merck Frosst, Merck Sharp & Dohme or
>> MSD and in Japan, as Banyu - direct contact information for affiliates is
>> available at http://www.merck.com/contact/contacts.html) that may be
>> confidential, proprietary copyrighted and/or legally privileged. It is
>> intended solely for the use of the individual or entity named on this
>> message. If you are not the intended recipient, and have received this
>> message in error, please notify us immediately by reply e-mail and
>> then delete it from your system.
>>
>>
>>
>
Dear All,
Do we have to assume the variability between all occasions are the same when
we estimate IOV? What will happen if I don't use the 'same' constrain in the
$OMEGA BLOCK statement? Any input will be appreciated.
Best,
Xia Li
Quoted reply history
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Johan Wallin
Sent: Wednesday, October 15, 2008 9:17 AM
To: [email protected]
Subject: RE: [NMusers] More Levels of Random Effects
Bill,
Is it really an eta you want, or is this rather solved by different error
models for the different machines?
If still want etas, one way would be to model in the same way as IOV. In the
case of intermachine-variability you would have to assume the variability
between all machines are the same...
Or would you rather assume interindividual variability is different with
different machine, and you then would want one eta for TH(X) for every
machine...? It depends on what you mean by different slope every day,
regarding on what your experiments like, but calibration differences should
perhaps be taken care of by looking into your error model, eta on epsilon
for starters...
Without knowing your structure of data, a short example of IOV-like
variability would be:
MA1=0
MA2=0
IF(MACH=1)MA1=1
IF(MACH=2)MA2=1
;Intermachine variability:
ETAM = MA1*ETA(Y)+MA2*ETA(Z)
PAR= TH(X) *EXP(ETA(X)+ETAM)
$OMEGA
value1
$OMEGA BLOCK(1) value2
$OMEGA BLOCK(1) same
/Johan
_________________________________________
Johan Wallin, M.Sci./Ph.D.-student
Pharmacometrics Group
Div. of Pharmacokinetics and Drug therapy
Uppsala University
_________________________________________
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Denney, William S.
Sent: den 15 oktober 2008 14:39
To: [email protected]
Subject: [NMusers] More Levels of Random Effects
Hello,
I'm trying to build a model where I need to have ETAs generated on
separately for the ID and another variable (MACH). What I have is a PD
experiment that was run on several different machines (MACH). Each
machine appears to have a different slope per day and a different
calibration. I still need to keep some ETAs on the ID column, so I
can't just assign MACH=ID.
I've heard that there are ways to do similar to this, but I have been
unable to find examples of how to set etas to key off of different
columns.
Thanks,
Bill
Notice: This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates (which may be known
outside the United States as Merck Frosst, Merck Sharp & Dohme or
MSD and in Japan, as Banyu - direct contact information for affiliates is
available at http://www.merck.com/contact/contacts.html) that may be
confidential, proprietary copyrighted and/or legally privileged. It is
intended solely for the use of the individual or entity named on this
message. If you are not the intended recipient, and have received this
message in error, please notify us immediately by reply e-mail and
then delete it from your system.
Xia,
There is no requirement to use the SAME option. However, it is a reasonable model for IOV that it has the same variability on each occasion.
If you dont use the SAME option then you just need to estimate an extra OMEGA parameter for each occasion you dont use SAME. You can test if the SAME assumption is supported by your data or not by comparing models with and without SAME.
Nick
PS Your computer clock seems to be more than 2 years out of date. Your email claimed it was sent in 17 Jan 2006.
Xia Li wrote:
> Dear All,
> Do we have to assume the variability between all occasions are the same when
> we estimate IOV? What will happen if I don't use the 'same' constrain in the
> $OMEGA BLOCK statement? Any input will be appreciated.
>
> Best,
>
> Xia Li
>
Quoted reply history
> -----Original Message-----
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
> Behalf Of Johan Wallin
> Sent: Wednesday, October 15, 2008 9:17 AM
> To: [email protected]
> Subject: RE: [NMusers] More Levels of Random Effects
>
> Bill,
> Is it really an eta you want, or is this rather solved by different error
> models for the different machines?
>
> If still want etas, one way would be to model in the same way as IOV. In the
> case of intermachine-variability you would have to assume the variability
>
> between all machines are the same... Or would you rather assume interindividual variability is different with
>
> different machine, and you then would want one eta for TH(X) for every
> machine...? It depends on what you mean by different slope every day,
> regarding on what your experiments like, but calibration differences should
> perhaps be taken care of by looking into your error model, eta on epsilon
> for starters...
>
> Without knowing your structure of data, a short example of IOV-like
> variability would be:
>
> MA1=0
> MA2=0
> IF(MACH=1)MA1=1
> IF(MACH=2)MA2=1
> ;Intermachine variability:
> ETAM = MA1*ETA(Y)+MA2*ETA(Z)
>
> PAR= TH(X) *EXP(ETA(X)+ETAM)
>
> $OMEGA value1
>
> $OMEGA BLOCK(1) value2
> $OMEGA BLOCK(1) same
>
> /Johan
>
> _________________________________________
> Johan Wallin, M.Sci./Ph.D.-student
> Pharmacometrics Group
> Div. of Pharmacokinetics and Drug therapy
> Uppsala University
> _________________________________________
>
> -----Original Message-----
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
> Behalf Of Denney, William S.
> Sent: den 15 oktober 2008 14:39
> To: [email protected]
> Subject: [NMusers] More Levels of Random Effects
>
> Hello,
>
> I'm trying to build a model where I need to have ETAs generated on
> separately for the ID and another variable (MACH). What I have is a PD
> experiment that was run on several different machines (MACH). Each
> machine appears to have a different slope per day and a different
> calibration. I still need to keep some ETAs on the ID column, so I
> can't just assign MACH=ID.
>
> I've heard that there are ways to do similar to this, but I have been
> unable to find examples of how to set etas to key off of different
> columns.
>
> Thanks,
>
> Bill
> Notice: This e-mail message, together with any attachments, contains
> information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
> New Jersey, USA 08889), and/or its affiliates (which may be known
> outside the United States as Merck Frosst, Merck Sharp & Dohme or
> MSD and in Japan, as Banyu - direct contact information for affiliates is
> available at http://www.merck.com/contact/contacts.html) that may be
> confidential, proprietary copyrighted and/or legally privileged. It is
> intended solely for the use of the individual or entity named on this
> message. If you are not the intended recipient, and have received this
> message in error, please notify us immediately by reply e-mail and
> then delete it from your system.
--
Nick Holford, 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
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
Hi Xia, Nick
Technically, one can use different variances on different occasions but
then we loose predictive power of the model: we do not know what will be
the variability on the next occasion. One can use occasion-dependent IOV
variance to check for trends (for example, to investigate the time
dependence of the IOV variability, or to check whether the first
occasion (e.g., after the first dose of a long-term study) is for some
reasons different from the others) but the final model should have some
condition that specifies the relations of IOV variances at different
occasion (SAME being the simplest, most reasonable and the most-often
used option).
Thanks
Leonid
--------------------------------------
Leonid Gibiansky, Ph.D.
President, QuantPharm LLC
web: www.quantpharm.com
e-mail: LGibiansky at quantpharm.com
tel: (301) 767 5566
Nick Holford wrote:
> Xia,
>
> There is no requirement to use the SAME option. However, it is a reasonable model for IOV that it has the same variability on each occasion.
>
> If you dont use the SAME option then you just need to estimate an extra OMEGA parameter for each occasion you dont use SAME. You can test if the SAME assumption is supported by your data or not by comparing models with and without SAME.
>
> Nick
>
> PS Your computer clock seems to be more than 2 years out of date. Your email claimed it was sent in 17 Jan 2006.
>
> Xia Li wrote:
>
> > Dear All,
> >
> > Do we have to assume the variability between all occasions are the same when we estimate IOV? What will happen if I don't use the 'same' constrain in the
> >
> > $OMEGA BLOCK statement? Any input will be appreciated.
> >
> > Best,
> >
> > Xia Li
> >
> > -----Original Message-----
> >
Quoted reply history
> > From: [EMAIL PROTECTED] [ mailto:[EMAIL PROTECTED] On
> >
> > Behalf Of Johan Wallin
> > Sent: Wednesday, October 15, 2008 9:17 AM
> > To: [email protected]
> > Subject: RE: [NMusers] More Levels of Random Effects
> >
> > Bill,
> > Is it really an eta you want, or is this rather solved by different error
> > models for the different machines?
> >
> > If still want etas, one way would be to model in the same way as IOV. In the
> >
> > case of intermachine-variability you would have to assume the variability
> >
> > between all machines are the same... Or would you rather assume interindividual variability is different with
> >
> > different machine, and you then would want one eta for TH(X) for every
> > machine...? It depends on what you mean by different slope every day,
> >
> > regarding on what your experiments like, but calibration differences should
> >
> > perhaps be taken care of by looking into your error model, eta on epsilon
> > for starters...
> >
> > Without knowing your structure of data, a short example of IOV-like
> > variability would be:
> >
> > MA1=0
> > MA2=0
> > IF(MACH=1)MA1=1
> > IF(MACH=2)MA2=1
> > ;Intermachine variability:
> > ETAM = MA1*ETA(Y)+MA2*ETA(Z)
> >
> > PAR= TH(X) *EXP(ETA(X)+ETAM)
> >
> > $OMEGA value1
> > $OMEGA BLOCK(1) value2
> > $OMEGA BLOCK(1) same
> >
> > /Johan
> >
> > _________________________________________
> > Johan Wallin, M.Sci./Ph.D.-student
> > Pharmacometrics Group
> > Div. of Pharmacokinetics and Drug therapy
> > Uppsala University
> > _________________________________________
> >
> > -----Original Message-----
> >
> > From: [EMAIL PROTECTED] [ mailto:[EMAIL PROTECTED] On
> >
> > Behalf Of Denney, William S.
> > Sent: den 15 oktober 2008 14:39
> > To: [email protected]
> > Subject: [NMusers] More Levels of Random Effects
> >
> > Hello,
> >
> > I'm trying to build a model where I need to have ETAs generated on
> > separately for the ID and another variable (MACH). What I have is a PD
> > experiment that was run on several different machines (MACH). Each
> > machine appears to have a different slope per day and a different
> > calibration. I still need to keep some ETAs on the ID column, so I
> > can't just assign MACH=ID.
> >
> > I've heard that there are ways to do similar to this, but I have been
> > unable to find examples of how to set etas to key off of different
> > columns.
> >
> > Thanks,
> >
> > Bill
> > Notice: This e-mail message, together with any attachments, contains
> > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
> > New Jersey, USA 08889), and/or its affiliates (which may be known
> > outside the United States as Merck Frosst, Merck Sharp & Dohme or
> > MSD and in Japan, as Banyu - direct contact information for affiliates is
> > available at http://www.merck.com/contact/contacts.html) that may be
> > confidential, proprietary copyrighted and/or legally privileged. It is
> > intended solely for the use of the individual or entity named on this
> > message. If you are not the intended recipient, and have received this
> > message in error, please notify us immediately by reply e-mail and
> > then delete it from your system.
I suppose it really comes down to what you are going to do with the model.
Many times I have checked the SAME assumption when modeling
inter-occasional variability, and found that sometimes, removing it does
indeed improve the fit significantly. In almost every case I've retained
it (despite the better fit) for the exact reasons Leonid cites: it makes
your model completely data-dependent. I suppose if the model was meant as
a description or summary of the data, then it would not matter, but I make
all of my models work for a living...
There is a related topic which I'd be interested in hearing from the group
about. Many times, we take several Phase 1 studies and put them together
in order to develop a population model early in development. I've learned
through experience to be careful when doing this, because often, one or
more studies will appear to have a different mean response for some
parameter, e.g., CL or V2. Of course, you can introduce study as a
covariate, but this intrduces the same problem as above; in a simulation
context, which CL value is correct? There is a work-around for this (use
both values) but this doubles the number of simulations you have to do,
and from a scientific stand-point it is not very satisfying. What we need
is another level of random effects at the STUDY level, similar to what is
routinely done when performing hierarchical modeling in something like
WinBUGS. I'd love to see this feature in a future version of NONMEM.
"Leonid Gibiansky" <LGibiansky
Sent by: owner-nmusers
17-Oct-2008 09:30
To
"Nick Holford" <n.holford
cc
"nmusers" <nmusers
Subject
Re: [NMusers] More Levels of Random Effects
Nick,
This is exactly what I meant. If you have a model for English, Irish and
Welsh, you may at least extrapolate it to Australians and New Zealanders
(of British descent :) ). With occasion treated as non-ordered
categorical covariate, you cannot extrapolate the model at all because
time cannot be repeated, so your covariate (occasion) will have
different value (level) at any future trial.
Leonid
--------------------------------------
Leonid Gibiansky, Ph.D.
President, QuantPharm LLC
web: www.quantpharm.com
e-mail: LGibiansky at quantpharm.com
tel: (301) 767 5566
Nick Holford wrote:
> Leonid,
>
> I dont understand what you mean by "we lose predictive power of the
> model: we do not know what will be
> the variability on the next occasion.".
>
> Or are you concerned about the situation where you have say 3 occasions
> and the IOV seems to be different on each occasion but you now want to
> predict the IOV for a future study on the 4th occasion?
>
> I agree it is hard to extrapolate to future occasions but this seems to
> be just like any other non-ordered categorical covariate - e.g. if we
> see differences between English, Irish and Welsh what difference would
> you expect for Russians? :-)
>
> Nick
>
>
> Leonid Gibiansky wrote:
>> Hi Xia, Nick
>> Technically, one can use different variances on different occasions but
>> then we loose predictive power of the model: we do not know what will
be
>> the variability on the next occasion. One can use occasion-dependent
IOV
>> variance to check for trends (for example, to investigate the time
>> dependence of the IOV variability, or to check whether the first
>> occasion (e.g., after the first dose of a long-term study) is for some
>> reasons different from the others) but the final model should have some
>> condition that specifies the relations of IOV variances at different
>> occasion (SAME being the simplest, most reasonable and the most-often
>> used option).
>>
>> Thanks
>> Leonid
>>
>> --------------------------------------
>> Leonid Gibiansky, Ph.D.
>> President, QuantPharm LLC
>> web: www.quantpharm.com
>> e-mail: LGibiansky at quantpharm.com
>> tel: (301) 767 5566
>>
>>
>>
>>
>> Nick Holford wrote:
>>> Xia,
>>>
>>> There is no requirement to use the SAME option. However, it is a
>>> reasonable model for IOV that it has the same variability on each
>>> occasion.
>>>
>>> If you dont use the SAME option then you just need to estimate an
>>> extra OMEGA parameter for each occasion you dont use SAME. You can
>>> test if the SAME assumption is supported by your data or not by
>>> comparing models with and without SAME.
>>>
>>> Nick
>>>
>>> PS Your computer clock seems to be more than 2 years out of date.
>>> Your email claimed it was sent in 17 Jan 2006.
>>>
>>> Xia Li wrote:
>>>> Dear All,
>>>> Do we have to assume the variability between all occasions are the
>>>> same when
>>>> we estimate IOV? What will happen if I don't use the 'same'
>>>> constrain in the
>>>> $OMEGA BLOCK statement? Any input will be appreciated.
>>>>
>>>> Best,
>>>>
>>>> Xia Li
>>>>
>>>> -----Original Message-----
Quoted reply history
>>>> From: owner-nmusers
>>>> [mailto:owner-nmusers
>>>> Behalf Of Johan Wallin
>>>> Sent: Wednesday, October 15, 2008 9:17 AM
>>>> To: nmusers
>>>> Subject: RE: [NMusers] More Levels of Random Effects
>>>>
>>>> Bill,
>>>> Is it really an eta you want, or is this rather solved by different
>>>> error
>>>> models for the different machines?
>>>>
>>>> If still want etas, one way would be to model in the same way as
>>>> IOV. In the
>>>> case of intermachine-variability you would have to assume the
>>>> variability
>>>> between all machines are the same... Or would you rather assume
>>>> interindividual variability is different with
>>>> different machine, and you then would want one eta for TH(X) for
every
>>>> machine...? It depends on what you mean by different slope every day,
>>>> regarding on what your experiments like, but calibration differences
>>>> should
>>>> perhaps be taken care of by looking into your error model, eta on
>>>> epsilon
>>>> for starters...
>>>>
>>>> Without knowing your structure of data, a short example of IOV-like
>>>> variability would be:
>>>>
>>>> MA1=0
>>>> MA2=0
>>>> IF(MACH=1)MA1=1
>>>> IF(MACH=2)MA2=1
>>>> ;Intermachine variability:
>>>> ETAM = MA1*ETA(Y)+MA2*ETA(Z)
>>>>
>>>> PAR= TH(X) *EXP(ETA(X)+ETAM)
>>>>
>>>> $OMEGA value1
>>>> $OMEGA BLOCK(1) value2
>>>> $OMEGA BLOCK(1) same
>>>>
>>>> /Johan
>>>>
>>>>
>>>> _________________________________________
>>>> Johan Wallin, M.Sci./Ph.D.-student
>>>> Pharmacometrics Group
>>>> Div. of Pharmacokinetics and Drug therapy
>>>> Uppsala University
>>>> _________________________________________
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: owner-nmusers
>>>> [mailto:owner-nmusers
>>>> Behalf Of Denney, William S.
>>>> Sent: den 15 oktober 2008 14:39
>>>> To: nmusers
>>>> Subject: [NMusers] More Levels of Random Effects
>>>>
>>>> Hello,
>>>>
>>>> I'm trying to build a model where I need to have ETAs generated on
>>>> separately for the ID and another variable (MACH). What I have is a
PD
>>>> experiment that was run on several different machines (MACH). Each
>>>> machine appears to have a different slope per day and a different
>>>> calibration. I still need to keep some ETAs on the ID column, so I
>>>> can't just assign MACH=ID.
>>>>
>>>> I've heard that there are ways to do similar to this, but I have been
>>>> unable to find examples of how to set etas to key off of different
>>>> columns.
>>>>
>>>> Thanks,
>>>>
>>>> Bill
>>>> Notice: This e-mail message, together with any attachments, contains
>>>> information of Merck & Co., Inc. (One Merck Drive, Whitehouse
Station,
>>>> New Jersey, USA 08889), and/or its affiliates (which may be known
>>>> outside the United States as Merck Frosst, Merck Sharp & Dohme or
>>>> MSD and in Japan, as Banyu - direct contact information for
>>>> affiliates is
>>>> available at http://www.merck.com/contact/contacts.html) that may be
>>>> confidential, proprietary copyrighted and/or legally privileged. It
is
>>>> intended solely for the use of the individual or entity named on this
>>>> message. If you are not the intended recipient, and have received
this
>>>> message in error, please notify us immediately by reply e-mail and
>>>> then delete it from your system.
>>>>
>>>>
>>>>
>>>
>>
>
I suppose it really comes down to what you are going to do with the model.
Many times I have checked the SAME assumption when modeling
inter-occasional variability, and found that sometimes, removing it does
indeed improve the fit significantly. In almost every case I've retained
it (despite the better fit) for the exact reasons Leonid cites: it makes
your model completely data-dependent. I suppose if the model was meant as
a description or summary of the data, then it would not matter, but I make
all of my models work for a living...
There is a related topic which I'd be interested in hearing from the group
about. Many times, we take several Phase 1 studies and put them together
in order to develop a population model early in development. I've learned
through experience to be careful when doing this, because often, one or
more studies will appear to have a different mean response for some
parameter, e.g., CL or V2. Of course, you can introduce study as a
covariate, but this intrduces the same problem as above; in a simulation
context, which CL value is correct? There is a work-around for this (use
both values) but this doubles the number of simulations you have to do,
and from a scientific stand-point it is not very satisfying. What we need
is another level of random effects at the STUDY level, similar to what is
routinely done when performing hierarchical modeling in something like
WinBUGS. I'd love to see this feature in a future version of NONMEM.
"Leonid Gibiansky" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
17-Oct-2008 09:30
To
"Nick Holford" <[EMAIL PROTECTED]>
cc
"nmusers" <[email protected]>
Subject
Re: [NMusers] More Levels of Random Effects
Nick,
This is exactly what I meant. If you have a model for English, Irish and
Welsh, you may at least extrapolate it to Australians and New Zealanders
(of British descent :) ). With occasion treated as non-ordered
categorical covariate, you cannot extrapolate the model at all because
time cannot be repeated, so your covariate (occasion) will have
different value (level) at any future trial.
Leonid
--------------------------------------
Leonid Gibiansky, Ph.D.
President, QuantPharm LLC
web: www.quantpharm.com
e-mail: LGibiansky at quantpharm.com
tel: (301) 767 5566
Nick Holford wrote:
> Leonid,
>
> I dont understand what you mean by "we lose predictive power of the
> model: we do not know what will be
> the variability on the next occasion.".
>
> Or are you concerned about the situation where you have say 3 occasions
> and the IOV seems to be different on each occasion but you now want to
> predict the IOV for a future study on the 4th occasion?
>
> I agree it is hard to extrapolate to future occasions but this seems to
> be just like any other non-ordered categorical covariate - e.g. if we
> see differences between English, Irish and Welsh what difference would
> you expect for Russians? :-)
>
> Nick
>
>
> Leonid Gibiansky wrote:
>> Hi Xia, Nick
>> Technically, one can use different variances on different occasions but
>> then we loose predictive power of the model: we do not know what will
be
>> the variability on the next occasion. One can use occasion-dependent
IOV
>> variance to check for trends (for example, to investigate the time
>> dependence of the IOV variability, or to check whether the first
>> occasion (e.g., after the first dose of a long-term study) is for some
>> reasons different from the others) but the final model should have some
>> condition that specifies the relations of IOV variances at different
>> occasion (SAME being the simplest, most reasonable and the most-often
>> used option).
>>
>> Thanks
>> Leonid
>>
>> --------------------------------------
>> Leonid Gibiansky, Ph.D.
>> President, QuantPharm LLC
>> web: www.quantpharm.com
>> e-mail: LGibiansky at quantpharm.com
>> tel: (301) 767 5566
>>
>>
>>
>>
>> Nick Holford wrote:
>>> Xia,
>>>
>>> There is no requirement to use the SAME option. However, it is a
>>> reasonable model for IOV that it has the same variability on each
>>> occasion.
>>>
>>> If you dont use the SAME option then you just need to estimate an
>>> extra OMEGA parameter for each occasion you dont use SAME. You can
>>> test if the SAME assumption is supported by your data or not by
>>> comparing models with and without SAME.
>>>
>>> Nick
>>>
>>> PS Your computer clock seems to be more than 2 years out of date.
>>> Your email claimed it was sent in 17 Jan 2006.
>>>
>>> Xia Li wrote:
>>>> Dear All,
>>>> Do we have to assume the variability between all occasions are the
>>>> same when
>>>> we estimate IOV? What will happen if I don't use the 'same'
>>>> constrain in the
>>>> $OMEGA BLOCK statement? Any input will be appreciated.
>>>>
>>>> Best,
>>>>
>>>> Xia Li
>>>>
>>>> -----Original Message-----
Quoted reply history
>>>> From: [EMAIL PROTECTED]
>>>> [mailto:[EMAIL PROTECTED] On
>>>> Behalf Of Johan Wallin
>>>> Sent: Wednesday, October 15, 2008 9:17 AM
>>>> To: [email protected]
>>>> Subject: RE: [NMusers] More Levels of Random Effects
>>>>
>>>> Bill,
>>>> Is it really an eta you want, or is this rather solved by different
>>>> error
>>>> models for the different machines?
>>>>
>>>> If still want etas, one way would be to model in the same way as
>>>> IOV. In the
>>>> case of intermachine-variability you would have to assume the
>>>> variability
>>>> between all machines are the same... Or would you rather assume
>>>> interindividual variability is different with
>>>> different machine, and you then would want one eta for TH(X) for
every
>>>> machine...? It depends on what you mean by different slope every day,
>>>> regarding on what your experiments like, but calibration differences
>>>> should
>>>> perhaps be taken care of by looking into your error model, eta on
>>>> epsilon
>>>> for starters...
>>>>
>>>> Without knowing your structure of data, a short example of IOV-like
>>>> variability would be:
>>>>
>>>> MA1=0
>>>> MA2=0
>>>> IF(MACH=1)MA1=1
>>>> IF(MACH=2)MA2=1
>>>> ;Intermachine variability:
>>>> ETAM = MA1*ETA(Y)+MA2*ETA(Z)
>>>>
>>>> PAR= TH(X) *EXP(ETA(X)+ETAM)
>>>>
>>>> $OMEGA value1
>>>> $OMEGA BLOCK(1) value2
>>>> $OMEGA BLOCK(1) same
>>>>
>>>> /Johan
>>>>
>>>>
>>>> _________________________________________
>>>> Johan Wallin, M.Sci./Ph.D.-student
>>>> Pharmacometrics Group
>>>> Div. of Pharmacokinetics and Drug therapy
>>>> Uppsala University
>>>> _________________________________________
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: [EMAIL PROTECTED]
>>>> [mailto:[EMAIL PROTECTED] On
>>>> Behalf Of Denney, William S.
>>>> Sent: den 15 oktober 2008 14:39
>>>> To: [email protected]
>>>> Subject: [NMusers] More Levels of Random Effects
>>>>
>>>> Hello,
>>>>
>>>> I'm trying to build a model where I need to have ETAs generated on
>>>> separately for the ID and another variable (MACH). What I have is a
PD
>>>> experiment that was run on several different machines (MACH). Each
>>>> machine appears to have a different slope per day and a different
>>>> calibration. I still need to keep some ETAs on the ID column, so I
>>>> can't just assign MACH=ID.
>>>>
>>>> I've heard that there are ways to do similar to this, but I have been
>>>> unable to find examples of how to set etas to key off of different
>>>> columns.
>>>>
>>>> Thanks,
>>>>
>>>> Bill
>>>> Notice: This e-mail message, together with any attachments, contains
>>>> information of Merck & Co., Inc. (One Merck Drive, Whitehouse
Station,
>>>> New Jersey, USA 08889), and/or its affiliates (which may be known
>>>> outside the United States as Merck Frosst, Merck Sharp & Dohme or
>>>> MSD and in Japan, as Banyu - direct contact information for
>>>> affiliates is
>>>> available at http://www.merck.com/contact/contacts.html) that may be
>>>> confidential, proprietary copyrighted and/or legally privileged. It
is
>>>> intended solely for the use of the individual or entity named on this
>>>> message. If you are not the intended recipient, and have received
this
>>>> message in error, please notify us immediately by reply e-mail and
>>>> then delete it from your system.
>>>>
>>>>
>>>>
>>>
>>
>
Title: Paul R
Please don't forget us Scots.
Paul
Leonid Gibiansky wrote:
Nick,
This is exactly what I meant. If you have a model for English, Irish
and Welsh, you may at least extrapolate it to Australians and New
Zealanders (of British descent :) ). With occasion treated as
non-ordered categorical covariate, you cannot extrapolate the model at
all because time cannot be repeated, so your covariate (occasion) will
have different value (level) at any future trial.
Leonid
--------------------------------------
Leonid Gibiansky, Ph.D.
President, QuantPharm LLC
web: www.quantpharm.com
e-mail: LGibiansky at quantpharm.com
tel: (301) 767 5566
Nick Holford wrote:
Leonid,
I dont understand what you mean by "we lose predictive power of the
model: we do not know what will be
the variability on the next occasion.".
Or are you concerned about the situation where you have say 3 occasions
and the IOV seems to be different on each occasion but you now want to
predict the IOV for a future study on the 4th occasion?
I agree it is hard to extrapolate to future occasions but this seems to
be just like any other non-ordered categorical covariate - e.g. if we
see differences between English, Irish and Welsh what difference would
you expect for Russians? :-)
Nick
Leonid Gibiansky wrote:
Hi Xia, Nick
Technically, one can use different variances on different occasions but
then we loose predictive power of the model: we do not know what will
be
the variability on the next occasion. One can use occasion-dependent
IOV
variance to check for trends (for example, to investigate the time
dependence of the IOV variability, or to check whether the first
occasion (e.g., after the first dose of a long-term study) is for some
reasons different from the others) but the final model should have some
condition that specifies the relations of IOV variances at different
occasion (SAME being the simplest, most reasonable and the most-often
used option).
Thanks
Leonid
--------------------------------------
Leonid Gibiansky, Ph.D.
President, QuantPharm LLC
web: www.quantpharm.com
e-mail: LGibiansky at quantpharm.com
tel: (301) 767 5566
Nick Holford wrote:
Xia,
There is no requirement to use the SAME option. However, it is a
reasonable model for IOV that it has the same variability on each
occasion.
If you dont use the SAME option then you just need to estimate an extra
OMEGA parameter for each occasion you dont use SAME. You can test if
the SAME assumption is supported by your data or not by comparing
models with and without SAME.
Nick
PS Your computer clock seems to be more than 2 years out of date. Your
email claimed it was sent in 17 Jan 2006.
Xia Li wrote:
Dear All,
Do we have to assume the variability between all occasions are the same
when
we estimate IOV? What will happen if I don't use the 'same' constrain
in the
$OMEGA BLOCK statement? Any input will be appreciated.
Best,
Xia Li
Quoted reply history
-----Original Message-----
From: [EMAIL PROTECTED]
[ mailto:[EMAIL PROTECTED] ] On
Behalf Of Johan Wallin
Sent: Wednesday, October 15, 2008 9:17 AM
To: [email protected]
Subject: RE: [NMusers] More Levels of Random Effects
Bill,
Is it really an eta you want, or is this rather solved by different
error
models for the different machines?
If still want etas, one way would be to model in the same way as IOV.
In the
case of intermachine-variability you would have to assume the
variability
between all machines are the same... Or would you rather assume
interindividual variability is different with
different machine, and you then would want one eta for TH(X) for every
machine...? It depends on what you mean by different slope every day,
regarding on what your experiments like, but calibration differences
should
perhaps be taken care of by looking into your error model, eta on
epsilon
for starters...
Without knowing your structure of data, a short example of IOV-like
variability would be:
MA1=0
MA2=0
IF(MACH=1)MA1=1
IF(MACH=2)MA2=1
;Intermachine variability:
ETAM = MA1*ETA(Y)+MA2*ETA(Z)
PAR= TH(X) *EXP(ETA(X)+ETAM)
$OMEGA value1
$OMEGA BLOCK(1) value2
$OMEGA BLOCK(1) same
/Johan
_________________________________________
Johan Wallin, M.Sci./Ph.D.-student
Pharmacometrics Group
Div. of Pharmacokinetics and Drug therapy
Uppsala University
_________________________________________
-----Original Message-----
From: [EMAIL PROTECTED]
[ mailto:[EMAIL PROTECTED] ] On
Behalf Of Denney, William S.
Sent: den 15 oktober 2008 14:39
To: [email protected]
Subject: [NMusers] More Levels of Random Effects
Hello,
I'm trying to build a model where I need to have ETAs generated on
separately for the ID and another variable (MACH). What I have is a PD
experiment that was run on several different machines (MACH). Each
machine appears to have a different slope per day and a different
calibration. I still need to keep some ETAs on the ID column, so I
can't just assign MACH=ID.
I've heard that there are ways to do similar to this, but I have been
unable to find examples of how to set etas to key off of different
columns.
Thanks,
Bill
Notice: This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse
Station,
New Jersey, USA 08889), and/or its affiliates (which may be known
outside the United States as Merck Frosst, Merck Sharp & Dohme or
MSD and in Japan, as Banyu - direct contact information for affiliates
is
available at http://www.merck.com/contact/contacts.html ) that may be
confidential, proprietary copyrighted and/or legally privileged. It is
intended solely for the use of the individual or entity named on this
message. If you are not the intended recipient, and have received this
message in error, please notify us immediately by reply e-mail and
then delete it from your system.
--
Paul R.
Hutson, Pharm.D.
Associate
Professor
UW School
of Pharmacy
777
Highland Avenue
Madison
WI 53705-2222
Tel 608.263.2496
Fax
608.265.5421
Pager
608.265.7000, p7856
Dear Michael,
You may want to have a look at :
Laporte-Simitsidis S, Girard P, ;Mismetti P, Chabaud S, Decousus H, Boissel JP
Inter-study variability in population pharmacokinetic meta-analysis: when and
how to estimate it?
J Pharm Sci. 2000 Feb;89(2):155-67. Review.
PMID: 10688745 [PubMed - indexed for MEDLINE]
Inter-Study variability was implemented in NONMEM ( and it is detailed in the
appendix of the reference) using a similar trick to the IOV one.
Hope this helps,
Bests,
Samer
Quoted reply history
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED]
Sent: Fri 10/17/2008 10:26
To: Leonid Gibiansky
Cc: nmusers; Nick Holford; [EMAIL PROTECTED]
Subject: Re: [NMusers] More Levels of Random Effects
I suppose it really comes down to what you are going to do with the model.
Many times I have checked the SAME assumption when modeling
inter-occasional variability, and found that sometimes, removing it does
indeed improve the fit significantly. In almost every case I've retained
it (despite the better fit) for the exact reasons Leonid cites: it makes
your model completely data-dependent. I suppose if the model was meant as
a description or summary of the data, then it would not matter, but I make
all of my models work for a living...
There is a related topic which I'd be interested in hearing from the group
about. Many times, we take several Phase 1 studies and put them together
in order to develop a population model early in development. I've learned
through experience to be careful when doing this, because often, one or
more studies will appear to have a different mean response for some
parameter, e.g., CL or V2. Of course, you can introduce study as a
covariate, but this intrduces the same problem as above; in a simulation
context, which CL value is correct? There is a work-around for this (use
both values) but this doubles the number of simulations you have to do,
and from a scientific stand-point it is not very satisfying. What we need
is another level of random effects at the STUDY level, similar to what is
routinely done when performing hierarchical modeling in something like
WinBUGS. I'd love to see this feature in a future version of NONMEM.
"Leonid Gibiansky" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
17-Oct-2008 09:30
To
"Nick Holford" <[EMAIL PROTECTED]>
cc
"nmusers" <[email protected]>
Subject
Re: [NMusers] More Levels of Random Effects
Nick,
This is exactly what I meant. If you have a model for English, Irish and
Welsh, you may at least extrapolate it to Australians and New Zealanders
(of British descent :) ). With occasion treated as non-ordered
categorical covariate, you cannot extrapolate the model at all because
time cannot be repeated, so your covariate (occasion) will have
different value (level) at any future trial.
Leonid
--------------------------------------
Leonid Gibiansky, Ph.D.
President, QuantPharm LLC
web: www.quantpharm.com
e-mail: LGibiansky at quantpharm.com
tel: (301) 767 5566
Nick Holford wrote:
> Leonid,
>
> I dont understand what you mean by "we lose predictive power of the
> model: we do not know what will be
> the variability on the next occasion.".
>
> Or are you concerned about the situation where you have say 3 occasions
> and the IOV seems to be different on each occasion but you now want to
> predict the IOV for a future study on the 4th occasion?
>
> I agree it is hard to extrapolate to future occasions but this seems to
> be just like any other non-ordered categorical covariate - e.g. if we
> see differences between English, Irish and Welsh what difference would
> you expect for Russians? :-)
>
> Nick
>
>
> Leonid Gibiansky wrote:
>> Hi Xia, Nick
>> Technically, one can use different variances on different occasions but
>> then we loose predictive power of the model: we do not know what will
be
>> the variability on the next occasion. One can use occasion-dependent
IOV
>> variance to check for trends (for example, to investigate the time
>> dependence of the IOV variability, or to check whether the first
>> occasion (e.g., after the first dose of a long-term study) is for some
>> reasons different from the others) but the final model should have some
>> condition that specifies the relations of IOV variances at different
>> occasion (SAME being the simplest, most reasonable and the most-often
>> used option).
>>
>> Thanks
>> Leonid
>>
>> --------------------------------------
>> Leonid Gibiansky, Ph.D.
>> President, QuantPharm LLC
>> web: www.quantpharm.com
>> e-mail: LGibiansky at quantpharm.com
>> tel: (301) 767 5566
>>
>>
>>
>>
>> Nick Holford wrote:
>>> Xia,
>>>
>>> There is no requirement to use the SAME option. However, it is a
>>> reasonable model for IOV that it has the same variability on each
>>> occasion.
>>>
>>> If you dont use the SAME option then you just need to estimate an
>>> extra OMEGA parameter for each occasion you dont use SAME. You can
>>> test if the SAME assumption is supported by your data or not by
>>> comparing models with and without SAME.
>>>
>>> Nick
>>>
>>> PS Your computer clock seems to be more than 2 years out of date.
>>> Your email claimed it was sent in 17 Jan 2006.
>>>
>>> Xia Li wrote:
>>>> Dear All,
>>>> Do we have to assume the variability between all occasions are the
>>>> same when
>>>> we estimate IOV? What will happen if I don't use the 'same'
>>>> constrain in the
>>>> $OMEGA BLOCK statement? Any input will be appreciated.
>>>>
>>>> Best,
>>>>
>>>> Xia Li
>>>>
>>>> -----Original Message-----
>>>> From: [EMAIL PROTECTED]
>>>> [mailto:[EMAIL PROTECTED] On
>>>> Behalf Of Johan Wallin
>>>> Sent: Wednesday, October 15, 2008 9:17 AM
>>>> To: [email protected]
>>>> Subject: RE: [NMusers] More Levels of Random Effects
>>>>
>>>> Bill,
>>>> Is it really an eta you want, or is this rather solved by different
>>>> error
>>>> models for the different machines?
>>>>
>>>> If still want etas, one way would be to model in the same way as
>>>> IOV. In the
>>>> case of intermachine-variability you would have to assume the
>>>> variability
>>>> between all machines are the same... Or would you rather assume
>>>> interindividual variability is different with
>>>> different machine, and you then would want one eta for TH(X) for
every
>>>> machine...? It depends on what you mean by different slope every day,
>>>> regarding on what your experiments like, but calibration differences
>>>> should
>>>> perhaps be taken care of by looking into your error model, eta on
>>>> epsilon
>>>> for starters...
>>>>
>>>> Without knowing your structure of data, a short example of IOV-like
>>>> variability would be:
>>>>
>>>> MA1=0
>>>> MA2=0
>>>> IF(MACH=1)MA1=1
>>>> IF(MACH=2)MA2=1
>>>> ;Intermachine variability:
>>>> ETAM = MA1*ETA(Y)+MA2*ETA(Z)
>>>>
>>>> PAR= TH(X) *EXP(ETA(X)+ETAM)
>>>>
>>>> $OMEGA value1
>>>> $OMEGA BLOCK(1) value2
>>>> $OMEGA BLOCK(1) same
>>>>
>>>> /Johan
>>>>
>>>>
>>>> _________________________________________
>>>> Johan Wallin, M.Sci./Ph.D.-student
>>>> Pharmacometrics Group
>>>> Div. of Pharmacokinetics and Drug therapy
>>>> Uppsala University
>>>> _________________________________________
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: [EMAIL PROTECTED]
>>>> [mailto:[EMAIL PROTECTED] On
>>>> Behalf Of Denney, William S.
>>>> Sent: den 15 oktober 2008 14:39
>>>> To: [email protected]
>>>> Subject: [NMusers] More Levels of Random Effects
>>>>
>>>> Hello,
>>>>
>>>> I'm trying to build a model where I need to have ETAs generated on
>>>> separately for the ID and another variable (MACH). What I have is a
PD
>>>> experiment that was run on several different machines (MACH). Each
>>>> machine appears to have a different slope per day and a different
>>>> calibration. I still need to keep some ETAs on the ID column, so I
>>>> can't just assign MACH=ID.
>>>>
>>>> I've heard that there are ways to do similar to this, but I have been
>>>> unable to find examples of how to set etas to key off of different
>>>> columns.
>>>>
>>>> Thanks,
>>>>
>>>> Bill
>>>> Notice: This e-mail message, together with any attachments, contains
>>>> information of Merck & Co., Inc. (One Merck Drive, Whitehouse
Station,
>>>> New Jersey, USA 08889), and/or its affiliates (which may be known
>>>> outside the United States as Merck Frosst, Merck Sharp & Dohme or
>>>> MSD and in Japan, as Banyu - direct contact information for
>>>> affiliates is
>>>> available at http://www.merck.com/contact/contacts.html) that may be
>>>> confidential, proprietary copyrighted and/or legally privileged. It
is
>>>> intended solely for the use of the individual or entity named on this
>>>> message. If you are not the intended recipient, and have received
this
>>>> message in error, please notify us immediately by reply e-mail and
>>>> then delete it from your system.
>>>>
>>>>
>>>>
>>>
>>
>
Hi Nick;
In your example, I would also do the latter, since I would have a rough
idea of the proportion of each of those groups living in the UK. But, I am
not sure your example is analagous to IOV, principally because, in your
example of Scots, Irish and Welsh, time is not involved. If you have 4
occasions, and you fit 4 variability terms as separate (no BLOCK SAME)
don't they now become ordered categories? If there is a definite pattern
to the variability changes as a function of time, wouldn't that change be
better modeled explicitly as a time-dependent change, rather than in an
implicit way?
I think your suggestion of running simulations based on the 1-4th occasion
when extrapolating is reasonable; however, the number of simulations that
might have to be performed may, in certain cases quickly add up.
Mike Fossler
GSK
"Nick Holford" <n.holford
Sent by: owner-nmusers
17-Oct-2008 15:38
To
"nmusers" <nmusers
cc
Subject
Re: [NMusers] More Levels of Random Effects
Mike,
So how do you deal with other non-ordered categorical variables? Suppose
you do your studies in Scotland, Ireland and Wales then need to predict
what will happen in England? Assuming you found 'significant'
differences in between subject variability in clearance between the
Scots, Irish and Welsh and wanted to predict a population in England do
you think it would better to take the average of the Scots, Irish and
Welsh (equivalent to using SAME) or do you think it would be better to
randomly choose from the 3 groups knowing that representatives of these
3 groups might be found living in England?
I would think the latter approach would be more realistic. I would
consider doing something similar for between occasion variability (aka
IOV) if I find 'significant' differences across 3 occasions and need to
predict a study which has 4 occasions. Rather than assume the 4th
occasion is the average of the other 3 I would consider randomly
assigning the 4th occasion data item to 1, 2 or 3.
Nick
Michael.J.Fossler
>
>
> I suppose it really comes down to what you are going to do with the
> model. Many times I have checked the SAME assumption when modeling
> inter-occasional variability, and found that sometimes, removing it
> does indeed improve the fit significantly. In almost every case I've
> retained it (despite the better fit) for the exact reasons Leonid
> cites: it makes your model completely data-dependent. I suppose if the
> model was meant as a description or summary of the data, then it would
> not matter, but I make all of my models work for a living...
>
--
Nick Holford, Dept Pharmacology & Clinical Pharmacology
University of Auckland, 85 Park Rd, Private Bag 92019, Auckland, New
Zealand
n.holford
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
Hi Nick;
In your example, I would also do the latter, since I would have a rough
idea of the proportion of each of those groups living in the UK. But, I am
not sure your example is analagous to IOV, principally because, in your
example of Scots, Irish and Welsh, time is not involved. If you have 4
occasions, and you fit 4 variability terms as separate (no BLOCK SAME)
don't they now become ordered categories? If there is a definite pattern
to the variability changes as a function of time, wouldn't that change be
better modeled explicitly as a time-dependent change, rather than in an
implicit way?
I think your suggestion of running simulations based on the 1-4th occasion
when extrapolating is reasonable; however, the number of simulations that
might have to be performed may, in certain cases quickly add up.
Mike Fossler
GSK
"Nick Holford" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
17-Oct-2008 15:38
To
"nmusers" <[email protected]>
cc
Subject
Re: [NMusers] More Levels of Random Effects
Mike,
So how do you deal with other non-ordered categorical variables? Suppose
you do your studies in Scotland, Ireland and Wales then need to predict
what will happen in England? Assuming you found 'significant'
differences in between subject variability in clearance between the
Scots, Irish and Welsh and wanted to predict a population in England do
you think it would better to take the average of the Scots, Irish and
Welsh (equivalent to using SAME) or do you think it would be better to
randomly choose from the 3 groups knowing that representatives of these
3 groups might be found living in England?
I would think the latter approach would be more realistic. I would
consider doing something similar for between occasion variability (aka
IOV) if I find 'significant' differences across 3 occasions and need to
predict a study which has 4 occasions. Rather than assume the 4th
occasion is the average of the other 3 I would consider randomly
assigning the 4th occasion data item to 1, 2 or 3.
Nick
[EMAIL PROTECTED] wrote:
>
>
> I suppose it really comes down to what you are going to do with the
> model. Many times I have checked the SAME assumption when modeling
> inter-occasional variability, and found that sometimes, removing it
> does indeed improve the fit significantly. In almost every case I've
> retained it (despite the better fit) for the exact reasons Leonid
> cites: it makes your model completely data-dependent. I suppose if the
> model was meant as a description or summary of the data, then it would
> not matter, but I make all of my models work for a living...
>
--
Nick Holford, 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
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
Mike,
I don't agree with you that occasion is necessarily linked through time. As already mentioned by Leonid, in the example we are discussing it is assumed that you are unable to find a predictable relationship between occasions in order to predict a future occasion. This would mean that there is no relationship of occasion to time or any other factor.
It makes no difference how you use the occasion value (say 1, 2 and 3) to the sequence of ETAs that you associate with the occasion e.g. you could use ETA(1) with occasion 2, ETA(2) with occasion 3 and ETA(3) with occasion 1. There is no intrinsic ordering to the occasion value if (as we assume) there is no relationship of IOV to time. Thus the occasions are non-ordered categories like race.
I agree that for race you may have some other clues to help you with expected proportions when you randomly select a category for future predictions. But if occasion is really random and you have no idea of the future proportions then a uniform distribution of occasions seems reasonable.
I dont understand your point about number of simulations. For whatever purpose you are planning to use the original model the need to randomly predict unknown occasions should not affect the number of simulations. It just becomes part of the prediction model which presumably already has stochastic elements in it anyway.
Best wishes
Nick
[EMAIL PROTECTED] wrote:
> Hi Nick;
>
> In your example, I would also do the latter, since I would have a rough idea of the proportion of each of those groups living in the UK. But, I am not sure your example is analagous to IOV, principally because, in your example of Scots, Irish and Welsh, time is not involved. If you have 4 occasions, and you fit 4 variability terms as separate (no BLOCK SAME) don't they now become ordered categories? If there is a definite pattern to the variability changes as a function of time, wouldn't that change be better modeled explicitly as a time-dependent change, rather than in an implicit way?
>
> I think your suggestion of running simulations based on the 1-4th occasion when extrapolating is reasonable; however, the number of simulations that might have to be performed may, in certain cases quickly add up.
>
> Mike Fossler
> GSK
>
> *"Nick Holford" <[EMAIL PROTECTED]>*
> Sent by: [EMAIL PROTECTED]
>
> 17-Oct-2008 15:38
>
> To
>
> "nmusers" <[email protected]>
> cc
>
> Subject
> Re: [NMusers] More Levels of Random Effects
>
> Mike,
>
> So how do you deal with other non-ordered categorical variables? Suppose
> you do your studies in Scotland, Ireland and Wales then need to predict
> what will happen in England? Assuming you found 'significant'
> differences in between subject variability in clearance between the
> Scots, Irish and Welsh and wanted to predict a population in England do
> you think it would better to take the average of the Scots, Irish and
> Welsh (equivalent to using SAME) or do you think it would be better to
> randomly choose from the 3 groups knowing that representatives of these
> 3 groups might be found living in England?
>
> I would think the latter approach would be more realistic. I would
> consider doing something similar for between occasion variability (aka
> IOV) if I find 'significant' differences across 3 occasions and need to
> predict a study which has 4 occasions. Rather than assume the 4th
> occasion is the average of the other 3 I would consider randomly
> assigning the 4th occasion data item to 1, 2 or 3.
>
> Nick
>
> [EMAIL PROTECTED] wrote:
> >
> >
> > I suppose it really comes down to what you are going to do with the
> > model. Many times I have checked the SAME assumption when modeling
> > inter-occasional variability, and found that sometimes, removing it
> > does indeed improve the fit significantly. In almost every case I've
> > retained it (despite the better fit) for the exact reasons Leonid
> > cites: it makes your model completely data-dependent. I suppose if the
> > model was meant as a description or summary of the data, then it would
> > not matter, but I make all of my models work for a living...
> >
>
> --
> Nick Holford, 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
> http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
--
Nick Holford, 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
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
Hi Leonid,
It is not obvious to me how to make use of the next level of random
effects using the PRIOR subroutine in the html help. Can you point me
to an example or other documentation of how to use PRIOR for this?
Thanks,
Bill
Quoted reply history
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Leonid Gibiansky
Sent: Friday, October 17, 2008 10:35 AM
To: [EMAIL PROTECTED]
Cc: nmusers; Nick Holford
Subject: Re: [NMusers] More Levels of Random Effects
The next level of random effects can be introduced in NONMEM using PRIOR
subroutine. It existed as undocumented feature even in Nonmem V. Now (in
Nonmem VI) it is official (see help).
Leonid
--------------------------------------
Leonid Gibiansky, Ph.D.
President, QuantPharm LLC
web: www.quantpharm.com
e-mail: LGibiansky at quantpharm.com
tel: (301) 767 5566
[EMAIL PROTECTED] wrote:
>
>
> I suppose it really comes down to what you are going to do with the
> model. Many times I have checked the SAME assumption when modeling
> inter-occasional variability, and found that sometimes, removing it
does
> indeed improve the fit significantly. In almost every case I've
> retained it (despite the better fit) for the exact reasons Leonid
cites:
> it makes your model completely data-dependent. I suppose if the model
> was meant as a description or summary of the data, then it would not
> matter, but I make all of my models work for a living...
>
> There is a related topic which I'd be interested in hearing from the
> group about. Many times, we take several Phase 1 studies and put them
> together in order to develop a population model early in development.
> I've learned through experience to be careful when doing this, because
> often, one or more studies will appear to have a different mean
response
> for some parameter, e.g., CL or V2. Of course, you can introduce study
> as a covariate, but this intrduces the same problem as above; in a
> simulation context, which CL value is correct? There is a work-around
> for this (use both values) but this doubles the number of simulations
> you have to do, and from a scientific stand-point it is not very
> satisfying. What we need is another level of random effects at the
STUDY
> level, similar to what is routinely done when performing hierarchical
> modeling in something like WinBUGS. I'd love to see this feature in a
> future version of NONMEM.
>
>
>
>
>
>
> *"Leonid Gibiansky" <[EMAIL PROTECTED]>*
> Sent by: [EMAIL PROTECTED]
>
> 17-Oct-2008 09:30
>
>
> To
> "Nick Holford" <[EMAIL PROTECTED]>
> cc
> "nmusers" <[email protected]>
> Subject
> Re: [NMusers] More Levels of Random Effects
>
>
>
>
>
>
>
>
> Nick,
>
> This is exactly what I meant. If you have a model for English, Irish
and
> Welsh, you may at least extrapolate it to Australians and New
Zealanders
> (of British descent :) ). With occasion treated as non-ordered
> categorical covariate, you cannot extrapolate the model at all because
> time cannot be repeated, so your covariate (occasion) will have
> different value (level) at any future trial.
>
> Leonid
>
> --------------------------------------
> Leonid Gibiansky, Ph.D.
> President, QuantPharm LLC
> web: www.quantpharm.com
> e-mail: LGibiansky at quantpharm.com
> tel: (301) 767 5566
>
>
>
>
> Nick Holford wrote:
> > Leonid,
> >
> > I dont understand what you mean by "we lose predictive power of the
> > model: we do not know what will be
> > the variability on the next occasion.".
> >
> > Or are you concerned about the situation where you have say 3
occasions
> > and the IOV seems to be different on each occasion but you now want
to
> > predict the IOV for a future study on the 4th occasion?
> >
> > I agree it is hard to extrapolate to future occasions but this
seems to
> > be just like any other non-ordered categorical covariate - e.g. if
we
> > see differences between English, Irish and Welsh what difference
would
> > you expect for Russians? :-)
> >
> > Nick
> >
> >
> > Leonid Gibiansky wrote:
> >> Hi Xia, Nick
> >> Technically, one can use different variances on different
occasions but
> >> then we loose predictive power of the model: we do not know what
will be
> >> the variability on the next occasion. One can use
occasion-dependent IOV
> >> variance to check for trends (for example, to investigate the time
> >> dependence of the IOV variability, or to check whether the first
> >> occasion (e.g., after the first dose of a long-term study) is for
some
> >> reasons different from the others) but the final model should have
some
> >> condition that specifies the relations of IOV variances at
different
> >> occasion (SAME being the simplest, most reasonable and the
most-often
> >> used option).
> >>
> >> Thanks
> >> Leonid
> >>
> >> --------------------------------------
> >> Leonid Gibiansky, Ph.D.
> >> President, QuantPharm LLC
> >> web: www.quantpharm.com
> >> e-mail: LGibiansky at quantpharm.com
> >> tel: (301) 767 5566
> >>
> >>
> >>
> >>
> >> Nick Holford wrote:
> >>> Xia,
> >>>
> >>> There is no requirement to use the SAME option. However, it is a
> >>> reasonable model for IOV that it has the same variability on each
> >>> occasion.
> >>>
> >>> If you dont use the SAME option then you just need to estimate an
> >>> extra OMEGA parameter for each occasion you dont use SAME. You
can
> >>> test if the SAME assumption is supported by your data or not by
> >>> comparing models with and without SAME.
> >>>
> >>> Nick
> >>>
> >>> PS Your computer clock seems to be more than 2 years out of date.
> >>> Your email claimed it was sent in 17 Jan 2006.
> >>>
> >>> Xia Li wrote:
> >>>> Dear All,
> >>>> Do we have to assume the variability between all occasions are
the
> >>>> same when
> >>>> we estimate IOV? What will happen if I don't use the 'same'
> >>>> constrain in the
> >>>> $OMEGA BLOCK statement? Any input will be appreciated.
> >>>>
> >>>> Best,
> >>>>
> >>>> Xia Li
> >>>>
> >>>> -----Original Message-----
> >>>> From: [EMAIL PROTECTED]
> >>>> [mailto:[EMAIL PROTECTED] On
> >>>> Behalf Of Johan Wallin
> >>>> Sent: Wednesday, October 15, 2008 9:17 AM
> >>>> To: [email protected]
> >>>> Subject: RE: [NMusers] More Levels of Random Effects
> >>>>
> >>>> Bill,
> >>>> Is it really an eta you want, or is this rather solved by
different
> >>>> error
> >>>> models for the different machines?
> >>>>
> >>>> If still want etas, one way would be to model in the same way as
> >>>> IOV. In the
> >>>> case of intermachine-variability you would have to assume the
> >>>> variability
> >>>> between all machines are the same... Or would you rather assume
> >>>> interindividual variability is different with
> >>>> different machine, and you then would want one eta for TH(X) for
every
> >>>> machine...? It depends on what you mean by different slope every
day,
> >>>> regarding on what your experiments like, but calibration
differences
> >>>> should
> >>>> perhaps be taken care of by looking into your error model, eta
on
> >>>> epsilon
> >>>> for starters...
> >>>>
> >>>> Without knowing your structure of data, a short example of
IOV-like
> >>>> variability would be:
> >>>>
> >>>> MA1=0
> >>>> MA2=0
> >>>> IF(MACH=1)MA1=1
> >>>> IF(MACH=2)MA2=1
> >>>> ;Intermachine variability:
> >>>> ETAM = MA1*ETA(Y)+MA2*ETA(Z)
> >>>>
> >>>> PAR= TH(X) *EXP(ETA(X)+ETAM)
> >>>>
> >>>> $OMEGA value1
> >>>> $OMEGA BLOCK(1) value2
> >>>> $OMEGA BLOCK(1) same
> >>>>
> >>>> /Johan
> >>>>
> >>>>
> >>>> _________________________________________
> >>>> Johan Wallin, M.Sci./Ph.D.-student
> >>>> Pharmacometrics Group
> >>>> Div. of Pharmacokinetics and Drug therapy
> >>>> Uppsala University
> >>>> _________________________________________
> >>>>
> >>>>
> >>>> -----Original Message-----
> >>>> From: [EMAIL PROTECTED]
> >>>> [mailto:[EMAIL PROTECTED] On
> >>>> Behalf Of Denney, William S.
> >>>> Sent: den 15 oktober 2008 14:39
> >>>> To: [email protected]
> >>>> Subject: [NMusers] More Levels of Random Effects
> >>>>
> >>>> Hello,
> >>>>
> >>>> I'm trying to build a model where I need to have ETAs generated
on
> >>>> separately for the ID and another variable (MACH). What I have
is
> a PD
> >>>> experiment that was run on several different machines (MACH).
Each
> >>>> machine appears to have a different slope per day and a
different
> >>>> calibration. I still need to keep some ETAs on the ID column,
so I
> >>>> can't just assign MACH=ID.
> >>>>
> >>>> I've heard that there are ways to do similar to this, but I have
been
> >>>> unable to find examples of how to set etas to key off of
different
> >>>> columns.
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Bill
Notice: This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates (which may be known
outside the United States as Merck Frosst, Merck Sharp & Dohme or
MSD and in Japan, as Banyu - direct contact information for affiliates is
available at http://www.merck.com/contact/contacts.html) that may be
confidential, proprietary copyrighted and/or legally privileged. It is
intended solely for the use of the individual or entity named on this
message. If you are not the intended recipient, and have received this
message in error, please notify us immediately by reply e-mail and
then delete it from your system.
Hi Bill,
I think, description in $PRIOR and nwpri help entries are the most helpful. The simplest 1-compartment problem example is below.
Good luck!
Leonid
--------------------------------------
Leonid Gibiansky, Ph.D.
President, QuantPharm LLC
web: www.quantpharm.com
e-mail: LGibiansky at quantpharm.com
tel: (301) 767 5566
----------
$PROBLEM 001, example
$INPUT ID,TIME,AMT,DV,MDV,EVID
$DATA data.csv
$SUBROUTINES ADVAN1 TRANS1
$PRIOR NWPRI NTHETA=3 NETA=2 NEPS=1 NTHP=3 NETP=2 NPEXP=1
$PK
CL = THETA(1)*EXP(ETA(1))
V = THETA(2)*EXP(ETA(2))
K=CL/V
SD1 = THETA(3)
S1=V
$ERROR
Y=A(1)/V*EXP(SD1*EPS(1))
$THETA ; INITIAL ESTIMATES FOR THETAS
(0,1) ; 1 CL
(0,1) ; 2 V
(0,0.3) ; 3 error SD
$THETA ; PRIOR MEAN OF THETAS
2 FIXED ; 1 CL
2 FIXED ; 2 V
0.3 FIXED ; 3 error SD
$THETA ; degrees of freedom for OMEGAs
20 FIXED ; 1 CL
20 FIXED ; 2 V1
$OMEGA ; current-problem omegas
0.1 ;[P] 1 V1
0.1 ;[P] 2 CL
$OMEGA ; variances of the distribution for thetas
1.5 FIXED ;[P] 1 CL
1.5 FIXED ;[P] 2 V
0.1 FIXED ;[P] 3 error SD
$OMEGA ; mode of priors for omegas
0.15 FIXED ; 1 CL
0.15 FIXED ; 2 V1
$SIGMA
1 FIXED ;[P]
$EST MAXEVAL=9999 NOABORT METHOD=1
----------
data.csv:
1,0,1000,0,1,1
1,0.1,0,1000,0,0
1,0.2,0,900,0,0
1,0.3,0,800,0,0
1,0.4,0,600,0,0
1,0.5,0,500,0,0
1,1,0,200,0,0
1,2,0,100,0,0
1,3,0,50,0,0
1,4,0,25,0,0
1,5,0,10,0,0
2,0,1000,0,1,1
2,0.1,0,1000,0,0
2,0.2,0,900,0,0
2,0.3,0,800,0,0
2,0.4,0,600,0,0
2,0.5,0,500,0,0
2,1,0,200,0,0
2,2,0,100,0,0
2,3,0,50,0,0
2,4,0,25,0,0
2,5,0,10,0,0
Denney, William S. wrote:
> Hi Leonid,
>
> It is not obvious to me how to make use of the next level of random
> effects using the PRIOR subroutine in the html help. Can you point me
> to an example or other documentation of how to use PRIOR for this?
>
> Thanks,
>
> Bill
>
Quoted reply history
> -----Original Message-----
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> On Behalf Of Leonid Gibiansky
> Sent: Friday, October 17, 2008 10:35 AM
> To: [EMAIL PROTECTED]
> Cc: nmusers; Nick Holford
> Subject: Re: [NMusers] More Levels of Random Effects
>
> The next level of random effects can be introduced in NONMEM using PRIOR
>
> subroutine. It existed as undocumented feature even in Nonmem V. Now (in
>
> Nonmem VI) it is official (see help).
> Leonid
>
> --------------------------------------
> Leonid Gibiansky, Ph.D.
> President, QuantPharm LLC
> web: www.quantpharm.com
> e-mail: LGibiansky at quantpharm.com
> tel: (301) 767 5566
>
> [EMAIL PROTECTED] wrote:
>
> > I suppose it really comes down to what you are going to do with the model. Many times I have checked the SAME assumption when modeling inter-occasional variability, and found that sometimes, removing it
>
> does
>
> > indeed improve the fit significantly. In almost every case I've retained it (despite the better fit) for the exact reasons Leonid
>
> cites:
>
> > it makes your model completely data-dependent. I suppose if the model was meant as a description or summary of the data, then it would not matter, but I make all of my models work for a living...
> >
> > There is a related topic which I'd be interested in hearing from the group about. Many times, we take several Phase 1 studies and put them together in order to develop a population model early in development. I've learned through experience to be careful when doing this, because
>
> > often, one or more studies will appear to have a different mean
>
> response
>
> > for some parameter, e.g., CL or V2. Of course, you can introduce study
>
> > as a covariate, but this intrduces the same problem as above; in a simulation context, which CL value is correct? There is a work-around for this (use both values) but this doubles the number of simulations you have to do, and from a scientific stand-point it is not very satisfying. What we need is another level of random effects at the
>
> STUDY
>
> > level, similar to what is routinely done when performing hierarchical modeling in something like WinBUGS. I'd love to see this feature in a future version of NONMEM.
> >
> > *"Leonid Gibiansky" <[EMAIL PROTECTED]>*
> > Sent by: [EMAIL PROTECTED]
> >
> > 17-Oct-2008 09:30
> >
> > To
> >
> > "Nick Holford" <[EMAIL PROTECTED]>
> > cc
> > "nmusers" <[email protected]>
> > Subject
> > Re: [NMusers] More Levels of Random Effects
> >
> > Nick,
> >
> > This is exactly what I meant. If you have a model for English, Irish
>
> and
>
> > Welsh, you may at least extrapolate it to Australians and New
>
> Zealanders
>
> > (of British descent :) ). With occasion treated as non-ordered
> > categorical covariate, you cannot extrapolate the model at all because
> > time cannot be repeated, so your covariate (occasion) will have
> > different value (level) at any future trial.
> >
> > Leonid
> >
> > --------------------------------------
> > Leonid Gibiansky, Ph.D.
> > President, QuantPharm LLC
> > web: www.quantpharm.com
> > e-mail: LGibiansky at quantpharm.com
> > tel: (301) 767 5566
> >
> > Nick Holford wrote:
> > > Leonid,
> > >
> > > I dont understand what you mean by "we lose predictive power of the
> > > model: we do not know what will be
> > > the variability on the next occasion.".
> > >
> > > Or are you concerned about the situation where you have say 3
>
> occasions
>
> > > and the IOV seems to be different on each occasion but you now want
>
> to
>
> > > predict the IOV for a future study on the 4th occasion?
> > >
> > > I agree it is hard to extrapolate to future occasions but this
>
> seems to
>
> > > be just like any other non-ordered categorical covariate - e.g. if
>
> we
>
> > > see differences between English, Irish and Welsh what difference
>
> would
>
> > > you expect for Russians? :-)
> > >
> > > Nick
> > >
> > >
> > > Leonid Gibiansky wrote:
> > >> Hi Xia, Nick
> > >> Technically, one can use different variances on different
>
> occasions but
>
> > >> then we loose predictive power of the model: we do not know what
>
> will be
>
> > >> the variability on the next occasion. One can use
>
> occasion-dependent IOV
>
> > >> variance to check for trends (for example, to investigate the time
> > >> dependence of the IOV variability, or to check whether the first
> > >> occasion (e.g., after the first dose of a long-term study) is for
>
> some
>
> > >> reasons different from the others) but the final model should have
>
> some
>
> > >> condition that specifies the relations of IOV variances at
>
> different
>
> > >> occasion (SAME being the simplest, most reasonable and the
>
> most-often
>
> > >> used option).
> > >>
> > >> Thanks
> > >> Leonid
> > >>
> > >> --------------------------------------
> > >> Leonid Gibiansky, Ph.D.
> > >> President, QuantPharm LLC
> > >> web: www.quantpharm.com
> > >> e-mail: LGibiansky at quantpharm.com
> > >> tel: (301) 767 5566
> > >>
> > >>
> > >>
> > >>
> > >> Nick Holford wrote:
> > >>> Xia,
> > >>>
> > >>> There is no requirement to use the SAME option. However, it is a
> > >>> reasonable model for IOV that it has the same variability on each
> > >>> occasion.
> > >>>
> > >>> If you dont use the SAME option then you just need to estimate an
> > >>> extra OMEGA parameter for each occasion you dont use SAME. You
>
> can
>
> > >>> test if the SAME assumption is supported by your data or not by
> > >>> comparing models with and without SAME.
> > >>>
> > >>> Nick
> > >>>
> > >>> PS Your computer clock seems to be more than 2 years out of date.
> > >>> Your email claimed it was sent in 17 Jan 2006.
> > >>>
> > >>> Xia Li wrote:
> > >>>> Dear All,
> > >>>> Do we have to assume the variability between all occasions are
>
> the
>
> > >>>> same when
> > >>>> we estimate IOV? What will happen if I don't use the 'same'
> > >>>> constrain in the
> > >>>> $OMEGA BLOCK statement? Any input will be appreciated.
> > >>>>
> > >>>> Best,
> > >>>>
> > >>>> Xia Li
> > >>>>
> > >>>> -----Original Message-----
> > >>>> From: [EMAIL PROTECTED]
> > >>>> [mailto:[EMAIL PROTECTED] On
> > >>>> Behalf Of Johan Wallin
> > >>>> Sent: Wednesday, October 15, 2008 9:17 AM
> > >>>> To: [email protected]
> > >>>> Subject: RE: [NMusers] More Levels of Random Effects
> > >>>>
> > >>>> Bill,
> > >>>> Is it really an eta you want, or is this rather solved by
>
> different
>
> > >>>> error
> > >>>> models for the different machines?
> > >>>>
> > >>>> If still want etas, one way would be to model in the same way as
> > >>>> IOV. In the
> > >>>> case of intermachine-variability you would have to assume the
> > >>>> variability
> > >>>> between all machines are the same... Or would you rather assume
> > >>>> interindividual variability is different with
> > >>>> different machine, and you then would want one eta for TH(X) for
>
> every
>
> > >>>> machine...? It depends on what you mean by different slope every
>
> day,
>
> > >>>> regarding on what your experiments like, but calibration
>
> differences
>
> > >>>> should
> > >>>> perhaps be taken care of by looking into your error model, eta
>
> on
>
> > >>>> epsilon
> > >>>> for starters...
> > >>>>
> > >>>> Without knowing your structure of data, a short example of
>
> IOV-like
>
> > >>>> variability would be:
> > >>>>
> > >>>> MA1=0
> > >>>> MA2=0
> > >>>> IF(MACH=1)MA1=1
> > >>>> IF(MACH=2)MA2=1
> > >>>> ;Intermachine variability:
> > >>>> ETAM = MA1*ETA(Y)+MA2*ETA(Z)
> > >>>>
> > >>>> PAR= TH(X) *EXP(ETA(X)+ETAM)
> > >>>>
> > >>>> $OMEGA value1
> > >>>> $OMEGA BLOCK(1) value2
> > >>>> $OMEGA BLOCK(1) same
> > >>>>
> > >>>> /Johan
> > >>>>
> > >>>>
> > >>>> _________________________________________
> > >>>> Johan Wallin, M.Sci./Ph.D.-student
> > >>>> Pharmacometrics Group
> > >>>> Div. of Pharmacokinetics and Drug therapy
> > >>>> Uppsala University
> > >>>> _________________________________________
> > >>>>
> > >>>>
> > >>>> -----Original Message-----
> > >>>> From: [EMAIL PROTECTED]
> > >>>> [mailto:[EMAIL PROTECTED] On
> > >>>> Behalf Of Denney, William S.
> > >>>> Sent: den 15 oktober 2008 14:39
> > >>>> To: [email protected]
> > >>>> Subject: [NMusers] More Levels of Random Effects
> > >>>>
> > >>>> Hello,
> > >>>>
> > >>>> I'm trying to build a model where I need to have ETAs generated
>
> on
>
> > >>>> separately for the ID and another variable (MACH). What I have
>
> is
>
> > a PD
> > >>>> experiment that was run on several different machines (MACH).
>
> Each
>
> > >>>> machine appears to have a different slope per day and a
>
> different
>
> > >>>> calibration. I still need to keep some ETAs on the ID column,
>
> so I
>
> > >>>> can't just assign MACH=ID.
> > >>>>
> > >>>> I've heard that there are ways to do similar to this, but I have
>
> been
>
> > >>>> unable to find examples of how to set etas to key off of
>
> different
>
> > >>>> columns.
> > >>>>
> > >>>> Thanks,
> > >>>>
> > >>>> Bill
>
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