Hi,
I’m working in NONMEM 7.4.1 with a model where I need to track 4 drugs
simultaneously. To increase the model quality, I’m making heavy use of
$ABBR REPLACE to keep track of THETA, ETA, and CMT numbers. I traced an
issue with my model where there was no gradient on a bioavailability term
to the fact that this substitution didn’t seem to be working:
$ABBR REPLACE FCMTD1GUT=F1
…
$PK
…
FCMTD1GUT = THETA(1)
FCMTD1GUT didn’t seem to be effectively replaced to F1, so the
bioavailability parameters had no effect. When I changed it to just
directly name F1, it worked as expected.
$PK
…
F1 = THETA(1)
It’s not obvious from the $ABBR REPLACE section of the manual that this is
a limitation of $ABBR REPLACE. Is this an issue or am I missing something?
Thanks,
Bill
------------------------------
http://www.humanpredictions.com[image: Human Predictions Logo]
http://www.humanpredictions.com/ http://www.humanpredictions.com*William
S. Denney, PhD*
Chief Scientist, Human Predictions LLC
+1-617-899-8123
[email protected]
This e-mail communication is confidential and is intended only for the
individual(s) or entity named above and others who have been specifically
authorized to receive it. If you are not the intended recipient, please do
not read, copy, use or disclose the contents of this communication to
others. Please notify the sender that you have received this e-mail in
error by replying to the e-mail or by calling +1-617-899-8123. Please then
delete the e-mail and any copies of it. Thank you.
$ABBR REPLACE Limitations?
Hi Luann,
I’m not having similar problems with other parameters with >6 characters.
I had a similar issue with ALAG1, so I think that there are limitations on
what types of variables you can remap. (Perhaps Allison or Bob could
confirm?)
Thanks,
Bill
*From:* Luann Phillips [mailto:[email protected]]
*Sent:* Tuesday, January 23, 2018 3:51 PM
*To:* Bill Denney <[email protected]>
*Cc:* nmusers <[email protected]>
*Subject:* Re: [NMusers] $ABBR REPLACE Limitations?
Bill,
I know at one time NM had a bug (haven't checked to see if it has been
fixed) that would cause variables with the first 6 characters the same to
be interpreted as the same variable even when later characters differed. I
wonder if this is a similar issue?
Have you tried a shorter variable name, such as FCD1GUT=F1?
Just a thought,
Luann
------------------------------
*From: *"Bill Denney" <[email protected]>
*To: *"nmusers" <[email protected]>
*Sent: *Tuesday, January 23, 2018 2:15:32 PM
*Subject: *[NMusers] $ABBR REPLACE Limitations?
Hi,
I’m working in NONMEM 7.4.1 with a model where I need to track 4 drugs
simultaneously. To increase the model quality, I’m making heavy use of
$ABBR REPLACE to keep track of THETA, ETA, and CMT numbers. I traced an
issue with my model where there was no gradient on a bioavailability term
to the fact that this substitution didn’t seem to be working:
$ABBR REPLACE FCMTD1GUT=F1
…
$PK
…
FCMTD1GUT = THETA(1)
FCMTD1GUT didn’t seem to be effectively replaced to F1, so the
bioavailability parameters had no effect. When I changed it to just
directly name F1, it worked as expected.
$PK
…
F1 = THETA(1)
It’s not obvious from the $ABBR REPLACE section of the manual that this is
a limitation of $ABBR REPLACE. Is this an issue or am I missing something?
Thanks,
Bill
------------------------------
http://www.humanpredictions.com/[image: Human Predictions Logo]
http://www.humanpredictions.com/ http://www.humanpredictions.com/*William
S. Denney, PhD*
Chief Scientist, Human Predictions LLC
+1-617-899-8123
[email protected]
This e-mail communication is confidential and is intended only for the
individual(s) or entity named above and others who have been specifically
authorized to receive it. If you are not the intended recipient, please do
not read, copy, use or disclose the contents of this communication to
others. Please notify the sender that you have received this e-mail in
error by replying to the e-mail or by calling +1-617-899-8123. Please then
delete the e-mail and any copies of it. Thank you.
This bug has been fixed since NONMEM 7.4
Bug #1, nm730_bug_list.pdf in https://nonmem.iconplc.com/nonmem730
Two variables with names longer than six characters, and identical in the first
six characters, defined in $PK, and used in $DES, will be seen as the same
variable. Use variable names that differ in the first six characters. This
occurs in NONMEM 7.1.0, 7.1.2, 7.2.0, and 7.3.0. A workaround is to move all
assignment statements for variables whose first 6 characters match to $DES.
Robert J. Bauer, Ph.D.
Senior Director
Pharmacometrics R&D
ICON Early Phase
820 W. Diamond Avenue
Suite 100
Gaithersburg, MD 20878
Office: (215) 616-6428
Mobile: (925) 286-0769
[email protected]<mailto:[email protected]>
http://www.iconplc.com/
Quoted reply history
From: [email protected] [mailto:[email protected]] On
Behalf Of Bill Denney
Sent: Tuesday, January 23, 2018 4:40 PM
To: Luann Phillips
Cc: nmusers
Subject: RE: [NMusers] $ABBR REPLACE Limitations?
Hi Luann,
I’m not having similar problems with other parameters with >6 characters. I
had a similar issue with ALAG1, so I think that there are limitations on what
types of variables you can remap. (Perhaps Allison or Bob could confirm?)
Thanks,
Bill
From: Luann Phillips
[mailto:[email protected]<mailto:[email protected]>]
Sent: Tuesday, January 23, 2018 3:51 PM
To: Bill Denney
<[email protected]<mailto:[email protected]>>
Cc: nmusers <[email protected]<mailto:[email protected]>>
Subject: Re: [NMusers] $ABBR REPLACE Limitations?
Bill,
I know at one time NM had a bug (haven't checked to see if it has been fixed)
that would cause variables with the first 6 characters the same to be
interpreted as the same variable even when later characters differed. I wonder
if this is a similar issue?
Have you tried a shorter variable name, such as FCD1GUT=F1?
Just a thought,
Luann
________________________________
From: "Bill Denney"
<[email protected]<mailto:[email protected]>>
To: "nmusers" <[email protected]<mailto:[email protected]>>
Sent: Tuesday, January 23, 2018 2:15:32 PM
Subject: [NMusers] $ABBR REPLACE Limitations?
Hi,
I’m working in NONMEM 7.4.1 with a model where I need to track 4 drugs
simultaneously. To increase the model quality, I’m making heavy use of $ABBR
REPLACE to keep track of THETA, ETA, and CMT numbers. I traced an issue with
my model where there was no gradient on a bioavailability term to the fact that
this substitution didn’t seem to be working:
$ABBR REPLACE FCMTD1GUT=F1
…
$PK
…
FCMTD1GUT = THETA(1)
FCMTD1GUT didn’t seem to be effectively replaced to F1, so the bioavailability
parameters had no effect. When I changed it to just directly name F1, it
worked as expected.
$PK
…
F1 = THETA(1)
It’s not obvious from the $ABBR REPLACE section of the manual that this is a
limitation of $ABBR REPLACE. Is this an issue or am I missing something?
Thanks,
Bill
________________________________
http://www.humanpredictions.com/[Image removed by sender. Human Predictions
http://www.humanpredictions.com/ http://www.humanpredictions.com/William
S. Denney, PhD
Chief Scientist, Human Predictions LLC
+1-617-899-8123
[email protected]<mailto:[email protected]>
This e-mail communication is confidential and is intended only for the
individual(s) or entity named above and others who have been specifically
authorized to receive it. If you are not the intended recipient, please do not
read, copy, use or disclose the contents of this communication to others.
Please notify the sender that you have received this e-mail in error by
replying to the e-mail or by calling +1-617-899-8123. Please then delete the
e-mail and any copies of it. Thank you.
Bill,
An alternative, and IMHO more convenient, method of coding parameters, written as THETA, ETA and EPS/ERR indexed variables, is to use the ntcs.awk script provided as part of Wings for NONMEM. < http://wfn.sourceforge.net/ > I developed WFN in 1990 and one its primary aims was to allow the user to code these variables as meaningful user defined names and stop having to count vector indices.
ntcs.awk is an awk script that can be used on any platform that can run awk (all NONMEM platforms as far as I know). You can use arbitrarily long names for your parameters as long as they are unique.
It should just be one line added to any script you currently use with standard NM-TRAN. You don't have to use any other part of WFN. You can then forgot about counting the parameter vector index and having to redo everything if you change the order parameters or insert parameters.
Best wishes,
Nick
Quoted reply history
On 24-Jan-18 13:40, Bill Denney wrote:
> Hi Luann,
>
> I’m not having similar problems with other parameters with >6 characters. I had a similar issue with ALAG1, so I think that there are limitations on what types of variables you can remap. (Perhaps Allison or Bob could confirm?)
>
> Thanks,
>
> Bill
>
> *From:* Luann Phillips [ mailto: [email protected] < mailto: [email protected] >]
>
> *Sent:* Tuesday, January 23, 2018 3:51 PM
>
> *To:* Bill Denney < [email protected] < mailto: [email protected] >>
>
> *Cc:* nmusers <[email protected] <mailto:[email protected]>>
> *Subject:* Re: [NMusers] $ABBR REPLACE Limitations?
>
> Bill,
>
> I know at one time NM had a bug (haven't checked to see if it has been fixed) that would cause variables with the first 6 characters the same to be interpreted as the same variable even when later characters differed. I wonder if this is a similar issue?
>
> Have you tried a shorter variable name, such as FCD1GUT=F1?
>
> Just a thought,
>
> Luann
>
> ------------------------------------------------------------------------
>
> *From: *"Bill Denney" < [email protected] < mailto: [email protected] >>
>
> *To: *"nmusers" <[email protected] <mailto:[email protected]>>
> *Sent: *Tuesday, January 23, 2018 2:15:32 PM
> *Subject: *[NMusers] $ABBR REPLACE Limitations?
>
> Hi,
>
> I’m working in NONMEM 7.4.1 with a model where I need to track 4 drugs simultaneously. To increase the model quality, I’m making heavy use of $ABBR REPLACE to keep track of THETA, ETA, and CMT numbers. I traced an issue with my model where there was no gradient on a bioavailability term to the fact that this substitution didn’t seem to be working:
>
> $ABBR REPLACE FCMTD1GUT=F1
>
> …
>
> $PK
>
> …
>
> FCMTD1GUT = THETA(1)
>
> FCMTD1GUT didn’t seem to be effectively replaced to F1, so the bioavailability parameters had no effect. When I changed it to just directly name F1, it worked as expected.
>
> $PK
>
> …
>
> F1 = THETA(1)
>
> It’s not obvious from the $ABBR REPLACE section of the manual that this is a limitation of $ABBR REPLACE. Is this an issue or am I missing something?
>
> Thanks,
>
> Bill
>
> ------------------------------------------------------------------------
>
> Human Predictions Logo < http://www.humanpredictions.com/ >*William S. Denney, PhD*
>
> Chief Scientist, Human Predictions LLC
> +1-617-899-8123
> [email protected] <mailto:[email protected]>
>
> This e-mail communication is confidential and is intended only for the individual(s) or entity named above and others who have been specifically authorized to receive it. If you are not the intended recipient, please do not read, copy, use or disclose the contents of this communication to others. Please notify the sender that you have received this e-mail in error by replying to the e-mail or by calling +1-617-899-8123. Please then delete the e-mail and any copies of it. Thank you.
--
Nick Holford, Professor Clinical Pharmacology
Dept Pharmacology & Clinical Pharmacology, Bldg 503 Room 302A
University of Auckland,85 Park Rd,Private Bag 92019,Auckland,New Zealand
office:+64(9)923-6730 mobile:NZ+64(21)46 23 53 FR+33(6)62 32 46 72
email: [email protected]
http://holford.fmhs.auckland.ac.nz/
http://orcid.org/0000-0002-4031-2514
Read the question, answer the question, attempt all questions
Hi Bob,
Thanks for this confirmation. I'm using 7.4.1.
For my other question, is there a limitation of $ABBR REPLACE which prevents
its use for parameters like F1 and ALAG1?
Thanks,
Bill
Quoted reply history
> On Jan 24, 2018, at 00:43, Bauer, Robert <[email protected]> wrote:
>
> This bug has been fixed since NONMEM 7.4
>
>
> Bug #1, nm730_bug_list.pdf in https://nonmem.iconplc.com/nonmem730
> Two variables with names longer than six characters, and identical in the
> first six characters, defined in $PK, and used in $DES, will be seen as the
> same variable. Use variable names that differ in the first six characters.
> This occurs in NONMEM 7.1.0, 7.1.2, 7.2.0, and 7.3.0. A workaround is to
> move all assignment statements for variables whose first 6 characters match
> to $DES.
>
> Robert J. Bauer, Ph.D.
> Senior Director
> Pharmacometrics R&D
> ICON Early Phase
> 820 W. Diamond Avenue
> Suite 100
> Gaithersburg, MD 20878
> Office: (215) 616-6428
> Mobile: (925) 286-0769
> [email protected]
> www.iconplc.com
>
> From: [email protected] [mailto:[email protected]] On
> Behalf Of Bill Denney
> Sent: Tuesday, January 23, 2018 4:40 PM
> To: Luann Phillips
> Cc: nmusers
> Subject: RE: [NMusers] $ABBR REPLACE Limitations?
>
> Hi Luann,
>
> I’m not having similar problems with other parameters with >6 characters. I
> had a similar issue with ALAG1, so I think that there are limitations on what
> types of variables you can remap. (Perhaps Allison or Bob could confirm?)
>
> Thanks,
>
> Bill
>
> From: Luann Phillips [mailto:[email protected]]
> Sent: Tuesday, January 23, 2018 3:51 PM
> To: Bill Denney <[email protected]>
> Cc: nmusers <[email protected]>
> Subject: Re: [NMusers] $ABBR REPLACE Limitations?
>
> Bill,
>
> I know at one time NM had a bug (haven't checked to see if it has been fixed)
> that would cause variables with the first 6 characters the same to be
> interpreted as the same variable even when later characters differed. I
> wonder if this is a similar issue?
> Have you tried a shorter variable name, such as FCD1GUT=F1?
>
> Just a thought,
> Luann
>
> From: "Bill Denney" <[email protected]>
> To: "nmusers" <[email protected]>
> Sent: Tuesday, January 23, 2018 2:15:32 PM
> Subject: [NMusers] $ABBR REPLACE Limitations?
>
> Hi,
>
> I’m working in NONMEM 7.4.1 with a model where I need to track 4 drugs
> simultaneously. To increase the model quality, I’m making heavy use of $ABBR
> REPLACE to keep track of THETA, ETA, and CMT numbers. I traced an issue with
> my model where there was no gradient on a bioavailability term to the fact
> that this substitution didn’t seem to be working:
>
> $ABBR REPLACE FCMTD1GUT=F1
> …
> $PK
> …
> FCMTD1GUT = THETA(1)
>
> FCMTD1GUT didn’t seem to be effectively replaced to F1, so the
> bioavailability parameters had no effect. When I changed it to just directly
> name F1, it worked as expected.
>
> $PK
> …
> F1 = THETA(1)
>
> It’s not obvious from the $ABBR REPLACE section of the manual that this is a
> limitation of $ABBR REPLACE. Is this an issue or am I missing something?
>
> Thanks,
>
> Bill
>
> <image001.jpg>William S. Denney, PhD
> Chief Scientist, Human Predictions LLC
> +1-617-899-8123
> [email protected]
> This e-mail communication is confidential and is intended only for the
> individual(s) or entity named above and others who have been specifically
> authorized to receive it. If you are not the intended recipient, please do
> not read, copy, use or disclose the contents of this communication to others.
> Please notify the sender that you have received this e-mail in error by
> replying to the e-mail or by calling +1-617-899-8123. Please then delete the
> e-mail and any copies of it. Thank you.
>
>
>
>
Bill:
If a substitution fails, you can more surely enforce its replacement if you
surround the variable to be substituted with parentheses.
In your example,
$ABBR REPLACE CMTUPGUT=1
$ABBR REPLACE CMTUPGUT2=15
…
$PK
…
IF (CMT.EQ.(CMTUPGUT).OR.CMT.EQ.(CMTUPGUT2).AND.AMTEFFSOLID.GT.0) THEN
…
ENDIF
…
Should work.
Robert J. Bauer, Ph.D.
Senior Director
Pharmacometrics R&D
ICON Early Phase
820 W. Diamond Avenue
Suite 100
Gaithersburg, MD 20878
Office: (215) 616-6428
Mobile: (925) 286-0769
[email protected]<mailto:[email protected]>
http://www.iconplc.com/
Quoted reply history
From: Bill Denney [mailto:[email protected]]
Sent: Saturday, February 03, 2018 11:35 AM
To: Alison Boeckmann
Cc: Bauer, Robert; Luann Phillips; nmusers
Subject: RE: [NMusers] $ABBR REPLACE Limitations?
Hi,
I hit another issue that I think may be related to the issue below. I’m still
in NONMEM 7.4.1, so if it’s fixed in 7.4.2, please let me know. I don’t have
any spaces , so I think that it’s at least subtly different than the related
issue discovered previously with spacing before and/or after substituted
parameters.
Is it possible to use replaced parameter in the beginning of a compound Boolean
statement in the $PK?
$ABBR REPLACE CMTUPGUT=1
$ABBR REPLACE CMTUPGUT2=15
…
$PK
…
IF (CMT.EQ.CMTUPGUT.OR.CMT.EQ.CMTUPGUT2.AND.AMTEFFSOLID.GT.0) THEN
…
ENDIF
…
Gives the error below:
AN ERROR WAS FOUND ON LINE 245 AT THE APPROXIMATE POSITION NOTED:
IF (CMT.EQ.CMTUPGUT.OR.CMT.EQ.CMTUPGUT2.AND.AMTEFFSOLID.GT.0) THEN
X
THE CHARACTERS IN ERROR ARE: CMTUPGUT
208 UNDEFINED VARIABLE.
Switching the order in the IF statement
$ABBR REPLACE CMTUPGUT=1
$ABBR REPLACE CMTUPGUT2=15
…
$PK
…
IF (CMT.EQ.CMTUPGUT2.OR.CMT.EQ.CMTUPGUT.AND.AMTEFFSOLID.GT.0) THEN
…
ENDIF
…
Gives the equivalent error for CMTUPGUT2.
Doing manual substitution of the first value in the IF statement makes the code
apparently work:
$ABBR REPLACE CMTUPGUT=1
$ABBR REPLACE CMTUPGUT2=15
…
$PK
…
IF (CMT.EQ.1.OR.CMT.EQ.CMTUPGUT2.AND.AMTEFFSOLID.GT.0) THEN
…
ENDIF
…
Thanks,
Bill