Re: [NMusers] $ABBR REPLACE Limitations?

From: Nick Holford <n.holford_at_auckland.ac.nz>
Date: Wed, 24 Jan 2018 20:59:51 +1300

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


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:luann_at_cognigencorp.com
> <mailto:luann_at_cognigencorp.com>]
> *Sent:* Tuesday, January 23, 2018 3:51 PM
> *To:* Bill Denney <wdenney_at_humanpredictions.com
> <mailto:wdenney_at_humanpredictions.com>>
> *Cc:* nmusers <nmusers_at_globomaxnm.com <mailto:nmusers_at_globomaxnm.com>>
> *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" <wdenney_at_humanpredictions.com
> <mailto:wdenney_at_humanpredictions.com>>
> *To: *"nmusers" <nmusers_at_globomaxnm.com <mailto:nmusers_at_globomaxnm.com>>
> *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
> wdenney_at_humanpredictions.com <mailto:wdenney_at_humanpredictions.com>
>
> 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: n.holford_at_auckland.ac.nz
http://holford.fmhs.auckland.ac.nz/
http://orcid.org/0000-0002-4031-2514
Read the question, answer the question, attempt all questions


Received on Wed Jan 24 2018 - 02:59:51 EST

This archive was generated by hypermail 2.3.0 : Fri Sep 27 2019 - 16:57:53 EDT