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Re: [NMusers] $ABBR REPLACE Limitations?

From: William Denney <wdenney_at_humanpredictions.com>
Date: Wed, 24 Jan 2018 07:09:27 -0500

Hi Nick,

I'll take a look.

Thanks,

Bill

> On Jan 24, 2018, at 02:59, Nick Holford <n.holford_at_auckland.ac.nz> wrote:
>
> Bill,
>
> An alternative, and IMHO more convenient, method of coding parameters, wri=
tten as THETA, ETA and EPS/ERR indexed variables, is to use the ntcs.awk scr=
ipt provided as part of Wings for NONMEM. <http://wfn.sourceforge.net/> I de=
veloped WFN in 1990 and one its primary aims was to allow the user to code t=
hese variables as meaningful user defined names and stop having to count vec=
tor indices.
>
> ntcs.awk is an awk script that can be used on any platform that can run aw=
k (all NONMEM platforms as far as I know). You can use arbitrarily long name=
s for your parameters as long as they are unique.
>
> It should just be one line added to any script you currently use with stan=
dard NM-TRAN. You don't have to use any other part of WFN. You can then forg=
ot about counting the parameter vector index and having to redo everything i=
f 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 cha=
racters. I had a similar issue with ALAG1, so I think that there are limita=
tions on what types of variables you can remap. (Perhaps Allison or Bob cou=
ld confirm?)
>>
>> Thanks,
>>
>> Bill
>>
>> *From:* Luann Phillips [mailto:luann_at_cognigencorp.com <mailto:luann_at_cogni=
gencorp.com>]
>> *Sent:* Tuesday, January 23, 2018 3:51 PM
>> *To:* Bill Denney <wdenney_at_humanpredictions.com <mailto:wdenney_at_humanpred=
ictions.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 fi=
xed) that would cause variables with the first 6 characters the same to be i=
nterpreted as the same variable even when later characters differed. I wonde=
r 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_human=
predictions.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 d=
rugs simultaneously. To increase the model quality, I’m making heav=
y use of $ABBR REPLACE to keep track of THETA, ETA, and CMT numbers. I trac=
ed an issue with my model where there was no gradient on a bioavailability t=
erm 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 bi=
oavailability parameters had no effect. When I changed it to just directly n=
ame F1, it worked as expected.
>>
>> $PK
>>
>> …
>>
>> F1 = THETA(1)
>>
>> It’s not obvious from the $ABBR REPLACE section of the manual tha=
t this is a limitation of $ABBR REPLACE. Is this an issue or am I missing s=
omething?
>>
>> Thanks,
>>
>> Bill
>>
>> ------------------------------------------------------------------------
>>
>> Human Predictions Logo <http://www.humanpredictions.com/>*William S. Denn=
ey, 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 in=
dividual(s) or entity named above and others who have been specifically auth=
orized to receive it. If you are not the intended recipient, please do not r=
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>
> --
> 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 - 07:09:27 EST

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