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RE: NONMEM 7.2 and Pirana/Xpose4

From: Bauer, Robert <Robert.Bauer>
Date: Wed, 10 Jul 2013 01:48:51 +0000

Sorry, I spotted a typo:

New bug item in nm7.2.0, which will be resolved in nm73:

When a series of $TABLE statements without FILE= specification is followe=
d by $TABLE statements with FILE= specification, not all tables print out=
, and an error is issued in the NONMEM report file: "0ERROR IN WRITING FILE=
 : TABLE FILE; USER FORMAT ERROR IN FORMAT_SWRITE". Work-around is to set =
LFORMAT=NONE and RFORMAT=NONE on the first $TABLE record with a FILE==
 option.


Robert J. Bauer, Ph.D.
Vice President, Pharmacometrics, R&D
ICON Development Solutions
7740 Milestone Parkway
Suite 150
Hanover, MD 21076
Tel: (215) 616-6428
Mob: (925) 286-0769
Email: Robert.Bauer
Web: www.iconplc.com<http://www.iconplc.com/>

From: owner-nmusers
 Behalf Of Bauer, Robert
Sent: Tuesday, July 09, 2013 9:17 PM
To: Ron Keizer; Thomson, Maggie
Cc: Mukul Minocha; nmusers
Subject: RE: [NMusers] NONMEM 7.2 and Pirana/Xpose4

Hello all:

New bug item in nm7.2.0, which will be resolved in nm73:

When a series of $TABLE statements without FILE= specification is followe=
d by $TABLE statements with FILE= specification, not all tables print out=
, and an error is issued in the NONMEM report file: "0ERROR IN WRITING FILE=
 : TABLE FILE; USER FORMAT ERROR IN FORMAT_SWRITE". Work-around is to set =
LFORMAT=NONE and FORMATR=NONE on the first $TABLE record with a FILE==
 option.

Robert J. Bauer, Ph.D.
Vice President, Pharmacometrics, R&D
ICON Development Solutions
7740 Milestone Parkway
Suite 150
Hanover, MD 21076
Tel: (215) 616-6428
Mob: (925) 286-0769
Email: Robert.Bauer
Web: www.iconplc.com<http://www.iconplc.com/>

From: owner-nmusers
ilto:owner-nmusers
Sent: Monday, July 08, 2013 3:23 PM
To: Thomson, Maggie
Cc: Mukul Minocha; nmusers
Subject: Re: [NMusers] NONMEM 7.2 and Pirana/Xpose4

hi Maggie,

the problem is with the first two tables you define:

$TABLE ID BW APAR CL V FIRSTONLY
$TABLE ID TIME DV PRED IPRED IWRES

Since you do not specify the FILE argument, these are not outputted to a fi=
le, but printed in the result file itself (usually .res or .lst). In princi=
ple this should be fine, but this causes the other four tables that you def=
ine (and for which you do specify FILE=...), not to be printed at all. Th=
is seems like a bug in NONMEM to me, or perhaps someone knows a reason for =
this behavior?
Anyway, if you remove the first two $TABLE records, or also specify FILE==
... in those $TABLE records, the tables are outputted fine (and you will be=
 able to make goodness of fit plots with Pirana / R / Xpose).

best regards,
Ron

PS. $SCATTER is kind of a rudimentary NONMEM function, we have so many nice=
 graphical tools these days...


----------------------------------------------
Ron Keizer, PharmD PhD
Post-doctoral fellow, Integrative Pharmacology
Dept. of Bioengineering & Therapeutic Sciences
University of California San Francisco (UCSF)
----------------------------------------------
Pirana Software & Consulting BV
USA / the Netherlands
www.pirana-software.com<http://www.pirana-software.com/>
----------------------------------------------
On Mon, Jul 8, 2013 at 10:27 AM, Ron Keizer <ron
:ron
hi Maggie,
Pirana, PsN and Xpose are all compatible with NM 7.2, no problem there. Not=
e that the problem seems not to be with Xpose or Pirana, but with generatin=
g output from NONMEM (the sdtab file is empty). And you can't plot data wit=
hout data :)
If you could share the control stream + dataset, I'd be happy to look into =
this.
best regards,
Ron

----------------------------------------------
Ron Keizer, PharmD PhD
Post-doctoral fellow, Integrative Pharmacology
Dept. of Bioengineering & Therapeutic Sciences
University of California San Francisco (UCSF)
----------------------------------------------
Pirana Software & Consulting BV
USA / the Netherlands
www.pirana-software.com<http://www.pirana-software.com/>
----------------------------------------------

On Mon, Jul 8, 2013 at 9:27 AM, Thomson, Maggie <mthomso1
mthomso1
Thank you for the response. I just copied the most recent control stream I =
had which had the sdtab file labelled as sdtab104 instead of sdtab101 I ini=
tially used in describing the problem. Regardless of the number extension o=
n the sdtab file it is not populated with any data; it is completely blank.=
 I have tried exploring all the GOF plot options in Pirana and have not bee=
n successful in creating a single one. After some research I learned that X=
pose4 uses the sdtab file which is why I have concentrated on figuring out =
why it is not created. In my group of at least 4 other people using NONMEM =
7.2, Pirana, and Xpose4 no one has been able to create the GOF plots or a p=
opulated sdtab file. Another person using NONMEM 7 appears to have had no p=
roblem creating the plots withina n the Pirana/Xpose environment. Is this a=
n incompatiability with Pirana/Xpose4 and NONMEM 7.2; and if so, is there a=
 workaround?

Maggie


From: Mukul Minocha [mailto:mukul.minocha
ail.com>]
Sent: Friday, July 05, 2013 11:32 AM
To: Thomson, Maggie
Cc: nmusers
Subject: Re: [NMusers] NONMEM 7.2 and Pirana/Xpose4

Hi Maggie,

The $TABLE code seems correct. However, I would like to point out you menti=
oned sdtab101 in the text while the code has sdtab104. Also in Pirana, you =
just need to highlight the model, the right hand side panel will give you s=
everal options under SCRIPTS for basic GOF plots. Also, my suggestion to yo=
u would be to table out all the continuous and categorical covariates in a =
separate $TABLE files for plotting purposes. Following is an example that w=
orks well for me and what I routinely use for my runs.

$TABLE ID TIME DV EVID NTIME OCC IPRED IWRES CWRES ONEHEADER NOPRINT FILE=
=sdtab005
$TABLE ID TIME KA V CL IIVKA IIVV IIVCL ONEHEADER NOPRINT FILE=patab005
$TABLE ID TIME AGE WT CRCL ONEHEADER NOPRINT FILE=cotab005
$TABLE ID TIME ISM RACE ONEHEADER NOPRINT FILE=catab005

See that Pirana requires these standard notations for continuous (cotab) an=
d categorical (catab) covariates.

Hope this helps,

Mukul Minocha
Research scientist
CTM,
University of Maryland Baltimore



On Fri, Jul 5, 2013 at 11:24 AM, Thomson, Maggie <mthomso1
:mthomso1
I am new to NONMEM 7.2 and am having some issues generating the goodness of=
 fit plots within Pirana or Xpose through the R console. I believe the prob=
lem is that the sdtab101 table is not created. When I try to open this file=
 it is completely blank. I am having this problem both with a practice data=
set as well as my own dataset. Below you will find the code that I am using=
 to create the sdtab file. I appreciate any help so that I can continue ana=
lyzing my data.

$TABLE ID TIME DV IPRED PRED IWRES CWRES WRES NOPRINT ONEHEADER FILE=sdta=
b104

Margaret Thomson, PharmD
PhD Candidate
University of Tennessee Health Science Center




--
-Mukul




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Received on Tue Jul 09 2013 - 21:48:51 EDT

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