RE: NONMEM 7.2 and Pirana/Xpose4

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 followed 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: 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 file, but printed in the result file itself (usually .res or .lst). In principle this should be fine, but this causes the other four tables that you define (and for which you do specify FILE=...), not to be printed at all. This 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 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. Note that the problem seems not to be with Xpose or Pirana, but with generating output from NONMEM (the sdtab file is empty). And you can't plot data without 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 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 initially used in describing the problem. Regardless of the number extension on 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 been successful in creating a single one. After some research I learned that Xpose4 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 populated sdtab file. Another person using NONMEM 7 appears to have had no problem creating the plots withina n the Pirana/Xpose environment. Is this an 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 mentioned 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 several options under SCRIPTS for basic GOF plots. Also, my suggestion to you would be to table out all the continuous and categorical covariates in a separate $TABLE files for plotting purposes. Following is an example that works 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 FILEtab005 See that Pirana requires these standard notations for continuous (cotab) and 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 problem 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 dataset 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 analyzing my data. $TABLE ID TIME DV IPRED PRED IWRES CWRES WRES NOPRINT ONEHEADER FILE=sdtab104 Margaret Thomson, PharmD PhD Candidate University of Tennessee Health Science Center -- -Mukul