RE: No Fit file -> bug or not a bug? -> simpler workaround for nmfe6.bat

-----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Sale - Next Level Solutions Sent: Wednesday, May 23, 2007 11:43 AM Cc: 'nmusers' Subject: RE: [NMusers] No Fit file -> bug or not a bug? Bill, I'm not sure there is a platform-independent-Fortran based fix (Alison would know better). You could edit nmfe6.bat to append a crlf, or go to another language for your front end application, one with more text processing flexibility. I assume it is part of everyone's QC to confirm that the number of observations and individuals in the output file matches what they expected. BTW, I think nmfe6.bat and be "fixed" by: Create a file c:\nmvi\util\end.txt put in it: ; end (note crlf before and after ; end - all you really need is a single crlf) add this text after the first line of c:\nmvi\util\nmfe6.bat type c:\nmvi\util\end.txt >> %1 Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > -------- Original Message -------- > Subject: RE: [NMusers] No Fit file -> bug or not a bug? > From: "Bill Bachman" <[EMAIL PROTECTED]> > Date: Wed, May 23, 2007 11:25 am > To: "'Mark Sale - Next Level Solutions'" <[EMAIL PROTECTED]> > Cc: "'nmusers'" <[email protected]> > > I guess this depends on how you define "bug". If a feature of an > application (NONMEM run with Fortran) causes an error (failure of a > table to > be created, as in this case, or a data record not to be included in > the data > set) on one of the intended operating systems (Windows), I would (in my > opinion) call it a bug. I would suggest fixing this known issue so > others > don't have to puzzle over it (or worse, omit a data record unknowingly). > > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On > Behalf Of Mark Sale - Next Level Solutions > Sent: Tuesday, May 22, 2007 7:04 PM > Cc: nmusers > Subject: RE: [NMusers] No Fit file > > Thanks for clarifying this Alison, I think I did know this is a fortran > I/O issue, not really a NMTRAN issue. Clearly we should all go back to > MS-DOS edit ;-) (only us really old people even remember MS-DOS). > > > > Mark Sale MD > Next Level Solutions, LLC > www.NextLevelSolns.com > > > > -------- Original Message -------- > > Subject: RE: [NMusers] No Fit file > > From: "Alison Boeckmann" <[EMAIL PROTECTED]> > > Date: Tue, May 22, 2007 5:41 pm > > To: "Mark Sale - Next Level Solutions" <[EMAIL PROTECTED]> > > Cc: "nmusers" <[email protected]> > > > > This is not a bug in NM-TRAN. But I can see how it happens in > > MS-DOS. Both wordpad and notepad (unlike ms-dos edit and unix vi) will > > write a file whose last line does not terminate with cr/lf. Such a line > > is invisible to the Fortran I/O libraries that are part of g77 > > (in the MS-DOS environment) and FORTRAN 77 5.0 (in the Solaris > > environment). > > > > I tested this in both MS-DOS and Solaris with a little fortran program > > that branches to statement 10 when an end of file condition occurs. > > > > > > program read > > character*10 text > > read (5,55,end=10) text > > print *,text > > 55 format (A10) > > stop > > 10 print *,'nothing read' > > end > > > > I created a file named infile containing only "1234567890" with no > cr/lf > > using notepad. I copied it to Solaris using ftp. In both environments, > > when the program is run with infile as input, it produces > > the output "nothing read". E.g., in Solaris, > > > > % f77 read.for > > read.for: > > MAIN read: > > % a.out<infile > > nothing read > > > > I don't know how to overcome this problem. Changing the format from A10 > > to (say) > > A1 or * does not help. It seems to me it is a bug (or maybe a design > > feature?) in the Fortran I/O library. > > > > > > On Tue, 22 May 2007 12:56:18 -0700, "Mark Sale - Next Level Solutions" > > <[EMAIL PROTECTED]> said: > > > Navin, If you're not getting the table file you expect, if may be > > > because NMtran (5 at least) seems to have a small bug that it will > > > sometimes ignore the last line of a control file if there isn't a > > > carriage return/line feed at the end. Try just hitting Enter after > > > the $TABLE record and saving. WRT plots, two options are Xpose from > > > the Upsala group (R/Splus, http://xpose.sourceforge.net) or an excel > > > macro from Next Level Solutions (www.nextlevelsolns.com) > > > > > > > > > > > > Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > > > > > > > > > > -------- Original Message -------- Subject: RE: [NMusers] No Fit > > > > file From: "Bachman, William (MYD)" <[EMAIL PROTECTED]> Date: > Tue, > > > > May 22, 2007 2:48 pm To: "navin goyal" <[EMAIL PROTECTED]>, > > > > "nmusers" <[email protected]> > > > > > > > > according to your code, your run should have created a file named > > > > "drug3.sdtab". this file contains a table with these columns "ID > > > > TIME AMT MDV DV EVID CMT" and DV PRED RES WRES. You can import > > > > this file into Excel. You will have to manually create the graphs > > > > unless you have a macro that can do it. > > > > > > > > ________________________________ > > > > > > > > From: [EMAIL PROTECTED] [mailto:owner- > > > > [EMAIL PROTECTED] On Behalf Of navin goyal Sent: Tuesday, May > > > > 22, 2007 2:20 PM To: nmusers Subject: [NMusers] No Fit file > > > > > > > > > > > > Hello everybody, I am trying to run a control stream for my data > > > > using NONMEM 6. I get the output file with the objective function > > > > and other estimates. The problem is that I do not get the fit > > > > file that can be opened in excel. I guess I am missing out > > > > something in the control stream, but just cannot figure it out. > > > > Any suggestions would be appreciated The last part in the control > > > > stream is posted below > > > > > > > > > > > > $ESTIMATION METHOD=1 MAXEVAL=9999 PRINT=5 POSTHOC $COVARIANCE > > > > > > > > $TABLE ID TIME AMT MDV DV EVID CMT NOPRINT ONEHEADER > > > > FILE=drug3.sdtab > > > > > > > > thanks a lot > > > > > > > > Navin > > > > > > > > > > > > > > > > > > > > > > > > > > > > ___________________________________________________________________- > > > > ____________________________________________________________________ > > > > > > > > > > > > > > > > > > > >